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mkutmonmkutmon
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generic regin creator that reads tab separated files and creates xgmml files based on config file
1 parent 4b99fd9 commit 8410b82

21 files changed

+1174
-5
lines changed

‎.gitignore

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*.class
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# Package Files #
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*.jar
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*.war
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*.ear
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GenericCreator/.settings*
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GenericCreator/dist*
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.metadata*

‎GenericCreator/.classpath

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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" path="src"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7"/>
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<classpathentry kind="lib" path="lib/jdom.jar"/>
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<classpathentry kind="lib" path="lib/jewelcli-0.6.jar"/>
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<classpathentry kind="lib" path="lib/derby.jar"/>
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<classpathentry kind="lib" path="lib/org.bridgedb.bio.jar"/>
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<classpathentry kind="lib" path="lib/org.bridgedb.jar"/>
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<classpathentry kind="lib" path="lib/org.bridgedb.rdb.jar"/>
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<classpathentry kind="output" path="bin"/>
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</classpath>

‎GenericCreator/.project

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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>GenericCreator</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.jdt.core.javanature</nature>
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</natures>
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</projectDescription>

‎GenericCreator/build.xml

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<?xml version="1.0"?>
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<project name="CyTargetLinker conversion scripts" default="dist" basedir=".">
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<property name="src.dir" value="src"/>
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<property name="build.dir" value="build"/>
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<property name="lib.dir" value="lib"/>
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<property name="dist.dir" value="dist"/>
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<property name="jar.name" value="conversion.jar"/>
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<path id="class.path">
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<fileset dir="lib">
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<include name="*.jar"/>
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</fileset>
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</path>
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<target name="prepare">
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<mkdir dir="${build.dir}"/>
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<mkdir dir="${dist.dir}"/>
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</target>
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<target name="clean" description="Remove all generated files.">
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<delete dir="${build.dir}"/>
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<delete dir="${dist.dir}"/>
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<delete file="${jar.name}"/>
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</target>
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<target name="compile" depends="prepare" description="Compile sources">
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<javac srcdir="${src.dir}"
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includes="**"
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destdir="${build.dir}"
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debug="true"
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source="1.5">
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<classpath refid="class.path"/>
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</javac>
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</target>
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<target name="jar" depends="compile" description="Generates executable jar file">
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<pathconvert refid="class.path" property="class.path.manifest" pathsep=" ">
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<mapper>
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<chainedmapper>
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<!-- remove absolute path -->
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<flattenmapper />
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<!-- add lib/ prefix -->
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<globmapper from="*" to="lib/*" />
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</chainedmapper>
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</mapper>
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</pathconvert>
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<jar jarfile="${jar.name}">
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<manifest>
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<attribute name="Class-Path" value="${class.path.manifest}"/>
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<attribute name="Main-Class" value="org.regin.creator.GenericCreator"/>
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</manifest>
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<fileset dir="${build.dir}" includes="**/*"/>
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<fileset dir="${src.dir}" includes="**/*.groovy"/>
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</jar>
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</target>
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<target name="dist" depends="jar" description="Copies jar and external libraries to dist path">
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<copy file="${jar.name}" toDir="${dist.dir}"/>
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<copy toDir="${dist.dir}/lib">
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<fileset dir="${lib.dir}">
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<include name="**/*.jar"/>
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</fileset>
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</copy>
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<delete file="${jar.name}"/>
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</target>
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</project>

‎GenericCreator/derby.log

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----------------------------------------------------------------
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2013-10-31 14:35:33.121 GMT:
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Booting Derby version The Apache Software Foundation - Apache Derby - 10.4.2.0 - (689064): instance a816c00e-0142-0ef0-d2d9-0000032e68f8
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on database directory jar:(/home/martina/Data/Pathvisio/databases/mirbase-v19.bridge)database in READ ONLY mode
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Database Class Loader started - derby.database.classpath=''
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----------------------------------------------------------------
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2013-10-31 14:35:33.768 GMT:
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Booting Derby version The Apache Software Foundation - Apache Derby - 10.4.2.0 - (689064): instance 582f8014-0142-0ef0-d2d9-0000032e68f8
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on database directory jar:(/home/martina/Data/Pathvisio/databases/Hs_Derby_20130701.bridge)database in READ ONLY mode
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Database Class Loader started - derby.database.classpath=''

‎GenericCreator/lib/derby.jar

2.45 MB
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‎GenericCreator/lib/jdom.jar

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‎GenericCreator/lib/jewelcli-0.6.jar

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‎GenericCreator/lib/org.bridgedb.bio.jar

21.6 KB
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‎GenericCreator/lib/org.bridgedb.jar

33.6 KB
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‎GenericCreator/lib/org.bridgedb.rdb.jar

21.4 KB
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