From f7c0f018943f80883edbc15ac9f26bd4ff79b861 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 10 May 2019 13:42:33 +0200
Subject: [PATCH] export to CellDesigner doesn't support z-index, therefore it
must be ignored in comparison
---
.../commands/CommandTestFunctions.java | 114 +++++++++++-------
.../mapviewer/commands/CopyCommandTest.java | 58 +--------
.../commands/SubModelCommandTest.java | 25 +---
.../lcsb/mapviewer/model/map/model/Model.java | 3 +-
.../model/map/model/ModelFullIndexed.java | 11 ++
5 files changed, 91 insertions(+), 120 deletions(-)
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index f975548de2..b003428d07 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -1,5 +1,8 @@
package lcsb.mapviewer.commands;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -8,58 +11,77 @@ import java.util.Map;
import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.Drawable;
+import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.GenericProtein;
public abstract class CommandTestFunctions {
- public double EPSILON = 1e-6;
-
- Logger logger = Logger.getLogger(CommandTestFunctions.class);
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- result.setName(null);
- return result;
- }
- Model result = models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- result.setName(null);
- models.put(fileName, result);
- }
- return result;
- }
-
- protected Model createSimpleModel() {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein alias = new GenericProtein("alias_id");
- alias.setNotes(null);
- List<String> list = new ArrayList<>();
- list.add("synonym");
- alias.addSynonyms(list);
- List<String> list2 = new ArrayList<>();
- list2.add("f_symbol");
- alias.setFormerSymbols(list2);
-
- Complex complexAlias = new Complex("complex_alias_id");
- model.addElement(complexAlias);
-
- complexAlias.addSpecies(alias);
-
- model.addElement(alias);
-
- return model;
- }
+ public double EPSILON = 1e-6;
+
+ Logger logger = Logger.getLogger(CommandTestFunctions.class);
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ result.setName(null);
+ return result;
+ }
+ Model result = models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ result.setName(null);
+ models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected Model createSimpleModel() {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein alias = new GenericProtein("alias_id");
+ alias.setNotes(null);
+ List<String> list = new ArrayList<>();
+ list.add("synonym");
+ alias.addSynonyms(list);
+ List<String> list2 = new ArrayList<>();
+ list2.add("f_symbol");
+ alias.setFormerSymbols(list2);
+
+ Complex complexAlias = new Complex("complex_alias_id");
+ model.addElement(complexAlias);
+
+ complexAlias.addSpecies(alias);
+
+ model.addElement(alias);
+
+ return model;
+ }
+
+ protected Model serializeViaCellDesigner(Model original)
+ throws InconsistentModelException, InvalidInputDataExecption {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.model2String(original);
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+ Model result = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+
+ for (Drawable bioEntity: original.getDrawables()) {
+ bioEntity.setZ(null);
+ }
+ for (Drawable bioEntity: result.getDrawables()) {
+ bioEntity.setZ(null);
+ }
+ return result;
+ }
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 42b20d1a12..a85f57116d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -7,9 +7,6 @@ import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
import java.util.Calendar;
import org.junit.After;
@@ -17,8 +14,6 @@ import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -43,6 +38,8 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
+ ModelComparator comparator = new ModelComparator();
+
@Before
public void setUp() throws Exception {
}
@@ -57,8 +54,6 @@ public class CopyCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/sample.xml", false);
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -72,8 +67,6 @@ public class CopyCommandTest extends CommandTestFunctions {
Model model = getModelForFile("testFiles/kinetics_with_compartment.xml", false);
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
for (Reaction reaction : copy.getReactions()) {
if (reaction.getKinetics() != null) {
@@ -109,8 +102,6 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -138,8 +129,6 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
@@ -155,12 +144,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
+ Model copy2 = serializeViaCellDesigner(copy);
// check if after conversion to xml everything works
assertEquals(0, comparator.compare(copy, copy2));
@@ -178,12 +162,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
+ Model copy2 = serializeViaCellDesigner(copy);
// check if after conversion to xml everything works
assertEquals(0, comparator.compare(copy, copy2));
@@ -202,12 +181,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
+ Model copy2 = serializeViaCellDesigner(copy);
new CreateHierarchyCommand(copy2, 2, 2).execute();
@@ -229,8 +203,6 @@ public class CopyCommandTest extends CommandTestFunctions {
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -253,8 +225,6 @@ public class CopyCommandTest extends CommandTestFunctions {
alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
Model copy = new CopyCommand(model2).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model2, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -274,8 +244,6 @@ public class CopyCommandTest extends CommandTestFunctions {
.setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -291,8 +259,6 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(model, copy));
} catch (Exception e) {
e.printStackTrace();
@@ -404,10 +370,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(copy, model));
-
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -422,10 +385,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(copy, model));
-
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -440,10 +400,7 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(copy, model));
-
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -458,16 +415,11 @@ public class CopyCommandTest extends CommandTestFunctions {
Model copy = new CopyCommand(model).execute();
- ModelComparator comparator = new ModelComparator();
-
assertEquals(0, comparator.compare(copy, model));
-
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
-
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
index 4a384fefa6..9eba9df40a 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
@@ -4,9 +4,6 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import java.awt.geom.Path2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.HashSet;
@@ -14,13 +11,13 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
public class SubModelCommandTest extends CommandTestFunctions {
+ ModelComparator comparator = new ModelComparator();
+
@Before
public void setUp() throws Exception {
}
@@ -104,12 +101,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(),
copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
+ Model copy2 = serializeViaCellDesigner(copy);
// check if after conversion to xml everything works
assertEquals(0, comparator.compare(copy, copy2));
@@ -156,16 +148,9 @@ public class SubModelCommandTest extends CommandTestFunctions {
Model copy = new SubModelCommand(model, polygon).execute();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.model2String(copy);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-
- ModelComparator mc = new ModelComparator();
- assertEquals(0, mc.compare(copy, model2));
+ Model model2 = serializeViaCellDesigner(copy);
+ assertEquals(0, comparator.compare(copy, model2));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index f9df9d1113..5450b22f0c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -8,6 +8,7 @@ import java.util.Set;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
@@ -550,5 +551,5 @@ public interface Model {
void addModificationDates(Collection<Calendar> modificationDatesFromRdf);
-
+ Set<Drawable> getDrawables();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 43480ff428..5487e7011d 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -15,6 +15,7 @@ import org.apache.log4j.Logger;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
@@ -717,4 +718,14 @@ public class ModelFullIndexed implements Model {
addModificationDate(calendar);
}
}
+
+ @Override
+ public Set<Drawable> getDrawables() {
+ Set<Drawable> result = new HashSet<>();
+ result.addAll(getBioEntities());
+ for (Layer layer: getLayers()) {
+ result.addAll(layer.getDrawables());
+ }
+ return result;
+ }
}
--
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