From 6fbe9845d776ad10e5f3ae92fc2e850999dcc974 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 31 Dec 2018 11:28:26 +0100
Subject: [PATCH] export refactored (it doesn't take layout is a constructor
parameter anymore)
---
.../model/sbml/SbmlBioEntityExporter.java | 58 +++++++++++++------
.../model/sbml/SbmlElementExporter.java | 6 +-
.../converter/model/sbml/SbmlExporter.java | 6 +-
.../compartment/SbmlCompartmentExporter.java | 12 ++--
.../sbml/reaction/SbmlReactionExporter.java | 14 ++---
.../sbml/species/SbmlSpeciesExporter.java | 6 +-
.../model/sbml/SbmlBioEntityExporterTest.java | 10 +---
.../reaction/SbmlReactionExporterTest.java | 7 +--
.../sbml/species/SbmlSpeciesExporterTest.java | 4 +-
9 files changed, 72 insertions(+), 51 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
index 62d6d3ab7c..45ac9e9392 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java
@@ -12,8 +12,10 @@ import javax.xml.stream.XMLStreamException;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.render.ColorDefinition;
import org.sbml.jsbml.ext.render.LocalRenderInformation;
@@ -31,12 +33,24 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase>
extends XmlParser {
- @SuppressWarnings("unused")
+ /**
+ * Default class logger.
+ */
private Logger logger = Logger.getLogger(SbmlBioEntityExporter.class);
+ /**
+ * SBML Layout used when exporting map.
+ */
private Layout layout;
+ /**
+ * Map that we are exporting.
+ */
private lcsb.mapviewer.model.map.model.Model minervaModel;
+
+ /**
+ * SBML model to which we are exporting.
+ */
private Model sbmlModel;
private Map<String, S> sbmlElementByElementId = new HashMap<>();
@@ -48,9 +62,10 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
private Set<SbmlExtension> sbmlExtensions = new HashSet<>();
- public SbmlBioEntityExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel,
+ public SbmlBioEntityExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
Collection<SbmlExtension> sbmlExtensions) {
- this.layout = sbmlLayout;
+ this.sbmlModel = sbmlModel;
+ this.layout = getLayout(sbmlModel);
this.minervaModel = minervaModel;
this.sbmlExtensions.addAll(sbmlExtensions);
}
@@ -129,25 +144,34 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
return (idCounter++) + "";
}
- protected Model getSbmlModel() {
- return sbmlModel;
- }
-
- protected void setSbmlModel(Model sbmlModel) {
- this.sbmlModel = sbmlModel;
+ private Layout getLayout(org.sbml.jsbml.Model sbmlModel) {
+ Layout layout = null;
+
+ if (sbmlModel.getExtensionCount() > 0) {
+ for (SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
+ if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
+ LayoutModelPlugin layoutPlugin = (LayoutModelPlugin) plugin;
+ if (layoutPlugin.getLayoutCount() == 0) {
+ logger.warn("Layout plugin available but no layouts defined");
+ } else if (layoutPlugin.getLayoutCount() > 1) {
+ logger.warn(layoutPlugin.getLayoutCount() + " layouts defined. Using first one.");
+ layout = layoutPlugin.getLayout(0);
+ } else {
+ layout = layoutPlugin.getLayout(0);
+ }
+ }
+ }
+ }
+ return layout;
}
protected Layout getLayout() {
return layout;
}
- protected void setLayout(Layout layout) {
- this.layout = layout;
- }
-
protected RenderLayoutPlugin getRenderPlugin() {
- if (layout.getExtensionCount() > 0) {
- return (RenderLayoutPlugin) layout.getExtension("render");
+ if (getLayout().getExtensionCount() > 0) {
+ return (RenderLayoutPlugin) getLayout().getExtension("render");
}
return null;
}
@@ -160,8 +184,8 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
return minervaModel;
}
- protected void setMinervaModel(lcsb.mapviewer.model.map.model.Model minervaModel) {
- this.minervaModel = minervaModel;
+ protected Model getSbmlModel() {
+ return sbmlModel;
}
public S getSbmlElementByElementId(String id) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
index 68a22e13e3..530dfa9c71 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -3,10 +3,10 @@ package lcsb.mapviewer.converter.model.sbml;
import java.util.Collection;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.render.ColorDefinition;
import org.sbml.jsbml.ext.render.LocalStyle;
@@ -22,9 +22,9 @@ public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(SbmlElementExporter.class);
- public SbmlElementExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel,
+ public SbmlElementExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
Collection<SbmlExtension> sbmlExtensions) {
- super(sbmlLayout, minervaModel, sbmlExtensions);
+ super(sbmlModel, minervaModel, sbmlExtensions);
}
protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph speciesGlyph) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 6ec05f80ef..db7b4bd519 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -98,11 +98,11 @@ public class SbmlExporter {
assignStructuralStatesToTypes(multiPlugin, model);
}
- SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model, usedExtensions);
- SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+ SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(result, model, usedExtensions);
+ SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(result, model,
usedExtensions,
compartmentExporter);
- SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
+ SbmlReactionExporter reactionExporter = new SbmlReactionExporter(result, model, speciesExporter,
usedExtensions, compartmentExporter);
SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
index c3f994b786..8b2a8bf0d5 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -5,11 +5,11 @@ import java.util.Collection;
import java.util.List;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.Dimensions;
-import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
@@ -18,10 +18,14 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.Compartment;
public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
- Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
- public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel, Collection<SbmlExtension> sbmlExtensions) {
- super(layout, minervaModel, sbmlExtensions);
+ public SbmlCompartmentExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel, Collection<SbmlExtension> sbmlExtensions) {
+ super(sbmlModel, minervaModel, sbmlExtensions);
}
@Override
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 93136ab5ee..257a39e6ce 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
@@ -48,15 +48,18 @@ import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.species.Element;
public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sbml.jsbml.Reaction> {
- Logger logger = Logger.getLogger(SbmlReactionExporter.class);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(SbmlReactionExporter.class);
private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
private SbmlBioEntityExporter<Compartment, org.sbml.jsbml.Compartment> compartmentExporter;
- public SbmlReactionExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
+ public SbmlReactionExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter,
Collection<SbmlExtension> sbmlExtensions,
SbmlBioEntityExporter<lcsb.mapviewer.model.map.compartment.Compartment, org.sbml.jsbml.Compartment> compartmentExporter) {
- super(layout, minervaModel, sbmlExtensions);
+ super(sbmlModel, minervaModel, sbmlExtensions);
this.speciesExporter = speciesExporter;
this.compartmentExporter = compartmentExporter;
}
@@ -319,11 +322,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
return curve;
}
- @Override
- protected void setSbmlModel(Model sbmlModel) {
- super.setSbmlModel(sbmlModel);
- }
-
@Override
protected String getSbmlIdKey(Reaction element) {
return element.getClass().getSimpleName() + "\n" + element.getElementId();
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index e875c3a389..6dc2dc133a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -4,8 +4,8 @@ import java.util.Collection;
import java.util.List;
import org.apache.log4j.Logger;
+import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
-import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
@@ -34,11 +34,11 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
private SbmlCompartmentExporter compartmentExporter;
- public SbmlSpeciesExporter(Layout layout,
+ public SbmlSpeciesExporter(Model sbmlModel,
lcsb.mapviewer.model.map.model.Model minervaModel,
Collection<SbmlExtension> sbmlExtensions,
SbmlCompartmentExporter compartmentExporter) {
- super(layout, minervaModel, sbmlExtensions);
+ super(sbmlModel, minervaModel, sbmlExtensions);
this.compartmentExporter = compartmentExporter;
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
index 471f844b46..d29f86f82f 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporterTest.java
@@ -11,9 +11,7 @@ import org.mockito.Mockito;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.render.ColorDefinition;
-import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -22,9 +20,8 @@ public class SbmlBioEntityExporterTest {
@Test
public void testEmptyGetRenderPlugin() {
@SuppressWarnings("rawtypes")
- SbmlBioEntityExporter exporter = Mockito.mock(SbmlBioEntityExporter.class, Mockito.CALLS_REAL_METHODS);
- Layout layout = new Layout();
- exporter.setLayout(layout);
+ SbmlBioEntityExporter exporter = createMockExporter();
+ Mockito.when(exporter.getLayout()).thenReturn(new Layout());
assertNull(exporter.getRenderPlugin());
}
@@ -45,8 +42,7 @@ public class SbmlBioEntityExporterTest {
SbmlExporter sbmlExporter = new SbmlExporter();
Layout layout = sbmlExporter.createSbmlLayout(new ModelFullIndexed(null), result);
- exporter.setSbmlModel(result);
- exporter.setLayout(layout);
+ Mockito.when(exporter.getLayout()).thenReturn(layout);
return exporter;
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
index 38378c18d7..ce2936868e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
@@ -72,15 +72,14 @@ public class SbmlReactionExporterTest {
plugin.add(layout);
result.addExtension("layout", plugin);
- SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model,
+ SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(result, model,
Arrays.asList(SbmlExtension.values()));
- SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+ SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(result, model,
Arrays.asList(SbmlExtension.values()),
compartmentExporter);
- SbmlReactionExporter exporter = new SbmlReactionExporter(layout, model, speciesExporter,
+ SbmlReactionExporter exporter = new SbmlReactionExporter(result, model, speciesExporter,
Arrays.asList(SbmlExtension.values()), compartmentExporter);
- exporter.setSbmlModel(result);
return exporter;
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
index c359e04bcd..954544c422 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java
@@ -74,10 +74,10 @@ public class SbmlSpeciesExporterTest {
SbmlExporter sbmlExporter = new SbmlExporter();
sbmlLayout = sbmlExporter.createSbmlLayout(model, sbmlModel);
- SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlLayout, model,
+ SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlModel, model,
Arrays.asList(SbmlExtension.values()));
compartmentExporter.exportElements(sbmlModel);
- SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlLayout, model,
+ SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlModel, model,
Arrays.asList(new SbmlExtension[] { SbmlExtension.RENDER, SbmlExtension.LAYOUT }),
compartmentExporter);
return result;
--
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