cd /path/to/moby-live/Java
From senger at dev.open-bio.org Tue Feb 3 01:28:43 2009
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 3 Feb 2009 01:28:43 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902030628.n136ShVe022706@dev.open-bio.org>
senger
Tue Feb 3 01:28:42 EST 2009
Update of /home/repository/moby/moby-live/Java/src/Clients
In directory dev.open-bio.org:/tmp/cvs-serv22691/src/Clients
Added Files:
PreferencesManager.java
Log Message:
added the beginning of the Java Preference Manager
moby-live/Java/src/Clients PreferencesManager.java,NONE,1.1
From senger at dev.open-bio.org Tue Feb 3 01:29:18 2009
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 3 Feb 2009 01:29:18 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902030629.n136TIS0022734@dev.open-bio.org>
senger
Tue Feb 3 01:29:18 EST 2009
Update of /home/repository/moby/moby-live/Java/src/Clients/help
In directory dev.open-bio.org:/tmp/cvs-serv22719/src/Clients/help
Added Files:
PreferencesManager_usage.txt
Log Message:
added the beginning of the Java Preference Manager
moby-live/Java/src/Clients/help PreferencesManager_usage.txt,NONE,1.1
From groscurt at dev.open-bio.org Tue Feb 3 03:59:20 2009
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Tue, 3 Feb 2009 03:59:20 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902030859.n138xKj4022960@dev.open-bio.org>
groscurt
Tue Feb 3 03:59:20 EST 2009
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv22917/xmls
Modified Files:
deployBuild.xml tomcat.xml servletsBuild.xml
Log Message:
corrected version for server deployment... backward compatible
moby-live/Java/xmls deployBuild.xml,1.9,1.10 tomcat.xml,1.5,1.6 servletsBuild.xml,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/deployBuild.xml,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2009/01/06 09:40:12 1.9
+++ /home/repository/moby/moby-live/Java/xmls/deployBuild.xml 2009/02/03 08:59:20 1.10
@@ -11,13 +11,13 @@
-
@@ -55,7 +55,7 @@
-
@@ -83,11 +83,11 @@
-
+
-
+
-
+
-
+
@@ -104,7 +104,7 @@
-
+
@@ -129,14 +129,14 @@
-
+
-
+
@@ -152,7 +152,7 @@
-
+
@@ -172,7 +172,7 @@
-
+
@@ -236,7 +236,7 @@
-
+
@@ -247,9 +247,9 @@
fork="true"
failonerror="true">
-
+
-
+
@@ -290,7 +290,7 @@
-
@@ -328,18 +328,20 @@
-
-
-
+
+
+
-
+
+
-
-
-
+
+
+
+
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/tomcat.xml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Java/xmls/tomcat.xml 2009/01/05 09:40:36 1.5
+++ /home/repository/moby/moby-live/Java/xmls/tomcat.xml 2009/02/03 08:59:20 1.6
@@ -4,59 +4,73 @@
-
+
-
-
-
+
+
+
-
+
-
-
-
+
+
+
+
-
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-
-
-
+ location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
+
+
+
'
-
ERROR: Server not found.
-------------------------------
Please set environment variable CATALINA_HOME to point to it,
or create a file 'build.properties' and put there the line:
- server.home = <location of your server>
+ catalina.home = <location of your server>
(do not include '<' and '>' there),
or start your Ant with this property on the command-line:
- ant -Dserver.home=<location of your server>
+ ant -Dcatalina.home=<location of your server>
-
-
-
+
+
+
-
+
'
-
ERROR: Server does not seem to be running.
------------------------------------------
- I have just checked ${server.host}:${server.port}...
+ I have just checked ${real.server.host}:${real.server.port}...
You may perhaps consider to start it.
Or to set differently the following properties:
- "server.host" (current value: ${server.host}), and
- "server.port" (current value: ${server.port})
+ "server.host" (current value: ${real.server.host}), and
+ "server.port" (current value: ${real.server.port}).
@@ -65,6 +79,6 @@
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml 2009/01/05 08:46:07 1.3
+++ /home/repository/moby/moby-live/Java/xmls/servletsBuild.xml 2009/02/03 08:59:20 1.4
@@ -10,7 +10,7 @@
-
From groscurt at dev.open-bio.org Tue Feb 3 03:59:35 2009
From: groscurt at dev.open-bio.org (Andreas Groscurth)
Date: Tue, 3 Feb 2009 03:59:35 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902030859.n138xZ1x023000@dev.open-bio.org>
groscurt
Tue Feb 3 03:59:35 EST 2009
Update of /home/repository/moby/moby-live/Java/src/webapps
In directory dev.open-bio.org:/tmp/cvs-serv22965/src/webapps
Modified Files:
remote.deploy.build.xml.template
Log Message:
corrected version for server deployment... backward compatible
moby-live/Java/src/webapps remote.deploy.build.xml.template,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2009/01/05 08:46:07 1.6
+++ /home/repository/moby/moby-live/Java/src/webapps/remote.deploy.build.xml.template 2009/02/03 08:59:35 1.7
@@ -20,13 +20,15 @@
-
-
-
-
+
+
+
+
+
+
@@ -37,22 +39,25 @@
The following properties define where and how the services
will be deployed. You can still define new values for them.
-server.home = ${server.home}
+tomcat.home = ${tomcat.home}
All libraries (.jar files) will be moved here.
-server.host = ${server.host}
- Where is your server installed. If this is not localhost
+tomcat.host = ${tomcat.host}
+ Where is your Tomcat installed. If this is not localhost
you may need to allow remote control in server-config.wsdd
before deploying services.
-server.port = ${server.port}
- Where is your server listening.
+tomcat.port = ${tomcat.port}
+ Where is your Tomcat listening.
+
+tomcat.webapps = ${tomcat.webapps}
+ Where the deployment directory is 'e.g. webapps'
axis.relative.path = ${axis.relative.path}
- Where is Axis installed within Tomcat's 'webapps' dir or JBoss 'server/default/deploy' dir
+ Where is Axis installed within Tomcat's 'webapps' dir.
axis.admin.url = ${axis.admin.url}
- How to access your server/Axis.
+ How to access your Tomcat/Axis.
For the list of services that will be deployed when you call
'ant deploy' (or undeploy when you call 'ant undeploy')
@@ -65,11 +70,27 @@
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ location="${real.catalina.home}/${tomcat.webapps}/${axis.relative.path}/WEB-INF"/>
@@ -88,7 +109,7 @@
-
-
-
+
-
-
-
+
+
+
- -
+ -
'
ERROR: Server does not seem to be running.
------------------------------------------
- I have just checked ${server.host}:${server.port}...
+ I have just checked ${real.server.host}:${real.server.port}...
You may perhaps consider to start it.
Or to set differently the following properties:
- "server.host" (current value: ${server.host}), and
- "server.port" (current value: ${server.port})
+ "server.host" (current value: ${real.server.host}), and
+ "server.port" (current value: ${real.server.port})
-
+
-
+
-
+
-
+
-
+
@@ -188,7 +209,7 @@
-
+
@@ -196,9 +217,9 @@
-
+
-
+
From kawas at dev.open-bio.org Tue Feb 3 11:39:42 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 3 Feb 2009 11:39:42 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902031639.n13Gdgwu024764@dev.open-bio.org>
kawas
Tue Feb 3 11:39:41 EST 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared
In directory dev.open-bio.org:/tmp/cvs-serv24729/src/main/org/biomoby/shared
Modified Files:
MobyUnitTest.java
Log Message:
added some documentation (mainly to make the javadoc look better when referring to it from biomoby.org doc)
moby-live/Java/src/main/org/biomoby/shared MobyUnitTest.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyUnitTest.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/shared/MobyUnitTest.java 2009/01/29 19:12:01 1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyUnitTest.java 2009/02/03 16:39:41 1.3
@@ -48,7 +48,7 @@
private String validXPath;
/**
- * Default Constructor
+ * Default Constructor - creates a blank MobyUnitTest object
*/
public MobyUnitTest() {
setExampleInput("");
@@ -58,6 +58,15 @@
init();
}
+ /*
+ * set up XMLUnit for doing our comparisons
+ *
+ * we would like to: -> ignore attribute order because it doesnt matter ->
+ * ignore XML comments, because they are irrelevant in moby -> ignore
+ * element whitespace because it doesnt change semantics -> treat CDATA
+ * sections and text nodes alike
+ *
+ */
private void init() {
// for comparing dom trees
XMLUnit.setIgnoreAttributeOrder(true);
@@ -67,6 +76,7 @@
}
/**
+ * Getter: get the example input that you can use to invoke this service
*
* @return a string of XML representing a services example input
*/
@@ -75,6 +85,8 @@
}
/**
+ * Setter: set the example input that can be passed to the service to invoke
+ * it
*
* @param exampleInput
* a string of XML representing a services example input
@@ -85,6 +97,8 @@
}
/**
+ * Getter: get the expected XML output for this service (usually by sending
+ * it the input from getExampleInput()
*
* @return a string of XML representing a services expected output
*/
@@ -93,6 +107,7 @@
}
/**
+ * Setter: set the expected XML output for this serivce
*
* @param validOutputXML
* a string of XML representing a services expected output
@@ -103,6 +118,7 @@
}
/**
+ * Getter: get the Regular Expression for this unit test
*
* @return a regular expression that can be used on a services output to
* determine validity
@@ -112,6 +128,7 @@
}
/**
+ * Setter: set the regular expression for this unit test
*
* @param validREGEX
* a regular expression that can be used on a services output
@@ -123,6 +140,7 @@
}
/**
+ * Getter: get the xpath expression for this unit test
*
* @return an xpath expression that can be used to drill into a services
* output
@@ -132,6 +150,7 @@
}
/**
+ * Setter: set the xpath expression for this unit test
*
* @param validXPath
* an xpath expression that can be used to drill into a
@@ -150,12 +169,16 @@
public String toString() {
StringBuffer buf = new StringBuffer();
buf.append("Unit Test:\n");
- buf.append(" Input \n" + Utils.format (getExampleInput(), 2) + "\n");
- buf.append(" Output \n" + Utils.format(getValidOutputXML(),2) + "\n");
- buf.append(" XPath \n" + Utils.format(getValidXPath(),2) + "\n");
- buf.append(" REGEX \n" + Utils.format(getValidREGEX(),2) + "\n");
- //return buf.toString();
- return Utils.format (buf.toString(), 1);
+ buf.append(" Input \n" + Utils.format(getExampleInput(), 2)
+ + "\n");
+ buf.append(" Output \n" + Utils.format(getValidOutputXML(), 2)
+ + "\n");
+ buf.append(" XPath \n" + Utils.format(getValidXPath(), 2)
+ + "\n");
+ buf.append(" REGEX \n" + Utils.format(getValidREGEX(), 2)
+ + "\n");
+ // return buf.toString();
+ return Utils.format(buf.toString(), 1);
}
/**
@@ -166,6 +189,9 @@
* the XML that you would like to compare to XML obtained
* from getValidOutputXML()
* @return true if the documents are semantically similar, false otherwise
+ *
+ * @throws MobyException
+ * if there is a problem reading/parsing the testXML
*/
public boolean compareOutputXML(String testXML) throws MobyException {
if (!getValidOutputXML().trim().equals(""))
@@ -191,6 +217,9 @@
* getValidXPath(), expression against
* @return true if the XPath expression matches at least one node in the
* testXML
+ * @throws MobyException
+ * if there is a problem compiling the XPATH expression, or
+ * reading/parsing the textXML
*/
public boolean compareXmlWithXpath(String testXML) throws MobyException {
if (!getValidXPath().trim().equals(""))
@@ -267,7 +296,8 @@
/**
* This inner class implements a 'Qualifier' used to compare XML documents
- * using the XMLUnit engine. It used both RecursiveElementNameAndTextQualifier and
+ * using the XMLUnit engine. It used both
+ * RecursiveElementNameAndTextQualifier and
* MultiLevelElementNameAndTextQualifier as a template.
*
* @author Eddie Kawas
@@ -275,40 +305,36 @@
*/
protected class MobyQualifier extends ElementNameQualifier {
/*
- ******************************************************************
- Copyright (c) 2008, Jeff Martin, Tim Bacon
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
- * Neither the name of the xmlunit.sourceforge.net nor the names
- of its contributors may be used to endorse or promote products
- derived from this software without specific prior written
- permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
- ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGE.
-
- ******************************************************************
- */
+ * *****************************************************************
+ * Copyright (c) 2008, Jeff Martin, Tim Bacon All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in the
+ * documentation and/or other materials provided with the distribution.
+ * Neither the name of the xmlunit.sourceforge.net nor the names of its
+ * contributors may be used to endorse or promote products derived from
+ * this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * *****************************************************************
+ */
private final String[] qualifyingAttrNames;
private final ElementNameQualifier NAME_QUALIFIER = new ElementNameQualifier();
@@ -373,7 +399,8 @@
Element currentControl = control;
Element currentTest = test;
- // we dont try to compare the Collection node because they have unordered children
+ // we dont try to compare the Collection node because they have
+ // unordered children
if (!control.getLocalName().equals("Collection")) {
// not a collection, match name and attributes
stillSimilar = NAME_QUALIFIER.qualifyForComparison(
From kawas at dev.open-bio.org Tue Feb 3 13:05:03 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 3 Feb 2009 13:05:03 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902031805.n13I53a9024979@dev.open-bio.org>
kawas
Tue Feb 3 13:05:03 EST 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
In directory dev.open-bio.org:/tmp/cvs-serv24944/Perl/MOBY-Server/lib/MOBY/RDF/Parsers
Modified Files:
ServiceParser.pm
Log Message:
updated these modules to be more like their java counterparts. Namely, lsids are okay as URI and moved parsing out of URIs to the RDF parser, rather than having it occur in the RDF generator.
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers ServiceParser.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceParser.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceParser.pm 2009/01/28 14:51:36 1.5
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Parsers/ServiceParser.pm 2009/02/03 18:05:03 1.6
@@ -773,25 +773,7 @@
}
}
$val = "" if ref($val) eq 'ARRAY';
-
- # check if $SI->type is an lsid or uri
- if ( $val =~ m/RESOURCES\/MOBY\-S\/Services(\/[A-Za-z0-9_\-]*)?$/ ) {
-
- # uri is /Services/
- $val = substr $1, 1 if $1;
- }
- elsif ( $val =~ m/RESOURCES\/MOBY\-S\/Services(\#[A-Za-z0-9_\-]*)?$/ ) {
-
- # uri is /Services#
- $val = substr $1, 1 if $1;
- }
- elsif ( $val =~ m/^urn\:lsid/i ) {
-
- # uri is an lsid
- my $lsid = LS::ID->new($val);
- $val = $lsid->object if $lsid;
- }
- $instance->type( MOBY::RDF::Utils::trim($val) );
+ $instance->type( $self->_unwrap_servicetype ( MOBY::RDF::Utils::trim($val) ) );
# dont need the performsTask node anymore
$performs = undef;
@@ -886,8 +868,8 @@
$uri =~ m/RESOURCES\/MOBY\-S\/Objects(\#[A-Za-z0-9_\-]*)?$/ ) {
$uri = substr $1, 1 if $1;
} elsif ( $uri =~ m/^urn\:lsid/i ) {
- my $lsid = LS::ID->new( $uri );
- $uri = $lsid->object if $lsid;
+ #my $lsid = LS::ID->new( $uri );
+ #$uri = $lsid->object if $lsid;
}
return $uri;
}
@@ -900,11 +882,26 @@
} elsif ($n =~ m/RESOURCES\/MOBY\-S\/Namespaces(\#[A-Za-z0-9_\-]*)?$/ ){
$n = substr $1, 1 if $1;
} elsif( $n =~ m/^urn\:lsid/i) {
- my $lsid = LS::ID->new($n);
- $n = $lsid->object if $lsid;
+ #my $lsid = LS::ID->new($n);
+ #$n = $lsid->object if $lsid;
+ }
+ return $n;
+}
+
+sub _unwrap_servicetype {
+ my ($self, $n) = @_;
+ # get only the servicetype name (strip from lsid or URI)
+ if ($n =~ m/RESOURCES\/MOBY\-S\/Services(\/[A-Za-z0-9_\-]*)?$/) {
+ $n = substr $1, 1 if $1;
+ } elsif ($n =~ m/RESOURCES\/MOBY\-S\/Services(\#[A-Za-z0-9_\-]*)?$/ ){
+ $n = substr $1, 1 if $1;
+ } elsif( $n =~ m/^urn\:lsid/i) {
+ #my $lsid = LS::ID->new($n);
+ #$n = $lsid->object if $lsid;
}
return $n;
}
+
1;
__END__
From kawas at dev.open-bio.org Tue Feb 3 13:05:04 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 3 Feb 2009 13:05:04 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902031805.n13I54tj024997@dev.open-bio.org>
kawas
Tue Feb 3 13:05:03 EST 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
In directory dev.open-bio.org:/tmp/cvs-serv24944/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies
Modified Files:
Services.pm
Log Message:
updated these modules to be more like their java counterparts. Namely, lsids are okay as URI and moved parsing out of URIs to the RDF parser, rather than having it occur in the RDF generator.
moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies Services.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2009/01/28 14:42:21 1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/RDF/Ontologies/Services.pm 2009/02/03 18:05:03 1.11
@@ -668,8 +668,10 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri} . $_->objectType
- )#TODO check for lsids
+ # check for lsids
+ LS::ID->new($_->objectType) ?
+ $_->objectType : $self->{datatype_uri} . $_->objectType
+ )
)
);
@@ -738,8 +740,9 @@
$inNamespaces,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{namespace_uri} . $n
- ) #TODO check for lsids
+ LS::ID->new($n) ?
+ $n : $self->{namespace_uri} . $n
+ ) # check for lsids
)
);
}
@@ -822,8 +825,9 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri} . $simp->objectType
- )#TODO check for lsids
+ LS::ID->new($simp->objectType) ?
+ $simp->objectType : $self->{datatype_uri} . $simp->objectType
+ )# check for lsids
)
);
my $namespaces = $simp->namespaces;
@@ -870,8 +874,9 @@
MOBY::RDF::Predicates::RDF->type
),
new RDF::Core::Resource(
- $self->{namespace_uri} . $n
- )#TODO check for lsids
+ LS::ID->new($n) ?
+ $n : $self->{namespace_uri} . $n
+ )# check for lsids
)
);
}
@@ -1075,8 +1080,9 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri} . $_->objectType
- )#TODO check for lsids
+ LS::ID->new($_->objectType) ?
+ $_->objectType : $self->{datatype_uri} . $_->objectType
+ )# check for lsids
)
);
@@ -1145,8 +1151,9 @@
$inNamespaces,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{namespace_uri} . $n
- )#TODO check for lsids
+ LS::ID->new($n) ?
+ $n : $self->{namespace_uri} . $n
+ )# check for lsids
)
);
}
@@ -1229,8 +1236,9 @@
$oType,
$resource->new( MOBY::RDF::Predicates::RDF->type ),
new RDF::Core::Resource(
- $self->{datatype_uri} . $simp->objectType
- )#TODO check for lsids
+ LS::ID->new($simp->objectType) ?
+ $simp->objectType : $self->{datatype_uri} . $simp->objectType
+ )# check for lsids
)
);
my $namespaces = $simp->namespaces;
@@ -1277,8 +1285,9 @@
MOBY::RDF::Predicates::RDF->type
),
new RDF::Core::Resource(
- $self->{namespace_uri} . $n
- )#TODO check for lsids
+ LS::ID->new($n) ?
+ $n : $self->{namespace_uri} . $n
+ )
)
);
}
From kawas at dev.open-bio.org Tue Feb 3 16:27:54 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 3 Feb 2009 16:27:54 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902032127.n13LRstj025399@dev.open-bio.org>
kawas
Tue Feb 3 16:27:54 EST 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv25364/Perl/MOBY-Server/lib/MOBY/Client
Modified Files:
ServiceInstance.pm
Log Message:
fixed the perldoc unitTests()
moby-live/Perl/MOBY-Server/lib/MOBY/Client ServiceInstance.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2009/01/28 14:37:02 1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/ServiceInstance.pm 2009/02/03 21:27:54 1.5
@@ -217,12 +217,12 @@
=cut
-=head2 unitTest
+=head2 unitTests
- Title : unitTest
- Usage : $test = $Service->unitTest()
- Function : get/set the MobyUnitTest for this service
- Returns : a MOBY::Client::MobyUnitTest object for this service
+ Title : unitTests
+ Usage : $test = $Service->unitTests()
+ Function : get/set the MobyUnitTests for this service
+ Returns : a listref of MOBY::Client::MobyUnitTest objects for this service
=cut
From kawas at dev.open-bio.org Tue Feb 3 16:56:19 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 3 Feb 2009 16:56:19 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902032156.n13LuJ3I025460@dev.open-bio.org>
kawas
Tue Feb 3 16:56:19 EST 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv25425/Perl/MOBY-Server/lib/MOBY/Client
Modified Files:
MobyUnitTest.pm
Log Message:
fixed a sub name in the perl doc
moby-live/Perl/MOBY-Server/lib/MOBY/Client MobyUnitTest.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm 2008/12/02 18:53:46 1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Client/MobyUnitTest.pm 2009/02/03 21:56:19 1.5
@@ -223,7 +223,7 @@
=cut
-=head2 example_output
+=head2 expected_output
getter/setter - use to get/set the expected output for the service that we are testing given C.
From senger at dev.open-bio.org Tue Feb 3 21:00:01 2009
From: senger at dev.open-bio.org (Martin Senger)
Date: Tue, 3 Feb 2009 21:00:01 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902040200.n14201WG025809@dev.open-bio.org>
senger
Tue Feb 3 21:00:01 EST 2009
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv25790/xmls
Modified Files:
install.xml
Log Message:
install task updated to include (some) Java preferences
moby-live/Java/xmls install.xml,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/install.xml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/xmls/install.xml 2008/10/24 01:41:37 1.6
+++ /home/repository/moby/moby-live/Java/xmls/install.xml 2009/02/04 02:00:01 1.7
@@ -82,6 +82,7 @@
+
@@ -180,3 +181,20 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
From kawas at dev.open-bio.org Thu Feb 5 12:38:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Feb 2009 12:38:10 -0500
Subject: [MOBY-guts] biomoby commit
Message-ID: <200902051738.n15HcAvN032260@dev.open-bio.org>
kawas
Thu Feb 5 12:38:09 EST 2009
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API
In directory dev.open-bio.org:/tmp/cvs-serv32225/Docs/MOBY-S_API
Modified Files:
XMLPayloads.html
Log Message:
fixed the service categories available for registerService
moby-live/Docs/MOBY-S_API XMLPayloads.html,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2008/02/13 04:05:01 1.22
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/XMLPayloads.html 2009/02/05 17:38:09 1.23
@@ -348,12 +348,13 @@
characters, like:
~`!@#$%^&*()=+{[]}:;'",.<>?/|\