From mwilkinson at pub.open-bio.org  Mon May  3 11:07:51 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 10:56:56 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031507.i43F7ptf011702@pub.open-bio.org>


mwilkinson
Mon May  3 11:07:51 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11683/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
more documentation and tools for dealing with secondary inputs

moby-live/Perl/MOBY CommonSubs.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/04/29 22:37:57	1.47
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
@@ -30,9 +30,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant "SIMPLE" or "COLLECTION"
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs));
@@ -163,7 +163,11 @@
 use MOBY::Client::OntologyServer;
 use strict;
 use warnings;
-
+use MOBY::Client::SimpleArticle;
+use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
+            
+            
 use constant COLLECTION => 1;
 use constant SIMPLE => 2;
 use constant SECONDARY => 3;
@@ -191,6 +195,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -223,6 +228,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -244,19 +250,18 @@
 
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node
 
 =cut
 
@@ -276,7 +281,7 @@
                 push @inputs, [COLLECTION,$queryID, \@simples];
             } elsif (isSimpleArticle($article)){
                 push @inputs, [SIMPLE,$queryID,$article];
-            } elsif (isSecondaryArticle($article)){
+            } elsif (isSecondaryArticle($article)){  # should never happen in a generic service parser!
                 push @inputs, [SECONDARY,$queryID,$article];
             }
         }
@@ -290,7 +295,7 @@
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -317,14 +322,14 @@
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs->{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [SIMPLE, $DOM_name1], # the <Simple> block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= <Parameter> block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
             to parse XML DOM objects.
-            
-            
+
+
             Collections --------------------
             
             With inputs that have collections these are presented as a
@@ -347,8 +352,8 @@
 
             will become
             
-            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the <Simple> Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = <Parameter> Block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
@@ -891,7 +896,7 @@
         } elsif ($child->getTagName =~ /Collection/){
             $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
         } elsif ($child->getTagName =~ /Parameter/){
-            $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
+            $object = MOBY::Client::SecondaryArticle->new(XML_DOM => $child);
         }
         next unless $object;
         push @articles, $object;   # take the child elements, which are <Simple/> or <Collection/>
@@ -1097,15 +1102,20 @@
 =head2 getNodeContentWithArticle
 
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or "Parameter" if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -1126,16 +1136,50 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, "String", "SequenceString");
-                     print "matching node contents were ".(join "\n\n", @sequences)."\n"; # join all lines of string
-                 }   
-              }
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
 
+            For Parameters, such as the following
+             ...
+             ...
+             <moby:mobyContent>
+                <moby:mobyData>
+                    <Simple>
+                      <Sequence namespace=blah id=blah>
+                           <Integer namespace='' id='' articleName="Length">3</Integer>
+                           <String namespace='' id='' articleName="SequenceString">ATG</String>
+                      </Sequence>
+                    </Simple>
+                    <Parameter articleName='cutoff'>
+                        <Value>24</Value>
+                    </Parameter>
+                </moby:mobyData>
+             </moby:mobyContent>
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
+              @cutoffs = getNodeContentWithArticle($input, "Parameter", "cutoff");
+
+
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs->{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs->{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, "Parameter", "cutoff");
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, "String", "SequenceString");
+                }
+             }
+           }
 
 =cut
 
@@ -1157,19 +1201,38 @@
     unless ($nodes->item(0)){
         $nodes = $node->getElementsByTagName("moby:$element");
     }
+
 	for (0..$nodes->getLength-1){
         my $child = $nodes->item($_);
-		if (
+        if (
             (($child->getAttribute("articleName")) && (($child->getAttribute("articleName") eq $articleName)))
             || (($child->getAttribute("moby:articleName")) && (($child->getAttribute("moby:articleName") eq $articleName)))){
-			# now we have a valid child, get the content... stringified... regardless of what it is
-			my $resp;
-			foreach ($child->getChildNodes){
-                next unless $_->getNodeType == TEXT_NODE;
-				$resp .= $_->toString;
-			}
-			push @contents, $resp;
-		}
+            # now we have a valid child, get the content... stringified... regardless of what it is
+            
+            if (isSecondaryArticle($child)){
+                my $resp;
+                my $valuenodes = $child->getElementsByTagName('Value');
+                unless ($valuenodes->item(0)){
+                    $valuenodes = $child->getElementsByTagName("moby:Value");
+                }
+                for (0..$valuenodes->getLength-1){
+                    my $valuenode = $valuenodes->item($_);
+                    foreach my $amount ($valuenode->getChildNodes){
+                        next unless $amount->getNodeType == TEXT_NODE;
+                        $resp .= $amount->toString;
+                    }
+                }
+                push @contents, $resp;
+                
+            } else {
+                my $resp;
+                foreach ($child->getChildNodes){
+                    next unless $_->getNodeType == TEXT_NODE;
+                    $resp .= $_->toString;
+                }
+                push @contents, $resp;
+            }
+        }
 	}
 	return @contents;
 }

From mwilkinson at pub.open-bio.org  Mon May  3 15:49:18 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 15:38:22 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031949.i43JnI0k012385@pub.open-bio.org>


mwilkinson
Mon May  3 15:49:18 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12366

Modified Files:
	Central.pm 
Added Files:
	SecondaryArticle.html SecondaryArticle.pm 
Log Message:
added an object to represent a parameter

moby-live/Perl/MOBY/Client SecondaryArticle.html,NONE,1.1 SecondaryArticle.pm,NONE,1.1 Central.pm,1.74,1.75
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.74
retrieving revision 1.75
diff -u -r1.74 -r1.75
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/04/14 19:56:59	1.74
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
@@ -75,14 +75,29 @@
  Function  :	connect to one or more MOBY-Central
                 registries for searching
  Returns   :	MOBY::Client::Central object
+ 
+ ENV & PROXY : you can set environment variables to change the defaults.
+             By default, a call to 'new' will initialize MOBY::Client::Central
+             to connect to the MOBY Central registry at:
+             http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl
+             If you wish to chose another registry by default, or if you need
+             to set up additional connection details (e.g. PROXY) then you may
+             set the following environment variables to whatever you
+             require:
+             MOBY_SERVER  (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
+             MOBY_URI     (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
+             MOBY_PROXY   (no default)
+                
  Args      :    Registries - optional.
                            - takes the form
                               {$NAME1 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                $NAME2 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                 }
                             - by default this becomes
                             {mobycentral => {
@@ -125,6 +140,7 @@
 				default_MOBY_servername => ['mobycentral',												'read/write'],
 				default_MOBY_server 	=> ['http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl', 	'read/write'],
 				default_MOBY_uri		=> ['http://mobycentral.cbr.nrc.ca/MOBY/Central',				'read/write'],
+                default_MOBY_proxy      => [undef,                                                      'read/write'],
 				default_MOBY_type		=> ['soap',                                                     'read/write'],
 				Registries              => [undef, 														'read/write'],
 				multiple_registries		=> [undef,														'read/write'],
@@ -238,6 +254,7 @@
 	$self->default_MOBY_server($ENV{MOBY_SERVER}) if $ENV{MOBY_SERVER};
 	$self->default_MOBY_uri($ENV{MOBY_URI}) if $ENV{MOBY_URI};
 	$self->default_MOBY_type($ENV{MOBY_TYPE}) if $ENV{MOBY_TYPE};
+	$self->default_MOBY_proxy($ENV{MOBY_PROXY}) if $ENV{MOBY_PROXY};
 	
 	
     if ($self->Registries){
@@ -248,11 +265,19 @@
 			my $url = $acc->{URL};
 			my $uri = $acc->{URI};
 			my $type = $acc->{TYPE};
+			my $proxy = $acc->{PROXY};
 			$type ||='soap';
 			if (lc($type) eq "get"){
 				push @{$self->Connections}, [$name, $type, $url];
 			} else {
-				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy($url)->uri($uri)->on_fault(
+                my @soapargs;
+                if ($proxy){
+                    @soapargs = ($url,
+                                proxy => ['http' => $proxy]);
+                } else {
+                    @soapargs = ($url);
+                }
+				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy(@soapargs)->uri($uri)->on_fault(
 					sub{
 						my($soap, $res) = @_; 
 						die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";
@@ -270,7 +295,16 @@
 								URI => $self->default_MOBY_uri
 							  }}
 							 );
-			push @{$self->Connections},[$self->default_MOBY_servername, $self->default_MOBY_type, SOAP::Lite->proxy($self->default_MOBY_server)->uri($self->default_MOBY_uri)->on_fault(
+            my @soapargs;
+            if ($self->default_MOBY_proxy){
+                @soapargs = ($self->default_MOBY_server,
+                            proxy => ['http' => $self->default_MOBY_proxy]);
+            } else {
+                @soapargs = ($self->default_MOBY_server);
+            }
+			push @{$self->Connections},[$self->default_MOBY_servername,
+                                        $self->default_MOBY_type,
+                                        SOAP::Lite->proxy(@soapargs)->uri($self->default_MOBY_uri)->on_fault(
 				sub{
 					my($soap, $res) = @_; 
 					die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";

From mwilkinson at pub.open-bio.org  Mon May  3 16:15:32 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 16:04:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032015.i43KFWrL012520@pub.open-bio.org>


mwilkinson
Mon May  3 16:15:32 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12497

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing documentation error that Bertrand spotted

moby-live/Perl/MOBY CommonSubs.pm,1.48,1.49 CommonSubs.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
@@ -314,7 +314,6 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/04/14 20:10:35	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
@@ -86,9 +86,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant &quot;SIMPLE&quot; or &quot;COLLECTION&quot;
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data-&gt;type('base64' =&gt; responseHeader(&quot;my.authURI.com&quot;) . responseFooter()) unless (scalar(@inputs));
@@ -206,25 +206,24 @@
 <pre>
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
-                            &lt;queryInput...&gt;...&lt;/queryInput&gt;
-                         b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node</pre>
+                            &lt;mobyData...&gt;...&lt;/mobyData&gt;
+                         b. \@article XML:DOM nodes for Collections</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
 <pre>
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -238,33 +237,31 @@
             
             for example, the input message:
             
-                &lt;queryInput queryID = '1'&gt;
+                &lt;mobyData queryID = '1'&gt;
                     &lt;Simple articleName='name1'&gt;
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1], # the &lt;Simple&gt; block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= &lt;Parameter&gt; block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
-            to parse XML DOM objects.
-            
-            
+            to parse XML DOM objects.</pre>
+<pre>
             Collections --------------------
             
             With inputs that have collections these are presented as a
             listref of Simple article DOM's.  So for the following message:
             
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -277,12 +274,12 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become
             
-            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the &lt;Simple&gt; Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = &lt;Parameter&gt; Block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
@@ -292,12 +289,11 @@
 <h2><a name="getarticles">getArticles</a></h2>
 <pre>
  name     : getArticles
- function : get the Simple/Collection/Parameter articles for a single queryInput
-            or queryResponse node
+ function : get the Simple/Collection/Parameter articles for a single mobyData
  usage    : @articles = getArticles($XML)
  args     : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs)
- returns  : a list of listrefs; each listref is one component of the queryInput.
-            a single queryInput/Response may consist of one or more named or unnamed
+ returns  : a list of listrefs; each listref is one component of the queryInput or mobyData block
+            a single block may consist of one or more named or unnamed
             simple, collection, or parameter articles.
             The listref structure is thus [name, $ARTICLE_DOM]:
             
@@ -305,17 +301,17 @@
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Simple articleName='name1'&gt;
                       &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
-                &lt;/queryInput&gt;
+                &lt;/mobyData&gt;
         
     or  :  @articles = ['name1', $COLL_DOM], ['paramname1', $PARAM_DOM]</pre>
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -328,7 +324,7 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <p>
 </p>
 <h2><a name="genericserviceinputparserasobject">genericServiceInputParserAsObject</a></h2>
@@ -381,13 +377,13 @@
 <h2><a name="simpleresponse">simpleResponse</a></h2>
 <pre>
  name     : simpleResponse
- function : wraps a simple article in the appropriate queryResponse structure
+ function : wraps a simple article in the appropriate (mobyData) structure
  usage    : $resp .= &amp;simpleResponse($object, 'MyArticleName', $queryID);
  args     : (in order)
             $object   - (optional) a MOBY Object as raw XML
             $article  - (optional) an articeName for this article
             $query    - (optional, but strongly recommended) the queryID value for the
-                        queryInput block to which you are responding
+                        mobyData block to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
             response by calling &amp;simpleResponse(undef, undef, $queryID) with no arguments.</pre>
@@ -396,12 +392,12 @@
 <h2><a name="collectionresponse">collectionResponse</a></h2>
 <pre>
  name     : collectionResponse
- function : wraps a set of articles in the appropriate queryResponse structure
+ function : wraps a set of articles in the appropriate mobyData structure
  usage    : return responseHeader . &amp;collectionResponse(\@objects, 'MyArticleName', $queryID) . responseFooter;
  args     : (in order)
             \@objects - (optional) a listref of MOBY Objects as raw XML
             $article  - (optional) an articeName for this article
-            $queryID  - (optional, but strongly recommended) the queryInput ID
+            $queryID  - (optional, but strongly recommended) the mobyData ID
                         to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
@@ -442,7 +438,7 @@
 <h2><a name="getinputs">getInputs</a></h2>
 <pre>
  name     : getInputs
- function : get the queryInput block(s) as XML::DOM nodes
+ function : get the mobyData block(s) as XML::DOM nodes
  usage    : @queryInputs = getInputArticles($XML)
  args     : the raw XML of a &lt;MOBY&gt; query, or an XML::DOM document
  returns  : a list of XML::DOM::Node's, each is a queryInput or mobyData block.
@@ -467,11 +463,11 @@
 <h2><a name="getarticlesasobjects">getArticlesAsObjects</a></h2>
 <pre>
  name     : DO NOT USE!!
- function : get the Simple/Collection articles for a single queryInput
+ function : get the Simple/Collection articles for a single mobyData
             or queryResponse node, rethrning them as SimpleArticle,
             SecondaryArticle, or ServiceInstance objects
  usage    : @articles = getArticles($XML)
- args     : raw XML or XML::DOM of a moby:queryInput, moby:queryResponse block
+ args     : raw XML or XML::DOM of a moby:mobyData block
  returns  :</pre>
 <p>
 </p>
@@ -555,15 +551,20 @@
 <h2><a name="getnodecontentwitharticle">getNodeContentWithArticle</a></h2>
 <pre>
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or &quot;Parameter&quot; if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -584,15 +585,49 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, &quot;String&quot;, &quot;SequenceString&quot;);
-                     print &quot;matching node contents were &quot;.(join &quot;\n\n&quot;, @sequences).&quot;\n&quot;; # join all lines of string
-                 }   
-              }</pre>
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);</pre>
+<pre>
+            For Parameters, such as the following
+             ...
+             ...
+             &lt;moby:mobyContent&gt;
+                &lt;moby:mobyData&gt;
+                    &lt;Simple&gt;
+                      &lt;Sequence namespace=blah id=blah&gt;
+                           &lt;Integer namespace='' id='' articleName=&quot;Length&quot;&gt;3&lt;/Integer&gt;
+                           &lt;String namespace='' id='' articleName=&quot;SequenceString&quot;&gt;ATG&lt;/String&gt;
+                      &lt;/Sequence&gt;
+                    &lt;/Simple&gt;
+                    &lt;Parameter articleName='cutoff'&gt;
+                        &lt;Value&gt;24&lt;/Value&gt;
+                    &lt;/Parameter&gt;
+                &lt;/moby:mobyData&gt;
+             &lt;/moby:mobyContent&gt;
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);
+              @cutoffs = getNodeContentWithArticle($input, &quot;Parameter&quot;, &quot;cutoff&quot;);</pre>
+<pre>
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs-&gt;{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs-&gt;{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, &quot;Parameter&quot;, &quot;cutoff&quot;);
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, &quot;String&quot;, &quot;SequenceString&quot;);
+                }
+             }
+           }</pre>
 <p>
 </p>
 <h2><a name="validatenamespaces">validateNamespaces</a></h2>

From mwilkinson at pub.open-bio.org  Mon May  3 16:39:11 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 16:28:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032039.i43KdBEA012659@pub.open-bio.org>


mwilkinson
Mon May  3 16:39:11 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12636/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.8,1.9 Service.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/04/01 21:23:47	1.8
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
@@ -181,6 +181,16 @@
                 This would cause a single invocation of a service requiring
                 two input parameters named "input1" and "input2" 
 
+                $Service->execute(XMLinputlist => [
+	                         [
+                             'input1', '<Object namespace="blah" id="123"/>',
+                             'input2', '<Object namespace="blah" id="234"/>',
+                             'param1', '<Value>0.001</Value>',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named "input1" and "input2" 
+
 
 =cut
 
@@ -198,8 +208,11 @@
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
                 $XML ||= "";
-                $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
-                
+                if (($XML =~ /\<Value\>/) || ($XML =~ /\<moby\:Value\>/)){
+                    $data .= "<moby:Parameter moby:articleName='$articleName'>$XML</moby:Parameter>";
+                } else {
+                    $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
+                }
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/04/01 21:23:47	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
@@ -110,6 +110,16 @@
                               ]);
                 This would cause a single invocation of a service requiring
                 two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+<pre>
+                $Service-&gt;execute(XMLinputlist =&gt; [
+                                 [
+                             'input1', '&lt;Object namespace=&quot;blah&quot; id=&quot;123&quot;/&gt;',
+                             'input2', '&lt;Object namespace=&quot;blah&quot; id=&quot;234&quot;/&gt;',
+                             'param1', '&lt;Value&gt;0.001&lt;/Value&gt;',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>

From mwilkinson at pub.open-bio.org  Mon May  3 16:44:41 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 16:33:45 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032044.i43KifVR012740@pub.open-bio.org>


mwilkinson
Mon May  3 16:44:41 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12717/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.9,1.10 Service.html,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
@@ -189,7 +189,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named "input1" and "input2" 
+                two input parameters named "input1" and "input2", and a
+                parameter named 'param1' with a value of 0.001
 
 
 =cut

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:44:41	1.6
@@ -119,7 +119,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;, and a
+                parameter named 'param1' with a value of 0.001</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>

From mwilkinson at pub.open-bio.org  Mon May  3 16:51:15 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon May  3 16:40:20 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032051.i43KpFUl012830@pub.open-bio.org>


mwilkinson
Mon May  3 16:51:15 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12807/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing more documentation errors

moby-live/Perl/MOBY CommonSubs.pm,1.49,1.50 CommonSubs.html,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.49
retrieving revision 1.50
diff -u -r1.49 -r1.50
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
@@ -344,7 +344,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>
@@ -422,7 +421,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='e value cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
@@ -271,7 +271,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
@@ -321,7 +320,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='e value cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>

From mwilkinson at pub.open-bio.org  Tue May  4 19:54:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue May  4 19:43:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405042354.i44NsGmZ018527@pub.open-bio.org>


mwilkinson
Tue May  4 19:54:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv18504/Perl/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing and improving documentation for the service input parser

moby-live/Perl/MOBY CommonSubs.pm,1.50,1.51 CommonSubs.html,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.50
retrieving revision 1.51
diff -u -r1.50 -r1.51
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
@@ -263,6 +263,41 @@
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
 
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+                <mobyData queryID = '2'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
+
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the <Simple> block
+
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Collection>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    </Collection>
+                </mobyData>
+
+            will become:
+
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the <Simple> block
+
 =cut
 
 
@@ -314,7 +349,7 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 
@@ -344,7 +379,7 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/04 23:54:16	1.12
@@ -218,6 +218,41 @@
                          a. $article XML::DOM node for Simples
                             &lt;mobyData...&gt;...&lt;/mobyData&gt;
                          b. \@article XML:DOM nodes for Collections</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;
+                &lt;mobyData queryID = '2'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)</pre>
+<pre>
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the &lt;Simple&gt; block</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Collection&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;/Collection&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:</pre>
+<pre>
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the &lt;Simple&gt; block</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
@@ -242,7 +277,7 @@
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>
@@ -271,7 +306,7 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>

From gordonp at pub.open-bio.org  Wed May  5 23:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed May  5 23:11:56 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3HG024197@pub.open-bio.org>


gordonp
Wed May  5 23:23:03 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/docs

Modified Files:
	ChangeLog 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/docs ChangeLog,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/04/21 17:56:49	1.12
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
@@ -1,3 +1,8 @@
+2004-05-05  Paul Gordon <gordonp@cbr.nrc.ca>
+
+	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 
+        have the same mobyContent/mobyData envelopes.
+
 2004-04-21  Paul Gordon <gordonp@cbr.nrc.ca>
 
         * Implemented Moby data instance classes for simples, collections, 

From gordonp at pub.open-bio.org  Wed May  5 23:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed May  5 23:12:00 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3D3024178@pub.open-bio.org>


gordonp
Wed May  5 23:23:02 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/04/21 17:28:58	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
@@ -102,7 +102,7 @@
 	// Now compile the XPath statements that will be used fetch data from the server response
 	try{
 	    base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT);
-	    queryResponseXPath = new XPath("//moby:queryResponse | //queryResponse", null, mobyPrefixResolver, XPath.SELECT);
+	    queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT);
 	    simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT);
 	    collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT);
 	}
@@ -428,8 +428,8 @@
 	// Start of envelope
 	String mobyRequest = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
 	    "       <moby:MOBY xmlns:moby=\"" + MobyPrefixResolver.MOBY_XML_NAMESPACE + "\">\n" +
-	    "          <moby:Query>\n" +
-	    "<moby:queryInput moby:queryID='1'>";
+	    "          <moby:mobyContent>\n" +
+	    "<moby:mobyData moby:queryID='1'>";
 
 	// Real input data payload
 	if(data != null){
@@ -458,8 +458,8 @@
 	
 	// End of envelope
 	mobyRequest +=
-	    "              </moby:queryInput>\n" +
-	    "          </moby:Query>\n" +
+	    "              </moby:mobyData>\n" +
+	    "          </moby:mobyContent>\n" +
 	    "       </moby:MOBY>\n";
 	if(debug){
 	    debugPS.println("Input to MOBY Service is:");
@@ -483,17 +483,17 @@
 	try{
 	    response_list = runXPath(queryResponseXPath, n);
      	}catch(TransformerException te){
-            throw new MobyException("Cannot select MOBY DOM queryResponse nodes due to exception "+
+            throw new MobyException("Cannot select MOBY DOM mobyContent nodes due to exception "+
 				    "while executing XPath statement: " +te);
 	}
 	
 	if(response_list == null || response_list.getLength() == 0){
-	    throw new MobyException("Could not find any queryResponse elements in the output");
+	    throw new MobyException("Could not find any mobyContent elements in the output");
 	}
 	if(debug){
-	    debugPS.println("Aha! Got " + response_list.getLength() + " queryResponses");
+	    debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements");
 	}
-	// Do data deserialization for each queryResponse
+	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
 	    debugPS.println("Got response " + response);
@@ -504,7 +504,7 @@
 	    try{
 		collections = runXPath(collectionChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    for(int j = 0; collections != null && j < collections.getLength(); j++){
@@ -517,7 +517,7 @@
 		NodeList subsimples = null;
 		try{subsimples = runXPath(simpleChildXPath, collections.item(j));}
 		catch(TransformerException te){
-		    throw new MobyException("Cannot select MOBY DOM queryResponse/Collection/Simple " +
+		    throw new MobyException("Cannot select MOBY DOM mobyData/Collection/Simple " +
 					    "nodes due to exception "+
 					    "while executing XPath statement: " +te);
 		}
@@ -542,12 +542,12 @@
 	    try{
 		simples = runXPath(simpleChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    if((collections == null || collections.getLength() == 0) &&
 	       (simples == null || simples.getLength() == 0)){
-		debugPS.println("WARNING: There appears to be no output data in queryResponse #" + i);
+		debugPS.println("WARNING: There appears to be no output data in mobyData #" + i);
 	    }
 	    for(int j = 0; simples != null && j < simples.getLength(); j++){
 		if(debug && j == 0)

From mwilkinson at pub.open-bio.org  Tue May 11 11:48:45 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue May 11 11:36:58 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405111548.i4BFmjSU023513@pub.open-bio.org>


mwilkinson
Tue May 11 11:48:45 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv23494/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixed blockers in the OntologyServer.pm module.  Debugging is now OFF by default, and the logging will correctly exit

moby-live/Perl/MOBY OntologyServer.pm,1.40,1.41
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -r1.40 -r1.41
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/04/20 23:24:25	1.40
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
@@ -75,7 +75,7 @@
 use DBI;
 use DBD::mysql;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data
@@ -998,7 +998,7 @@
 
 
 sub _LOG {
-	#return unless $debug;
+	return unless $debug;
 	#print join "\n", @_;
 	#print  "\n---\n";
 	#return;

From mwilkinson at pub.open-bio.org  Thu May 13 13:56:33 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu May 13 13:44:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131756.i4DHuXHq032273@pub.open-bio.org>


mwilkinson
Thu May 13 13:56:33 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32254

Modified Files:
	OntologyServer.pm 
Added Files:
	OntologyServer.html 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.html,NONE,1.1 OntologyServer.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2003/07/10 20:43:09	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
@@ -41,7 +41,8 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (markw@illuminae.com)
+Mark Wilkinson (markw at illuminae.com)
+Nina Opushneva (opushneva at yahoo.ca)
 
 BioMOBY Project:  http://www.biomoby.org
 
@@ -57,7 +58,8 @@
  Usage     :	my $OS = MOBY::OntologyServer->new(%args)
  Function  :	
  Returns   :	MOBY::OntologyServer object
- Args      :    host =>  URL to ontolgy_server script
+ Args      :    host =>  URL to ontolgy_server script (default http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi)
+                proxy => URL to an HTTP proxy server if necessarray (optional)
 
 =cut
 
@@ -80,6 +82,8 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
                     host    =>      ["http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi",         'read/write'],
+					proxy	=>		[undef, 				'read/write'],
+					
                     );
 
    #_____________________________________________________________
@@ -121,6 +125,8 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
+    
+
     return undef unless $self->host;
     return $self;
 }
@@ -135,7 +141,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("objectExists=$term");
     my $res = $ua->request($req);
@@ -157,7 +163,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("serviceExists=$term");
     my $res = $ua->request($req);
@@ -178,7 +184,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("namespaceExists=$term");
     my $res = $ua->request($req);
@@ -199,7 +205,7 @@
     
     my $term = $args{'term'};
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("relationshipExists=$term");
     my $res = $ua->request($req);
@@ -210,6 +216,17 @@
     }
 }
 
+sub getUserAgent{
+	my ($self, @args) = @_;
+  my $ua = LWP::UserAgent->new;
+    my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment
+	$proxy = $self->proxy if $self->proxy;  # but if the object was initialized with a proxy argument then use that instead
+    if($proxy){
+       $ua->proxy('http', $proxy);
+    }
+  return $ua;
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {

From mwilkinson at pub.open-bio.org  Thu May 13 13:57:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu May 13 13:45:30 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131757.i4DHvYEs032321@pub.open-bio.org>


mwilkinson
Thu May 13 13:57:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32302

Modified Files:
	OntologyServer.pm 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:57:34	1.5
@@ -72,7 +72,7 @@
 use vars qw($AUTOLOAD);
 use LWP::UserAgent;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data

From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:00:50 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6K026303@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs/dist
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs/dist

Modified Files:
	_README_ 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs/dist _README_,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/dist/_README_	2003/11/08 00:27:24	1.1
+++ /home/repository/moby/moby-live/Java/docs/dist/_README_	2004/05/18 10:13:16	1.2
@@ -8,7 +8,7 @@
    jMoby-<date>.zip
 
 Servlet distribution - for those who want to run servlet producing
-BioMoby Graphs. Just rename the file ti jmoby.war and throw it into
+BioMoby Graphs. Just rename the file to jmoby.war and throw it into
 your <tomcat-home>/webapps directory, and restart Tomcat:
    jmoby-<date>.war
 

From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:00:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6Q026322@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients

Modified Files:
	MobyCmdLineClient.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients MobyCmdLineClient.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2003/11/25 13:18:10	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2004/05/18 10:13:16	1.4
@@ -443,25 +443,22 @@
 		    pattern.setAuthority (param.substring (pos+1));
 		    services = worker.findService (pattern);
 		}
-		if (services != null) {
-		    for (int i = 0; i < services.length; i++)
-			System.out.println (services[i]);
-		}
+		printServices (services, cmd.hasOption ("-on"));
 	    }
 	    if ((param = cmd.getParam ("-f")) != null ) {
 		decorationLn ("Looking for services related to: '" + param + "':");
 		decorationLn ("--------------------------------");
-		MobyService[] services = worker.findService (StringUtils.split (param, ","));
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		printServices (worker.findService (StringUtils.split (param, ",")),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if ((param = cmd.getParam ("-ft")) != null ) {
 		decorationLn ("Looking for services of type '" + param + "':");
 		decorationLn ("----------------------------");
-		MobyService[] services = worker.findService (param);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		MobyService pattern = new MobyService ("dummy");
+		pattern.setType (param);
+		printServices (worker.findService (pattern, null, !cmd.hasOption ("-nc"), true),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if (cmd.hasParam ("-fs-type") || cmd.hasParam ("-fs-auth") ||
@@ -474,24 +471,30 @@
 		    String[] inputs = StringUtils.split (param, ",");
 		    for (int i = 0; i < inputs.length; i++) {
 			String[] parts = StringUtils.split (inputs[i], "=");
-			if (parts.length >= 2) {
-// 			    pattern.addInput (parts[0], parts[1]);
-			} else {
-// 			    pattern.addInput (parts[0], "");
-			}
+			MobyPrimaryDataSimple input = new MobyPrimaryDataSimple ("dummy");
+			input.setDataType (new MobyDataType (parts[0]));
+			if (parts.length >= 2)
+			    input.addNamespace (new MobyNamespace (parts[1]));
+			pattern.addInput (input);
 		    }
 		}
                 if ((param = cmd.getParam ("-fs-out")) != null ) {
 		    String[] outs = StringUtils.split (param, ",");
 		    for (int i = 0; i < outs.length; i++) {
+			MobyPrimaryDataSimple output = new MobyPrimaryDataSimple ("dummy");
+			output.setDataType (new MobyDataType (outs[i]));
+			pattern.addOutput (output);
 // 			pattern.addOutputType (outs [i]);
 		    }
 		}
 		decoration (pattern.toString());
 		decorationLn ("-----------------------------------------------");
-		MobyService[] services = worker.findService (pattern);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		boolean includeChildrenServiceTypes = !cmd.hasOption ("-nc");
+		boolean includeParentDataTypes = !cmd.hasOption ("-np");
+		printServices (worker.findService (pattern, null,
+						   includeChildrenServiceTypes,
+						   includeParentDataTypes),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    //
@@ -560,4 +563,15 @@
 	}
     }
 
+    static void printServices (MobyService[] services, boolean onlyNames) {
+	if (services != null) {
+	    for (int i = 0; i < services.length; i++) {
+		if (onlyNames)
+		    System.out.println (services[i].getName());
+		else
+		    System.out.println (services[i]);
+	    }
+	}
+    }
+
 }

From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:01:12 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHaL026383@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/shared

Modified Files:
	Central.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/shared Central.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/04/02 16:40:23	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/05/18 10:13:17	1.5
@@ -308,6 +308,23 @@
 	throws MobyException;
 
     /**************************************************************************
+     * Find service matching both all non-empty fields in the 'pattern' and
+     * the 'keywords', and take into account also the whole ontology tree:
+     * <p>
+     * @param includeChildrenServiceTypes - if true (which is default)
+     * then it discovers also services that are child types (more
+     * specific) than the service type in 'pattern'
+     * @param includeParentDataTypes - if true (which is default) then
+     * it finds services that operate not only on the input/output
+     * data types defined in 'pattern', but also any ontolological
+     * parent types of that data types
+     *************************************************************************/
+    MobyService[] findService (MobyService pattern, String[] keywords,
+			       boolean includeChildrenServiceTypes,
+			       boolean includeParentDataTypes)
+	throws MobyException;
+
+    /**************************************************************************
      * Call Moby registry's method with given XML as input and return whatever
      * you get back. If 'inputXML' is null or empty, the method is called
      * without any parameters.

From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:01:13 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADGTP026284@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs

Modified Files:
	ChangeLog 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs ChangeLog,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
@@ -1,3 +1,12 @@
+2004-05-18  Martin Senger  <senger@ebi.ac.uk>
+
+	* Added a new displaying option (-on) to MobyCmdLineClient
+
+	* Added a new findService() method to Central.java allowing to set
+	also 'expandObjects' and 'expandServices' attributes.
+
+	* Added/fixed MobyCmdLineClient to to able to find service by input/output.
+
 2004-05-05  Paul Gordon <gordonp@cbr.nrc.ca>
 
 	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 

From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:01:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADH8J026343@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients/help

Modified Files:
	MobyCmdLineClient_usage.txt 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2003/11/24 18:45:25	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2004/05/18 10:13:16	1.4
@@ -58,7 +58,8 @@
       find services by keywords (apply logical OR if more keywords);
       <keywords> is a comma-delimited lists of keywords
 
- To find services by their input and/or output data types:
+ To find services by their input and/or output data types
+ (note that this works only for simple data, not for collections):
 
    -fs-type <service-type>
    -fs-auth <authority>
@@ -69,6 +70,16 @@
    -fs-out   <outputs>
       <outputs> are comma-delimited names of output types
 
+   You may limit the number of found services by specifying:
+   -nc ... do not include services that are child types (more
+           specific) than the type you requested
+           (this option also applies when searching with -ft)
+   -np ... do not include services operating on parent types of
+           the data types you requested
+
+ The found services are printed in details, unless:
+   -on ... print only names of found services
+
  To register a data type:
 
    -rd-name  <data-type-name>
@@ -149,7 +160,4 @@
      is a name of an existing file, the contents of this file
      is used as an input parameter to the called mathod
 
-     Note that this method is meant mostly for debugging and may
-     be depracated later.
-
    -debug  ... print debug messages

From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue May 18 06:01:21 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHfE026364@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/04/21 17:22:26	1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/05/18 10:13:17	1.13
@@ -1140,12 +1140,42 @@
      *************************************************************************/
     public MobyService[] findService (MobyService pattern, String[] keywords)
 	throws MobyException {
+	return findService (pattern, keywords, true, true);
+// 	if (pattern == null)
+// 	    pattern = new MobyService ("dummy");
+
+// 	String[] query = new String[] { 
+// 				"<findService>" +
+// 				buildQueryObject (pattern, keywords, true, true, false) + 
+// 				"</findService>"
+// 	};
+// 	if(useCache && cache.containsKey("findService"+query[0]))
+// 	    return (MobyService[]) cache.get("findService"+query[0]);
+	
+// 	String result = (String) doCall ("findService", query);
+// 	MobyService[] services = extractServices (result);
+
+// 	if(useCache)
+// 	    cache.put("findService"+query[0], services);
+// 	return services;
+    }
+
+    /**************************************************************************
+     *
+     *************************************************************************/
+    public MobyService[] findService (MobyService pattern, String[] keywords,
+				      boolean includeChildrenServiceTypes,
+				      boolean includeParentDataTypes)
+	throws MobyException {
 	if (pattern == null)
 	    pattern = new MobyService ("dummy");
 
 	String[] query = new String[] { 
 				"<findService>" +
-				buildQueryObject (pattern, keywords, true, true, false) + 
+				buildQueryObject (pattern, keywords,
+						  includeParentDataTypes,
+						  includeChildrenServiceTypes,
+						  false) + 
 				"</findService>"
 	};
 	if(useCache && cache.containsKey("findService"+query[0]))

From mwilkinson at pub.open-bio.org  Wed May 19 10:58:36 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed May 19 10:45:56 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191458.i4JEwaVu031596@pub.open-bio.org>


mwilkinson
Wed May 19 10:58:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv31577/Perl/MOBY/Client

Modified Files:
	Service.pm 
Log Message:
fixed errors in tags surrounding collections.  Updated with API changes to the Query and Queryinput tags

moby-live/Perl/MOBY/Client Service.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/19 14:58:36	1.11
@@ -204,7 +204,7 @@
 	foreach (@inputs){
 		return "ERROR:  expected listref [articleName, XML] for data element" unless (ref($_) =~ /array/i); 
 		my $qID = $self->_nextQueryID;
-        $data .= "<moby:queryInput queryID='$qID'>";
+        $data .= "<moby:mobyData queryID='$qID'>";
 		while (my ($articleName, $XML) = splice (@{$_}, 0, 2)){
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
@@ -217,20 +217,20 @@
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};
-                $data .="<moby:queryInput queryID='$qID'><moby:Collection moby:articleName='$articleName'>\n";
+                $data .="<moby:Collection moby:articleName='$articleName'>\n";
                 foreach (@objs){
-                    $data .= "$_\n";
+                    $data .= "<moby:Simple>$_</moby:Simple>\n";
                 }
                 $data .="</moby:Collection>\n";
             }
         }
-        $data .="</moby:queryInput>\n";
+        $data .="</moby:mobyData>\n";
 	}
 	$data = "<![CDATA[<?xml version='1.0' encoding='UTF-8'?>
 	<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
-	      <moby:Query>
+	      <moby:mobyContent>
 	          $data
-	      </moby:Query>
+	      </moby:mobyContent>
 	</moby:MOBY>]]>";
 	my $METHOD = $self->ServiceName;
 	&_LOG(%args, $METHOD);

From gss at pub.open-bio.org  Wed May 19 14:26:22 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:13:41 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQMU5000526@pub.open-bio.org>


gss
Wed May 19 14:26:22 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv501/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/04/01 00:30:54	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
@@ -1,6 +1,7 @@
 package org.sgd.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class SGD extends VocabularyDescription

From gss at pub.open-bio.org  Wed May 19 14:26:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:13:43 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQPB1000561@pub.open-bio.org>


gss
Wed May 19 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv534/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/04/01 00:35:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
@@ -1,6 +1,7 @@
 package org.pubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Pubs extends VocabularyDescription

From gss at pub.open-bio.org  Wed May 19 14:26:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:13:47 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQTSO000600@pub.open-bio.org>


gss
Wed May 19 14:26:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv575/.externalToolBuilders

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders added to the repository

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQetK000655@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot

Added Files:
	terms.n3 log4j.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,NONE,1.1 log4j.properties,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQebL000708@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv634

Modified Files:
	.classpath 
Added Files:
	.xdoclet xdoclet-build.xml 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server .xdoclet,NONE,1.1 xdoclet-build.xml,NONE,1.1 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/03/22 22:14:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/05/19 18:26:40	1.4
@@ -5,7 +5,7 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry exported="true" kind="src" path="/Jena2"/>
 	<classpathentry exported="true" kind="src" path="/HttpClient"/>
-	<classpathentry kind="lib" path="C:/cvs-repository/httpclient/lib/commons-logging.jar"/>
+	<classpathentry kind="lib" path="C:/commons-logging-1.0.3/commons-logging.jar"/>
 	<classpathentry exported="true" kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>

From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:02 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeiH000688@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java ProviderListServlet.java 
	GraphConversionServlet.java MOBYGraphValidationServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.1,1.2 ProviderListServlet.java,1.1,1.2 GraphConversionServlet.java,1.1,1.2 MOBYGraphValidationServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.ontology.*;
 import com.hp.hpl.jena.ontology.tidy.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,9 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.*;
+import org.smoby.servlet.*;
+import org.smoby.tools.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 import java.io.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.rdf.model.*;
 

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,8 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.parser.Parser;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 
@@ -23,18 +24,19 @@
 			Model baseModel = ModelFactory.createDefaultModel();
 			StringReader reader = new StringReader(graphString);
 			baseModel.read(reader, null);
-			new MOBYGraph(baseModel);
+			Parser parser = new Parser(baseModel);
+			parser.parseProvider();
 			out.println("Model is canonical");
 		}
         catch (ParameterException e)
         {
             response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, e.getMessage());
         }
-		catch (NonCanonicalException e)
-		{
-			out.println("Model failed canonicality test:");
-			out.println(e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			out.println("Model failed canonicality test:");
+//			out.println(e);
+//		}
 		catch (IllegalArgumentException e) {}
 	}
 }

From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:03 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQesY000741@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java DiscoveryQuery.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.2,1.3 DiscoveryQuery.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/03/27 01:27:51	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
@@ -3,11 +3,13 @@
 import java.util.*;
 import java.io.*;
 import javax.servlet.http.*;
-import org.smoby.tools.common.*;
+
+import org.smoby.tools.*;
+import org.smoby.http.*;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.http.*;
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
 import org.apache.commons.httpclient.util.*;
 import org.apache.commons.logging.*;
 
@@ -50,7 +52,7 @@
         synchronized (instances)
         {
         	if (instances.get(providerURL) != null) {
-                syncLog.warn("Already investigating " + providerURL);
+        		syncLog.warn("Already investigating " + providerURL);
                 return;
             }
             
@@ -97,7 +99,7 @@
         }
         catch (MissingPropertyException e)
         {
-            syncLog.error("Missing DB_REPOSITORY_NAME property");
+        	syncLog.error("Missing DB_REPOSITORY_NAME property");
         }
         finally
         {
@@ -140,7 +142,7 @@
         }
         catch (StorageException e)
         {
-            syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
             return;
         }
         
@@ -151,7 +153,7 @@
             }
             catch (StorageException e)
             {
-                syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
+            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
                 return;
             }
         }
@@ -164,7 +166,9 @@
         // be sent if it has been modified since that date
         //
         if (lastModifiedDate != null) {
-            request.addHeader(MOBY.IF_MODIFIED_HEADER,  Util.formatDateForHTTP(lastModifiedDate));
+            request.addHeader(
+                MOBY.IF_MODIFIED_HEADER,
+                Util.formatDateForHTTP(lastModifiedDate));
         }
         
         // Send the request and check the response code
@@ -178,7 +182,7 @@
         }
         catch (HTTPException e)
         {
-            syncLog.warn("Couldn't reach suggested provider " + providerURI);
+        	syncLog.warn("Couldn't reach suggested provider " + providerURI);
             return;
         }
         
@@ -203,7 +207,7 @@
                     // Log a message about the last modified date not being
                     // retrievable, but register the graph anyway
                     //
-                    syncLog.warn("Unable to get Last-Modified date for "
+                	syncLog.warn("Unable to get Last-Modified date for "
                                  + providerURI + "; ignoring");
                 }
                 catch (Throwable t)
@@ -211,7 +215,7 @@
                     // Log a message about the last modified date not being
                     // parsable, but register the graph anyway
                     //
-                    syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
+                	syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
                                 "\") for " + providerURI + "; ignoring");
                 }
 
@@ -219,25 +223,24 @@
                 // provider was already registered, then first de-register
                 // its currently stored description graph.
                 //
-                String graphString = "";
-                
+                InputStream in = null;
                 try {
-                	graphString = response.getBody();
+                	in = response.getBodyAsStream();
                 }
                 catch (HTTPException e)
                 {
-                    syncLog.error("Couldn't retrieve graph from " + providerURI);
+                	syncLog.error("Couldn't retrieve graph from " + providerURI);
                     return;
                 }
                 
-                Model graph = null;
-                
+                MOBYProvider provider = null;
                 try {
-                    graph = MOBYGraph.parseModel(graphString);
+                    Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
+                    provider = parser.parseProvider();
                 }
-                catch (UnparsableModelException e)
+                catch (UnparsableGraphException e)
                 {
-                    syncLog.warn("Unparsable graph found at " + providerURI +
+                	syncLog.warn("Unparsable graph found at " + providerURI +
                         (alreadyRegistered ? "; deregistering" : "; ignoring"));
                     if (alreadyRegistered) {
                         deregisterProvider(manager);
@@ -251,14 +254,14 @@
                 
                 try
                 {
-                    manager.registerGraph(graph, providerURI, lastModifiedDate);
+                    manager.registerProvider(provider, lastModifiedDate);
                     
                     // Log a message about successfully registering the graph:
                     //
                     syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
                 }
                 catch (StorageException e) {
-                    syncLog.error("Error storing graph for " + providerURI, e);
+                	syncLog.error("Error storing graph for " + providerURI, e);
                 }
                 
                 break;
@@ -268,7 +271,7 @@
                 // The resource has not been modified since it was
                 // registered, so there is nothing to do but log a message.
                 //
-                syncLog.info("IN-SYNC : " + providerURI);
+            	syncLog.info("IN-SYNC : " + providerURI);
                 break;
             
             case HttpServletResponse.SC_NOT_FOUND:
@@ -281,7 +284,7 @@
                     try
                     {
                     	manager.deregisterProvider(providerURI);
-                        syncLog.info("REMOVED : " + providerURI);
+                    	syncLog.info("REMOVED : " + providerURI);
                     }
                     catch (StorageException e) {
                     	syncLog.error("Unable to de-register provider " + providerURI, e);
@@ -296,7 +299,7 @@
                 
                 // Log a message about the failed attempt to contact the URL
                 //
-                syncLog.error("Status " + status + " received while trying " +
+            	syncLog.error("Status " + status + " received while trying " +
                              "to contact provider " + providerURI);
                 break;
         }

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/03/30 23:54:34	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
@@ -4,9 +4,12 @@
 import java.text.*;
 import java.util.*;
 
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.vocabulary.MOBY;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
+import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.graph.*;
@@ -41,7 +44,7 @@
     /**
      * The graph that serves as a template for providers that match.
      */
-    private MOBYGraph queryGraph;
+    private MOBYProvider queryProvider;
     
     /**
      * Flag indicating which statements should be returned: URI_ONLY,
@@ -67,9 +70,9 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYGraph queryGraph, int statementsToReturn)
+    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
-    	this.queryGraph = queryGraph;
+    	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
     }
     
@@ -83,22 +86,21 @@
         lastBnodeNumber = 0;
     }
     
-	public ProviderDescriptionGraph[] findMatchingGraphs()
+    public MOBYCollection findMatchingGraphs()
 	{
         init();
         
 		try
 		{
-            String queryString = buildQueryString(queryGraph);
+		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
+            String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-
             Model model = manager.openDBModel();
             ((ModelRDB) model).setDoFastpath(false);
             
 			// Execute the query
 			//
 			QueryResults results = Query.exec(queryString, model);
-
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -108,17 +110,19 @@
 			}
 			results.close();
 			
-			ProviderDescriptionGraph[] graphs =
-                new ProviderDescriptionGraph[matching.size()];
-			int i = 0;
-			for (Iterator it = matching.iterator(); it.hasNext(); i++)
+			List returnList = new ArrayList();
+			
+			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next());
-				graphs[i] = new ProviderDescriptionGraph(
-					new MOBYGraph(manager.openModel(mg.getProvider().getURI())));
+				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
+				String uri = mp.getURI();
+				// YUCK!
+				Model providerModel = manager.openModel(uri);
+				Parser parser = new Parser(providerModel);
+				returnList.add(parser.parseProvider());
 			}
 			
-			return graphs;
+			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
 			
 		} catch (Throwable t) {
 			return null;
@@ -128,10 +132,8 @@
 	/**
 	 * Build and return an RDQL query string for the reified Model
 	 */
-	private String buildQueryString(MOBYGraph queryGraph)
+	private String buildQueryString(Model queryModel)
 	{
-        Model queryModel = queryGraph.getModel();
-        
         String SPACES = "      ";
         
         Map nsMap = queryModel.getNsPrefixMap();
@@ -220,12 +222,8 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYGraph buildGraphModel(MOBYGraph queryGraph,
-                                      ResultBinding binding)
-		throws NonCanonicalException
+	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
 	{
-        Model queryModel = queryGraph.getModel();
-        
 		// Create a default model to return
 		//
 		Model model = ModelFactory.createDefaultModel();
@@ -247,7 +245,8 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		return new MOBYGraph(model);
+		Parser parser = new Parser(model);
+		return parser.parseProvider();
 	}
 	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)

From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfX1000828@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/03/29 19:40:08	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
@@ -1,10 +1,9 @@
 package org.smoby.ref.tools.db;
 
-import org.smoby.tools.common.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYProviderImpl;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.common.vocabulary.*;
-
+import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.shared.*;
@@ -65,28 +64,16 @@
      * are in the provider graph's namespace will be stored in the global repository,
      * and all statements from the provider graph are stored in a separate model
      * that has as its name the fully expanded URI of the provider.
-     * @param providerGraph the graph to store
+     * @param provider the Provider to store
      * @param lastModifiedDate when the graph was last modified
      * @throws StorageException if unable to access the database
      */
-	public void registerProviderGraph(MOBYGraph providerGraph, Date lastModifiedDate)
-        throws StorageException
-	{
-        registerGraph(providerGraph.getModel(),
-                      providerGraph.getProvider(),
-                      lastModifiedDate);
-	}
-    
-    public void registerGraph(Model graph, String uri, Date lastModifiedDate)
-        throws StorageException
-    {
-    	registerGraph(graph, graph.createResource(uri), lastModifiedDate);
-    }
-    
-    public void registerGraph(Model graph, Resource uri, Date lastModifiedDate)
+	public void registerProvider(MOBYProvider provider, Date lastModifiedDate)
         throws StorageException
 	{
+	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
+        Resource uri = model.createResource(provider.getURI());
         
         try
         {
@@ -114,7 +101,7 @@
             //
             String providerNameSpace = uri.getNameSpace();
             
-            for (StmtIterator it = graph.listStatements(); it.hasNext();)
+            for (StmtIterator it = model.listStatements(); it.hasNext();)
             {
                 Statement stmt = it.nextStatement();
                 Resource subject = stmt.getSubject();
@@ -132,8 +119,8 @@
             // Add to the database another model, with the provider URL as its name
             //
             Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(graph);
-            providerModel.setNsPrefixes(graph.getNsPrefixMap());
+            providerModel.add(model);
+            providerModel.setNsPrefixes(model.getNsPrefixMap());
             
             // Add a statement asserting when the model was added to the database
             //

From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfJi000807@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot/WEB-INF/classes

Modified Files:
	smoby.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/04/02 00:08:26	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/05/19 18:26:40	1.4
@@ -5,11 +5,11 @@
 #
 DB_USER_ID            = smobydev
 DB_PASSWORD           = 
-DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 DB_REPOSITORY_NAME    = smoby-dev
 
 # Uncomment if using MySQL
 #
+# DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 # DB_URL                = jdbc:mysql://localhost/smoby-dev
 # DB_TYPE               = MySQL
 

From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:14:08 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfu4000786@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv634/.externalToolBuilders

Added Files:
	XDoclet Builder.launch 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmg6000901@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv876/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
@@ -8,36 +8,36 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <megapubs:literatureGuideURL rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <megapubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Cool new search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
+  <rdf:Description rdf:nodeID="A2">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
+    <moby:hasMapping rdf:nodeID="A3"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqjx000978@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/04/02 00:03:39	1.7
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
@@ -2,17 +2,13 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.go.vocabulary.Go;
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.vocabulary.MOBY;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
-import com.acmepubs.vocabulary.AcmePubs;
-
-import com.hp.hpl.jena.rdf.model.*;
+import org.go.vocabulary.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
+import com.acmepubs.vocabulary.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -39,47 +35,47 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
         // Retrieve the subject of the moby:operatesOn statement (there is only
     	// one operatesOn statement in a valid MOBY graph)
         //
-        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-        
-        // There may be multiple moby:hasMapping statements. For each one,
-        // map its geneSymbol to a literatureGuideURL
-        //
-        StmtIterator it = graph.getModel().listStatements(
-        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-        
-        while (it.hasNext())
-        {
-    		try
-			{
-	        	Statement hasMappingStmt = it.nextStatement();
-	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-	        	
-	        	Statement geneSymbolStmt =
-	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-	        	
-    			String geneSymbol = geneSymbolStmt.getString();
-    			
-    			Statement mapsToStmt = 
-    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-    			
-				Resource mobyObject = (Resource) mapsToStmt.getObject();
-				
-				Statement literatureGuideURLStmt =
-					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-				
-				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-        	}
-    		catch (Throwable t)
-			{
-    			// Something went wrong, so proceed to next hasMapping statement
-    		}
-        }
+//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
+//        
+//        // There may be multiple moby:hasMapping statements. For each one,
+//        // map its geneSymbol to a literatureGuideURL
+//        //
+//        StmtIterator it = graph.getModel().listStatements(
+//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
+//        
+//        while (it.hasNext())
+//        {
+//    		try
+//			{
+//	        	Statement hasMappingStmt = it.nextStatement();
+//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
+//	        	
+//	        	Statement geneSymbolStmt =
+//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
+//	        	
+//    			String geneSymbol = geneSymbolStmt.getString();
+//    			
+//    			Statement mapsToStmt = 
+//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
+//    			
+//				Resource mobyObject = (Resource) mapsToStmt.getObject();
+//				
+//				Statement literatureGuideURLStmt =
+//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
+//				
+//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
+//        	}
+//    		catch (Throwable t)
+//			{
+//    			// Something went wrong, so proceed to next hasMapping statement
+//    		}
+//        }
     }
     
     /**

From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQq7s000997@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv953/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
@@ -14,30 +14,30 @@
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <acmepubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <acmepubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file

From gss at pub.open-bio.org  Wed May 19 14:26:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQtu5001055@pub.open-bio.org>


gss
Wed May 19 14:26:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1030/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
@@ -1,6 +1,7 @@
 package org.go.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Go extends VocabularyDescription

From gss at pub.open-bio.org  Wed May 19 14:26:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQihp000868@pub.open-bio.org>


gss
Wed May 19 14:26:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv843

Modified Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager SimpleProviderEngagerPanel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/05/19 18:26:44	1.2
@@ -4,13 +4,20 @@
 import javax.swing.border.*;
 import javax.swing.event.*;
 
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.graph.NonCanonicalException;
-import org.smoby.tools.common.graph.UnparsableModelException;
-import org.smoby.tools.common.http.HTTPException;
-import org.smoby.tools.common.http.HTTPRequest;
-import org.smoby.tools.common.http.HTTPResponse;
+import org.smoby.http.*;
+import org.smoby.graph.*;
+import org.smoby.parser.*;
 
+/**
+ * This class is a simple two-pane window for engaging Semantic MOBY
+ * providers. The user first pastes into the input pane a canonical graph
+ * of the form that is acceptable to the provider (i.e. the graph
+ * returned by doing an HTTP GET on the provider URI, with some of
+ * the blank nodes filled in). When the user presses the "Engage Provider"
+ * button, the graph is submitted, via HTTP POST, to the provider embedded
+ * in the graph; the results of the HTTP POST, as written by the provider,
+ * are then printed to the lower pane.
+ */
 public class SimpleProviderEngagerPanel extends JPanel
 {
 	private JTextArea inputArea = new JTextArea();
@@ -31,8 +38,7 @@
 		Font plain = new Font("Monospaced", Font.PLAIN, 12);
 		inputArea.setFont(plain);
 		outputArea.setFont(plain);
-		inputArea.setEditable(true);
-		outputArea.setEditable(false);
+		
 		engageButton.setEnabled(false);
 		
 		addListeners();
@@ -104,26 +110,26 @@
 		String graphString = inputArea.getText();
 		try
 		{
-			MOBYGraph mobyGraph = MOBYGraph.fromString(graphString, false);
-			String graphURI = mobyGraph.getProvider().getURI();
+		    Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+		    MOBYProvider provider = parser.parseProvider();
+			String graphURI = provider.getURI();
 			HTTPRequest request = HTTPRequest.newPostRequest(graphURI);
 			request.addParameter("graph", graphString);
 			HTTPResponse response = request.send();
 			outputArea.setText(response.getBody());
-//			inputArea.setText("");
 		}
-		catch (UnparsableModelException e)
+		catch (UnparsableGraphException e)
 		{
 			JOptionPane.showMessageDialog(this,
 				"The graph could not be parsed", "Unparsable",
 				JOptionPane.ERROR_MESSAGE);
 		}
-		catch (NonCanonicalException e)
-		{
-			JOptionPane.showMessageDialog(this,
-					"The graph is not canonical", "Non-canonoical",
-					JOptionPane.ERROR_MESSAGE);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			JOptionPane.showMessageDialog(this,
+//					"The graph is not canonical", "Non-canonoical",
+//					JOptionPane.ERROR_MESSAGE);
+//		}
 		catch (HTTPException e)
 		{
 			JOptionPane.showMessageDialog(this,

From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8U1001275@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/graph

Removed Files:
	ProviderDescriptionGraph.java NonCanonicalException.java 
	MOBYGraph.java UnparsableModelException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.java,1.1,NONE NonCanonicalException.java,1.1,NONE MOBYGraph.java,1.3,NONE UnparsableModelException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:30 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqrC001016@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
@@ -1,6 +1,7 @@
 package com.acmepubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class AcmePubs extends VocabularyDescription

From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8tS001385@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/io

Removed Files:
	TransceiverBase.java TokenSeparatedTransceiver.java 
	GraphListTransmitter.java ZipStreamTransceiver.java 
	GraphListTransceiverFactory.java GraphListReceiver.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io TransceiverBase.java,1.1,NONE TokenSeparatedTransceiver.java,1.1,NONE GraphListTransmitter.java,1.1,NONE ZipStreamTransceiver.java,1.1,NONE GraphListTransceiverFactory.java,1.1,NONE GraphListReceiver.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9QR001496@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common

Removed Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:27:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR7U5001256@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/server/servlet

Removed Files:
	ParamReader.java ParameterException.java 
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,1.1,NONE ParameterException.java,1.1,NONE AbstractMobyServlet.java,1.6,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8bH001324@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph/impl

Added Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYOntologyImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NO!
NE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:33 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8dY001291@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser

Added Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,NONE,1.1 UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:33 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQm02000920@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/03/27 01:17:58	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:48	1.4
@@ -2,12 +2,10 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -36,7 +34,7 @@
      * a gene symbol and returning a list of publication
      * abstracts.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
     }
     

From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:34 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9fT001458@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/vocabulary

Removed Files:
	MOBY.java VocabularyDescription.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,1.2,NONE VocabularyDescription.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8E6001358@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/http

Added Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9rs001480@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/http

Removed Files:
	HTTPException.java HTTPResponse.java HTTPRequest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPException.java,1.2,NONE HTTPResponse.java,1.3,NONE HTTPRequest.java,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9sx001439@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/servlet

Added Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 ParameterException.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmRJ000940@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/04/02 00:04:21	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
@@ -1,6 +1,7 @@
 package com.megapubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class MegaPubs extends VocabularyDescription

From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8lW001343@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8qw001309@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph

Added Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYDocument.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1 MOBYGraph.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8oF001420@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8pP001405@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:15:41 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeuc000765@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.2,1.3 DiscoveryServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/03/22 22:13:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
@@ -6,9 +6,9 @@
 import javax.servlet.http.*;
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
 import org.smoby.ref.tools.URIInvestigator;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.servlet.*;
 
 /**
  * This servlet class is used to request that S-MOBY investigate a URL for the

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,10 @@
 package org.smoby.ref.servlets;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.io.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.parser.NonCanonicalException;
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
 import java.io.*;
@@ -37,26 +38,18 @@
             //
 			String graphString = ParamReader.getParameter("query-graph", request);
             
-            // Does the requester want the matching graphs sent back in a
-            // binary format?
-            //
-            boolean binary = false;
-            try {
-            	ParamReader.getParameter("binary-return", request);
-                binary = true;
-            } catch (ParameterException e) {}
-            
             // Parse the query graph into a MOBYGraph object
             //
-			MOBYGraph g = MOBYGraph.fromString(graphString, true);
+			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+			MOBYProvider provider = parser.parseProvider();
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(g, DiscoveryQuery.ALL_STMTS);
-			ProviderDescriptionGraph[] matching = q.findMatchingGraphs();
+            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
+			MOBYCollection matching = q.findMatchingGraphs();
 			
-            if ((matching.length == 0) && (! binary))
+            if ((matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -66,23 +59,20 @@
             }
             else
             {
-                // Otherwise, create an object capable of transmitting the
-                // graphs (in either binary or human-readable text format)
-                // and use the object to send the matching graphs.
-                //
-                GraphListTransmitter transmitter =
-                    GraphListTransceiverFactory.newTransmitter(out, binary);
-                transmitter.transmit(matching);
+                for (Iterator it = matching.iterator(); it.hasNext();) {
+                    MOBYProvider p = (MOBYProvider) it.next();
+                    p.serialize(out);
+                }
 			}
             
 		}
-		catch (NonCanonicalException e)
-		{
-            // The query graph did not have the required canonical form
-            //
-			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-				"Query graph is not canonical:\n" + e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//            // The query graph did not have the required canonical form
+//            //
+//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
+//				"Query graph is not canonical:\n" + e);
+//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxY4001087@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:24 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQx3w001105@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:26 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxXt001123@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:27 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxkI001142@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxS8001185@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxUh001164@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 14:24:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxh9001203@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Wed May 19 16:42:30 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 16:29:48 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgUSK001852@pub.open-bio.org>


gss
Wed May 19 16:42:30 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv1831

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/server .encoding,NONE,1.1
From gss at pub.open-bio.org  Wed May 19 16:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 16:29:53 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgYQS001889@pub.open-bio.org>


gss
Wed May 19 16:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1860/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.4,1.5 citationSearch.rdf,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
@@ -10,28 +10,32 @@
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Cool new search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    megapubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    megapubs:literatureGuideURL _:bnode6 .
+    moby:name "MegaPubs Citation Search" ;
+    moby:oneLineDescription "Cool new search" ;
+    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                megapubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    megapubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 megapubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 megapubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
@@ -8,36 +8,43 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
+  <rdf:Description rdf:nodeID="A0">
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A0">
-    <megapubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
     <moby:operatesOn rdf:nodeID="A2"/>
+    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <moby:name>MegaPubs Citation Search</moby:name>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Cool new search</rdfs:comment>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A3"/>
+    <rdf:_1 rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
+    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-  </rdf:Description>
-</rdf:RDF>
\ No newline at end of file
+</rdf:RDF>

From gss at pub.open-bio.org  Wed May 19 16:42:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 16:29:58 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgbYu001926@pub.open-bio.org>


gss
Wed May 19 16:42:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1897/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.5,1.6 citationSearch.n3,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
@@ -12,31 +12,38 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
     <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A2"/>
-    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <acmepubs:geneSymbol rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:operatesOn rdf:nodeID="A4"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
+    <moby:name>AcmePubs Citation Search</moby:name>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
@@ -10,28 +10,32 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file

From gss at pub.open-bio.org  Wed May 19 19:33:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 19:20:23 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX5Ru002275@pub.open-bio.org>


gss
Wed May 19 19:33:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv2250/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
@@ -7,6 +7,7 @@
 import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
 import org.smoby.vocabulary.*;
 import com.acmepubs.vocabulary.*;
 
@@ -35,47 +36,54 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYProvider graph)
+    protected void handleRequest(MOBYProvider provider)
     {
-        // Retrieve the subject of the moby:operatesOn statement (there is only
-    	// one operatesOn statement in a valid MOBY graph)
-        //
-//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-//        
-//        // There may be multiple moby:hasMapping statements. For each one,
-//        // map its geneSymbol to a literatureGuideURL
-//        //
-//        StmtIterator it = graph.getModel().listStatements(
-//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-//        
-//        while (it.hasNext())
-//        {
-//    		try
-//			{
-//	        	Statement hasMappingStmt = it.nextStatement();
-//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-//	        	
-//	        	Statement geneSymbolStmt =
-//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-//	        	
-//    			String geneSymbol = geneSymbolStmt.getString();
-//    			
-//    			Statement mapsToStmt = 
-//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-//    			
-//				Resource mobyObject = (Resource) mapsToStmt.getObject();
-//				
-//				Statement literatureGuideURLStmt =
-//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-//				
-//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-//        	}
-//    		catch (Throwable t)
-//			{
-//    			// Something went wrong, so proceed to next hasMapping statement
-//    		}
-//        }
+        try
+        {
+            // There should be only one operatesOn subgraph, which should be
+            // a collection of MOBYGraph objects.
+            //
+            MOBYCollection coll = (MOBYCollection)
+            	provider.getOperatesOn().iterator().next();
+            
+            // Iterate over the MOBYGraph objects
+            //
+            Iterator it = coll.iterator();
+            while (it.hasNext())
+            {
+                MOBYGraph graph = (MOBYGraph) it.next();
+                
+                // The subject of the graph should be a MOBYSubject
+                //
+                MOBYSubject subject = (MOBYSubject) graph.gethasMapping();
+                
+                // That object should have a single subproperty of moby:Property,
+                // namely geneSymbol; its value should be a literal
+                //
+                MOBYPropertyValueStatement stmt = (MOBYPropertyValueStatement)
+                    subject.getPropertyValueStatements().iterator().next();
+                MOBYLiteral literal = (MOBYLiteral) stmt.getValue();
+                String geneSymbol = literal.getStringValue();
+                
+                // The object of the MOBYSubject should be a MOBYObject. That
+                // object should have a single subproperty of moby:Property,
+                // namely literatureGuideURL
+                //
+                MOBYObject object = (MOBYObject)
+                	subject.getDirectMappings().iterator().next();
+                stmt = (MOBYPropertyValueStatement)
+                	object.getPropertyValueStatements().iterator().next();
+                
+                // Set the value of the literatureGuideURL to a literal value
+                // based on a base URI string and the geneSymbol that was passed
+                //
+                String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+                literal = MOBYObjectFactory.newLiteralValue(
+                        baseURI + geneSymbol);
+                stmt.setPropertyValue(literal);
+            }
+        }
+        catch (Throwable t) {System.out.println(t);} // No feedback on failure...
     }
     
     /**

From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 19:20:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Lr002327@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 18:27:07	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 23:33:08	1.2
@@ -375,10 +375,7 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
-            boolean blankVal = pval.canAs(Resource.class) &&
-                               ((Resource) pval.as(Resource.class)).isAnon();
-            
-            if (blankVal && model.contains(res, p, pval) &&
+            if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
                 MOBYPropertyValueStatement pvalStmt =

From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 19:20:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9jX002373@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/servlet

Modified Files:
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet AbstractMobyServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 23:33:09	1.2
@@ -100,11 +100,12 @@
         
         try
         {
-            // Read the invocation graph from the "query-graph" parameter
+            // Read the invocation graph from the "graph" parameter
             // and parse it into a MOBYGraph object
             //
-            Parser parser = Parser.forInputStream(
-                   request.getInputStream(), Parser.LANGUAGE_RDF_XML);
+            String graphString = ParamReader.getParameter("graph", request);
+            Parser parser = Parser.forString(
+                   graphString, Parser.LANGUAGE_RDF_XML);
             MOBYProvider provider = parser.parseProvider();
             
             // Invoke the abstract handleRequest() method in order for the

From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 19:20:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9PQ002308@pub.open-bio.org>


gss
Wed May 19 19:33:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph

Modified Files:
	MOBYPropertyValueStatement.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYPropertyValueStatement.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 23:33:08	1.2
@@ -3,9 +3,17 @@
 
 public interface MOBYPropertyValueStatement
 {
+    /**
+     * Return the name of this property
+     */
     public String getPropertyName();
     
     /**
+     * Return the value currently associated with this property
+     */
+    public MOBYPropertyValue getValue();
+    
+    /**
      * Set the property value. This is just a placeholder; values of
      * different property types will be set to different types of
      * values.

From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 19 19:20:30 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Fj002352@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph/impl

Modified Files:
	MOBYPropertyValueStatementImpl.java MOBYObjectFactory.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYPropertyValueStatementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 23:33:09	1.2
@@ -8,11 +8,19 @@
 	implements MOBYPropertyValueStatement
 {
     Statement jenaStatement;
+    MOBYPropertyValue currentValue;
     MOBYPropertyValueConstraint constraint;
     
     MOBYPropertyValueStatementImpl(Statement jenaStatement, Model underlying) {
         super(null, underlying);
         this.jenaStatement = jenaStatement;
+        if (jenaStatement.getObject().canAs(Resource.class)) {
+            Resource value = (Resource) jenaStatement.getObject();
+            currentValue = new MOBYResourceImpl(value);
+        } else {
+            Literal value = (Literal) jenaStatement.getObject();
+            currentValue = new MOBYLiteralImpl(value.getString());
+        }
     }
     
     public String getPropertyName() {
@@ -23,6 +31,10 @@
         return jenaStatement.toString();
     }
     
+    public MOBYPropertyValue getValue() {
+        return currentValue;
+    }
+    
     public void setPropertyValue(MOBYPropertyValue newValue)
     	throws MOBYPropertyValueException
     {

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 23:33:09	1.2
@@ -66,6 +66,11 @@
         return new MOBYPropertyValueStatementImpl(statement, underlying);
     }
     
+    public static MOBYLiteral newLiteralValue(String value)
+    {
+        return new MOBYLiteralImpl(value);
+    }
+    
     public static MOBYPropertyValueConstraint newIntegerConstraint()
     {
         return new MOBYIntegerConstraintImpl();

From gordonp at pub.open-bio.org  Thu May 20 12:08:05 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu May 20 11:55:18 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201608.i4KG85q1004928@pub.open-bio.org>


gordonp
Thu May 20 12:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv4903

Modified Files:
	MobyRequest.java 
Log Message:
Just got rid of some debug statements

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/20 16:08:05	1.3
@@ -381,7 +381,6 @@
             throw new SOAPException("Cannot select SOAP nodes due to exception "+
 				    "while executing XPath statement:" +te);
 	}
-	debugPS.println("Result is " + node_list);
 
 	if(node_list == null || node_list.getLength() == 0){
 	    // Note: before giving up we should really have a plain string check as per the MOBY API 0.6
@@ -496,7 +495,6 @@
 	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
-	    debugPS.println("Got response " + response);
 	    
 	    Vector out = new Vector();
 	    // Find all the collections in the response
@@ -578,7 +576,6 @@
 	XObject xobject = xpath.execute(xpath_context, n, node_prefix_resolver);
 	if(xobject instanceof XNodeSet){
 	    result = ((XNodeSet) xobject).nodelist();
-	    debugPS.println("Result is " + result);
 	}
 	else if(debug && xobject != null){
 	    debugPS.println("Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName());

From gordonp at pub.open-bio.org  Thu May 20 12:18:46 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu May 20 12:06:01 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201618.i4KGIkaq004981@pub.open-bio.org>


gordonp
Thu May 20 12:18:46 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv4960

Added Files:
	MobyServiceInvocationExample.java 
Log Message:
Example class that uses jMOBY to find and invoke services based on seed data

moby-live/Java/src/Clients MobyServiceInvocationExample.java,NONE,1.1
From gordonp at pub.open-bio.org  Thu May 20 12:23:15 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu May 20 12:10:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201623.i4KGNFCo005051@pub.open-bio.org>


gordonp
Thu May 20 12:23:15 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv5026

Modified Files:
	ChangeLog 
Log Message:
Note location of good new service invocation example

moby-live/Java/docs ChangeLog,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/20 16:23:15	1.15
@@ -1,3 +1,9 @@
+2004-05-20  Paul Gordon <gordonp@cbr.nrc.ca>
+
+        * Added full working example of service discovery and invocation in 
+          src/Client/MobyServiceInvocationExample
+          Use that one instead of the example in this ChangeLog
+
 2004-05-18  Martin Senger  <senger@ebi.ac.uk>
 
 	* Added a new displaying option (-on) to MobyCmdLineClient

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQm028394@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:14 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PXV028354@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:15 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5P3v028299@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org added to the repository

moby-live/S-MOBY/ref-impl/core/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:16 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PMo028372@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:17 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PJH028316@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:17 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q1l028433@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:18 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Ph3028413@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:19 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Pvv028282@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src
In directory pub.open-bio.org:/tmp/cvs-serv28258/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src added to the repository

moby-live/S-MOBY/ref-impl/core/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:20 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q3K028470@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:22 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQd028336@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:23 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5QUV028452@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/tools

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Z0C028564@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph/impl

Added Files:
	MOBYOntologyImpl.java MOBYResourceImpl.java MOBYGraphImpl.java 
	MOBYPropertyValueConstraintImpl.java MOBYDescriptorImpl.java 
	MOBYOrderedCollectionImpl.java MOBYIntegerConstraintImpl.java 
	MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java 
	MOBYPropertyValueImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java 
	MOBYProviderImpl.java MOBYEnumerationImpl.java 
	MOBYLiteralImpl.java MOBYSingleElementImpl.java 
	MOBYDocumentImpl.java MOBYUnorderedCollectionImpl.java 
	MOBYNumericConstraintImpl.java MOBYGraphNodeImpl.java 
	MOBYObjectImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java MOBYCollectionImpl.java 
	MOBYObjectFactory.java MOBYMappingElementImpl.java 
	MOBYPropertyValueStatementImpl.java 
	MOBYResizableCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYOntologyImpl.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.jav!
a,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:29 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5YpV028532@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/servlet

Added Files:
	AbstractMobyServlet.java ParamReader.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet AbstractMobyServlet.java,NONE,1.1 ParamReader.java,NONE,1.1 ParameterException.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:31 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZUB028579@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph

Added Files:
	MOBYDocument.java MOBYOntology.java MOBYProvider.java 
	MOBYResource.java MOBYOrderedCollection.java MOBYSubject.java 
	MOBYSingleElement.java MOBYEnumeration.java 
	MOBYDescriptor.java MOBYPropertyValueStatement.java 
	MOBYLiteral.java MOBYCollection.java MOBYFixedCollection.java 
	MOBYPropertyValueException.java MOBYGraphNode.java 
	MOBYObject.java MOBYUnorderedCollection.java MOBYGraph.java 
	MOBYMappingElement.java MOBYResizableCollection.java 
	MOBYPropertyValueConstraint.java MOBYPropertyValue.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDocument.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYProvider.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYGraph.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a0h028675@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZZ6028594@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:36 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZSW028614@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/http

Added Files:
	HTTPException.java HTTPRequest.java HTTPResponse.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http HTTPException.java,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5aH2028631@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser

Added Files:
	UnparsableGraphException.java NonCanonicalException.java 
	Parser.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 Parser.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a8O028660@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv28511

Modified Files:
	build.xml .classpath 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
@@ -1,2 +1,3 @@
 <project name="core" basedir=".">
+    <property name="src" value="build"/>
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/03/27 01:14:22	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/05/24 22:05:35	1.4
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>

From gss at pub.open-bio.org  Mon May 24 18:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:52:40 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Yhf028547@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1
From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:03 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HX1028729@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser

Removed Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.2,NONE UnparsableGraphException.java,1.1,NONE NonCanonicalException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/Parser.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/UnparsableGraphException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/NonCanonicalException.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HRN028767@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph

Removed Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,1.1,NONE MOBYPropertyValueConstraint.java,1.1,NONE MOBYOntology.java,1.1,NONE MOBYPropertyValueStatement.java,1.2,NONE MOBYDescriptor.java,1.1,NONE MOBYFixedCollection.java,1.1,NONE MOBYMappingElement.java,1.1,NONE MOBYSingleElement.java,1.1,NONE MOBYUnorderedCollection.java,1.1,NONE MOBYEnumeration.java,1.1,NONE MOBYObject.java,1.1,NONE MOBYResizableCollection.java,1.1,NONE MOBYSubject.java,1.1,NONE MOBYResource.java,1.1,NONE MOBYOrderedCollection.java,1.1,NONE MOBYPropertyValueException.java,1.1,NONE MOBYDocument.java,1.1,NONE MOBYCollection.java,1.1,NONE MOBYGraphNode.java,1.1,NONE MOBYLiteral.java,1.1,NONE MOBYPropertyValue.java,1.1,NONE MOBYGraph.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYProvider.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueConstraint.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOntology.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueStatement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDescriptor.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYFixedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYMappingElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSingleElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYUnorderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYEnumeration.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYObject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResizableCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSubject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResource.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOrderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDocument.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraphNode.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYLiteral.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValue.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraph.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:08 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7H0j028830@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/tools

Removed Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/Util.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:09 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4r028906@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/servlet

Removed Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,1.1,NONE AbstractMobyServlet.java,1.2,NONE ParameterException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParameterException.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:10 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HlJ028849@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/http

Removed Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,1.1,NONE HTTPResponse.java,1.1,NONE HTTPException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPRequest.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPException.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7ID1028887@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/vocabulary

Removed Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,1.1,NONE MOBY.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/MOBY.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HtL028814@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph/impl

Removed Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,1.1,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYOntologyImpl.java,1.1,NONE MOBYDocumentImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.1,NONE MOBYResizableCollectionImpl.java,1.1,NONE MOBYDescriptorImpl.java,1.1,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.1,NONE MOBYObjectFactory.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYSingleElementImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYProviderImpl.java,1.1,NONE MOBYLiteralImpl.java,1.1,NONE MOBYGraphNodeImpl.java,1.1,NONE MOBYCollectionImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.1,NONE MOBYFixedCollectionImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYSubjectImpl.java,1.1,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.1,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.!
1,NONE MOBYUnorderedCollectionImpl.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory

From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon May 24 17:54:12 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4o028866@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser/test

Removed Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,1.1,NONE ParserTest.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/Test.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/ParserTest.java,v: No such file or directory

From gss at pub.open-bio.org  Wed May 26 19:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed May 26 19:14:19 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405262327.i4QNRlVa003497@pub.open-bio.org>


gss
Wed May 26 19:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv3472

Modified Files:
	.cvsignore 
Log Message:
Ignore build directory

moby-live/S-MOBY/ref-impl/core .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/03/22 22:21:39	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
@@ -1 +1,2 @@
-classes
\ No newline at end of file
+classes
+build

From gss at pub.open-bio.org  Thu May 27 11:30:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:17:09 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271530.i4RFUek4006236@pub.open-bio.org>


gss
Thu May 27 11:30:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6210

Modified Files:
	.cvsignore 
Log Message:
Removed blank line

moby-live/S-MOBY/ref-impl/core .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
@@ -1,2 +1,2 @@
 classes
-build
+build
\ No newline at end of file

From gss at pub.open-bio.org  Thu May 27 11:31:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:17:58 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271531.i4RFVVL8006281@pub.open-bio.org>


gss
Thu May 27 11:31:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv6256/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Remove go.org import

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/27 15:31:31	1.10
@@ -4,7 +4,6 @@
 import java.util.*;
 import javax.servlet.*;
 import javax.servlet.http.*;
-import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.MOBYObjectFactory;

From gss at pub.open-bio.org  Thu May 27 11:54:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:40:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFs8NB006492@pub.open-bio.org>


gss
Thu May 27 11:54:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv6471

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,NONE,1.1 .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 11:54:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:40:39 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsCqr006525@pub.open-bio.org>


gss
Thu May 27 11:54:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv6500

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/server build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/03/12 17:48:32	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
@@ -1,2 +1,29 @@
-<project name="server" basedir=".">
+<!-- Apache Ant format build file for s-moby.org example provider -->
+
+<project name="s-moby.org" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="s-moby.org.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>

From gss at pub.open-bio.org  Thu May 27 11:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:40:47 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKMG006565@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv6544

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,NONE,1.1 .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 11:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:40:48 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKIa006580@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv6544/WebRoot/WEB-INF

Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 11:54:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:40:55 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsSar006627@pub.open-bio.org>


gss
Thu May 27 11:54:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6602

Modified Files:
	build.xml 
Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,NONE,1.1 build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/03/12 17:48:33	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
@@ -1,2 +1,29 @@
-<project name="megapubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="megapubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="megapubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>

From gss at pub.open-bio.org  Thu May 27 11:54:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:41:07 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFseHV006690@pub.open-bio.org>


gss
Thu May 27 11:54:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6657

Modified Files:
	build.xml .classpath 
Added Files:
	.cvsignore .xdoclet 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,NONE,1.1 .xdoclet,1.2,1.3 build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.xdoclet,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
@@ -1,2 +1,29 @@
-<project name="acmepubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="acmepubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="acmepubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/05/27 15:54:40	1.4
@@ -5,9 +5,6 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>
-	<classpathentry kind="src" path="/www.go.org"/>
-	<classpathentry kind="src" path="/www.pubs.org"/>
-	<classpathentry kind="src" path="/www.sgd.org"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>

From gss at pub.open-bio.org  Thu May 27 11:54:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:41:13 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsiWe006723@pub.open-bio.org>


gss
Thu May 27 11:54:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6698

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/core build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
@@ -1,3 +1,26 @@
-<project name="core" basedir=".">
-    <property name="src" value="build"/>
+<!-- Apache Ant format build file for Semantic MOBY core library -->
+
+<project name="smoby-core" default="jar" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../library.xml"/>
+
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+    <!-- Compile all the source files that go into the library -->
+    <target name="compile">
+        <mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="core.classpath"/>
+        </javac>
+    </target>
+    
+    <!-- Deploy the jar file to the Tomcat shared library directory -->
+    <target name="deploy-to-tomcat" depends="jar">
+        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
 </project>

From gss at pub.open-bio.org  Thu May 27 12:03:43 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:50:09 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271603.i4RG3hAF006842@pub.open-bio.org>


gss
Thu May 27 12:03:42 EDT 2004
Update of /home/repository/moby/www.go.org
In directory pub.open-bio.org:/tmp/cvs-serv6818/www.go.org

Log Message:
Directory /home/repository/moby/www.go.org added to the repository

www.go.org - New directory
rcsdiff: /home/repository/moby/www.go.org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 12:11:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 11:57:41 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271611.i4RGBFHF007039@pub.open-bio.org>


gss
Thu May 27 12:11:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv7018

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .encoding,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 12:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 12:10:26 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271623.i4RGNxH0007277@pub.open-bio.org>


gss
Thu May 27 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv7256

Added Files:
	.cvsignore build.xml 
Log Message:
Oops, had released to wrong directory

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,NONE,1.1 build.xml,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 14:31:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 14:18:11 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271831.i4RIVkXZ008515@pub.open-bio.org>


gss
Thu May 27 14:31:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv8494

Added Files:
	.cvsignore 
Log Message:


moby-live/S-MOBY/ref-impl/server .cvsignore,NONE,1.1
From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:32 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3cg009360@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src
In directory pub.open-bio.org:/tmp/cvs-serv9336/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:33 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Gl009378@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:34 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Jq009397@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:35 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Js009416@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby/exampleclients

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/directory,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 15:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbAZ5009474@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv9444

Modified Files:
	.classpath .cvsignore 
Added Files:
	build.xml 
Removed Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,NONE,1.1 .classpath,1.1,1.2 .cvsignore,1.1,1.2 SimpleProviderEngagerPanel.java,1.2,NONE
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/05/27 19:37:10	1.2
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="src" path="/Jena2"/>
 	<classpathentry kind="src" path="/HttpClient"/>
-	<classpathentry kind="output" path=""/>
+	<classpathentry kind="output" path="build"/>
 </classpath>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/04/02 00:45:31	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
@@ -1,2 +1,2 @@
 classes
-*.class
\ No newline at end of file
+build

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/SimpleProviderEngagerPanel.java,v: No such file or directory

From gss at pub.open-bio.org  Thu May 27 15:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu May 27 15:23:38 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbA5Z009489@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9444/src/org/smoby/exampleclients

Added Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,NONE,1.1
From ambrose at pub.open-bio.org  Fri May 28 16:54:08 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri May 28 16:40:28 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282054.i4SKs8F0013990@pub.open-bio.org>


ambrose
Fri May 28 16:54:08 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv13964

Modified Files:
	NamespaceMaintenance.cgi 
Log Message:
fixed mysql duplicate entry problem caused by updating form field error

moby-live/Perl/Accessories NamespaceMaintenance.cgi,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/04/29 18:03:52	1.2
+++ /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/05/28 20:54:08	1.3
@@ -6,18 +6,31 @@
 my $namespace_id;
 my $authabvr;
 my $namespacetype;
-    if (param('ns')) { #ns param specified; user intends to load from database so open database and load up parameters
-        my @ns = split (/\_/,param('ns'));
-        param('authabvr'=>$ns[0]);
-        param('namespacetype'=>$ns[1]);
-        $authabvr=$ns[0];
-        $namespacetype=$ns[1];
-        my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
-        my $dbh1 = open_dbi();
-        my $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
-        $sth1->execute($retrieve);
+    if (param('ns') or param('id')) { #ns or id param specified; user intends to load from database so open database and load up parameters
+        my $sth1;
+        if (param('ns')) {
+            my @ns = split (/\_/,param('ns'));
+            param('authabvr'=>$ns[0]);
+            param('namespacetype'=>$ns[1]);
+            $authabvr=$ns[0];
+            $namespacetype=$ns[1];
+            my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
+            $sth1->execute($retrieve);
+        }
+        else {
+            my $retrieve = param('id');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_id = ?});
+            $sth1->execute($retrieve);
+        }
         my ($id, $namespace_lsid,  $namespace_type, $desc, $auth, $contactemail, $object,  $generic_url,  $synonym,  $urlsyntax,  $urlexample,  $shorthandname, $example_id, $note) = $sth1->fetchrow_array();
         $namespace_id = $id;
+        my @split = split(/\:/, $namespace_lsid);
+        ($authabvr, $namespacetype) = split(/\_/,$split[4]);
+        param('authabvr'=>$authabvr);
+        param('namespacetype'=>$namespacetype);
         param('desc'=>$desc);
         param('auth'=>$auth);
         param('object'=>$object);
@@ -58,20 +71,22 @@
         param('shorthand_name'=>$shorthandname);
         param('example_id'=>$example_id);
         param('note'=>$note);
+        param('continue'=>1);
+        param('nsid'=>$id);
     }
 
     print header,
-        start_html(-title => 'Namespace Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}),
-        
-        h1('Namespace Form');
+        start_html(-title => 'Namespace Update Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}, -class => "update"),
+        h1('Namespace Update Form');
+        print "Database search page is located here: ",a({href=>'http://mobycentral.cbr.nrc.ca/cgi-bin/search.cgi'}, "Search Page"),p,; 
         if (!$namespace_id) {
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         "Full abbreviation will be \"authority abbreviation_identifier abbreviation\" e.g. \"GeneDB_Tbrucei\"",
         start_form,
         table(
-        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB")),
+        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB"),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation* "),td(textfield(-name =>'namespacetype', -class => "require"),"e.g.: Tbrucei")),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name => 'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -105,11 +120,11 @@
         else {
             param('namespace_id'=>$namespace_id);
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         start_form,
         table(
-        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id'))),
+        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id')),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation: "),td($namespacetype),(hidden('namespacetype'))),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name =>'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -135,7 +150,7 @@
         Tr(td("url_example "),td(textfield('url_iec'),"e.g.: http\:\/\/www.genedb.org\/genedb\/Search\?organism=tryp&name=Tb927.1.5250")),
         Tr(td("shorthand_names "),td(textarea('shorthand_name'),"e.g.: Tbrucei. one entry per line")),
         Tr(td("note "),td(textarea('note'))),
-    Tr(td(submit)),
+    Tr(td(submit -name => 'submit values', -class => 'submit')),
     Tr(td(reset)),
     end_form,),p,
         $namespace_id,p,
@@ -168,31 +183,29 @@
         if (param('note')) {$Param{note}=param('note');}
         if (param('syn')) {$Param{syn} = param('syn');}
         
-if (param() and !param('ns')) {
-        my $error = chkerrors(%Param);
-        my %variables;
-        if ($error == 0){
-            %variables = setvariables(%Param);
-
-        
+if (param() and !param('ns') and !param('id')) {
+    my $error = chkerrors(%Param);
+    my %variables;
+    if ($error == 0){
+        %variables = setvariables(%Param);
         my $dbh = open_dbi();
-        my $sth;
- 
-        if (!param('namespace_id')) {
+        my $sth; 
+        if (!param('namespace_id') and param('continue') != 1) {
             adddata ($dbh, $sth, %variables);
         }
         else {
-            my $nsid = (param('namespace_id'));
+            my $nsid;
+            if (param('namespace_id')) {
+            $nsid = (param('namespace_id')); }
+            elsif (param('nsid')) { $nsid= param('nsid'); }
             updatedata ($dbh, $sth, $nsid, %variables);
         }
         $variables{authabvr} = param('authabvr');
         finalprinttoscreen (%variables);
-        param('namespace_id')=>undef;
-        }
+    }
+    #elsif ($error == 1) { print hidden('continue'=>1); }
 }
 
-elsif (param('ns')){ param('ns')=>undef;
-                    }
 #########
 
 
@@ -267,11 +280,7 @@
         print "invalid url_synonym header",hr;
         return 1;
     }
-    #elsif ($Param{example_id} =~ /\W/)  {
-     #   print "invalid characters in example_id",hr;
-      #  return 1;
-    #}
-    
+   
     else { return 0; }
 }
 sub setvariables {
@@ -358,7 +367,7 @@
         }
 sub finalprinttoscreen { #final printing to screen after updating database
     my (%variables) = @_;
-            print pre(
+            print pre(p,"successful!",p
         "namespace_type = ",$variables{namespacetype},p,
         "lsid = ",$variables{lsid},p,
         "description = ",$variables{desc},p,

From gss at pub.open-bio.org  Fri May 28 17:35:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri May 28 17:21:37 2004
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282135.i4SLZIbg014116@pub.open-bio.org>


gss
Fri May 28 17:35:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv14091

Modified Files:
	build.xml 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/27 19:37:10	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
@@ -1,26 +1,24 @@
-<!-- Apache Ant format build file for Semantic MOBY core library -->
+<!-- Apache Ant format build file for the SimpleEngager client GUI -->
 
-<project name="smoby-core" default="jar" basedir=".">
+<project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../../library.xml"/>
+
+    <!-- The main jar file -->
+    <property name="jar-file" value="${build-dir}/engager.jar"/>
 
     <!-- Package the compiled source files into the main jar file -->
     <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
     </target>
     
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
         <javac srcdir="${src-dir}" destdir="${classes-dir}">
-            <classpath refid="core.classpath"/>
+            <classpath refid="common.classpath"/>
         </javac>
     </target>
     
-    <!-- Deploy the jar file to the Tomcat shared library directory -->
-    <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
-    </target>
-    
 </project>

From mwilkinson at pub.open-bio.org  Mon May  3 11:07:51 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 11:07:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031507.i43F7ptf011702@pub.open-bio.org>


mwilkinson
Mon May  3 11:07:51 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11683/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
more documentation and tools for dealing with secondary inputs

moby-live/Perl/MOBY CommonSubs.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/04/29 22:37:57	1.47
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
@@ -30,9 +30,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant "SIMPLE" or "COLLECTION"
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs));
@@ -163,7 +163,11 @@
 use MOBY::Client::OntologyServer;
 use strict;
 use warnings;
-
+use MOBY::Client::SimpleArticle;
+use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
+            
+            
 use constant COLLECTION => 1;
 use constant SIMPLE => 2;
 use constant SECONDARY => 3;
@@ -191,6 +195,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -223,6 +228,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -244,19 +250,18 @@
 
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node
 
 =cut
 
@@ -276,7 +281,7 @@
                 push @inputs, [COLLECTION,$queryID, \@simples];
             } elsif (isSimpleArticle($article)){
                 push @inputs, [SIMPLE,$queryID,$article];
-            } elsif (isSecondaryArticle($article)){
+            } elsif (isSecondaryArticle($article)){  # should never happen in a generic service parser!
                 push @inputs, [SECONDARY,$queryID,$article];
             }
         }
@@ -290,7 +295,7 @@
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -317,14 +322,14 @@
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs->{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [SIMPLE, $DOM_name1], # the <Simple> block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= <Parameter> block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
             to parse XML DOM objects.
-            
-            
+
+
             Collections --------------------
             
             With inputs that have collections these are presented as a
@@ -347,8 +352,8 @@
 
             will become
             
-            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the <Simple> Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = <Parameter> Block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
@@ -891,7 +896,7 @@
         } elsif ($child->getTagName =~ /Collection/){
             $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
         } elsif ($child->getTagName =~ /Parameter/){
-            $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
+            $object = MOBY::Client::SecondaryArticle->new(XML_DOM => $child);
         }
         next unless $object;
         push @articles, $object;   # take the child elements, which are <Simple/> or <Collection/>
@@ -1097,15 +1102,20 @@
 =head2 getNodeContentWithArticle
 
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or "Parameter" if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -1126,16 +1136,50 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, "String", "SequenceString");
-                     print "matching node contents were ".(join "\n\n", @sequences)."\n"; # join all lines of string
-                 }   
-              }
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
 
+            For Parameters, such as the following
+             ...
+             ...
+             <moby:mobyContent>
+                <moby:mobyData>
+                    <Simple>
+                      <Sequence namespace=blah id=blah>
+                           <Integer namespace='' id='' articleName="Length">3</Integer>
+                           <String namespace='' id='' articleName="SequenceString">ATG</String>
+                      </Sequence>
+                    </Simple>
+                    <Parameter articleName='cutoff'>
+                        <Value>24</Value>
+                    </Parameter>
+                </moby:mobyData>
+             </moby:mobyContent>
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
+              @cutoffs = getNodeContentWithArticle($input, "Parameter", "cutoff");
+
+
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs->{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs->{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, "Parameter", "cutoff");
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, "String", "SequenceString");
+                }
+             }
+           }
 
 =cut
 
@@ -1157,19 +1201,38 @@
     unless ($nodes->item(0)){
         $nodes = $node->getElementsByTagName("moby:$element");
     }
+
 	for (0..$nodes->getLength-1){
         my $child = $nodes->item($_);
-		if (
+        if (
             (($child->getAttribute("articleName")) && (($child->getAttribute("articleName") eq $articleName)))
             || (($child->getAttribute("moby:articleName")) && (($child->getAttribute("moby:articleName") eq $articleName)))){
-			# now we have a valid child, get the content... stringified... regardless of what it is
-			my $resp;
-			foreach ($child->getChildNodes){
-                next unless $_->getNodeType == TEXT_NODE;
-				$resp .= $_->toString;
-			}
-			push @contents, $resp;
-		}
+            # now we have a valid child, get the content... stringified... regardless of what it is
+            
+            if (isSecondaryArticle($child)){
+                my $resp;
+                my $valuenodes = $child->getElementsByTagName('Value');
+                unless ($valuenodes->item(0)){
+                    $valuenodes = $child->getElementsByTagName("moby:Value");
+                }
+                for (0..$valuenodes->getLength-1){
+                    my $valuenode = $valuenodes->item($_);
+                    foreach my $amount ($valuenode->getChildNodes){
+                        next unless $amount->getNodeType == TEXT_NODE;
+                        $resp .= $amount->toString;
+                    }
+                }
+                push @contents, $resp;
+                
+            } else {
+                my $resp;
+                foreach ($child->getChildNodes){
+                    next unless $_->getNodeType == TEXT_NODE;
+                    $resp .= $_->toString;
+                }
+                push @contents, $resp;
+            }
+        }
 	}
 	return @contents;
 }



From mwilkinson at pub.open-bio.org  Mon May  3 15:49:18 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 15:49:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031949.i43JnI0k012385@pub.open-bio.org>


mwilkinson
Mon May  3 15:49:18 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12366

Modified Files:
	Central.pm 
Added Files:
	SecondaryArticle.html SecondaryArticle.pm 
Log Message:
added an object to represent a parameter

moby-live/Perl/MOBY/Client SecondaryArticle.html,NONE,1.1 SecondaryArticle.pm,NONE,1.1 Central.pm,1.74,1.75
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.74
retrieving revision 1.75
diff -u -r1.74 -r1.75
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/04/14 19:56:59	1.74
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
@@ -75,14 +75,29 @@
  Function  :	connect to one or more MOBY-Central
                 registries for searching
  Returns   :	MOBY::Client::Central object
+ 
+ ENV & PROXY : you can set environment variables to change the defaults.
+             By default, a call to 'new' will initialize MOBY::Client::Central
+             to connect to the MOBY Central registry at:
+             http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl
+             If you wish to chose another registry by default, or if you need
+             to set up additional connection details (e.g. PROXY) then you may
+             set the following environment variables to whatever you
+             require:
+             MOBY_SERVER  (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
+             MOBY_URI     (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
+             MOBY_PROXY   (no default)
+                
  Args      :    Registries - optional.
                            - takes the form
                               {$NAME1 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                $NAME2 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                 }
                             - by default this becomes
                             {mobycentral => {
@@ -125,6 +140,7 @@
 				default_MOBY_servername => ['mobycentral',												'read/write'],
 				default_MOBY_server 	=> ['http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl', 	'read/write'],
 				default_MOBY_uri		=> ['http://mobycentral.cbr.nrc.ca/MOBY/Central',				'read/write'],
+                default_MOBY_proxy      => [undef,                                                      'read/write'],
 				default_MOBY_type		=> ['soap',                                                     'read/write'],
 				Registries              => [undef, 														'read/write'],
 				multiple_registries		=> [undef,														'read/write'],
@@ -238,6 +254,7 @@
 	$self->default_MOBY_server($ENV{MOBY_SERVER}) if $ENV{MOBY_SERVER};
 	$self->default_MOBY_uri($ENV{MOBY_URI}) if $ENV{MOBY_URI};
 	$self->default_MOBY_type($ENV{MOBY_TYPE}) if $ENV{MOBY_TYPE};
+	$self->default_MOBY_proxy($ENV{MOBY_PROXY}) if $ENV{MOBY_PROXY};
 	
 	
     if ($self->Registries){
@@ -248,11 +265,19 @@
 			my $url = $acc->{URL};
 			my $uri = $acc->{URI};
 			my $type = $acc->{TYPE};
+			my $proxy = $acc->{PROXY};
 			$type ||='soap';
 			if (lc($type) eq "get"){
 				push @{$self->Connections}, [$name, $type, $url];
 			} else {
-				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy($url)->uri($uri)->on_fault(
+                my @soapargs;
+                if ($proxy){
+                    @soapargs = ($url,
+                                proxy => ['http' => $proxy]);
+                } else {
+                    @soapargs = ($url);
+                }
+				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy(@soapargs)->uri($uri)->on_fault(
 					sub{
 						my($soap, $res) = @_; 
 						die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";
@@ -270,7 +295,16 @@
 								URI => $self->default_MOBY_uri
 							  }}
 							 );
-			push @{$self->Connections},[$self->default_MOBY_servername, $self->default_MOBY_type, SOAP::Lite->proxy($self->default_MOBY_server)->uri($self->default_MOBY_uri)->on_fault(
+            my @soapargs;
+            if ($self->default_MOBY_proxy){
+                @soapargs = ($self->default_MOBY_server,
+                            proxy => ['http' => $self->default_MOBY_proxy]);
+            } else {
+                @soapargs = ($self->default_MOBY_server);
+            }
+			push @{$self->Connections},[$self->default_MOBY_servername,
+                                        $self->default_MOBY_type,
+                                        SOAP::Lite->proxy(@soapargs)->uri($self->default_MOBY_uri)->on_fault(
 				sub{
 					my($soap, $res) = @_; 
 					die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";



From mwilkinson at pub.open-bio.org  Mon May  3 16:15:32 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:15:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032015.i43KFWrL012520@pub.open-bio.org>


mwilkinson
Mon May  3 16:15:32 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12497

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing documentation error that Bertrand spotted

moby-live/Perl/MOBY CommonSubs.pm,1.48,1.49 CommonSubs.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
@@ -314,7 +314,6 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/04/14 20:10:35	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
@@ -86,9 +86,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant &quot;SIMPLE&quot; or &quot;COLLECTION&quot;
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data-&gt;type('base64' =&gt; responseHeader(&quot;my.authURI.com&quot;) . responseFooter()) unless (scalar(@inputs));
@@ -206,25 +206,24 @@
 <pre>
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
-                            &lt;queryInput...&gt;...&lt;/queryInput&gt;
-                         b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node</pre>
+                            &lt;mobyData...&gt;...&lt;/mobyData&gt;
+                         b. \@article XML:DOM nodes for Collections</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
 <pre>
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -238,33 +237,31 @@
             
             for example, the input message:
             
-                &lt;queryInput queryID = '1'&gt;
+                &lt;mobyData queryID = '1'&gt;
                     &lt;Simple articleName='name1'&gt;
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1], # the &lt;Simple&gt; block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= &lt;Parameter&gt; block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
-            to parse XML DOM objects.
-            
-            
+            to parse XML DOM objects.</pre>
+<pre>
             Collections --------------------
             
             With inputs that have collections these are presented as a
             listref of Simple article DOM's.  So for the following message:
             
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -277,12 +274,12 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become
             
-            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the &lt;Simple&gt; Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = &lt;Parameter&gt; Block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
@@ -292,12 +289,11 @@
 <h2><a name="getarticles">getArticles</a></h2>
 <pre>
  name     : getArticles
- function : get the Simple/Collection/Parameter articles for a single queryInput
-            or queryResponse node
+ function : get the Simple/Collection/Parameter articles for a single mobyData
  usage    : @articles = getArticles($XML)
  args     : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs)
- returns  : a list of listrefs; each listref is one component of the queryInput.
-            a single queryInput/Response may consist of one or more named or unnamed
+ returns  : a list of listrefs; each listref is one component of the queryInput or mobyData block
+            a single block may consist of one or more named or unnamed
             simple, collection, or parameter articles.
             The listref structure is thus [name, $ARTICLE_DOM]:
             
@@ -305,17 +301,17 @@
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Simple articleName='name1'&gt;
                       &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
-                &lt;/queryInput&gt;
+                &lt;/mobyData&gt;
         
     or  :  @articles = ['name1', $COLL_DOM], ['paramname1', $PARAM_DOM]</pre>
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -328,7 +324,7 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <p>
 </p>
 <h2><a name="genericserviceinputparserasobject">genericServiceInputParserAsObject</a></h2>
@@ -381,13 +377,13 @@
 <h2><a name="simpleresponse">simpleResponse</a></h2>
 <pre>
  name     : simpleResponse
- function : wraps a simple article in the appropriate queryResponse structure
+ function : wraps a simple article in the appropriate (mobyData) structure
  usage    : $resp .= &amp;simpleResponse($object, 'MyArticleName', $queryID);
  args     : (in order)
             $object   - (optional) a MOBY Object as raw XML
             $article  - (optional) an articeName for this article
             $query    - (optional, but strongly recommended) the queryID value for the
-                        queryInput block to which you are responding
+                        mobyData block to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
             response by calling &amp;simpleResponse(undef, undef, $queryID) with no arguments.</pre>
@@ -396,12 +392,12 @@
 <h2><a name="collectionresponse">collectionResponse</a></h2>
 <pre>
  name     : collectionResponse
- function : wraps a set of articles in the appropriate queryResponse structure
+ function : wraps a set of articles in the appropriate mobyData structure
  usage    : return responseHeader . &amp;collectionResponse(\@objects, 'MyArticleName', $queryID) . responseFooter;
  args     : (in order)
             \@objects - (optional) a listref of MOBY Objects as raw XML
             $article  - (optional) an articeName for this article
-            $queryID  - (optional, but strongly recommended) the queryInput ID
+            $queryID  - (optional, but strongly recommended) the mobyData ID
                         to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
@@ -442,7 +438,7 @@
 <h2><a name="getinputs">getInputs</a></h2>
 <pre>
  name     : getInputs
- function : get the queryInput block(s) as XML::DOM nodes
+ function : get the mobyData block(s) as XML::DOM nodes
  usage    : @queryInputs = getInputArticles($XML)
  args     : the raw XML of a &lt;MOBY&gt; query, or an XML::DOM document
  returns  : a list of XML::DOM::Node's, each is a queryInput or mobyData block.
@@ -467,11 +463,11 @@
 <h2><a name="getarticlesasobjects">getArticlesAsObjects</a></h2>
 <pre>
  name     : DO NOT USE!!
- function : get the Simple/Collection articles for a single queryInput
+ function : get the Simple/Collection articles for a single mobyData
             or queryResponse node, rethrning them as SimpleArticle,
             SecondaryArticle, or ServiceInstance objects
  usage    : @articles = getArticles($XML)
- args     : raw XML or XML::DOM of a moby:queryInput, moby:queryResponse block
+ args     : raw XML or XML::DOM of a moby:mobyData block
  returns  :</pre>
 <p>
 </p>
@@ -555,15 +551,20 @@
 <h2><a name="getnodecontentwitharticle">getNodeContentWithArticle</a></h2>
 <pre>
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or &quot;Parameter&quot; if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -584,15 +585,49 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, &quot;String&quot;, &quot;SequenceString&quot;);
-                     print &quot;matching node contents were &quot;.(join &quot;\n\n&quot;, @sequences).&quot;\n&quot;; # join all lines of string
-                 }   
-              }</pre>
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);</pre>
+<pre>
+            For Parameters, such as the following
+             ...
+             ...
+             &lt;moby:mobyContent&gt;
+                &lt;moby:mobyData&gt;
+                    &lt;Simple&gt;
+                      &lt;Sequence namespace=blah id=blah&gt;
+                           &lt;Integer namespace='' id='' articleName=&quot;Length&quot;&gt;3&lt;/Integer&gt;
+                           &lt;String namespace='' id='' articleName=&quot;SequenceString&quot;&gt;ATG&lt;/String&gt;
+                      &lt;/Sequence&gt;
+                    &lt;/Simple&gt;
+                    &lt;Parameter articleName='cutoff'&gt;
+                        &lt;Value&gt;24&lt;/Value&gt;
+                    &lt;/Parameter&gt;
+                &lt;/moby:mobyData&gt;
+             &lt;/moby:mobyContent&gt;
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);
+              @cutoffs = getNodeContentWithArticle($input, &quot;Parameter&quot;, &quot;cutoff&quot;);</pre>
+<pre>
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs-&gt;{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs-&gt;{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, &quot;Parameter&quot;, &quot;cutoff&quot;);
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, &quot;String&quot;, &quot;SequenceString&quot;);
+                }
+             }
+           }</pre>
 <p>
 </p>
 <h2><a name="validatenamespaces">validateNamespaces</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 16:39:11 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:39:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032039.i43KdBEA012659@pub.open-bio.org>


mwilkinson
Mon May  3 16:39:11 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12636/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.8,1.9 Service.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/04/01 21:23:47	1.8
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
@@ -181,6 +181,16 @@
                 This would cause a single invocation of a service requiring
                 two input parameters named "input1" and "input2" 
 
+                $Service->execute(XMLinputlist => [
+	                         [
+                             'input1', '<Object namespace="blah" id="123"/>',
+                             'input2', '<Object namespace="blah" id="234"/>',
+                             'param1', '<Value>0.001</Value>',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named "input1" and "input2" 
+
 
 =cut
 
@@ -198,8 +208,11 @@
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
                 $XML ||= "";
-                $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
-                
+                if (($XML =~ /\<Value\>/) || ($XML =~ /\<moby\:Value\>/)){
+                    $data .= "<moby:Parameter moby:articleName='$articleName'>$XML</moby:Parameter>";
+                } else {
+                    $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
+                }
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/04/01 21:23:47	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
@@ -110,6 +110,16 @@
                               ]);
                 This would cause a single invocation of a service requiring
                 two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+<pre>
+                $Service-&gt;execute(XMLinputlist =&gt; [
+                                 [
+                             'input1', '&lt;Object namespace=&quot;blah&quot; id=&quot;123&quot;/&gt;',
+                             'input2', '&lt;Object namespace=&quot;blah&quot; id=&quot;234&quot;/&gt;',
+                             'param1', '&lt;Value&gt;0.001&lt;/Value&gt;',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 16:44:41 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:44:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032044.i43KifVR012740@pub.open-bio.org>


mwilkinson
Mon May  3 16:44:41 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12717/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.9,1.10 Service.html,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
@@ -189,7 +189,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named "input1" and "input2" 
+                two input parameters named "input1" and "input2", and a
+                parameter named 'param1' with a value of 0.001
 
 
 =cut

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:44:41	1.6
@@ -119,7 +119,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;, and a
+                parameter named 'param1' with a value of 0.001</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 16:51:15 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:51:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032051.i43KpFUl012830@pub.open-bio.org>


mwilkinson
Mon May  3 16:51:15 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12807/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing more documentation errors

moby-live/Perl/MOBY CommonSubs.pm,1.49,1.50 CommonSubs.html,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.49
retrieving revision 1.50
diff -u -r1.49 -r1.50
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
@@ -344,7 +344,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>
@@ -422,7 +421,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='e value cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
@@ -271,7 +271,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
@@ -321,7 +320,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='e value cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>



From mwilkinson at pub.open-bio.org  Tue May  4 19:54:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 4 May 2004 19:54:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405042354.i44NsGmZ018527@pub.open-bio.org>


mwilkinson
Tue May  4 19:54:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv18504/Perl/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing and improving documentation for the service input parser

moby-live/Perl/MOBY CommonSubs.pm,1.50,1.51 CommonSubs.html,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.50
retrieving revision 1.51
diff -u -r1.50 -r1.51
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
@@ -263,6 +263,41 @@
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
 
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+                <mobyData queryID = '2'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
+
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the <Simple> block
+
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Collection>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    </Collection>
+                </mobyData>
+
+            will become:
+
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the <Simple> block
+
 =cut
 
 
@@ -314,7 +349,7 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 
@@ -344,7 +379,7 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/04 23:54:16	1.12
@@ -218,6 +218,41 @@
                          a. $article XML::DOM node for Simples
                             &lt;mobyData...&gt;...&lt;/mobyData&gt;
                          b. \@article XML:DOM nodes for Collections</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;
+                &lt;mobyData queryID = '2'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)</pre>
+<pre>
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the &lt;Simple&gt; block</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Collection&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;/Collection&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:</pre>
+<pre>
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the &lt;Simple&gt; block</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
@@ -242,7 +277,7 @@
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>
@@ -271,7 +306,7 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>



From gordonp at pub.open-bio.org  Wed May  5 23:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 5 May 2004 23:23:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3HG024197@pub.open-bio.org>


gordonp
Wed May  5 23:23:03 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/docs

Modified Files:
	ChangeLog 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/docs ChangeLog,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/04/21 17:56:49	1.12
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
@@ -1,3 +1,8 @@
+2004-05-05  Paul Gordon <gordonp at cbr.nrc.ca>
+
+	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 
+        have the same mobyContent/mobyData envelopes.
+
 2004-04-21  Paul Gordon <gordonp at cbr.nrc.ca>
 
         * Implemented Moby data instance classes for simples, collections, 



From gordonp at pub.open-bio.org  Wed May  5 23:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 5 May 2004 23:23:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3D3024178@pub.open-bio.org>


gordonp
Wed May  5 23:23:02 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/04/21 17:28:58	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
@@ -102,7 +102,7 @@
 	// Now compile the XPath statements that will be used fetch data from the server response
 	try{
 	    base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT);
-	    queryResponseXPath = new XPath("//moby:queryResponse | //queryResponse", null, mobyPrefixResolver, XPath.SELECT);
+	    queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT);
 	    simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT);
 	    collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT);
 	}
@@ -428,8 +428,8 @@
 	// Start of envelope
 	String mobyRequest = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
 	    "       <moby:MOBY xmlns:moby=\"" + MobyPrefixResolver.MOBY_XML_NAMESPACE + "\">\n" +
-	    "          <moby:Query>\n" +
-	    "<moby:queryInput moby:queryID='1'>";
+	    "          <moby:mobyContent>\n" +
+	    "<moby:mobyData moby:queryID='1'>";
 
 	// Real input data payload
 	if(data != null){
@@ -458,8 +458,8 @@
 	
 	// End of envelope
 	mobyRequest +=
-	    "              </moby:queryInput>\n" +
-	    "          </moby:Query>\n" +
+	    "              </moby:mobyData>\n" +
+	    "          </moby:mobyContent>\n" +
 	    "       </moby:MOBY>\n";
 	if(debug){
 	    debugPS.println("Input to MOBY Service is:");
@@ -483,17 +483,17 @@
 	try{
 	    response_list = runXPath(queryResponseXPath, n);
      	}catch(TransformerException te){
-            throw new MobyException("Cannot select MOBY DOM queryResponse nodes due to exception "+
+            throw new MobyException("Cannot select MOBY DOM mobyContent nodes due to exception "+
 				    "while executing XPath statement: " +te);
 	}
 	
 	if(response_list == null || response_list.getLength() == 0){
-	    throw new MobyException("Could not find any queryResponse elements in the output");
+	    throw new MobyException("Could not find any mobyContent elements in the output");
 	}
 	if(debug){
-	    debugPS.println("Aha! Got " + response_list.getLength() + " queryResponses");
+	    debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements");
 	}
-	// Do data deserialization for each queryResponse
+	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
 	    debugPS.println("Got response " + response);
@@ -504,7 +504,7 @@
 	    try{
 		collections = runXPath(collectionChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    for(int j = 0; collections != null && j < collections.getLength(); j++){
@@ -517,7 +517,7 @@
 		NodeList subsimples = null;
 		try{subsimples = runXPath(simpleChildXPath, collections.item(j));}
 		catch(TransformerException te){
-		    throw new MobyException("Cannot select MOBY DOM queryResponse/Collection/Simple " +
+		    throw new MobyException("Cannot select MOBY DOM mobyData/Collection/Simple " +
 					    "nodes due to exception "+
 					    "while executing XPath statement: " +te);
 		}
@@ -542,12 +542,12 @@
 	    try{
 		simples = runXPath(simpleChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    if((collections == null || collections.getLength() == 0) &&
 	       (simples == null || simples.getLength() == 0)){
-		debugPS.println("WARNING: There appears to be no output data in queryResponse #" + i);
+		debugPS.println("WARNING: There appears to be no output data in mobyData #" + i);
 	    }
 	    for(int j = 0; simples != null && j < simples.getLength(); j++){
 		if(debug && j == 0)



From mwilkinson at pub.open-bio.org  Tue May 11 11:48:45 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 11 May 2004 11:48:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405111548.i4BFmjSU023513@pub.open-bio.org>


mwilkinson
Tue May 11 11:48:45 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv23494/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixed blockers in the OntologyServer.pm module.  Debugging is now OFF by default, and the logging will correctly exit

moby-live/Perl/MOBY OntologyServer.pm,1.40,1.41
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -r1.40 -r1.41
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/04/20 23:24:25	1.40
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
@@ -75,7 +75,7 @@
 use DBI;
 use DBD::mysql;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data
@@ -998,7 +998,7 @@
 
 
 sub _LOG {
-	#return unless $debug;
+	return unless $debug;
 	#print join "\n", @_;
 	#print  "\n---\n";
 	#return;



From mwilkinson at pub.open-bio.org  Thu May 13 13:56:33 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 13 May 2004 13:56:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131756.i4DHuXHq032273@pub.open-bio.org>


mwilkinson
Thu May 13 13:56:33 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32254

Modified Files:
	OntologyServer.pm 
Added Files:
	OntologyServer.html 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.html,NONE,1.1 OntologyServer.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2003/07/10 20:43:09	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
@@ -41,7 +41,8 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (markw at illuminae.com)
+Mark Wilkinson (markw at illuminae.com)
+Nina Opushneva (opushneva at yahoo.ca)
 
 BioMOBY Project:  http://www.biomoby.org
 
@@ -57,7 +58,8 @@
  Usage     :	my $OS = MOBY::OntologyServer->new(%args)
  Function  :	
  Returns   :	MOBY::OntologyServer object
- Args      :    host =>  URL to ontolgy_server script
+ Args      :    host =>  URL to ontolgy_server script (default http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi)
+                proxy => URL to an HTTP proxy server if necessarray (optional)
 
 =cut
 
@@ -80,6 +82,8 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
                     host    =>      ["http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi",         'read/write'],
+					proxy	=>		[undef, 				'read/write'],
+					
                     );
 
    #_____________________________________________________________
@@ -121,6 +125,8 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
+    
+
     return undef unless $self->host;
     return $self;
 }
@@ -135,7 +141,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("objectExists=$term");
     my $res = $ua->request($req);
@@ -157,7 +163,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("serviceExists=$term");
     my $res = $ua->request($req);
@@ -178,7 +184,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("namespaceExists=$term");
     my $res = $ua->request($req);
@@ -199,7 +205,7 @@
     
     my $term = $args{'term'};
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("relationshipExists=$term");
     my $res = $ua->request($req);
@@ -210,6 +216,17 @@
     }
 }
 
+sub getUserAgent{
+	my ($self, @args) = @_;
+  my $ua = LWP::UserAgent->new;
+    my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment
+	$proxy = $self->proxy if $self->proxy;  # but if the object was initialized with a proxy argument then use that instead
+    if($proxy){
+       $ua->proxy('http', $proxy);
+    }
+  return $ua;
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {



From mwilkinson at pub.open-bio.org  Thu May 13 13:57:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 13 May 2004 13:57:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131757.i4DHvYEs032321@pub.open-bio.org>


mwilkinson
Thu May 13 13:57:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32302

Modified Files:
	OntologyServer.pm 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:57:34	1.5
@@ -72,7 +72,7 @@
 use vars qw($AUTOLOAD);
 use LWP::UserAgent;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data



From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6K026303@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs/dist
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs/dist

Modified Files:
	_README_ 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs/dist _README_,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/dist/_README_	2003/11/08 00:27:24	1.1
+++ /home/repository/moby/moby-live/Java/docs/dist/_README_	2004/05/18 10:13:16	1.2
@@ -8,7 +8,7 @@
    jMoby-<date>.zip
 
 Servlet distribution - for those who want to run servlet producing
-BioMoby Graphs. Just rename the file ti jmoby.war and throw it into
+BioMoby Graphs. Just rename the file to jmoby.war and throw it into
 your <tomcat-home>/webapps directory, and restart Tomcat:
    jmoby-<date>.war
 



From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6Q026322@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients

Modified Files:
	MobyCmdLineClient.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients MobyCmdLineClient.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2003/11/25 13:18:10	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2004/05/18 10:13:16	1.4
@@ -443,25 +443,22 @@
 		    pattern.setAuthority (param.substring (pos+1));
 		    services = worker.findService (pattern);
 		}
-		if (services != null) {
-		    for (int i = 0; i < services.length; i++)
-			System.out.println (services[i]);
-		}
+		printServices (services, cmd.hasOption ("-on"));
 	    }
 	    if ((param = cmd.getParam ("-f")) != null ) {
 		decorationLn ("Looking for services related to: '" + param + "':");
 		decorationLn ("--------------------------------");
-		MobyService[] services = worker.findService (StringUtils.split (param, ","));
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		printServices (worker.findService (StringUtils.split (param, ",")),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if ((param = cmd.getParam ("-ft")) != null ) {
 		decorationLn ("Looking for services of type '" + param + "':");
 		decorationLn ("----------------------------");
-		MobyService[] services = worker.findService (param);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		MobyService pattern = new MobyService ("dummy");
+		pattern.setType (param);
+		printServices (worker.findService (pattern, null, !cmd.hasOption ("-nc"), true),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if (cmd.hasParam ("-fs-type") || cmd.hasParam ("-fs-auth") ||
@@ -474,24 +471,30 @@
 		    String[] inputs = StringUtils.split (param, ",");
 		    for (int i = 0; i < inputs.length; i++) {
 			String[] parts = StringUtils.split (inputs[i], "=");
-			if (parts.length >= 2) {
-// 			    pattern.addInput (parts[0], parts[1]);
-			} else {
-// 			    pattern.addInput (parts[0], "");
-			}
+			MobyPrimaryDataSimple input = new MobyPrimaryDataSimple ("dummy");
+			input.setDataType (new MobyDataType (parts[0]));
+			if (parts.length >= 2)
+			    input.addNamespace (new MobyNamespace (parts[1]));
+			pattern.addInput (input);
 		    }
 		}
                 if ((param = cmd.getParam ("-fs-out")) != null ) {
 		    String[] outs = StringUtils.split (param, ",");
 		    for (int i = 0; i < outs.length; i++) {
+			MobyPrimaryDataSimple output = new MobyPrimaryDataSimple ("dummy");
+			output.setDataType (new MobyDataType (outs[i]));
+			pattern.addOutput (output);
 // 			pattern.addOutputType (outs [i]);
 		    }
 		}
 		decoration (pattern.toString());
 		decorationLn ("-----------------------------------------------");
-		MobyService[] services = worker.findService (pattern);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		boolean includeChildrenServiceTypes = !cmd.hasOption ("-nc");
+		boolean includeParentDataTypes = !cmd.hasOption ("-np");
+		printServices (worker.findService (pattern, null,
+						   includeChildrenServiceTypes,
+						   includeParentDataTypes),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    //
@@ -560,4 +563,15 @@
 	}
     }
 
+    static void printServices (MobyService[] services, boolean onlyNames) {
+	if (services != null) {
+	    for (int i = 0; i < services.length; i++) {
+		if (onlyNames)
+		    System.out.println (services[i].getName());
+		else
+		    System.out.println (services[i]);
+	    }
+	}
+    }
+
 }



From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHaL026383@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/shared

Modified Files:
	Central.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/shared Central.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/04/02 16:40:23	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/05/18 10:13:17	1.5
@@ -308,6 +308,23 @@
 	throws MobyException;
 
     /**************************************************************************
+     * Find service matching both all non-empty fields in the 'pattern' and
+     * the 'keywords', and take into account also the whole ontology tree:
+     * <p>
+     * @param includeChildrenServiceTypes - if true (which is default)
+     * then it discovers also services that are child types (more
+     * specific) than the service type in 'pattern'
+     * @param includeParentDataTypes - if true (which is default) then
+     * it finds services that operate not only on the input/output
+     * data types defined in 'pattern', but also any ontolological
+     * parent types of that data types
+     *************************************************************************/
+    MobyService[] findService (MobyService pattern, String[] keywords,
+			       boolean includeChildrenServiceTypes,
+			       boolean includeParentDataTypes)
+	throws MobyException;
+
+    /**************************************************************************
      * Call Moby registry's method with given XML as input and return whatever
      * you get back. If 'inputXML' is null or empty, the method is called
      * without any parameters.



From senger at pub.open-bio.org  Tue May 18 06:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADGTP026284@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs

Modified Files:
	ChangeLog 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs ChangeLog,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
@@ -1,3 +1,12 @@
+2004-05-18  Martin Senger  <senger at ebi.ac.uk>
+
+	* Added a new displaying option (-on) to MobyCmdLineClient
+
+	* Added a new findService() method to Central.java allowing to set
+	also 'expandObjects' and 'expandServices' attributes.
+
+	* Added/fixed MobyCmdLineClient to to able to find service by input/output.
+
 2004-05-05  Paul Gordon <gordonp at cbr.nrc.ca>
 
 	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 



From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADH8J026343@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients/help

Modified Files:
	MobyCmdLineClient_usage.txt 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2003/11/24 18:45:25	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2004/05/18 10:13:16	1.4
@@ -58,7 +58,8 @@
       find services by keywords (apply logical OR if more keywords);
       <keywords> is a comma-delimited lists of keywords
 
- To find services by their input and/or output data types:
+ To find services by their input and/or output data types
+ (note that this works only for simple data, not for collections):
 
    -fs-type <service-type>
    -fs-auth <authority>
@@ -69,6 +70,16 @@
    -fs-out   <outputs>
       <outputs> are comma-delimited names of output types
 
+   You may limit the number of found services by specifying:
+   -nc ... do not include services that are child types (more
+           specific) than the type you requested
+           (this option also applies when searching with -ft)
+   -np ... do not include services operating on parent types of
+           the data types you requested
+
+ The found services are printed in details, unless:
+   -on ... print only names of found services
+
  To register a data type:
 
    -rd-name  <data-type-name>
@@ -149,7 +160,4 @@
      is a name of an existing file, the contents of this file
      is used as an input parameter to the called mathod
 
-     Note that this method is meant mostly for debugging and may
-     be depracated later.
-
    -debug  ... print debug messages



From senger at pub.open-bio.org  Tue May 18 06:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHfE026364@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/04/21 17:22:26	1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/05/18 10:13:17	1.13
@@ -1140,12 +1140,42 @@
      *************************************************************************/
     public MobyService[] findService (MobyService pattern, String[] keywords)
 	throws MobyException {
+	return findService (pattern, keywords, true, true);
+// 	if (pattern == null)
+// 	    pattern = new MobyService ("dummy");
+
+// 	String[] query = new String[] { 
+// 				"<findService>" +
+// 				buildQueryObject (pattern, keywords, true, true, false) + 
+// 				"</findService>"
+// 	};
+// 	if(useCache && cache.containsKey("findService"+query[0]))
+// 	    return (MobyService[]) cache.get("findService"+query[0]);
+	
+// 	String result = (String) doCall ("findService", query);
+// 	MobyService[] services = extractServices (result);
+
+// 	if(useCache)
+// 	    cache.put("findService"+query[0], services);
+// 	return services;
+    }
+
+    /**************************************************************************
+     *
+     *************************************************************************/
+    public MobyService[] findService (MobyService pattern, String[] keywords,
+				      boolean includeChildrenServiceTypes,
+				      boolean includeParentDataTypes)
+	throws MobyException {
 	if (pattern == null)
 	    pattern = new MobyService ("dummy");
 
 	String[] query = new String[] { 
 				"<findService>" +
-				buildQueryObject (pattern, keywords, true, true, false) + 
+				buildQueryObject (pattern, keywords,
+						  includeParentDataTypes,
+						  includeChildrenServiceTypes,
+						  false) + 
 				"</findService>"
 	};
 	if(useCache && cache.containsKey("findService"+query[0]))



From mwilkinson at pub.open-bio.org  Wed May 19 10:58:36 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 19 May 2004 10:58:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191458.i4JEwaVu031596@pub.open-bio.org>


mwilkinson
Wed May 19 10:58:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv31577/Perl/MOBY/Client

Modified Files:
	Service.pm 
Log Message:
fixed errors in tags surrounding collections.  Updated with API changes to the Query and Queryinput tags

moby-live/Perl/MOBY/Client Service.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/19 14:58:36	1.11
@@ -204,7 +204,7 @@
 	foreach (@inputs){
 		return "ERROR:  expected listref [articleName, XML] for data element" unless (ref($_) =~ /array/i); 
 		my $qID = $self->_nextQueryID;
-        $data .= "<moby:queryInput queryID='$qID'>";
+        $data .= "<moby:mobyData queryID='$qID'>";
 		while (my ($articleName, $XML) = splice (@{$_}, 0, 2)){
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
@@ -217,20 +217,20 @@
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};
-                $data .="<moby:queryInput queryID='$qID'><moby:Collection moby:articleName='$articleName'>\n";
+                $data .="<moby:Collection moby:articleName='$articleName'>\n";
                 foreach (@objs){
-                    $data .= "$_\n";
+                    $data .= "<moby:Simple>$_</moby:Simple>\n";
                 }
                 $data .="</moby:Collection>\n";
             }
         }
-        $data .="</moby:queryInput>\n";
+        $data .="</moby:mobyData>\n";
 	}
 	$data = "<![CDATA[<?xml version='1.0' encoding='UTF-8'?>
 	<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
-	      <moby:Query>
+	      <moby:mobyContent>
 	          $data
-	      </moby:Query>
+	      </moby:mobyContent>
 	</moby:MOBY>]]>";
 	my $METHOD = $self->ServiceName;
 	&_LOG(%args, $METHOD);



From gss at pub.open-bio.org  Wed May 19 14:26:22 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:22 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQMU5000526@pub.open-bio.org>


gss
Wed May 19 14:26:22 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv501/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/04/01 00:30:54	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
@@ -1,6 +1,7 @@
 package org.sgd.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class SGD extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 14:26:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQPB1000561@pub.open-bio.org>


gss
Wed May 19 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv534/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/04/01 00:35:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
@@ -1,6 +1,7 @@
 package org.pubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Pubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 14:26:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQTSO000600@pub.open-bio.org>


gss
Wed May 19 14:26:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv575/.externalToolBuilders

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders added to the repository

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQetK000655@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot

Added Files:
	terms.n3 log4j.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,NONE,1.1 log4j.properties,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQebL000708@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv634

Modified Files:
	.classpath 
Added Files:
	.xdoclet xdoclet-build.xml 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server .xdoclet,NONE,1.1 xdoclet-build.xml,NONE,1.1 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/03/22 22:14:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/05/19 18:26:40	1.4
@@ -5,7 +5,7 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry exported="true" kind="src" path="/Jena2"/>
 	<classpathentry exported="true" kind="src" path="/HttpClient"/>
-	<classpathentry kind="lib" path="C:/cvs-repository/httpclient/lib/commons-logging.jar"/>
+	<classpathentry kind="lib" path="C:/commons-logging-1.0.3/commons-logging.jar"/>
 	<classpathentry exported="true" kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>



From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeiH000688@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java ProviderListServlet.java 
	GraphConversionServlet.java MOBYGraphValidationServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.1,1.2 ProviderListServlet.java,1.1,1.2 GraphConversionServlet.java,1.1,1.2 MOBYGraphValidationServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.ontology.*;
 import com.hp.hpl.jena.ontology.tidy.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,9 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.*;
+import org.smoby.servlet.*;
+import org.smoby.tools.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 import java.io.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.rdf.model.*;
 

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,8 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.parser.Parser;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 
@@ -23,18 +24,19 @@
 			Model baseModel = ModelFactory.createDefaultModel();
 			StringReader reader = new StringReader(graphString);
 			baseModel.read(reader, null);
-			new MOBYGraph(baseModel);
+			Parser parser = new Parser(baseModel);
+			parser.parseProvider();
 			out.println("Model is canonical");
 		}
         catch (ParameterException e)
         {
             response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, e.getMessage());
         }
-		catch (NonCanonicalException e)
-		{
-			out.println("Model failed canonicality test:");
-			out.println(e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			out.println("Model failed canonicality test:");
+//			out.println(e);
+//		}
 		catch (IllegalArgumentException e) {}
 	}
 }



From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQesY000741@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java DiscoveryQuery.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.2,1.3 DiscoveryQuery.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/03/27 01:27:51	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
@@ -3,11 +3,13 @@
 import java.util.*;
 import java.io.*;
 import javax.servlet.http.*;
-import org.smoby.tools.common.*;
+
+import org.smoby.tools.*;
+import org.smoby.http.*;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.http.*;
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
 import org.apache.commons.httpclient.util.*;
 import org.apache.commons.logging.*;
 
@@ -50,7 +52,7 @@
         synchronized (instances)
         {
         	if (instances.get(providerURL) != null) {
-                syncLog.warn("Already investigating " + providerURL);
+        		syncLog.warn("Already investigating " + providerURL);
                 return;
             }
             
@@ -97,7 +99,7 @@
         }
         catch (MissingPropertyException e)
         {
-            syncLog.error("Missing DB_REPOSITORY_NAME property");
+        	syncLog.error("Missing DB_REPOSITORY_NAME property");
         }
         finally
         {
@@ -140,7 +142,7 @@
         }
         catch (StorageException e)
         {
-            syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
             return;
         }
         
@@ -151,7 +153,7 @@
             }
             catch (StorageException e)
             {
-                syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
+            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
                 return;
             }
         }
@@ -164,7 +166,9 @@
         // be sent if it has been modified since that date
         //
         if (lastModifiedDate != null) {
-            request.addHeader(MOBY.IF_MODIFIED_HEADER,  Util.formatDateForHTTP(lastModifiedDate));
+            request.addHeader(
+                MOBY.IF_MODIFIED_HEADER,
+                Util.formatDateForHTTP(lastModifiedDate));
         }
         
         // Send the request and check the response code
@@ -178,7 +182,7 @@
         }
         catch (HTTPException e)
         {
-            syncLog.warn("Couldn't reach suggested provider " + providerURI);
+        	syncLog.warn("Couldn't reach suggested provider " + providerURI);
             return;
         }
         
@@ -203,7 +207,7 @@
                     // Log a message about the last modified date not being
                     // retrievable, but register the graph anyway
                     //
-                    syncLog.warn("Unable to get Last-Modified date for "
+                	syncLog.warn("Unable to get Last-Modified date for "
                                  + providerURI + "; ignoring");
                 }
                 catch (Throwable t)
@@ -211,7 +215,7 @@
                     // Log a message about the last modified date not being
                     // parsable, but register the graph anyway
                     //
-                    syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
+                	syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
                                 "\") for " + providerURI + "; ignoring");
                 }
 
@@ -219,25 +223,24 @@
                 // provider was already registered, then first de-register
                 // its currently stored description graph.
                 //
-                String graphString = "";
-                
+                InputStream in = null;
                 try {
-                	graphString = response.getBody();
+                	in = response.getBodyAsStream();
                 }
                 catch (HTTPException e)
                 {
-                    syncLog.error("Couldn't retrieve graph from " + providerURI);
+                	syncLog.error("Couldn't retrieve graph from " + providerURI);
                     return;
                 }
                 
-                Model graph = null;
-                
+                MOBYProvider provider = null;
                 try {
-                    graph = MOBYGraph.parseModel(graphString);
+                    Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
+                    provider = parser.parseProvider();
                 }
-                catch (UnparsableModelException e)
+                catch (UnparsableGraphException e)
                 {
-                    syncLog.warn("Unparsable graph found at " + providerURI +
+                	syncLog.warn("Unparsable graph found at " + providerURI +
                         (alreadyRegistered ? "; deregistering" : "; ignoring"));
                     if (alreadyRegistered) {
                         deregisterProvider(manager);
@@ -251,14 +254,14 @@
                 
                 try
                 {
-                    manager.registerGraph(graph, providerURI, lastModifiedDate);
+                    manager.registerProvider(provider, lastModifiedDate);
                     
                     // Log a message about successfully registering the graph:
                     //
                     syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
                 }
                 catch (StorageException e) {
-                    syncLog.error("Error storing graph for " + providerURI, e);
+                	syncLog.error("Error storing graph for " + providerURI, e);
                 }
                 
                 break;
@@ -268,7 +271,7 @@
                 // The resource has not been modified since it was
                 // registered, so there is nothing to do but log a message.
                 //
-                syncLog.info("IN-SYNC : " + providerURI);
+            	syncLog.info("IN-SYNC : " + providerURI);
                 break;
             
             case HttpServletResponse.SC_NOT_FOUND:
@@ -281,7 +284,7 @@
                     try
                     {
                     	manager.deregisterProvider(providerURI);
-                        syncLog.info("REMOVED : " + providerURI);
+                    	syncLog.info("REMOVED : " + providerURI);
                     }
                     catch (StorageException e) {
                     	syncLog.error("Unable to de-register provider " + providerURI, e);
@@ -296,7 +299,7 @@
                 
                 // Log a message about the failed attempt to contact the URL
                 //
-                syncLog.error("Status " + status + " received while trying " +
+            	syncLog.error("Status " + status + " received while trying " +
                              "to contact provider " + providerURI);
                 break;
         }

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/03/30 23:54:34	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
@@ -4,9 +4,12 @@
 import java.text.*;
 import java.util.*;
 
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.vocabulary.MOBY;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
+import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.graph.*;
@@ -41,7 +44,7 @@
     /**
      * The graph that serves as a template for providers that match.
      */
-    private MOBYGraph queryGraph;
+    private MOBYProvider queryProvider;
     
     /**
      * Flag indicating which statements should be returned: URI_ONLY,
@@ -67,9 +70,9 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYGraph queryGraph, int statementsToReturn)
+    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
-    	this.queryGraph = queryGraph;
+    	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
     }
     
@@ -83,22 +86,21 @@
         lastBnodeNumber = 0;
     }
     
-	public ProviderDescriptionGraph[] findMatchingGraphs()
+    public MOBYCollection findMatchingGraphs()
 	{
         init();
         
 		try
 		{
-            String queryString = buildQueryString(queryGraph);
+		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
+            String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-
             Model model = manager.openDBModel();
             ((ModelRDB) model).setDoFastpath(false);
             
 			// Execute the query
 			//
 			QueryResults results = Query.exec(queryString, model);
-
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -108,17 +110,19 @@
 			}
 			results.close();
 			
-			ProviderDescriptionGraph[] graphs =
-                new ProviderDescriptionGraph[matching.size()];
-			int i = 0;
-			for (Iterator it = matching.iterator(); it.hasNext(); i++)
+			List returnList = new ArrayList();
+			
+			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next());
-				graphs[i] = new ProviderDescriptionGraph(
-					new MOBYGraph(manager.openModel(mg.getProvider().getURI())));
+				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
+				String uri = mp.getURI();
+				// YUCK!
+				Model providerModel = manager.openModel(uri);
+				Parser parser = new Parser(providerModel);
+				returnList.add(parser.parseProvider());
 			}
 			
-			return graphs;
+			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
 			
 		} catch (Throwable t) {
 			return null;
@@ -128,10 +132,8 @@
 	/**
 	 * Build and return an RDQL query string for the reified Model
 	 */
-	private String buildQueryString(MOBYGraph queryGraph)
+	private String buildQueryString(Model queryModel)
 	{
-        Model queryModel = queryGraph.getModel();
-        
         String SPACES = "      ";
         
         Map nsMap = queryModel.getNsPrefixMap();
@@ -220,12 +222,8 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYGraph buildGraphModel(MOBYGraph queryGraph,
-                                      ResultBinding binding)
-		throws NonCanonicalException
+	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
 	{
-        Model queryModel = queryGraph.getModel();
-        
 		// Create a default model to return
 		//
 		Model model = ModelFactory.createDefaultModel();
@@ -247,7 +245,8 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		return new MOBYGraph(model);
+		Parser parser = new Parser(model);
+		return parser.parseProvider();
 	}
 	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)



From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfX1000828@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/03/29 19:40:08	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
@@ -1,10 +1,9 @@
 package org.smoby.ref.tools.db;
 
-import org.smoby.tools.common.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYProviderImpl;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.common.vocabulary.*;
-
+import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.shared.*;
@@ -65,28 +64,16 @@
      * are in the provider graph's namespace will be stored in the global repository,
      * and all statements from the provider graph are stored in a separate model
      * that has as its name the fully expanded URI of the provider.
-     * @param providerGraph the graph to store
+     * @param provider the Provider to store
      * @param lastModifiedDate when the graph was last modified
      * @throws StorageException if unable to access the database
      */
-	public void registerProviderGraph(MOBYGraph providerGraph, Date lastModifiedDate)
-        throws StorageException
-	{
-        registerGraph(providerGraph.getModel(),
-                      providerGraph.getProvider(),
-                      lastModifiedDate);
-	}
-    
-    public void registerGraph(Model graph, String uri, Date lastModifiedDate)
-        throws StorageException
-    {
-    	registerGraph(graph, graph.createResource(uri), lastModifiedDate);
-    }
-    
-    public void registerGraph(Model graph, Resource uri, Date lastModifiedDate)
+	public void registerProvider(MOBYProvider provider, Date lastModifiedDate)
         throws StorageException
 	{
+	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
+        Resource uri = model.createResource(provider.getURI());
         
         try
         {
@@ -114,7 +101,7 @@
             //
             String providerNameSpace = uri.getNameSpace();
             
-            for (StmtIterator it = graph.listStatements(); it.hasNext();)
+            for (StmtIterator it = model.listStatements(); it.hasNext();)
             {
                 Statement stmt = it.nextStatement();
                 Resource subject = stmt.getSubject();
@@ -132,8 +119,8 @@
             // Add to the database another model, with the provider URL as its name
             //
             Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(graph);
-            providerModel.setNsPrefixes(graph.getNsPrefixMap());
+            providerModel.add(model);
+            providerModel.setNsPrefixes(model.getNsPrefixMap());
             
             // Add a statement asserting when the model was added to the database
             //



From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfJi000807@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot/WEB-INF/classes

Modified Files:
	smoby.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/04/02 00:08:26	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/05/19 18:26:40	1.4
@@ -5,11 +5,11 @@
 #
 DB_USER_ID            = smobydev
 DB_PASSWORD           = 
-DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 DB_REPOSITORY_NAME    = smoby-dev
 
 # Uncomment if using MySQL
 #
+# DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 # DB_URL                = jdbc:mysql://localhost/smoby-dev
 # DB_TYPE               = MySQL
 



From gss at pub.open-bio.org  Wed May 19 14:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfu4000786@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv634/.externalToolBuilders

Added Files:
	XDoclet Builder.launch 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmg6000901@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv876/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
@@ -8,36 +8,36 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <megapubs:literatureGuideURL rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <megapubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Cool new search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
+  <rdf:Description rdf:nodeID="A2">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
+    <moby:hasMapping rdf:nodeID="A3"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqjx000978@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/04/02 00:03:39	1.7
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
@@ -2,17 +2,13 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.go.vocabulary.Go;
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.vocabulary.MOBY;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
-import com.acmepubs.vocabulary.AcmePubs;
-
-import com.hp.hpl.jena.rdf.model.*;
+import org.go.vocabulary.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
+import com.acmepubs.vocabulary.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -39,47 +35,47 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
         // Retrieve the subject of the moby:operatesOn statement (there is only
     	// one operatesOn statement in a valid MOBY graph)
         //
-        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-        
-        // There may be multiple moby:hasMapping statements. For each one,
-        // map its geneSymbol to a literatureGuideURL
-        //
-        StmtIterator it = graph.getModel().listStatements(
-        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-        
-        while (it.hasNext())
-        {
-    		try
-			{
-	        	Statement hasMappingStmt = it.nextStatement();
-	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-	        	
-	        	Statement geneSymbolStmt =
-	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-	        	
-    			String geneSymbol = geneSymbolStmt.getString();
-    			
-    			Statement mapsToStmt = 
-    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-    			
-				Resource mobyObject = (Resource) mapsToStmt.getObject();
-				
-				Statement literatureGuideURLStmt =
-					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-				
-				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-        	}
-    		catch (Throwable t)
-			{
-    			// Something went wrong, so proceed to next hasMapping statement
-    		}
-        }
+//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
+//        
+//        // There may be multiple moby:hasMapping statements. For each one,
+//        // map its geneSymbol to a literatureGuideURL
+//        //
+//        StmtIterator it = graph.getModel().listStatements(
+//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
+//        
+//        while (it.hasNext())
+//        {
+//    		try
+//			{
+//	        	Statement hasMappingStmt = it.nextStatement();
+//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
+//	        	
+//	        	Statement geneSymbolStmt =
+//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
+//	        	
+//    			String geneSymbol = geneSymbolStmt.getString();
+//    			
+//    			Statement mapsToStmt = 
+//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
+//    			
+//				Resource mobyObject = (Resource) mapsToStmt.getObject();
+//				
+//				Statement literatureGuideURLStmt =
+//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
+//				
+//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
+//        	}
+//    		catch (Throwable t)
+//			{
+//    			// Something went wrong, so proceed to next hasMapping statement
+//    		}
+//        }
     }
     
     /**



From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQq7s000997@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv953/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
@@ -14,30 +14,30 @@
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <acmepubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <acmepubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 14:26:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQtu5001055@pub.open-bio.org>


gss
Wed May 19 14:26:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1030/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
@@ -1,6 +1,7 @@
 package org.go.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Go extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 14:26:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQihp000868@pub.open-bio.org>


gss
Wed May 19 14:26:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv843

Modified Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager SimpleProviderEngagerPanel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/05/19 18:26:44	1.2
@@ -4,13 +4,20 @@
 import javax.swing.border.*;
 import javax.swing.event.*;
 
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.graph.NonCanonicalException;
-import org.smoby.tools.common.graph.UnparsableModelException;
-import org.smoby.tools.common.http.HTTPException;
-import org.smoby.tools.common.http.HTTPRequest;
-import org.smoby.tools.common.http.HTTPResponse;
+import org.smoby.http.*;
+import org.smoby.graph.*;
+import org.smoby.parser.*;
 
+/**
+ * This class is a simple two-pane window for engaging Semantic MOBY
+ * providers. The user first pastes into the input pane a canonical graph
+ * of the form that is acceptable to the provider (i.e. the graph
+ * returned by doing an HTTP GET on the provider URI, with some of
+ * the blank nodes filled in). When the user presses the "Engage Provider"
+ * button, the graph is submitted, via HTTP POST, to the provider embedded
+ * in the graph; the results of the HTTP POST, as written by the provider,
+ * are then printed to the lower pane.
+ */
 public class SimpleProviderEngagerPanel extends JPanel
 {
 	private JTextArea inputArea = new JTextArea();
@@ -31,8 +38,7 @@
 		Font plain = new Font("Monospaced", Font.PLAIN, 12);
 		inputArea.setFont(plain);
 		outputArea.setFont(plain);
-		inputArea.setEditable(true);
-		outputArea.setEditable(false);
+		
 		engageButton.setEnabled(false);
 		
 		addListeners();
@@ -104,26 +110,26 @@
 		String graphString = inputArea.getText();
 		try
 		{
-			MOBYGraph mobyGraph = MOBYGraph.fromString(graphString, false);
-			String graphURI = mobyGraph.getProvider().getURI();
+		    Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+		    MOBYProvider provider = parser.parseProvider();
+			String graphURI = provider.getURI();
 			HTTPRequest request = HTTPRequest.newPostRequest(graphURI);
 			request.addParameter("graph", graphString);
 			HTTPResponse response = request.send();
 			outputArea.setText(response.getBody());
-//			inputArea.setText("");
 		}
-		catch (UnparsableModelException e)
+		catch (UnparsableGraphException e)
 		{
 			JOptionPane.showMessageDialog(this,
 				"The graph could not be parsed", "Unparsable",
 				JOptionPane.ERROR_MESSAGE);
 		}
-		catch (NonCanonicalException e)
-		{
-			JOptionPane.showMessageDialog(this,
-					"The graph is not canonical", "Non-canonoical",
-					JOptionPane.ERROR_MESSAGE);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			JOptionPane.showMessageDialog(this,
+//					"The graph is not canonical", "Non-canonoical",
+//					JOptionPane.ERROR_MESSAGE);
+//		}
 		catch (HTTPException e)
 		{
 			JOptionPane.showMessageDialog(this,



From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8U1001275@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/graph

Removed Files:
	ProviderDescriptionGraph.java NonCanonicalException.java 
	MOBYGraph.java UnparsableModelException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.java,1.1,NONE NonCanonicalException.java,1.1,NONE MOBYGraph.java,1.3,NONE UnparsableModelException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqrC001016@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
@@ -1,6 +1,7 @@
 package com.acmepubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class AcmePubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8tS001385@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/io

Removed Files:
	TransceiverBase.java TokenSeparatedTransceiver.java 
	GraphListTransmitter.java ZipStreamTransceiver.java 
	GraphListTransceiverFactory.java GraphListReceiver.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io TransceiverBase.java,1.1,NONE TokenSeparatedTransceiver.java,1.1,NONE GraphListTransmitter.java,1.1,NONE ZipStreamTransceiver.java,1.1,NONE GraphListTransceiverFactory.java,1.1,NONE GraphListReceiver.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9QR001496@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common

Removed Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:27:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR7U5001256@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/server/servlet

Removed Files:
	ParamReader.java ParameterException.java 
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,1.1,NONE ParameterException.java,1.1,NONE AbstractMobyServlet.java,1.6,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8bH001324@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph/impl

Added Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYOntologyImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NO!
NE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8dY001291@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser

Added Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,NONE,1.1 UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQm02000920@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/03/27 01:17:58	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:48	1.4
@@ -2,12 +2,10 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -36,7 +34,7 @@
      * a gene symbol and returning a list of publication
      * abstracts.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
     }
     



From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9fT001458@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/vocabulary

Removed Files:
	MOBY.java VocabularyDescription.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,1.2,NONE VocabularyDescription.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8E6001358@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/http

Added Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9rs001480@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/http

Removed Files:
	HTTPException.java HTTPResponse.java HTTPRequest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPException.java,1.2,NONE HTTPResponse.java,1.3,NONE HTTPRequest.java,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9sx001439@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/servlet

Added Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 ParameterException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmRJ000940@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/04/02 00:04:21	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
@@ -1,6 +1,7 @@
 package com.megapubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class MegaPubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8lW001343@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8qw001309@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph

Added Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYDocument.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1 MOBYGraph.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8oF001420@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8pP001405@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 14:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeuc000765@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.2,1.3 DiscoveryServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/03/22 22:13:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
@@ -6,9 +6,9 @@
 import javax.servlet.http.*;
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
 import org.smoby.ref.tools.URIInvestigator;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.servlet.*;
 
 /**
  * This servlet class is used to request that S-MOBY investigate a URL for the

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,10 @@
 package org.smoby.ref.servlets;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.io.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.parser.NonCanonicalException;
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
 import java.io.*;
@@ -37,26 +38,18 @@
             //
 			String graphString = ParamReader.getParameter("query-graph", request);
             
-            // Does the requester want the matching graphs sent back in a
-            // binary format?
-            //
-            boolean binary = false;
-            try {
-            	ParamReader.getParameter("binary-return", request);
-                binary = true;
-            } catch (ParameterException e) {}
-            
             // Parse the query graph into a MOBYGraph object
             //
-			MOBYGraph g = MOBYGraph.fromString(graphString, true);
+			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+			MOBYProvider provider = parser.parseProvider();
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(g, DiscoveryQuery.ALL_STMTS);
-			ProviderDescriptionGraph[] matching = q.findMatchingGraphs();
+            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
+			MOBYCollection matching = q.findMatchingGraphs();
 			
-            if ((matching.length == 0) && (! binary))
+            if ((matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -66,23 +59,20 @@
             }
             else
             {
-                // Otherwise, create an object capable of transmitting the
-                // graphs (in either binary or human-readable text format)
-                // and use the object to send the matching graphs.
-                //
-                GraphListTransmitter transmitter =
-                    GraphListTransceiverFactory.newTransmitter(out, binary);
-                transmitter.transmit(matching);
+                for (Iterator it = matching.iterator(); it.hasNext();) {
+                    MOBYProvider p = (MOBYProvider) it.next();
+                    p.serialize(out);
+                }
 			}
             
 		}
-		catch (NonCanonicalException e)
-		{
-            // The query graph did not have the required canonical form
-            //
-			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-				"Query graph is not canonical:\n" + e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//            // The query graph did not have the required canonical form
+//            //
+//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
+//				"Query graph is not canonical:\n" + e);
+//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxY4001087@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQx3w001105@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxXt001123@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxkI001142@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxS8001185@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxUh001164@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 14:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxh9001203@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 16:42:30 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgUSK001852@pub.open-bio.org>


gss
Wed May 19 16:42:30 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv1831

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/server .encoding,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 16:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgYQS001889@pub.open-bio.org>


gss
Wed May 19 16:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1860/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.4,1.5 citationSearch.rdf,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
@@ -10,28 +10,32 @@
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Cool new search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    megapubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    megapubs:literatureGuideURL _:bnode6 .
+    moby:name "MegaPubs Citation Search" ;
+    moby:oneLineDescription "Cool new search" ;
+    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                megapubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    megapubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 megapubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 megapubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
@@ -8,36 +8,43 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
+  <rdf:Description rdf:nodeID="A0">
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A0">
-    <megapubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
     <moby:operatesOn rdf:nodeID="A2"/>
+    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <moby:name>MegaPubs Citation Search</moby:name>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Cool new search</rdfs:comment>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A3"/>
+    <rdf:_1 rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
+    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-  </rdf:Description>
-</rdf:RDF>
\ No newline at end of file
+</rdf:RDF>



From gss at pub.open-bio.org  Wed May 19 16:42:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgbYu001926@pub.open-bio.org>


gss
Wed May 19 16:42:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1897/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.5,1.6 citationSearch.n3,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
@@ -12,31 +12,38 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
     <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A2"/>
-    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <acmepubs:geneSymbol rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:operatesOn rdf:nodeID="A4"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
+    <moby:name>AcmePubs Citation Search</moby:name>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
@@ -10,28 +10,32 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 19:33:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX5Ru002275@pub.open-bio.org>


gss
Wed May 19 19:33:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv2250/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
@@ -7,6 +7,7 @@
 import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
 import org.smoby.vocabulary.*;
 import com.acmepubs.vocabulary.*;
 
@@ -35,47 +36,54 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYProvider graph)
+    protected void handleRequest(MOBYProvider provider)
     {
-        // Retrieve the subject of the moby:operatesOn statement (there is only
-    	// one operatesOn statement in a valid MOBY graph)
-        //
-//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-//        
-//        // There may be multiple moby:hasMapping statements. For each one,
-//        // map its geneSymbol to a literatureGuideURL
-//        //
-//        StmtIterator it = graph.getModel().listStatements(
-//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-//        
-//        while (it.hasNext())
-//        {
-//    		try
-//			{
-//	        	Statement hasMappingStmt = it.nextStatement();
-//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-//	        	
-//	        	Statement geneSymbolStmt =
-//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-//	        	
-//    			String geneSymbol = geneSymbolStmt.getString();
-//    			
-//    			Statement mapsToStmt = 
-//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-//    			
-//				Resource mobyObject = (Resource) mapsToStmt.getObject();
-//				
-//				Statement literatureGuideURLStmt =
-//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-//				
-//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-//        	}
-//    		catch (Throwable t)
-//			{
-//    			// Something went wrong, so proceed to next hasMapping statement
-//    		}
-//        }
+        try
+        {
+            // There should be only one operatesOn subgraph, which should be
+            // a collection of MOBYGraph objects.
+            //
+            MOBYCollection coll = (MOBYCollection)
+            	provider.getOperatesOn().iterator().next();
+            
+            // Iterate over the MOBYGraph objects
+            //
+            Iterator it = coll.iterator();
+            while (it.hasNext())
+            {
+                MOBYGraph graph = (MOBYGraph) it.next();
+                
+                // The subject of the graph should be a MOBYSubject
+                //
+                MOBYSubject subject = (MOBYSubject) graph.gethasMapping();
+                
+                // That object should have a single subproperty of moby:Property,
+                // namely geneSymbol; its value should be a literal
+                //
+                MOBYPropertyValueStatement stmt = (MOBYPropertyValueStatement)
+                    subject.getPropertyValueStatements().iterator().next();
+                MOBYLiteral literal = (MOBYLiteral) stmt.getValue();
+                String geneSymbol = literal.getStringValue();
+                
+                // The object of the MOBYSubject should be a MOBYObject. That
+                // object should have a single subproperty of moby:Property,
+                // namely literatureGuideURL
+                //
+                MOBYObject object = (MOBYObject)
+                	subject.getDirectMappings().iterator().next();
+                stmt = (MOBYPropertyValueStatement)
+                	object.getPropertyValueStatements().iterator().next();
+                
+                // Set the value of the literatureGuideURL to a literal value
+                // based on a base URI string and the geneSymbol that was passed
+                //
+                String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+                literal = MOBYObjectFactory.newLiteralValue(
+                        baseURI + geneSymbol);
+                stmt.setPropertyValue(literal);
+            }
+        }
+        catch (Throwable t) {System.out.println(t);} // No feedback on failure...
     }
     
     /**



From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Lr002327@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 18:27:07	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 23:33:08	1.2
@@ -375,10 +375,7 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
-            boolean blankVal = pval.canAs(Resource.class) &&
-                               ((Resource) pval.as(Resource.class)).isAnon();
-            
-            if (blankVal && model.contains(res, p, pval) &&
+            if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
                 MOBYPropertyValueStatement pvalStmt =



From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9jX002373@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/servlet

Modified Files:
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet AbstractMobyServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 23:33:09	1.2
@@ -100,11 +100,12 @@
         
         try
         {
-            // Read the invocation graph from the "query-graph" parameter
+            // Read the invocation graph from the "graph" parameter
             // and parse it into a MOBYGraph object
             //
-            Parser parser = Parser.forInputStream(
-                   request.getInputStream(), Parser.LANGUAGE_RDF_XML);
+            String graphString = ParamReader.getParameter("graph", request);
+            Parser parser = Parser.forString(
+                   graphString, Parser.LANGUAGE_RDF_XML);
             MOBYProvider provider = parser.parseProvider();
             
             // Invoke the abstract handleRequest() method in order for the



From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9PQ002308@pub.open-bio.org>


gss
Wed May 19 19:33:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph

Modified Files:
	MOBYPropertyValueStatement.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYPropertyValueStatement.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 23:33:08	1.2
@@ -3,9 +3,17 @@
 
 public interface MOBYPropertyValueStatement
 {
+    /**
+     * Return the name of this property
+     */
     public String getPropertyName();
     
     /**
+     * Return the value currently associated with this property
+     */
+    public MOBYPropertyValue getValue();
+    
+    /**
      * Set the property value. This is just a placeholder; values of
      * different property types will be set to different types of
      * values.



From gss at pub.open-bio.org  Wed May 19 19:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Fj002352@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph/impl

Modified Files:
	MOBYPropertyValueStatementImpl.java MOBYObjectFactory.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYPropertyValueStatementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 23:33:09	1.2
@@ -8,11 +8,19 @@
 	implements MOBYPropertyValueStatement
 {
     Statement jenaStatement;
+    MOBYPropertyValue currentValue;
     MOBYPropertyValueConstraint constraint;
     
     MOBYPropertyValueStatementImpl(Statement jenaStatement, Model underlying) {
         super(null, underlying);
         this.jenaStatement = jenaStatement;
+        if (jenaStatement.getObject().canAs(Resource.class)) {
+            Resource value = (Resource) jenaStatement.getObject();
+            currentValue = new MOBYResourceImpl(value);
+        } else {
+            Literal value = (Literal) jenaStatement.getObject();
+            currentValue = new MOBYLiteralImpl(value.getString());
+        }
     }
     
     public String getPropertyName() {
@@ -23,6 +31,10 @@
         return jenaStatement.toString();
     }
     
+    public MOBYPropertyValue getValue() {
+        return currentValue;
+    }
+    
     public void setPropertyValue(MOBYPropertyValue newValue)
     	throws MOBYPropertyValueException
     {

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 23:33:09	1.2
@@ -66,6 +66,11 @@
         return new MOBYPropertyValueStatementImpl(statement, underlying);
     }
     
+    public static MOBYLiteral newLiteralValue(String value)
+    {
+        return new MOBYLiteralImpl(value);
+    }
+    
     public static MOBYPropertyValueConstraint newIntegerConstraint()
     {
         return new MOBYIntegerConstraintImpl();



From gordonp at pub.open-bio.org  Thu May 20 12:08:05 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:08:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201608.i4KG85q1004928@pub.open-bio.org>


gordonp
Thu May 20 12:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv4903

Modified Files:
	MobyRequest.java 
Log Message:
Just got rid of some debug statements

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/20 16:08:05	1.3
@@ -381,7 +381,6 @@
             throw new SOAPException("Cannot select SOAP nodes due to exception "+
 				    "while executing XPath statement:" +te);
 	}
-	debugPS.println("Result is " + node_list);
 
 	if(node_list == null || node_list.getLength() == 0){
 	    // Note: before giving up we should really have a plain string check as per the MOBY API 0.6
@@ -496,7 +495,6 @@
 	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
-	    debugPS.println("Got response " + response);
 	    
 	    Vector out = new Vector();
 	    // Find all the collections in the response
@@ -578,7 +576,6 @@
 	XObject xobject = xpath.execute(xpath_context, n, node_prefix_resolver);
 	if(xobject instanceof XNodeSet){
 	    result = ((XNodeSet) xobject).nodelist();
-	    debugPS.println("Result is " + result);
 	}
 	else if(debug && xobject != null){
 	    debugPS.println("Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName());



From gordonp at pub.open-bio.org  Thu May 20 12:18:46 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:18:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201618.i4KGIkaq004981@pub.open-bio.org>


gordonp
Thu May 20 12:18:46 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv4960

Added Files:
	MobyServiceInvocationExample.java 
Log Message:
Example class that uses jMOBY to find and invoke services based on seed data

moby-live/Java/src/Clients MobyServiceInvocationExample.java,NONE,1.1


From gordonp at pub.open-bio.org  Thu May 20 12:23:15 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:23:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201623.i4KGNFCo005051@pub.open-bio.org>


gordonp
Thu May 20 12:23:15 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv5026

Modified Files:
	ChangeLog 
Log Message:
Note location of good new service invocation example

moby-live/Java/docs ChangeLog,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/20 16:23:15	1.15
@@ -1,3 +1,9 @@
+2004-05-20  Paul Gordon <gordonp at cbr.nrc.ca>
+
+        * Added full working example of service discovery and invocation in 
+          src/Client/MobyServiceInvocationExample
+          Use that one instead of the example in this ChangeLog
+
 2004-05-18  Martin Senger  <senger at ebi.ac.uk>
 
 	* Added a new displaying option (-on) to MobyCmdLineClient



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQm028394@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PXV028354@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5P3v028299@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org added to the repository

moby-live/S-MOBY/ref-impl/core/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PMo028372@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PJH028316@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q1l028433@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Ph3028413@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Pvv028282@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src
In directory pub.open-bio.org:/tmp/cvs-serv28258/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src added to the repository

moby-live/S-MOBY/ref-impl/core/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q3K028470@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQd028336@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5QUV028452@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/tools

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Z0C028564@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph/impl

Added Files:
	MOBYOntologyImpl.java MOBYResourceImpl.java MOBYGraphImpl.java 
	MOBYPropertyValueConstraintImpl.java MOBYDescriptorImpl.java 
	MOBYOrderedCollectionImpl.java MOBYIntegerConstraintImpl.java 
	MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java 
	MOBYPropertyValueImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java 
	MOBYProviderImpl.java MOBYEnumerationImpl.java 
	MOBYLiteralImpl.java MOBYSingleElementImpl.java 
	MOBYDocumentImpl.java MOBYUnorderedCollectionImpl.java 
	MOBYNumericConstraintImpl.java MOBYGraphNodeImpl.java 
	MOBYObjectImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java MOBYCollectionImpl.java 
	MOBYObjectFactory.java MOBYMappingElementImpl.java 
	MOBYPropertyValueStatementImpl.java 
	MOBYResizableCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYOntologyImpl.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.jav!
a,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5YpV028532@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/servlet

Added Files:
	AbstractMobyServlet.java ParamReader.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet AbstractMobyServlet.java,NONE,1.1 ParamReader.java,NONE,1.1 ParameterException.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZUB028579@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph

Added Files:
	MOBYDocument.java MOBYOntology.java MOBYProvider.java 
	MOBYResource.java MOBYOrderedCollection.java MOBYSubject.java 
	MOBYSingleElement.java MOBYEnumeration.java 
	MOBYDescriptor.java MOBYPropertyValueStatement.java 
	MOBYLiteral.java MOBYCollection.java MOBYFixedCollection.java 
	MOBYPropertyValueException.java MOBYGraphNode.java 
	MOBYObject.java MOBYUnorderedCollection.java MOBYGraph.java 
	MOBYMappingElement.java MOBYResizableCollection.java 
	MOBYPropertyValueConstraint.java MOBYPropertyValue.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDocument.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYProvider.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYGraph.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a0h028675@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZZ6028594@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZSW028614@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/http

Added Files:
	HTTPException.java HTTPRequest.java HTTPResponse.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http HTTPException.java,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5aH2028631@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser

Added Files:
	UnparsableGraphException.java NonCanonicalException.java 
	Parser.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 Parser.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a8O028660@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv28511

Modified Files:
	build.xml .classpath 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
@@ -1,2 +1,3 @@
 <project name="core" basedir=".">
+    <property name="src" value="build"/>
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/03/27 01:14:22	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/05/24 22:05:35	1.4
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>



From gss at pub.open-bio.org  Mon May 24 18:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Yhf028547@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HX1028729@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser

Removed Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.2,NONE UnparsableGraphException.java,1.1,NONE NonCanonicalException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/Parser.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/UnparsableGraphException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/NonCanonicalException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HRN028767@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph

Removed Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,1.1,NONE MOBYPropertyValueConstraint.java,1.1,NONE MOBYOntology.java,1.1,NONE MOBYPropertyValueStatement.java,1.2,NONE MOBYDescriptor.java,1.1,NONE MOBYFixedCollection.java,1.1,NONE MOBYMappingElement.java,1.1,NONE MOBYSingleElement.java,1.1,NONE MOBYUnorderedCollection.java,1.1,NONE MOBYEnumeration.java,1.1,NONE MOBYObject.java,1.1,NONE MOBYResizableCollection.java,1.1,NONE MOBYSubject.java,1.1,NONE MOBYResource.java,1.1,NONE MOBYOrderedCollection.java,1.1,NONE MOBYPropertyValueException.java,1.1,NONE MOBYDocument.java,1.1,NONE MOBYCollection.java,1.1,NONE MOBYGraphNode.java,1.1,NONE MOBYLiteral.java,1.1,NONE MOBYPropertyValue.java,1.1,NONE MOBYGraph.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYProvider.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueConstraint.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOntology.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueStatement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDescriptor.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYFixedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYMappingElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSingleElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYUnorderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYEnumeration.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYObject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResizableCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSubject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResource.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOrderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDocument.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraphNode.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYLiteral.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValue.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraph.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7H0j028830@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/tools

Removed Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/Util.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4r028906@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/servlet

Removed Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,1.1,NONE AbstractMobyServlet.java,1.2,NONE ParameterException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParameterException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HlJ028849@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/http

Removed Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,1.1,NONE HTTPResponse.java,1.1,NONE HTTPException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPRequest.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7ID1028887@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/vocabulary

Removed Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,1.1,NONE MOBY.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/MOBY.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HtL028814@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph/impl

Removed Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,1.1,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYOntologyImpl.java,1.1,NONE MOBYDocumentImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.1,NONE MOBYResizableCollectionImpl.java,1.1,NONE MOBYDescriptorImpl.java,1.1,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.1,NONE MOBYObjectFactory.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYSingleElementImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYProviderImpl.java,1.1,NONE MOBYLiteralImpl.java,1.1,NONE MOBYGraphNodeImpl.java,1.1,NONE MOBYCollectionImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.1,NONE MOBYFixedCollectionImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYSubjectImpl.java,1.1,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.1,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.!
1,NONE MOBYUnorderedCollectionImpl.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 18:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4o028866@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser/test

Removed Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,1.1,NONE ParserTest.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/Test.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/ParserTest.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 26 19:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 26 May 2004 19:27:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405262327.i4QNRlVa003497@pub.open-bio.org>


gss
Wed May 26 19:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv3472

Modified Files:
	.cvsignore 
Log Message:
Ignore build directory

moby-live/S-MOBY/ref-impl/core .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/03/22 22:21:39	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
@@ -1 +1,2 @@
-classes
\ No newline at end of file
+classes
+build



From gss at pub.open-bio.org  Thu May 27 11:30:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:30:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271530.i4RFUek4006236@pub.open-bio.org>


gss
Thu May 27 11:30:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6210

Modified Files:
	.cvsignore 
Log Message:
Removed blank line

moby-live/S-MOBY/ref-impl/core .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
@@ -1,2 +1,2 @@
 classes
-build
+build
\ No newline at end of file



From gss at pub.open-bio.org  Thu May 27 11:31:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271531.i4RFVVL8006281@pub.open-bio.org>


gss
Thu May 27 11:31:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv6256/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Remove go.org import

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/27 15:31:31	1.10
@@ -4,7 +4,6 @@
 import java.util.*;
 import javax.servlet.*;
 import javax.servlet.http.*;
-import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.MOBYObjectFactory;



From gss at pub.open-bio.org  Thu May 27 11:54:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFs8NB006492@pub.open-bio.org>


gss
Thu May 27 11:54:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv6471

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,NONE,1.1 .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 11:54:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsCqr006525@pub.open-bio.org>


gss
Thu May 27 11:54:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv6500

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/server build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/03/12 17:48:32	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
@@ -1,2 +1,29 @@
-<project name="server" basedir=".">
+<!-- Apache Ant format build file for s-moby.org example provider -->
+
+<project name="s-moby.org" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="s-moby.org.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>



From gss at pub.open-bio.org  Thu May 27 11:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKMG006565@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv6544

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,NONE,1.1 .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 11:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKIa006580@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv6544/WebRoot/WEB-INF

Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 11:54:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsSar006627@pub.open-bio.org>


gss
Thu May 27 11:54:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6602

Modified Files:
	build.xml 
Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,NONE,1.1 build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/03/12 17:48:33	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
@@ -1,2 +1,29 @@
-<project name="megapubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="megapubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="megapubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>



From gss at pub.open-bio.org  Thu May 27 11:54:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFseHV006690@pub.open-bio.org>


gss
Thu May 27 11:54:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6657

Modified Files:
	build.xml .classpath 
Added Files:
	.cvsignore .xdoclet 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,NONE,1.1 .xdoclet,1.2,1.3 build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.xdoclet,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
@@ -1,2 +1,29 @@
-<project name="acmepubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="acmepubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="acmepubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/05/27 15:54:40	1.4
@@ -5,9 +5,6 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>
-	<classpathentry kind="src" path="/www.go.org"/>
-	<classpathentry kind="src" path="/www.pubs.org"/>
-	<classpathentry kind="src" path="/www.sgd.org"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>



From gss at pub.open-bio.org  Thu May 27 11:54:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsiWe006723@pub.open-bio.org>


gss
Thu May 27 11:54:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6698

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/core build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
@@ -1,3 +1,26 @@
-<project name="core" basedir=".">
-    <property name="src" value="build"/>
+<!-- Apache Ant format build file for Semantic MOBY core library -->
+
+<project name="smoby-core" default="jar" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../library.xml"/>
+
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+    <!-- Compile all the source files that go into the library -->
+    <target name="compile">
+        <mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="core.classpath"/>
+        </javac>
+    </target>
+    
+    <!-- Deploy the jar file to the Tomcat shared library directory -->
+    <target name="deploy-to-tomcat" depends="jar">
+        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
 </project>



From gss at pub.open-bio.org  Thu May 27 12:03:43 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:03:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271603.i4RG3hAF006842@pub.open-bio.org>


gss
Thu May 27 12:03:42 EDT 2004
Update of /home/repository/moby/www.go.org
In directory pub.open-bio.org:/tmp/cvs-serv6818/www.go.org

Log Message:
Directory /home/repository/moby/www.go.org added to the repository

www.go.org - New directory
rcsdiff: /home/repository/moby/www.go.org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 12:11:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:11:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271611.i4RGBFHF007039@pub.open-bio.org>


gss
Thu May 27 12:11:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv7018

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .encoding,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 12:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:23:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271623.i4RGNxH0007277@pub.open-bio.org>


gss
Thu May 27 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv7256

Added Files:
	.cvsignore build.xml 
Log Message:
Oops, had released to wrong directory

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,NONE,1.1 build.xml,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 14:31:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 14:31:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271831.i4RIVkXZ008515@pub.open-bio.org>


gss
Thu May 27 14:31:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv8494

Added Files:
	.cvsignore 
Log Message:


moby-live/S-MOBY/ref-impl/server .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3cg009360@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src
In directory pub.open-bio.org:/tmp/cvs-serv9336/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Gl009378@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Jq009397@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 15:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Js009416@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby/exampleclients

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 15:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbAZ5009474@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv9444

Modified Files:
	.classpath .cvsignore 
Added Files:
	build.xml 
Removed Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,NONE,1.1 .classpath,1.1,1.2 .cvsignore,1.1,1.2 SimpleProviderEngagerPanel.java,1.2,NONE
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/05/27 19:37:10	1.2
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="src" path="/Jena2"/>
 	<classpathentry kind="src" path="/HttpClient"/>
-	<classpathentry kind="output" path=""/>
+	<classpathentry kind="output" path="build"/>
 </classpath>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/04/02 00:45:31	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
@@ -1,2 +1,2 @@
 classes
-*.class
\ No newline at end of file
+build

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/SimpleProviderEngagerPanel.java,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 15:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbA5Z009489@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9444/src/org/smoby/exampleclients

Added Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,NONE,1.1


From ambrose at pub.open-bio.org  Fri May 28 16:54:08 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri, 28 May 2004 16:54:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282054.i4SKs8F0013990@pub.open-bio.org>


ambrose
Fri May 28 16:54:08 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv13964

Modified Files:
	NamespaceMaintenance.cgi 
Log Message:
fixed mysql duplicate entry problem caused by updating form field error

moby-live/Perl/Accessories NamespaceMaintenance.cgi,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/04/29 18:03:52	1.2
+++ /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/05/28 20:54:08	1.3
@@ -6,18 +6,31 @@
 my $namespace_id;
 my $authabvr;
 my $namespacetype;
-    if (param('ns')) { #ns param specified; user intends to load from database so open database and load up parameters
-        my @ns = split (/\_/,param('ns'));
-        param('authabvr'=>$ns[0]);
-        param('namespacetype'=>$ns[1]);
-        $authabvr=$ns[0];
-        $namespacetype=$ns[1];
-        my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
-        my $dbh1 = open_dbi();
-        my $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
-        $sth1->execute($retrieve);
+    if (param('ns') or param('id')) { #ns or id param specified; user intends to load from database so open database and load up parameters
+        my $sth1;
+        if (param('ns')) {
+            my @ns = split (/\_/,param('ns'));
+            param('authabvr'=>$ns[0]);
+            param('namespacetype'=>$ns[1]);
+            $authabvr=$ns[0];
+            $namespacetype=$ns[1];
+            my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
+            $sth1->execute($retrieve);
+        }
+        else {
+            my $retrieve = param('id');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_id = ?});
+            $sth1->execute($retrieve);
+        }
         my ($id, $namespace_lsid,  $namespace_type, $desc, $auth, $contactemail, $object,  $generic_url,  $synonym,  $urlsyntax,  $urlexample,  $shorthandname, $example_id, $note) = $sth1->fetchrow_array();
         $namespace_id = $id;
+        my @split = split(/\:/, $namespace_lsid);
+        ($authabvr, $namespacetype) = split(/\_/,$split[4]);
+        param('authabvr'=>$authabvr);
+        param('namespacetype'=>$namespacetype);
         param('desc'=>$desc);
         param('auth'=>$auth);
         param('object'=>$object);
@@ -58,20 +71,22 @@
         param('shorthand_name'=>$shorthandname);
         param('example_id'=>$example_id);
         param('note'=>$note);
+        param('continue'=>1);
+        param('nsid'=>$id);
     }
 
     print header,
-        start_html(-title => 'Namespace Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}),
-        
-        h1('Namespace Form');
+        start_html(-title => 'Namespace Update Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}, -class => "update"),
+        h1('Namespace Update Form');
+        print "Database search page is located here: ",a({href=>'http://mobycentral.cbr.nrc.ca/cgi-bin/search.cgi'}, "Search Page"),p,; 
         if (!$namespace_id) {
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         "Full abbreviation will be \"authority abbreviation_identifier abbreviation\" e.g. \"GeneDB_Tbrucei\"",
         start_form,
         table(
-        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB")),
+        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB"),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation* "),td(textfield(-name =>'namespacetype', -class => "require"),"e.g.: Tbrucei")),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name => 'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -105,11 +120,11 @@
         else {
             param('namespace_id'=>$namespace_id);
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         start_form,
         table(
-        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id'))),
+        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id')),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation: "),td($namespacetype),(hidden('namespacetype'))),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name =>'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -135,7 +150,7 @@
         Tr(td("url_example "),td(textfield('url_iec'),"e.g.: http\:\/\/www.genedb.org\/genedb\/Search\?organism=tryp&name=Tb927.1.5250")),
         Tr(td("shorthand_names "),td(textarea('shorthand_name'),"e.g.: Tbrucei. one entry per line")),
         Tr(td("note "),td(textarea('note'))),
-    Tr(td(submit)),
+    Tr(td(submit -name => 'submit values', -class => 'submit')),
     Tr(td(reset)),
     end_form,),p,
         $namespace_id,p,
@@ -168,31 +183,29 @@
         if (param('note')) {$Param{note}=param('note');}
         if (param('syn')) {$Param{syn} = param('syn');}
         
-if (param() and !param('ns')) {
-        my $error = chkerrors(%Param);
-        my %variables;
-        if ($error == 0){
-            %variables = setvariables(%Param);
-
-        
+if (param() and !param('ns') and !param('id')) {
+    my $error = chkerrors(%Param);
+    my %variables;
+    if ($error == 0){
+        %variables = setvariables(%Param);
         my $dbh = open_dbi();
-        my $sth;
- 
-        if (!param('namespace_id')) {
+        my $sth; 
+        if (!param('namespace_id') and param('continue') != 1) {
             adddata ($dbh, $sth, %variables);
         }
         else {
-            my $nsid = (param('namespace_id'));
+            my $nsid;
+            if (param('namespace_id')) {
+            $nsid = (param('namespace_id')); }
+            elsif (param('nsid')) { $nsid= param('nsid'); }
             updatedata ($dbh, $sth, $nsid, %variables);
         }
         $variables{authabvr} = param('authabvr');
         finalprinttoscreen (%variables);
-        param('namespace_id')=>undef;
-        }
+    }
+    #elsif ($error == 1) { print hidden('continue'=>1); }
 }
 
-elsif (param('ns')){ param('ns')=>undef;
-                    }
 #########
 
 
@@ -267,11 +280,7 @@
         print "invalid url_synonym header",hr;
         return 1;
     }
-    #elsif ($Param{example_id} =~ /\W/)  {
-     #   print "invalid characters in example_id",hr;
-      #  return 1;
-    #}
-    
+   
     else { return 0; }
 }
 sub setvariables {
@@ -358,7 +367,7 @@
         }
 sub finalprinttoscreen { #final printing to screen after updating database
     my (%variables) = @_;
-            print pre(
+            print pre(p,"successful!",p
         "namespace_type = ",$variables{namespacetype},p,
         "lsid = ",$variables{lsid},p,
         "description = ",$variables{desc},p,



From gss at pub.open-bio.org  Fri May 28 17:35:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 28 May 2004 17:35:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282135.i4SLZIbg014116@pub.open-bio.org>


gss
Fri May 28 17:35:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv14091

Modified Files:
	build.xml 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/27 19:37:10	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
@@ -1,26 +1,24 @@
-<!-- Apache Ant format build file for Semantic MOBY core library -->
+<!-- Apache Ant format build file for the SimpleEngager client GUI -->
 
-<project name="smoby-core" default="jar" basedir=".">
+<project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../../library.xml"/>
+
+    <!-- The main jar file -->
+    <property name="jar-file" value="${build-dir}/engager.jar"/>
 
     <!-- Package the compiled source files into the main jar file -->
     <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
     </target>
     
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
         <javac srcdir="${src-dir}" destdir="${classes-dir}">
-            <classpath refid="core.classpath"/>
+            <classpath refid="common.classpath"/>
         </javac>
     </target>
     
-    <!-- Deploy the jar file to the Tomcat shared library directory -->
-    <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
-    </target>
-    
 </project>



From mwilkinson at pub.open-bio.org  Mon May  3 15:07:51 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 11:07:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031507.i43F7ptf011702@pub.open-bio.org>


mwilkinson
Mon May  3 11:07:51 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv11683/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
more documentation and tools for dealing with secondary inputs

moby-live/Perl/MOBY CommonSubs.pm,1.47,1.48
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -r1.47 -r1.48
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/04/29 22:37:57	1.47
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
@@ -30,9 +30,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant "SIMPLE" or "COLLECTION"
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data->type('base64' => responseHeader("my.authURI.com") . responseFooter()) unless (scalar(@inputs));
@@ -163,7 +163,11 @@
 use MOBY::Client::OntologyServer;
 use strict;
 use warnings;
-
+use MOBY::Client::SimpleArticle;
+use MOBY::Client::CollectionArticle;
+use MOBY::Client::SecondaryArticle;
+            
+            
 use constant COLLECTION => 1;
 use constant SIMPLE => 2;
 use constant SECONDARY => 3;
@@ -191,6 +195,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -223,6 +228,7 @@
     validateThisNamespace
     isSimpleArticle
     isCollectionArticle
+    isSecondaryArticle
     extractResponseArticles
     getResponseArticles
     getCrossReferences
@@ -244,19 +250,18 @@
 
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node
 
 =cut
 
@@ -276,7 +281,7 @@
                 push @inputs, [COLLECTION,$queryID, \@simples];
             } elsif (isSimpleArticle($article)){
                 push @inputs, [SIMPLE,$queryID,$article];
-            } elsif (isSecondaryArticle($article)){
+            } elsif (isSecondaryArticle($article)){  # should never happen in a generic service parser!
                 push @inputs, [SECONDARY,$queryID,$article];
             }
         }
@@ -290,7 +295,7 @@
 =head2 complexServiceInputParser
 
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -317,14 +322,14 @@
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs->{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [SIMPLE, $DOM_name1], # the <Simple> block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= <Parameter> block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
             to parse XML DOM objects.
-            
-            
+
+
             Collections --------------------
             
             With inputs that have collections these are presented as a
@@ -347,8 +352,8 @@
 
             will become
             
-            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs->{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the <Simple> Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = <Parameter> Block
                            ]
 
             Please see the XML::DOM pod documentation for information about how
@@ -891,7 +896,7 @@
         } elsif ($child->getTagName =~ /Collection/){
             $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
         } elsif ($child->getTagName =~ /Parameter/){
-            $object = MOBY::Client::CollectionArticle->new(XML_DOM => $child);
+            $object = MOBY::Client::SecondaryArticle->new(XML_DOM => $child);
         }
         next unless $object;
         push @articles, $object;   # take the child elements, which are <Simple/> or <Collection/>
@@ -1097,15 +1102,20 @@
 =head2 getNodeContentWithArticle
 
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or "Parameter" if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -1126,16 +1136,50 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, "String", "SequenceString");
-                     print "matching node contents were ".(join "\n\n", @sequences)."\n"; # join all lines of string
-                 }   
-              }
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
 
+            For Parameters, such as the following
+             ...
+             ...
+             <moby:mobyContent>
+                <moby:mobyData>
+                    <Simple>
+                      <Sequence namespace=blah id=blah>
+                           <Integer namespace='' id='' articleName="Length">3</Integer>
+                           <String namespace='' id='' articleName="SequenceString">ATG</String>
+                      </Sequence>
+                    </Simple>
+                    <Parameter articleName='cutoff'>
+                        <Value>24</Value>
+                    </Parameter>
+                </moby:mobyData>
+             </moby:mobyContent>
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, "String", "SequenceString");
+              @cutoffs = getNodeContentWithArticle($input, "Parameter", "cutoff");
+
+
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs->{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs->{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, "Parameter", "cutoff");
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, "String", "SequenceString");
+                }
+             }
+           }
 
 =cut
 
@@ -1157,19 +1201,38 @@
     unless ($nodes->item(0)){
         $nodes = $node->getElementsByTagName("moby:$element");
     }
+
 	for (0..$nodes->getLength-1){
         my $child = $nodes->item($_);
-		if (
+        if (
             (($child->getAttribute("articleName")) && (($child->getAttribute("articleName") eq $articleName)))
             || (($child->getAttribute("moby:articleName")) && (($child->getAttribute("moby:articleName") eq $articleName)))){
-			# now we have a valid child, get the content... stringified... regardless of what it is
-			my $resp;
-			foreach ($child->getChildNodes){
-                next unless $_->getNodeType == TEXT_NODE;
-				$resp .= $_->toString;
-			}
-			push @contents, $resp;
-		}
+            # now we have a valid child, get the content... stringified... regardless of what it is
+            
+            if (isSecondaryArticle($child)){
+                my $resp;
+                my $valuenodes = $child->getElementsByTagName('Value');
+                unless ($valuenodes->item(0)){
+                    $valuenodes = $child->getElementsByTagName("moby:Value");
+                }
+                for (0..$valuenodes->getLength-1){
+                    my $valuenode = $valuenodes->item($_);
+                    foreach my $amount ($valuenode->getChildNodes){
+                        next unless $amount->getNodeType == TEXT_NODE;
+                        $resp .= $amount->toString;
+                    }
+                }
+                push @contents, $resp;
+                
+            } else {
+                my $resp;
+                foreach ($child->getChildNodes){
+                    next unless $_->getNodeType == TEXT_NODE;
+                    $resp .= $_->toString;
+                }
+                push @contents, $resp;
+            }
+        }
 	}
 	return @contents;
 }



From mwilkinson at pub.open-bio.org  Mon May  3 19:49:18 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 15:49:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405031949.i43JnI0k012385@pub.open-bio.org>


mwilkinson
Mon May  3 15:49:18 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12366

Modified Files:
	Central.pm 
Added Files:
	SecondaryArticle.html SecondaryArticle.pm 
Log Message:
added an object to represent a parameter

moby-live/Perl/MOBY/Client SecondaryArticle.html,NONE,1.1 SecondaryArticle.pm,NONE,1.1 Central.pm,1.74,1.75
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.74
retrieving revision 1.75
diff -u -r1.74 -r1.75
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/04/14 19:56:59	1.74
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2004/05/03 19:49:18	1.75
@@ -75,14 +75,29 @@
  Function  :	connect to one or more MOBY-Central
                 registries for searching
  Returns   :	MOBY::Client::Central object
+ 
+ ENV & PROXY : you can set environment variables to change the defaults.
+             By default, a call to 'new' will initialize MOBY::Client::Central
+             to connect to the MOBY Central registry at:
+             http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl
+             If you wish to chose another registry by default, or if you need
+             to set up additional connection details (e.g. PROXY) then you may
+             set the following environment variables to whatever you
+             require:
+             MOBY_SERVER  (default http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl)
+             MOBY_URI     (default http://mobycentral.cbr.nrc.ca/MOBY/Central)
+             MOBY_PROXY   (no default)
+                
  Args      :    Registries - optional.
                            - takes the form
                               {$NAME1 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                $NAME2 => {
                                     URL => $URL,
-                                    URI => $URI},
+                                    URI => $URI,
+                                    PROXY => $proxy_server},
                                 }
                             - by default this becomes
                             {mobycentral => {
@@ -125,6 +140,7 @@
 				default_MOBY_servername => ['mobycentral',												'read/write'],
 				default_MOBY_server 	=> ['http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY05/mobycentral.pl', 	'read/write'],
 				default_MOBY_uri		=> ['http://mobycentral.cbr.nrc.ca/MOBY/Central',				'read/write'],
+                default_MOBY_proxy      => [undef,                                                      'read/write'],
 				default_MOBY_type		=> ['soap',                                                     'read/write'],
 				Registries              => [undef, 														'read/write'],
 				multiple_registries		=> [undef,														'read/write'],
@@ -238,6 +254,7 @@
 	$self->default_MOBY_server($ENV{MOBY_SERVER}) if $ENV{MOBY_SERVER};
 	$self->default_MOBY_uri($ENV{MOBY_URI}) if $ENV{MOBY_URI};
 	$self->default_MOBY_type($ENV{MOBY_TYPE}) if $ENV{MOBY_TYPE};
+	$self->default_MOBY_proxy($ENV{MOBY_PROXY}) if $ENV{MOBY_PROXY};
 	
 	
     if ($self->Registries){
@@ -248,11 +265,19 @@
 			my $url = $acc->{URL};
 			my $uri = $acc->{URI};
 			my $type = $acc->{TYPE};
+			my $proxy = $acc->{PROXY};
 			$type ||='soap';
 			if (lc($type) eq "get"){
 				push @{$self->Connections}, [$name, $type, $url];
 			} else {
-				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy($url)->uri($uri)->on_fault(
+                my @soapargs;
+                if ($proxy){
+                    @soapargs = ($url,
+                                proxy => ['http' => $proxy]);
+                } else {
+                    @soapargs = ($url);
+                }
+				push @{$self->Connections}, [$name, $type, SOAP::Lite->proxy(@soapargs)->uri($uri)->on_fault(
 					sub{
 						my($soap, $res) = @_; 
 						die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";
@@ -270,7 +295,16 @@
 								URI => $self->default_MOBY_uri
 							  }}
 							 );
-			push @{$self->Connections},[$self->default_MOBY_servername, $self->default_MOBY_type, SOAP::Lite->proxy($self->default_MOBY_server)->uri($self->default_MOBY_uri)->on_fault(
+            my @soapargs;
+            if ($self->default_MOBY_proxy){
+                @soapargs = ($self->default_MOBY_server,
+                            proxy => ['http' => $self->default_MOBY_proxy]);
+            } else {
+                @soapargs = ($self->default_MOBY_server);
+            }
+			push @{$self->Connections},[$self->default_MOBY_servername,
+                                        $self->default_MOBY_type,
+                                        SOAP::Lite->proxy(@soapargs)->uri($self->default_MOBY_uri)->on_fault(
 				sub{
 					my($soap, $res) = @_; 
 					die ref $res ? $res->faultstring : $soap->transport->status, "\n ERROR ERROR ERROR\n";



From mwilkinson at pub.open-bio.org  Mon May  3 20:15:32 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:15:32 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032015.i43KFWrL012520@pub.open-bio.org>


mwilkinson
Mon May  3 16:15:32 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12497

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing documentation error that Bertrand spotted

moby-live/Perl/MOBY CommonSubs.pm,1.48,1.49 CommonSubs.html,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 15:07:51	1.48
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
@@ -314,7 +314,6 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/04/14 20:10:35	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
@@ -86,9 +86,9 @@
         # Each element of the array is a queryInput block, or a mobyData block
         # the arrayref has the following structure:
         # [SIMPLE, $queryID, $simple]
-        # the first element is a constant &quot;SIMPLE&quot; or &quot;COLLECTION&quot;
+        # the first element is an exported constant SIMPLE, COLLECTION, SECONDARY
         # the second element is the queryID (required for enumerating the responses)
-        # the third element is the XML::DOM for the Simple or Collection block    
+        # the third element is the XML::DOM for the Simple, Collection, or Parameter block    
     my (@inputs)= genericServiceInputParser($data); 
         # or fail properly with an empty response
     return SOAP::Data-&gt;type('base64' =&gt; responseHeader(&quot;my.authURI.com&quot;) . responseFooter()) unless (scalar(@inputs));
@@ -206,25 +206,24 @@
 <pre>
  name     : genericServiceInputParser
  function : For the MOST SIMPLE SERVICES that take single Simple or Collection inputs
-            and no Secondaries this routine takes the MOBY message and
+            and no Secondaries/Parameters this routine takes the MOBY message and
             breaks the objects out of it in a useful way
  usage    : my @inputs = genericServiceInputParser($MOBY_mssage));
  args     : $message - this is the SOAP payload; i.e. the XML document containing the MOBY message
  returns  : @inputs - the structure of @inputs is a list of listrefs.
             Each listref has three components:
-                1. COLLECTION|SIMPLE|SECONDARY (i.e. constants 1, 2, 3)
-                2. queryID (undef for Secondary parameters)
+                1. COLLECTION|SIMPLE (i.e. constants 1, 2)
+                2. queryID
                 3. $data - the data takes several forms
                          a. $article XML::DOM node for Simples
-                            &lt;queryInput...&gt;...&lt;/queryInput&gt;
-                         b. \@article XML:DOM nodes for Collections
-                         c. $secondary XML::DOM node</pre>
+                            &lt;mobyData...&gt;...&lt;/mobyData&gt;
+                         b. \@article XML:DOM nodes for Collections</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
 <pre>
  name     : complexServiceInputParser
- function : For more complex services taht have multiple articles for each input
+ function : For more complex services that have multiple articles for each input
             and/or accept parameters, this routine will take a MOBY message and
             extract the Simple/Collection/Parameter objects out of it in a
             useful way.
@@ -238,33 +237,31 @@
             
             for example, the input message:
             
-                &lt;queryInput queryID = '1'&gt;
+                &lt;mobyData queryID = '1'&gt;
                     &lt;Simple articleName='name1'&gt;
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become:
             (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
             
-            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [SIMPLE, $DOM_name1], # the &lt;Simple&gt; block
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff= &lt;Parameter&gt; block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
-            to parse XML DOM objects.
-            
-            
+            to parse XML DOM objects.</pre>
+<pre>
             Collections --------------------
             
             With inputs that have collections these are presented as a
             listref of Simple article DOM's.  So for the following message:
             
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -277,12 +274,12 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <pre>
             will become
             
-            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ],
-                             [SECONDARY, $DOM_cutoff]
+            $inputs-&gt;{1} = [ [COLLECTION, [$DOM, $DOM] ], # $DOM is the &lt;Simple&gt; Block!
+                             [SECONDARY, $DOM_cutoff]  # $DOM_cutoff = &lt;Parameter&gt; Block
                            ]</pre>
 <pre>
             Please see the XML::DOM pod documentation for information about how
@@ -292,12 +289,11 @@
 <h2><a name="getarticles">getArticles</a></h2>
 <pre>
  name     : getArticles
- function : get the Simple/Collection/Parameter articles for a single queryInput
-            or queryResponse node
+ function : get the Simple/Collection/Parameter articles for a single mobyData
  usage    : @articles = getArticles($XML)
  args     : raw XML or XML::DOM of a queryInput, mobyData, or queryResponse block (e.g. from getInputs)
- returns  : a list of listrefs; each listref is one component of the queryInput.
-            a single queryInput/Response may consist of one or more named or unnamed
+ returns  : a list of listrefs; each listref is one component of the queryInput or mobyData block
+            a single block may consist of one or more named or unnamed
             simple, collection, or parameter articles.
             The listref structure is thus [name, $ARTICLE_DOM]:
             
@@ -305,17 +301,17 @@
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Simple articleName='name1'&gt;
                       &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
-                &lt;/queryInput&gt;
+                &lt;/mobyData&gt;
         
     or  :  @articles = ['name1', $COLL_DOM], ['paramname1', $PARAM_DOM]</pre>
 <pre>
             generated from the following sample XML:</pre>
 <pre>
-                &lt;queryInput&gt;
+                &lt;mobyData&gt;
                     &lt;Collection articleName='name1'&gt;
                       &lt;Simple&gt;
                        &lt;Object namespace=blah id=blah/&gt;
@@ -328,7 +324,7 @@
                        &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
-                &lt;/queryInput&gt;</pre>
+                &lt;/mobyData&gt;</pre>
 <p>
 </p>
 <h2><a name="genericserviceinputparserasobject">genericServiceInputParserAsObject</a></h2>
@@ -381,13 +377,13 @@
 <h2><a name="simpleresponse">simpleResponse</a></h2>
 <pre>
  name     : simpleResponse
- function : wraps a simple article in the appropriate queryResponse structure
+ function : wraps a simple article in the appropriate (mobyData) structure
  usage    : $resp .= &amp;simpleResponse($object, 'MyArticleName', $queryID);
  args     : (in order)
             $object   - (optional) a MOBY Object as raw XML
             $article  - (optional) an articeName for this article
             $query    - (optional, but strongly recommended) the queryID value for the
-                        queryInput block to which you are responding
+                        mobyData block to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
             response by calling &amp;simpleResponse(undef, undef, $queryID) with no arguments.</pre>
@@ -396,12 +392,12 @@
 <h2><a name="collectionresponse">collectionResponse</a></h2>
 <pre>
  name     : collectionResponse
- function : wraps a set of articles in the appropriate queryResponse structure
+ function : wraps a set of articles in the appropriate mobyData structure
  usage    : return responseHeader . &amp;collectionResponse(\@objects, 'MyArticleName', $queryID) . responseFooter;
  args     : (in order)
             \@objects - (optional) a listref of MOBY Objects as raw XML
             $article  - (optional) an articeName for this article
-            $queryID  - (optional, but strongly recommended) the queryInput ID
+            $queryID  - (optional, but strongly recommended) the mobyData ID
                         to which you are responding
  notes    : as required by the API you must return a response for every input.
             If one of the inputs was invalid, you return a valid (empty) MOBY
@@ -442,7 +438,7 @@
 <h2><a name="getinputs">getInputs</a></h2>
 <pre>
  name     : getInputs
- function : get the queryInput block(s) as XML::DOM nodes
+ function : get the mobyData block(s) as XML::DOM nodes
  usage    : @queryInputs = getInputArticles($XML)
  args     : the raw XML of a &lt;MOBY&gt; query, or an XML::DOM document
  returns  : a list of XML::DOM::Node's, each is a queryInput or mobyData block.
@@ -467,11 +463,11 @@
 <h2><a name="getarticlesasobjects">getArticlesAsObjects</a></h2>
 <pre>
  name     : DO NOT USE!!
- function : get the Simple/Collection articles for a single queryInput
+ function : get the Simple/Collection articles for a single mobyData
             or queryResponse node, rethrning them as SimpleArticle,
             SecondaryArticle, or ServiceInstance objects
  usage    : @articles = getArticles($XML)
- args     : raw XML or XML::DOM of a moby:queryInput, moby:queryResponse block
+ args     : raw XML or XML::DOM of a moby:mobyData block
  returns  :</pre>
 <p>
 </p>
@@ -555,15 +551,20 @@
 <h2><a name="getnodecontentwitharticle">getNodeContentWithArticle</a></h2>
 <pre>
  name     : getNodeContentWithArticle
- function : get the stringified content of a node that has the correct element and article name
+ function : a very flexible way to get the stringified content of a node
+            that has the correct element and article name
+            or get the value of a Parameter element.
  usage    : @strings = getNodeContentWithArticle($node, $tagname, $articleName)
  args     : (in order)
-            $node        - the XML::DOM node we are searching
-            $tagname     - the tagname (effectively from the Object type ontology)
+            $node        - an XML::DOM node, or straight XML.  It may even
+                           be the entire mobyData block.
+            $tagname     - the tagname (effectively from the Object type ontology),
+                           or &quot;Parameter&quot; if you are trying to get secondaries
             $articleName - the articleName that we are searching for
             
  returns  : an array of the stringified text content for each
             node that matched the tagname/articleName specified.
+            note that each line of content is an element of the string.
  notes    : This was written for the purpose of getting the values of
             String, Integer, Float, Date_Time, and other such primitives.
             For example, in the following XML:
@@ -584,15 +585,49 @@
              
             would be analysed as follows:
               
-              my ($query) = @_;  # get the incoming MOBY query XML
-              my @queries = getInputArticles($query);  # returns DOM nodes
-              foreach (@queries){
-                 my @inputs = @{$_}; #(may be more than one Simple/Collection input per query)
-                 foreach my $input(@inputs){
-                     @sequences = getNodeContentWithArticle($_, &quot;String&quot;, &quot;SequenceString&quot;);
-                     print &quot;matching node contents were &quot;.(join &quot;\n\n&quot;, @sequences).&quot;\n&quot;; # join all lines of string
-                 }   
-              }</pre>
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);</pre>
+<pre>
+            For Parameters, such as the following
+             ...
+             ...
+             &lt;moby:mobyContent&gt;
+                &lt;moby:mobyData&gt;
+                    &lt;Simple&gt;
+                      &lt;Sequence namespace=blah id=blah&gt;
+                           &lt;Integer namespace='' id='' articleName=&quot;Length&quot;&gt;3&lt;/Integer&gt;
+                           &lt;String namespace='' id='' articleName=&quot;SequenceString&quot;&gt;ATG&lt;/String&gt;
+                      &lt;/Sequence&gt;
+                    &lt;/Simple&gt;
+                    &lt;Parameter articleName='cutoff'&gt;
+                        &lt;Value&gt;24&lt;/Value&gt;
+                    &lt;/Parameter&gt;
+                &lt;/moby:mobyData&gt;
+             &lt;/moby:mobyContent&gt;
+             ...
+             ...
+            
+            You would parse it as follows:
+            
+              # get $input - e.g. from genericServiceInputParser or complexServiceInputParser
+              @sequences = getNodeContentWithArticle($input, &quot;String&quot;, &quot;SequenceString&quot;);
+              @cutoffs = getNodeContentWithArticle($input, &quot;Parameter&quot;, &quot;cutoff&quot;);</pre>
+<pre>
+ EXAMPLE  :
+           my $inputs = complexServiceInputParser($MOBY_mssage));
+               # $inputs-&gt;{$queryID} = [ [TYPE, $DOM], [TYPE, $DOM], [TYPE, $DOM] ]
+           my (@enumerated) = keys %{$inputs};
+           foreach $no (@enumerated){
+             my @articles = @{$inputs-&gt;{$no}};
+             foreach my $article(@articles){
+                my ($type, $DOM) = @{$article};
+                if ($type == SECONDARY){
+                    $cutoff = getNodeContentsWithArticle($DOM, &quot;Parameter&quot;, &quot;cutoff&quot;);
+                } else {
+                   $sequences = getNodeContentWithArticle($DOM, &quot;String&quot;, &quot;SequenceString&quot;);
+                }
+             }
+           }</pre>
 <p>
 </p>
 <h2><a name="validatenamespaces">validateNamespaces</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 20:39:11 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:39:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032039.i43KdBEA012659@pub.open-bio.org>


mwilkinson
Mon May  3 16:39:11 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12636/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.8,1.9 Service.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/04/01 21:23:47	1.8
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
@@ -181,6 +181,16 @@
                 This would cause a single invocation of a service requiring
                 two input parameters named "input1" and "input2" 
 
+                $Service->execute(XMLinputlist => [
+	                         [
+                             'input1', '<Object namespace="blah" id="123"/>',
+                             'input2', '<Object namespace="blah" id="234"/>',
+                             'param1', '<Value>0.001</Value>',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named "input1" and "input2" 
+
 
 =cut
 
@@ -198,8 +208,11 @@
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
                 $XML ||= "";
-                $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
-                
+                if (($XML =~ /\<Value\>/) || ($XML =~ /\<moby\:Value\>/)){
+                    $data .= "<moby:Parameter moby:articleName='$articleName'>$XML</moby:Parameter>";
+                } else {
+                    $data .= "<moby:Simple moby:articleName='$articleName'>\n$XML\n</moby:Simple>\n";
+                }
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/04/01 21:23:47	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
@@ -110,6 +110,16 @@
                               ]);
                 This would cause a single invocation of a service requiring
                 two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+<pre>
+                $Service-&gt;execute(XMLinputlist =&gt; [
+                                 [
+                             'input1', '&lt;Object namespace=&quot;blah&quot; id=&quot;123&quot;/&gt;',
+                             'input2', '&lt;Object namespace=&quot;blah&quot; id=&quot;234&quot;/&gt;',
+                             'param1', '&lt;Value&gt;0.001&lt;/Value&gt;',
+                             ]
+                              ]);
+                This would cause a single invocation of a service requiring
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 20:44:41 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:44:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032044.i43KifVR012740@pub.open-bio.org>


mwilkinson
Mon May  3 16:44:41 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv12717/MOBY/Client

Modified Files:
	Service.pm Service.html 
Log Message:
enable execution of services that require parameters

moby-live/Perl/MOBY/Client Service.pm,1.9,1.10 Service.html,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:39:11	1.9
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
@@ -189,7 +189,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named "input1" and "input2" 
+                two input parameters named "input1" and "input2", and a
+                parameter named 'param1' with a value of 0.001
 
 
 =cut

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:39:11	1.5
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.html	2004/05/03 20:44:41	1.6
@@ -119,7 +119,8 @@
                              ]
                               ]);
                 This would cause a single invocation of a service requiring
-                two input parameters named &quot;input1&quot; and &quot;input2&quot;</pre>
+                two input parameters named &quot;input1&quot; and &quot;input2&quot;, and a
+                parameter named 'param1' with a value of 0.001</pre>
 <p>
 </p>
 <h2><a name="servicename">ServiceName</a></h2>



From mwilkinson at pub.open-bio.org  Mon May  3 20:51:15 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Mon, 3 May 2004 16:51:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405032051.i43KpFUl012830@pub.open-bio.org>


mwilkinson
Mon May  3 16:51:15 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv12807/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing more documentation errors

moby-live/Perl/MOBY CommonSubs.pm,1.49,1.50 CommonSubs.html,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.49
retrieving revision 1.50
diff -u -r1.49 -r1.50
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:15:32	1.49
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
@@ -344,7 +344,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>
@@ -422,7 +421,6 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='e value cutoff'>
-                       <datatype>Float</datatype>
                        <default>10</default>
                     </Parameter>
                 </mobyData>

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:15:32	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
@@ -271,7 +271,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
@@ -321,7 +320,6 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='e value cutoff'&gt;
-                       &lt;datatype&gt;Float&lt;/datatype&gt;
                        &lt;default&gt;10&lt;/default&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>



From mwilkinson at pub.open-bio.org  Tue May  4 23:54:16 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 4 May 2004 19:54:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405042354.i44NsGmZ018527@pub.open-bio.org>


mwilkinson
Tue May  4 19:54:16 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv18504/Perl/MOBY

Modified Files:
	CommonSubs.pm CommonSubs.html 
Log Message:
fixing and improving documentation for the service input parser

moby-live/Perl/MOBY CommonSubs.pm,1.50,1.51 CommonSubs.html,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.50
retrieving revision 1.51
diff -u -r1.50 -r1.51
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/03 20:51:15	1.50
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2004/05/04 23:54:16	1.51
@@ -263,6 +263,41 @@
                             <mobyData...>...</mobyData>
                          b. \@article XML:DOM nodes for Collections
 
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+                <mobyData queryID = '2'>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                </mobyData>
+
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)
+
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the <Simple> block
+
+            for example, the input message:
+            
+                <mobyData queryID = '1'>
+                    <Collection>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    <Simple>
+                       <Object namespace=blah id=blah/>
+                    </Simple>
+                    </Collection>
+                </mobyData>
+
+            will become:
+
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the <Simple> block
+
 =cut
 
 
@@ -314,7 +349,7 @@
                        <Object namespace=blah id=blah/>
                     </Simple>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 
@@ -344,7 +379,7 @@
                       </Simple>
                     </Collection>
                     <Parameter articleName='cutoff'>
-                       <default>10</default>
+                       <Value>10</Value>
                     </Parameter>
                 </mobyData>
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/03 20:51:15	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.html	2004/05/04 23:54:16	1.12
@@ -218,6 +218,41 @@
                          a. $article XML::DOM node for Simples
                             &lt;mobyData...&gt;...&lt;/mobyData&gt;
                          b. \@article XML:DOM nodes for Collections</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;
+                &lt;mobyData queryID = '2'&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:
+            (note that SIMPLE, COLLECTION, and SECONDARY are exported constants from this module)</pre>
+<pre>
+            @inputs = ([SIMPLE, 1, $DOM], [SIMPLE, 2, $DOM]) # the &lt;Simple&gt; block</pre>
+<pre>
+            for example, the input message:
+            
+                &lt;mobyData queryID = '1'&gt;
+                    &lt;Collection&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;Simple&gt;
+                       &lt;Object namespace=blah id=blah/&gt;
+                    &lt;/Simple&gt;
+                    &lt;/Collection&gt;
+                &lt;/mobyData&gt;</pre>
+<pre>
+            will become:</pre>
+<pre>
+            @inputs = ( [COLLECTION, 1, [$DOM, $DOM]] ) # the &lt;Simple&gt; block</pre>
 <p>
 </p>
 <h2><a name="complexserviceinputparser">complexServiceInputParser</a></h2>
@@ -242,7 +277,7 @@
                        &lt;Object namespace=blah id=blah/&gt;
                     &lt;/Simple&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>
@@ -271,7 +306,7 @@
                       &lt;/Simple&gt;
                     &lt;/Collection&gt;
                     &lt;Parameter articleName='cutoff'&gt;
-                       &lt;default&gt;10&lt;/default&gt;
+                       &lt;Value&gt;10&lt;/Value&gt;
                     &lt;/Parameter&gt;
                 &lt;/mobyData&gt;</pre>
 <pre>



From gordonp at pub.open-bio.org  Thu May  6 03:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 5 May 2004 23:23:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3HG024197@pub.open-bio.org>


gordonp
Wed May  5 23:23:03 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/docs

Modified Files:
	ChangeLog 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/docs ChangeLog,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/04/21 17:56:49	1.12
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
@@ -1,3 +1,8 @@
+2004-05-05  Paul Gordon <gordonp at cbr.nrc.ca>
+
+	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 
+        have the same mobyContent/mobyData envelopes.
+
 2004-04-21  Paul Gordon <gordonp at cbr.nrc.ca>
 
         * Implemented Moby data instance classes for simples, collections, 



From gordonp at pub.open-bio.org  Thu May  6 03:23:03 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Wed, 5 May 2004 23:23:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405060323.i463N3D3024178@pub.open-bio.org>


gordonp
Wed May  5 23:23:02 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv24153/Java/src/main/org/biomoby/client

Modified Files:
	MobyRequest.java 
Log Message:
Updated to use new mobyContent/mobyData structure of 0.7 API

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/04/21 17:28:58	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
@@ -102,7 +102,7 @@
 	// Now compile the XPath statements that will be used fetch data from the server response
 	try{
 	    base64EncodedXPath = new XPath("//*[@xsi:type=\"SOAP-ENC:base64\"]", null, mobyPrefixResolver, XPath.SELECT);
-	    queryResponseXPath = new XPath("//moby:queryResponse | //queryResponse", null, mobyPrefixResolver, XPath.SELECT);
+	    queryResponseXPath = new XPath("//moby:mobyData | //mobyData", null, mobyPrefixResolver, XPath.SELECT);
 	    simpleChildXPath = new XPath("moby:Simple | Simple", null, mobyPrefixResolver, XPath.SELECT);
 	    collectionChildXPath = new XPath("moby:Collection | Collection", null, mobyPrefixResolver, XPath.SELECT);
 	}
@@ -428,8 +428,8 @@
 	// Start of envelope
 	String mobyRequest = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
 	    "       <moby:MOBY xmlns:moby=\"" + MobyPrefixResolver.MOBY_XML_NAMESPACE + "\">\n" +
-	    "          <moby:Query>\n" +
-	    "<moby:queryInput moby:queryID='1'>";
+	    "          <moby:mobyContent>\n" +
+	    "<moby:mobyData moby:queryID='1'>";
 
 	// Real input data payload
 	if(data != null){
@@ -458,8 +458,8 @@
 	
 	// End of envelope
 	mobyRequest +=
-	    "              </moby:queryInput>\n" +
-	    "          </moby:Query>\n" +
+	    "              </moby:mobyData>\n" +
+	    "          </moby:mobyContent>\n" +
 	    "       </moby:MOBY>\n";
 	if(debug){
 	    debugPS.println("Input to MOBY Service is:");
@@ -483,17 +483,17 @@
 	try{
 	    response_list = runXPath(queryResponseXPath, n);
      	}catch(TransformerException te){
-            throw new MobyException("Cannot select MOBY DOM queryResponse nodes due to exception "+
+            throw new MobyException("Cannot select MOBY DOM mobyContent nodes due to exception "+
 				    "while executing XPath statement: " +te);
 	}
 	
 	if(response_list == null || response_list.getLength() == 0){
-	    throw new MobyException("Could not find any queryResponse elements in the output");
+	    throw new MobyException("Could not find any mobyContent elements in the output");
 	}
 	if(debug){
-	    debugPS.println("Aha! Got " + response_list.getLength() + " queryResponses");
+	    debugPS.println("Aha! Got " + response_list.getLength() + " mobyContent response elements");
 	}
-	// Do data deserialization for each queryResponse
+	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
 	    debugPS.println("Got response " + response);
@@ -504,7 +504,7 @@
 	    try{
 		collections = runXPath(collectionChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    for(int j = 0; collections != null && j < collections.getLength(); j++){
@@ -517,7 +517,7 @@
 		NodeList subsimples = null;
 		try{subsimples = runXPath(simpleChildXPath, collections.item(j));}
 		catch(TransformerException te){
-		    throw new MobyException("Cannot select MOBY DOM queryResponse/Collection/Simple " +
+		    throw new MobyException("Cannot select MOBY DOM mobyData/Collection/Simple " +
 					    "nodes due to exception "+
 					    "while executing XPath statement: " +te);
 		}
@@ -542,12 +542,12 @@
 	    try{
 		simples = runXPath(simpleChildXPath, response);
 	    }catch(TransformerException te){
-		throw new MobyException("Cannot select MOBY DOM queryResponse/Collection nodes due to exception "+
+		throw new MobyException("Cannot select MOBY DOM mobyData/Collection nodes due to exception "+
 					"while executing XPath statement: " +te);
 	    }
 	    if((collections == null || collections.getLength() == 0) &&
 	       (simples == null || simples.getLength() == 0)){
-		debugPS.println("WARNING: There appears to be no output data in queryResponse #" + i);
+		debugPS.println("WARNING: There appears to be no output data in mobyData #" + i);
 	    }
 	    for(int j = 0; simples != null && j < simples.getLength(); j++){
 		if(debug && j == 0)



From mwilkinson at pub.open-bio.org  Tue May 11 15:48:45 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Tue, 11 May 2004 11:48:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405111548.i4BFmjSU023513@pub.open-bio.org>


mwilkinson
Tue May 11 11:48:45 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv23494/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixed blockers in the OntologyServer.pm module.  Debugging is now OFF by default, and the logging will correctly exit

moby-live/Perl/MOBY OntologyServer.pm,1.40,1.41
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -r1.40 -r1.41
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/04/20 23:24:25	1.40
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/05/11 15:48:45	1.41
@@ -75,7 +75,7 @@
 use DBI;
 use DBD::mysql;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data
@@ -998,7 +998,7 @@
 
 
 sub _LOG {
-	#return unless $debug;
+	return unless $debug;
 	#print join "\n", @_;
 	#print  "\n---\n";
 	#return;



From mwilkinson at pub.open-bio.org  Thu May 13 17:56:33 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 13 May 2004 13:56:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131756.i4DHuXHq032273@pub.open-bio.org>


mwilkinson
Thu May 13 13:56:33 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32254

Modified Files:
	OntologyServer.pm 
Added Files:
	OntologyServer.html 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.html,NONE,1.1 OntologyServer.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2003/07/10 20:43:09	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
@@ -41,7 +41,8 @@
 
 =head1 AUTHORS
 
-Mark Wilkinson (markw at illuminae.com)
+Mark Wilkinson (markw at illuminae.com)
+Nina Opushneva (opushneva at yahoo.ca)
 
 BioMOBY Project:  http://www.biomoby.org
 
@@ -57,7 +58,8 @@
  Usage     :	my $OS = MOBY::OntologyServer->new(%args)
  Function  :	
  Returns   :	MOBY::OntologyServer object
- Args      :    host =>  URL to ontolgy_server script
+ Args      :    host =>  URL to ontolgy_server script (default http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi)
+                proxy => URL to an HTTP proxy server if necessarray (optional)
 
 =cut
 
@@ -80,6 +82,8 @@
     my %_attr_data = #     				DEFAULT    	ACCESSIBILITY
                   (
                     host    =>      ["http://mobycentral.cbr.nrc.ca/cgi-bin/OntologyServer.cgi",         'read/write'],
+					proxy	=>		[undef, 				'read/write'],
+					
                     );
 
    #_____________________________________________________________
@@ -121,6 +125,8 @@
     else {
 		$self->{$attrname} = $self->_default_for($attrname) }
     }
+    
+
     return undef unless $self->host;
     return $self;
 }
@@ -135,7 +141,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("objectExists=$term");
     my $res = $ua->request($req);
@@ -157,7 +163,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("serviceExists=$term");
     my $res = $ua->request($req);
@@ -178,7 +184,7 @@
     
     my $term = $args{'term'};    
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("namespaceExists=$term");
     my $res = $ua->request($req);
@@ -199,7 +205,7 @@
     
     my $term = $args{'term'};
     $term =~ s/^moby://;   # if the term is namespaced, then remove that
-    my $ua = LWP::UserAgent->new;
+    my $ua = $self->getUserAgent;
     my $req = HTTP::Request->new(POST => $self->host);
     $req->content("relationshipExists=$term");
     my $res = $ua->request($req);
@@ -210,6 +216,17 @@
     }
 }
 
+sub getUserAgent{
+	my ($self, @args) = @_;
+  my $ua = LWP::UserAgent->new;
+    my $proxy = $ENV{PROXY} if $ENV{PROXY}; # first check the environment
+	$proxy = $self->proxy if $self->proxy;  # but if the object was initialized with a proxy argument then use that instead
+    if($proxy){
+       $ua->proxy('http', $proxy);
+    }
+  return $ua;
+}
+
 sub DESTROY {}
 
 sub AUTOLOAD {



From mwilkinson at pub.open-bio.org  Thu May 13 17:57:34 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Thu, 13 May 2004 13:57:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405131757.i4DHvYEs032321@pub.open-bio.org>


mwilkinson
Thu May 13 13:57:34 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv32302

Modified Files:
	OntologyServer.pm 
Log Message:
changes to Ontology Server to allow for proxies.  More changes coming.

moby-live/Perl/MOBY/Client OntologyServer.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:56:33	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/OntologyServer.pm	2004/05/13 17:57:34	1.5
@@ -72,7 +72,7 @@
 use vars qw($AUTOLOAD);
 use LWP::UserAgent;
 
-my $debug = 1;
+my $debug = 0;
 
 {
 	#Encapsulated class data



From senger at pub.open-bio.org  Tue May 18 10:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6K026303@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs/dist
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs/dist

Modified Files:
	_README_ 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs/dist _README_,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/dist/_README_,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/dist/_README_	2003/11/08 00:27:24	1.1
+++ /home/repository/moby/moby-live/Java/docs/dist/_README_	2004/05/18 10:13:16	1.2
@@ -8,7 +8,7 @@
    jMoby-<date>.zip
 
 Servlet distribution - for those who want to run servlet producing
-BioMoby Graphs. Just rename the file ti jmoby.war and throw it into
+BioMoby Graphs. Just rename the file to jmoby.war and throw it into
 your <tomcat-home>/webapps directory, and restart Tomcat:
    jmoby-<date>.war
 



From senger at pub.open-bio.org  Tue May 18 10:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADG6Q026322@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients

Modified Files:
	MobyCmdLineClient.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients MobyCmdLineClient.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2003/11/25 13:18:10	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java	2004/05/18 10:13:16	1.4
@@ -443,25 +443,22 @@
 		    pattern.setAuthority (param.substring (pos+1));
 		    services = worker.findService (pattern);
 		}
-		if (services != null) {
-		    for (int i = 0; i < services.length; i++)
-			System.out.println (services[i]);
-		}
+		printServices (services, cmd.hasOption ("-on"));
 	    }
 	    if ((param = cmd.getParam ("-f")) != null ) {
 		decorationLn ("Looking for services related to: '" + param + "':");
 		decorationLn ("--------------------------------");
-		MobyService[] services = worker.findService (StringUtils.split (param, ","));
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		printServices (worker.findService (StringUtils.split (param, ",")),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if ((param = cmd.getParam ("-ft")) != null ) {
 		decorationLn ("Looking for services of type '" + param + "':");
 		decorationLn ("----------------------------");
-		MobyService[] services = worker.findService (param);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		MobyService pattern = new MobyService ("dummy");
+		pattern.setType (param);
+		printServices (worker.findService (pattern, null, !cmd.hasOption ("-nc"), true),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    if (cmd.hasParam ("-fs-type") || cmd.hasParam ("-fs-auth") ||
@@ -474,24 +471,30 @@
 		    String[] inputs = StringUtils.split (param, ",");
 		    for (int i = 0; i < inputs.length; i++) {
 			String[] parts = StringUtils.split (inputs[i], "=");
-			if (parts.length >= 2) {
-// 			    pattern.addInput (parts[0], parts[1]);
-			} else {
-// 			    pattern.addInput (parts[0], "");
-			}
+			MobyPrimaryDataSimple input = new MobyPrimaryDataSimple ("dummy");
+			input.setDataType (new MobyDataType (parts[0]));
+			if (parts.length >= 2)
+			    input.addNamespace (new MobyNamespace (parts[1]));
+			pattern.addInput (input);
 		    }
 		}
                 if ((param = cmd.getParam ("-fs-out")) != null ) {
 		    String[] outs = StringUtils.split (param, ",");
 		    for (int i = 0; i < outs.length; i++) {
+			MobyPrimaryDataSimple output = new MobyPrimaryDataSimple ("dummy");
+			output.setDataType (new MobyDataType (outs[i]));
+			pattern.addOutput (output);
 // 			pattern.addOutputType (outs [i]);
 		    }
 		}
 		decoration (pattern.toString());
 		decorationLn ("-----------------------------------------------");
-		MobyService[] services = worker.findService (pattern);
-		for (int i = 0; i < services.length; i++)
-		    System.out.println (services[i]);
+		boolean includeChildrenServiceTypes = !cmd.hasOption ("-nc");
+		boolean includeParentDataTypes = !cmd.hasOption ("-np");
+		printServices (worker.findService (pattern, null,
+						   includeChildrenServiceTypes,
+						   includeParentDataTypes),
+			       cmd.hasOption ("-on"));
 	    }
 
 	    //
@@ -560,4 +563,15 @@
 	}
     }
 
+    static void printServices (MobyService[] services, boolean onlyNames) {
+	if (services != null) {
+	    for (int i = 0; i < services.length; i++) {
+		if (onlyNames)
+		    System.out.println (services[i].getName());
+		else
+		    System.out.println (services[i]);
+	    }
+	}
+    }
+
 }



From senger at pub.open-bio.org  Tue May 18 10:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHaL026383@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/shared

Modified Files:
	Central.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/shared Central.java,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/04/02 16:40:23	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java	2004/05/18 10:13:17	1.5
@@ -308,6 +308,23 @@
 	throws MobyException;
 
     /**************************************************************************
+     * Find service matching both all non-empty fields in the 'pattern' and
+     * the 'keywords', and take into account also the whole ontology tree:
+     * <p>
+     * @param includeChildrenServiceTypes - if true (which is default)
+     * then it discovers also services that are child types (more
+     * specific) than the service type in 'pattern'
+     * @param includeParentDataTypes - if true (which is default) then
+     * it finds services that operate not only on the input/output
+     * data types defined in 'pattern', but also any ontolological
+     * parent types of that data types
+     *************************************************************************/
+    MobyService[] findService (MobyService pattern, String[] keywords,
+			       boolean includeChildrenServiceTypes,
+			       boolean includeParentDataTypes)
+	throws MobyException;
+
+    /**************************************************************************
      * Call Moby registry's method with given XML as input and return whatever
      * you get back. If 'inputXML' is null or empty, the method is called
      * without any parameters.



From senger at pub.open-bio.org  Tue May 18 10:13:16 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:16 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADGTP026284@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv26265/docs

Modified Files:
	ChangeLog 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/docs ChangeLog,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/06 03:23:02	1.13
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
@@ -1,3 +1,12 @@
+2004-05-18  Martin Senger  <senger at ebi.ac.uk>
+
+	* Added a new displaying option (-on) to MobyCmdLineClient
+
+	* Added a new findService() method to Central.java allowing to set
+	also 'expandObjects' and 'expandServices' attributes.
+
+	* Added/fixed MobyCmdLineClient to to able to find service by input/output.
+
 2004-05-05  Paul Gordon <gordonp at cbr.nrc.ca>
 
 	* Changed MobyRequest to reflect new 0.7 API, i.e. queries and responses 



From senger at pub.open-bio.org  Tue May 18 10:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADH8J026343@pub.open-bio.org>


senger
Tue May 18 06:13:16 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/Clients/help

Modified Files:
	MobyCmdLineClient_usage.txt 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2003/11/24 18:45:25	1.3
+++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt	2004/05/18 10:13:16	1.4
@@ -58,7 +58,8 @@
       find services by keywords (apply logical OR if more keywords);
       <keywords> is a comma-delimited lists of keywords
 
- To find services by their input and/or output data types:
+ To find services by their input and/or output data types
+ (note that this works only for simple data, not for collections):
 
    -fs-type <service-type>
    -fs-auth <authority>
@@ -69,6 +70,16 @@
    -fs-out   <outputs>
       <outputs> are comma-delimited names of output types
 
+   You may limit the number of found services by specifying:
+   -nc ... do not include services that are child types (more
+           specific) than the type you requested
+           (this option also applies when searching with -ft)
+   -np ... do not include services operating on parent types of
+           the data types you requested
+
+ The found services are printed in details, unless:
+   -on ... print only names of found services
+
  To register a data type:
 
    -rd-name  <data-type-name>
@@ -149,7 +160,4 @@
      is a name of an existing file, the contents of this file
      is used as an input parameter to the called mathod
 
-     Note that this method is meant mostly for debugging and may
-     be depracated later.
-
    -debug  ... print debug messages



From senger at pub.open-bio.org  Tue May 18 10:13:17 2004
From: senger at pub.open-bio.org (senger@ebi.ac.uk)
Date: Tue, 18 May 2004 06:13:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405181013.i4IADHfE026364@pub.open-bio.org>


senger
Tue May 18 06:13:17 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv26265/src/main/org/biomoby/client

Modified Files:
	CentralImpl.java 
Log Message:
improved finding services in MobyCmdLineClient

moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/04/21 17:22:26	1.12
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java	2004/05/18 10:13:17	1.13
@@ -1140,12 +1140,42 @@
      *************************************************************************/
     public MobyService[] findService (MobyService pattern, String[] keywords)
 	throws MobyException {
+	return findService (pattern, keywords, true, true);
+// 	if (pattern == null)
+// 	    pattern = new MobyService ("dummy");
+
+// 	String[] query = new String[] { 
+// 				"<findService>" +
+// 				buildQueryObject (pattern, keywords, true, true, false) + 
+// 				"</findService>"
+// 	};
+// 	if(useCache && cache.containsKey("findService"+query[0]))
+// 	    return (MobyService[]) cache.get("findService"+query[0]);
+	
+// 	String result = (String) doCall ("findService", query);
+// 	MobyService[] services = extractServices (result);
+
+// 	if(useCache)
+// 	    cache.put("findService"+query[0], services);
+// 	return services;
+    }
+
+    /**************************************************************************
+     *
+     *************************************************************************/
+    public MobyService[] findService (MobyService pattern, String[] keywords,
+				      boolean includeChildrenServiceTypes,
+				      boolean includeParentDataTypes)
+	throws MobyException {
 	if (pattern == null)
 	    pattern = new MobyService ("dummy");
 
 	String[] query = new String[] { 
 				"<findService>" +
-				buildQueryObject (pattern, keywords, true, true, false) + 
+				buildQueryObject (pattern, keywords,
+						  includeParentDataTypes,
+						  includeChildrenServiceTypes,
+						  false) + 
 				"</findService>"
 	};
 	if(useCache && cache.containsKey("findService"+query[0]))



From mwilkinson at pub.open-bio.org  Wed May 19 14:58:36 2004
From: mwilkinson at pub.open-bio.org (Mark Wilkinson)
Date: Wed, 19 May 2004 10:58:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191458.i4JEwaVu031596@pub.open-bio.org>


mwilkinson
Wed May 19 10:58:36 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory pub.open-bio.org:/tmp/cvs-serv31577/Perl/MOBY/Client

Modified Files:
	Service.pm 
Log Message:
fixed errors in tags surrounding collections.  Updated with API changes to the Query and Queryinput tags

moby-live/Perl/MOBY/Client Service.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/03 20:44:41	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Service.pm	2004/05/19 14:58:36	1.11
@@ -204,7 +204,7 @@
 	foreach (@inputs){
 		return "ERROR:  expected listref [articleName, XML] for data element" unless (ref($_) =~ /array/i); 
 		my $qID = $self->_nextQueryID;
-        $data .= "<moby:queryInput queryID='$qID'>";
+        $data .= "<moby:mobyData queryID='$qID'>";
 		while (my ($articleName, $XML) = splice (@{$_}, 0, 2)){
             if (!(ref($XML)=~/array/i)){
                 $articleName ||="";
@@ -217,20 +217,20 @@
             # need to do this for collections also!!!!!!    
             } elsif (ref($XML)=~/array/i){
                 my @objs = @{$XML};
-                $data .="<moby:queryInput queryID='$qID'><moby:Collection moby:articleName='$articleName'>\n";
+                $data .="<moby:Collection moby:articleName='$articleName'>\n";
                 foreach (@objs){
-                    $data .= "$_\n";
+                    $data .= "<moby:Simple>$_</moby:Simple>\n";
                 }
                 $data .="</moby:Collection>\n";
             }
         }
-        $data .="</moby:queryInput>\n";
+        $data .="</moby:mobyData>\n";
 	}
 	$data = "<![CDATA[<?xml version='1.0' encoding='UTF-8'?>
 	<moby:MOBY xmlns:moby='http://www.biomoby.org/moby-s'>
-	      <moby:Query>
+	      <moby:mobyContent>
 	          $data
-	      </moby:Query>
+	      </moby:mobyContent>
 	</moby:MOBY>]]>";
 	my $METHOD = $self->ServiceName;
 	&_LOG(%args, $METHOD);



From gss at pub.open-bio.org  Wed May 19 18:26:22 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:22 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQMU5000526@pub.open-bio.org>


gss
Wed May 19 14:26:22 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv501/src/org/sgd/vocabulary

Modified Files:
	SGD.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary SGD.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/04/01 00:30:54	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/src/org/sgd/vocabulary/SGD.java	2004/05/19 18:26:22	1.2
@@ -1,6 +1,7 @@
 package org.sgd.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class SGD extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 18:26:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQPB1000561@pub.open-bio.org>


gss
Wed May 19 14:26:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv534/src/org/pubs/vocabulary

Modified Files:
	Pubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary Pubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/04/01 00:35:06	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org/src/org/pubs/vocabulary/Pubs.java	2004/05/19 18:26:25	1.3
@@ -1,6 +1,7 @@
 package org.pubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Pubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 18:26:29 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:29 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQTSO000600@pub.open-bio.org>


gss
Wed May 19 14:26:29 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv575/.externalToolBuilders

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders added to the repository

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQetK000655@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot

Added Files:
	terms.n3 log4j.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot terms.n3,NONE,1.1 log4j.properties,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQebL000708@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv634

Modified Files:
	.classpath 
Added Files:
	.xdoclet xdoclet-build.xml 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server .xdoclet,NONE,1.1 xdoclet-build.xml,NONE,1.1 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/03/22 22:14:01	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.classpath	2004/05/19 18:26:40	1.4
@@ -5,7 +5,7 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry exported="true" kind="src" path="/Jena2"/>
 	<classpathentry exported="true" kind="src" path="/HttpClient"/>
-	<classpathentry kind="lib" path="C:/cvs-repository/httpclient/lib/commons-logging.jar"/>
+	<classpathentry kind="lib" path="C:/commons-logging-1.0.3/commons-logging.jar"/>
 	<classpathentry exported="true" kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>



From gss at pub.open-bio.org  Wed May 19 18:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeiH000688@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets/dev

Modified Files:
	OWLValidationServlet.java ProviderListServlet.java 
	GraphConversionServlet.java MOBYGraphValidationServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev OWLValidationServlet.java,1.1,1.2 ProviderListServlet.java,1.1,1.2 GraphConversionServlet.java,1.1,1.2 MOBYGraphValidationServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/OWLValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.ontology.*;
 import com.hp.hpl.jena.ontology.tidy.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/ProviderListServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,9 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.*;
+import org.smoby.servlet.*;
+import org.smoby.tools.*;
 import org.smoby.ref.tools.db.*;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 import java.io.*;

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/GraphConversionServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,7 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.server.servlet.ParamReader;
-import org.smoby.tools.server.servlet.ParameterException;
+import org.smoby.servlet.ParamReader;
+import org.smoby.servlet.ParameterException;
 
 import com.hp.hpl.jena.rdf.model.*;
 

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/03/20 00:36:47	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/dev/MOBYGraphValidationServlet.java	2004/05/19 18:26:40	1.2
@@ -1,7 +1,8 @@
 package org.smoby.ref.servlets.dev;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.parser.Parser;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 import com.hp.hpl.jena.rdf.model.*;
 
@@ -23,18 +24,19 @@
 			Model baseModel = ModelFactory.createDefaultModel();
 			StringReader reader = new StringReader(graphString);
 			baseModel.read(reader, null);
-			new MOBYGraph(baseModel);
+			Parser parser = new Parser(baseModel);
+			parser.parseProvider();
 			out.println("Model is canonical");
 		}
         catch (ParameterException e)
         {
             response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE, e.getMessage());
         }
-		catch (NonCanonicalException e)
-		{
-			out.println("Model failed canonicality test:");
-			out.println(e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			out.println("Model failed canonicality test:");
+//			out.println(e);
+//		}
 		catch (IllegalArgumentException e) {}
 	}
 }



From gss at pub.open-bio.org  Wed May 19 18:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQesY000741@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools

Modified Files:
	URIInvestigator.java DiscoveryQuery.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools URIInvestigator.java,1.2,1.3 DiscoveryQuery.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/03/27 01:27:51	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/URIInvestigator.java	2004/05/19 18:26:40	1.3
@@ -3,11 +3,13 @@
 import java.util.*;
 import java.io.*;
 import javax.servlet.http.*;
-import org.smoby.tools.common.*;
+
+import org.smoby.tools.*;
+import org.smoby.http.*;
+import org.smoby.parser.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.http.*;
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
 import org.apache.commons.httpclient.util.*;
 import org.apache.commons.logging.*;
 
@@ -50,7 +52,7 @@
         synchronized (instances)
         {
         	if (instances.get(providerURL) != null) {
-                syncLog.warn("Already investigating " + providerURL);
+        		syncLog.warn("Already investigating " + providerURL);
                 return;
             }
             
@@ -97,7 +99,7 @@
         }
         catch (MissingPropertyException e)
         {
-            syncLog.error("Missing DB_REPOSITORY_NAME property");
+        	syncLog.error("Missing DB_REPOSITORY_NAME property");
         }
         finally
         {
@@ -140,7 +142,7 @@
         }
         catch (StorageException e)
         {
-            syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
+        	syncLog.error("Couldn't check if provider URL " + providerURI + " exists", e);
             return;
         }
         
@@ -151,7 +153,7 @@
             }
             catch (StorageException e)
             {
-                syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
+            	syncLog.error("Couldn't check for last modified date of provider URL " + providerURI, e);
                 return;
             }
         }
@@ -164,7 +166,9 @@
         // be sent if it has been modified since that date
         //
         if (lastModifiedDate != null) {
-            request.addHeader(MOBY.IF_MODIFIED_HEADER,  Util.formatDateForHTTP(lastModifiedDate));
+            request.addHeader(
+                MOBY.IF_MODIFIED_HEADER,
+                Util.formatDateForHTTP(lastModifiedDate));
         }
         
         // Send the request and check the response code
@@ -178,7 +182,7 @@
         }
         catch (HTTPException e)
         {
-            syncLog.warn("Couldn't reach suggested provider " + providerURI);
+        	syncLog.warn("Couldn't reach suggested provider " + providerURI);
             return;
         }
         
@@ -203,7 +207,7 @@
                     // Log a message about the last modified date not being
                     // retrievable, but register the graph anyway
                     //
-                    syncLog.warn("Unable to get Last-Modified date for "
+                	syncLog.warn("Unable to get Last-Modified date for "
                                  + providerURI + "; ignoring");
                 }
                 catch (Throwable t)
@@ -211,7 +215,7 @@
                     // Log a message about the last modified date not being
                     // parsable, but register the graph anyway
                     //
-                    syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
+                	syncLog.warn("Unparsable Last-Modified date " + "(\"" + dateString +
                                 "\") for " + providerURI + "; ignoring");
                 }
 
@@ -219,25 +223,24 @@
                 // provider was already registered, then first de-register
                 // its currently stored description graph.
                 //
-                String graphString = "";
-                
+                InputStream in = null;
                 try {
-                	graphString = response.getBody();
+                	in = response.getBodyAsStream();
                 }
                 catch (HTTPException e)
                 {
-                    syncLog.error("Couldn't retrieve graph from " + providerURI);
+                	syncLog.error("Couldn't retrieve graph from " + providerURI);
                     return;
                 }
                 
-                Model graph = null;
-                
+                MOBYProvider provider = null;
                 try {
-                    graph = MOBYGraph.parseModel(graphString);
+                    Parser parser = Parser.forInputStream(in, Parser.LANGUAGE_RDF_XML);
+                    provider = parser.parseProvider();
                 }
-                catch (UnparsableModelException e)
+                catch (UnparsableGraphException e)
                 {
-                    syncLog.warn("Unparsable graph found at " + providerURI +
+                	syncLog.warn("Unparsable graph found at " + providerURI +
                         (alreadyRegistered ? "; deregistering" : "; ignoring"));
                     if (alreadyRegistered) {
                         deregisterProvider(manager);
@@ -251,14 +254,14 @@
                 
                 try
                 {
-                    manager.registerGraph(graph, providerURI, lastModifiedDate);
+                    manager.registerProvider(provider, lastModifiedDate);
                     
                     // Log a message about successfully registering the graph:
                     //
                     syncLog.info((alreadyRegistered ? "UPDATED : " : "ADDED   : ") + providerURI);
                 }
                 catch (StorageException e) {
-                    syncLog.error("Error storing graph for " + providerURI, e);
+                	syncLog.error("Error storing graph for " + providerURI, e);
                 }
                 
                 break;
@@ -268,7 +271,7 @@
                 // The resource has not been modified since it was
                 // registered, so there is nothing to do but log a message.
                 //
-                syncLog.info("IN-SYNC : " + providerURI);
+            	syncLog.info("IN-SYNC : " + providerURI);
                 break;
             
             case HttpServletResponse.SC_NOT_FOUND:
@@ -281,7 +284,7 @@
                     try
                     {
                     	manager.deregisterProvider(providerURI);
-                        syncLog.info("REMOVED : " + providerURI);
+                    	syncLog.info("REMOVED : " + providerURI);
                     }
                     catch (StorageException e) {
                     	syncLog.error("Unable to de-register provider " + providerURI, e);
@@ -296,7 +299,7 @@
                 
                 // Log a message about the failed attempt to contact the URL
                 //
-                syncLog.error("Status " + status + " received while trying " +
+            	syncLog.error("Status " + status + " received while trying " +
                              "to contact provider " + providerURI);
                 break;
         }

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/03/30 23:54:34	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/DiscoveryQuery.java	2004/05/19 18:26:40	1.4
@@ -4,9 +4,12 @@
 import java.text.*;
 import java.util.*;
 
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.vocabulary.MOBY;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
+import org.smoby.graph.impl.MOBYProviderImpl;
+import org.smoby.vocabulary.*;
 
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.graph.*;
@@ -41,7 +44,7 @@
     /**
      * The graph that serves as a template for providers that match.
      */
-    private MOBYGraph queryGraph;
+    private MOBYProvider queryProvider;
     
     /**
      * Flag indicating which statements should be returned: URI_ONLY,
@@ -67,9 +70,9 @@
      * @param statementsToReturn which statements should be returned: URI_ONLY,
      * QUERY_STMTS_ONLY, or ALL_STMTS (use the static constants on this class).
      */
-    public DiscoveryQuery(MOBYGraph queryGraph, int statementsToReturn)
+    public DiscoveryQuery(MOBYProvider queryProvider, int statementsToReturn)
     {
-    	this.queryGraph = queryGraph;
+    	this.queryProvider = queryProvider;
         this.statementsToReturn = statementsToReturn;
     }
     
@@ -83,22 +86,21 @@
         lastBnodeNumber = 0;
     }
     
-	public ProviderDescriptionGraph[] findMatchingGraphs()
+    public MOBYCollection findMatchingGraphs()
 	{
         init();
         
 		try
 		{
-            String queryString = buildQueryString(queryGraph);
+		    Model queryModel = ((MOBYProviderImpl) queryProvider).getUnderlying();
+            String queryString = buildQueryString(queryModel);
             StorageManager manager = new StorageManager();
-
             Model model = manager.openDBModel();
             ((ModelRDB) model).setDoFastpath(false);
             
 			// Execute the query
 			//
 			QueryResults results = Query.exec(queryString, model);
-
 			ArrayList matching = new ArrayList();
             
 			while (results.hasNext())
@@ -108,17 +110,19 @@
 			}
 			results.close();
 			
-			ProviderDescriptionGraph[] graphs =
-                new ProviderDescriptionGraph[matching.size()];
-			int i = 0;
-			for (Iterator it = matching.iterator(); it.hasNext(); i++)
+			List returnList = new ArrayList();
+			
+			for (Iterator it = matching.iterator(); it.hasNext();)
 			{
-				MOBYGraph mg = buildGraphModel(queryGraph, (ResultBinding) it.next());
-				graphs[i] = new ProviderDescriptionGraph(
-					new MOBYGraph(manager.openModel(mg.getProvider().getURI())));
+				MOBYProvider mp = buildGraphModel(queryModel, (ResultBinding) it.next());
+				String uri = mp.getURI();
+				// YUCK!
+				Model providerModel = manager.openModel(uri);
+				Parser parser = new Parser(providerModel);
+				returnList.add(parser.parseProvider());
 			}
 			
-			return graphs;
+			return MOBYObjectFactory.newUnorderedCollection(null, returnList, null);
 			
 		} catch (Throwable t) {
 			return null;
@@ -128,10 +132,8 @@
 	/**
 	 * Build and return an RDQL query string for the reified Model
 	 */
-	private String buildQueryString(MOBYGraph queryGraph)
+	private String buildQueryString(Model queryModel)
 	{
-        Model queryModel = queryGraph.getModel();
-        
         String SPACES = "      ";
         
         Map nsMap = queryModel.getNsPrefixMap();
@@ -220,12 +222,8 @@
 	 * @param binding bindings for variables
 	 * @return
 	 */
-	private MOBYGraph buildGraphModel(MOBYGraph queryGraph,
-                                      ResultBinding binding)
-		throws NonCanonicalException
+	private MOBYProvider buildGraphModel(Model queryModel, ResultBinding binding)
 	{
-        Model queryModel = queryGraph.getModel();
-        
 		// Create a default model to return
 		//
 		Model model = ModelFactory.createDefaultModel();
@@ -247,7 +245,8 @@
 			Statement copy = model.createStatement(subject, property, object);
 			model.add(copy);
 		}
-		return new MOBYGraph(model);
+		Parser parser = new Parser(model);
+		return parser.parseProvider();
 	}
 	
 	private RDFNode getBinding(RDFNode node, ResultBinding binding)



From gss at pub.open-bio.org  Wed May 19 18:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfX1000828@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/tools/db

Modified Files:
	StorageManager.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db StorageManager.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/03/29 19:40:08	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/tools/db/StorageManager.java	2004/05/19 18:26:41	1.3
@@ -1,10 +1,9 @@
 package org.smoby.ref.tools.db;
 
-import org.smoby.tools.common.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYProviderImpl;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.common.vocabulary.*;
-
+import org.smoby.vocabulary.*;
 import com.hp.hpl.jena.db.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.shared.*;
@@ -65,28 +64,16 @@
      * are in the provider graph's namespace will be stored in the global repository,
      * and all statements from the provider graph are stored in a separate model
      * that has as its name the fully expanded URI of the provider.
-     * @param providerGraph the graph to store
+     * @param provider the Provider to store
      * @param lastModifiedDate when the graph was last modified
      * @throws StorageException if unable to access the database
      */
-	public void registerProviderGraph(MOBYGraph providerGraph, Date lastModifiedDate)
-        throws StorageException
-	{
-        registerGraph(providerGraph.getModel(),
-                      providerGraph.getProvider(),
-                      lastModifiedDate);
-	}
-    
-    public void registerGraph(Model graph, String uri, Date lastModifiedDate)
-        throws StorageException
-    {
-    	registerGraph(graph, graph.createResource(uri), lastModifiedDate);
-    }
-    
-    public void registerGraph(Model graph, Resource uri, Date lastModifiedDate)
+	public void registerProvider(MOBYProvider provider, Date lastModifiedDate)
         throws StorageException
 	{
+	    Model model = ((MOBYProviderImpl) provider).getUnderlying();
         Model dbModel = null;
+        Resource uri = model.createResource(provider.getURI());
         
         try
         {
@@ -114,7 +101,7 @@
             //
             String providerNameSpace = uri.getNameSpace();
             
-            for (StmtIterator it = graph.listStatements(); it.hasNext();)
+            for (StmtIterator it = model.listStatements(); it.hasNext();)
             {
                 Statement stmt = it.nextStatement();
                 Resource subject = stmt.getSubject();
@@ -132,8 +119,8 @@
             // Add to the database another model, with the provider URL as its name
             //
             Model providerModel = maker.createModel(uri.getURI());
-            providerModel.add(graph);
-            providerModel.setNsPrefixes(graph.getNsPrefixMap());
+            providerModel.add(model);
+            providerModel.setNsPrefixes(model.getNsPrefixMap());
             
             // Add a statement asserting when the model was added to the database
             //



From gss at pub.open-bio.org  Wed May 19 18:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfJi000807@pub.open-bio.org>


gss
Wed May 19 14:26:41 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes
In directory pub.open-bio.org:/tmp/cvs-serv634/WebRoot/WEB-INF/classes

Modified Files:
	smoby.properties 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes smoby.properties,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/04/02 00:08:26	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/WebRoot/WEB-INF/classes/smoby.properties	2004/05/19 18:26:40	1.4
@@ -5,11 +5,11 @@
 #
 DB_USER_ID            = smobydev
 DB_PASSWORD           = 
-DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 DB_REPOSITORY_NAME    = smoby-dev
 
 # Uncomment if using MySQL
 #
+# DB_DRIVER_CLASS_NAME  = com.mysql.jdbc.Driver
 # DB_URL                = jdbc:mysql://localhost/smoby-dev
 # DB_TYPE               = MySQL
 



From gss at pub.open-bio.org  Wed May 19 18:26:41 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQfu4000786@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders
In directory pub.open-bio.org:/tmp/cvs-serv634/.externalToolBuilders

Added Files:
	XDoclet Builder.launch 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/.externalToolBuilders XDoclet Builder.launch,NONE,1.1
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/.externalToolBuilders/RCS/XDoclet,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmg6000901@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv876/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
@@ -8,36 +8,36 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
     <megapubs:literatureGuideURL rdf:nodeID="A1"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
     <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <megapubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Cool new search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
-  </rdf:Description>
-  <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
-    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
-    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
-    <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
+  <rdf:Description rdf:nodeID="A2">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
+    <moby:hasMapping rdf:nodeID="A3"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
+    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <moby:mapsTo rdf:nodeID="A0"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 18:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqjx000978@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/04/02 00:03:39	1.7
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
@@ -2,17 +2,13 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.go.vocabulary.Go;
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.vocabulary.MOBY;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
-import com.acmepubs.vocabulary.AcmePubs;
-
-import com.hp.hpl.jena.rdf.model.*;
+import org.go.vocabulary.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.vocabulary.*;
+import com.acmepubs.vocabulary.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -39,47 +35,47 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
         // Retrieve the subject of the moby:operatesOn statement (there is only
     	// one operatesOn statement in a valid MOBY graph)
         //
-        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-        
-        // There may be multiple moby:hasMapping statements. For each one,
-        // map its geneSymbol to a literatureGuideURL
-        //
-        StmtIterator it = graph.getModel().listStatements(
-        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-        
-        while (it.hasNext())
-        {
-    		try
-			{
-	        	Statement hasMappingStmt = it.nextStatement();
-	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-	        	
-	        	Statement geneSymbolStmt =
-	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-	        	
-    			String geneSymbol = geneSymbolStmt.getString();
-    			
-    			Statement mapsToStmt = 
-    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-    			
-				Resource mobyObject = (Resource) mapsToStmt.getObject();
-				
-				Statement literatureGuideURLStmt =
-					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-				
-				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-        	}
-    		catch (Throwable t)
-			{
-    			// Something went wrong, so proceed to next hasMapping statement
-    		}
-        }
+//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
+//        
+//        // There may be multiple moby:hasMapping statements. For each one,
+//        // map its geneSymbol to a literatureGuideURL
+//        //
+//        StmtIterator it = graph.getModel().listStatements(
+//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
+//        
+//        while (it.hasNext())
+//        {
+//    		try
+//			{
+//	        	Statement hasMappingStmt = it.nextStatement();
+//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
+//	        	
+//	        	Statement geneSymbolStmt =
+//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
+//	        	
+//    			String geneSymbol = geneSymbolStmt.getString();
+//    			
+//    			Statement mapsToStmt = 
+//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
+//    			
+//				Resource mobyObject = (Resource) mapsToStmt.getObject();
+//				
+//				Statement literatureGuideURLStmt =
+//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
+//				
+//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
+//        	}
+//    		catch (Throwable t)
+//			{
+//    			// Something went wrong, so proceed to next hasMapping statement
+//    		}
+//        }
     }
     
     /**



From gss at pub.open-bio.org  Wed May 19 18:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQq7s000997@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv953/WebRoot

Modified Files:
	citationSearch.rdf 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
@@ -14,30 +14,30 @@
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <acmepubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <acmepubs:geneSymbol rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-    <moby:mapsTo rdf:nodeID="A0"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A2"/>
+    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:operatesOn rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
     <rdfs:comment>Industry standard search</rdfs:comment>
-    <moby:operatesOn rdf:nodeID="A4"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A4">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A2"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
 </rdf:RDF>
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 18:26:55 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQtu5001055@pub.open-bio.org>


gss
Wed May 19 14:26:55 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1030/src/org/go/vocabulary

Modified Files:
	Go.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary Go.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/04/01 00:30:50	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org/src/org/go/vocabulary/Go.java	2004/05/19 18:26:55	1.2
@@ -1,6 +1,7 @@
 package org.go.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class Go extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 18:26:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQihp000868@pub.open-bio.org>


gss
Wed May 19 14:26:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv843

Modified Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager SimpleProviderEngagerPanel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/SimpleProviderEngagerPanel.java	2004/05/19 18:26:44	1.2
@@ -4,13 +4,20 @@
 import javax.swing.border.*;
 import javax.swing.event.*;
 
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.common.graph.NonCanonicalException;
-import org.smoby.tools.common.graph.UnparsableModelException;
-import org.smoby.tools.common.http.HTTPException;
-import org.smoby.tools.common.http.HTTPRequest;
-import org.smoby.tools.common.http.HTTPResponse;
+import org.smoby.http.*;
+import org.smoby.graph.*;
+import org.smoby.parser.*;
 
+/**
+ * This class is a simple two-pane window for engaging Semantic MOBY
+ * providers. The user first pastes into the input pane a canonical graph
+ * of the form that is acceptable to the provider (i.e. the graph
+ * returned by doing an HTTP GET on the provider URI, with some of
+ * the blank nodes filled in). When the user presses the "Engage Provider"
+ * button, the graph is submitted, via HTTP POST, to the provider embedded
+ * in the graph; the results of the HTTP POST, as written by the provider,
+ * are then printed to the lower pane.
+ */
 public class SimpleProviderEngagerPanel extends JPanel
 {
 	private JTextArea inputArea = new JTextArea();
@@ -31,8 +38,7 @@
 		Font plain = new Font("Monospaced", Font.PLAIN, 12);
 		inputArea.setFont(plain);
 		outputArea.setFont(plain);
-		inputArea.setEditable(true);
-		outputArea.setEditable(false);
+		
 		engageButton.setEnabled(false);
 		
 		addListeners();
@@ -104,26 +110,26 @@
 		String graphString = inputArea.getText();
 		try
 		{
-			MOBYGraph mobyGraph = MOBYGraph.fromString(graphString, false);
-			String graphURI = mobyGraph.getProvider().getURI();
+		    Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+		    MOBYProvider provider = parser.parseProvider();
+			String graphURI = provider.getURI();
 			HTTPRequest request = HTTPRequest.newPostRequest(graphURI);
 			request.addParameter("graph", graphString);
 			HTTPResponse response = request.send();
 			outputArea.setText(response.getBody());
-//			inputArea.setText("");
 		}
-		catch (UnparsableModelException e)
+		catch (UnparsableGraphException e)
 		{
 			JOptionPane.showMessageDialog(this,
 				"The graph could not be parsed", "Unparsable",
 				JOptionPane.ERROR_MESSAGE);
 		}
-		catch (NonCanonicalException e)
-		{
-			JOptionPane.showMessageDialog(this,
-					"The graph is not canonical", "Non-canonoical",
-					JOptionPane.ERROR_MESSAGE);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//			JOptionPane.showMessageDialog(this,
+//					"The graph is not canonical", "Non-canonoical",
+//					JOptionPane.ERROR_MESSAGE);
+//		}
 		catch (HTTPException e)
 		{
 			JOptionPane.showMessageDialog(this,



From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8U1001275@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/graph

Removed Files:
	ProviderDescriptionGraph.java NonCanonicalException.java 
	MOBYGraph.java UnparsableModelException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph ProviderDescriptionGraph.java,1.1,NONE NonCanonicalException.java,1.1,NONE MOBYGraph.java,1.3,NONE UnparsableModelException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/ProviderDescriptionGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/NonCanonicalException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/MOBYGraph.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/graph/RCS/UnparsableModelException.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:52 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:52 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQqrC001016@pub.open-bio.org>


gss
Wed May 19 14:26:52 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv953/src/com/acmepubs/vocabulary

Modified Files:
	AcmePubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary AcmePubs.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/vocabulary/AcmePubs.java	2004/05/19 18:26:52	1.4
@@ -1,6 +1,7 @@
 package com.acmepubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class AcmePubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8tS001385@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/io

Removed Files:
	TransceiverBase.java TokenSeparatedTransceiver.java 
	GraphListTransmitter.java ZipStreamTransceiver.java 
	GraphListTransceiverFactory.java GraphListReceiver.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io TransceiverBase.java,1.1,NONE TokenSeparatedTransceiver.java,1.1,NONE GraphListTransmitter.java,1.1,NONE ZipStreamTransceiver.java,1.1,NONE GraphListTransceiverFactory.java,1.1,NONE GraphListReceiver.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TransceiverBase.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/TokenSeparatedTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransmitter.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/ZipStreamTransceiver.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListTransceiverFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/io/RCS/GraphListReceiver.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9QR001496@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common

Removed Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/RCS/Util.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:27:07 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR7U5001256@pub.open-bio.org>


gss
Wed May 19 14:27:07 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/server/servlet

Removed Files:
	ParamReader.java ParameterException.java 
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet ParamReader.java,1.1,NONE ParameterException.java,1.1,NONE AbstractMobyServlet.java,1.6,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/ParameterException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/server/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8bH001324@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph/impl

Added Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYOntologyImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NO!
NE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8dY001291@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser

Added Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,NONE,1.1 UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQm02000920@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets CitationSearchServlet.java,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/03/27 01:17:58	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:48	1.4
@@ -2,12 +2,10 @@
 
 import java.io.*;
 import java.util.*;
-
 import javax.servlet.*;
 import javax.servlet.http.*;
-
-import org.smoby.tools.common.graph.MOBYGraph;
-import org.smoby.tools.server.servlet.AbstractMobyServlet;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
 
 /**
  * This class is a concrete subclass of AbstractMobyServlet that illustrates
@@ -36,7 +34,7 @@
      * a gene symbol and returning a list of publication
      * abstracts.
      */
-    protected void handleRequest(MOBYGraph graph)
+    protected void handleRequest(MOBYProvider graph)
     {
     }
     



From gss at pub.open-bio.org  Wed May 19 18:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9fT001458@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/vocabulary

Removed Files:
	MOBY.java VocabularyDescription.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary MOBY.java,1.2,NONE VocabularyDescription.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/MOBY.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8E6001358@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/http

Added Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1 HTTPException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9rs001480@pub.open-bio.org>


gss
Wed May 19 14:27:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools/common/http

Removed Files:
	HTTPException.java HTTPResponse.java HTTPRequest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http HTTPException.java,1.2,NONE HTTPResponse.java,1.3,NONE HTTPRequest.java,1.3,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/common/http/RCS/HTTPRequest.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:27:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR9sx001439@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/servlet

Added Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,NONE,1.1 AbstractMobyServlet.java,NONE,1.1 ParameterException.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:26:48 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQmRJ000940@pub.open-bio.org>


gss
Wed May 19 14:26:48 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv876/src/com/megapubs/vocabulary

Modified Files:
	MegaPubs.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary MegaPubs.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/04/02 00:04:21	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/src/com/megapubs/vocabulary/MegaPubs.java	2004/05/19 18:26:48	1.3
@@ -1,6 +1,7 @@
 package com.megapubs.vocabulary;
 
-import org.smoby.tools.common.vocabulary.*;
+import org.smoby.vocabulary.*;
+
 import com.hp.hpl.jena.rdf.model.*;
 
 public class MegaPubs extends VocabularyDescription



From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8lW001343@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8qw001309@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/graph

Added Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYDocument.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1 MOBYGraph.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8oF001420@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:27:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:27:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191827.i4JIR8pP001405@pub.open-bio.org>


gss
Wed May 19 14:27:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1232/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 18:26:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQeuc000765@pub.open-bio.org>


gss
Wed May 19 14:26:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets
In directory pub.open-bio.org:/tmp/cvs-serv634/src/org/smoby/ref/servlets

Modified Files:
	ProviderInvestigationServlet.java DiscoveryServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets ProviderInvestigationServlet.java,1.2,1.3 DiscoveryServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/03/22 22:13:13	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/ProviderInvestigationServlet.java	2004/05/19 18:26:40	1.3
@@ -6,9 +6,9 @@
 import javax.servlet.http.*;
 import org.apache.commons.logging.*;
 import org.smoby.ref.tools.db.*;
-import org.smoby.tools.common.graph.*;
+import org.smoby.graph.*;
 import org.smoby.ref.tools.URIInvestigator;
-import org.smoby.tools.server.servlet.*;
+import org.smoby.servlet.*;
 
 /**
  * This servlet class is used to request that S-MOBY investigate a URL for the

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/03/20 00:36:48	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/src/org/smoby/ref/servlets/DiscoveryServlet.java	2004/05/19 18:26:40	1.2
@@ -1,9 +1,10 @@
 package org.smoby.ref.servlets;
 
-import org.smoby.tools.common.graph.*;
-import org.smoby.tools.common.io.*;
+import org.smoby.servlet.*;
+import org.smoby.graph.*;
+import org.smoby.parser.NonCanonicalException;
+import org.smoby.parser.Parser;
 import org.smoby.ref.tools.*;
-import org.smoby.tools.server.servlet.*;
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.rdql.*;
 import java.io.*;
@@ -37,26 +38,18 @@
             //
 			String graphString = ParamReader.getParameter("query-graph", request);
             
-            // Does the requester want the matching graphs sent back in a
-            // binary format?
-            //
-            boolean binary = false;
-            try {
-            	ParamReader.getParameter("binary-return", request);
-                binary = true;
-            } catch (ParameterException e) {}
-            
             // Parse the query graph into a MOBYGraph object
             //
-			MOBYGraph g = MOBYGraph.fromString(graphString, true);
+			Parser parser = Parser.forString(graphString, Parser.LANGUAGE_RDF_XML);
+			MOBYProvider provider = parser.parseProvider();
             
             // Retrieve an array of provider description graphs that unify with
             // the query graph.
             //
-            DiscoveryQuery q = new DiscoveryQuery(g, DiscoveryQuery.ALL_STMTS);
-			ProviderDescriptionGraph[] matching = q.findMatchingGraphs();
+            DiscoveryQuery q = new DiscoveryQuery(provider, DiscoveryQuery.ALL_STMTS);
+			MOBYCollection matching = q.findMatchingGraphs();
 			
-            if ((matching.length == 0) && (! binary))
+            if ((matching.size() == 0))
             {
                 // The client doesn't want the graphs sent in a binary
                 // format, so show a text message indicating that there
@@ -66,23 +59,20 @@
             }
             else
             {
-                // Otherwise, create an object capable of transmitting the
-                // graphs (in either binary or human-readable text format)
-                // and use the object to send the matching graphs.
-                //
-                GraphListTransmitter transmitter =
-                    GraphListTransceiverFactory.newTransmitter(out, binary);
-                transmitter.transmit(matching);
+                for (Iterator it = matching.iterator(); it.hasNext();) {
+                    MOBYProvider p = (MOBYProvider) it.next();
+                    p.serialize(out);
+                }
 			}
             
 		}
-		catch (NonCanonicalException e)
-		{
-            // The query graph did not have the required canonical form
-            //
-			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
-				"Query graph is not canonical:\n" + e);
-		}
+//		catch (NonCanonicalException e)
+//		{
+//            // The query graph did not have the required canonical form
+//            //
+//			response.sendError(HttpServletResponse.SC_NOT_ACCEPTABLE,
+//				"Query graph is not canonical:\n" + e);
+//		}
 		catch (ParameterException e)
         {
             // The graph parameter was missing



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxY4001087@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQx3w001105@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxXt001123@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxkI001142@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxS8001185@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxUh001164@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 18:26:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 14:26:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405191826.i4JIQxh9001203@pub.open-bio.org>


gss
Wed May 19 14:26:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv1063/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Wed May 19 20:42:30 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgUSK001852@pub.open-bio.org>


gss
Wed May 19 16:42:30 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv1831

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/server .encoding,NONE,1.1


From gss at pub.open-bio.org  Wed May 19 20:42:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgYQS001889@pub.open-bio.org>


gss
Wed May 19 16:42:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1860/WebRoot

Modified Files:
	citationSearch.n3 citationSearch.rdf 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot citationSearch.n3,1.4,1.5 citationSearch.rdf,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/04/02 00:04:21	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:33	1.5
@@ -10,28 +10,32 @@
 
 megapubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Cool new search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    megapubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    megapubs:literatureGuideURL _:bnode6 .
+    moby:name "MegaPubs Citation Search" ;
+    moby:oneLineDescription "Cool new search" ;
+    moby:aboutURI "http://www.megapubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                megapubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    megapubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 megapubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 megapubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:48	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:34	1.6
@@ -8,36 +8,43 @@
     xmlns:pubs="http://www.pubs.org:8081/terms#"
     xmlns:moby="http://www.s-moby.org:8080/terms#"
     xmlns:sgd="http://www.sgd.org:8080/terms#" >
+  <rdf:Description rdf:nodeID="A0">
+    <moby:hasMapping rdf:nodeID="A1"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A0">
-    <megapubs:literatureGuideURL rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
+    <moby:oneLineDescription>Cool new search</moby:oneLineDescription>
     <moby:operatesOn rdf:nodeID="A2"/>
+    <moby:aboutURI>http://www.megapubs.com/about/citationSearch</moby:aboutURI>
+    <moby:name>MegaPubs Citation Search</moby:name>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Cool new search</rdfs:comment>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A2">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
-    <moby:hasMapping rdf:nodeID="A3"/>
+    <rdf:_1 rdf:nodeID="A0"/>
     <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
   </rdf:Description>
+  <rdf:Description rdf:nodeID="A1">
+    <moby:mapsTo rdf:nodeID="A3"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <megapubs:geneSymbol rdf:nodeID="A4"/>
+    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <megapubs:literatureGuideURL rdf:nodeID="A5"/>
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+  </rdf:Description>
   <rdf:Description rdf:about="http://www.megapubs.com:8080/geneSymbol">
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
   </rdf:Description>
-  <rdf:Description rdf:nodeID="A3">
-    <moby:mapsTo rdf:nodeID="A0"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <megapubs:geneSymbol rdf:nodeID="A4"/>
-    <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
-  </rdf:Description>
-</rdf:RDF>
\ No newline at end of file
+</rdf:RDF>



From gss at pub.open-bio.org  Wed May 19 20:42:37 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 16:42:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192042.i4JKgbYu001926@pub.open-bio.org>


gss
Wed May 19 16:42:37 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot
In directory pub.open-bio.org:/tmp/cvs-serv1897/WebRoot

Modified Files:
	citationSearch.rdf citationSearch.n3 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot citationSearch.rdf,1.5,1.6 citationSearch.n3,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 18:26:52	1.5
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.rdf	2004/05/19 20:42:37	1.6
@@ -12,31 +12,38 @@
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A0">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
     <moby:hasMapping rdf:nodeID="A1"/>
-    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
-  </rdf:Description>
-  <rdf:Description rdf:nodeID="A2">
-    <acmepubs:literatureGuideURL rdf:nodeID="A3"/>
-    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Graph"/>
   </rdf:Description>
   <rdf:Description rdf:nodeID="A1">
-    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
-    <moby:mapsTo rdf:nodeID="A2"/>
-    <acmepubs:geneSymbol rdf:nodeID="A4"/>
+    <acmepubs:geneSymbol rdf:nodeID="A2"/>
     <rdf:type rdf:resource="http://www.go.org:8080/terms#GeneSymbol"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Subject"/>
+    <moby:mapsTo rdf:nodeID="A3"/>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A4">
+    <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
+    <rdf:_1 rdf:nodeID="A0"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/citationSearch">
     <rdf:type rdf:resource="http://www.pubs.org:8081/terms#citationSearch"/>
-    <moby:operatesOn rdf:nodeID="A0"/>
+    <moby:operatesOn rdf:nodeID="A4"/>
+    <moby:oneLineDescription>Industry standard search</moby:oneLineDescription>
+    <moby:aboutURI>http://www.acmepubs.com/about/citationSearch</moby:aboutURI>
     <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Provider"/>
-    <rdfs:comment>Industry standard search</rdfs:comment>
+    <moby:name>AcmePubs Citation Search</moby:name>
+  </rdf:Description>
+  <rdf:Description rdf:nodeID="A3">
+    <rdf:type rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
+    <rdf:type rdf:resource="http://www.s-moby.org:8080/terms#Object"/>
+    <acmepubs:literatureGuideURL rdf:nodeID="A5"/>
   </rdf:Description>
   <rdf:Description rdf:about="http://www.acmepubs.com:8080/literatureGuideURL">
     <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#anyURI"/>
+    <rdfs:subPropertyOf rdf:resource="http://www.s-moby.org:8080/terms#Property"/>
     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DataTypeProperty"/>
     <rdfs:domain rdf:resource="http://www.sgd.org:8080/terms#LiteratureGuide"/>
   </rdf:Description>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/04/01 00:33:35	1.4
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/WebRoot/citationSearch.n3	2004/05/19 20:42:37	1.5
@@ -10,28 +10,32 @@
 
 acmepubs:citationSearch
     a moby:Provider, pubs:citationSearch ;
-    rdfs:comment "Industry standard search" ;
-    moby:operatesOn _:bnode1 .
-
-_:bnode1
-    a moby:Graph, rdf:Bag ;
-    moby:hasMapping _:bnode2 .
-
-_:bnode2
-    a moby:Subject, go:GeneSymbol ;
-    moby:mapsTo _:bnode3 ;
-    acmepubs:geneSymbol _:bnode4 .
-
-_:bnode3
-    a moby:Object, sgd:LiteratureGuide ;
-    acmepubs:literatureGuideURL _:bnode6 .
+    moby:name "AcmePubs Citation Search" ;
+    moby:oneLineDescription "Industry standard search" ;
+    moby:aboutURI "http://www.acmepubs.com/about/citationSearch" ;
+    moby:operatesOn [
+        a rdf:Bag ;
+        rdf:_1 [
+            a moby:Graph ;
+            moby:hasMapping [
+                a moby:Subject, go:GeneSymbol ;
+                acmepubs:geneSymbol _:bnode1 ;
+                moby:mapsTo [
+                    a moby:Object, sgd:LiteratureGuide ;
+                    acmepubs:literatureGuideURL _:bnode2
+                ]
+            ]
+        ]
+    ] .
 
 acmepubs:geneSymbol
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain go:GeneSymbol ;
     rdfs:range xsd:string .
 
 acmepubs:literatureGuideURL
     a owl:DataTypeProperty ;
+    rdfs:subPropertyOf moby:Property ;
     rdfs:domain sgd:LiteratureGuide ;
     rdfs:range xsd:anyURI .
\ No newline at end of file



From gss at pub.open-bio.org  Wed May 19 23:33:05 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX5Ru002275@pub.open-bio.org>


gss
Wed May 19 19:33:05 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv2250/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 18:26:52	1.8
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
@@ -7,6 +7,7 @@
 import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
+import org.smoby.graph.impl.MOBYObjectFactory;
 import org.smoby.vocabulary.*;
 import com.acmepubs.vocabulary.*;
 
@@ -35,47 +36,54 @@
      * a gene symbol and returning a URL for querying the
      * SGD database for literature pertaining to that URL.
      */
-    protected void handleRequest(MOBYProvider graph)
+    protected void handleRequest(MOBYProvider provider)
     {
-        // Retrieve the subject of the moby:operatesOn statement (there is only
-    	// one operatesOn statement in a valid MOBY graph)
-        //
-//        Resource mobyGraphSubject = (Resource) graph.getOperatesOnStmt().getObject();
-//        
-//        // There may be multiple moby:hasMapping statements. For each one,
-//        // map its geneSymbol to a literatureGuideURL
-//        //
-//        StmtIterator it = graph.getModel().listStatements(
-//        		mobyGraphSubject, MOBY.hasMapping, (RDFNode) null);
-//        
-//        while (it.hasNext())
-//        {
-//    		try
-//			{
-//	        	Statement hasMappingStmt = it.nextStatement();
-//	        	Resource mobySubject = (Resource) hasMappingStmt.getObject();
-//	        	
-//	        	Statement geneSymbolStmt =
-//	        		getFirstStatement(graph, mobySubject, AcmePubs.geneSymbol, null);
-//	        	
-//    			String geneSymbol = geneSymbolStmt.getString();
-//    			
-//    			Statement mapsToStmt = 
-//    				getFirstStatement(graph, mobySubject, MOBY.mapsTo, null);
-//    			
-//				Resource mobyObject = (Resource) mapsToStmt.getObject();
-//				
-//				Statement literatureGuideURLStmt =
-//					getFirstStatement(graph, mobyObject, AcmePubs.literatureGuideURL, null);
-//				
-//				String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
-//				literatureGuideURLStmt.changeObject(baseURI + geneSymbol);
-//        	}
-//    		catch (Throwable t)
-//			{
-//    			// Something went wrong, so proceed to next hasMapping statement
-//    		}
-//        }
+        try
+        {
+            // There should be only one operatesOn subgraph, which should be
+            // a collection of MOBYGraph objects.
+            //
+            MOBYCollection coll = (MOBYCollection)
+            	provider.getOperatesOn().iterator().next();
+            
+            // Iterate over the MOBYGraph objects
+            //
+            Iterator it = coll.iterator();
+            while (it.hasNext())
+            {
+                MOBYGraph graph = (MOBYGraph) it.next();
+                
+                // The subject of the graph should be a MOBYSubject
+                //
+                MOBYSubject subject = (MOBYSubject) graph.gethasMapping();
+                
+                // That object should have a single subproperty of moby:Property,
+                // namely geneSymbol; its value should be a literal
+                //
+                MOBYPropertyValueStatement stmt = (MOBYPropertyValueStatement)
+                    subject.getPropertyValueStatements().iterator().next();
+                MOBYLiteral literal = (MOBYLiteral) stmt.getValue();
+                String geneSymbol = literal.getStringValue();
+                
+                // The object of the MOBYSubject should be a MOBYObject. That
+                // object should have a single subproperty of moby:Property,
+                // namely literatureGuideURL
+                //
+                MOBYObject object = (MOBYObject)
+                	subject.getDirectMappings().iterator().next();
+                stmt = (MOBYPropertyValueStatement)
+                	object.getPropertyValueStatements().iterator().next();
+                
+                // Set the value of the literatureGuideURL to a literal value
+                // based on a base URI string and the geneSymbol that was passed
+                //
+                String baseURI = "http://db.yeastgenome.org/cgi-bin/SGD/reference/geneinfo.pl?locus=";
+                literal = MOBYObjectFactory.newLiteralValue(
+                        baseURI + geneSymbol);
+                stmt.setPropertyValue(literal);
+            }
+        }
+        catch (Throwable t) {System.out.println(t);} // No feedback on failure...
     }
     
     /**



From gss at pub.open-bio.org  Wed May 19 23:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Lr002327@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/parser

Modified Files:
	Parser.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 18:27:07	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/Parser.java	2004/05/19 23:33:08	1.2
@@ -375,10 +375,7 @@
             Property p = stmt.getPredicate();
             RDFNode pval = stmt.getObject();
             
-            boolean blankVal = pval.canAs(Resource.class) &&
-                               ((Resource) pval.as(Resource.class)).isAnon();
-            
-            if (blankVal && model.contains(res, p, pval) &&
+            if (model.contains(res, p, pval) &&
                 inferenceModel.contains(p, RDFS.subPropertyOf, MOBY.Property))
             {
                 MOBYPropertyValueStatement pvalStmt =



From gss at pub.open-bio.org  Wed May 19 23:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9jX002373@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/servlet

Modified Files:
	AbstractMobyServlet.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet AbstractMobyServlet.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/AbstractMobyServlet.java	2004/05/19 23:33:09	1.2
@@ -100,11 +100,12 @@
         
         try
         {
-            // Read the invocation graph from the "query-graph" parameter
+            // Read the invocation graph from the "graph" parameter
             // and parse it into a MOBYGraph object
             //
-            Parser parser = Parser.forInputStream(
-                   request.getInputStream(), Parser.LANGUAGE_RDF_XML);
+            String graphString = ParamReader.getParameter("graph", request);
+            Parser parser = Parser.forString(
+                   graphString, Parser.LANGUAGE_RDF_XML);
             MOBYProvider provider = parser.parseProvider();
             
             // Invoke the abstract handleRequest() method in order for the



From gss at pub.open-bio.org  Wed May 19 23:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9PQ002308@pub.open-bio.org>


gss
Wed May 19 19:33:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph

Modified Files:
	MOBYPropertyValueStatement.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYPropertyValueStatement.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/MOBYPropertyValueStatement.java	2004/05/19 23:33:08	1.2
@@ -3,9 +3,17 @@
 
 public interface MOBYPropertyValueStatement
 {
+    /**
+     * Return the name of this property
+     */
     public String getPropertyName();
     
     /**
+     * Return the value currently associated with this property
+     */
+    public MOBYPropertyValue getValue();
+    
+    /**
      * Set the property value. This is just a placeholder; values of
      * different property types will be set to different types of
      * values.



From gss at pub.open-bio.org  Wed May 19 23:33:09 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 19 May 2004 19:33:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405192333.i4JNX9Fj002352@pub.open-bio.org>


gss
Wed May 19 19:33:09 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv2283/org/smoby/graph/impl

Modified Files:
	MOBYPropertyValueStatementImpl.java MOBYObjectFactory.java 
Log Message:
Incorporation of new parser

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYPropertyValueStatementImpl.java,1.1,1.2 MOBYObjectFactory.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYPropertyValueStatementImpl.java	2004/05/19 23:33:09	1.2
@@ -8,11 +8,19 @@
 	implements MOBYPropertyValueStatement
 {
     Statement jenaStatement;
+    MOBYPropertyValue currentValue;
     MOBYPropertyValueConstraint constraint;
     
     MOBYPropertyValueStatementImpl(Statement jenaStatement, Model underlying) {
         super(null, underlying);
         this.jenaStatement = jenaStatement;
+        if (jenaStatement.getObject().canAs(Resource.class)) {
+            Resource value = (Resource) jenaStatement.getObject();
+            currentValue = new MOBYResourceImpl(value);
+        } else {
+            Literal value = (Literal) jenaStatement.getObject();
+            currentValue = new MOBYLiteralImpl(value.getString());
+        }
     }
     
     public String getPropertyName() {
@@ -23,6 +31,10 @@
         return jenaStatement.toString();
     }
     
+    public MOBYPropertyValue getValue() {
+        return currentValue;
+    }
+    
     public void setPropertyValue(MOBYPropertyValue newValue)
     	throws MOBYPropertyValueException
     {

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 18:27:08	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/MOBYObjectFactory.java	2004/05/19 23:33:09	1.2
@@ -66,6 +66,11 @@
         return new MOBYPropertyValueStatementImpl(statement, underlying);
     }
     
+    public static MOBYLiteral newLiteralValue(String value)
+    {
+        return new MOBYLiteralImpl(value);
+    }
+    
     public static MOBYPropertyValueConstraint newIntegerConstraint()
     {
         return new MOBYIntegerConstraintImpl();



From gordonp at pub.open-bio.org  Thu May 20 16:08:05 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:08:05 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201608.i4KG85q1004928@pub.open-bio.org>


gordonp
Thu May 20 12:08:05 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory pub.open-bio.org:/tmp/cvs-serv4903

Modified Files:
	MobyRequest.java 
Log Message:
Just got rid of some debug statements

moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/06 03:23:02	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java	2004/05/20 16:08:05	1.3
@@ -381,7 +381,6 @@
             throw new SOAPException("Cannot select SOAP nodes due to exception "+
 				    "while executing XPath statement:" +te);
 	}
-	debugPS.println("Result is " + node_list);
 
 	if(node_list == null || node_list.getLength() == 0){
 	    // Note: before giving up we should really have a plain string check as per the MOBY API 0.6
@@ -496,7 +495,6 @@
 	// Do data deserialization for each response's mobyData
 	for(int i = 0; i < response_list.getLength(); i++){
 	    Node response = response_list.item(i);
-	    debugPS.println("Got response " + response);
 	    
 	    Vector out = new Vector();
 	    // Find all the collections in the response
@@ -578,7 +576,6 @@
 	XObject xobject = xpath.execute(xpath_context, n, node_prefix_resolver);
 	if(xobject instanceof XNodeSet){
 	    result = ((XNodeSet) xobject).nodelist();
-	    debugPS.println("Result is " + result);
 	}
 	else if(debug && xobject != null){
 	    debugPS.println("Output of XPath was not a XNodeSet as expected, found " + xobject.getClass().getName());



From gordonp at pub.open-bio.org  Thu May 20 16:18:46 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:18:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201618.i4KGIkaq004981@pub.open-bio.org>


gordonp
Thu May 20 12:18:46 EDT 2004
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory pub.open-bio.org:/tmp/cvs-serv4960

Added Files:
	MobyServiceInvocationExample.java 
Log Message:
Example class that uses jMOBY to find and invoke services based on seed data

moby-live/Java/src/Clients MobyServiceInvocationExample.java,NONE,1.1


From gordonp at pub.open-bio.org  Thu May 20 16:23:15 2004
From: gordonp at pub.open-bio.org (Paul Gordon)
Date: Thu, 20 May 2004 12:23:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405201623.i4KGNFCo005051@pub.open-bio.org>


gordonp
Thu May 20 12:23:15 EDT 2004
Update of /home/repository/moby/moby-live/Java/docs
In directory pub.open-bio.org:/tmp/cvs-serv5026

Modified Files:
	ChangeLog 
Log Message:
Note location of good new service invocation example

moby-live/Java/docs ChangeLog,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/18 10:13:16	1.14
+++ /home/repository/moby/moby-live/Java/docs/ChangeLog	2004/05/20 16:23:15	1.15
@@ -1,3 +1,9 @@
+2004-05-20  Paul Gordon <gordonp at cbr.nrc.ca>
+
+        * Added full working example of service discovery and invocation in 
+          src/Client/MobyServiceInvocationExample
+          Use that one instead of the example in this ChangeLog
+
 2004-05-18  Martin Senger  <senger at ebi.ac.uk>
 
 	* Added a new displaying option (-on) to MobyCmdLineClient



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQm028394@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PXV028354@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph/impl

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5P3v028299@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org added to the repository

moby-live/S-MOBY/ref-impl/core/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PMo028372@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/http

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PJH028316@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q1l028433@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/servlet

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Ph3028413@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/parser/test

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Pvv028282@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src
In directory pub.open-bio.org:/tmp/cvs-serv28258/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src added to the repository

moby-live/S-MOBY/ref-impl/core/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Q3K028470@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/vocabulary

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:25 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5PQd028336@pub.open-bio.org>


gss
Mon May 24 18:05:25 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/graph

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:26 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5QUV028452@pub.open-bio.org>


gss
Mon May 24 18:05:26 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28258/src/org/smoby/tools

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools added to the repository

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Z0C028564@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph/impl

Added Files:
	MOBYOntologyImpl.java MOBYResourceImpl.java MOBYGraphImpl.java 
	MOBYPropertyValueConstraintImpl.java MOBYDescriptorImpl.java 
	MOBYOrderedCollectionImpl.java MOBYIntegerConstraintImpl.java 
	MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java 
	MOBYPropertyValueImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java 
	MOBYProviderImpl.java MOBYEnumerationImpl.java 
	MOBYLiteralImpl.java MOBYSingleElementImpl.java 
	MOBYDocumentImpl.java MOBYUnorderedCollectionImpl.java 
	MOBYNumericConstraintImpl.java MOBYGraphNodeImpl.java 
	MOBYObjectImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java MOBYCollectionImpl.java 
	MOBYObjectFactory.java MOBYMappingElementImpl.java 
	MOBYPropertyValueStatementImpl.java 
	MOBYResizableCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph/impl MOBYOntologyImpl.java,NONE,1.1 MOBYResourceImpl.java,NONE,1.1 MOBYGraphImpl.java,NONE,1.1 MOBYPropertyValueConstraintImpl.java,NONE,1.1 MOBYDescriptorImpl.java,NONE,1.1 MOBYOrderedCollectionImpl.java,NONE,1.1 MOBYIntegerConstraintImpl.java,NONE,1.1 MOBYFixedCollectionImpl.java,NONE,1.1 MOBYNonNegativeIntegerConstraintImpl.java,NONE,1.1 MOBYPropertyValueImpl.java,NONE,1.1 MOBYNonPositiveIntegerConstraintImpl.java,NONE,1.1 MOBYProviderImpl.java,NONE,1.1 MOBYEnumerationImpl.java,NONE,1.1 MOBYLiteralImpl.java,NONE,1.1 MOBYSingleElementImpl.java,NONE,1.1 MOBYDocumentImpl.java,NONE,1.1 MOBYUnorderedCollectionImpl.java,NONE,1.1 MOBYNumericConstraintImpl.java,NONE,1.1 MOBYGraphNodeImpl.java,NONE,1.1 MOBYObjectImpl.java,NONE,1.1 MOBYSubjectImpl.java,NONE,1.1 MOBYDateConstraintImpl.java,NONE,1.1 MOBYCollectionImpl.java,NONE,1.1 MOBYObjectFactory.java,NONE,1.1 MOBYMappingElementImpl.java,NONE,1.1 MOBYPropertyValueStatementImpl.jav!
a,NONE,1.1 MOBYResizableCollectionImpl.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5YpV028532@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/servlet

Added Files:
	AbstractMobyServlet.java ParamReader.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/servlet AbstractMobyServlet.java,NONE,1.1 ParamReader.java,NONE,1.1 ParameterException.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZUB028579@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/graph

Added Files:
	MOBYDocument.java MOBYOntology.java MOBYProvider.java 
	MOBYResource.java MOBYOrderedCollection.java MOBYSubject.java 
	MOBYSingleElement.java MOBYEnumeration.java 
	MOBYDescriptor.java MOBYPropertyValueStatement.java 
	MOBYLiteral.java MOBYCollection.java MOBYFixedCollection.java 
	MOBYPropertyValueException.java MOBYGraphNode.java 
	MOBYObject.java MOBYUnorderedCollection.java MOBYGraph.java 
	MOBYMappingElement.java MOBYResizableCollection.java 
	MOBYPropertyValueConstraint.java MOBYPropertyValue.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/graph MOBYDocument.java,NONE,1.1 MOBYOntology.java,NONE,1.1 MOBYProvider.java,NONE,1.1 MOBYResource.java,NONE,1.1 MOBYOrderedCollection.java,NONE,1.1 MOBYSubject.java,NONE,1.1 MOBYSingleElement.java,NONE,1.1 MOBYEnumeration.java,NONE,1.1 MOBYDescriptor.java,NONE,1.1 MOBYPropertyValueStatement.java,NONE,1.1 MOBYLiteral.java,NONE,1.1 MOBYCollection.java,NONE,1.1 MOBYFixedCollection.java,NONE,1.1 MOBYPropertyValueException.java,NONE,1.1 MOBYGraphNode.java,NONE,1.1 MOBYObject.java,NONE,1.1 MOBYUnorderedCollection.java,NONE,1.1 MOBYGraph.java,NONE,1.1 MOBYMappingElement.java,NONE,1.1 MOBYResizableCollection.java,NONE,1.1 MOBYPropertyValueConstraint.java,NONE,1.1 MOBYPropertyValue.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a0h028675@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/tools

Added Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/tools Util.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZZ6028594@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser/test

Added Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser/test Test.java,NONE,1.1 ParserTest.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:35 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5ZSW028614@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/http

Added Files:
	HTTPException.java HTTPRequest.java HTTPResponse.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/http HTTPException.java,NONE,1.1 HTTPRequest.java,NONE,1.1 HTTPResponse.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5aH2028631@pub.open-bio.org>


gss
Mon May 24 18:05:35 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/parser

Added Files:
	UnparsableGraphException.java NonCanonicalException.java 
	Parser.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/parser UnparsableGraphException.java,NONE,1.1 NonCanonicalException.java,NONE,1.1 Parser.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:05:36 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5a8O028660@pub.open-bio.org>


gss
Mon May 24 18:05:36 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv28511

Modified Files:
	build.xml .classpath 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
@@ -1,2 +1,3 @@
 <project name="core" basedir=".">
+    <property name="src" value="build"/>
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/03/27 01:14:22	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.classpath	2004/05/24 22:05:35	1.4
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>



From gss at pub.open-bio.org  Mon May 24 22:05:34 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:05:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242205.i4OM5Yhf028547@pub.open-bio.org>


gss
Mon May 24 18:05:34 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28511/src/org/smoby/vocabulary

Added Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/src/org/smoby/vocabulary VocabularyDescription.java,NONE,1.1 MOBY.java,NONE,1.1


From gss at pub.open-bio.org  Mon May 24 22:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HX1028729@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser

Removed Files:
	Parser.java UnparsableGraphException.java 
	NonCanonicalException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser Parser.java,1.2,NONE UnparsableGraphException.java,1.1,NONE NonCanonicalException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/Parser.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/UnparsableGraphException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/RCS/NonCanonicalException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HRN028767@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph

Removed Files:
	MOBYProvider.java MOBYPropertyValueConstraint.java 
	MOBYOntology.java MOBYPropertyValueStatement.java 
	MOBYDescriptor.java MOBYFixedCollection.java 
	MOBYMappingElement.java MOBYSingleElement.java 
	MOBYUnorderedCollection.java MOBYEnumeration.java 
	MOBYObject.java MOBYResizableCollection.java MOBYSubject.java 
	MOBYResource.java MOBYOrderedCollection.java 
	MOBYPropertyValueException.java MOBYDocument.java 
	MOBYCollection.java MOBYGraphNode.java MOBYLiteral.java 
	MOBYPropertyValue.java MOBYGraph.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph MOBYProvider.java,1.1,NONE MOBYPropertyValueConstraint.java,1.1,NONE MOBYOntology.java,1.1,NONE MOBYPropertyValueStatement.java,1.2,NONE MOBYDescriptor.java,1.1,NONE MOBYFixedCollection.java,1.1,NONE MOBYMappingElement.java,1.1,NONE MOBYSingleElement.java,1.1,NONE MOBYUnorderedCollection.java,1.1,NONE MOBYEnumeration.java,1.1,NONE MOBYObject.java,1.1,NONE MOBYResizableCollection.java,1.1,NONE MOBYSubject.java,1.1,NONE MOBYResource.java,1.1,NONE MOBYOrderedCollection.java,1.1,NONE MOBYPropertyValueException.java,1.1,NONE MOBYDocument.java,1.1,NONE MOBYCollection.java,1.1,NONE MOBYGraphNode.java,1.1,NONE MOBYLiteral.java,1.1,NONE MOBYPropertyValue.java,1.1,NONE MOBYGraph.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYProvider.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueConstraint.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOntology.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueStatement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDescriptor.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYFixedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYMappingElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSingleElement.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYUnorderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYEnumeration.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYObject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResizableCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYSubject.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYResource.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYOrderedCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValueException.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYDocument.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYCollection.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraphNode.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYLiteral.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYPropertyValue.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/RCS/MOBYGraph.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7H0j028830@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/tools

Removed Files:
	Util.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/tools Util.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/tools/RCS/Util.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4r028906@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/servlet

Removed Files:
	ParamReader.java AbstractMobyServlet.java 
	ParameterException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/servlet ParamReader.java,1.1,NONE AbstractMobyServlet.java,1.2,NONE ParameterException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParamReader.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/AbstractMobyServlet.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/servlet/RCS/ParameterException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HlJ028849@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/http

Removed Files:
	HTTPRequest.java HTTPResponse.java HTTPException.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/http HTTPRequest.java,1.1,NONE HTTPResponse.java,1.1,NONE HTTPException.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPRequest.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPResponse.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/http/RCS/HTTPException.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7ID1028887@pub.open-bio.org>


gss
Mon May 24 18:07:18 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/vocabulary

Removed Files:
	VocabularyDescription.java MOBY.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary VocabularyDescription.java,1.1,NONE MOBY.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/VocabularyDescription.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/vocabulary/RCS/MOBY.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:17 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:17 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7HtL028814@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/graph/impl

Removed Files:
	MOBYGraphImpl.java MOBYPropertyValueConstraintImpl.java 
	MOBYOntologyImpl.java MOBYDocumentImpl.java 
	MOBYOrderedCollectionImpl.java 
	MOBYResizableCollectionImpl.java MOBYDescriptorImpl.java 
	MOBYNonPositiveIntegerConstraintImpl.java MOBYObjectImpl.java 
	MOBYObjectFactory.java MOBYResourceImpl.java 
	MOBYSingleElementImpl.java MOBYPropertyValueImpl.java 
	MOBYProviderImpl.java MOBYLiteralImpl.java 
	MOBYGraphNodeImpl.java MOBYCollectionImpl.java 
	MOBYMappingElementImpl.java MOBYFixedCollectionImpl.java 
	MOBYNonNegativeIntegerConstraintImpl.java MOBYSubjectImpl.java 
	MOBYDateConstraintImpl.java 
	MOBYPropertyValueStatementImpl.java MOBYEnumerationImpl.java 
	MOBYIntegerConstraintImpl.java MOBYNumericConstraintImpl.java 
	MOBYUnorderedCollectionImpl.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl MOBYGraphImpl.java,1.1,NONE MOBYPropertyValueConstraintImpl.java,1.1,NONE MOBYOntologyImpl.java,1.1,NONE MOBYDocumentImpl.java,1.1,NONE MOBYOrderedCollectionImpl.java,1.1,NONE MOBYResizableCollectionImpl.java,1.1,NONE MOBYDescriptorImpl.java,1.1,NONE MOBYNonPositiveIntegerConstraintImpl.java,1.1,NONE MOBYObjectImpl.java,1.1,NONE MOBYObjectFactory.java,1.2,NONE MOBYResourceImpl.java,1.1,NONE MOBYSingleElementImpl.java,1.1,NONE MOBYPropertyValueImpl.java,1.1,NONE MOBYProviderImpl.java,1.1,NONE MOBYLiteralImpl.java,1.1,NONE MOBYGraphNodeImpl.java,1.1,NONE MOBYCollectionImpl.java,1.1,NONE MOBYMappingElementImpl.java,1.1,NONE MOBYFixedCollectionImpl.java,1.1,NONE MOBYNonNegativeIntegerConstraintImpl.java,1.1,NONE MOBYSubjectImpl.java,1.1,NONE MOBYDateConstraintImpl.java,1.1,NONE MOBYPropertyValueStatementImpl.java,1.2,NONE MOBYEnumerationImpl.java,1.1,NONE MOBYIntegerConstraintImpl.java,1.1,NONE MOBYNumericConstraintImpl.java,1.!
1,NONE MOBYUnorderedCollectionImpl.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOntologyImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDocumentImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYOrderedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResizableCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDescriptorImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonPositiveIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYObjectFactory.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYResourceImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSingleElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYProviderImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYLiteralImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYGraphNodeImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYMappingElementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYFixedCollectionImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNonNegativeIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYSubjectImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYDateConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYPropertyValueStatementImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYEnumerationImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYIntegerConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYNumericConstraintImpl.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/graph/impl/RCS/MOBYUnorderedCollectionImpl.java,v: No such file or directory



From gss at pub.open-bio.org  Mon May 24 22:07:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Mon, 24 May 2004 18:07:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405242207.i4OM7I4o028866@pub.open-bio.org>


gss
Mon May 24 18:07:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test
In directory pub.open-bio.org:/tmp/cvs-serv28705/org/smoby/parser/test

Removed Files:
	Test.java ParserTest.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test Test.java,1.1,NONE ParserTest.java,1.1,NONE
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/Test.java,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/org/smoby/parser/test/RCS/ParserTest.java,v: No such file or directory



From gss at pub.open-bio.org  Wed May 26 23:27:47 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Wed, 26 May 2004 19:27:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405262327.i4QNRlVa003497@pub.open-bio.org>


gss
Wed May 26 19:27:47 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv3472

Modified Files:
	.cvsignore 
Log Message:
Ignore build directory

moby-live/S-MOBY/ref-impl/core .cvsignore,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/03/22 22:21:39	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
@@ -1 +1,2 @@
-classes
\ No newline at end of file
+classes
+build



From gss at pub.open-bio.org  Thu May 27 15:30:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:30:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271530.i4RFUek4006236@pub.open-bio.org>


gss
Thu May 27 11:30:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6210

Modified Files:
	.cvsignore 
Log Message:
Removed blank line

moby-live/S-MOBY/ref-impl/core .cvsignore,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/26 23:27:47	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/.cvsignore	2004/05/27 15:30:40	1.4
@@ -1,2 +1,2 @@
 classes
-build
+build
\ No newline at end of file



From gss at pub.open-bio.org  Thu May 27 15:31:31 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:31:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271531.i4RFVVL8006281@pub.open-bio.org>


gss
Thu May 27 11:31:31 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets
In directory pub.open-bio.org:/tmp/cvs-serv6256/src/com/acmepubs/servlets

Modified Files:
	CitationSearchServlet.java 
Log Message:
Remove go.org import

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets CitationSearchServlet.java,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/19 23:33:05	1.9
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/src/com/acmepubs/servlets/CitationSearchServlet.java	2004/05/27 15:31:31	1.10
@@ -4,7 +4,6 @@
 import java.util.*;
 import javax.servlet.*;
 import javax.servlet.http.*;
-import org.go.vocabulary.*;
 import org.smoby.servlet.*;
 import org.smoby.graph.*;
 import org.smoby.graph.impl.MOBYObjectFactory;



From gss at pub.open-bio.org  Thu May 27 15:54:08 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFs8NB006492@pub.open-bio.org>


gss
Thu May 27 11:54:08 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/pubs.org
In directory pub.open-bio.org:/tmp/cvs-serv6471

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/pubs.org build.xml,NONE,1.1 .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 15:54:12 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsCqr006525@pub.open-bio.org>


gss
Thu May 27 11:54:12 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv6500

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/server build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/03/12 17:48:32	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/server/build.xml	2004/05/27 15:54:12	1.2
@@ -1,2 +1,29 @@
-<project name="server" basedir=".">
+<!-- Apache Ant format build file for s-moby.org example provider -->
+
+<project name="s-moby.org" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="s-moby.org.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>



From gss at pub.open-bio.org  Thu May 27 15:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKMG006565@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv6544

Added Files:
	build.xml .cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org build.xml,NONE,1.1 .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 15:54:20 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsKIa006580@pub.open-bio.org>


gss
Thu May 27 11:54:20 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF
In directory pub.open-bio.org:/tmp/cvs-serv6544/WebRoot/WEB-INF

Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/sgd.org/WebRoot/WEB-INF .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 15:54:28 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsSar006627@pub.open-bio.org>


gss
Thu May 27 11:54:28 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6602

Modified Files:
	build.xml 
Added Files:
	.cvsignore 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/megapubs.com .cvsignore,NONE,1.1 build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/03/12 17:48:33	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/megapubs.com/build.xml	2004/05/27 15:54:28	1.2
@@ -1,2 +1,29 @@
-<project name="megapubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="megapubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="megapubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>



From gss at pub.open-bio.org  Thu May 27 15:54:40 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFseHV006690@pub.open-bio.org>


gss
Thu May 27 11:54:40 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com
In directory pub.open-bio.org:/tmp/cvs-serv6657

Modified Files:
	build.xml .classpath 
Added Files:
	.cvsignore .xdoclet 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com .cvsignore,NONE,1.1 .xdoclet,1.2,1.3 build.xml,1.1,1.2 .classpath,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.xdoclet,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/03/12 17:48:34	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/build.xml	2004/05/27 15:54:40	1.2
@@ -1,2 +1,29 @@
-<project name="acmepubs.com" basedir=".">
+<!-- Apache Ant format build file for acmepubs.com example provider -->
+
+<project name="acmepubs.com" default="war" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../../servlet.xml"/>
+
+	<!-- The full path of the web archive file to be built -->
+    <property name="war-file" value="acmepubs.com.war"/>
+	
+	<!-- Package the compiled source files into the main jar file -->
+	<target name="war" depends="compile">
+        <jar destfile="${war-file}" basedir="${web-root}"/>
+	</target>
+	
+	<!-- Compile all the source files that go into the library -->
+	<target name="compile">
+		<mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="common.classpath"/>
+        </javac>
+	</target>
+
+    <!-- Clean the build directory and the war file -->
+    <target name="clean" depends="clean-build">
+        <delete file="${war-file}"/>
+    </target>
+	
 </project>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/04/02 00:03:39	1.3
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/acmepubs.com/.classpath	2004/05/27 15:54:40	1.4
@@ -5,9 +5,6 @@
 	<classpathentry kind="con" path="com.genuitec.eclipse.j2eedt.core.J2EE13_CONTAINER"/>
 	<classpathentry kind="src" path="/HttpClient"/>
 	<classpathentry kind="src" path="/Jena2"/>
-	<classpathentry kind="src" path="/www.go.org"/>
-	<classpathentry kind="src" path="/www.pubs.org"/>
-	<classpathentry kind="src" path="/www.sgd.org"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="output" path="WebRoot/WEB-INF/classes"/>
 </classpath>



From gss at pub.open-bio.org  Thu May 27 15:54:44 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 11:54:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271554.i4RFsiWe006723@pub.open-bio.org>


gss
Thu May 27 11:54:44 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/core
In directory pub.open-bio.org:/tmp/cvs-serv6698

Modified Files:
	build.xml 
Log Message:
Finally, some build scripts

moby-live/S-MOBY/ref-impl/core build.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/24 22:05:35	1.2
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/core/build.xml	2004/05/27 15:54:44	1.3
@@ -1,3 +1,26 @@
-<project name="core" basedir=".">
-    <property name="src" value="build"/>
+<!-- Apache Ant format build file for Semantic MOBY core library -->
+
+<project name="smoby-core" default="jar" basedir=".">
+
+    <!-- Import shared stuff -->
+    <import file="../library.xml"/>
+
+    <!-- Package the compiled source files into the main jar file -->
+    <target name="jar" depends="compile">
+        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+    </target>
+    
+    <!-- Compile all the source files that go into the library -->
+    <target name="compile">
+        <mkdir dir="${classes-dir}"/>
+        <javac srcdir="${src-dir}" destdir="${classes-dir}">
+            <classpath refid="core.classpath"/>
+        </javac>
+    </target>
+    
+    <!-- Deploy the jar file to the Tomcat shared library directory -->
+    <target name="deploy-to-tomcat" depends="jar">
+        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
+    </target>
+    
 </project>



From gss at pub.open-bio.org  Thu May 27 16:03:43 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:03:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271603.i4RG3hAF006842@pub.open-bio.org>


gss
Thu May 27 12:03:42 EDT 2004
Update of /home/repository/moby/www.go.org
In directory pub.open-bio.org:/tmp/cvs-serv6818/www.go.org

Log Message:
Directory /home/repository/moby/www.go.org added to the repository

www.go.org - New directory
rcsdiff: /home/repository/moby/www.go.org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/www.go.org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 16:11:15 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:11:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271611.i4RGBFHF007039@pub.open-bio.org>


gss
Thu May 27 12:11:15 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/sgd.org
In directory pub.open-bio.org:/tmp/cvs-serv7018

Added Files:
	.encoding 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-providers/sgd.org .encoding,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 16:23:59 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 12:23:59 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271623.i4RGNxH0007277@pub.open-bio.org>


gss
Thu May 27 12:23:59 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-providers/go.org
In directory pub.open-bio.org:/tmp/cvs-serv7256

Added Files:
	.cvsignore build.xml 
Log Message:
Oops, had released to wrong directory

moby-live/S-MOBY/ref-impl/example-providers/go.org .cvsignore,NONE,1.1 build.xml,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 18:31:46 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 14:31:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271831.i4RIVkXZ008515@pub.open-bio.org>


gss
Thu May 27 14:31:46 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/server
In directory pub.open-bio.org:/tmp/cvs-serv8494

Added Files:
	.cvsignore 
Log Message:


moby-live/S-MOBY/ref-impl/server .cvsignore,NONE,1.1


From gss at pub.open-bio.org  Thu May 27 19:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3cg009360@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src
In directory pub.open-bio.org:/tmp/cvs-serv9336/src

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 19:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Gl009378@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 19:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Jq009397@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 19:37:03 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJb3Js009416@pub.open-bio.org>


gss
Thu May 27 15:37:03 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9336/src/org/smoby/exampleclients

Log Message:
Directory /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients added to the repository

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients - New directory
rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/-,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/New,v: No such file or directory

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients/RCS/directory,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 19:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbAZ5009474@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv9444

Modified Files:
	.classpath .cvsignore 
Added Files:
	build.xml 
Removed Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,NONE,1.1 .classpath,1.1,1.2 .cvsignore,1.1,1.2 SimpleProviderEngagerPanel.java,1.2,NONE
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/03/30 21:41:36	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.classpath	2004/05/27 19:37:10	1.2
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="src" path=""/>
+	<classpathentry kind="src" path="src"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="src" path="/S-MOBY_Core"/>
 	<classpathentry kind="src" path="/Jena2"/>
 	<classpathentry kind="src" path="/HttpClient"/>
-	<classpathentry kind="output" path=""/>
+	<classpathentry kind="output" path="build"/>
 </classpath>

===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/04/02 00:45:31	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/.cvsignore	2004/05/27 19:37:10	1.2
@@ -1,2 +1,2 @@
 classes
-*.class
\ No newline at end of file
+build

rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/RCS/SimpleProviderEngagerPanel.java,v: No such file or directory



From gss at pub.open-bio.org  Thu May 27 19:37:10 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Thu, 27 May 2004 15:37:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405271937.i4RJbA5Z009489@pub.open-bio.org>


gss
Thu May 27 15:37:10 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients
In directory pub.open-bio.org:/tmp/cvs-serv9444/src/org/smoby/exampleclients

Added Files:
	SimpleProviderEngagerPanel.java 
Log Message:
Moved source files to src/ subdirectory

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/src/org/smoby/exampleclients SimpleProviderEngagerPanel.java,NONE,1.1


From ambrose at pub.open-bio.org  Fri May 28 20:54:08 2004
From: ambrose at pub.open-bio.org (Ambrose Ng)
Date: Fri, 28 May 2004 16:54:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282054.i4SKs8F0013990@pub.open-bio.org>


ambrose
Fri May 28 16:54:08 EDT 2004
Update of /home/repository/moby/moby-live/Perl/Accessories
In directory pub.open-bio.org:/tmp/cvs-serv13964

Modified Files:
	NamespaceMaintenance.cgi 
Log Message:
fixed mysql duplicate entry problem caused by updating form field error

moby-live/Perl/Accessories NamespaceMaintenance.cgi,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/04/29 18:03:52	1.2
+++ /home/repository/moby/moby-live/Perl/Accessories/NamespaceMaintenance.cgi	2004/05/28 20:54:08	1.3
@@ -6,18 +6,31 @@
 my $namespace_id;
 my $authabvr;
 my $namespacetype;
-    if (param('ns')) { #ns param specified; user intends to load from database so open database and load up parameters
-        my @ns = split (/\_/,param('ns'));
-        param('authabvr'=>$ns[0]);
-        param('namespacetype'=>$ns[1]);
-        $authabvr=$ns[0];
-        $namespacetype=$ns[1];
-        my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
-        my $dbh1 = open_dbi();
-        my $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
-        $sth1->execute($retrieve);
+    if (param('ns') or param('id')) { #ns or id param specified; user intends to load from database so open database and load up parameters
+        my $sth1;
+        if (param('ns')) {
+            my @ns = split (/\_/,param('ns'));
+            param('authabvr'=>$ns[0]);
+            param('namespacetype'=>$ns[1]);
+            $authabvr=$ns[0];
+            $namespacetype=$ns[1];
+            my $retrieve = 'urn:lsid:biomoby.org:namespacetype:'.param('ns');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_lsid = ?});
+            $sth1->execute($retrieve);
+        }
+        else {
+            my $retrieve = param('id');
+            my $dbh1 = open_dbi();
+            $sth1 = $dbh1->prepare(qq{SELECT * FROM namespace WHERE namespace_id = ?});
+            $sth1->execute($retrieve);
+        }
         my ($id, $namespace_lsid,  $namespace_type, $desc, $auth, $contactemail, $object,  $generic_url,  $synonym,  $urlsyntax,  $urlexample,  $shorthandname, $example_id, $note) = $sth1->fetchrow_array();
         $namespace_id = $id;
+        my @split = split(/\:/, $namespace_lsid);
+        ($authabvr, $namespacetype) = split(/\_/,$split[4]);
+        param('authabvr'=>$authabvr);
+        param('namespacetype'=>$namespacetype);
         param('desc'=>$desc);
         param('auth'=>$auth);
         param('object'=>$object);
@@ -58,20 +71,22 @@
         param('shorthand_name'=>$shorthandname);
         param('example_id'=>$example_id);
         param('note'=>$note);
+        param('continue'=>1);
+        param('nsid'=>$id);
     }
 
     print header,
-        start_html(-title => 'Namespace Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}),
-        
-        h1('Namespace Form');
+        start_html(-title => 'Namespace Update Form', -style => {-src => 'http://mobycentral.cbr.nrc.ca/stylesheets/ambrose.css'}, -class => "update"),
+        h1('Namespace Update Form');
+        print "Database search page is located here: ",a({href=>'http://mobycentral.cbr.nrc.ca/cgi-bin/search.cgi'}, "Search Page"),p,; 
         if (!$namespace_id) {
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         "Full abbreviation will be \"authority abbreviation_identifier abbreviation\" e.g. \"GeneDB_Tbrucei\"",
         start_form,
         table(
-        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB")),
+        Tr(td("authority abbreviation* "),td(textfield(-name => 'authabvr', -class => "require"),"e.g.: GeneDB"),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation* "),td(textfield(-name =>'namespacetype', -class => "require"),"e.g.: Tbrucei")),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name => 'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -105,11 +120,11 @@
         else {
             param('namespace_id'=>$namespace_id);
             print
-        "* = required fields",p,
+        "* = required fields (highlighted)",p,
         " --------",p,
         start_form,
         table(
-        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id'))),
+        Tr(td("authority abbreviation: "),td($authabvr),(hidden('authabvr')),(hidden('namespace_id')),(hidden('continue')),(hidden('nsid'))),
         Tr(td("identifier abbreviation: "),td($namespacetype),(hidden('namespacetype'))),
         Tr(td"--------"),
         Tr(td("description* "),td(textarea(-name =>'desc', -class => "require"),"Type a short description here about the entry.")),
@@ -135,7 +150,7 @@
         Tr(td("url_example "),td(textfield('url_iec'),"e.g.: http\:\/\/www.genedb.org\/genedb\/Search\?organism=tryp&name=Tb927.1.5250")),
         Tr(td("shorthand_names "),td(textarea('shorthand_name'),"e.g.: Tbrucei. one entry per line")),
         Tr(td("note "),td(textarea('note'))),
-    Tr(td(submit)),
+    Tr(td(submit -name => 'submit values', -class => 'submit')),
     Tr(td(reset)),
     end_form,),p,
         $namespace_id,p,
@@ -168,31 +183,29 @@
         if (param('note')) {$Param{note}=param('note');}
         if (param('syn')) {$Param{syn} = param('syn');}
         
-if (param() and !param('ns')) {
-        my $error = chkerrors(%Param);
-        my %variables;
-        if ($error == 0){
-            %variables = setvariables(%Param);
-
-        
+if (param() and !param('ns') and !param('id')) {
+    my $error = chkerrors(%Param);
+    my %variables;
+    if ($error == 0){
+        %variables = setvariables(%Param);
         my $dbh = open_dbi();
-        my $sth;
- 
-        if (!param('namespace_id')) {
+        my $sth; 
+        if (!param('namespace_id') and param('continue') != 1) {
             adddata ($dbh, $sth, %variables);
         }
         else {
-            my $nsid = (param('namespace_id'));
+            my $nsid;
+            if (param('namespace_id')) {
+            $nsid = (param('namespace_id')); }
+            elsif (param('nsid')) { $nsid= param('nsid'); }
             updatedata ($dbh, $sth, $nsid, %variables);
         }
         $variables{authabvr} = param('authabvr');
         finalprinttoscreen (%variables);
-        param('namespace_id')=>undef;
-        }
+    }
+    #elsif ($error == 1) { print hidden('continue'=>1); }
 }
 
-elsif (param('ns')){ param('ns')=>undef;
-                    }
 #########
 
 
@@ -267,11 +280,7 @@
         print "invalid url_synonym header",hr;
         return 1;
     }
-    #elsif ($Param{example_id} =~ /\W/)  {
-     #   print "invalid characters in example_id",hr;
-      #  return 1;
-    #}
-    
+   
     else { return 0; }
 }
 sub setvariables {
@@ -358,7 +367,7 @@
         }
 sub finalprinttoscreen { #final printing to screen after updating database
     my (%variables) = @_;
-            print pre(
+            print pre(p,"successful!",p
         "namespace_type = ",$variables{namespacetype},p,
         "lsid = ",$variables{lsid},p,
         "description = ",$variables{desc},p,



From gss at pub.open-bio.org  Fri May 28 21:35:18 2004
From: gss at pub.open-bio.org (Gary Schlitz)
Date: Fri, 28 May 2004 17:35:18 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200405282135.i4SLZIbg014116@pub.open-bio.org>


gss
Fri May 28 17:35:17 EDT 2004
Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager
In directory pub.open-bio.org:/tmp/cvs-serv14091

Modified Files:
	build.xml 
Log Message:
Misc fixes

moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager build.xml,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/27 19:37:10	1.1
+++ /home/repository/moby/moby-live/S-MOBY/ref-impl/example-clients/SimpleEngager/build.xml	2004/05/28 21:35:17	1.2
@@ -1,26 +1,24 @@
-<!-- Apache Ant format build file for Semantic MOBY core library -->
+<!-- Apache Ant format build file for the SimpleEngager client GUI -->
 
-<project name="smoby-core" default="jar" basedir=".">
+<project name="simple-engager" default="jar" basedir=".">
 
     <!-- Import shared stuff -->
-    <import file="../library.xml"/>
+    <import file="../../library.xml"/>
+
+    <!-- The main jar file -->
+    <property name="jar-file" value="${build-dir}/engager.jar"/>
 
     <!-- Package the compiled source files into the main jar file -->
     <target name="jar" depends="compile">
-        <jar destfile="${core-jar-file}" basedir="${classes-dir}"/>
+        <jar destfile="${jar-file}" basedir="${classes-dir}"/>
     </target>
     
     <!-- Compile all the source files that go into the library -->
     <target name="compile">
         <mkdir dir="${classes-dir}"/>
         <javac srcdir="${src-dir}" destdir="${classes-dir}">
-            <classpath refid="core.classpath"/>
+            <classpath refid="common.classpath"/>
         </javac>
     </target>
     
-    <!-- Deploy the jar file to the Tomcat shared library directory -->
-    <target name="deploy-to-tomcat" depends="jar">
-        <copy file="${core-jar-file}" todir="${tomcat-shared-lib-dir}"/>
-    </target>
-    
 </project>