From 97f0c33a90d2b8fe702fe6c5d8b75a11a18ed844 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 9 Jan 2018 15:43:32 +0100
Subject: [PATCH] export of sbml reaction with few graphical representation
handled
---
.../model/sbml/SbmlBioEntityParser.java | 6 ++++
.../converter/model/sbml/SbmlParser.java | 5 +--
.../model/sbml/SbmlReactionExporter.java | 31 +++++++++++++++++--
.../model/sbml/SbmlReactionParser.java | 2 +-
.../model/sbml/SbmlExporterTest.java | 28 +++++++++++++++++
.../layout/ApplyLayoutModelCommand.java | 19 ++++++++++--
.../layout/ApplySimpleLayoutModelCommand.java | 16 ++++++++--
.../layout/ApplyLayoutModelCommandTest.java | 4 +--
8 files changed, 99 insertions(+), 12 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index c4fcd05ea7..2a03a7bd52 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -21,6 +21,8 @@ public class SbmlBioEntityParser {
protected Layout layout;
protected lcsb.mapviewer.model.map.model.Model minervaModel;
+ private int idCounter = 0;
+
public SbmlBioEntityParser() {
super();
}
@@ -65,4 +67,8 @@ public class SbmlBioEntityParser {
return notes;
}
+ protected String getNextId() {
+ return (idCounter++) + "";
+ }
+
}
\ No newline at end of file
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 8014fbbc69..b72c589162 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -59,6 +59,7 @@ public class SbmlParser implements IConverter {
model.setIdModel(sbmlModel.getId());
Layout layout = getSbmlLayout(sbmlModel);
+ boolean layoutExists = layout != null;
SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
@@ -72,7 +73,7 @@ public class SbmlParser implements IConverter {
model.addElements(speciesParser.parseList(sbmlModel));
model.addReactions(reactionParser.parseList(sbmlModel));
- if (layout != null) {
+ if (layoutExists) {
if (layout.getDimensions() != null) {
model.setWidth(layout.getDimensions().getWidth());
model.setHeight(layout.getDimensions().getHeight());
@@ -149,7 +150,7 @@ public class SbmlParser implements IConverter {
}
}
try {
- new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout).execute();
+ new ApplySimpleLayoutModelCommand(model, bioEntitesRequiringLayout, true).execute();
} catch (CommandExecutionException e) {
throw new InvalidInputDataExecption("Problem with generating layout", e);
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
index 55b4d7cac4..82f63a0e25 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
@@ -40,7 +40,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
@Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
- org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
+ String reactionId = getReactionId(reaction);
+ logger.debug(reactionId);
+ org.sbml.jsbml.Reaction result = super.sbmlElementByElementId.get(reactionId);
+ if (result != null) {
+ return result;
+ }
+ result = sbmlModel.createReaction(reactionId);
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
@@ -59,9 +65,30 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return result;
}
+ private String getReactionId(Reaction reaction) {
+ int separatorIndex = reaction.getElementId().indexOf("__");
+ if (separatorIndex > 0) {
+ return reaction.getElementId().substring(0, separatorIndex);
+ }
+ return reaction.getElementId();
+ }
+
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
- ReactionGlyph reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+ int separatorIndex = glyphId.indexOf("__");
+ if (separatorIndex > 0) {
+ glyphId = glyphId.substring(separatorIndex + 2);
+ }
+ logger.debug(glyphId);
+ ReactionGlyph reactionGlyph;
+ try {
+ // handle case when input data cannot doesn't come from SBML parser and contains
+ // "__" that mess up identifier uniqueness
+ reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+ } catch (IllegalArgumentException e) {
+ glyphId += "_" + getNextId();
+ reactionGlyph = layout.createReactionGlyph(glyphId, sbmlElementId);
+ }
return reactionGlyph;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index 02364cefab..fc91aa0314 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -96,7 +96,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
try {
Reaction reactionWithLayout = source.copy();
// getId doesn't have to be unique, therefore we concatenate with reaction
- reactionWithLayout.setIdReaction(glyph.getId() + "_" + glyph.getReaction());
+ reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
for (SpeciesReferenceGlyph speciesRefernceGlyph : glyph.getListOfSpeciesReferenceGlyphs()) {
SpeciesGlyph speciesGlyph = layout.getSpeciesGlyph(speciesRefernceGlyph.getSpeciesGlyph());
ReactionNode minervaNode = null;
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index 520b8295c0..cde6d4d78d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -16,12 +16,14 @@ import org.junit.Test;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
@@ -218,4 +220,30 @@ public class SbmlExporterTest {
}
+ @Test
+ public void testExportModelWithReaction() throws Exception {
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
+ model.setName(null);
+
+ converter.exportModelToFile(model, "tmp.xml");
+
+ Model model2 = converter.createModel(new ConverterParams().filename("tmp.xml"));
+ model2.setName(null);
+
+ for (Reaction r: model.getReactions()) {
+ logger.debug(r.getIdReaction());
+ }
+ logger.debug("---");
+ for (Reaction r: model2.getReactions()) {
+ logger.debug(r.getIdReaction());
+ }
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+
+ }
+
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
index f3c17b1e67..fe321ba070 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommand.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.commands.layout;
-import java.awt.Dimension;
import java.awt.geom.Dimension2D;
import java.awt.geom.Point2D;
import java.util.Collection;
@@ -25,9 +24,12 @@ public abstract class ApplyLayoutModelCommand extends ModelCommand {
private Double minY;
private Double maxX;
private Double maxY;
+ private boolean addReactionPrefixes;
+
+ private int idCounter = 0;
public ApplyLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, Double minX, Double minY, Double maxX,
- Double maxY) {
+ Double maxY, boolean addReactionPrefixes) {
super(model);
if (bioEntities == null) {
bioEntities = new HashSet<>();
@@ -43,6 +45,7 @@ public abstract class ApplyLayoutModelCommand extends ModelCommand {
this.setMinY(minY);
this.setMaxX(maxX);
this.setMaxY(maxY);
+ this.addReactionPrefixes = addReactionPrefixes;
}
protected Collection<BioEntity> getBioEntities() {
@@ -101,4 +104,16 @@ public abstract class ApplyLayoutModelCommand extends ModelCommand {
}
}
+ public boolean isAddReactionPrefixes() {
+ return addReactionPrefixes;
+ }
+
+ public void setAddReactionPrefixes(boolean addReactionPrefixes) {
+ this.addReactionPrefixes = addReactionPrefixes;
+ }
+
+ protected String getNextId() {
+ return (idCounter++) + "";
+ }
+
}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 041820ea04..9d89405b3b 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -50,12 +50,16 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
private static final double COMPLEX_PADDING = 5;
public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, Double minX, Double minY,
- Double maxX, Double maxY) {
- super(model, bioEntities, minX, minY, maxX, maxY);
+ Double maxX, Double maxY, boolean addReactionPrefixes) {
+ super(model, bioEntities, minX, minY, maxX, maxY, addReactionPrefixes);
}
public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities) {
- this(model, bioEntities, null, null, null, null);
+ this(model, bioEntities, null, null, null, null, false);
+ }
+
+ public ApplySimpleLayoutModelCommand(Model model, Collection<BioEntity> bioEntities, boolean addReactionPrefixes) {
+ this(model, bioEntities, null, null, null, null, addReactionPrefixes);
}
public ApplySimpleLayoutModelCommand(Model model) {
@@ -217,6 +221,12 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
modifyProducts(reaction, middle);
modifyReactants(reaction, middle);
modifyModifiers(reaction, middle);
+
+ if (super.isAddReactionPrefixes()) {
+ super.getModel().removeReaction(reaction);
+ reaction.setIdReaction("reaction_glyph_" + getNextId() + "__" + reaction.getIdReaction());
+ super.getModel().addReaction(reaction);
+ }
}
private Point2D.Double getMiddlePoint(Point2D middle, Point2D productPoint) {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommandTest.java
index ab4e586288..df63c2e9c2 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/layout/ApplyLayoutModelCommandTest.java
@@ -18,7 +18,7 @@ public class ApplyLayoutModelCommandTest {
Double minX = 1.0;
Double minY = 2.0;
ApplyLayoutModelCommand command = new ApplySimpleLayoutModelCommand(new ModelFullIndexed(null), new ArrayList<>(),
- minX, minY, null, null);
+ minX, minY, null, null, false);
Point2D minPoint = command.getStartPoint();
assertNotNull(minPoint);
@@ -31,7 +31,7 @@ public class ApplyLayoutModelCommandTest {
Double maxX = 1.0;
Double maxY = 2.0;
ApplyLayoutModelCommand command = new ApplySimpleLayoutModelCommand(new ModelFullIndexed(null), new ArrayList<>(),
- 0.0, 0.0, maxX, maxY);
+ 0.0, 0.0, maxX, maxY, false);
Dimension2D minPoint = command.getStartDimension();
assertNotNull(minPoint);
--
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