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Updated build script for new third-party libraries and more parsimone…
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…ous use of JSBML. Corrections from SysBio (use of identifiers.org URIs instead of MIRIAM URNs) also adopted.
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@draeger
draeger committed Sep 14, 2015
1 parent c2e77c3 commit 36cf7c9
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Showing 2 changed files with 39 additions and 27 deletions.
66 changes: 39 additions & 27 deletions dist/build.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@
<filter token="date" value="${TODAY}"/>

<property name="Name" value="KEGGtranslator"/>
<property name="version" value="2.4"/>
<property name="version" value="2.5"/>
<property name="build.number" value="${DSTAMP}-${TSTAMP}"/>
<property name="build.name" value="${version} (build ${build.number})"/>
<property name="build.dir" value="${base}/build"/>
Expand Down Expand Up @@ -104,7 +104,7 @@

<!-- the path to JSBML -->
<property name="JSBMLPath" location="${base}/../JSBML" />
<property name="jsbml.version" value="1.0"/>
<property name="jsbml.version" value="1.1"/>

<!-- the path to SBML2LaTeX -->
<property name="SBML2LaTeXPath" location="${base}/../SBML2LaTeX" />
Expand Down Expand Up @@ -415,14 +415,20 @@
<exclude name="de.zbit.graph.SearchSupport"/>
<exclude name="de.zbit.graph.StackingNodeLayout"/>

<exclude name="de.zbit.graph.gui.options.GraphBackgroundImageProvider"/>
<exclude name="de.zbit.graph.gui.LayoutGraphPanel"/>
<exclude name="de.zbit.graph.gui.TranslatorGraphLayerPanel"/>
<exclude name="de.zbit.graph.gui.TranslatorSBMLgraphPanel"/>

<exclude name="de.zbit.graph.gui.options.*"/>

<exclude name="de.zbit.graph.io.*"/>
<exclude name="de.zbit.graph.io.def.GenericDataMap"/>
<exclude name="de.zbit.graph.io.def.SBGNVisualizationProperties"/>

<exclude name="de.zbit.graph.sbgn.*"/>

<exclude name="de.zbit.sbml.layout.y.*"/>

<exclude name="de.zbit.util.TranslatorTools"/>

<!-- Obfuscate the included y.jar -->
Expand Down Expand Up @@ -634,13 +640,13 @@
</path>

<echo message="Determining the revision number of SysBio"/>
<!--<exec executable="svn" outputproperty="${SysBioPath}/svninfo.xml">
<arg line="info MINUSMINUSxml ${SysBioPath}"/>
<exec executable="svn" outputproperty="${SysBioPath}/svninfo.xml">
<arg line="info --xml ${SysBioPath}"/>
</exec>
<xmlproperty collapseAttributes="true">
<propertyresource name="${SysBioPath}/svninfo.xml"/>
</xmlproperty>-->
<property name="sysbio.revision" value="1367"/> <!--${info.entry.revision}"/>-->
</xmlproperty>
<property name="sysbio.revision" value="${info.entry.revision}"/><!-- 1379 -->

<echo message="Deleting all previous versions of SysBio JAR files"/>
<delete verbose="true">
Expand Down Expand Up @@ -769,20 +775,21 @@


<echo message="Determining the revision number of JSBML"/>
<!--<exec executable="svn" outputproperty="${jsbml.dir}/svninfo.xml">
<arg line="info MINUSMINUSxml ${jsbml.dir}"/>
<exec executable="svn" outputproperty="${jsbml.dir}/svninfo.xml">
<arg line="info --xml ${jsbml.dir}"/>
</exec>
<xmlproperty collapseAttributes="true">
<propertyresource name="${jsbml.dir}/svninfo.xml"/>
</xmlproperty>-->
<property name="jsbml.revision" value="2116"/> <!-- ${info.entry.revision}"/>-->
</xmlproperty>
<property name="jsbml.revision" value="${info.entry.revision}"/><!-- 2358 -->

<echo message="Compiling the entire JSBML project for revision ${jsbml.revision}"/>
<delete dir="${jsbml.dir}/bin"/>
<mkdir dir="${jsbml.dir}/bin"/>

<path id="jsbml.classpath">
<fileset dir="${jsbml.dir}/core/lib" includes="**.jar, **/**.jar, **.zip"/>
<fileset dir="${jsbml.dir}/core/lib" includes="**.jar, **/**.jar, **.zip"/>
<fileset dir="${jsbml.dir}/modules/tidy/lib" includes="**.jar, **/**.jar, **.zip"/>
</path>

<!-- Compile JSBML including core and all extension packages -->
Expand All @@ -804,30 +811,34 @@
>
<!-- Source -->
<src path="${jsbml.dir}/core/src"/>
<src path="${jsbml.dir}/extensions/arrays/src"/>
<!--<src path="${jsbml.dir}/extensions/arrays/src"/>
<src path="${jsbml.dir}/extensions/comp/src"/>
<src path="${jsbml.dir}/extensions/dyn/src"/>
<src path="${jsbml.dir}/extensions/distrib/src"/>
<src path="${jsbml.dir}/extensions/dyn/src"/>-->
<src path="${jsbml.dir}/extensions/fbc/src"/>
<src path="${jsbml.dir}/extensions/groups/src"/>
<src path="${jsbml.dir}/extensions/layout/src"/>
<src path="${jsbml.dir}/extensions/multi/src"/>
<!--<src path="${jsbml.dir}/extensions/multi/src"/>-->
<src path="${jsbml.dir}/extensions/qual/src"/>
<src path="${jsbml.dir}/extensions/render/src"/>
<!--<src path="${jsbml.dir}/extensions/render/src"/>
<src path="${jsbml.dir}/extensions/req/src"/>
<src path="${jsbml.dir}/extensions/spatial/src"/>
<src path="${jsbml.dir}/extensions/spatial/src"/>-->
<src path="${jsbml.dir}/modules/tidy/src"/>
<!-- Resources -->
<src path="${jsbml.dir}/core/resources"/>
<src path="${jsbml.dir}/extensions/arrays/resources"/>
<!--<src path="${jsbml.dir}/extensions/arrays/resources"/>
<src path="${jsbml.dir}/extensions/comp/resources"/>
<src path="${jsbml.dir}/extensions/dyn/resources"/>
<src path="${jsbml.dir}/extensions/distrib/resources"/>
<src path="${jsbml.dir}/extensions/dyn/resources"/>-->
<src path="${jsbml.dir}/extensions/fbc/resources"/>
<src path="${jsbml.dir}/extensions/groups/resources"/>
<src path="${jsbml.dir}/extensions/layout/resources"/>
<src path="${jsbml.dir}/extensions/multi/resources"/>
<!--<src path="${jsbml.dir}/extensions/multi/resources"/>-->
<src path="${jsbml.dir}/extensions/qual/resources"/>
<src path="${jsbml.dir}/extensions/render/resources"/>
<!--<src path="${jsbml.dir}/extensions/render/resources"/>
<src path="${jsbml.dir}/extensions/req/resources"/>
<src path="${jsbml.dir}/extensions/spatial/resources"/>
<src path="${jsbml.dir}/extensions/spatial/resources"/>-->
<src path="${jsbml.dir}/modules/tidy/resources"/>
</javac>

<copy file="${jsbml.dir}/AUTHORS.txt" tofile="${jsbml.dir}/core/licenses/JSBML-AUTHORS.txt"/>
Expand Down Expand Up @@ -882,17 +893,17 @@
/>
<!-- Resources -->
<fileset dir="${jsbml.dir}/core/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/arrays/resources" includes="${jsbml.includes}"/>
<!--<fileset dir="${jsbml.dir}/extensions/arrays/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/comp/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/dyn/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/dyn/resources" includes="${jsbml.includes}"/>-->
<fileset dir="${jsbml.dir}/extensions/fbc/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/groups/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/layout/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/multi/resources" includes="${jsbml.includes}"/>
<!--<fileset dir="${jsbml.dir}/extensions/multi/resources" includes="${jsbml.includes}"/>-->
<fileset dir="${jsbml.dir}/extensions/qual/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/render/resources" includes="${jsbml.includes}"/>
<!--<fileset dir="${jsbml.dir}/extensions/render/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/req/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/spatial/resources" includes="${jsbml.includes}"/>
<fileset dir="${jsbml.dir}/extensions/spatial/resources" includes="${jsbml.includes}"/>-->
<!-- 3rd party libraries -->
<zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/**.java readme.txt LICENSE" src="${jsbml.dir}/core/lib/biojava3-ontology-3.1.0.jar"/>
<zipfileset excludes="${EXCL}" src="${jsbml.dir}/core/lib/jigsaw-dateParser.jar"/>
Expand All @@ -903,6 +914,7 @@
<zipfileset excludes="${EXCL}" src="${jsbml.dir}/core/lib/woodstox-core-lgpl-4.0.9.jar"/>
<zipfileset excludes="${EXCL}" src="${jsbml.dir}/core/lib/xstream-1.3.1.jar"/>
<zipfileset excludes="${EXCL}" src="${jsbml.dir}/core/lib/spi-full-0.2.4.jar"/>
<zipfileset excludes="${EXCL}" src="${jsbml.dir}/modules/tidy/lib/jtidy-r938.jar"/>
</jar>

<!-- Remove temporary file again: -->
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