From c679cf77decd7a07fb0022ec63b41e0fd43c535c Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Thu, 13 Mar 2025 15:10:48 +0100
Subject: [PATCH] export submodels
---
.../lcsb/mapviewer/common/Comparator.java | 2 +-
.../common/comparator/SetComparator.java | 16 +++----
.../CellDesignerTestFunctions.java | 16 +++++--
.../model/celldesigner/ProjectExportTest.java | 43 ++++++++++++++++---
.../mapviewer/converter/ProjectFactory.java | 20 ++++++---
.../mapviewer/model/ProjectComparator.java | 5 ++-
.../model/SubmodelConnectionComparator.java | 19 ++++----
7 files changed, 82 insertions(+), 39 deletions(-)
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
index 772b161ba7..e908c2846b 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
@@ -9,7 +9,7 @@ import java.util.List;
public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
protected static Logger logger = LogManager.getLogger();
-
+
private final Class<T> comparatorClazz;
private final boolean exactClassMatch;
private final List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
index 1f178fbfcb..f237a1a15d 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
@@ -1,22 +1,21 @@
package lcsb.mapviewer.common.comparator;
-import java.util.Comparator;
-import java.util.Set;
-
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import java.util.Comparator;
+import java.util.Set;
+
/**
* Comparator used for comparing sets of strings.
- *
+ *
* @author Piotr Gawron
- *
*/
public class SetComparator<T> implements Comparator<Set<T>> {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
private Comparator<T> objectComparator;
@@ -41,6 +40,7 @@ public class SetComparator<T> implements Comparator<Set<T>> {
for (final T objectInList0 : arg0) {
if (objectComparator.compare(objectInList0, objectInList1) == 0) {
found = true;
+ break;
}
}
if (!found) {
@@ -54,11 +54,11 @@ public class SetComparator<T> implements Comparator<Set<T>> {
for (final T objectInList1 : arg1) {
if (objectComparator.compare(objectInList0, objectInList1) == 0) {
found = true;
+ break;
}
}
if (!found) {
- new Exception().printStackTrace();
- logger.debug("Cannot find object " + objectInList0 + " in set: " + arg1);
+ logger.debug("Cannot find object {} in set: {}", objectInList0, arg1);
return 1;
}
}
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 ca10f5af92..aa357bbda2 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
@@ -24,6 +24,7 @@ import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
@@ -91,13 +92,19 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
final InputStream is = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
final Model model2 = parser.createModel(new ConverterParams().inputStream(is, model.getName()).sizeAutoAdjust(false));
- for (final Drawable bioEntity : model2.getDrawables()) {
- bioEntity.setZ(null);
- }
+ clearModelFromZ(model2);
+ clearModelFromZ(model);
+ return model2;
+ }
+
+ protected void clearModelFromZ(final Model model) {
for (final Drawable bioEntity : model.getDrawables()) {
bioEntity.setZ(null);
}
- return model2;
+ }
+
+ protected void clearModelFromZ(final ModelData modelData) {
+ clearModelFromZ(modelData.getModel());
}
private static int idCounter = 0;
@@ -246,6 +253,7 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
protected static Model createEmptyModel() {
final Model model = new ModelFullIndexed(null);
+ model.setName(faker.witcher().monster());
model.setIdModel("as");
model.setWidth(100);
model.setHeight(100);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
index e2a0795446..8b04264dc6 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
@@ -2,12 +2,18 @@ package lcsb.mapviewer.converter.model.celldesigner;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.ProjectFactory;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectComparator;
+import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -27,8 +33,13 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
private final ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
+ private ComplexZipConverter parser;
+ private ProjectFactory projectFactory;
+
@Before
public void setUp() throws Exception {
+ parser = new ComplexZipConverter(CellDesignerXmlParser.class);
+ projectFactory = new ProjectFactory(parser);
}
@After
@@ -41,22 +52,40 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
Model model = createEmptyModel();
project.addModel(model);
- final ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
- final ProjectFactory projectFactory = new ProjectFactory(parser);
+ testSerializationOverZip(project);
+ }
- byte[] data = projectFactory.project2zip(project);
+ @Test
+ public void testWithManyModels() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ project.addModel(model);
- File tempFile = File.createTempFile("CD-", ".zip");
+ Model model2 = createEmptyModel();
+ model2.setWidth(260);
+ model2.addElement(createProtein());
+ project.addModel(model2);
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, model2.getName()));
+ testSerializationOverZip(project);
+ }
+
+ private void testSerializationOverZip(final Project project) throws IOException, ConverterException, InconsistentModelException, InvalidInputDataExecption {
+ File tempFile = File.createTempFile("CD-", ".zip");
try (FileOutputStream outputStream = new FileOutputStream(tempFile)) {
+ byte[] data = projectFactory.project2zip(project);
outputStream.write(data);
}
- logger.debug(tempFile.getAbsolutePath());
-
final ComplexZipConverterParams complexParams = createDefaultParams(tempFile);
-
Project project2 = projectFactory.create(complexParams);
+ for (ModelData model : project.getModels()) {
+ clearModelFromZ(model);
+ }
+ for (ModelData model : project2.getModels()) {
+ clearModelFromZ(model);
+ }
+
assertEquals(0, projectComparator.compare(project, project2));
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index fe2b69e772..812e84783a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -155,18 +155,26 @@ public class ProjectFactory {
public byte[] project2zip(final Project project) throws ConverterException, InconsistentModelException {
Converter converter = this.converter.createConverterInstance();
- String topModelContent = converter.model2String(project.getTopModel());
ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
try (ZipOutputStream zos = new ZipOutputStream(byteArrayOutputStream)) {
- ZipEntry entry = new ZipEntry(project.getTopModel().getName() + "." + converter.getFileExtensions().get(0));
-
- zos.putNextEntry(entry);
- zos.write(topModelContent.getBytes());
- zos.closeEntry();
+ addModelFileToZip(project.getTopModel(), project.getTopModel().getName() + "." + converter.getFileExtensions().get(0), converter, zos);
+ for (ModelData model : project.getModels()) {
+ if (model != project.getTopModelData()) {
+ addModelFileToZip(model.getModel(), "submaps/" + model.getName() + "." + converter.getFileExtensions().get(0), converter, zos);
+ }
+ }
} catch (IOException ioe) {
throw new ConverterException(ioe);
}
return byteArrayOutputStream.toByteArray();
}
+
+ private static void addModelFileToZip(final Model model, final String filename, final Converter converter, final ZipOutputStream zos) throws IOException, InconsistentModelException, ConverterException {
+ ZipEntry entry = new ZipEntry(filename);
+ zos.putNextEntry(entry);
+ String topModelContent = converter.model2String(model);
+ zos.write(topModelContent.getBytes());
+ zos.closeEntry();
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
index 0aa6694500..b1862ab796 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
@@ -28,9 +28,10 @@ public class ProjectComparator extends Comparator<Project> {
@Override
protected int internalCompare(final Project arg0, final Project arg1) {
- if (modelComparator.compare(arg0.getTopModel(), arg1.getTopModel()) != 0) {
+ int compareResult = modelComparator.compare(arg0.getTopModel(), arg1.getTopModel());
+ if (compareResult != 0) {
logger.debug("Top model different: {}, {}", arg0.getTopModel(), arg1.getTopModel());
- return modelComparator.compare(arg0.getTopModel(), arg1.getTopModel());
+ return compareResult;
}
if (modelDataSetComparator.compare(arg0.getModels(), arg1.getModels()) != 0) {
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
index ecbd93fbac..2cb72be7eb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
@@ -1,36 +1,33 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link SubmodelConnection}. It
* handles comparison of subclasses of {@link SubmodelConnection} class.
- *
+ *
* @author Piotr Gawron
- *
*/
public class SubmodelConnectionComparator extends Comparator<SubmodelConnection> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public SubmodelConnectionComparator(final double epsilon) {
super(SubmodelConnection.class, true);
@@ -60,7 +57,7 @@ public class SubmodelConnectionComparator extends Comparator<SubmodelConnection>
}
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
return stringComparator.compare(arg0.getName(), arg1.getName());
}
--
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