From 0bc2881ecc6bc5c6bf4266212a4c0acf7c5a8473 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 8 May 2019 21:02:56 +0200
Subject: [PATCH] unit tests fixed
---
.../CellDesignerTestFunctions.java | 25 ++++++++++++++++---
.../CellDesignerXmlParserTest.java | 12 ++-------
.../celldesigner/ComplexParserTests.java | 22 ++--------------
.../model/sbml/GenericSbmlParserTest.java | 8 +++++-
.../model/sbml/SbmlTestFunctions.java | 18 +++++++++++++
.../commands/CreateHierarchyCommandTest.java | 1 +
.../testFiles/layer_text_with_notes.xml | 1 +
7 files changed, 52 insertions(+), 35 deletions(-)
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
index f05ce4c064..fa6ea6d6b3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
@@ -44,6 +44,7 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -234,14 +235,30 @@ public abstract class CellDesignerTestFunctions {
protected void testXmlSerialization(Model model)
throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model);
- InputStream is = new ByteArrayInputStream(xml.getBytes("UTF-8"));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ for (BioEntity bioEntity : model.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+
+ Model model2 = serializeModel(model);
model.setName(null);
ModelComparator comparator = new ModelComparator();
assertEquals(0, comparator.compare(model, model2));
}
+
+ protected Model serializeModel(Model model)
+ throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.model2String(model);
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ for (BioEntity bioEntity : model2.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+ return model2;
+ }
+
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 0323096e10..2f0d754c17 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -470,11 +470,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
alias2.setName("PDK2");
model.addElement(alias2);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.model2String(model);
-
- InputStream is = new ByteArrayInputStream(xmlString.getBytes());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModel(model);
assertEquals(0, modelComparator.compare(model, model2));
@@ -1078,11 +1074,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
protein.addSynonym("&");
model.addElement(protein);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.model2String(model);
- InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+ Model model2 = serializeModel(model);
assertEquals(0, modelComparator.compare(model, model2));
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
index 022d79dc5c..5c62f1ecae 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java
@@ -7,8 +7,6 @@ import static org.junit.Assert.assertTrue;
import java.awt.Color;
import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
@@ -98,7 +96,6 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
-
@Test
public void testParseTextWithBackground() throws Exception {
try {
@@ -413,14 +410,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
alias.setName("name & no-name");
model.addElement(alias);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.model2String(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
+ Model model2 = serializeModel(model);
ModelComparator comparator = new ModelComparator();
@@ -443,14 +433,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
alias.setName("name\rno-name");
model.addElement(alias);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String string = parser.model2String(model);
-
- InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
- ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
- Model model2 = parser.createModel(params);
+ Model model2 = serializeModel(model);
ModelComparator comparator = new ModelComparator();
@@ -485,5 +468,4 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
}
}
-
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index 7d324d25bb..bb885faf54 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -26,6 +26,7 @@ import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -91,11 +92,16 @@ public class GenericSbmlParserTest {
assertNotNull(model2);
ModelComparator comparator = new ModelComparator(1.0);
+ for (BioEntity bioEntity: model.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+ for (BioEntity bioEntity: model2.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
assertEquals(0, comparator.compare(model, model2));
FileUtils.deleteDirectory(new File(dir));
} catch (Exception e) {
- // TODO Auto-generated catch block
e.printStackTrace();
throw e;
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
index 933b781dc2..4b9e2610e2 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlTestFunctions.java
@@ -4,6 +4,7 @@ import java.awt.Desktop;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
import java.io.File;
+import java.io.InputStream;
import java.nio.file.Files;
import java.util.List;
@@ -17,7 +18,9 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -117,6 +120,21 @@ public class SbmlTestFunctions {
// showImage(result);
return result;
}
+
+ protected Model getModelAfterCellDEsignerSerializing(Model model) throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.model2String(model);
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ for (BioEntity bioEntity : model2.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+ for (BioEntity bioEntity : model.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+ return model2;
+ }
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index f952fbb959..70809cf5ae 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -385,6 +385,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
assertEquals("test", pathway.getName());
assertEquals("5", pathway.getVisibilityLevel());
+ assertEquals((Integer)11, pathway.getZ());
} catch (Exception e) {
e.printStackTrace();
diff --git a/model-command/testFiles/layer_text_with_notes.xml b/model-command/testFiles/layer_text_with_notes.xml
index 690a38abda..426b06f1c1 100644
--- a/model-command/testFiles/layer_text_with_notes.xml
+++ b/model-command/testFiles/layer_text_with_notes.xml
@@ -42,6 +42,7 @@
<celldesigner:layerNotes>
test
SemanticZoomLevelVisibility: 5
+Z-Index: 11
</celldesigner:layerNotes>
<celldesigner:bounds x="140.0" y="173.0" w="242.0" h="178.0"/>
<celldesigner:paint color="ff000000"/>
--
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