 |
Page History
...
As primary reference, see the Installation and Administration Guide :
...
in the GForge archive.
Building the LexBIG Installer from CVS
...
| Code Block |
|---|
Link provided for historical purposes: cbiocvs2.nci.nih.gov:/share/content/gforge/lexbig |
...
Development and build processes are not dependent on a particular CVS client or programming environment. However, files with the extension '.classpath' and '.project' have been inserted into each project folder to help facilitate compilation and use within the Eclipse development environment
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
Folder content and purpose
...
- Command line: Download and unzip the latest stable version of Ant from the [Apache site|http://ant.apache.org/bindownload.cgi.
. Check out all project folders from CVS, and then run the Ant command against the build.xml file provided in lbCVSDeploy. If successful, files will be created in /lbCVSDeploy/dist/.Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include - Eclipse: Open the build.xml file in the Eclipse Ant view and run the default task. If successful, refresh the /lbCVSDeploy folder; files will be created in /lbCVSDeploy/dist.
How to enable ydoc
- yDoc
offers the capability to add UML diagrams to the generated LexBIG JavaDoc.Multiexcerpt include nopanel true MultiExcerptName ExitDisclaimer PageWithExcerpt wikicontent:Exit Disclaimer to Include
If the yDoc directory is present and a valid license is located in the /yDoc/resources directory, the enhanced yDoc support is automatically enabled and used. If not, standard JavaDoc is produced.
...
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:
| Code Block | ||||
|---|---|---|---|---|
| ||||
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
|
...
Try the following values in the config.props file for the DB_URL:
| Code Block | ||||
|---|---|---|---|---|
| ||||
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=
|
...
A coding scheme manifest file is a valid XML file, conforming to the schema defined by http://LexGrid.org/schema/LexBIG/2007/01/CodingSchemeManifestList.xsd]
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
This XML file can define values for one or more coding schemes you are dealing with. Some coding scheme meta-information may not easily map to information in the source file. In this case a manifest file is of great help to bridge the gap and control the information flow while mapping to the LexGrid model. A detailed model of the LexGrid Coding Scheme and its fields can be found online. Structure of the schema for the manifest file is explained in the following table (manifest components refer to the original LexGrid model schema namespaces and types):
- Coding Scheme Manifest entry field: '''id'''
- Type: lgCommon:registeredName
- Required: Yes
- Override flag set: Not applicable
Description:
is
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
.Code Block Historical link 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.
- Coding Scheme Manifest entry field: '''codingScheme'''
- Type: lgBuiltin:localId
- Required: No
- Override flag set: Yes
- Description:
This value will be set for 'coding scheme name' in the LexGrid format counterpart. If the override flag is set to 'true', the value provided in the source file will be replaced with this one. Otherwise, this value is treated as a default value and used only if the value is not provided in the source file.
...
Here are some example coding scheme manifest entries:
| Code Block | ||||
|---|---|---|---|---|
| ||||
<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>
|
...
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:
| Code Block | ||||
|---|---|---|---|---|
| ||||
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.load()"
"org.LexGrid.LexBIG.Extensions.Load.OWL_Loader.validate()"
|
An example code snippet:
| Code Block | ||||
|---|---|---|---|---|
| ||||
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);
}
|
...
