From 0e9f18f5c9ae54ce97be10d4074579cace70a678 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 18:02:43 +0100
Subject: [PATCH] export of modifier type added
---
.../sbml/reaction/SBOTermModifierType.java | 24 +++++++-
.../sbml/reaction/SbmlReactionExporter.java | 4 ++
.../sbml/reaction/SbmlReactionParser.java | 55 ++++++++++---------
.../sbml/GenericSbmlToXmlParserTest.java | 3 +-
.../sbml/species/SbmlSpeciesParserTest.java | 2 +
5 files changed, 59 insertions(+), 29 deletions(-)
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
index 605f4b8c5f..580deecbb6 100644
--- 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
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
import org.apache.log4j.Logger;
@@ -19,7 +19,7 @@ public enum SBOTermModifierType {
;
private static Logger logger = Logger.getLogger(SBOTermModifierType.class);
- private Set<String> sboTerms = new HashSet<>();
+ private List<String> sboTerms = new ArrayList<>();
Class<? extends Modifier> clazz;
private SBOTermModifierType(Class<? extends Modifier> clazz, String[] inputSboTerms) {
@@ -47,4 +47,22 @@ public enum SBOTermModifierType {
}
return result;
}
+
+ public static String getTermByType(Class<? extends Modifier> clazz) {
+ for (SBOTermModifierType term : values()) {
+ if (clazz.equals(term.clazz)) {
+ return term.getSBO();
+ }
+ }
+ logger.warn("Cannot find SBO term for class: " + clazz);
+ return null;
+ }
+
+ private String getSBO() {
+ if (sboTerms.size() != 0) {
+ return sboTerms.get(0);
+ }
+ logger.warn("Cannot find SBO term for class: " + clazz);
+ return null;
+ }
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
index 67e1391847..ef9da4db73 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java
@@ -78,6 +78,10 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(modifier.getElement().getElementId());
SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
speciesReferenceByReactionNode.put(modifier, speciesReference);
+ String term = SBOTermModifierType.getTermByType(modifier.getClass());
+ if (term != null) {
+ speciesReference.setSBOTerm(term);
+ }
}
if (reaction.getKinetics() != null) {
result.setKineticLaw(createKineticLaw(reaction));
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 876a08866d..af039111eb 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
@@ -109,32 +109,33 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
Class<? extends ReactionNode> nodeClass = null;
- switch (speciesRefernceGlyph.getRole()) {
- case ACTIVATOR:
- nodeClass = Trigger.class;
- break;
- case INHIBITOR:
- nodeClass = Inhibition.class;
- break;
- case MODIFIER:
- nodeClass = Modulation.class;
- break;
- case PRODUCT:
- nodeClass = Product.class;
- break;
- case SIDEPRODUCT:
- nodeClass = Product.class;
- break;
- case SIDESUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case SUBSTRATE:
- nodeClass = Reactant.class;
- break;
- case UNDEFINED:
- nodeClass = null;
- break;
+ if (speciesRefernceGlyph.getRole() != null) {
+ switch (speciesRefernceGlyph.getRole()) {
+ case ACTIVATOR:
+ nodeClass = Trigger.class;
+ break;
+ case INHIBITOR:
+ nodeClass = Inhibition.class;
+ break;
+ case PRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDEPRODUCT:
+ nodeClass = Product.class;
+ break;
+ case SIDESUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case SUBSTRATE:
+ nodeClass = Reactant.class;
+ break;
+ case UNDEFINED:
+ case MODIFIER:
+ nodeClass = null;
+ break;
+ }
}
+
if (reactionWithLayout.isReversible() && (nodeClass == Reactant.class || nodeClass == Product.class)) {
nodeClass = null;
}
@@ -148,7 +149,11 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
}
+ if (nodeClass == Modifier.class) {
+ nodeClass = Modulation.class;
+ }
if (minervaNode == null) {
+ logger.debug(nodeClass);
throw new InvalidInputDataExecption(
"Cannot find reaction node for layouted reaction: " + speciesGlyph.getSpecies() + ", " + glyph.getId());
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index 4b17dfa771..c3f9c5bfa6 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -53,6 +53,7 @@ public class GenericSbmlToXmlParserTest {
@Test
public void toXmlModelTest() throws Exception {
try {
+
String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
IConverter converter = new SbmlParser();
@@ -64,7 +65,7 @@ public class GenericSbmlToXmlParserTest {
+ filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
String xmlFilePath = pathWithouExtension.concat(".xml");
converter.exportModelToFile(model, xmlFilePath);
-
+
Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath));
model2.setName(null);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
index 2a049eecec..c82b00a7e4 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParserTest.java
@@ -6,6 +6,7 @@ import java.io.FileNotFoundException;
import org.apache.log4j.Logger;
import org.junit.Test;
+import org.sbml.jsbml.SBMLDocument;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -128,4 +129,5 @@ public class SbmlSpeciesParserTest {
assertTrue(element instanceof Unknown);
}
+
}
--
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