From 3dcf521fe53bebbee3a6ed72ea8b5df283c0d0c8 Mon Sep 17 00:00:00 2001
From: sherzinger <sascha.herzinger@uni.lu>
Date: Tue, 19 Feb 2019 08:49:28 +0100
Subject: [PATCH] fixing sbml converter tests
---
.../converter/model/sbml/CellDesignerToMultiExportTest.java | 4 ++--
.../mapviewer/converter/model/sbml/CopasiImportTest.java | 6 +++---
.../converter/model/sbml/GenericSbmlParserTest.java | 6 +++---
.../converter/model/sbml/GenericSbmlToXmlParserTest.java | 3 +--
.../mapviewer/converter/model/sbml/MultiParserTest.java | 6 +++---
.../model/sbml/SbmlExporterFromCellDesignerTest.java | 2 +-
.../mapviewer/converter/model/sbml/SbmlExporterTest.java | 6 +++---
.../model/sbml/SbmlPareserForInvalidReactionTest.java | 4 ++--
.../model/sbml/reaction/SbmlReactionExportArrowType.java | 2 +-
9 files changed, 19 insertions(+), 20 deletions(-)
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
index 396c75e683..143ef22ff0 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CellDesignerToMultiExportTest.java
@@ -19,7 +19,7 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -49,7 +49,7 @@ public class CellDesignerToMultiExportTest {
@Test
public void createModelTest() throws Exception {
try {
- IConverter converter = new CellDesignerXmlParser();
+ Converter converter = new CellDesignerXmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
index edcb085e39..224f3b60e4 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/CopasiImportTest.java
@@ -16,7 +16,7 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.model.map.model.Model;
@RunWith(Parameterized.class)
@@ -44,11 +44,11 @@ public class CopasiImportTest extends SbmlTestFunctions{
@Test
public void createModelTest() throws Exception {
try {
- IConverter converter = new SbmlParser();
+ Converter converter = new SbmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
assertNotNull(model);
- converter.exportModelToInputStream(model);
+ converter.model2InputStream(model);
} catch (Exception e) {
e.printStackTrace();
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 409a17a491..69a896c9d5 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
@@ -21,7 +21,7 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
@@ -61,7 +61,7 @@ public class GenericSbmlParserTest {
try {
String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
- IConverter converter = new SbmlParser();
+ Converter converter = new SbmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
@@ -77,7 +77,7 @@ public class GenericSbmlParserTest {
// Desktop.getDesktop().open(new File(pngFilePath));
CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
+ String xmlString = cellDesignerXmlParser.model2Xml(model);
InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
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 327a004943..a01e176e6c 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
@@ -19,7 +19,6 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -65,7 +64,7 @@ public class GenericSbmlToXmlParserTest {
String pathWithouExtension = dir + "/"
+ filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
String xmlFilePath = pathWithouExtension.concat(".xml");
- converter.exportModelToFile(model, xmlFilePath);
+ converter.model2File(model, xmlFilePath);
Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath).sizeAutoAdjust(false));
model2.setName(null);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
index 9636bdb54b..c941ab79f8 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/MultiParserTest.java
@@ -21,7 +21,7 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
import lcsb.mapviewer.converter.graphics.PngImageGenerator;
@@ -56,7 +56,7 @@ public class MultiParserTest {
try {
String dir = Files.createTempDirectory("sbml-temp-images-dir").toFile().getAbsolutePath();
- IConverter converter = new SbmlParser();
+ Converter converter = new SbmlParser();
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
@@ -72,7 +72,7 @@ public class MultiParserTest {
// Desktop.getDesktop().open(new File(pngFilePath));
CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
+ String xmlString = cellDesignerXmlParser.model2Xml(model);
InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
index 2a33f3f0af..bee52e3765 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterFromCellDesignerTest.java
@@ -36,7 +36,7 @@ public class SbmlExporterFromCellDesignerTest extends SbmlTestFunctions {
model.setName(originalModel.getName());
- String cellDesignerXml = cellDesignerXmlParser.toXml(model);
+ String cellDesignerXml = cellDesignerXmlParser.model2Xml(model);
ByteArrayInputStream stream = new ByteArrayInputStream(cellDesignerXml.getBytes("UTF-8"));
assertEquals(0, comparator.compare(model, originalModel));
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 2d45276826..115bbf5c12 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
@@ -239,7 +239,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
Model model = converter.createModel(new ConverterParams().filename("testFiles/layoutExample/example1.xml"));
model.setName(null);
- converter.exportModelToFile(model, tempFilename);
+ converter.model2File(model, tempFilename);
Model model2 = converter.createModel(new ConverterParams().filename(tempFilename));
model2.setName(null);
@@ -258,7 +258,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
Model model = createEmptyModel();
- converter.exportModelToFile(model, tempFilename);
+ converter.model2File(model, tempFilename);
Model model2 = converter.createModel(new ConverterParams().filename(tempFilename));
@@ -666,7 +666,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
.createModel(new ConverterParams().filename("testFiles/cell_designer_problems/boolean_logic_gate.xml"));
Model model = getModelAfterSerializing(originalModel);
- new CellDesignerXmlParser().toXml(model);
+ new CellDesignerXmlParser().model2Xml(model);
List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
index d1dd68b432..f8c7079da0 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlPareserForInvalidReactionTest.java
@@ -16,7 +16,7 @@ import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
@RunWith(Parameterized.class)
@@ -44,7 +44,7 @@ public class SbmlPareserForInvalidReactionTest {
@Test
public void createModelTest() throws Exception {
try {
- IConverter converter = new SbmlParser();
+ Converter converter = new SbmlParser();
converter.createModel(new ConverterParams().filename(filePath.toString()));
fail("Exception expected when parsing file: " + filePath.toString());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
index efaf38757f..de716fd561 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExportArrowType.java
@@ -113,7 +113,7 @@ public class SbmlReactionExportArrowType {
model.addReaction(reaction);
CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
- String xmlString = cellDesignerXmlParser.toXml(model);
+ String xmlString = cellDesignerXmlParser.model2Xml(model);
Model modelAfterSerialization = cellDesignerXmlParser
.createModel(new ConverterParams().inputStream(new ByteArrayInputStream(xmlString.getBytes())));
return modelAfterSerialization;
--
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