From 791b6fafd086cd828e13a8c0c67a7c7cf3134369 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 16:22:42 +0100
Subject: [PATCH] parsing of sbo terms for modifiers added
---
.../sbml/reaction/SBOTermModifierType.java | 50 ++++++++++++++++
.../sbml/reaction/SbmlReactionParser.java | 13 ++++-
.../model/sbml/AllSbmlConverterTests.java | 2 +
.../sbml/reaction/SbmlReactionParserTest.java | 57 +++++++++++++++++++
.../testFiles/small/modifier/catalysis.xml | 45 +++++++++++++++
.../testFiles/small/modifier/inhibition.xml | 45 +++++++++++++++
.../small/modifier/unknown_catalysis.xml | 45 +++++++++++++++
.../small/modifier/unknown_inhibition.xml | 45 +++++++++++++++
8 files changed, 299 insertions(+), 3 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
create mode 100644 converter-sbml/testFiles/small/modifier/catalysis.xml
create mode 100644 converter-sbml/testFiles/small/modifier/inhibition.xml
create mode 100644 converter-sbml/testFiles/small/modifier/unknown_catalysis.xml
create mode 100644 converter-sbml/testFiles/small/modifier/unknown_inhibition.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
new file mode 100644
index 0000000000..605f4b8c5f
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java
@@ -0,0 +1,50 @@
+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+
+public enum SBOTermModifierType {
+ CATALYSIS(Catalysis.class, new String[] { "SBO:0000013" }), //
+ INHIBITION(Inhibition.class, new String[] { "SBO:0000537" }), //
+ UNKNOWN_CATALYSIS(UnknownCatalysis.class, new String[] { "SBO:0000462" }), //
+ UNKNOWN_INHIBITION(UnknownInhibition.class, new String[] { "SBO:0000536" }), //
+ ;
+
+ private static Logger logger = Logger.getLogger(SBOTermModifierType.class);
+ private Set<String> sboTerms = new HashSet<>();
+ Class<? extends Modifier> clazz;
+
+ private SBOTermModifierType(Class<? extends Modifier> clazz, String[] inputSboTerms) {
+ this.clazz = clazz;
+ for (String string : inputSboTerms) {
+ sboTerms.add(string);
+ }
+ }
+
+ public static Class<? extends Modifier> getTypeSBOTerm(String sboTerm) {
+ if (sboTerm == null || sboTerm.isEmpty()) {
+ return Modifier.class;
+ }
+ Class<? extends Modifier> result = null;
+ for (SBOTermModifierType term : values()) {
+ for (String string : term.sboTerms) {
+ if (string.equalsIgnoreCase(sboTerm)) {
+ result = term.clazz;
+ }
+ }
+ }
+ if (result == null) {
+ logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
+ result = Modifier.class;
+ }
+ return result;
+ }
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index bbd35ecbd8..d92ca8f6ea 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -235,7 +235,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
operator.setLine(line);
reactionWithLayout.addNode(operator);
}
- minervaModel.addReaction(new StateTransitionReaction(reactionWithLayout));
+ minervaModel.addReaction(reactionWithLayout);
} catch (InvalidArgumentException e) {
throw new InvalidInputDataExecption(e);
}
@@ -295,7 +295,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
for (ModifierSpeciesReference modifier : sbmlReaction.getListOfModifiers()) {
Species element = minervaModel.getElementByElementId(modifier.getSpecies());
- reaction.addModifier(new Modifier(element));
+ Class<? extends Modifier> nodeClass = SBOTermModifierType.getTypeSBOTerm(modifier.getSBOTermID());
+ try {
+ Modifier newNode = nodeClass.getConstructor(Element.class).newInstance(element);
+ reaction.addModifier(newNode);
+ } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException
+ | NoSuchMethodException | SecurityException e) {
+ throw new InvalidInputDataExecption("Problem with creating modifier", e);
+ }
}
return reaction;
@@ -306,7 +313,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
result.setDefinition(kineticLaw.getMath().toMathML());
SbmlParameterParser parameterParser = new SbmlParameterParser(minervaModel);
- result.addParameters(parameterParser.parseList((Collection<LocalParameter>)kineticLaw.getListOfLocalParameters()));
+ result.addParameters(parameterParser.parseList((Collection<LocalParameter>) kineticLaw.getListOfLocalParameters()));
try {
Node node = super.getXmlDocumentFromString(result.getDefinition());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index c6ec3e57c9..8996139330 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -4,6 +4,7 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
+import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParserTest;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
@RunWith(Suite.class)
@@ -12,6 +13,7 @@ import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParserTest;
SbmlExporterTest.class, //
SbmlPareserForInvalidReactionTest.class, //
SbmlParserTest.class, //
+ SbmlReactionParserTest.class, //
SbmlSpeciesParserTest.class,//
})
public class AllSbmlConverterTests {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
new file mode 100644
index 0000000000..ac66ea7393
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
@@ -0,0 +1,57 @@
+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.FileNotFoundException;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbml.SbmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.modifier.Catalysis;
+import lcsb.mapviewer.model.map.modifier.Inhibition;
+import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
+import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+public class SbmlReactionParserTest {
+ Logger logger = Logger.getLogger(SbmlReactionParserTest.class);
+ SbmlParser parser = new SbmlParser();
+
+ @Test
+ public void testParseCatalysis() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/modifier/catalysis.xml"));
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction);
+ assertTrue(reaction.getModifiers().iterator().next() instanceof Catalysis);
+ }
+
+ @Test
+ public void testParseInhibition() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/modifier/inhibition.xml"));
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction);
+ assertTrue(reaction.getModifiers().iterator().next() instanceof Inhibition);
+ }
+
+ @Test
+ public void testParseUnknownCatalysis() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/modifier/unknown_catalysis.xml"));
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction);
+ assertTrue(reaction.getModifiers().iterator().next() instanceof UnknownCatalysis);
+ }
+
+ @Test
+ public void testParseUnknownInhibition() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/small/modifier/unknown_inhibition.xml"));
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction);
+ assertTrue(reaction.getModifiers().iterator().next() instanceof UnknownInhibition);
+ }
+
+}
diff --git a/converter-sbml/testFiles/small/modifier/catalysis.xml b/converter-sbml/testFiles/small/modifier/catalysis.xml
new file mode 100644
index 0000000000..5e7ce9c465
--- /dev/null
+++ b/converter-sbml/testFiles/small/modifier/catalysis.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species compartment="cell" initialConcentration="1" id="s1" name="nm1">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s2" name="nm2">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s3" name="nm3">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="re1">
+ <listOfReactants>
+ <speciesReference species="s1" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s2" stoichiometry="1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="s3" sboTerm="SBO:0000013"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/small/modifier/inhibition.xml b/converter-sbml/testFiles/small/modifier/inhibition.xml
new file mode 100644
index 0000000000..e40bd9cb5f
--- /dev/null
+++ b/converter-sbml/testFiles/small/modifier/inhibition.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species compartment="cell" initialConcentration="1" id="s1" name="nm1">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s2" name="nm2">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s3" name="nm3">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="re1">
+ <listOfReactants>
+ <speciesReference species="s1" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s2" stoichiometry="1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="s3" sboTerm="SBO:0000537"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/small/modifier/unknown_catalysis.xml b/converter-sbml/testFiles/small/modifier/unknown_catalysis.xml
new file mode 100644
index 0000000000..d3f6a2c8e1
--- /dev/null
+++ b/converter-sbml/testFiles/small/modifier/unknown_catalysis.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species compartment="cell" initialConcentration="1" id="s1" name="nm1">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s2" name="nm2">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s3" name="nm3">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="re1">
+ <listOfReactants>
+ <speciesReference species="s1" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s2" stoichiometry="1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="s3" sboTerm="SBO:0000462"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file
diff --git a/converter-sbml/testFiles/small/modifier/unknown_inhibition.xml b/converter-sbml/testFiles/small/modifier/unknown_inhibition.xml
new file mode 100644
index 0000000000..ae574907ea
--- /dev/null
+++ b/converter-sbml/testFiles/small/modifier/unknown_inhibition.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+ <model id="TestGEN">
+ <annotation/>
+ <listOfCompartments>
+ <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+ <annotation>
+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+ <rdf:Description rdf:about="#">
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ </rdf:Description>
+ </rdf:RDF>
+ </annotation>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species compartment="cell" initialConcentration="1" id="s1" name="nm1">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s2" name="nm2">
+ <annotation/>
+ </species>
+ <species compartment="cell" initialConcentration="1" id="s3" name="nm3">
+ <annotation/>
+ </species>
+ </listOfSpecies>
+ <listOfReactions>
+ <reaction id="re1">
+ <listOfReactants>
+ <speciesReference species="s1" stoichiometry="1"/>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference species="s2" stoichiometry="1"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="s3" sboTerm="SBO:0000536"/>
+ </listOfModifiers>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file
--
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