From f1e4eb0fa3f801de80678ad83060a561f48915c3 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Fri, 14 Mar 2025 13:21:42 +0100
Subject: [PATCH] export of glyphs added
---
.../CellDesignerTestFunctions.java | 24 +++
.../model/celldesigner/ProjectExportTest.java | 17 ++
.../testFiles/glyphs/uni.png | Bin 0 -> 25059 bytes
.../converter/ComplexZipConverter.java | 67 +++++--
.../mapviewer/converter/OverviewParser.java | 179 +++++++-----------
.../mapviewer/converter/ProjectFactory.java | 52 +++--
.../converter/ComplexZipConverterTest.java | 27 +--
.../converter/OverviewParserTest.java | 77 ++++----
.../converter/ProjectFactoryTest.java | 4 +-
.../commands/ColorModelCommandTest.java | 56 +++---
.../mapviewer/model/ProjectComparator.java | 15 +-
.../cache/UploadedFileEntryComparator.java | 32 ++++
.../map/layout/graphics/GlyphComparator.java | 24 +++
.../model/map/species/ElementComparator.java | 7 +
14 files changed, 356 insertions(+), 225 deletions(-)
create mode 100644 converter-CellDesigner/testFiles/glyphs/uni.png
create mode 100644 model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java
create mode 100644 model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java
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 aa357bbda2..24e3bebbca 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
@@ -7,6 +7,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.Drawable;
@@ -20,6 +21,7 @@ import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
@@ -46,9 +48,13 @@ import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
@@ -299,4 +305,22 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
return project;
}
+ protected Glyph createGlyph() throws IOException {
+ Glyph glyph = new Glyph();
+ glyph.setFile(createFile("testFiles/glyphs/uni.png"));
+
+ return glyph;
+ }
+
+ private UploadedFileEntry createFile(final String filePath) throws IOException {
+ UploadedFileEntry uploadedFileEntry = new UploadedFileEntry();
+ byte[] byteArray = Files.readAllBytes(Paths.get(filePath));
+ uploadedFileEntry.setFileContent(byteArray);
+ uploadedFileEntry.setOriginalFileName("glyphs/" + new File(filePath).getName());
+ uploadedFileEntry.setLength(byteArray.length);
+ uploadedFileEntry.setLocalPath(null);
+ return uploadedFileEntry;
+
+ }
+
}
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 57001079c8..1f5034282d 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
@@ -7,6 +7,7 @@ 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.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -99,6 +100,22 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
testSerializationOverZip(project);
}
+ @Test
+ public void testGlyph() throws Exception {
+ Glyph glyph = createGlyph();
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ protein.setGlyph(glyph);
+ model.addElement(protein);
+ project.addModel(model);
+ project.addGlyph(glyph);
+
+ testSerializationOverZip(project);
+ }
+
+
private void testSerializationOverZip(final Project project) throws Exception {
File tempFile = File.createTempFile("CD-", ".zip");
try (FileOutputStream outputStream = new FileOutputStream(tempFile)) {
diff --git a/converter-CellDesigner/testFiles/glyphs/uni.png b/converter-CellDesigner/testFiles/glyphs/uni.png
new file mode 100644
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diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 5d6bc2741c..c00117499d 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -10,9 +10,11 @@ import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -40,6 +42,7 @@ import java.lang.reflect.Modifier;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
@@ -65,6 +68,7 @@ public class ComplexZipConverter {
*/
private static final Logger logger = LogManager.getLogger();
protected static final String IMMEDIATE_LINK_PREFIX = "IMMEDIATE_LINK:";
+ protected static final String GLYPH_PREFIX = "Glyph:";
/**
* Class used to create single submap from a file.
@@ -97,7 +101,7 @@ public class ComplexZipConverter {
* @return complex {@link Model} created from input data
* @throws InvalidInputDataExecption thrown when there is a problem with accessing input data
*/
- public Model createModel(final ComplexZipConverterParams params) throws InvalidInputDataExecption, ConverterException {
+ public Model createModel(final ComplexZipConverterParams params, final Project project) throws InvalidInputDataExecption, ConverterException {
try {
ZipFile zipFile = params.getZipFile();
Enumeration<? extends ZipEntry> entries;
@@ -154,16 +158,22 @@ public class ComplexZipConverter {
processReaction(mapping, nameModelMap, result, reaction);
}
for (final Species species : mappingModel.getSpeciesList()) {
- processSpecies(species, nameModelMap);
+ processSpecies(species, nameModelMap, project.getGlyphs());
}
}
+
+ project.addModel(result);
+ for (final Model model : result.getSubmodels()) {
+ project.addModel(model);
+ }
+
return result;
} catch (final IOException e) {
throw new InvalidArgumentException(e);
}
}
- private void processSpecies(final Species species, final Map<String, Model> nameModelMap) {
+ private void processSpecies(final Species species, final Map<String, Model> nameModelMap, final List<Glyph> glyphs) {
String notes = species.getNotes();
if (notes != null) {
String[] lines = notes.split("\n");
@@ -172,28 +182,49 @@ public class ComplexZipConverter {
if (line.startsWith(IMMEDIATE_LINK_PREFIX)) {
String link = line.replace(IMMEDIATE_LINK_PREFIX, "").trim();
- Compartment compartment = species.getCompartment();
- if (compartment == null) {
- logger.warn("[SUBMODEL MAPPING] Species {} in mapping file doesn't start inside compartment. Skipped. Link skipped",
- species.getElementId());
- } else {
- String modelName = compartment.getName().toLowerCase();
- Model model = nameModelMap.get(modelName);
- if (model == null) {
- throw new InvalidArgumentException("Mapping file references to " + modelName + " submodel. But such model doesn't exist");
- }
- Element elementToChange = model.getElementByElementId(species.getName());
- if (elementToChange == null) {
- throw new InvalidArgumentException("Mapping file references to element with alias: " + species.getName()
- + ". But such element doesn't exist");
- }
+ Element elementToChange = getElementToChange(species, nameModelMap);
+ if (elementToChange != null) {
elementToChange.setImmediateLink(link);
}
+ } else if (line.startsWith(GLYPH_PREFIX)) {
+ String filename = line.replace(GLYPH_PREFIX, "").trim();
+
+ Element elementToChange = getElementToChange(species, nameModelMap);
+ if (elementToChange != null) {
+ for (Glyph glyph : glyphs) {
+ if (glyph.getFile().getOriginalFileName().equalsIgnoreCase(filename)) {
+ elementToChange.setGlyph(glyph);
+ }
+ }
+ }
}
}
}
}
+ private static Element getElementToChange(
+ final Species species,
+ final Map<String, Model> nameModelMap) {
+ Compartment compartment = species.getCompartment();
+ if (compartment == null) {
+ logger.warn("[SUBMODEL MAPPING] Species {} in mapping file doesn't start inside compartment. Skipped. Link skipped",
+ species.getElementId());
+ } else {
+ String modelName = compartment.getName().toLowerCase();
+ Model model = nameModelMap.get(modelName);
+ if (model == null) {
+ throw new InvalidArgumentException("Mapping file references to " + modelName + " submodel. But such model doesn't exist");
+ }
+ Element result = model.getElementByElementId(species.getName());
+ if (result == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + species.getName()
+ + ". But such element doesn't exist");
+ }
+ return result;
+ }
+ return null;
+ }
+
protected boolean isIgnoredFile(final String name) {
if (name == null) {
return true;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index 6be2c06671..00f51f01df 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -1,5 +1,23 @@
package lcsb.mapviewer.converter;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.OverviewLinkDeserializer;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.OverviewSearchLink;
+import lcsb.mapviewer.model.map.model.ModelData;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import javax.imageio.ImageIO;
import java.awt.Polygon;
import java.awt.geom.Area;
import java.awt.geom.Point2D;
@@ -20,33 +38,11 @@ import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import javax.imageio.ImageIO;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.module.SimpleModule;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.OverviewLinkDeserializer;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.OverviewSearchLink;
-import lcsb.mapviewer.model.map.model.Model;
-
/**
* Parser used to extract data about {@link OverviewImage overview images} from
* zip file.
- *
+ *
* @author Piotr Gawron
- *
*/
public class OverviewParser {
/**
@@ -58,37 +54,17 @@ public class OverviewParser {
private static final String JSON_COORDINATES_FILENAME = "coords.json";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#zoomLevel} is stored.
- */
private static final String ZOOM_LEVEL_COORDINATES_COLUMN = "MODEL_ZOOM_LEVEL";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#xCoord},{@link OverviewModelLink#yCoord} is stored.
- */
+
private static final String REDIRECTION_COORDINATES_COORDINATE_COLUMN = "MODEL_COORDINATES";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#linkedModel} or
- * {@link OverviewImageLink#linkedOverviewImage} is stored.
- */
+
private static final String TARGET_FILENAME_COORDINATE_COLUMN = "LINK_TARGET";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#polygon} is stored.
- */
+
private static final String POLYGON_COORDINATE_COLUMN = "POLYGON";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#overviewImage source of the image} is stored.
- */
+
private static final String FILENAME_COORDINATE_COLUMN = "FILE";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * type of the link (implementation of {@link OverviewLink} class) is stored.
- */
+
private static final String TARGET_TYPE_COORDINATE_COLUMN = "LINK_TYPE";
/**
@@ -126,20 +102,16 @@ public class OverviewParser {
* Method that parse zip file and creates list of {@link OverviewImage images}
* from it.
*
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param files
- * list with files to parse
- * @param outputDirectory
- * directory where images should be stored, directory path should be
- * absolute
+ * @param models map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param files list with files to parse
+ * @param outputDirectory directory where images should be stored, directory path should be
+ * absolute
* @return list of {@link OverviewImage images}
- * @throws InvalidOverviewFile
- * thrown when the zip file contains invalid data
+ * @throws InvalidOverviewFile thrown when the zip file contains invalid data
*/
- public List<OverviewImage> parseOverviewLinks(final Set<Model> models, final List<ImageZipEntryFile> files,
- final String outputDirectory, final ZipFile zipFile) throws InvalidOverviewFile {
+ public List<OverviewImage> parseOverviewLinks(final Set<ModelData> models, final List<ImageZipEntryFile> files,
+ final String outputDirectory, final ZipFile zipFile) throws InvalidOverviewFile {
if (outputDirectory != null) {
File f = new File(outputDirectory);
if (!f.exists()) {
@@ -220,9 +192,9 @@ public class OverviewParser {
}
}
- private Map<String, Model> createMapping(final Set<Model> models) {
- Map<String, Model> result = new HashMap<>();
- for (final Model model : models) {
+ private Map<String, ModelData> createMapping(final Set<ModelData> models) {
+ Map<String, ModelData> result = new HashMap<>();
+ for (final ModelData model : models) {
result.put(model.getName().toLowerCase(), model);
}
return result;
@@ -232,20 +204,16 @@ public class OverviewParser {
* This method process data from {@link #COORDINATES_FILENAME} in zip archive.
* This method adds connections between images and between images and models.
*
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param images
- * list of {@link OverviewImage images} that should be connected
- * @param coordinatesData
- * {@link String} with the data taken from
- * {@link #COORDINATES_FILENAME} file
- * @throws InvalidOverviewFile
- * thrown when the data are invalid
+ * @param models map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param images list of {@link OverviewImage images} that should be connected
+ * @param coordinatesData {@link String} with the data taken from
+ * {@link #COORDINATES_FILENAME} file
+ * @throws InvalidOverviewFile thrown when the data are invalid
*/
- protected List<OverviewImage> processCoordinates(final Set<Model> models, final List<OverviewImage> images, final String coordinatesData)
+ protected List<OverviewImage> processCoordinates(final Set<ModelData> models, final List<OverviewImage> images, final String coordinatesData)
throws InvalidOverviewFile {
- Map<String, Model> modelMapping = createMapping(models);
+ Map<String, ModelData> modelMapping = createMapping(models);
String[] rows = coordinatesData.replaceAll("\r", "\n").split("\n");
Integer filenameColumn = null;
Integer polygonColumn = null;
@@ -399,9 +367,9 @@ public class OverviewParser {
return images;
}
- protected List<OverviewImage> processJsonCoordinates(final Set<Model> models, final List<OverviewImage> images, final String json)
+ protected List<OverviewImage> processJsonCoordinates(final Set<ModelData> models, final List<OverviewImage> images, final String json)
throws InvalidOverviewFile {
- Map<String, Model> modelMapping = createMapping(models);
+ Map<String, ModelData> modelMapping = createMapping(models);
ObjectMapper mapper = new ObjectMapper();
final SimpleModule module = new SimpleModule();
module.addDeserializer(OverviewLink.class, new OverviewLinkDeserializer());
@@ -429,7 +397,7 @@ public class OverviewParser {
((OverviewImageLink) link).setLinkedOverviewImage(linkImage);
}
if (link instanceof OverviewModelLink) {
- Model model = modelMapping.get(((OverviewModelLink) link).getLinkedModel().getName().toLowerCase());
+ ModelData model = modelMapping.get(((OverviewModelLink) link).getLinkedModel().getName().toLowerCase());
if (model == null) {
throw new InvalidOverviewFile(((OverviewModelLink) link).getLinkedModel().getName() + " is missing");
@@ -454,35 +422,32 @@ public class OverviewParser {
* Creates a link from parameters and place it in appropriate
* {@link OverviewImage}.
*
- * @param filename
- * {@link OverviewImage#filename name of the image}
- * @param polygon
- * {@link OverviewImage#polygon polygon} describing link
- * @param linkTarget
- * defines target that should be invoked when the link is activated.
- * This target is either a file name (in case of
- * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
- * string (in case of {@link #SEARCH_LINK_TYPE}).
- * @param coord
- * coordinates on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param zoomLevel
- * zoom level on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param linkType
- * type of the connection. This will define implementation of
- * {@link OverviewImage} that will be used. For now three values are
- * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
- * {@link #SEARCH_LINK_TYPE}.
- * @param images
- * list of images that are available
- * @param models
- * list of models that are available
- * @throws InvalidCoordinatesFile
- * thrown when one of the input parameters is invalid
+ * @param filename filename name of the image
+ * @param polygon polygon polygon describing link
+ * @param linkTarget defines target that should be invoked when the link is activated.
+ * This target is either a file name (in case of
+ * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
+ * string (in case of {@link #SEARCH_LINK_TYPE}).
+ * @param coord coordinates on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param zoomLevel zoom level on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param linkType type of the connection. This will define implementation of
+ * {@link OverviewImage} that will be used. For now three values are
+ * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
+ * {@link #SEARCH_LINK_TYPE}.
+ * @param images list of images that are available
+ * @param models list of models that are available
+ * @throws InvalidCoordinatesFile thrown when one of the input parameters is invalid
*/
- private void createOverviewLink(final String filename, final String polygon, final String linkTarget, final String coord, final String zoomLevel,
- final String linkType, final List<OverviewImage> images, final Map<String, Model> models) throws InvalidCoordinatesFile {
+ private void createOverviewLink(final String filename,
+ final String polygon,
+ final String linkTarget,
+ final String coord,
+ final String zoomLevel,
+ final String linkType,
+ final List<OverviewImage> images,
+ final Map<String, ModelData> models) throws InvalidCoordinatesFile {
OverviewImage image = null;
for (final OverviewImage oi : images) {
if (oi.getFilename().equalsIgnoreCase(filename)) {
@@ -494,7 +459,7 @@ public class OverviewParser {
}
OverviewLink ol = null;
if (linkType.equals(MODEL_LINK_TYPE)) {
- Model model = models.get(linkTarget.toLowerCase());
+ ModelData model = models.get(linkTarget.toLowerCase());
if (model == null) {
throw new InvalidCoordinatesFile("Unknown model in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index b5f450031f..51e60b8766 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -7,6 +7,7 @@ import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
@@ -30,6 +31,7 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.io.ByteArrayOutputStream;
+import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Enumeration;
@@ -72,17 +74,6 @@ public class ProjectFactory {
public Project create(final ComplexZipConverterParams params, final Project project)
throws InvalidInputDataExecption, ConverterException {
try {
- Model model = converter.createModel(params);
-
- Set<Model> models = new HashSet<>();
- models.add(model);
- models.addAll(model.getSubmodels());
-
- project.addModel(model);
- for (final Model m : model.getSubmodels()) {
- project.addModel(m);
- }
-
ZipFile zipFile = params.getZipFile();
Enumeration<? extends ZipEntry> entries;
@@ -103,10 +94,12 @@ public class ProjectFactory {
}
}
}
+ converter.createModel(params, project);
+
+
if (!imageEntries.isEmpty()) {
OverviewParser parser = new OverviewParser();
- project
- .addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir(), zipFile));
+ project.addOverviewImages(parser.parseOverviewLinks(project.getModels(), imageEntries, params.getVisualizationDir(), zipFile));
}
if (!project.getGlyphs().isEmpty()) {
assignGlyphsToElements(project);
@@ -151,7 +144,7 @@ public class ProjectFactory {
String[] lines = notes.split("[\n\r]+");
StringBuilder result = new StringBuilder();
for (final String line : lines) {
- if (!line.startsWith("Glyph:")) {
+ if (!line.startsWith(ComplexZipConverter.GLYPH_PREFIX)) {
result.append(line).append("\n");
}
}
@@ -161,8 +154,8 @@ public class ProjectFactory {
Glyph extractGlyph(final Project project, final String notes) throws InvalidGlyphFile {
String[] lines = notes.split("[\n\r]+");
for (final String line : lines) {
- if (line.startsWith("Glyph:")) {
- String glyphString = line.replace("Glyph:", "").trim().toLowerCase();
+ if (line.startsWith(ComplexZipConverter.GLYPH_PREFIX)) {
+ String glyphString = line.replace(ComplexZipConverter.GLYPH_PREFIX, "").trim().toLowerCase();
for (final Glyph glyph : project.getGlyphs()) {
if (glyph.getFile().getOriginalFileName().toLowerCase().equalsIgnoreCase(glyphString)) {
return glyph;
@@ -189,12 +182,28 @@ public class ProjectFactory {
addModelFileToZip(mapping, "submaps/mapping." + converter.getFileExtensions().get(0), converter, zos);
+ for (ModelData model : project.getModels()) {
+ addGlyphsToZip(model.getModel(), zos);
+ }
+
} catch (IOException ioe) {
throw new ConverterException(ioe);
}
return byteArrayOutputStream.toByteArray();
}
+ private void addGlyphsToZip(final Model model, final ZipOutputStream zos) throws IOException {
+ for (Element element : model.getElements()) {
+ if (element.getGlyph() != null) {
+ UploadedFileEntry uploadedFileEntry = element.getGlyph().getFile();
+ ZipEntry entry = new ZipEntry("glyphs/" + new File(uploadedFileEntry.getOriginalFileName()).getName());
+ zos.putNextEntry(entry);
+ zos.write(uploadedFileEntry.getFileContent());
+ zos.closeEntry();
+ }
+ }
+ }
+
private int idCounter = 0;
private Model createMappingModel(final Set<ModelData> models) {
@@ -228,7 +237,16 @@ public class ProjectFactory {
Species sourceElement = getCompartmentChildForConnection(parentElement.getElementId(), mappingParentCompartment);
String notes = sourceElement.getNotes();
- notes += ComplexZipConverter.IMMEDIATE_LINK_PREFIX + parentElement.getImmediateLink() + "\n";
+ notes += "\n" + ComplexZipConverter.IMMEDIATE_LINK_PREFIX + parentElement.getImmediateLink();
+ sourceElement.setNotes(notes);
+ }
+ if (parentElement.getGlyph() != null) {
+ UploadedFileEntry uploadedFileEntry = parentElement.getGlyph().getFile();
+ Compartment mappingParentCompartment = getCompartmentForConnection(parentModel.getName(), mapping);
+
+ Species sourceElement = getCompartmentChildForConnection(parentElement.getElementId(), mappingParentCompartment);
+ String notes = sourceElement.getNotes();
+ notes += "\n" + ComplexZipConverter.GLYPH_PREFIX + "glyphs/" + new File(uploadedFileEntry.getOriginalFileName()).getName();
sourceElement.setNotes(notes);
}
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 5850f0dad1..bea7c1a888 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -4,6 +4,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
@@ -40,7 +41,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
}
@Test
- public void testConstructor3() throws Exception {
+ public void testConstructor3() {
new ComplexZipConverter(MockConverter.class);
}
@@ -54,7 +55,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -108,7 +109,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -160,7 +161,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -174,7 +175,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -188,7 +189,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -202,7 +203,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test
@@ -216,7 +217,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
@@ -247,7 +248,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -258,11 +259,11 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test
- public void testIsIgnoredFileForMac() throws Exception {
+ public void testIsIgnoredFileForMac() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertTrue(converter.isIgnoredFile("__MACOSX/.desc"));
assertTrue(converter.isIgnoredFile(".DS_Store"));
@@ -272,13 +273,13 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
}
@Test
- public void testIsIgnoredFileForOldMacEntries() throws Exception {
+ public void testIsIgnoredFileForOldMacEntries() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertTrue(converter.isIgnoredFile(".DS_Store/.desc"));
}
@Test
- public void testIsIgnoredFileForValidFiles() throws Exception {
+ public void testIsIgnoredFileForValidFiles() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertFalse(converter.isIgnoredFile("mapping.xml"));
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
index 02ddc58b20..1485ed9620 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
@@ -1,8 +1,16 @@
package lcsb.mapviewer.converter;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import org.apache.commons.io.FileUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import java.awt.geom.Point2D;
import java.io.File;
@@ -16,23 +24,15 @@ import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.commons.io.FileUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
public class OverviewParserTest extends ConverterTestFunctions {
private static final String TEST_FILES_VALID_OVERVIEW_ZIP = "testFiles/valid_overview.zip";
private static final String TEST_FILES_VALID_OVERVIEW_CASE_SENSITIVE_ZIP = "testFiles/valid_overview_case_sensitive.zip";
- private OverviewParser parser = new OverviewParser();
+ private final OverviewParser parser = new OverviewParser();
@Before
public void setUp() throws Exception {
@@ -44,7 +44,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParsingValidFile() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<ImageZipEntryFile> imageEntries = createImageEntries(TEST_FILES_VALID_OVERVIEW_ZIP);
List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null,
new ZipFile(TEST_FILES_VALID_OVERVIEW_ZIP));
@@ -66,8 +66,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
assertTrue(link instanceof OverviewModelLink);
OverviewModelLink modelLink = (OverviewModelLink) link;
- Model mainModel = models.iterator().next();
- assertEquals(mainModel.getModelData(), modelLink.getLinkedModel());
+ ModelData mainModel = models.iterator().next();
+ assertEquals(mainModel, modelLink.getLinkedModel());
assertEquals((Integer) 10, modelLink.getxCoord());
assertEquals((Integer) 10, modelLink.getyCoord());
assertEquals((Integer) 3, modelLink.getZoomLevel());
@@ -75,7 +75,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParsingValidCaseSensitiveFile() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<ImageZipEntryFile> imageEntries = createImageEntries(TEST_FILES_VALID_OVERVIEW_CASE_SENSITIVE_ZIP);
for (final ImageZipEntryFile imageZipEntryFile : imageEntries) {
imageZipEntryFile.setFilename(imageZipEntryFile.getFilename().toLowerCase());
@@ -99,8 +99,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
assertTrue(link instanceof OverviewModelLink);
OverviewModelLink modelLink = (OverviewModelLink) link;
- Model mainModel = models.iterator().next();
- assertEquals(mainModel.getModelData(), modelLink.getLinkedModel());
+ ModelData mainModel = models.iterator().next();
+ assertEquals(mainModel, modelLink.getLinkedModel());
assertEquals((Integer) 10, modelLink.getxCoord());
assertEquals((Integer) 10, modelLink.getyCoord());
assertEquals((Integer) 3, modelLink.getZoomLevel());
@@ -109,8 +109,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
private List<ImageZipEntryFile> createImageEntries(final String string) throws IOException {
List<ImageZipEntryFile> result = new ArrayList<>();
- ZipFile zipFile = new ZipFile(string);
- try {
+ try (ZipFile zipFile = new ZipFile(string)) {
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
@@ -119,14 +118,12 @@ public class OverviewParserTest extends ConverterTestFunctions {
}
}
return result;
- } finally {
- zipFile.close();
}
}
@Test
public void testParsingValidFile2() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
String tmpDir = Files.createTempDirectory("tmp").toFile().getAbsolutePath();
@@ -145,7 +142,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile1() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_1.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_1.zip"));
}
@@ -153,7 +150,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile2() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_2.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_2.zip"));
}
@@ -161,16 +158,16 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile3() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_3.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_3.zip"));
}
- private Set<Model> createValidTestMapModel() {
- Set<Model> result = new HashSet<>();
+ private Set<ModelData> createValidTestMapModel() {
+ Set<ModelData> result = new HashSet<>();
Model model = new ModelFullIndexed(null);
model.setName("main");
- result.add(model);
+ result.add(model.getModelData());
return result;
}
@@ -181,9 +178,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
public void testParseInvalidCoordinates() throws Exception {
String invalidCoordinates = "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n"
+ "test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4";
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
- List<OverviewImage> images = new ArrayList<OverviewImage>();
+ List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
oi.setFilename("test.png");
oi.setWidth(1000);
@@ -198,9 +195,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
String invalidCoordinates = "FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n"
+ "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n"
+ "test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL";
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
- List<OverviewImage> images = new ArrayList<OverviewImage>();
+ List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
oi.setFilename("test.png");
oi.setWidth(1000);
@@ -215,7 +212,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParseValidComplexCoordinates() throws Exception {
String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"), "UTF-8");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
@@ -239,7 +236,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParseValidComplexCoordinatesWithExtraImages() throws Exception {
String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"), "UTF-8");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
@@ -267,10 +264,10 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testJsonCoordinates() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
Model child = new ModelFullIndexed(null);
child.setName("child");
- models.add(child);
+ models.add(child.getModelData());
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/valid_overview_with_json.zip");
List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/valid_overview_with_json.zip"));
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
index 327f984bdc..ea88c76453 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
@@ -149,7 +149,7 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
public void testParseGlyphsAndPutThemAsElementGlyphs() throws Exception {
Model model = new ModelFullIndexed(null);
final GenericProtein protein = createProtein();
- protein.setNotes("Glyph: glyphs/g1.png");
+ protein.setNotes(ComplexZipConverter.GLYPH_PREFIX + "glyphs/g1.png");
model.addElement(protein);
MockConverter.modelToBeReturned = model;
@@ -188,7 +188,7 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
final Layer layer = new Layer();
final LayerText text = new LayerText();
- text.setNotes("Glyph: glyphs/g1.png");
+ text.setNotes(ComplexZipConverter.GLYPH_PREFIX + " glyphs/g1.png");
layer.addLayerText(text);
model.addLayer(layer);
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 5d2fdaadc9..2a3b2cebfc 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -45,7 +45,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testAliasMatchWithInvalidElementId() throws Exception {
+ public void testAliasMatchWithInvalidElementId() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.setName(null);
colorSchema.setElementId("1");
@@ -65,7 +65,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testSpeciesMatchWithProteinType() throws Exception {
+ public void testSpeciesMatchWithProteinType() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.setName("s1");
colorSchema.addType(Protein.class);
@@ -82,7 +82,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testSpeciesMatchWithMiriamData() throws Exception {
+ public void testSpeciesMatchWithMiriamData() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.setName("s1");
colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
@@ -105,7 +105,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testSpeciesMatchWithMiriamDataDifferentAnnotator() throws Exception {
+ public void testSpeciesMatchWithMiriamDataDifferentAnnotator() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.setName("s1");
colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
@@ -123,7 +123,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionMatchWithProteinMiriamData() throws Exception {
+ public void testReactionMatchWithProteinMiriamData() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
@@ -138,7 +138,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionMatchWithMiriamData() throws Exception {
+ public void testReactionMatchWithMiriamData() {
GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
@@ -155,7 +155,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
@Test
- public void testGetModifiedElements() throws Exception {
+ public void testGetModifiedElements() {
Reaction reaction = new Reaction("re");
reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
@@ -174,7 +174,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testApplyColorToReaction() throws Exception {
+ public void testApplyColorToReaction() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -249,7 +249,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoring2() throws Exception {
+ public void testColoring2() {
Model model = createSimpleModel();
GenericProtein protein = createProteinWithLayout();
protein.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
@@ -280,7 +280,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColorTheSameElementTwiceUsingDifferentSelector() throws Exception {
+ public void testColorTheSameElementTwiceUsingDifferentSelector() {
Model model = createSimpleModel();
GenericProtein protein = createProteinWithLayout();
protein.setName("SNCA");
@@ -304,7 +304,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoring1() throws Exception {
+ public void testReactionColoring1() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -326,7 +326,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoring2() throws Exception {
+ public void testReactionColoring2() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -335,7 +335,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction reaction = createReactionWithLayout(protein1, protein1);
model.addReaction(reaction);
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setElementId(reaction.getIdReaction());
schema.setColor(Color.RED);
@@ -351,7 +351,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoring3() throws Exception {
+ public void testReactionColoring3() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -360,7 +360,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Reaction reaction = createReactionWithLayout(protein1, protein1);
model.addReaction(reaction);
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setElementId(reaction.getIdReaction());
schema.setValue(-1.0);
@@ -376,7 +376,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoring4() throws Exception {
+ public void testReactionColoring4() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -386,7 +386,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
model.addReaction(reaction);
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
schema.setValue(-1.0);
@@ -403,7 +403,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoringComplexModel() throws Exception {
+ public void testColoringComplexModel() {
Model model = createSimpleModel();
Model model2 = createSimpleModel();
@@ -420,8 +420,10 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
- assertNotEquals(coloredModel2.getElementByElementId(protein1.getElementId()).getFillColor(), model2.getElementByElementId(protein1.getElementId()).getFillColor());
- assertNotEquals(coloredModel3.getElementByElementId(protein1.getElementId()).getFillColor(), model2.getElementByElementId(protein1.getElementId()).getFillColor());
+ assertNotEquals(coloredModel2.getElementByElementId(protein1.getElementId()).getFillColor(),
+ model2.getElementByElementId(protein1.getElementId()).getFillColor());
+ assertNotEquals(coloredModel3.getElementByElementId(protein1.getElementId()).getFillColor(),
+ model2.getElementByElementId(protein1.getElementId()).getFillColor());
}
@Test
@@ -453,7 +455,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoredReactions() throws Exception {
+ public void testColoredReactions() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -477,7 +479,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoredReactions2() throws Exception {
+ public void testColoredReactions2() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -506,7 +508,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoringWithModelNotMatching() throws Exception {
+ public void testReactionColoringWithModelNotMatching() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -529,7 +531,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testReactionColoringWithModelMatch() throws Exception {
+ public void testReactionColoringWithModelMatch() {
Model model = createSimpleModel();
Protein protein1 = createProteinWithLayout();
Protein protein2 = createProteinWithLayout();
@@ -552,7 +554,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testAliasColoringWithModelNotMatching() throws Exception {
+ public void testAliasColoringWithModelNotMatching() {
Model model = createSimpleModel();
Protein p1 = createProtein();
p1.setName("CNC");
@@ -571,7 +573,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testAliasColoringWithModelMatch() throws Exception {
+ public void testAliasColoringWithModelMatch() {
Model model = createSimpleModel();
Protein p1 = createProtein();
p1.setName("CNC");
@@ -606,7 +608,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testAliasColoringWithElementIdMatch() throws Exception {
+ public void testAliasColoringWithElementIdMatch() {
Model model = createSimpleModel();
model.addElement(createProtein());
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
index b1862ab796..776c2556b7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
@@ -3,23 +3,29 @@ package lcsb.mapviewer.model;
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
+import lcsb.mapviewer.model.map.layout.graphics.GlyphComparator;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelDataComparator;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import java.util.HashSet;
+
public class ProjectComparator extends Comparator<Project> {
private static final Logger logger = LogManager.getLogger();
private final ModelComparator modelComparator;
private final SetComparator<ModelData> modelDataSetComparator;
+ private final SetComparator<Glyph> glyphSetComparator;
public ProjectComparator(final double epsilon) {
super(Project.class);
modelComparator = new ModelComparator(epsilon);
modelDataSetComparator = new SetComparator<>(new ModelDataComparator(epsilon));
+ glyphSetComparator = new SetComparator<>(new GlyphComparator());
}
public ProjectComparator() {
@@ -28,7 +34,13 @@ public class ProjectComparator extends Comparator<Project> {
@Override
protected int internalCompare(final Project arg0, final Project arg1) {
- int compareResult = modelComparator.compare(arg0.getTopModel(), arg1.getTopModel());
+ int compareResult = glyphSetComparator.compare(new HashSet<>(arg0.getGlyphs()), new HashSet<>(arg1.getGlyphs()));
+ if (compareResult != 0) {
+ logger.debug("Glyphs different");
+ return compareResult;
+ }
+
+ compareResult = modelComparator.compare(arg0.getTopModel(), arg1.getTopModel());
if (compareResult != 0) {
logger.debug("Top model different: {}, {}", arg0.getTopModel(), arg1.getTopModel());
return compareResult;
@@ -38,6 +50,7 @@ public class ProjectComparator extends Comparator<Project> {
logger.debug("Models different");
return modelDataSetComparator.compare(arg0.getModels(), arg1.getModels());
}
+
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java
new file mode 100644
index 0000000000..2dda81abcb
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java
@@ -0,0 +1,32 @@
+package lcsb.mapviewer.model.cache;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+import java.util.Arrays;
+
+public class UploadedFileEntryComparator extends Comparator<UploadedFileEntry> {
+
+ public UploadedFileEntryComparator() {
+ super(UploadedFileEntry.class, true);
+ }
+
+
+ @Override
+ protected int internalCompare(final UploadedFileEntry arg0, final UploadedFileEntry arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getOriginalFileName(), arg1.getOriginalFileName()) != 0) {
+ logger.debug("Original file name is different: {} != {}", arg0.getOriginalFileName(), arg1.getOriginalFileName());
+ return stringComparator.compare(arg0.getOriginalFileName(), arg1.getOriginalFileName());
+ }
+
+ if (!Arrays.equals(arg0.getFileContent(), arg1.getFileContent())) {
+ logger.debug("Glyph content different for file {}.", arg0.getOriginalFileName());
+ return -1;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java
new file mode 100644
index 0000000000..e217a4bc5d
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.model.cache.UploadedFileEntryComparator;
+
+public class GlyphComparator extends Comparator<Glyph> {
+
+
+ public GlyphComparator() {
+ super(Glyph.class, true);
+ }
+
+ @Override
+ protected int internalCompare(final Glyph arg0, final Glyph arg1) {
+ UploadedFileEntryComparator fileComparator = new UploadedFileEntryComparator();
+
+ if (fileComparator.compare(arg0.getFile(), arg1.getFile()) != 0) {
+ return fileComparator.compare(arg0.getFile(), arg1.getFile());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index 72997425c9..e4cd56e751 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.layout.graphics.GlyphComparator;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
/**
@@ -63,6 +64,7 @@ public class ElementComparator extends Comparator<Element> {
StringComparator stringComparator = new StringComparator();
ColorComparator colorComparator = new ColorComparator();
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ GlyphComparator glyphComparator = new GlyphComparator();
if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
logger.debug("ElementId different: {}, {}", arg0.getElementId(), arg1.getElementId());
@@ -216,6 +218,11 @@ public class ElementComparator extends Comparator<Element> {
return stringComparator.compare(arg0.getImmediateLink(), arg1.getImmediateLink());
}
+ if (glyphComparator.compare(arg0.getGlyph(), arg1.getGlyph()) != 0) {
+ logger.debug("Glyph different: {}, {}", arg0.getGlyph(), arg1.getGlyph());
+ return glyphComparator.compare(arg0.getGlyph(), arg1.getGlyph());
+ }
+
return 0;
}
--
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