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[Sbfc-svn] SF.net SVN: sbfc:[731] trunk
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From: <nik...@us...> - 2018-05-25 12:02:13
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Revision: 731
http://sourceforge.net/p/sbfc/code/731
Author: niko-rodrigue
Date: 2018-05-25 12:02:10 +0000 (Fri, 25 May 2018)
Log Message:
-----------
corrected linux scripts to include the paxtools jar. Put back the creation of BioPAX EntityReferences that will old the annotations
Modified Paths:
--------------
trunk/build.xml
trunk/lib/sbfc-1.3.8-SNAPSHOT.jar
trunk/sbfConverter.sh
trunk/sbfConverterGUI.sh
trunk/sbfConverterList.sh
trunk/sbfModelList.sh
trunk/sbml2biopax.sh
trunk/sbml2biopax3.bat
trunk/sbml2biopax3.sh
trunk/sbml2biopax_gsoc16.sh
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_Tramy.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l2.java
trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java
trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/build.xml 2018-05-25 12:02:10 UTC (rev 731)
@@ -59,7 +59,7 @@
<include name="*.jar"/>
<exclude name="{name}.jar"/>
</fileset>
- <fileset dir="${jars.dir}/paxtools-4.2/">
+ <fileset dir="${jars.dir}/paxtools/">
<include name="*.jar"/>
<exclude name="{name}.jar"/>
</fileset>
@@ -271,7 +271,7 @@
<!-- all the dependencies jars -->
<zipgroupfileset dir="${jars.dir}" includes="*.jar" />
<!-- latest paxtools jar -->
- <zipgroupfileset dir="${jars.dir}/paxtools-4.2" includes="*.jar" />
+ <zipgroupfileset dir="${jars.dir}/paxtools" includes="*.jar" />
</jar>
</target>
@@ -305,7 +305,7 @@
<!-- Copy all the dependencies jar files -->
<copy todir="${dist.dir}/lib"><fileset dir="${jars.dir}/" includes="*.jar"/></copy>
<copy todir="${dist.dir}/lib/pathvisio"><fileset dir="${jars.dir}/pathvisio/" includes="*.jar"/></copy>
- <copy todir="${dist.dir}/lib/paxtools-4.2"><fileset dir="${jars.dir}/paxtools-4.2/" includes="*.jar"/></copy>
+ <copy todir="${dist.dir}/lib/paxtools"><fileset dir="${jars.dir}/paxtools/" includes="*.jar"/></copy>
<copy todir="${dist.dir}">
@@ -342,7 +342,7 @@
<!-- Restores the *.sh and lib folder -->
<copy todir="${dist.dir}/lib"><fileset dir="${jars.dir}/" includes="*.jar"/></copy>
<copy todir="${dist.dir}/lib/pathvisio"><fileset dir="${jars.dir}/pathvisio/" includes="*.jar"/></copy>
- <copy todir="${dist.dir}/lib/paxtools-4.2"><fileset dir="${jars.dir}/paxtools-4.2/" includes="*.jar"/></copy>
+ <copy todir="${dist.dir}/lib/paxtools"><fileset dir="${jars.dir}/paxtools/" includes="*.jar"/></copy>
<copy todir="${dist.dir}">
<fileset dir="${basedir}/" includes="*.sh *.bat"/>
@@ -465,7 +465,7 @@
<!-- Including only the necessary jar files -->
<copy todir="${dist.dir}/lib"><fileset dir="${jars.dir}/" includes="jsbml*.jar ${name}-${version}.jar miriam*"/></copy>
- <copy todir="${dist.dir}/lib/paxtools-4.2"><fileset dir="${jars.dir}/paxtools-4.2/" includes="*.jar"/></copy>
+ <copy todir="${dist.dir}/lib/paxtools"><fileset dir="${jars.dir}/paxtools/" includes="*.jar"/></copy>
<antcall target="converter.generic.package"/>
Modified: trunk/lib/sbfc-1.3.8-SNAPSHOT.jar
===================================================================
(Binary files differ)
Modified: trunk/sbfConverter.sh
===================================================================
--- trunk/sbfConverter.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbfConverter.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -70,7 +70,11 @@
if [ ${PATHVISIO_CONVERTER} == "no" ];
then
- export CLASSPATH=$CLASSPATH:$LIB_PATH/paxtools/paxtools*.jar
+ for jarFile in $LIB_PATH/paxtools/*.jar
+ do
+ export CLASSPATH=$CLASSPATH:$jarFile
+ done
+
else
for jarFile in $LIB_PATH/pathvisio/*.jar
do
Modified: trunk/sbfConverterGUI.sh
===================================================================
--- trunk/sbfConverterGUI.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbfConverterGUI.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -23,7 +23,10 @@
do
export CLASSPATH=$CLASSPATH:$jarFile
done
-export CLASSPATH=$CLASSPATH:$LIB_PATH/paxtools/paxtools*.jar
+for jarFile in $LIB_PATH/paxtools/*.jar
+do
+ export CLASSPATH=$CLASSPATH:$jarFile
+done
java -Dmiriam.xml.export=${SBF_CONVERTER_HOME}/miriam.xml org.sbfc.converter.ConverterGUI
Modified: trunk/sbfConverterList.sh
===================================================================
--- trunk/sbfConverterList.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbfConverterList.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -11,7 +11,10 @@
do
export CLASSPATH=$CLASSPATH:$jarFile
done
-export CLASSPATH=$CLASSPATH:$LIB_PATH/paxtools/paxtools-*.jar
+for jarFile in $LIB_PATH/paxtools/*.jar
+do
+ export CLASSPATH=$CLASSPATH:$jarFile
+done
COMMAND="java "
Modified: trunk/sbfModelList.sh
===================================================================
--- trunk/sbfModelList.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbfModelList.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -11,7 +11,10 @@
do
export CLASSPATH=$CLASSPATH:$jarFile
done
-export CLASSPATH=$CLASSPATH:$LIB_PATH/paxtools/paxtools*.jar
+for jarFile in $LIB_PATH/paxtools/*.jar
+do
+ export CLASSPATH=$CLASSPATH:$jarFile
+done
COMMAND="java "
Modified: trunk/sbml2biopax.sh
===================================================================
--- trunk/sbml2biopax.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbml2biopax.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -6,7 +6,7 @@
SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
-${SBF_CONVERTER_HOME}/sbml2biopax2.sh $@
+# ${SBF_CONVERTER_HOME}/sbml2biopax2.sh $@
${SBF_CONVERTER_HOME}/sbml2biopax3.sh $@
Modified: trunk/sbml2biopax3.bat
===================================================================
--- trunk/sbml2biopax3.bat 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbml2biopax3.bat 2018-05-25 12:02:10 UTC (rev 731)
@@ -4,4 +4,4 @@
set CONVERTER_HOME=%~dp0
-%CONVERTER_HOME%\sbfConverter.bat SBMLModel SBML2BioPAX_l3 %*
+%CONVERTER_HOME%\sbfConverter.bat SBMLModel SBML2BioPAX_Tramy %*
Modified: trunk/sbml2biopax3.sh
===================================================================
--- trunk/sbml2biopax3.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbml2biopax3.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -7,5 +7,5 @@
SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
-${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel SBML2BioPAX_l3 $1
+${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel SBML2BioPAX_Tramy $1
Modified: trunk/sbml2biopax_gsoc16.sh
===================================================================
--- trunk/sbml2biopax_gsoc16.sh 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/sbml2biopax_gsoc16.sh 2018-05-25 12:02:10 UTC (rev 731)
@@ -5,6 +5,6 @@
SBF_CONVERTER_HOME=`dirname ${RESOLVE_LINK}`
-${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel SBML2BioPAX_Arman $1
+${SBF_CONVERTER_HOME}/sbfConverter.sh SBMLModel SBML2BioPAX_Tramy $1
Modified: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_Tramy.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_Tramy.java 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_Tramy.java 2018-05-25 12:02:10 UTC (rev 731)
@@ -99,7 +99,7 @@
@Override
public String getName() {
- return "SBML2BioPAX GSOC 2016";
+ return "SBML2BioPAX";
}
@Override
Modified: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l2.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l2.java 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l2.java 2018-05-25 12:02:10 UTC (rev 731)
@@ -316,7 +316,7 @@
@Override
public String getName() {
- return "SBML2BioPAX_l2";
+ return "SBML to BioPAX Level 2 (old)";
}
@Override
Modified: trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/src/org/sbfc/converter/sbml2biopax/SBML2BioPAX_l3.java 2018-05-25 12:02:10 UTC (rev 731)
@@ -43,7 +43,7 @@
@Override
public String getName() {
- return "SBML2BioPAX_l3";
+ return "SBML to BioPAX Level 3 (old converter)";
}
@Override
Modified: trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java
===================================================================
--- trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2018-05-24 14:35:27 UTC (rev 730)
+++ trunk/src/org/sbfc/converter/sbml2biopax/arman/SBML2BioPAXUtilities.java 2018-05-25 12:02:10 UTC (rev 731)
@@ -36,7 +36,6 @@
import org.biopax.paxtools.model.level3.GeneticInteraction;
import org.biopax.paxtools.model.level3.Interaction;
import org.biopax.paxtools.model.level3.KPrime;
-import org.biopax.paxtools.model.level3.Modulation;
import org.biopax.paxtools.model.level3.MolecularInteraction;
import org.biopax.paxtools.model.level3.Named;
import org.biopax.paxtools.model.level3.Pathway;
@@ -58,6 +57,7 @@
import org.biopax.paxtools.model.level3.Transport;
import org.biopax.paxtools.model.level3.TransportWithBiochemicalReaction;
import org.biopax.paxtools.model.level3.UnificationXref;
+import org.biopax.paxtools.model.level3.XReferrable;
import org.biopax.paxtools.model.level3.Xref;
import org.identifiers.registry.RegistryUtilities;
import org.identifiers.registry.data.DataType;
@@ -585,26 +585,31 @@
*/
public <T extends SimplePhysicalEntity, S extends EntityReference> T convertSpeciesToSPE(Model bpModel, Class<T> entityClass, Class<S> refClass, Species species) {
T entity = createBPEfromSBMLE(bpModel, entityClass, species);
- for (Xref xref : generateXrefsForSBase(bpModel, species)) {
- entity.addXref(xref);
- }
+ Set<Xref> xrefs = generateXrefsForSBase(bpModel, species);
+
+// for (Xref xref : xrefs) {
+// entity.addXref(xref);
+// }
+
+
// TODO: check if there is an sbml group element that can be used to create the biopax entityReference
// TODO - if the group package is not defined and/or we could not linked a group to the species, create a new EntityReference for the species
/*
- * old deleted code to put back
- *
+ * case where there are no sbml group associated with the Species
+ * We create an EntityReference for each Species.
+ */
HashSet<XReferrable> ers = new HashSet<XReferrable>();
- for (Xref xref : xrefs) {
- for (XReferrable xReferrable : xref.getXrefOf()) {
- // Only add the entity references
- if(xReferrable instanceof EntityReference) {
- ers.add(xReferrable);
- }
- }
- }
+ for (Xref xref : xrefs) {
+ for (XReferrable xReferrable : xref.getXrefOf()) {
+ // Only add the entity references
+ if(xReferrable instanceof EntityReference) {
+ ers.add(xReferrable);
+ }
+ }
+ }
S reference;
if(ers.isEmpty()) {
@@ -615,17 +620,16 @@
} else if(ers.size() == 1) { // There shouldn't be more than one
reference = (S) ers.iterator().next();
} else {
- log.warn(
- "There are more than one EntityReferences that match with the same unification xref for species: "
- + species.getName()
- + ". Picking the first one: "
- + ers.iterator().next().getRDFId()
- );
+ log.warn(
+ "There are more than one EntityReferences that match with the same unification xref for species: "
+ + species.getName()
+ + ". Picking the first one: "
+ + ers.iterator().next().getUri()
+ );
- reference = (S) ers.iterator().next();
+ reference = (S) ers.iterator().next();
}
- T entity = createBPEfromSBMLE(bpModel, entityClass, species);
entity.setEntityReference(reference);
// Clean-up non-used xrefs
@@ -633,9 +637,8 @@
if(xref.getXrefOf().isEmpty()) {
bpModel.remove(xref);
}
- }*/
+ }
- //entity.setEntityReference(reference);
return entity;
}
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