From kawas at dev.open-bio.org  Mon Oct  1 15:05:38 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 1 Oct 2007 15:05:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710011905.l91J5cBl013641@dev.open-bio.org>


kawas
Mon Oct  1 15:05:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv13606

Modified Files:
	InstallingLocalMOBYCentral.html 
Log Message:
mention that MOBY_ONTOLOGYSERVER needs to be added to the environment and added it in the appropriate spots during installation
moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/02/22 16:22:24	1.8
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/10/01 19:05:38	1.9
@@ -154,6 +154,10 @@
         # from the mobycentral databases.
         #
         SetEnv MOBY_CENTRAL_CONFIG "/etc/apache2/conf/mobycentral.config"
+        # Full URL to the <a href="#ONTOLOGYSERVER">OntologyServer.cgi</a> script 
+        # that is copied to the cgi-bin
+        #
+        SetEnv MOBY_ONTOLOGY_SERVER "http://<i>your.domain</i>/cgi-bin/OntologyServer.cgi"
         # 
         # Path to additional Perl modules.
         # Tell Apache where to find Perl modules,
@@ -460,11 +464,6 @@
      <li>Copy the 
       <pre>    ~/moby-live/Perl/scripts/OntologyServer.cgi </pre>
          CGI script into your webserver cgi-bin folder.     </li>
-     <li>You will now have to edit the MOBY::Client::OntologyServer.pm module manually (sorry!). 
-         This module was hardcoded to point to the OntologyServer.cgi at THE central BioMOBY Central.  
-         You will have to change the line that reads 
-      <pre>    host => ["http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi",'read/write'] </pre>
-         to point to the URL of your OntologyServer.cgi that you just set up.     </li>
 	</ul>
    </li>
    <!--
@@ -545,12 +544,16 @@
          then set up the following environment variables. <br/>
          For bash, ksh, etc. in your ~/.bashrc or ~/.kshrc or etc.: 
        <pre>
-    export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central </pre>
+export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central
+export MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
          For csh or tcsh in your ~/.cshrc or ~/.tcshrc: <br/> 
        <pre>
-    setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central </pre>
+setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central
+setenv MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
      </li>
     </ul>
    </li>
@@ -563,7 +566,8 @@
    <b>To test your BioMOBY Central:</b>
    <ul>
     <li>Ensure that the following environment variables are set:
-      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above </pre>
+      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above</pre>
+	  <pre>    MOBY_ONTOLOGYSERVER - the url to your <a href="#ONTOLOGYSERVER">OntologyServer.cgi file</a> created above</pre>
       <pre>    MOBY_SERVER - the endpoint of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
       <pre>    MOBY_URI - the namespace of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
     </li>


From kawas at dev.open-bio.org  Thu Oct 18 10:26:25 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:26:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181426.l9IEQP6R003605@dev.open-bio.org>


kawas
Thu Oct 18 10:26:24 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService
In directory dev.open-bio.org:/tmp/cvs-serv3570

Modified Files:
	findService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/findService findService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd	2007/08/27 19:36:45	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd	2007/10/18 14:26:24	1.2
@@ -9,7 +9,7 @@
 				using the BioMOBY API.
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType>
 			<xs:sequence>
 				<xs:element minOccurs="0" maxOccurs="1"
 					name="Category">
@@ -258,7 +258,7 @@
 						<xs:sequence>
 							<xs:element name="serviceType" minOccurs="1"
 								maxOccurs="1">
-								<xs:complexType mixed="true">
+								<xs:complexType>
 									<xs:attribute name="lsid"
 										use="required">
 										<xs:simpleType>
@@ -315,7 +315,7 @@
 													<xs:element
 														name="objectType" minOccurs="1" maxOccurs="1">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid">
 																<xs:simpleType>
@@ -331,7 +331,7 @@
 													<xs:element
 														name="Namespace" minOccurs="0" maxOccurs="unbounded">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid" use="required">
 																<xs:simpleType>
@@ -368,7 +368,7 @@
 																<xs:element
 																	name="objectType" maxOccurs="1" minOccurs="1">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid">
 																			<xs:simpleType>
@@ -384,7 +384,7 @@
 																<xs:element
 																	name="Namespace" minOccurs="0" maxOccurs="unbounded">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid" use="required">
 																			<xs:simpleType>
@@ -430,7 +430,7 @@
 													<xs:element
 														name="objectType" minOccurs="1" maxOccurs="1">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid">
 																<xs:simpleType>
@@ -446,7 +446,7 @@
 													<xs:element
 														name="Namespace" minOccurs="0" maxOccurs="unbounded">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid" use="required">
 																<xs:simpleType>
@@ -483,7 +483,7 @@
 																<xs:element
 																	name="objectType" minOccurs="1" maxOccurs="1">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid">
 																			<xs:simpleType>
@@ -499,7 +499,7 @@
 																<xs:element
 																	name="Namespace" minOccurs="0" maxOccurs="unbounded">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid" use="required">
 																			<xs:simpleType>


From kawas at dev.open-bio.org  Thu Oct 18 10:26:54 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:26:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181426.l9IEQsKm003652@dev.open-bio.org>


kawas
Thu Oct 18 10:26:53 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService
In directory dev.open-bio.org:/tmp/cvs-serv3613

Modified Files:
	registerService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/registerService registerService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd	2007/08/27 19:39:03	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd	2007/10/18 14:26:53	1.2
@@ -9,7 +9,7 @@
 				using the BioMOBY API.
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType>
 			<xs:sequence>
 				<xs:element minOccurs="1" maxOccurs="1"
 					name="Category">


From kawas at dev.open-bio.org  Thu Oct 18 10:27:38 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:27:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181427.l9IERcwe003695@dev.open-bio.org>


kawas
Thu Oct 18 10:27:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService
In directory dev.open-bio.org:/tmp/cvs-serv3660

Modified Files:
	retrieveService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveService retrieveService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd	2007/08/27 19:49:55	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd	2007/10/18 14:27:38	1.2
@@ -2,7 +2,7 @@
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
 	targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central">
 	<xs:element name="retrieveService">
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:sequence>
 				<xs:annotation>
 					<xs:documentation>
@@ -13,7 +13,7 @@
 				</xs:annotation>
 				<xs:element name="Service" nillable="true" minOccurs="1"
 					maxOccurs="1" fixed="">
-					<xs:complexType mixed="true">
+					<xs:complexType >
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
 								<xs:attribute name="authURI"
@@ -52,7 +52,7 @@
 				for the service (usually wrapped in a CDATA section).
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:simpleContent>
 				<xs:extension base="xs:string">
 					<xs:attribute name="authURI" use="required">


From kawas at dev.open-bio.org  Thu Oct 18 10:28:40 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:28:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181428.l9IESex2003738@dev.open-bio.org>


kawas
Thu Oct 18 10:28:40 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders
In directory dev.open-bio.org:/tmp/cvs-serv3703

Modified Files:
	retrieveServiceProviders.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders retrieveServiceProviders.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd	2007/08/27 19:51:08	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd	2007/10/18 14:28:40	1.2
@@ -5,7 +5,7 @@
 	<xs:element name="serviceProviders">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="serviceProviders" minOccurs="0"
+				<xs:element name="serviceProvider" minOccurs="0"
 					maxOccurs="unbounded">
 					<xs:complexType>
 								<xs:attribute name="name"


From kawas at dev.open-bio.org  Thu Oct 18 12:38:42 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 12:38:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181638.l9IGcgY5003964@dev.open-bio.org>


kawas
Thu Oct 18 12:38:42 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames
In directory dev.open-bio.org:/tmp/cvs-serv3932

Modified Files:
	 retrieveServiceNames.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames  retrieveServiceNames.xsd,1.1,1.2
rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/retrieveServiceNames.xsd,v: No such file or directory


From kawas at dev.open-bio.org  Thu Oct 18 12:39:49 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 12:39:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181639.l9IGdnKc004028@dev.open-bio.org>


kawas
Thu Oct 18 12:39:48 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition
In directory dev.open-bio.org:/tmp/cvs-serv3993

Modified Files:
	retrieveObjectDefinitionOutput.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition retrieveObjectDefinitionOutput.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd	2007/08/27 19:48:18	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd	2007/10/18 16:39:48	1.2
@@ -2,7 +2,7 @@
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
 	targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central">
 	<xs:element name="retrieveObjectDefinition">
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:sequence>
 				<xs:annotation>
 					<xs:documentation>
@@ -11,7 +11,7 @@
 				</xs:annotation>
 				<xs:element name="objectType" minOccurs="1"
 					maxOccurs="1">
-					<xs:complexType mixed="true">
+					<xs:complexType >
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
 								<xs:attribute name="lsid"
@@ -36,7 +36,7 @@
 						<xs:sequence>
 							<xs:element name="objectType" minOccurs="1"
 								maxOccurs="1">
-								<xs:complexType mixed="true">
+								<xs:complexType >
 									<xs:simpleContent>
 										<xs:extension
 											base="xs:string">


From mwilkinson at dev.open-bio.org  Mon Oct 22 16:52:38 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 16:52:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222052.l9MKqcg5017902@dev.open-bio.org>


mwilkinson
Mon Oct 22 16:52:37 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17883/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.104,1.105
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.104
retrieving revision 1.105
diff -u -r1.104 -r1.105
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 16:26:50	1.104
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 20:52:37	1.105
@@ -1343,10 +1343,27 @@
 	my $incls = $self->_getInclusions($relHash,$node,[$rel], $incExpand);
 	foreach my $triplet ( @$incls ) {
 	  my ($inclId, $inclArtName, $inclAssert) = @$triplet;
-	  $hasRelDetails->{$inclId}->{$inclAssert} = $inclArtName;
+	  $hasRelDetails->{$inclId}->{$inclAssert} = $inclArtName;  # can be more than one articleName for each included Object
 	  push @entityResultList, $inclId;
 	}
       }
+	# we have the following structure now for the HAS and HASA...
+	#       DB<35> x $hasRelDetails
+	#	0  HASH(0x95cd1bc)
+	#	5371 => HASH(0x95f7fd8)   # object type
+	#	10795 => 'Tiny'		  # related to parent by $ rel relationship 
+	#	10796 => 'Small'
+	#	10797 => 'Aliphatic'
+	#	10798 => 'Aromatic'
+	#	10799 => 'Non-polar'
+	#	10800 => 'Polar'
+	#	10801 => 'Charged'
+	#	10802 => 'Positive'
+	#	10803 => 'Negative'
+	#	10804 => 'Hydropathy_KD'
+	#	10805 => 'Hydropathy_OHM'
+	#	10806 => 'Consensus'
+
       # set up list of unique object ids for the database lookup
       @entityQueryList = keys %$hasRelDetails;
     }
@@ -1358,16 +1375,23 @@
     
     # now it's time to move away from pure ids, retrieve details from database:
     my $details = $adaptor->get_details_for_id_list($ontology, \@fields, \@entityQueryList);
-
+    my $newstructure;
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
-      if ( exists $hasRelDetails->{$entityId} ) {
+      if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
-	  $details->{$entityId}->{'articleName'} = $hasRelDetails->{$entityId}->{$assert};
+	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE
+	  # NEEDS TO BE REVERSED!
+	  my $articleName = $hasRelDetails->{$entityId}->{$assert};
+	  my $objectTypeLSID = $details->{entityId}->{object_lsid};
+	  $details->{$entityId}->{'articleName'}->{$articleName} = "Related_by";  # I know, this is a very goofy data structure.  What we really
+				# want are keys $details->{entitId}->{articleName}
+				# so taht we can see how often that object is included
+				# by a has or hasa relationship
 	}
       }
-      elsif ( $ontology eq 'object') {
+      elsif ( $ontology eq 'object') {  # if it doesn't have a RelDetail, and it is the object ontology we are querying, then its an ISA
 	# for isa, articleName is the empty string
 	$details->{$entityId}->{'articleName'} = '';
       }


From mwilkinson at dev.open-bio.org  Mon Oct 22 16:52:56 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 16:52:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222052.l9MKqu8m017939@dev.open-bio.org>


mwilkinson
Mon Oct 22 16:52:56 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17920/MOBY

Modified Files:
	Central.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY Central.pm,1.291,1.292
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.291
retrieving revision 1.292
diff -u -r1.291 -r1.292
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/24 18:53:32	1.291
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/10/22 20:52:56	1.292
@@ -3102,10 +3102,17 @@
 		foreach my $lsid_article ( @lsids_articles ) {
 			my $lsid = $lsid_article->{lsid};
 			my $term = $lsid_article->{term};
-			my $articleName = $lsid_article->{articleName};
-			$response .= "<${ontology}Type lsid='$lsid' ";
-			$response .= "articleName='$articleName'" if $articleName;  # wont be there for Service type ontology
-			$response .= ">$term</${ontology}Type>\n";
+			if ($this_rel =~ /isa/i){
+				$response .= "<${ontology}Type lsid='$lsid' ";
+				$response .= ">$term</${ontology}Type>\n";
+			} else {
+				my @articleNames = keys %{$lsid_article->{'articleName'}};
+				foreach my $articleName(@articleNames){
+					$response .= "<${ontology}Type lsid='$lsid' ";
+					$response .= "articleName='$articleName'" if $articleName;  # wont be there for Service type ontology
+					$response .= ">$term</${ontology}Type>\n";
+				}
+			}
 		}
 		$response .= "</Relationship>\n";
 	}


From mwilkinson at dev.open-bio.org  Mon Oct 22 17:15:37 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 17:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222115.l9MLFb6n018018@dev.open-bio.org>


mwilkinson
Mon Oct 22 17:15:37 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17999/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.105,1.106
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.105
retrieving revision 1.106
diff -u -r1.105 -r1.106
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 20:52:37	1.105
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:15:37	1.106
@@ -1379,6 +1379,7 @@
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
+      next if $details->{$entityId};  # we've already processed this one
       if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
 	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE


From mwilkinson at dev.open-bio.org  Mon Oct 22 17:19:21 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 17:19:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222119.l9MLJLes018070@dev.open-bio.org>


mwilkinson
Mon Oct 22 17:19:21 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv18051/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.106,1.107
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.106
retrieving revision 1.107
diff -u -r1.106 -r1.107
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:15:37	1.106
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:19:21	1.107
@@ -1379,7 +1379,7 @@
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
-      next if $details->{$entityId};  # we've already processed this one
+      next if $details->{$entityId}->{'articleName'};  # we've already processed this one
       if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
 	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE


From gordonp at dev.open-bio.org  Thu Oct 25 17:29:33 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:29:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252129.l9PLTXsu008780@dev.open-bio.org>


gordonp
Thu Oct 25 17:29:33 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8744/org/biomoby/service/test

Modified Files:
	mobyAASeq.xml 
Log Message:
Removed secondaries, as this interfered with MobyServlet tutorial usage
moby-live/Java/src/main/org/biomoby/service/test mobyAASeq.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/mobyAASeq.xml,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/service/test/mobyAASeq.xml	2006/12/07 16:37:36	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/mobyAASeq.xml	2007/10/25 21:29:32	1.3
@@ -8,11 +8,6 @@
           <Integer namespace='' id='' articleName='Length'>499</Integer>
         </AminoAcidSequence>
       </moby:Simple>
-      <moby:Parameter articleName='filter'><Value>true</Value></moby:Parameter>	
-      <moby:Parameter articleName='hits'><Value>100</Value></moby:Parameter>	
-      <moby:Parameter articleName='db'><Value>nr</Value></moby:Parameter>	
-      <moby:Parameter articleName='threshold'><Value>1.0e-5</Value></moby:Parameter>	
-      <moby:Parameter articleName='since'><Value>2005-08-13</Value></moby:Parameter>	
     </moby:mobyData>
   </moby:mobyContent>
 </moby:MOBY>


From gordonp at dev.open-bio.org  Thu Oct 25 17:30:43 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:30:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252130.l9PLUhUg008842@dev.open-bio.org>


gordonp
Thu Oct 25 17:30:43 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8810/org/biomoby/service/test

Added Files:
	mobyAASeqWithSecondaries.xml 
Log Message:
Moved from mobySeqAA.xml, since that one needs to be without secondaries for proper MobyServlet tutorial usage
moby-live/Java/src/main/org/biomoby/service/test mobyAASeqWithSecondaries.xml,NONE,1.1

From gordonp at dev.open-bio.org  Thu Oct 25 17:31:48 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:31:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252131.l9PLVmkl008886@dev.open-bio.org>


gordonp
Thu Oct 25 17:31:48 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8850/org/biomoby/service/test

Modified Files:
	MobyServletTestCase.java 
Log Message:
Changed example XML file due to conflict with MobyServlet tutorial
moby-live/Java/src/main/org/biomoby/service/test MobyServletTestCase.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/07/23 21:32:27	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/10/25 21:31:48	1.6
@@ -20,7 +20,7 @@
 import java.util.Vector;
 
 public class MobyServletTestCase extends TestCase{
-    private final static String TEST_MOBY_XML = "org/biomoby/service/test/mobyAASeq.xml";
+    private final static String TEST_MOBY_XML = "org/biomoby/service/test/mobyAASeqWithSecondaries.xml";
     private final static String SERVLET_TEST_WEBXML = "org/biomoby/service/test/web.xml";
     private final static String SERVLET_TEST_URL = "http://moby.ucalgary.ca:8080/MobyServlet";
     private final static String TEST_MAIN_CLASS_NAME = "org.biomoby.service.test.ConvertAAtoFASTA_AA";


From gordonp at dev.open-bio.org  Wed Oct 31 11:35:56 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 31 Oct 2007 11:35:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710311535.l9VFZugD029097@dev.open-bio.org>


gordonp
Wed Oct 31 11:35:55 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv29055/src/main/org/biomoby/shared/data

Modified Files:
	MobyDataComposite.java MobyDataObject.java 
Log Message:
Fixed registry propagation
moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.18,1.19 MobyDataObject.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java	2007/08/10 20:23:01	1.18
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java	2007/10/31 15:35:55	1.19
@@ -93,7 +93,7 @@
     }
 
     public MobyDataComposite(MobyDataType type, String name, String namespace, String id){
-	super(namespace, id);
+	super(namespace, id, type.getRegistry());
 	setName(name);
 	setDataType(type);
 	members = new ConcurrentHashMap<String, MobyDataObject>();
@@ -108,7 +108,7 @@
     }
 
     public MobyDataComposite(String typeName, String name, String namespace, String id, Registry registry){
-	super(namespace, id);
+	super(namespace, id, registry);
 	setName(name);
 	setDataType(MobyDataType.getDataType(typeName, registry));
 	members = new ConcurrentHashMap<String, MobyDataObject>();

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2007/07/27 21:44:21	1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2007/10/31 15:35:55	1.20
@@ -82,7 +82,7 @@
 	setDataType(MobyDataType.getDataType(MobyTags.MOBYOBJECT, registry));
 	setId(id);	
 
-	MobyNamespace nsObj = MobyNamespace.getNamespace(namespace);
+	MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, registry);
 	if(nsObj == null){
 	    // Not in the ontology, so create a token namespace
 	    nsObj = new MobyNamespace(namespace == null ? "" : namespace);


From kawas at dev.open-bio.org  Mon Oct  1 19:05:38 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 1 Oct 2007 15:05:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710011905.l91J5cBl013641@dev.open-bio.org>


kawas
Mon Oct  1 15:05:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv13606

Modified Files:
	InstallingLocalMOBYCentral.html 
Log Message:
mention that MOBY_ONTOLOGYSERVER needs to be added to the environment and added it in the appropriate spots during installation
moby-live/Docs/MOBY-S_API InstallingLocalMOBYCentral.html,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/02/22 16:22:24	1.8
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html	2007/10/01 19:05:38	1.9
@@ -154,6 +154,10 @@
         # from the mobycentral databases.
         #
         SetEnv MOBY_CENTRAL_CONFIG "/etc/apache2/conf/mobycentral.config"
+        # Full URL to the <a href="#ONTOLOGYSERVER">OntologyServer.cgi</a> script 
+        # that is copied to the cgi-bin
+        #
+        SetEnv MOBY_ONTOLOGY_SERVER "http://<i>your.domain</i>/cgi-bin/OntologyServer.cgi"
         # 
         # Path to additional Perl modules.
         # Tell Apache where to find Perl modules,
@@ -460,11 +464,6 @@
      <li>Copy the 
       <pre>    ~/moby-live/Perl/scripts/OntologyServer.cgi </pre>
          CGI script into your webserver cgi-bin folder.     </li>
-     <li>You will now have to edit the MOBY::Client::OntologyServer.pm module manually (sorry!). 
-         This module was hardcoded to point to the OntologyServer.cgi at THE central BioMOBY Central.  
-         You will have to change the line that reads 
-      <pre>    host => ["http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi",'read/write'] </pre>
-         to point to the URL of your OntologyServer.cgi that you just set up.     </li>
 	</ul>
    </li>
    <!--
@@ -545,12 +544,16 @@
          then set up the following environment variables. <br/>
          For bash, ksh, etc. in your ~/.bashrc or ~/.kshrc or etc.: 
        <pre>
-    export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central </pre>
+export MOBY_SERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+export MOBY_URI=http://<i>your.host.name</i>t/MOBY/Central
+export MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
          For csh or tcsh in your ~/.cshrc or ~/.tcshrc: <br/> 
        <pre>
-    setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
-    setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central </pre>
+setenv MOBY_SERVER http://<i>your.host.name</i>/biomoby/central/cgi-bin/MOBY-Central.pl
+setenv MOBY_URI http://<i>your.host.name</i>/MOBY/Central
+setenv MOBY_ONTOLOGYSERVER=http://<i>your.host.name</i>/biomoby/central/cgi-bin/OntologyServer.cgi
+	   </pre>
      </li>
     </ul>
    </li>
@@ -563,7 +566,8 @@
    <b>To test your BioMOBY Central:</b>
    <ul>
     <li>Ensure that the following environment variables are set:
-      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above </pre>
+      <pre>    MOBY_CENTRAL_CONFIG - the path to your <a href="#mobycentral.config">mobycentral.config file</a> created above</pre>
+	  <pre>    MOBY_ONTOLOGYSERVER - the url to your <a href="#ONTOLOGYSERVER">OntologyServer.cgi file</a> created above</pre>
       <pre>    MOBY_SERVER - the endpoint of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
       <pre>    MOBY_URI - the namespace of your local registry (see above, <a href="#CLIENTS">Configure your clients</a>)</pre>
     </li>



From kawas at dev.open-bio.org  Thu Oct 18 14:26:25 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:26:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181426.l9IEQP6R003605@dev.open-bio.org>


kawas
Thu Oct 18 10:26:24 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService
In directory dev.open-bio.org:/tmp/cvs-serv3570

Modified Files:
	findService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/findService findService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd	2007/08/27 19:36:45	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/findService/findService.xsd	2007/10/18 14:26:24	1.2
@@ -9,7 +9,7 @@
 				using the BioMOBY API.
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType>
 			<xs:sequence>
 				<xs:element minOccurs="0" maxOccurs="1"
 					name="Category">
@@ -258,7 +258,7 @@
 						<xs:sequence>
 							<xs:element name="serviceType" minOccurs="1"
 								maxOccurs="1">
-								<xs:complexType mixed="true">
+								<xs:complexType>
 									<xs:attribute name="lsid"
 										use="required">
 										<xs:simpleType>
@@ -315,7 +315,7 @@
 													<xs:element
 														name="objectType" minOccurs="1" maxOccurs="1">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid">
 																<xs:simpleType>
@@ -331,7 +331,7 @@
 													<xs:element
 														name="Namespace" minOccurs="0" maxOccurs="unbounded">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid" use="required">
 																<xs:simpleType>
@@ -368,7 +368,7 @@
 																<xs:element
 																	name="objectType" maxOccurs="1" minOccurs="1">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid">
 																			<xs:simpleType>
@@ -384,7 +384,7 @@
 																<xs:element
 																	name="Namespace" minOccurs="0" maxOccurs="unbounded">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid" use="required">
 																			<xs:simpleType>
@@ -430,7 +430,7 @@
 													<xs:element
 														name="objectType" minOccurs="1" maxOccurs="1">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid">
 																<xs:simpleType>
@@ -446,7 +446,7 @@
 													<xs:element
 														name="Namespace" minOccurs="0" maxOccurs="unbounded">
 														<xs:complexType
-															mixed="true">
+															>
 															<xs:attribute
 																name="lsid" use="required">
 																<xs:simpleType>
@@ -483,7 +483,7 @@
 																<xs:element
 																	name="objectType" minOccurs="1" maxOccurs="1">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid">
 																			<xs:simpleType>
@@ -499,7 +499,7 @@
 																<xs:element
 																	name="Namespace" minOccurs="0" maxOccurs="unbounded">
 																	<xs:complexType
-																		mixed="true">
+																		>
 																		<xs:attribute
 																			name="lsid" use="required">
 																			<xs:simpleType>



From kawas at dev.open-bio.org  Thu Oct 18 14:26:54 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:26:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181426.l9IEQsKm003652@dev.open-bio.org>


kawas
Thu Oct 18 10:26:53 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService
In directory dev.open-bio.org:/tmp/cvs-serv3613

Modified Files:
	registerService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/registerService registerService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd	2007/08/27 19:39:03	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/registerService/registerService.xsd	2007/10/18 14:26:53	1.2
@@ -9,7 +9,7 @@
 				using the BioMOBY API.
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType>
 			<xs:sequence>
 				<xs:element minOccurs="1" maxOccurs="1"
 					name="Category">



From kawas at dev.open-bio.org  Thu Oct 18 14:27:38 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:27:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181427.l9IERcwe003695@dev.open-bio.org>


kawas
Thu Oct 18 10:27:38 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService
In directory dev.open-bio.org:/tmp/cvs-serv3660

Modified Files:
	retrieveService.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveService retrieveService.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd	2007/08/27 19:49:55	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveService/retrieveService.xsd	2007/10/18 14:27:38	1.2
@@ -2,7 +2,7 @@
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
 	targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central">
 	<xs:element name="retrieveService">
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:sequence>
 				<xs:annotation>
 					<xs:documentation>
@@ -13,7 +13,7 @@
 				</xs:annotation>
 				<xs:element name="Service" nillable="true" minOccurs="1"
 					maxOccurs="1" fixed="">
-					<xs:complexType mixed="true">
+					<xs:complexType >
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
 								<xs:attribute name="authURI"
@@ -52,7 +52,7 @@
 				for the service (usually wrapped in a CDATA section).
 			</xs:documentation>
 		</xs:annotation>
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:simpleContent>
 				<xs:extension base="xs:string">
 					<xs:attribute name="authURI" use="required">



From kawas at dev.open-bio.org  Thu Oct 18 14:28:40 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 10:28:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181428.l9IESex2003738@dev.open-bio.org>


kawas
Thu Oct 18 10:28:40 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders
In directory dev.open-bio.org:/tmp/cvs-serv3703

Modified Files:
	retrieveServiceProviders.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders retrieveServiceProviders.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd	2007/08/27 19:51:08	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceProviders/retrieveServiceProviders.xsd	2007/10/18 14:28:40	1.2
@@ -5,7 +5,7 @@
 	<xs:element name="serviceProviders">
 		<xs:complexType>
 			<xs:sequence>
-				<xs:element name="serviceProviders" minOccurs="0"
+				<xs:element name="serviceProvider" minOccurs="0"
 					maxOccurs="unbounded">
 					<xs:complexType>
 								<xs:attribute name="name"



From kawas at dev.open-bio.org  Thu Oct 18 16:38:42 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 12:38:42 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181638.l9IGcgY5003964@dev.open-bio.org>


kawas
Thu Oct 18 12:38:42 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames
In directory dev.open-bio.org:/tmp/cvs-serv3932

Modified Files:
	 retrieveServiceNames.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames  retrieveServiceNames.xsd,1.1,1.2
rcsdiff: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveServiceNames/RCS/retrieveServiceNames.xsd,v: No such file or directory



From kawas at dev.open-bio.org  Thu Oct 18 16:39:49 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 18 Oct 2007 12:39:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710181639.l9IGdnKc004028@dev.open-bio.org>


kawas
Thu Oct 18 12:39:48 EDT 2007
Update of /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition
In directory dev.open-bio.org:/tmp/cvs-serv3993

Modified Files:
	retrieveObjectDefinitionOutput.xsd 
Log Message:

moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition retrieveObjectDefinitionOutput.xsd,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd	2007/08/27 19:48:18	1.1
+++ /home/repository/moby/moby-live/Docs/Schemas/RegistryAPI/retrieveObjectDefinition/retrieveObjectDefinitionOutput.xsd	2007/10/18 16:39:48	1.2
@@ -2,7 +2,7 @@
 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"
 	targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central">
 	<xs:element name="retrieveObjectDefinition">
-		<xs:complexType mixed="true">
+		<xs:complexType >
 			<xs:sequence>
 				<xs:annotation>
 					<xs:documentation>
@@ -11,7 +11,7 @@
 				</xs:annotation>
 				<xs:element name="objectType" minOccurs="1"
 					maxOccurs="1">
-					<xs:complexType mixed="true">
+					<xs:complexType >
 						<xs:simpleContent>
 							<xs:extension base="xs:string">
 								<xs:attribute name="lsid"
@@ -36,7 +36,7 @@
 						<xs:sequence>
 							<xs:element name="objectType" minOccurs="1"
 								maxOccurs="1">
-								<xs:complexType mixed="true">
+								<xs:complexType >
 									<xs:simpleContent>
 										<xs:extension
 											base="xs:string">



From mwilkinson at dev.open-bio.org  Mon Oct 22 20:52:38 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 16:52:38 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222052.l9MKqcg5017902@dev.open-bio.org>


mwilkinson
Mon Oct 22 16:52:37 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17883/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.104,1.105
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.104
retrieving revision 1.105
diff -u -r1.104 -r1.105
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 16:26:50	1.104
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 20:52:37	1.105
@@ -1343,10 +1343,27 @@
 	my $incls = $self->_getInclusions($relHash,$node,[$rel], $incExpand);
 	foreach my $triplet ( @$incls ) {
 	  my ($inclId, $inclArtName, $inclAssert) = @$triplet;
-	  $hasRelDetails->{$inclId}->{$inclAssert} = $inclArtName;
+	  $hasRelDetails->{$inclId}->{$inclAssert} = $inclArtName;  # can be more than one articleName for each included Object
 	  push @entityResultList, $inclId;
 	}
       }
+	# we have the following structure now for the HAS and HASA...
+	#       DB<35> x $hasRelDetails
+	#	0  HASH(0x95cd1bc)
+	#	5371 => HASH(0x95f7fd8)   # object type
+	#	10795 => 'Tiny'		  # related to parent by $ rel relationship 
+	#	10796 => 'Small'
+	#	10797 => 'Aliphatic'
+	#	10798 => 'Aromatic'
+	#	10799 => 'Non-polar'
+	#	10800 => 'Polar'
+	#	10801 => 'Charged'
+	#	10802 => 'Positive'
+	#	10803 => 'Negative'
+	#	10804 => 'Hydropathy_KD'
+	#	10805 => 'Hydropathy_OHM'
+	#	10806 => 'Consensus'
+
       # set up list of unique object ids for the database lookup
       @entityQueryList = keys %$hasRelDetails;
     }
@@ -1358,16 +1375,23 @@
     
     # now it's time to move away from pure ids, retrieve details from database:
     my $details = $adaptor->get_details_for_id_list($ontology, \@fields, \@entityQueryList);
-
+    my $newstructure;
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
-      if ( exists $hasRelDetails->{$entityId} ) {
+      if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
-	  $details->{$entityId}->{'articleName'} = $hasRelDetails->{$entityId}->{$assert};
+	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE
+	  # NEEDS TO BE REVERSED!
+	  my $articleName = $hasRelDetails->{$entityId}->{$assert};
+	  my $objectTypeLSID = $details->{entityId}->{object_lsid};
+	  $details->{$entityId}->{'articleName'}->{$articleName} = "Related_by";  # I know, this is a very goofy data structure.  What we really
+				# want are keys $details->{entitId}->{articleName}
+				# so taht we can see how often that object is included
+				# by a has or hasa relationship
 	}
       }
-      elsif ( $ontology eq 'object') {
+      elsif ( $ontology eq 'object') {  # if it doesn't have a RelDetail, and it is the object ontology we are querying, then its an ISA
 	# for isa, articleName is the empty string
 	$details->{$entityId}->{'articleName'} = '';
       }



From mwilkinson at dev.open-bio.org  Mon Oct 22 20:52:56 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 16:52:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222052.l9MKqu8m017939@dev.open-bio.org>


mwilkinson
Mon Oct 22 16:52:56 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17920/MOBY

Modified Files:
	Central.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY Central.pm,1.291,1.292
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.291
retrieving revision 1.292
diff -u -r1.291 -r1.292
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/24 18:53:32	1.291
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/10/22 20:52:56	1.292
@@ -3102,10 +3102,17 @@
 		foreach my $lsid_article ( @lsids_articles ) {
 			my $lsid = $lsid_article->{lsid};
 			my $term = $lsid_article->{term};
-			my $articleName = $lsid_article->{articleName};
-			$response .= "<${ontology}Type lsid='$lsid' ";
-			$response .= "articleName='$articleName'" if $articleName;  # wont be there for Service type ontology
-			$response .= ">$term</${ontology}Type>\n";
+			if ($this_rel =~ /isa/i){
+				$response .= "<${ontology}Type lsid='$lsid' ";
+				$response .= ">$term</${ontology}Type>\n";
+			} else {
+				my @articleNames = keys %{$lsid_article->{'articleName'}};
+				foreach my $articleName(@articleNames){
+					$response .= "<${ontology}Type lsid='$lsid' ";
+					$response .= "articleName='$articleName'" if $articleName;  # wont be there for Service type ontology
+					$response .= ">$term</${ontology}Type>\n";
+				}
+			}
 		}
 		$response .= "</Relationship>\n";
 	}



From mwilkinson at dev.open-bio.org  Mon Oct 22 21:15:37 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 17:15:37 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222115.l9MLFb6n018018@dev.open-bio.org>


mwilkinson
Mon Oct 22 17:15:37 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv17999/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.105,1.106
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.105
retrieving revision 1.106
diff -u -r1.105 -r1.106
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 20:52:37	1.105
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:15:37	1.106
@@ -1379,6 +1379,7 @@
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
+      next if $details->{$entityId};  # we've already processed this one
       if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
 	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE



From mwilkinson at dev.open-bio.org  Mon Oct 22 21:19:21 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Mon, 22 Oct 2007 17:19:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710222119.l9MLJLes018070@dev.open-bio.org>


mwilkinson
Mon Oct 22 17:19:21 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv18051/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
fixing Relationships code
moby-live/Perl/MOBY OntologyServer.pm,1.106,1.107
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.106
retrieving revision 1.107
diff -u -r1.106 -r1.107
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:15:37	1.106
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/10/22 21:19:21	1.107
@@ -1379,7 +1379,7 @@
     # enhance details with information about relationships and build result hash
     foreach my $entityId (@entityResultList) {
       # add articleName slot if necessary
-      next if $details->{$entityId};  # we've already processed this one
+      next if $details->{$entityId}->{'articleName'};  # we've already processed this one
       if ( exists $hasRelDetails->{$entityId} ) {  # the only things that have RelDetails are HASA/HAS EntityIDs
 	foreach my $assert ( keys %{$hasRelDetails->{$entityId}} ) {
 	  # THIS DATA STRUCTURE IS WRONG - IT ASSUMES ONE ARTICLE NAME FOR EACH CONTAINED OBJECT TYPE



From gordonp at dev.open-bio.org  Thu Oct 25 21:29:33 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:29:33 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252129.l9PLTXsu008780@dev.open-bio.org>


gordonp
Thu Oct 25 17:29:33 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8744/org/biomoby/service/test

Modified Files:
	mobyAASeq.xml 
Log Message:
Removed secondaries, as this interfered with MobyServlet tutorial usage
moby-live/Java/src/main/org/biomoby/service/test mobyAASeq.xml,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/mobyAASeq.xml,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/service/test/mobyAASeq.xml	2006/12/07 16:37:36	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/mobyAASeq.xml	2007/10/25 21:29:32	1.3
@@ -8,11 +8,6 @@
           <Integer namespace='' id='' articleName='Length'>499</Integer>
         </AminoAcidSequence>
       </moby:Simple>
-      <moby:Parameter articleName='filter'><Value>true</Value></moby:Parameter>	
-      <moby:Parameter articleName='hits'><Value>100</Value></moby:Parameter>	
-      <moby:Parameter articleName='db'><Value>nr</Value></moby:Parameter>	
-      <moby:Parameter articleName='threshold'><Value>1.0e-5</Value></moby:Parameter>	
-      <moby:Parameter articleName='since'><Value>2005-08-13</Value></moby:Parameter>	
     </moby:mobyData>
   </moby:mobyContent>
 </moby:MOBY>



From gordonp at dev.open-bio.org  Thu Oct 25 21:30:43 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:30:43 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252130.l9PLUhUg008842@dev.open-bio.org>


gordonp
Thu Oct 25 17:30:43 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8810/org/biomoby/service/test

Added Files:
	mobyAASeqWithSecondaries.xml 
Log Message:
Moved from mobySeqAA.xml, since that one needs to be without secondaries for proper MobyServlet tutorial usage
moby-live/Java/src/main/org/biomoby/service/test mobyAASeqWithSecondaries.xml,NONE,1.1


From gordonp at dev.open-bio.org  Thu Oct 25 21:31:48 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Thu, 25 Oct 2007 17:31:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710252131.l9PLVmkl008886@dev.open-bio.org>


gordonp
Thu Oct 25 17:31:48 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test
In directory dev.open-bio.org:/tmp/cvs-serv8850/org/biomoby/service/test

Modified Files:
	MobyServletTestCase.java 
Log Message:
Changed example XML file due to conflict with MobyServlet tutorial
moby-live/Java/src/main/org/biomoby/service/test MobyServletTestCase.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/07/23 21:32:27	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/test/MobyServletTestCase.java	2007/10/25 21:31:48	1.6
@@ -20,7 +20,7 @@
 import java.util.Vector;
 
 public class MobyServletTestCase extends TestCase{
-    private final static String TEST_MOBY_XML = "org/biomoby/service/test/mobyAASeq.xml";
+    private final static String TEST_MOBY_XML = "org/biomoby/service/test/mobyAASeqWithSecondaries.xml";
     private final static String SERVLET_TEST_WEBXML = "org/biomoby/service/test/web.xml";
     private final static String SERVLET_TEST_URL = "http://moby.ucalgary.ca:8080/MobyServlet";
     private final static String TEST_MAIN_CLASS_NAME = "org.biomoby.service.test.ConvertAAtoFASTA_AA";



From gordonp at dev.open-bio.org  Wed Oct 31 15:35:56 2007
From: gordonp at dev.open-bio.org (Paul Gordon)
Date: Wed, 31 Oct 2007 11:35:56 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200710311535.l9VFZugD029097@dev.open-bio.org>


gordonp
Wed Oct 31 11:35:55 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data
In directory dev.open-bio.org:/tmp/cvs-serv29055/src/main/org/biomoby/shared/data

Modified Files:
	MobyDataComposite.java MobyDataObject.java 
Log Message:
Fixed registry propagation
moby-live/Java/src/main/org/biomoby/shared/data MobyDataComposite.java,1.18,1.19 MobyDataObject.java,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java	2007/08/10 20:23:01	1.18
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataComposite.java	2007/10/31 15:35:55	1.19
@@ -93,7 +93,7 @@
     }
 
     public MobyDataComposite(MobyDataType type, String name, String namespace, String id){
-	super(namespace, id);
+	super(namespace, id, type.getRegistry());
 	setName(name);
 	setDataType(type);
 	members = new ConcurrentHashMap<String, MobyDataObject>();
@@ -108,7 +108,7 @@
     }
 
     public MobyDataComposite(String typeName, String name, String namespace, String id, Registry registry){
-	super(namespace, id);
+	super(namespace, id, registry);
 	setName(name);
 	setDataType(MobyDataType.getDataType(typeName, registry));
 	members = new ConcurrentHashMap<String, MobyDataObject>();

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2007/07/27 21:44:21	1.19
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/data/MobyDataObject.java	2007/10/31 15:35:55	1.20
@@ -82,7 +82,7 @@
 	setDataType(MobyDataType.getDataType(MobyTags.MOBYOBJECT, registry));
 	setId(id);	
 
-	MobyNamespace nsObj = MobyNamespace.getNamespace(namespace);
+	MobyNamespace nsObj = MobyNamespace.getNamespace(namespace, registry);
 	if(nsObj == null){
 	    // Not in the ontology, so create a token namespace
 	    nsObj = new MobyNamespace(namespace == null ? "" : namespace);