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Link provided for historical purposes; contact the page author for access: https://gforge.nci.nih.gov/frs/?group_id=14 |
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Link provided for historical purposes: cbiocvs2.nci.nih.gov:/share/content/gforge/lexbig |
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JBoss tends to run out of memory while running with the default settings of JBoss. To fix the problem, modify the run.conf file under JBOSS_home/bin to change the memory setting and how frequently the rmi garbage collector runs, by editing the JAVA_OPTS line as follows:
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if [[ "x$JAVA_OPTS" = "x" ]; then
JAVA_OPTS="-server -XX:!MaxPermSize=128m -Xms256m -Xmx2000m -Dsun.rmi.dgc.client.gcInterval=120000
-Dsun.rmi.dgc.server.gcInterval=120000"
fi
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Try the following values in the config.props file for the DB_URL:
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SINGLE_DB_MODE=true
DB_URL=jdbc:mysql:///<dbname>?socketFactory=com.mysql.jdbc.NamedPipeSocketFactory
DB_DRIVER=org.gjt.mm.mysql.Driver
DB_USER=root
DB_PASSWORD=
DB_PREFIX=lb
DB_PARAM=
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- Coding Scheme Manifest entry field: '''id'''
- Type: lgCommon:registeredName
- Required: Yes
- Override flag set: Not applicable
- Description:
The registered name is the key used to find a coding scheme (for example a unique URL or namespace by which other people access same coding scheme). This String value will be used to identify the manifest entry in the manifest file for the coding scheme too. For example the registered name for coding scheme "Amino-acid" is http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#. This string is also set as the coding scheme's registered name field in the LexGrid model.
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Here are some example coding scheme manifest entries:
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<CodingSchemeManifestList
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList
http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd"
xmlns:owldef="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList"
xmlns="http://LexGrid.org/schema/2006/01/LexOnt/CodingSchemeManifestList">
<entry id="http://www.co-ode.org/ontologies/amino-acid/2006/05/18/amino-acid.owl#">
<codingScheme>amino</codingScheme>
<entityDescription>This is AminoAcide Description from Manifest.</entityDescription>
<formalName>Amino Acid Ontology</formalName>
<defaultLanguage>en</defaultLanguage>
<representsVersion>2005/10/11</representsVersion>
<localName>myLocalName</localName>
<source subRef="ontologies">COODE</source>
<copyright>This is copyright</copyright>
<owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes">
<supportedLanguage localId="en" urn="urn:oid:2.16.840.1.113883.6.84:en"/>
<supportedFormat localId="text_plain" urn="urn:oid:2.16.840.1.113883.6.10:text_plain"/>
<supportedSource localId="COODE" urn="http://www.co-ode.org/"/>
</owldef:mappings>
<associationDefinitions>
<assoc association="testRelation" forwardName="testRelation"
reverseName="testRelationInverse"
isTransitive="true" isReflexive="true"
targetCodingScheme=
"http://www.co-ode.org/ontologies/amino-acid/2006/05/18/outside#"/>
</associationDefinitions>
</entry>
<entry id="urn:oid:2.16.840.1.113883.3.26.1.1">
<codingScheme>NCI Thesaurus CS Manifest</codingScheme>
<entityDescription>This is NCI Thesaurus Description from Manifest.</entityDescription>
<formalName>NCI Thesaurus Formal From Manifest</formalName>
<defaultLanguage>en</defaultLanguage>
<representsVersion>manifestVersion</representsVersion>
<localName>NCILocalName</localName>
<source subRef="ontologies" >NCIManifestSource</source>
<copyright>This is copyright for NCI Thesaurus</copyright> %%%
<owldef:mappings dc="mappings" xmlns="http://LexGrid.org/schema/2006/01/LexGrid/codingSchemes">
<supportedSource localId="COODE" urn="http://www.co-ode.org/"/>
</owldef:mappings>
<associationDefinitions>
<assoc association="testRelation" forwardName="testRelation"
reverseName="testRelationInverse"
isTransitive="true" isReflexive="true"
targetCodingScheme=
"urn:oid:2.16.840.1.113883.3.26.1.1"/>
</associationDefinitions>
</entry>
</CodingSchemeManifestList>
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Currently a coding scheme manifest file is only supported when loading OWL sources. Support for other formats is in-works. If you want to use the manifest file, you can supply the manifest file URI to the following methods:
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"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.load()"
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.validate()"
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An example code snippet:
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LexBIGService lbs = new LexBIGServiceImpl();
LexBIGServiceManager lbsm = lbs.getServiceManager(null);
OWL_Loader loader = (OWL_Loader) lbsm.getLoader("OWLLoader");
if (toValidateOnly)
{
loader.'''validate'''(source, manifest, vl);
System.out.println("VALIDATION SUCCESSFUL");
}
else
{
loader.'''load'''(new File("resources/testData/amino-cid.owl").toURI(),%%%new File
("resources/testData/aa-manifest.xml").toURI(), true, true);
}
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