diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index adc4fbff1c1912131303412721531f3133b0e74a..dc91e510ca4d12a82a54da6a2767154608083e17 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -49,26 +49,24 @@ import lcsb.mapviewer.model.map.species.Species;
*
* @author Piotr Gawron
*
- * @param <T>
- * class used to create single submap from a file
*/
-public class ComplexZipConverter<T extends IConverter> {
+public class ComplexZipConverter {
/**
* Size of the buffer used for accessing single chunk of data from input
* stream.
*/
- private static final int BUFFER_SIZE = 1024;
-
+ private static final int BUFFER_SIZE = 1024;
+
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
-
+ private static Logger logger = Logger.getLogger(ComplexZipConverter.class);
+
/**
* Class used to create single submap from a file.
*/
- private Class<T> converterClazz;
+ private Class<? extends IConverter> converterClazz;
/**
* Default constructor. Checks if the class given in the parameter is proper
@@ -77,7 +75,7 @@ public class ComplexZipConverter<T extends IConverter> {
* @param clazz
* {@link IConverter} class used for creation of the single submap
*/
- public ComplexZipConverter(Class<T> clazz) {
+ public ComplexZipConverter(Class<? extends IConverter> clazz) {
if (Modifier.isAbstract(clazz.getModifiers())) {
throw new InvalidClassException("Param class cannot be abstract");
}
@@ -112,8 +110,7 @@ public class ComplexZipConverter<T extends IConverter> {
entries = zipFile.entries();
Model result = null;
List<Layout> layouts = new ArrayList<Layout>();
- List<ImageZipEntryFile> imageEntries = new ArrayList<ImageZipEntryFile>();
- List<DataMiningSet> dataMiningSets = new ArrayList<DataMiningSet>();
+ List<DataMiningSet> dataMiningSets = new ArrayList<>();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
if (!entry.isDirectory()) {
@@ -133,7 +130,8 @@ public class ComplexZipConverter<T extends IConverter> {
} else if (zef instanceof LayoutZipEntryFile) {
layouts.add(layoutZipEntryFileToLayout(params, zipFile, entry, (LayoutZipEntryFile) zef));
} else if (zef instanceof ImageZipEntryFile) {
- imageEntries.add((ImageZipEntryFile) zef);
+ continue;
+ // imageEntries.add((ImageZipEntryFile) zef);
} else if (zef instanceof DataMiningZipEntryFile) {
dataMiningSets.add(dataMiningZipEntryToDataMiningSet(zipFile, entry, (DataMiningZipEntryFile) zef));
} else {
@@ -142,10 +140,6 @@ public class ComplexZipConverter<T extends IConverter> {
}
}
- if (imageEntries.size() > 0) {
- OverviewParser parser = new OverviewParser();
- result.setOverviewImages(parser.parseOverviewLinks(filenameModelMap, imageEntries, params.getVisualizationDir()));
- }
result.addDataMiningSets(dataMiningSets);
for (Entry<String, Model> entry : filenameModelMap.entrySet()) {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
index 6b0b1642b98b2a66360afcfb5bb3c46ad3c39e94..2001d886edaea980a216be9fb586c2060a19d534 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
@@ -34,7 +34,7 @@ public class ComplexZipConverterParams {
* Mapping between filename and information provided by the user about the
* file.
*/
- private Map<String, ZipEntryFile> entries = new HashMap<String, ZipEntryFile>();
+ private Map<String, ZipEntryFile> entries = new HashMap<>();
/**
* Directory where additional visualization files should be stored.
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index b9388ab2b7cda60cdf0849a52b72dc4dc8feb366..134f9ddb91de60742bb98ed094477bbca56fb842 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -9,11 +9,16 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import javax.imageio.ImageIO;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.model.map.OverviewImage;
@@ -23,9 +28,6 @@ import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.OverviewSearchLink;
import lcsb.mapviewer.model.map.model.Model;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.log4j.Logger;
-
/**
* Parser used to extract data about {@link OverviewImage overview images} from
* zip file.
@@ -40,72 +42,72 @@ public class OverviewParser {
* separated file where every row contains information about single
* connection.
*/
- private static final String COORDINATES_FILENAME = "coords.txt";
+ private static final String COORDINATES_FILENAME = "coords.txt";
/**
* 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";
+ 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";
+ 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";
+ 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";
+ 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";
+ 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";
+ private static final String TARGET_TYPE_COORDINATE_COLUMN = "LINK_TYPE";
/**
* Name of the column in {@link #COORDINATES_FILENAME} where comment about
* link is stored.
*/
- private static final String COMMENT_COORDINATE_COLUMN = "COMMENT";
+ private static final String COMMENT_COORDINATE_COLUMN = "COMMENT";
/**
* Size of the buffer used to access data from input stream.
*/
- private static final Integer BUFFER_SIZE = 1024;
+ private static final Integer BUFFER_SIZE = 1024;
/**
* String identifing {@link OverviewModelLink} connections.
*/
- private static final String MODEL_LINK_TYPE = "MODEL";
+ private static final String MODEL_LINK_TYPE = "MODEL";
/**
* String identifing {@link OverviewImageLink} connections between images.
*/
- private static final String IMAGE_LINK_TYPE = "IMAGE";
+ private static final String IMAGE_LINK_TYPE = "IMAGE";
/**
* String identifing {@link OverviewSearchLink} connections.
*/
- private static final String SEARCH_LINK_TYPE = "SEARCH";
+ private static final String SEARCH_LINK_TYPE = "SEARCH";
/**
* Default class logger.
*/
- private final Logger logger = Logger.getLogger(OverviewParser.class);
+ private final Logger logger = Logger.getLogger(OverviewParser.class);
/**
* Method that parse zip file and creates list of {@link OverviewImage images}
@@ -123,7 +125,7 @@ public class OverviewParser {
* @throws InvalidOverviewFile
* thrown when the zip file contains invalid data
*/
- public List<OverviewImage> parseOverviewLinks(Map<String, Model> models, List<ImageZipEntryFile> files, String outputDirectory) throws InvalidOverviewFile {
+ public List<OverviewImage> parseOverviewLinks(Set<Model> models, List<ImageZipEntryFile> files, String outputDirectory) throws InvalidOverviewFile {
if (outputDirectory != null) {
File f = new File(outputDirectory);
if (!f.exists()) {
@@ -188,10 +190,19 @@ public class OverviewParser {
if (coordinates == null) {
throw new InvalidOverviewFile("File with coordinates (\"" + COORDINATES_FILENAME + "\") doesn't exist in overview images zip archive.");
}
+
processCoordinates(models, result, coordinates);
return result;
}
+ private Map<String, Model> createMapping(Set<Model> models) {
+ Map<String, Model> result = new HashMap<>();
+ for (Model model : models) {
+ result.put(model.getName(), model);
+ }
+ return result;
+ }
+
/**
* This method process data from {@link #COORDINATES_FILENAME} in zip archive.
* This method adds connections between images and between images and models.
@@ -207,7 +218,8 @@ public class OverviewParser {
* @throws InvalidOverviewFile
* thrown when the data are invalid
*/
- protected void processCoordinates(Map<String, Model> models, List<OverviewImage> images, String coordinatesData) throws InvalidOverviewFile {
+ protected void processCoordinates(Set<Model> models, List<OverviewImage> images, String coordinatesData) throws InvalidOverviewFile {
+ Map<String, Model> modelMapping = createMapping(models);
String[] rows = coordinatesData.replaceAll("\r", "\n").split("\n");
Integer filenameColumn = null;
Integer polygonColumn = null;
@@ -292,16 +304,16 @@ public class OverviewParser {
if (!row.isEmpty() && !row.startsWith("#")) {
columns = row.split("\t", -1);
if (columns.length != headerColumns) {
- throw new InvalidCoordinatesFile("Invalid number of columns (" + columns.length + " found, but " + headerColumns + " expected). Row: \"" + row
- + "\"");
+ throw new InvalidCoordinatesFile(
+ "Invalid number of columns (" + columns.length + " found, but " + headerColumns + " expected). Row: \"" + row + "\"");
}
String filename = columns[filenameColumn];
String polygon = columns[polygonColumn];
- String modelName = columns[targetFilenameColumn];
+ String modelName = FilenameUtils.removeExtension(columns[targetFilenameColumn]);
String coord = columns[redirectionCoordinatesColumn];
String zoomLevel = columns[zoomLevelColumn];
String linkType = columns[targetTypeColumn];
- createOverviewLink(filename, polygon, modelName, coord, zoomLevel, linkType, images, models);
+ createOverviewLink(filename, polygon, modelName, coord, zoomLevel, linkType, images, modelMapping);
}
}
for (OverviewImage image : images) {
@@ -322,8 +334,9 @@ public class OverviewParser {
Area area2 = new Area(polygon2);
area.intersect(area2);
if (!area.isEmpty()) {
- throw new InvalidOverviewFile("Polygon coordinates in " + COORDINATES_FILENAME + " file overlap. Image: " + image.getFilename() + "; polgyon1 = "
- + ol.getPolygon() + "; polygon2 = " + ol2.getPolygon());
+ throw new InvalidOverviewFile(
+ "Polygon coordinates in " + COORDINATES_FILENAME + " file overlap. Image: " + image.getFilename() + "; polgyon1 = " + ol.getPolygon()
+ + "; polygon2 = " + ol2.getPolygon());
}
}
}
@@ -397,7 +410,7 @@ public class OverviewParser {
} else if (linkType.equals(IMAGE_LINK_TYPE)) {
OverviewImage targetImage = null;
for (OverviewImage oi : images) {
- if (oi.getFilename().equalsIgnoreCase(linkTarget)) {
+ if (FilenameUtils.removeExtension(oi.getFilename()).equalsIgnoreCase(linkTarget)) {
targetImage = oi;
}
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..e73da9a7687e613d79658c674fddc5b1304745c8
--- /dev/null
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -0,0 +1,62 @@
+package lcsb.mapviewer.converter;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class ProjectFactory {
+ Logger logger = Logger.getLogger(ProjectFactory.class);
+ private ComplexZipConverter converter;
+
+ public ProjectFactory(ComplexZipConverter converter) {
+ this.converter = converter;
+ }
+
+ public Project create(ComplexZipConverterParams params) throws InvalidInputDataExecption {
+ return create(params, new Project());
+ }
+
+ public Project create(ComplexZipConverterParams params, Project project) throws InvalidInputDataExecption {
+ Model model = converter.createModel(params);
+
+ Set<Model> models = new HashSet<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+
+ project.addModel(model);
+ ZipFile zipFile = params.getZipFile();
+ Enumeration<? extends ZipEntry> entries;
+
+
+ entries = zipFile.entries();
+ List<ImageZipEntryFile> imageEntries = new ArrayList<>();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ ZipEntryFile zef = params.getEntry(entry.getName());
+ if (zef instanceof ImageZipEntryFile) {
+ imageEntries.add((ImageZipEntryFile) zef);
+ }
+ }
+ }
+
+ if (imageEntries.size() > 0) {
+ OverviewParser parser = new OverviewParser();
+ project.addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir()));
+ }
+ return project;
+ }
+}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
index 19a555096aca975a490583e4de9cbd11bf6b347b..f69bc17894122004b4ff0bd1f69def8e6998dd80 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/AllTests.java
@@ -6,7 +6,8 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ ComplexZipConverterTest.class, //
- OverviewParserTest.class,//
+ OverviewParserTest.class, //
+ ProjectFactoryTest.class,//
})
public class AllTests {
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index d80cfce64501edbf5388c8501bdab8a80910eb2f..8ac95951d99da55c05bbe7c154e1a29ecc48c5cc 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -3,15 +3,10 @@ package lcsb.mapviewer.converter;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import java.awt.geom.Point2D;
import java.io.File;
import java.io.InputStream;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import org.apache.log4j.Logger;
@@ -23,11 +18,7 @@ import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.map.InconsistentModelException;
-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 lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -161,12 +152,10 @@ public class ComplexZipConverterTest {
@Test
public void testConstructor() throws Exception {
try {
- try {
- new ComplexZipConverter<AbstractConverter>(AbstractConverter.class);
- fail("Exception expected");
- } catch (InvalidClassException e) {
+ new ComplexZipConverter(AbstractConverter.class);
+ fail("Exception expected");
- }
+ } catch (InvalidClassException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -177,12 +166,10 @@ public class ComplexZipConverterTest {
@Test
public void testConstructor2() throws Exception {
try {
- try {
- new ComplexZipConverter<InterfaceConverter>(InterfaceConverter.class);
- fail("Exception expected");
- } catch (InvalidClassException e) {
+ new ComplexZipConverter(InterfaceConverter.class);
+ fail("Exception expected");
- }
+ } catch (InvalidClassException e) {
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -193,7 +180,7 @@ public class ComplexZipConverterTest {
@Test
public void testConstructor3() throws Exception {
try {
- new ComplexZipConverter<MockConverter>(MockConverter.class);
+ new ComplexZipConverter(MockConverter.class);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -204,7 +191,7 @@ public class ComplexZipConverterTest {
@Test
public void testParamsOk() throws Exception {
try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -264,7 +251,7 @@ public class ComplexZipConverterTest {
@Test
public void testChangeModelZipEntry() throws Exception {
try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -324,7 +311,7 @@ public class ComplexZipConverterTest {
@Test
public void testParamsMissing() throws Exception {
try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -349,7 +336,7 @@ public class ComplexZipConverterTest {
public void testParamsInvalid1() throws Exception {
try {
// two mains
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -375,7 +362,7 @@ public class ComplexZipConverterTest {
public void testParamsInvalid2() throws Exception {
try {
// zero mains
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", false, false, null));
@@ -401,7 +388,7 @@ public class ComplexZipConverterTest {
public void testParamsInvalid3() throws Exception {
try {
// two mappings
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -427,7 +414,7 @@ public class ComplexZipConverterTest {
public void testParamsMissingMapping() throws Exception {
try {
// zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -463,7 +450,7 @@ public class ComplexZipConverterTest {
public void testTooManyParams() throws Exception {
try {
// zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/complex_model.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -488,7 +475,7 @@ public class ComplexZipConverterTest {
public void testInvalidMappingFile() throws Exception {
try {
// zero mappings (should be ok)
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
ComplexZipConverterParams params = new ComplexZipConverterParams();
params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
@@ -505,56 +492,4 @@ public class ComplexZipConverterTest {
}
}
- @Test
- public void testOverviewImageLink() throws Exception {
- try {
- ComplexZipConverter<MockConverter> converter = new ComplexZipConverter<MockConverter>(MockConverter.class);
- ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
- ComplexZipConverterParams params = new ComplexZipConverterParams();
- params.zipFile(zipFile);
-
- ZipEntryFileFactory factory = new ZipEntryFileFactory();
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- if (!entry.isDirectory()) {
- params.entry(factory.createZipEntryFile(entry, zipFile));
- }
- }
-
- Model model = converter.createModel(params);
- assertNotNull(model);
- assertEquals("main", model.getName());
-
- List<OverviewImage> result = model.getOverviewImages();
-
- assertNotNull(result);
- assertEquals(1, result.size());
-
- OverviewImage img = result.get(0);
-
- assertEquals("test.png", img.getFilename());
- assertEquals((Integer) 639, img.getHeight());
- assertEquals((Integer) 963, img.getWidth());
- assertEquals(2, img.getLinks().size());
-
- OverviewLink link = img.getLinks().get(0);
- List<Point2D> polygon = link.getPolygonCoordinates();
- assertEquals(4, polygon.size());
-
- assertTrue(link instanceof OverviewModelLink);
-
- OverviewModelLink mLink = (OverviewModelLink) link;
- assertEquals((Integer) 10, mLink.getxCoord());
- assertEquals((Integer) 10, mLink.getyCoord());
- assertEquals((Integer) 3, mLink.getZoomLevel());
- assertEquals(model.getModelData(), mLink.getLinkedModel());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
index dc8a7187a3ec6bf8f050ebbf94f4e85bbbe463c3..50777ea476c2b48bf91f150162df8119b0e9cb58 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
@@ -10,9 +10,15 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
-import java.util.Map;
+import java.util.Set;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.model.map.OverviewImage;
@@ -21,15 +27,9 @@ import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
public class OverviewParserTest {
- Logger logger = Logger.getLogger(OverviewParserTest.class);
- OverviewParser parser = new OverviewParser();
+ Logger logger = Logger.getLogger(OverviewParserTest.class);
+ OverviewParser parser = new OverviewParser();
@Before
public void setUp() throws Exception {
@@ -42,7 +42,7 @@ public class OverviewParserTest {
@Test
public void testParsingValidFile() throws Exception {
try {
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/valid_overview");
List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null);
assertNotNull(result);
@@ -62,7 +62,8 @@ public class OverviewParserTest {
assertTrue(link instanceof OverviewModelLink);
OverviewModelLink mLink = (OverviewModelLink) link;
- assertEquals(models.get("main.xml").getModelData(), mLink.getLinkedModel());
+ Model mainModel = models.iterator().next();
+ assertEquals(mainModel.getModelData(), mLink.getLinkedModel());
assertEquals((Integer) 10, mLink.getxCoord());
assertEquals((Integer) 10, mLink.getyCoord());
assertEquals((Integer) 3, mLink.getZoomLevel());
@@ -86,7 +87,7 @@ public class OverviewParserTest {
@Test
public void testParsingValidFile2() throws Exception {
try {
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
String tmpDir = "tmp";
@@ -113,7 +114,7 @@ public class OverviewParserTest {
public void testParsingInvalidFile1() throws Exception {
try {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_1");
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null);
fail("Exception expected");
@@ -129,7 +130,7 @@ public class OverviewParserTest {
public void testParsingInvalidFile2() throws Exception {
try {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_2");
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null);
fail("Exception expected");
@@ -145,7 +146,7 @@ public class OverviewParserTest {
public void testParsingInvalidFile3() throws Exception {
try {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_3");
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null);
fail("Exception expected");
@@ -157,9 +158,11 @@ public class OverviewParserTest {
}
}
- private Map<String, Model> createValidTestMapModel() {
- Map<String, Model> result = new HashMap<String, Model>();
- result.put("main.xml", new ModelFullIndexed(null));
+ private Set<Model> createValidTestMapModel() {
+ Set<Model> result = new HashSet<>();
+ Model model = new ModelFullIndexed(null);
+ model.setName("main");
+ result.add(model);
return result;
}
@@ -173,7 +176,7 @@ public class OverviewParserTest {
try {
String invalidCoordinates = "test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3\n" + //
"test.png 10,10 10,400 400,400 400,10 main.xml 10,10 4";
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<OverviewImage>();
OverviewImage oi = new OverviewImage();
@@ -198,7 +201,7 @@ public class OverviewParserTest {
String invalidCoordinates = "FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE\n" + //
"test.png 10,10 100,10 100,100 10,10 main.xml 10,10 3 MODEL\n" + //
"test.png 200,200 200,400 400,400 400,200 main.xml 10,10 4 MODEL";
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<OverviewImage>();
OverviewImage oi = new OverviewImage();
@@ -221,9 +224,9 @@ public class OverviewParserTest {
public void testParseValidComplexCoordinates() throws Exception {
try {
String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"));
- Map<String, Model> models = createValidTestMapModel();
+ Set<Model> models = createValidTestMapModel();
- List<OverviewImage> images = new ArrayList<OverviewImage>();
+ List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
oi.setFilename("test.png");
oi.setWidth(1000);
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..fc1d6640bb293a149fe830c972bd2ec29aff3492
--- /dev/null
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
@@ -0,0 +1,94 @@
+package lcsb.mapviewer.converter;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.geom.Point2D;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ComplexZipConverterTest.MockConverter;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.model.ModelData;
+
+public class ProjectFactoryTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testOverviewImageLink() throws Exception {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
+ ProjectFactory projectFactory = new ProjectFactory(converter);
+ ZipFile zipFile = new ZipFile("testFiles/complex_model_with_img.zip");
+ ComplexZipConverterParams params = new ComplexZipConverterParams();
+ params.zipFile(zipFile);
+
+ ZipEntryFileFactory factory = new ZipEntryFileFactory();
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ params.entry(factory.createZipEntryFile(entry, zipFile));
+ }
+ }
+
+ Project project = projectFactory.create(params);
+ assertNotNull(project);
+ ModelData model = project.getModels().iterator().next();
+ assertEquals("main", model.getName());
+
+ List<OverviewImage> result = project.getOverviewImages();
+
+ assertNotNull(result);
+ assertEquals(1, result.size());
+
+ OverviewImage img = result.get(0);
+
+ assertEquals("test.png", img.getFilename());
+ assertEquals((Integer) 639, img.getHeight());
+ assertEquals((Integer) 963, img.getWidth());
+ assertEquals(2, img.getLinks().size());
+
+ OverviewLink link = img.getLinks().get(0);
+ List<Point2D> polygon = link.getPolygonCoordinates();
+ assertEquals(4, polygon.size());
+
+ assertTrue(link instanceof OverviewModelLink);
+
+ OverviewModelLink mLink = (OverviewModelLink) link;
+ assertEquals((Integer) 10, mLink.getxCoord());
+ assertEquals((Integer) 10, mLink.getyCoord());
+ assertEquals((Integer) 3, mLink.getZoomLevel());
+ assertEquals(model, mLink.getLinkedModel());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 203c3070a339c83fc2f9f2fb4f0106a376d8a896..e9cf25c19222055ce89eb8d154d13725f76362b6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -232,9 +232,6 @@ public class CopyCommand extends NewModelCommand {
for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
result.addSubmodelConnection(connection.copy());
}
- for (OverviewImage oi : model.getOverviewImages()) {
- result.addOverviewImage(oi.copy());
- }
for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
result.addDataMiningSet(new DataMiningSet(dataMiningSet));
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 6ff5608d3cc46fafcfa79118f2217a9c9badac07..6519c2bcd95dca3a335b81db11de75d9fad45a13 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -300,27 +300,6 @@ public class CopyCommandTest extends CommandTestFunctions {
return model;
}
- @Test
- public void testCopyModelWithImages() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- OverviewImage oi = new OverviewImage();
- OverviewModelLink oml = new OverviewModelLink();
- oml.setLinkedModel(model);
- oml.setPolygon("1,2");
- oi.addLink(oml);
- model.addOverviewImage(oi);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testCopyModelReaction() throws Exception {
try {
diff --git a/model/src/main/java/lcsb/mapviewer/model/Project.java b/model/src/main/java/lcsb/mapviewer/model/Project.java
index 556ee98b37396f84f3444ff5eed907f13d9f9968..c14db03b826653f26ad8344b009844d6384421a1 100644
--- a/model/src/main/java/lcsb/mapviewer/model/Project.java
+++ b/model/src/main/java/lcsb/mapviewer/model/Project.java
@@ -15,6 +15,7 @@ import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
+import javax.persistence.OrderBy;
import javax.persistence.Table;
import org.apache.log4j.Appender;
@@ -22,10 +23,15 @@ import org.apache.log4j.Logger;
import org.apache.log4j.spi.LoggingEvent;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.LazyCollection;
+import org.hibernate.annotations.LazyCollectionOption;
import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -43,12 +49,12 @@ public class Project implements Serializable {
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(Project.class);
+ private static Logger logger = Logger.getLogger(Project.class);
/**
*
*/
- private static final long serialVersionUID = 1L;
+ private static final long serialVersionUID = 1L;
/**
* Unique database identifier.
@@ -56,86 +62,98 @@ public class Project implements Serializable {
@Id
@GeneratedValue(strategy = GenerationType.IDENTITY)
@Column(name = "idDb", unique = true, nullable = false)
- private int id;
+ private int id;
/**
* Project identifier defined by the user (some meaningful string).
*/
@Column(name = "project_id", unique = true, nullable = false)
- private String projectId;
+ private String projectId;
/**
* Project disease.
*/
@Cascade({ CascadeType.ALL })
@OneToOne
- private MiriamData disease;
+ private MiriamData disease;
/**
* Name of the project.
*/
- private String name;
+ private String name;
/**
* Version of the project.
*/
- private String version;
+ private String version;
/**
* Directory where the images on the server will be stored for this project.
*/
- private String directory;
+ private String directory;
/**
* Status of the project used during uploading the project to the system.
*/
- private ProjectStatus status = ProjectStatus.UNKNOWN;
+ private ProjectStatus status = ProjectStatus.UNKNOWN;
/**
* Progress of single step of project uploading.
*/
- private double progress = 0;
+ private double progress = 0;
/**
* Errors connected with the project.
*/
- private String errors = null;
+ private String errors = null;
/**
* Short description of the map.
*/
@Column(columnDefinition = "TEXT")
- private String warnings;
+ private String warnings;
/**
* Map models in the project.
*/
@Cascade({ CascadeType.ALL })
@OneToMany(mappedBy = "project", orphanRemoval = true)
- private Set<ModelData> models = new HashSet<>();
+ private Set<ModelData> models = new HashSet<>();
/**
* Here we store input file.
*/
@Basic(fetch = FetchType.LAZY)
- private byte[] inputData;
+ private byte[] inputData;
/**
* Here we store input file.
*/
- private String inputFileName;
+ private String inputFileName;
/**
* Organism associated with the project.
*/
@Cascade({ CascadeType.ALL })
@OneToOne
- private MiriamData organism;
+ private MiriamData organism;
/**
* SBGN format selection. Set, if map is to be displayed in SBGN format
*/
- private boolean sbgnFormat = false;
+ private boolean sbgnFormat = false;
+
+ /**
+ * List of overview images describing this {@link Project}. The elements on
+ * the list can create a hierarchy that describe dependencies, however now
+ * matter if the image is a top-level object or a leaf it should be placed on
+ * this list.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "project", orphanRemoval = true)
+ @OrderBy("id")
+ @LazyCollection(LazyCollectionOption.FALSE)
+ private List<OverviewImage> overviewImages = new ArrayList<>();
/**
* Default constructor.
@@ -504,4 +522,62 @@ public class Project implements Serializable {
this.version = version;
}
+ /**
+ * @return the overviewImages
+ * @see #overviewImages
+ */
+ public List<OverviewImage> getOverviewImages() {
+ return overviewImages;
+ }
+
+ /**
+ * @param overviewImages
+ * the overviewImages to set
+ * @see #overviewImages
+ */
+ public void setOverviewImages(List<OverviewImage> overviewImages) {
+ this.overviewImages = overviewImages;
+ for (OverviewImage overviewImage : overviewImages) {
+ overviewImage.setProject(this);
+ }
+ }
+
+ /**
+ * Returns top level {@link OverviewImage} that should be present as a first
+ * one when switching to view data by the overview images.
+ *
+ * @return top level {@link OverviewImage}
+ */
+ public OverviewImage getTopOverviewImage() {
+ Set<OverviewImage> set = new HashSet<OverviewImage>();
+ set.addAll(getOverviewImages());
+ for (OverviewImage image : getOverviewImages()) {
+ for (OverviewLink ol : image.getLinks()) {
+ if (ol instanceof OverviewImageLink) {
+ set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
+ }
+ }
+ }
+ if (set.size() > 0) {
+ return set.iterator().next();
+ } else if (getOverviewImages().size() > 0) {
+ logger.warn("Cannot determine top level image. Taking first one: " + getOverviewImages().get(0).getFilename());
+ return getOverviewImages().get(0);
+ } else {
+ return null;
+ }
+ }
+
+ public void addOverviewImage(OverviewImage oi) {
+ this.overviewImages.add(oi);
+ oi.setProject(this);
+ }
+
+ public void addOverviewImages(List<OverviewImage> parseOverviewLinks) {
+ for (OverviewImage overviewImage : parseOverviewLinks) {
+ this.addOverviewImage(overviewImage);
+ }
+
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
index f71cfa88baf07f6e0aed5e7102d6a2f2347267e8..e837b18f77bc1da132973b4fe6e205284dfd131b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
@@ -19,6 +19,7 @@ import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.ModelData;
/**
@@ -48,11 +49,11 @@ public class OverviewImage implements Serializable {
private int id;
/**
- * The description belongs to this model. It doesn't mean that {@link #links}
- * will point to this model. Links can also point to submodel.
+ * The image belongs to this {@link Project}. Links can point to any
+ * (sub)model in this project.
*/
@ManyToOne(fetch = FetchType.LAZY, optional = false)
- private ModelData model;
+ private Project project;
/**
* Name of the file in file system that reresent this overview image.
@@ -76,7 +77,7 @@ public class OverviewImage implements Serializable {
@Cascade({ CascadeType.ALL })
@OneToMany(fetch = FetchType.EAGER, mappedBy = "overviewImage", orphanRemoval = true)
@OrderBy("id")
- private List<OverviewLink> links = new ArrayList<OverviewLink>();
+ private List<OverviewLink> links = new ArrayList<>();
/**
* Default constructor.
@@ -94,7 +95,7 @@ public class OverviewImage implements Serializable {
*/
public OverviewImage(OverviewImage overviewImage) {
this.setId(overviewImage.getId());
- this.setModel(overviewImage.getModel());
+ this.setProject(overviewImage.getProject());
this.setFilename(overviewImage.getFilename());
this.setWidth(overviewImage.getWidth());
this.setHeight(overviewImage.getHeight());
@@ -171,23 +172,6 @@ public class OverviewImage implements Serializable {
this.links = links;
}
- /**
- * @return the model
- * @see #model
- */
- public ModelData getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModel(ModelData model) {
- this.model = model;
- }
-
/**
* @return the id
* @see #id
@@ -228,4 +212,20 @@ public class OverviewImage implements Serializable {
throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
}
}
+
+ /**
+ * @return the project
+ * @see #project
+ */
+ public Project getProject() {
+ return project;
+ }
+
+ /**
+ * @param project the project to set
+ * @see #project
+ */
+ public void setProject(Project project) {
+ this.project = project;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 62bc8dff797dcf613e3ac5756f8115f353372d5e..5f7e5f5e87d2b42694aaf322317191ef5147fbcb 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -8,7 +8,6 @@ import java.util.Set;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.OverviewImage;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
@@ -525,37 +524,6 @@ public interface Model {
*/
Model getSubmodelByName(String name);
- /**
- * Returns list of {@link OverviewImage overview images}.
- *
- * @return list of {@link OverviewImage overview images}.
- */
- List<OverviewImage> getOverviewImages();
-
- /**
- * Adds new {@link OverviewImage} to list of available overview images.
- *
- * @param overviewImage
- * new {@link OverviewImage}
- */
- void addOverviewImage(OverviewImage overviewImage);
-
- /**
- * Sets list of {@link OverviewImage overview images}.
- *
- * @param overviewImages
- * list of overview images
- */
- void setOverviewImages(List<OverviewImage> overviewImages);
-
- /**
- * Returns top level {@link OverviewImage} that should be present as a first
- * one when switching to view data by the overview images.
- *
- * @return top level {@link OverviewImage}
- */
- OverviewImage getTopOverviewImage();
-
/**
* Adds layout to list of layouts on a given position.
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index c20239a5e02705aab8d06fbf2e17e449e7b435b1..89b885d430c2d0af22ae480171f3a9724ec9c1c0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -161,11 +161,6 @@ public class ModelComparator implements Comparator<Model> {
return status;
}
- status = compareOverviewImages(arg0.getOverviewImages(), arg1.getOverviewImages());
- if (status != 0) {
- logger.debug("Set of overview images different");
- return status;
- }
status = integerComparator.compare(arg0.getDataMiningSets().size(), arg1.getDataMiningSets().size());
if (status != 0) {
logger.debug("Set of data mining sets different");
@@ -183,30 +178,6 @@ public class ModelComparator implements Comparator<Model> {
return 0;
}
- /**
- * Compares two lists of {@link OverviewImage}.
- *
- * @param overviewImages
- * first list to compare
- * @param overviewImages2
- * second list to compare
- * @return 0 if both lists are equal, -1/1 otherwise
- */
- private int compareOverviewImages(List<OverviewImage> overviewImages, List<OverviewImage> overviewImages2) {
- if (overviewImages.size() != overviewImages2.size()) {
- return overviewImages.size() - overviewImages2.size();
- } else {
- OverviewImageComparator oic = new OverviewImageComparator(epsilon);
- for (int i = 0; i < overviewImages.size(); i++) {
- int status = oic.compare(overviewImages.get(i), overviewImages2.get(i));
- if (status != 0) {
- return status;
- }
- }
- }
- return 0;
- }
-
/**
* Compares two set of reactions.
*
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index dddf43d1533ba578aba8e6e72cc7d734deea0815..b8e548c4d2c9134b5885517030d2b76330a8a911 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -187,17 +187,6 @@ public class ModelData implements Serializable {
@OneToMany(fetch = FetchType.LAZY, mappedBy = "submodel")
private Set<SubmodelConnection> parentModels = new HashSet<>();
- /**
- * List of overview images describing this model. This list should be set only
- * in the top-level model. The elements on the list can create a hierarchy
- * that describe dependencies, however now matter if the image is a top-level
- * object or a leaf it should be placed on this list.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "model", orphanRemoval = true)
- @OrderBy("id")
- private List<OverviewImage> overviewImages = new ArrayList<>();
-
/**
* List of {@link DataMiningSet} in the model. These data mining sets are used
* to create suggested (but missing) connections in the model.
@@ -699,26 +688,6 @@ public class ModelData implements Serializable {
this.parentModels = parentModels;
}
- /**
- * @return the overviewImages
- * @see #overviewImages
- */
- public List<OverviewImage> getOverviewImages() {
- return overviewImages;
- }
-
- /**
- * @param overviewImages
- * the overviewImages to set
- * @see #overviewImages
- */
- public void setOverviewImages(List<OverviewImage> overviewImages) {
- this.overviewImages = overviewImages;
- for (OverviewImage overviewImage : overviewImages) {
- overviewImage.setModel(this);
- }
- }
-
/**
* @return the dataMining
* @see #dataMiningSets
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 67ba368bf5e408664e341a271d5aee87cd513fef..a1c335748b8f773f792ffb802c46c4c960ffed01 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -571,44 +571,6 @@ public class ModelFullIndexed implements Model {
return null;
}
- @Override
- public List<OverviewImage> getOverviewImages() {
- return modelData.getOverviewImages();
- }
-
- @Override
- public void addOverviewImage(OverviewImage overviewImage) {
- modelData.getOverviewImages().add(overviewImage);
- overviewImage.setModel(modelData);
- }
-
- @Override
- public void setOverviewImages(List<OverviewImage> parseOverviewLinks) {
- for (OverviewImage overviewImage : parseOverviewLinks) {
- addOverviewImage(overviewImage);
- }
- }
-
- @Override
- public OverviewImage getTopOverviewImage() {
- Set<OverviewImage> set = new HashSet<OverviewImage>();
- set.addAll(getOverviewImages());
- for (OverviewImage image : getOverviewImages()) {
- for (OverviewLink ol : image.getLinks()) {
- if (ol instanceof OverviewImageLink) {
- set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
- }
- }
- }
- if (set.size() > 0) {
- return set.iterator().next();
- } else if (getOverviewImages().size() > 0) {
- logger.warn("Cannot determine top level image. Taking first one: " + getOverviewImages().get(0).getFilename());
- return getOverviewImages().get(0);
- } else {
- return null;
- }
- }
@Override
public void addLayout(int index, Layout layout) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
index e56c03e4d21fb31417165a794ce17b2ebd31199b..839e29e072f2af7e03642d9c9bdeca6972951054 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelComparatorTest.java
@@ -50,10 +50,6 @@ public class ModelComparatorTest {
assertEquals(0, comparator.compare(model1, model1));
assertEquals(0, comparator.compare(null, null));
- model1.addOverviewImage(new OverviewImage());
- model2.addOverviewImage(new OverviewImage());
- assertEquals(0, comparator.compare(model1, model2));
-
model1.addDataMiningSet(new DataMiningSet());
model2.addDataMiningSet(new DataMiningSet());
assertEquals(0, comparator.compare(model1, model2));
@@ -270,14 +266,6 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addOverviewImage(new OverviewImage());
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
model1.setIdModel("asdsdasd");
assertTrue(comparator.compare(model1, model2) != 0);
@@ -337,17 +325,6 @@ public class ModelComparatorTest {
model1 = getModel();
model2 = getModel();
- model1.addOverviewImage(new OverviewImage());
- OverviewImage oi = new OverviewImage();
- oi.setWidth(12);
- model2.addOverviewImage(oi);
-
- assertTrue(comparator.compare(model1, model2) != 0);
- assertTrue(comparator.compare(model2, model1) != 0);
-
- model1 = getModel();
- model2 = getModel();
-
model1.addReaction(new Reaction());
model2.addReaction(new Reaction());
Reaction reaction = new Reaction();
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
index 39915cd053894642025d70acd9b61c961ec0b448..cd9c2d92d35f5da166c46a21b0f918c45bff8184 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelDataTest.java
@@ -301,9 +301,6 @@ public class ModelDataTest {
md.setParentModels(parents);
assertEquals(parents, md.getParentModels());
- md.setOverviewImages(overviewImages);
- assertEquals(overviewImages, md.getOverviewImages());
-
md.setDataMiningSets(dataMiningSets);
assertEquals(dataMiningSets, md.getDataMiningSets());
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index 9390fbbf6a43ccc3a4a7e4ab81a9a36dd8d4a5d5..9a6b0c0ed0a23ecda95fb4a3c4f309de718eb7e8 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -628,40 +628,6 @@ public class ModelFullIndexedTest {
}
}
- @Test
- public void testGetTopOverviewImage() {
- try {
- ModelFullIndexed model = new ModelFullIndexed(null);
- assertNull(model.getTopOverviewImage());
-
- OverviewImage image1 = new OverviewImage();
- OverviewImage image2 = new OverviewImage();
-
- OverviewImageLink link = new OverviewImageLink();
- link.setLinkedOverviewImage(image1);
- image2.addLink(link);
-
- List<OverviewImage> images = new ArrayList<>();
- images.add(image1);
- images.add(image2);
- model.setOverviewImages(images);
-
- OverviewImage top = model.getTopOverviewImage();
- assertEquals(top, image2);
-
- link = new OverviewImageLink();
- link.setLinkedOverviewImage(image2);
- image1.addLink(link);
-
- top = model.getTopOverviewImage();
- assertEquals(top, image1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
@Test
public void testGetSubmodelByName() {
try {
diff --git a/persist/src/db/11.1.0/fix_db_20170808.sql b/persist/src/db/11.1.0/fix_db_20170808.sql
index 1d4d4c9bd6ca0a30ad7a256571d49582ac8d13ca..d416c7dd5429385c284bb0bb0fd53407e4f8eb40 100644
--- a/persist/src/db/11.1.0/fix_db_20170808.sql
+++ b/persist/src/db/11.1.0/fix_db_20170808.sql
@@ -1,4 +1,6 @@
--- version moved from model into project
-alter table model_table drop column mapversion character varying default '';
-alter table model_table drop column mapversion;
-update project_table set version = model_table.mapversion from model_table where project_table.iddb = model_table.project_iddb;
\ No newline at end of file
+-- images moved to project
+alter table overview_image_table add column project_iddb integer;
+update overview_image_table set project_iddb = model_table.project_iddb from model_table where model_table.iddb = overview_image_table.model_iddb;
+select * from overview_image_table;
+delete from overview_image_table where project_iddb is null;
+alter table overview_image_table drop column model_iddb;
\ No newline at end of file
diff --git a/persist/src/db/11.1.0/fix_db_20170809.sql b/persist/src/db/11.1.0/fix_db_20170809.sql
new file mode 100644
index 0000000000000000000000000000000000000000..1d4d4c9bd6ca0a30ad7a256571d49582ac8d13ca
--- /dev/null
+++ b/persist/src/db/11.1.0/fix_db_20170809.sql
@@ -0,0 +1,4 @@
+-- version moved from model into project
+alter table model_table drop column mapversion character varying default '';
+alter table model_table drop column mapversion;
+update project_table set version = model_table.mapversion from model_table where project_table.iddb = model_table.project_iddb;
\ No newline at end of file
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index 75636b31ce21634d1418faeffcad20a67b951329..39b526739e865711edead551cd28ab9ee4290260 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -236,7 +236,7 @@ public class ProjectDaoTest extends PersistTestFunctions {
oml.setyCoord(2);
oml.setZoomLevel(3);
oi.addLink(oml);
- model.addOverviewImage(oi);
+ project.addOverviewImage(oi);
project.addModel(model);
projectDao.add(project);
@@ -246,7 +246,7 @@ public class ProjectDaoTest extends PersistTestFunctions {
assertNotNull(project2);
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
- OverviewImage oi2 = model2.getOverviewImages().get(0);
+ OverviewImage oi2 = project2.getOverviewImages().get(0);
OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);
assertEquals(oi.getFilename(), oi2.getFilename());
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 93c268e01338165570cb1b9a3d5600791eb11783..529e8792c63d95a2a1c58797e75bc9da6c4cc8a9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
@@ -106,31 +106,28 @@ public class ProjectRestImpl extends BaseRestImpl {
private ProjectMetaData createData(Project project, AuthenticationToken token) {
ProjectMetaData result = new ProjectMetaData();
- Model model = getModelService().getLastModelByProjectId(project.getProjectId(), token);
result.setName(project.getName());
result.setProjectId(project.getProjectId());
result.setIdObject(project.getId());
result.setVersion(project.getVersion());
- if (model != null) {
- result.setOverviewImageViews(factory.createList(model.getOverviewImages()));
+ result.setOverviewImageViews(factory.createList(project.getOverviewImages()));
- Set<OverviewImage> set = new HashSet<>();
- set.addAll(model.getOverviewImages());
- for (OverviewImage image : model.getOverviewImages()) {
- for (OverviewLink ol : image.getLinks()) {
- if (ol instanceof OverviewImageLink) {
- set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
- }
+ Set<OverviewImage> set = new HashSet<>();
+ set.addAll(project.getOverviewImages());
+ for (OverviewImage image : project.getOverviewImages()) {
+ for (OverviewLink ol : image.getLinks()) {
+ if (ol instanceof OverviewImageLink) {
+ set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
}
}
- if (set.size() > 0) {
- result.setTopOverviewImage(factory.create(set.iterator().next()));
- } else if (model.getOverviewImages().size() > 0) {
- logger.warn("Cannot determine top level image. Taking first one. " + model.getOverviewImages().get(0).getFilename());
- result.setTopOverviewImage(factory.create(model.getOverviewImages().get(0)));
- }
+ }
+ if (set.size() > 0) {
+ result.setTopOverviewImage(factory.create(set.iterator().next()));
+ } else if (project.getOverviewImages().size() > 0) {
+ logger.warn("Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
+ result.setTopOverviewImage(factory.create(project.getOverviewImages().get(0)));
}
return result;
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index af2f8dcf6120fddefb942ed728c8a84d9e044e8e..a1a84dbd5fbca70097ba3fb8377466d6decb3cba 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -186,7 +186,7 @@ public abstract class RestTestFunctions {
private Model getModelForFile(String fileName) throws InvalidInputDataExecption, IOException {
if (fileName.endsWith("zip")) {
- ComplexZipConverter<CellDesignerXmlParser> parser = new ComplexZipConverter<CellDesignerXmlParser>(CellDesignerXmlParser.class);
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
ComplexZipConverterParams complexParams;
complexParams = new ComplexZipConverterParams().zipFile(fileName);
ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index a0b34ce3fd4af3340a40e993b4bc85e028f420c4..ee67364eb830c52470c347b423fffacb13bf2eed 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -50,6 +50,7 @@ import lcsb.mapviewer.converter.ComplexZipConverterParams;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ProjectFactory;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
@@ -665,7 +666,7 @@ public class ProjectService implements IProjectService {
* @throws InvalidInputDataExecption
* thrown when there is a problem with input file
*/
- protected Model createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
+ protected void createModel(final CreateProjectParams params, Project dbProject) throws InvalidInputDataExecption {
ModelData modelData = modelDao.getLastModelForProjectIdentifier(params.getProjectId(), false);
if (modelData != null) {
throw new InvalidArgumentException("Model with the given name already exists");
@@ -674,17 +675,17 @@ public class ProjectService implements IProjectService {
final Project project = dbProject;
updateProjectStatus(project, ProjectStatus.PARSING_DATA, 0.0, params);
- Model model = null;
if (params.isComplex()) {
try {
- ComplexZipConverter<CellDesignerXmlParser> parser = new ComplexZipConverter<CellDesignerXmlParser>(CellDesignerXmlParser.class);
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
ComplexZipConverterParams complexParams;
complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
complexParams.visualizationDir(params.getProjectDir());
for (ZipEntryFile entry : params.getZipEntries()) {
complexParams.entry(entry);
}
- model = parser.createModel(complexParams);
+ ProjectFactory projectFactory = new ProjectFactory(parser);
+ projectFactory.create(complexParams, dbProject);
} catch (IOException e) {
throw new InvalidInputDataExecption(e);
}
@@ -696,17 +697,24 @@ public class ProjectService implements IProjectService {
parser = new CellDesignerXmlParser();
}
try {
- model = parser
+ Model model = parser
.createModel(new ConverterParams().filename(params.getProjectFile()).sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
model.setName(params.getProjectName());
+ project.addModel(model);
} catch (FileNotFoundException ex) {
throw new InvalidInputDataExecption(ex);
}
}
- updateProjectStatus(project, ProjectStatus.PARSING_DATA, IProgressUpdater.MAX_PROGRESS, params);
- model.setNotes(params.getDescription());
- model.setZoomLevels(generator.computeZoomLevels(model));
- model.setTileSize(MapGenerator.TILE_SIZE);
+ Model topModel = project.getModels().iterator().next().getModel();
+ topModel.setZoomLevels(generator.computeZoomLevels(topModel));
+ topModel.setTileSize(MapGenerator.TILE_SIZE);
+ topModel.setNotifyEmail(params.getNotifyEmail());
+
+ updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
+ dbUtils.setAutoFlush(false);
+ projectDao.update(project);
+ dbUtils.setAutoFlush(true);
+ projectDao.flush();
List<BuildInLayout> buildInLayouts = new ArrayList<>();
BuildInLayout nested = null;
@@ -729,26 +737,27 @@ public class ProjectService implements IProjectService {
Collections.reverse(buildInLayouts);
for (BuildInLayout buildInLayout : buildInLayouts) {
- Layout topLayout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + model.getId() + "/", true);
+ Layout topLayout = new Layout(
+ buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + topModel.getId() + "/", true);
topLayout.setStatus(LayoutStatus.NA);
topLayout.setProgress(0.0);
topLayout.setHierarchicalView(buildInLayout.isNested());
- model.addLayout(0, topLayout);
+ topModel.addLayout(0, topLayout);
int submodelId = 1;
List<Layout> semanticLevelOverlays = new ArrayList<>();
if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- for (int i = 0; i <= model.getZoomLevels(); i++) {
- String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-" + model.getId() + "/";
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
+ String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-" + topModel.getId() + "/";
Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
semanticOverlay.setStatus(LayoutStatus.NA);
semanticOverlay.setProgress(0.0);
semanticOverlay.setHierarchicalView(buildInLayout.isNested());
semanticOverlay.setHierarchyViewLevel(i);
semanticLevelOverlays.add(semanticOverlay);
- model.addLayout(1, semanticOverlay);
+ topModel.addLayout(1, semanticOverlay);
}
}
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ for (ModelSubmodelConnection connection : topModel.getSubmodelConnections()) {
Layout layout = new Layout(buildInLayout.getTitle(), params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + submodelId + "/", true);
layout.setStatus(LayoutStatus.NA);
layout.setProgress(0.0);
@@ -759,7 +768,7 @@ public class ProjectService implements IProjectService {
connection.getSubmodel().setZoomLevels(generator.computeZoomLevels(connection.getSubmodel().getModel()));
connection.getSubmodel().setTileSize(MapGenerator.TILE_SIZE);
if (buildInLayout.equals(BuildInLayout.SEMANTIC)) {
- for (int i = 0; i <= model.getZoomLevels(); i++) {
+ for (int i = 0; i <= topModel.getZoomLevels(); i++) {
String directory = params.getProjectDir() + "/" + buildInLayout.getDirectorySuffix() + "-" + i + "-" + submodelId + "/";
Layout semanticOverlay = new Layout(buildInLayout.getTitle() + "-" + i, directory, true);
semanticOverlay.setStatus(LayoutStatus.NA);
@@ -783,7 +792,7 @@ public class ProjectService implements IProjectService {
}
}
logger.debug("Updating annotations");
- modelAnnotator.performAnnotations(model, new IProgressUpdater() {
+ modelAnnotator.performAnnotations(topModel, new IProgressUpdater() {
@Override
public void setProgress(final double progress) {
@@ -792,14 +801,8 @@ public class ProjectService implements IProjectService {
}, annotators);
logger.debug("Annotations updated");
}
- updateProjectStatus(project, ProjectStatus.UPLOADING_TO_DB, 0.0, params);
- dbUtils.setAutoFlush(false);
- project.addModel(model);
- projectDao.update(project);
- dbUtils.setAutoFlush(true);
- projectDao.flush();
updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, 0.0, params);
- processDataMining(model, model.getDataMiningSets(), new IProgressUpdater() {
+ processDataMining(topModel, topModel.getDataMiningSets(), new IProgressUpdater() {
@Override
public void setProgress(double progress) {
@@ -810,9 +813,6 @@ public class ProjectService implements IProjectService {
updateProjectStatus(project, ProjectStatus.EXTENDING_MODEL, IProgressUpdater.MAX_PROGRESS, params);
logger.debug("Model created");
- model.setNotifyEmail(params.getNotifyEmail());
-
- return model;
}
/**
@@ -951,7 +951,8 @@ public class ProjectService implements IProjectService {
project.setInputFileName(FilenameUtils.getName(params.getProjectFile()));
}
- Model originalModel = createModel(params, project);
+ createModel(params, project);
+ Model originalModel = project.getModels().iterator().next().getModel();
if (!params.isSemanticZoom()) {
new CreateHierarchyCommand(originalModel, generator.computeZoomLevels(originalModel), generator.computeZoomFactor(originalModel)).execute();
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
index a218e76b52736eb4a6c6f7bb4ae84fd265e9240c..673700f9f80f8d1d5c4286c8225740ab6829c875 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/ModelViewFactory.java
@@ -52,6 +52,10 @@ public class ModelViewFactory extends AbstractViewFactory<Model, ModelView> {
}
if (model.getProject() != null) {
result.setProjectId(model.getProject().getProjectId());
+ result.setOverviewImageViews(overviewImageViewFactory.createList(model.getProject().getOverviewImages()));
+ if (result.getOverviewImageViews().size() > 0) {
+ result.setTopOverviewImage(overviewImageViewFactory.create(model.getProject().getTopOverviewImage()));
+ }
}
result.setLayouts(new ArrayList<LayoutView>());
result.setCustomLayouts(new ArrayList<LayoutView>());
@@ -80,10 +84,6 @@ public class ModelViewFactory extends AbstractViewFactory<Model, ModelView> {
submodels.add(create(connection.getSubmodel().getModel()));
}
result.setSubmodels(submodels);
- result.setOverviewImageViews(overviewImageViewFactory.createList(model.getOverviewImages()));
- if (result.getOverviewImageViews().size() > 0) {
- result.setTopOverviewImage(overviewImageViewFactory.create(model.getTopOverviewImage()));
- }
return result;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java b/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
index 0df765808e7a6ad9e95dd391c9416ae0616d8df2..4b4bc5b1508d4cc089d8ed6dce75e738a4461b2c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
+++ b/service/src/main/java/lcsb/mapviewer/services/view/OverviewImageViewFactory.java
@@ -36,8 +36,8 @@ public class OverviewImageViewFactory extends AbstractViewFactory<OverviewImage,
logger.warn("Empty image...");
return result;
}
- if (object.getModel() != null && object.getModel().getProject() != null) {
- result.setFilename(object.getModel().getProject().getDirectory() + "/" + object.getFilename());
+ if (object.getProject() != null) {
+ result.setFilename(object.getProject().getDirectory() + "/" + object.getFilename());
} else {
result.setFilename(object.getFilename());
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index ea47b42d45c8e4b1fd84a0ea16876ddf0edea198..101892cd487cc00c34ea5f1c8678aeaa2d734e82 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -434,7 +434,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
projectDir(tmpResultDir).//
analyzeAnnotations(false);
- ComplexZipConverter<CellDesignerXmlParser> parser = new ComplexZipConverter<CellDesignerXmlParser>(CellDesignerXmlParser.class);
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
ComplexZipConverterParams complexParams;
complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
for (ZipEntryFile entry : params.getZipEntries()) {
@@ -718,7 +718,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Cannot find overview images the model", 2, model.getOverviewImages().size());
+ assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
assertEquals("Number of layouts doesn't match", BuildInLayout.values().length-1, model.getLayouts().size());
assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(0).getTitle());
assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(1).getTitle());
@@ -762,7 +762,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Cannot find overview images the model", 2, model.getOverviewImages().size());
+ assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
assertEquals("Number of layouts doesn't match", BuildInLayout.values().length-1, model.getLayouts().size());
assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(1).getTitle());
assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(0).getTitle());