diff --git a/.idea/modules.xml b/.idea/modules.xml
index 6e6dd9acbdd939bf1c110062e928a9ee7c27aa96..ae3706f24995e2278ace6b3dbfc2415ef574834a 100644
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
@@ -2,7 +2,28 @@
<project version="4">
<component name="ProjectModuleManager">
<modules>
+ <module fileurl="file://$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" filepath="$PROJECT_DIR$/CellDesigner-plugin/CellDesigner-plugin.iml" />
+ <module fileurl="file://$PROJECT_DIR$/annotation/annotation.iml" filepath="$PROJECT_DIR$/annotation/annotation.iml" />
+ <module fileurl="file://$PROJECT_DIR$/commons/commons.iml" filepath="$PROJECT_DIR$/commons/commons.iml" />
+ <module fileurl="file://$PROJECT_DIR$/comparison/comparison.iml" filepath="$PROJECT_DIR$/comparison/comparison.iml" />
+ <module fileurl="file://$PROJECT_DIR$/console/console.iml" filepath="$PROJECT_DIR$/console/console.iml" />
+ <module fileurl="file://$PROJECT_DIR$/converter/converter.iml" filepath="$PROJECT_DIR$/converter/converter.iml" />
+ <module fileurl="file://$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" filepath="$PROJECT_DIR$/converter-CellDesigner/converter-CellDesigner.iml" />
+ <module fileurl="file://$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" filepath="$PROJECT_DIR$/converter-SBGNML/converter-SBGNML.iml" />
+ <module fileurl="file://$PROJECT_DIR$/converter-graphics/converter-graphics.iml" filepath="$PROJECT_DIR$/converter-graphics/converter-graphics.iml" />
+ <module fileurl="file://$PROJECT_DIR$/editor/editor.iml" filepath="$PROJECT_DIR$/editor/editor.iml" />
+ <module fileurl="file://$PROJECT_DIR$/frontend-js/frontend-js.iml" filepath="$PROJECT_DIR$/frontend-js/frontend-js.iml" />
<module fileurl="file://$PROJECT_DIR$/.idea/minerva.iml" filepath="$PROJECT_DIR$/.idea/minerva.iml" />
+ <module fileurl="file://$PROJECT_DIR$/model/model.iml" filepath="$PROJECT_DIR$/model/model.iml" />
+ <module fileurl="file://$PROJECT_DIR$/model-command/model-command.iml" filepath="$PROJECT_DIR$/model-command/model-command.iml" />
+ <module fileurl="file://$PROJECT_DIR$/parent.iml" filepath="$PROJECT_DIR$/parent.iml" />
+ <module fileurl="file://$PROJECT_DIR$/pathvisio/pathvisio.iml" filepath="$PROJECT_DIR$/pathvisio/pathvisio.iml" />
+ <module fileurl="file://$PROJECT_DIR$/persist/persist.iml" filepath="$PROJECT_DIR$/persist/persist.iml" />
+ <module fileurl="file://$PROJECT_DIR$/quadTrees/quadTrees.iml" filepath="$PROJECT_DIR$/quadTrees/quadTrees.iml" />
+ <module fileurl="file://$PROJECT_DIR$/reactome/reactome.iml" filepath="$PROJECT_DIR$/reactome/reactome.iml" />
+ <module fileurl="file://$PROJECT_DIR$/rest-api/rest-api.iml" filepath="$PROJECT_DIR$/rest-api/rest-api.iml" />
+ <module fileurl="file://$PROJECT_DIR$/service/service.iml" filepath="$PROJECT_DIR$/service/service.iml" />
+ <module fileurl="file://$PROJECT_DIR$/web/web.iml" filepath="$PROJECT_DIR$/web/web.iml" />
</modules>
</component>
</project>
\ No newline at end of file
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index 134f9ddb91de60742bb98ed094477bbca56fb842..b04589b96d9b7d64f661fa3fa45410365397d679 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -13,6 +13,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.zip.ZipFile;
import javax.imageio.ImageIO;
@@ -90,17 +91,17 @@ public class OverviewParser {
private static final Integer BUFFER_SIZE = 1024;
/**
- * String identifing {@link OverviewModelLink} connections.
+ * String identifying {@link OverviewModelLink} connections.
*/
private static final String MODEL_LINK_TYPE = "MODEL";
/**
- * String identifing {@link OverviewImageLink} connections between images.
+ * String identifying {@link OverviewImageLink} connections between images.
*/
private static final String IMAGE_LINK_TYPE = "IMAGE";
/**
- * String identifing {@link OverviewSearchLink} connections.
+ * String identifying {@link OverviewSearchLink} connections.
*/
private static final String SEARCH_LINK_TYPE = "SEARCH";
@@ -125,7 +126,7 @@ public class OverviewParser {
* @throws InvalidOverviewFile
* thrown when the zip file contains invalid data
*/
- public List<OverviewImage> parseOverviewLinks(Set<Model> models, List<ImageZipEntryFile> files, String outputDirectory) throws InvalidOverviewFile {
+ public List<OverviewImage> parseOverviewLinks(Set<Model> models, List<ImageZipEntryFile> files, String outputDirectory, ZipFile zipFile) throws InvalidOverviewFile {
if (outputDirectory != null) {
File f = new File(outputDirectory);
if (!f.exists()) {
@@ -151,14 +152,14 @@ public class OverviewParser {
// copy file to file system
if (outputDirectory != null) {
imageFile = new File(outputDirectory + "/" + filename);
- } else { // or temp file
+ } else { // or temporary file
imageFile = File.createTempFile("temp-file-name", ".png");
imageFile.deleteOnExit();
}
FileOutputStream fos = new FileOutputStream(imageFile);
byte[] bytes = new byte[BUFFER_SIZE];
int length;
- InputStream is = entry.getInputStream();
+ InputStream is = zipFile.getInputStream(zipFile.getEntry(entry.getFilename()));
while ((length = is.read(bytes)) >= 0) {
fos.write(bytes, 0, length);
}
@@ -175,7 +176,7 @@ public class OverviewParser {
StringBuilder sb = new StringBuilder("");
byte[] buffer = new byte[BUFFER_SIZE];
int read = 0;
- InputStream is = entry.getInputStream();
+ InputStream is = zipFile.getInputStream(zipFile.getEntry(entry.getFilename()));
while ((read = is.read(buffer)) >= 0) {
sb.append(new String(buffer, 0, read));
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index 11c34bf4ef262a1ceda2b7d412082c57e99aac5c..357a3da36158df62a51e1db9fc4d6a05f5980526 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -58,7 +58,7 @@ public class ProjectFactory {
if (imageEntries.size() > 0) {
OverviewParser parser = new OverviewParser();
- project.addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir()));
+ project.addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir(), zipFile));
}
return project;
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
index 5b930d5dfb2237bb2320da91643ae352f25757c1..cef2d1956bf09943b4b837f36245625cc1abc5a6 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.converter.zip;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
import java.io.IOException;
-import java.io.InputStream;
import java.io.Serializable;
/**
@@ -15,67 +12,31 @@ import java.io.Serializable;
*/
public class ImageZipEntryFile extends ZipEntryFile implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ImageZipEntryFile() {
+
+ }
+
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link ZipEntryFile#filename}
+ * @param inputStream
+ * input stream with the data for this entry.
+ * @see #baos
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public ImageZipEntryFile(String filename) {
+ super(filename);
+ }
- /**
- * Size of the buffer used to copy input streams.
- */
- private static final int BUFFER_SIZE = 1024;
-
- /**
- * Copy of the {@link InputStream} of the file.
- */
- private byte[] bytes;
-
- /**
- * Default constructor.
- */
- public ImageZipEntryFile() {
-
- }
-
- /**
- * Default constructor.
- *
- * @param filename
- * {@link ZipEntryFile#filename}
- * @param inputStream
- * input stream with the data for this entry.
- * @see #baos
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public ImageZipEntryFile(String filename, InputStream inputStream) throws IOException {
- super(filename);
- setInputStream(inputStream);
- }
-
- /**
- * @return the inputStream
- * @see #inputStream
- */
- public InputStream getInputStream() {
- return new ByteArrayInputStream(bytes);
- }
-
- /**
- * @param inputStream
- * the inputStream to set
- * @throws IOException
- * thrown when there is aproblem with accessing inputStream
- * @see #inputStream
- */
- public void setInputStream(InputStream inputStream) throws IOException {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- byte[] buffer = new byte[BUFFER_SIZE];
- int len;
- while ((len = inputStream.read(buffer)) > -1) {
- baos.write(buffer, 0, len);
- }
- baos.flush();
- bytes = baos.toByteArray();
- }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
index 164b0aeba75d212a4f09c981faa4954e0d4b34a4..99b30c9a5e02cc81a1d4598c8c52a31a378b1aa5 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
@@ -11,70 +11,72 @@ import java.io.Serializable;
*/
public class LayoutZipEntryFile extends ZipEntryFile implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Name of the layout.
- */
- private String name = "";
+ /**
+ * Name of the layout.
+ */
+ private String name = "";
- /**
- * Description of the layout.
- */
- private String description = "";
+ /**
+ * Description of the layout.
+ */
+ private String description = "";
- /**
- * Default constructor.
- */
- public LayoutZipEntryFile() {
+ /**
+ * Default constructor.
+ */
+ public LayoutZipEntryFile() {
- }
+ }
- /**
- * Default constructor.
- *
- * @param filename
- * {@link ZipEntryFile#filename}
- */
- public LayoutZipEntryFile(String filename) {
- super(filename);
- }
+ /**
+ * Default constructor.
+ *
+ * @param filename
+ * {@link ZipEntryFile#filename}
+ */
+ public LayoutZipEntryFile(String filename, String name, String description) {
+ super(filename);
+ this.name = name;
+ this.description = description;
+ }
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
- /**
- * @param description
- * the description to set
- * @see #description
- */
- public void setDescription(String description) {
- this.description = description;
- }
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
index 084e575cd01cac40a83cbe5d336b070865b62328..1bcdc4b20e5ebcf96f9b4efce7de1af63a80a909 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -165,7 +165,7 @@ public class ZipEntryFileFactory {
}
return zesf;
} else if (directory.equals(IMAGES_DIRECTORY)) {
- ImageZipEntryFile result = new ImageZipEntryFile(entry.getName(), zipFile.getInputStream(entry));
+ ImageZipEntryFile result = new ImageZipEntryFile(entry.getName());
return result;
} else if (directory.equals(LAYOUT_DIRECTORY)) {
LayoutZipEntryFile result = createLayoutZipEntryFile(entry.getName(), zipFile.getInputStream(entry));
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
index 50777ea476c2b48bf91f150162df8119b0e9cb58..feace015aecc51cdc5e9432d02f5f178aa45b73d 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
@@ -10,9 +10,12 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.Enumeration;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
@@ -28,226 +31,237 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class OverviewParserTest {
- Logger logger = Logger.getLogger(OverviewParserTest.class);
- OverviewParser parser = new OverviewParser();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParsingValidFile() throws Exception {
- try {
- Set<Model> models = createValidTestMapModel();
- List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/valid_overview");
- List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null);
- 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;
- 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());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private List<ImageZipEntryFile> createImageEntries(String string) throws IOException {
- List<ImageZipEntryFile> result = new ArrayList<ImageZipEntryFile>();
- for (final File fileEntry : new File(string).listFiles()) {
- if (!fileEntry.isDirectory()) {
- result.add(new ImageZipEntryFile(fileEntry.getName(), new FileInputStream(fileEntry)));
- }
- }
- return result;
- }
-
- @Test
- public void testParsingValidFile2() throws Exception {
- try {
- Set<Model> models = createValidTestMapModel();
-
- String tmpDir = "tmp";
-
- new File(tmpDir).mkdirs();
- List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/valid_overview");
- List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, tmpDir);
-
- assertTrue(new File(tmpDir + "/test.png").exists());
-
- assertNotNull(result);
- assertEquals(1, result.size());
- OverviewImage img = result.get(0);
- assertEquals("test.png", img.getFilename());
-
- new File(tmpDir).delete();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingInvalidFile1() throws Exception {
- try {
- List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_1");
- Set<Model> models = createValidTestMapModel();
-
- parser.parseOverviewLinks(models, imageEntries, null);
- fail("Exception expected");
- } catch (InvalidOverviewFile e) {
- assertTrue(e.getMessage().contains("Unknown image filename"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingInvalidFile2() throws Exception {
- try {
- List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_2");
- Set<Model> models = createValidTestMapModel();
-
- parser.parseOverviewLinks(models, imageEntries, null);
- fail("Exception expected");
- } catch (InvalidOverviewFile e) {
- assertTrue(e.getMessage().contains("Unknown model"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParsingInvalidFile3() throws Exception {
- try {
- List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_3");
- Set<Model> models = createValidTestMapModel();
-
- parser.parseOverviewLinks(models, imageEntries, null);
- fail("Exception expected");
- } catch (InvalidOverviewFile e) {
- assertTrue(e.getMessage().contains("coordinates outside image"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Set<Model> createValidTestMapModel() {
- Set<Model> result = new HashSet<>();
- Model model = new ModelFullIndexed(null);
- model.setName("main");
- result.add(model);
- return result;
- }
-
- /**
- * Test coordinates that overlap (exception is expected).
- *
- * @throws Exception
- */
- @Test
- public void testParseInvalidCoordinates() throws Exception {
- 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";
- Set<Model> models = createValidTestMapModel();
-
- List<OverviewImage> images = new ArrayList<OverviewImage>();
- OverviewImage oi = new OverviewImage();
- oi.setFilename("test.png");
- oi.setWidth(1000);
- oi.setHeight(1000);
- images.add(oi);
-
- parser.processCoordinates(models, images, invalidCoordinates);
-
- fail("Exception expected");
- } catch (InvalidOverviewFile e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseValidCoordinates() throws Exception {
- try {
- 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";
- Set<Model> models = createValidTestMapModel();
-
- List<OverviewImage> images = new ArrayList<OverviewImage>();
- OverviewImage oi = new OverviewImage();
- oi.setFilename("test.png");
- oi.setWidth(1000);
- oi.setHeight(1000);
- images.add(oi);
-
- parser.processCoordinates(models, images, invalidCoordinates);
-
- assertEquals(2, oi.getLinks().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseValidComplexCoordinates() throws Exception {
- try {
- String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"));
- Set<Model> models = createValidTestMapModel();
-
- List<OverviewImage> images = new ArrayList<>();
- OverviewImage oi = new OverviewImage();
- oi.setFilename("test.png");
- oi.setWidth(1000);
- oi.setHeight(1000);
- images.add(oi);
-
- OverviewImage oi2 = new OverviewImage();
- oi2.setFilename("test2.png");
- oi2.setWidth(1000);
- oi2.setHeight(1000);
- images.add(oi2);
-
- parser.processCoordinates(models, images, invalidCoordinates);
-
- assertEquals(2, oi.getLinks().size());
- assertEquals(1, oi2.getLinks().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ private static final String TEST_FILES_VALID_OVERVIEW_ZIP = "testFiles/valid_overview.zip";
+ Logger logger = Logger.getLogger(OverviewParserTest.class);
+ OverviewParser parser = new OverviewParser();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParsingValidFile() throws Exception {
+ try {
+ Set<Model> 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));
+ 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;
+ 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());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<ImageZipEntryFile> createImageEntries(String string) throws IOException {
+ List<ImageZipEntryFile> result = new ArrayList<>();
+
+ ZipFile zipFile = new ZipFile(string);
+ try {
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ if (!entry.isDirectory()) {
+ result.add(new ImageZipEntryFile(entry.getName()));
+ }
+ }
+ return result;
+ } finally {
+ zipFile.close();
+ }
+ }
+
+ @Test
+ public void testParsingValidFile2() throws Exception {
+ try {
+ Set<Model> models = createValidTestMapModel();
+
+ String tmpDir = "tmp";
+
+ new File(tmpDir).mkdirs();
+ List<ImageZipEntryFile> imageEntries = createImageEntries(TEST_FILES_VALID_OVERVIEW_ZIP);
+ List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, tmpDir,
+ new ZipFile(TEST_FILES_VALID_OVERVIEW_ZIP));
+
+ assertTrue(new File(tmpDir + "/test.png").exists());
+
+ assertNotNull(result);
+ assertEquals(1, result.size());
+ OverviewImage img = result.get(0);
+ assertEquals("test.png", img.getFilename());
+
+ new File(tmpDir).delete();
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingInvalidFile1() throws Exception {
+ try {
+ List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_1.zip");
+ Set<Model> models = createValidTestMapModel();
+
+ parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_1.zip"));
+ fail("Exception expected");
+ } catch (InvalidOverviewFile e) {
+ assertTrue(e.getMessage().contains("Unknown image filename"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingInvalidFile2() throws Exception {
+ try {
+ List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_2.zip");
+ Set<Model> models = createValidTestMapModel();
+
+ parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_2.zip"));
+ fail("Exception expected");
+ } catch (InvalidOverviewFile e) {
+ assertTrue(e.getMessage().contains("Unknown model"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParsingInvalidFile3() throws Exception {
+ try {
+ List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_3.zip");
+ Set<Model> models = createValidTestMapModel();
+
+ parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_3.zip"));
+ fail("Exception expected");
+ } catch (InvalidOverviewFile e) {
+ assertTrue(e.getMessage().contains("coordinates outside image"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Set<Model> createValidTestMapModel() {
+ Set<Model> result = new HashSet<>();
+ Model model = new ModelFullIndexed(null);
+ model.setName("main");
+ result.add(model);
+ return result;
+ }
+
+ /**
+ * Test coordinates that overlap (exception is expected).
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testParseInvalidCoordinates() throws Exception {
+ 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";
+ Set<Model> models = createValidTestMapModel();
+
+ List<OverviewImage> images = new ArrayList<OverviewImage>();
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename("test.png");
+ oi.setWidth(1000);
+ oi.setHeight(1000);
+ images.add(oi);
+
+ parser.processCoordinates(models, images, invalidCoordinates);
+
+ fail("Exception expected");
+ } catch (InvalidOverviewFile e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseValidCoordinates() throws Exception {
+ try {
+ 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";
+ Set<Model> models = createValidTestMapModel();
+
+ List<OverviewImage> images = new ArrayList<OverviewImage>();
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename("test.png");
+ oi.setWidth(1000);
+ oi.setHeight(1000);
+ images.add(oi);
+
+ parser.processCoordinates(models, images, invalidCoordinates);
+
+ assertEquals(2, oi.getLinks().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseValidComplexCoordinates() throws Exception {
+ try {
+ String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"));
+ Set<Model> models = createValidTestMapModel();
+
+ List<OverviewImage> images = new ArrayList<>();
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename("test.png");
+ oi.setWidth(1000);
+ oi.setHeight(1000);
+ images.add(oi);
+
+ OverviewImage oi2 = new OverviewImage();
+ oi2.setFilename("test2.png");
+ oi2.setWidth(1000);
+ oi2.setHeight(1000);
+ images.add(oi2);
+
+ parser.processCoordinates(models, images, invalidCoordinates);
+
+ assertEquals(2, oi.getLinks().size());
+ assertEquals(1, oi2.getLinks().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter/src/test/resources/log4j.properties b/converter/src/test/resources/log4j.properties
index ec610a35af6964418be577ea1bce3ed615e8f91e..4d46bcbdbbff98b6f0ab577993b51da5a200c6d3 100644
--- a/converter/src/test/resources/log4j.properties
+++ b/converter/src/test/resources/log4j.properties
@@ -1,5 +1,5 @@
#Set root logger 's level and its appender to an appender called CONSOLE which is defined below.
-log4j.rootLogger=info, CONSOLE, R
+log4j.rootLogger=info, CONSOLE
#Set the behavior of the CONSOLE appender
log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
diff --git a/converter/testFiles/invalid_overview_1.zip b/converter/testFiles/invalid_overview_1.zip
new file mode 100644
index 0000000000000000000000000000000000000000..b3040204788c875114301808c2920fee4dda812b
Binary files /dev/null and b/converter/testFiles/invalid_overview_1.zip differ
diff --git a/converter/testFiles/invalid_overview_1/coords.txt b/converter/testFiles/invalid_overview_1/coords.txt
deleted file mode 100644
index 6b604ee16c9737e8fce2be69ca0064314a1a141c..0000000000000000000000000000000000000000
--- a/converter/testFiles/invalid_overview_1/coords.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE
-unknowntest.png 10,10 100,10 100,100 100,10 main.xml 10,10 3 MODEL
-test.png 200,200 200,400 400,400 400,200 main.xml 1000,1000 4 MODEL
-
diff --git a/converter/testFiles/invalid_overview_1/test.png b/converter/testFiles/invalid_overview_1/test.png
deleted file mode 100644
index adbe702689a43364dc6f0a6cebedcc9277388a9c..0000000000000000000000000000000000000000
Binary files a/converter/testFiles/invalid_overview_1/test.png and /dev/null differ
diff --git a/converter/testFiles/invalid_overview_2.zip b/converter/testFiles/invalid_overview_2.zip
new file mode 100644
index 0000000000000000000000000000000000000000..c2d52c9ce246a4df4b3563863c1ca122927c7958
Binary files /dev/null and b/converter/testFiles/invalid_overview_2.zip differ
diff --git a/converter/testFiles/invalid_overview_2/coords.txt b/converter/testFiles/invalid_overview_2/coords.txt
deleted file mode 100644
index d25072502f67096da21cace09230e9eb01e87cc5..0000000000000000000000000000000000000000
--- a/converter/testFiles/invalid_overview_2/coords.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE
-test.png 10,10 100,10 100,100 100,10 unknown_main.xml 10,10 3 MODEL
-test.png 200,200 200,400 400,400 400,200 main.xml 1000,1000 4 MODEL
-
diff --git a/converter/testFiles/invalid_overview_2/test.png b/converter/testFiles/invalid_overview_2/test.png
deleted file mode 100644
index adbe702689a43364dc6f0a6cebedcc9277388a9c..0000000000000000000000000000000000000000
Binary files a/converter/testFiles/invalid_overview_2/test.png and /dev/null differ
diff --git a/converter/testFiles/invalid_overview_3.zip b/converter/testFiles/invalid_overview_3.zip
new file mode 100644
index 0000000000000000000000000000000000000000..9b995cf8be6b2a267e7f4f440bfce870ecbf761a
Binary files /dev/null and b/converter/testFiles/invalid_overview_3.zip differ
diff --git a/converter/testFiles/invalid_overview_3/coords.txt b/converter/testFiles/invalid_overview_3/coords.txt
deleted file mode 100644
index 63839f6e7d91535a62b50690b3ca1d662ac65dcf..0000000000000000000000000000000000000000
--- a/converter/testFiles/invalid_overview_3/coords.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE
-test.png 10,10 100,10 100,100 10000,10 main.xml 10,10 3 MODEL
-test.png 200,200 200,400 400,400 400,200 main.xml 1000,1000 4 MODEL
-
diff --git a/converter/testFiles/invalid_overview_3/test.png b/converter/testFiles/invalid_overview_3/test.png
deleted file mode 100644
index adbe702689a43364dc6f0a6cebedcc9277388a9c..0000000000000000000000000000000000000000
Binary files a/converter/testFiles/invalid_overview_3/test.png and /dev/null differ
diff --git a/converter/testFiles/valid_overview.zip b/converter/testFiles/valid_overview.zip
new file mode 100644
index 0000000000000000000000000000000000000000..edfff4deed85439da9ae079ad6a22be298f9a42a
Binary files /dev/null and b/converter/testFiles/valid_overview.zip differ
diff --git a/converter/testFiles/valid_overview/coords.txt b/converter/testFiles/valid_overview/coords.txt
deleted file mode 100644
index 6cc5a4478fdef368e2c1e9e1f21e54fc9794e308..0000000000000000000000000000000000000000
--- a/converter/testFiles/valid_overview/coords.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-FILE POLYGON LINK_TARGET MODEL_COORDINATES MODEL_ZOOM_LEVEL LINK_TYPE
-test.png 10,10 100,10 100,100 100,10 main.xml 10,10 3 MODEL
-test.png 200,200 200,400 400,400 400,200 main.xml 1000,1000 4 MODEL
-
diff --git a/converter/testFiles/valid_overview/test.png b/converter/testFiles/valid_overview/test.png
deleted file mode 100644
index adbe702689a43364dc6f0a6cebedcc9277388a9c..0000000000000000000000000000000000000000
Binary files a/converter/testFiles/valid_overview/test.png and /dev/null differ
diff --git a/frontend-js/.idea/frontend-js.iml b/frontend-js/.idea/frontend-js.iml
index 4feb4987b6dd589318a78302c0367c39c36535a9..217608cacb6a1c303a5e7e7c1b1ad8b1338de378 100644
--- a/frontend-js/.idea/frontend-js.iml
+++ b/frontend-js/.idea/frontend-js.iml
@@ -4,11 +4,12 @@
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/src/test" isTestSource="true" />
<excludeFolder url="file://$MODULE_DIR$/.tmp" />
- <excludeFolder url="file://$MODULE_DIR$/temp" />
<excludeFolder url="file://$MODULE_DIR$/dist" />
+ <excludeFolder url="file://$MODULE_DIR$/temp" />
<excludeFolder url="file://$MODULE_DIR$/tmp" />
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
+ <orderEntry type="library" name="chai-DefinitelyTyped" level="application" />
</component>
-</module>
+</module>
\ No newline at end of file
diff --git a/frontend-js/package.json b/frontend-js/package.json
index dbf87572a8bb5b7aac10a6b456fcb358ff06198e..6608366a592f90159e988c0da56c07e56cc6ad30 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -43,6 +43,7 @@
"http-status-codes": "^1.3.0",
"js-cookie": "^2.1.3",
"jstree": "^3.3.4",
+ "jszip": "^3.1.4",
"log4js": "0.6.38",
"pileup": "^0.6.8",
"request": "^2.82.0"
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index f8bf26513b79f892ac70104ce220e94ed300fe0c..5dc187dd7cf1af381eddfbba546837ad98233358 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -49,6 +49,7 @@ function Configuration(json) {
self.setElementTypes(json.elementTypes);
self.setReactionTypes(json.reactionTypes);
self.setMiriamTypes(json.miriamTypes);
+ self.setMapTypes(json.mapTypes);
self.setModificationStateTypes(json.modificationStateTypes);
self.setPrivilegeTypes(json.privilegeTypes);
self.setAnnotators(json.annotators);
@@ -98,12 +99,12 @@ Configuration.prototype.getElementTypeNames = function () {
Configuration.prototype.getParentType = function (elementType) {
var i;
- for (var i = 0; i < this._elementTypes.length; i++) {
+ for (i = 0; i < this._elementTypes.length; i++) {
if (this._elementTypes[i].className === elementType.parentClass) {
return this._elementTypes[i];
}
}
- for (var i = 0; i < this._reactionTypes.length; i++) {
+ for (i = 0; i < this._reactionTypes.length; i++) {
if (this._reactionTypes[i].className === elementType.parentClass) {
return this._reactionTypes[i];
}
@@ -152,6 +153,13 @@ Configuration.prototype.setMiriamTypes = function (miriamTypes) {
);
};
+Configuration.prototype.setMapTypes = function (mapTypes) {
+ this._mapTypes = mapTypes;
+};
+Configuration.prototype.getMapTypes = function () {
+ return this._mapTypes;
+};
+
Configuration.prototype.setPrivilegeTypes = function (privilegeTypes) {
this._privilegeTypes = [];
for (var key in privilegeTypes) {
@@ -206,7 +214,7 @@ Configuration.prototype.setAnnotators = function (annotators) {
for (var key in annotators) {
if (annotators.hasOwnProperty(key)) {
var annotator = annotators[key];
- this._annotators.push(new Annotator(annotators[key], this));
+ this._annotators.push(new Annotator(annotator, this));
}
}
};
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index b78dc728ab4ed3fc4cb752f5e0a19e7e646f5394..857b2930e528de8b0b724b91be4ce5276d0d0a70 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -8,6 +8,8 @@ var GuiUtils = require('./leftPanel/GuiUtils');
var LayoutData = require('../map/data/LayoutData');
var NetworkError = require('../NetworkError');
+var OverlayParser = require('../map/OverlayParser');
+
var Functions = require('../Functions');
var logger = require('../logger');
var HttpStatus = require('http-status-codes');
@@ -24,7 +26,7 @@ function AddOverlayDialog(params) {
AddOverlayDialog.prototype = Object.create(AbstractGuiElement.prototype);
AddOverlayDialog.prototype.constructor = AddOverlayDialog;
-AddOverlayDialog.prototype.createGui = function() {
+AddOverlayDialog.prototype.createGui = function () {
var self = this;
var guiUtils = new GuiUtils();
var content = document.createElement("div");
@@ -32,9 +34,9 @@ AddOverlayDialog.prototype.createGui = function() {
content.style.height = "100%";
content.appendChild(guiUtils.createLabel("Name: "));
var nameInput = Functions.createElement({
- type : "input",
- inputType : "text",
- name : "overlay-name",
+ type: "input",
+ inputType: "text",
+ name: "overlay-name",
});
content.appendChild(nameInput);
content.appendChild(guiUtils.createNewLine());
@@ -42,19 +44,19 @@ AddOverlayDialog.prototype.createGui = function() {
content.appendChild(guiUtils.createLabel("Description: "));
content.appendChild(guiUtils.createNewLine());
var descriptionInput = Functions.createElement({
- type : "textarea",
- name : "overlay-description",
+ type: "textarea",
+ name: "overlay-description",
});
content.appendChild(descriptionInput);
content.appendChild(guiUtils.createNewLine());
content.appendChild(guiUtils.createLabel("Upload file: "));
var fileInput = Functions.createElement({
- type : "input",
- inputType : "file",
- name : "overlay-file",
+ type: "input",
+ inputType: "file",
+ name: "overlay-file",
});
- fileInput.addEventListener("change", function() {
+ fileInput.addEventListener("change", function () {
return self.processFile(fileInput.files[0]);
}, false);
content.appendChild(fileInput);
@@ -63,8 +65,8 @@ AddOverlayDialog.prototype.createGui = function() {
content.appendChild(guiUtils.createLabel("Or provide list of elements here (one per line): "));
content.appendChild(guiUtils.createNewLine());
var contentInput = Functions.createElement({
- type : "textarea",
- name : "overlay-content",
+ type: "textarea",
+ name: "overlay-content",
});
content.appendChild(contentInput);
content.appendChild(guiUtils.createNewLine());
@@ -72,21 +74,22 @@ AddOverlayDialog.prototype.createGui = function() {
self.getElement().appendChild(content);
};
-AddOverlayDialog.prototype.processFile = function(file) {
+AddOverlayDialog.prototype.processFile = function (file) {
var self = this;
self.setFileContent(null);
if (file) {
- return new Promise(function(resolve, reject) {
+ return new Promise(function (resolve, reject) {
var reader = new FileReader();
reader.readAsText(file, "UTF-8");
- reader.onload = function(evt) {
+ reader.onload = function (evt) {
try {
+ var overlayParser = new OverlayParser();
self.setFileContent(evt.target.result);
- var data = self.parseFile(evt.target.result);
+ var overlay = overlayParser.parse(evt.target.result);
var nameInput = $("[name='overlay-name']", self.getElement())[0];
var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
- if (data.name !== undefined) {
- nameInput.value = data.name;
+ if (overlay.getName() !== undefined) {
+ nameInput.value = overlay.getName();
} else {
var filename = $("[name='overlay-file']", self.getElement())[0].value;
if (filename.indexOf(".") > 0) {
@@ -97,15 +100,15 @@ AddOverlayDialog.prototype.processFile = function(file) {
}
nameInput.value = filename;
}
- if (data.description !== undefined) {
- descriptionInput.value = data.description;
+ if (overlay.getDescription() !== undefined) {
+ descriptionInput.value = overlay.getDescription();
}
resolve(self.getFileContent());
} catch (error) {
reject(error);
}
};
- reader.onerror = function() {
+ reader.onerror = function () {
reject(new Error("Problem reading file"));
};
});
@@ -114,11 +117,11 @@ AddOverlayDialog.prototype.processFile = function(file) {
}
};
-AddOverlayDialog.prototype.setFileContent = function(fileContent) {
+AddOverlayDialog.prototype.setFileContent = function (fileContent) {
this._fileContent = fileContent;
};
-AddOverlayDialog.prototype.getFileContent = function() {
+AddOverlayDialog.prototype.getFileContent = function () {
var self = this;
var contentInput = $("[name='overlay-content']", self.getElement())[0];
@@ -135,43 +138,43 @@ AddOverlayDialog.prototype.getFileContent = function() {
}
};
-AddOverlayDialog.prototype.init = function() {
+AddOverlayDialog.prototype.init = function () {
return Promise.resolve();
};
-AddOverlayDialog.prototype.addOverlay = function() {
+AddOverlayDialog.prototype.addOverlay = function () {
var self = this;
var nameInput = $("[name='overlay-name']", self.getElement())[0];
var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
var filename = $("[name='overlay-file']", self.getElement())[0].value;
var overlay = new LayoutData({
- name : nameInput.value,
- description : descriptionInput.value,
- content : self.getFileContent(),
- filename : filename,
+ name: nameInput.value,
+ description: descriptionInput.value,
+ content: self.getFileContent(),
+ filename: filename,
});
GuiConnector.showProcessing();
return ServerConnector.addOverlay({
- overlay : overlay,
- projectId : self.getProject().getProjectId(),
- }).then(function(result) {
+ overlay: overlay,
+ projectId: self.getProject().getProjectId(),
+ }).then(function (result) {
overlay = result;
GuiConnector.hideProcessing();
return self.callListeners("onAddOverlay", overlay);
});
};
-AddOverlayDialog.prototype.destroy = function() {
+AddOverlayDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
-AddOverlayDialog.prototype.open = function() {
+AddOverlayDialog.prototype.open = function () {
var self = this;
var div = self.getElement();
if (!$(div).hasClass("ui-dialog-content")) {
- var buttons = [ {
- text : "UPLOAD",
- click : function() {
+ var buttons = [{
+ text: "UPLOAD",
+ click: function () {
var dialog = this;
var fileContent = self.getFileContent();
if (fileContent === null) {
@@ -179,10 +182,10 @@ AddOverlayDialog.prototype.open = function() {
} else if (fileContent.length > 1024 * 256) {
GuiConnector.alert("File to big.<br>Please reduce file size or contact administrators.");
} else {
- return self.addOverlay().then(function(result) {
+ return self.addOverlay().then(function (result) {
$(dialog).dialog("close");
return result;
- }, function(error) {
+ }, function (error) {
GuiConnector.hideProcessing();
if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
var errorMessage = JSON.parse(error.content);
@@ -194,46 +197,20 @@ AddOverlayDialog.prototype.open = function() {
}
}
}, {
- text : "CANCEL",
- click : function() {
+ text: "CANCEL",
+ click: function () {
$(this).dialog("close");
}
- } ];
+ }];
$(div).dialog({
- title : "Add overlay",
- buttons : buttons,
- modal : true,
+ title: "Add overlay",
+ buttons: buttons,
+ modal: true,
});
}
$(div).dialog("open");
};
-AddOverlayDialog.prototype.parseFile = function(fileContent) {
- var result = {};
- var lines = fileContent.split("\n");
- for (var i = 0; i < lines.length; i++) {
- var line = lines[i];
- if (line.startsWith("#")) {
- if (line.indexOf("=") > 0) {
- var name = line.substring(1, line.indexOf("=")).trim();
- var value = line.substring(line.indexOf("=") + 1).trim();
- if (name === "NAME") {
- result.name = value;
- } else if (name === "DESCRIPTION") {
- result.description = value;
- } else if (name === "TYPE") {
- result.type = value;
- }
- } else {
- logger.warn("Invalid overlay header line: " + line);
- }
- } else {
- break;
- }
- }
- return result;
-};
-
module.exports = AddOverlayDialog;
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 26dea5dfd6dd9bdc3a4793fc5dead2f571d1f640..966d914461424cdbc1c4fb1672b782fa37b0c029 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -2,12 +2,14 @@
/* exported logger */
var Promise = require("bluebird");
+var JSZip = require("jszip");
var AbstractGuiElement = require('../AbstractGuiElement');
var ChooseAnnotatorsDialog = require('./ChooseAnnotatorsDialog');
var ChooseValidatorsDialog = require('./ChooseValidatorsDialog');
var GuiConnector = require('../../GuiConnector');
-var UserPreferences = require("../../map/data/UserPreferences");
+var OverlayParser = require('../../map/OverlayParser');
+var ZipEntry = require('./ZipEntry');
var Functions = require('../../Functions');
var logger = require('../../logger');
@@ -21,7 +23,10 @@ function AddProjectDialog(params) {
AbstractGuiElement.call(this, params);
var self = this;
self.registerListenerType("onFileUpload");
+ self.registerListenerType("onZipFileUpload");
+ self.setZipEntries([]);
$(self.getElement()).addClass("minerva-edit-project-dialog");
+ $(self.getElement()).css({overflow: "hidden"});
self.createGui();
}
@@ -36,7 +41,8 @@ AddProjectDialog.prototype.createGui = function () {
var tabDiv = Functions.createElement({
type: "div",
name: "tabView",
- className: "tabbable boxed parentTabs"
+ className: "tabbable boxed parentTabs",
+ style: "position:absolute;top:40px;bottom:10px;left:10px;right:10px"
});
element.appendChild(tabDiv);
@@ -48,7 +54,8 @@ AddProjectDialog.prototype.createGui = function () {
var tabContentDiv = Functions.createElement({
type: "div",
- className: "tab-content"
+ className: "tab-content",
+ style: "height:100%"
});
tabDiv.appendChild(tabContentDiv);
@@ -83,6 +90,7 @@ AddProjectDialog.prototype.addTab = function (params) {
navigationObject: navLi,
navigationBar: params.tabMenuDiv
});
+ contentDiv.style.overflow = "auto";
if (params.content !== undefined) {
contentDiv.appendChild(params.content);
@@ -148,6 +156,10 @@ AddProjectDialog.prototype.createGeneralTabContent = function () {
var file = e.arg;
return self.processFile(file);
});
+ self.addListener("onFileUpload", function (e) {
+ var file = e.arg;
+ return self.setZipFileContent(file);
+ });
self.addListener("onFileUpload", function (e) {
var file = e.arg;
if (file.name.lastIndexOf('.') > 0) {
@@ -308,11 +320,59 @@ AddProjectDialog.prototype.createOverlaysTabContent = function () {
};
AddProjectDialog.prototype._createOverlayTable = function () {
+ var self = this;
var result = Functions.createElement({
type: "div",
style: "margin-top:10px;"
});
+ var overlaysTable = Functions.createElement({
+ type: "table",
+ name: "overlaysTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(overlaysTable);
+
+ $(overlaysTable).DataTable({
+ columns: [{
+ title: 'File name'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Description'
+ }]
+ });
+
+ $(overlaysTable).on("input", "[name='overlayName']", function () {
+ var input = this;
+ var filename = $(input).attr("data");
+ self.getEntryByFilename(filename).getData().name = $(input).val();
+ });
+
+ $(overlaysTable).on("input", "[name='overlayDescription']", function () {
+ var input = this;
+ var filename = $(input).attr("data");
+ self.getEntryByFilename(filename).getData().description = $(input).val();
+ });
+
+ self.addListener("onZipFileUpload", function () {
+ var entries = self.getZipEntries();
+ var dataTable = $($("[name='overlaysTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < entries.length; i++) {
+ var entry = entries[i];
+ if (entry.getType() === "OVERLAY") {
+ var row = [];
+ row[0] = entry.getFilename();
+ row[1] = "<input data='" + entry.getFilename() + "' name='overlayName' value='" + entry.getData().name + "'/>";
+ row[2] = "<input data='" + entry.getFilename() + "' name='overlayDescription' value='" + entry.getData().description + "'/>";
+ data.push(row);
+ }
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+
return result;
};
@@ -321,17 +381,142 @@ AddProjectDialog.prototype.createSubmapsTab = function (tabMenuDiv, tabContentDi
self.addTab({
tabMenuDiv: tabMenuDiv,
tabContentDiv: tabContentDiv,
- name: "USERS",
+ name: "SUBMAPS",
id: "project_submaps_tab",
content: self.createSubmapsTabContent()
});
};
AddProjectDialog.prototype.createSubmapsTabContent = function () {
+ var self = this;
var result = Functions.createElement({
type: "div",
style: "margin-top:10px;"
});
+ var submapsTable = Functions.createElement({
+ type: "table",
+ name: "submapsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(submapsTable);
+
+ $(submapsTable).DataTable({
+ columns: [{
+ title: 'File name'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Root map'
+ }, {
+ title: 'Mapping file'
+ }, {
+ title: 'Map type'
+ }]
+ });
+
+ $(submapsTable).on("input", "[name='submapName']", function () {
+ var input = this;
+ var filename = $(input).attr("data");
+ self.getEntryByFilename(filename).getData().name = $(input).val();
+ });
+
+ $(submapsTable).on("change", "[name='submapRoot']", function () {
+ var input = this;
+ if (!$(input).is(":checked")) {
+ this.checked = true;
+ GuiConnector.info("One model must be marked as a root");
+ return false;
+ }
+
+ var filename = $(input).attr("data");
+ var checkboxes = $("[name='submapRoot']", submapsTable);
+ for (var i = 0; i < checkboxes.length; i++) {
+ var checkbox = checkboxes[i];
+ if ($(checkbox).attr("data") !== filename) {
+ $(checkbox).attr('checked', false);
+ self.getEntryByFilename($(checkbox).attr("data")).getData().root = false;
+ }
+ }
+ self.getEntryByFilename(filename).getData().root = $(input).is(":checked");
+ });
+
+ $(submapsTable).on("change", "[name='submapMapping']", function () {
+ var input = this;
+ var filename = $(input).attr("data");
+ var checkboxes = $("[name='submapMapping']", submapsTable);
+ for (var i = 0; i < checkboxes.length; i++) {
+ var checkbox = checkboxes[i];
+ if ($(checkbox).attr("data") !== filename) {
+ $(checkbox).attr('checked', false);
+ self.getEntryByFilename($(checkbox).attr("data")).getData().mapping = false;
+ }
+ }
+ self.getEntryByFilename(filename).getData().mapping = $(input).is(":checked");
+ });
+
+ $(submapsTable).on("change", "[name='submapType']", function () {
+ var input = this;
+ var filename = $(input).attr("data");
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var mapTypes = configuration.getMapTypes();
+ for (var j = 0; j < mapTypes.length; j++) {
+ var mapType = mapTypes[j];
+ if (mapType.id === $(input).val()) {
+ self.getEntryByFilename(filename).getData().type = mapType;
+ }
+ }
+ });
+ });
+
+ self.addListener("onZipFileUpload", function () {
+ return ServerConnector.getConfiguration().then(function (configuration) {
+
+ var entries = self.getZipEntries();
+ var dataTable = $($("[name='submapsTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < entries.length; i++) {
+ var entry = entries[i];
+ if (entry.getType() === "MAP") {
+ var row = [];
+ var rootCheckbox;
+ if (entry.getData().root) {
+ rootCheckbox = "<input name='submapRoot' type='checkbox' data='" + entry.getFilename() + "' checked='checked'/>";
+ } else {
+ rootCheckbox = "<input name='submapRoot' type='checkbox' data='" + entry.getFilename() + "'/>";
+ }
+ var mappingCheckbox;
+ if (entry.getData().mapping) {
+ mappingCheckbox = "<input name='submapMapping' type='checkbox' data='" + entry.getFilename() + "' checked='checked'/>";
+ } else {
+ mappingCheckbox = "<input name='submapMapping' type='checkbox' data='" + entry.getFilename() + "'/>";
+ }
+
+ var typeSelect = "<select data='" + entry.getFilename() + "' name='submapType'>";
+
+ typeSelect += "<option value='" + entry.getData().type.id + "' selected>" + entry.getData().type.name + "</option>";
+ var mapTypes = configuration.getMapTypes();
+ for (var j = 0; j < mapTypes.length; j++) {
+ var mapType = mapTypes[j];
+ if (mapType !== entry.getData().type) {
+ typeSelect += "<option value='" + mapType.id + "' >" + mapType.name + "</option>";
+ }
+ }
+ typeSelect += "</select>";
+
+
+ row[0] = entry.getFilename();
+ row[1] = "<input data='" + entry.getFilename() + "' name='submapName' value='" + entry.getData().name + "'/>";
+ row[2] = rootCheckbox;
+ row[3] = mappingCheckbox;
+ row[4] = typeSelect;
+ data.push(row);
+ }
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+ });
+
return result;
};
@@ -340,17 +525,48 @@ AddProjectDialog.prototype.createOverviewImagesTab = function (tabMenuDiv, tabCo
self.addTab({
tabMenuDiv: tabMenuDiv,
tabContentDiv: tabContentDiv,
- name: "USERS",
+ name: "IMAGES",
id: "project_overview_images_tab",
content: self.createOverviewImagesTabContent()
});
};
AddProjectDialog.prototype.createOverviewImagesTabContent = function () {
+ var self = this;
var result = Functions.createElement({
type: "div",
style: "margin-top:10px;"
});
+
+ var imagesTable = Functions.createElement({
+ type: "table",
+ name: "imagesTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(imagesTable);
+
+ $(imagesTable).DataTable({
+ columns: [{
+ title: 'File name'
+ }]
+ });
+
+ self.addListener("onZipFileUpload", function () {
+ var entries = self.getZipEntries();
+ var dataTable = $($("[name='imagesTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < entries.length; i++) {
+ var entry = entries[i];
+ if (entry.getType() === "IMAGE") {
+ var row = [];
+ row[0] = entry.getFilename();
+ data.push(row);
+ }
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+
return result;
};
@@ -412,6 +628,20 @@ AddProjectDialog.prototype.destroy = function () {
if (self._validatorsDialog !== undefined) {
self._validatorsDialog.destroy();
}
+ var overlaysTable = $("[name=overlaysTable]", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(overlaysTable)) {
+ $(overlaysTable).DataTable().destroy();
+ }
+ var submapsTable = $("[name=submapsTable]", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(submapsTable)) {
+ $(submapsTable).DataTable().destroy();
+ }
+
+ var imagesTable = $("[name=imagesTable]", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(imagesTable)) {
+ $(imagesTable).DataTable().destroy();
+ }
+
};
AddProjectDialog.prototype.open = function () {
@@ -445,7 +675,7 @@ AddProjectDialog.prototype.processFile = function (file) {
if (file) {
return new Promise(function (resolve, reject) {
var reader = new FileReader();
- reader.readAsText(file, "UTF-8");
+ reader.readAsText(file);
reader.onload = function (evt) {
try {
self.setFileContent(evt.target.result);
@@ -464,6 +694,7 @@ AddProjectDialog.prototype.processFile = function (file) {
};
AddProjectDialog.prototype.setFileContent = function (fileContent) {
+ logger.debug(fileContent);
this._fileContent = fileContent;
};
AddProjectDialog.prototype.getFileContent = function () {
@@ -593,7 +824,7 @@ AddProjectDialog.prototype.onSaveClicked = function () {
"semantic-zoom": self.isSemanticZooming(),
"annotate": self.isAnnotateAutomatically(),
"verify-annotations": self.isVerifyAnnotations(),
-
+ "zip-entries": self.getZipEntries()
};
return ServerConnector.addProject(options);
});
@@ -627,4 +858,124 @@ AddProjectDialog.prototype.checkValidity = function () {
});
};
+AddProjectDialog.prototype.setZipFileContent = function (file) {
+ var self = this;
+ if (file.name.toLowerCase().endsWith("zip")) {
+ var jsZip = new JSZip();
+ return jsZip.loadAsync(file).then(function (zip) {
+ var files = zip.files;
+ var promises = [];
+ var entries = [];
+ for (var key in files) {
+ if (files.hasOwnProperty(key)) {
+ promises.push(self.createZipEntry(files[key], zip));
+ }
+ }
+ return Promise.all(promises).then(function (result) {
+ for (var i = 0; i < result.length; i++) {
+ if (result[i] !== null) {
+ entries.push(result[i]);
+ }
+ }
+ return self.setZipEntries(entries);
+ });
+ });
+ } else {
+ return self.setZipEntries([]);
+ }
+};
+
+AddProjectDialog.prototype.createZipEntry = function (jsZipEntry, zipObject) {
+ if (jsZipEntry.dir) {
+ return null;
+ }
+ var filename = jsZipEntry.name.toLowerCase();
+ var type = null;
+ var data = {};
+ var processingPromise = Promise.resolve();
+ if (filename.startsWith("submaps")) {
+ type = "MAP";
+ if (filename.endsWith("mapping.xml")) {
+ data.mapping = true;
+ }
+ } else if (filename.startsWith("images")) {
+ type = "IMAGE";
+ } else if (filename.startsWith("layouts") || filename.startsWith("overlays")) {
+ type = "OVERLAY";
+ processingPromise = zipObject.file(jsZipEntry.name).async("string").then(function (content) {
+ var overlayParser = new OverlayParser();
+ var overlay = overlayParser.parse(content);
+ if (overlay.getName()) {
+ data.name = overlay.getName();
+ } else {
+ data.name = "";
+ }
+ if (overlay.getDescription()) {
+ data.description = overlay.getDescription();
+ } else {
+ data.description = "";
+ }
+ });
+ } else if (filename.indexOf("\\") === -1 && filename.indexOf("/") === -1) {
+ type = "MAP";
+ data.root = true;
+ } else {
+ throw new Error("Unrecognized file: " + filename);
+ }
+ if (type === "MAP") {
+ var name = jsZipEntry.name.toLowerCase();
+ this.setFileParserForFilename(name);
+ if (name.indexOf(".") > 0) {
+ name = name.substr(0, name.indexOf("."));
+ }
+ if (name.lastIndexOf("\\") >= 0) {
+ name = name.substr(name.lastIndexOf("\\") + 1);
+ }
+ if (name.lastIndexOf("/") >= 0) {
+ name = name.substr(name.lastIndexOf("/") + 1);
+ }
+ data.name = name;
+
+ processingPromise = processingPromise.then(function () {
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var mapTypes = configuration.getMapTypes();
+ for (var i = 0; i < mapTypes.length; i++) {
+ if (mapTypes[i].id === "UNKNOWN") {
+ data.type = mapTypes[i];
+ }
+ }
+ if (data.type === undefined) {
+ data.type = mapTypes[0];
+ }
+ });
+ });
+ }
+
+ return processingPromise.then(function () {
+ return new ZipEntry({filename: filename, type: type, data: data});
+ });
+};
+
+AddProjectDialog.prototype.getZipEntries = function () {
+ return this._zipEntries;
+};
+AddProjectDialog.prototype.setZipEntries = function (entries) {
+ var self = this;
+ self._zipEntries = entries;
+ return self.callListeners("onZipFileUpload", entries);
+
+};
+
+AddProjectDialog.prototype.getEntryByFilename = function (filename) {
+ var self = this;
+ var entries = self.getZipEntries();
+ for (var i = 0; i < entries.length; i++) {
+ var entry = entries[i];
+ if (entry.getFilename() === filename) {
+ return entry;
+ }
+ }
+ return null;
+};
+
module.exports = AddProjectDialog;
diff --git a/frontend-js/src/main/js/gui/admin/ZipEntry.js b/frontend-js/src/main/js/gui/admin/ZipEntry.js
new file mode 100644
index 0000000000000000000000000000000000000000..c3891a3a013e1b131353649c320471edd8671b7c
--- /dev/null
+++ b/frontend-js/src/main/js/gui/admin/ZipEntry.js
@@ -0,0 +1,37 @@
+"use strict";
+
+var types = ["IMAGE", "OVERLAY", "MAP"];
+
+function ZipEntry(params) {
+ var self = this;
+ self.setType(params.type);
+ self.setFilename(params.filename);
+ self.setData(params.data);
+}
+
+ZipEntry.prototype.setType = function (type) {
+ if (types.indexOf(type) === -1) {
+ throw new Error("Unknown ZipEntryType: " + type + ".")
+ }
+ this._type = type;
+};
+ZipEntry.prototype.getType = function () {
+ return this._type;
+};
+
+ZipEntry.prototype.setFilename = function (filename) {
+ this._filename = filename;
+};
+
+ZipEntry.prototype.getFilename = function () {
+ return this._filename;
+};
+
+ZipEntry.prototype.setData = function (data) {
+ this._data = data;
+};
+ZipEntry.prototype.getData = function () {
+ return this._data;
+};
+
+module.exports = ZipEntry;
diff --git a/frontend-js/src/main/js/map/OverlayParser.js b/frontend-js/src/main/js/map/OverlayParser.js
new file mode 100644
index 0000000000000000000000000000000000000000..31fc9bc086d2884189449f5c1b9c4bacc07d1e2c
--- /dev/null
+++ b/frontend-js/src/main/js/map/OverlayParser.js
@@ -0,0 +1,37 @@
+"use strict";
+
+var logger = require('./../logger');
+var LayoutData = require('./data/LayoutData');
+
+function OverlayParser() {
+}
+
+OverlayParser.prototype.parse = function (content) {
+ var data = {content: content};
+ var lines = content.split("\n");
+ for (var i = 0; i < lines.length; i++) {
+ var line = lines[i];
+ if (line.startsWith("#")) {
+ if (line.indexOf("=") > 0) {
+ var name = line.substring(1, line.indexOf("=")).trim();
+ var value = line.substring(line.indexOf("=") + 1).trim();
+ if (name === "NAME") {
+ data.name = value;
+ } else if (name === "DESCRIPTION") {
+ data.description = value;
+ } else if (name === "TYPE") {
+ data.type = value;
+ }
+ } else {
+ logger.warn("Invalid overlay header line: " + line);
+ }
+ } else {
+ break;
+ }
+ }
+
+ return new LayoutData(data);
+};
+
+
+module.exports = OverlayParser;
diff --git a/frontend-js/src/main/js/map/data/LayoutData.js b/frontend-js/src/main/js/map/data/LayoutData.js
index 8d8c29ba94f124cee4f4eb3394a0a187c4492e94..2e2fa6d043921a6775537c2e2c06d08dec809113 100644
--- a/frontend-js/src/main/js/map/data/LayoutData.js
+++ b/frontend-js/src/main/js/map/data/LayoutData.js
@@ -27,6 +27,7 @@ function LayoutData(layoutId, name) {
this.setFilename(object.filename);
this.setPublicOverlay(object.publicOverlay);
this.setInputDataAvailable(object.inputDataAvailable);
+ this.setType(object.type);
if (!this.getInputDataAvailable()) {
this.setInitialized(true);
}
@@ -42,54 +43,54 @@ function LayoutData(layoutId, name) {
/**
* Adds alias to the {@link LayoutData}
- *
+ *
* @param layoutAlias
* information about alias in a layout
*/
-LayoutData.prototype.addAlias = function(layoutAlias) {
+LayoutData.prototype.addAlias = function (layoutAlias) {
this.aliases.push(layoutAlias);
this.aliasById[layoutAlias.getId()] = layoutAlias;
};
/**
* Adds reaction to the {@link LayoutData}
- *
+ *
* @param layoutReaction
* information about reaction in a layout
*/
-LayoutData.prototype.addReaction = function(layoutReaction) {
+LayoutData.prototype.addReaction = function (layoutReaction) {
this.reactions.push(layoutReaction);
};
-LayoutData.prototype.getId = function() {
+LayoutData.prototype.getId = function () {
return this.id;
};
-LayoutData.prototype.setId = function(id) {
+LayoutData.prototype.setId = function (id) {
this.id = parseInt(id);
};
-LayoutData.prototype.getDescription = function() {
+LayoutData.prototype.getDescription = function () {
return this._description;
};
-LayoutData.prototype.setDescription = function(description) {
+LayoutData.prototype.setDescription = function (description) {
this._description = description;
};
-LayoutData.prototype.getCreator = function() {
+LayoutData.prototype.getCreator = function () {
return this._creator;
};
-LayoutData.prototype.setCreator = function(creator) {
+LayoutData.prototype.setCreator = function (creator) {
this._creator = creator;
};
-LayoutData.prototype.getInputDataAvailable = function() {
+LayoutData.prototype.getInputDataAvailable = function () {
return this._inputDataAvailable;
};
-LayoutData.prototype.setInputDataAvailable = function(inputDataAvailable) {
+LayoutData.prototype.setInputDataAvailable = function (inputDataAvailable) {
var value = inputDataAvailable;
if (inputDataAvailable === undefined) {
value = false;
@@ -104,23 +105,23 @@ LayoutData.prototype.setInputDataAvailable = function(inputDataAvailable) {
this._inputDataAvailable = value;
};
-LayoutData.prototype.getName = function() {
+LayoutData.prototype.getName = function () {
return this.name;
};
-LayoutData.prototype.setName = function(name) {
+LayoutData.prototype.setName = function (name) {
this.name = name;
};
-LayoutData.prototype.getDirectory = function() {
+LayoutData.prototype.getDirectory = function () {
return this._directory;
};
-LayoutData.prototype.setDirectory = function(directory) {
+LayoutData.prototype.setDirectory = function (directory) {
this._directory = directory;
};
-LayoutData.prototype.updateAlias = function(layoutAlias) {
+LayoutData.prototype.updateAlias = function (layoutAlias) {
if (this.aliasById[layoutAlias.getId()] === undefined) {
logger.warn("Cannot update alias, it doesn't exist. Alias: ", layoutAlias.getId());
} else {
@@ -129,19 +130,19 @@ LayoutData.prototype.updateAlias = function(layoutAlias) {
};
-LayoutData.prototype.getAliasById = function(id) {
+LayoutData.prototype.getAliasById = function (id) {
return this.aliasById[id];
};
-LayoutData.prototype.getFullAliasById = function(id) {
+LayoutData.prototype.getFullAliasById = function (id) {
var self = this;
var alias = self.getAliasById(id);
if (alias !== undefined) {
if (alias.getType() === LayoutAlias.LIGTH) {
return ServerConnector.getFullOverlayElement({
- element : new IdentifiedElement(alias),
- overlay : self,
- }).then(function(data) {
+ element: new IdentifiedElement(alias),
+ overlay: self,
+ }).then(function (data) {
self.updateAlias(data);
return alias;
});
@@ -150,28 +151,28 @@ LayoutData.prototype.getFullAliasById = function(id) {
return Promise.resolve(alias);
};
-LayoutData.prototype.setInitialized = function(value) {
+LayoutData.prototype.setInitialized = function (value) {
this._initialized = value;
};
-LayoutData.prototype.isInitialized = function() {
+LayoutData.prototype.isInitialized = function () {
return this._initialized;
};
-LayoutData.prototype.getAliases = function() {
+LayoutData.prototype.getAliases = function () {
return this.aliases;
};
-LayoutData.prototype.getReactions = function() {
+LayoutData.prototype.getReactions = function () {
return this.reactions;
};
-LayoutData.prototype.init = function() {
+LayoutData.prototype.init = function () {
var self = this;
if (this.isInitialized()) {
return Promise.resolve();
}
- return ServerConnector.getOverlayElements(self.getId()).then(function(data) {
+ return ServerConnector.getOverlayElements(self.getId()).then(function (data) {
for (var i = 0; i < data.length; i++) {
if (data[i] instanceof LayoutAlias) {
self.addAlias(data[i]);
@@ -187,28 +188,36 @@ LayoutData.prototype.init = function() {
};
-LayoutData.prototype.getPublicOverlay = function() {
+LayoutData.prototype.getPublicOverlay = function () {
return this._publicOverlay;
};
-LayoutData.prototype.setPublicOverlay = function(publicOverlay) {
+LayoutData.prototype.setPublicOverlay = function (publicOverlay) {
this._publicOverlay = publicOverlay;
};
-LayoutData.prototype.getContent = function() {
+LayoutData.prototype.getContent = function () {
return this._content;
};
-LayoutData.prototype.setContent = function(content) {
+LayoutData.prototype.setContent = function (content) {
this._content = content;
};
-LayoutData.prototype.getFilename = function() {
+LayoutData.prototype.getFilename = function () {
return this._filename;
};
-LayoutData.prototype.setFilename= function(filename) {
+LayoutData.prototype.setFilename = function (filename) {
this._filename = filename;
};
+LayoutData.prototype.getType = function () {
+ return this._type;
+};
+
+LayoutData.prototype.setType = function (type) {
+ this._type = type;
+};
+
module.exports = LayoutData;
diff --git a/frontend-js/src/test/js/gui/AddOverlayDialog-test.js b/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
index b9700d844df392ad345f93cc76c5bc4b49060e01..26b190671ff0b2a9a19e5d807e1f8ad46559dbc6 100644
--- a/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
+++ b/frontend-js/src/test/js/gui/AddOverlayDialog-test.js
@@ -12,23 +12,6 @@ var logger = require('../logger');
describe('AddOverlayDialog', function() {
- describe('processFile', function() {
- it('default', function() {
- return ServerConnector.getProject().then(function(project) {
- var dialog = new AddOverlayDialog({
- element : testDiv,
- project : project,
- customMap : null
- });
-
- var file = new Blob([ "#DESCRIPTION=xxx\nname\tvalue\ns1\t1" ]);
- return dialog.processFile(file).then(function(content) {
- assert.ok(content !== null);
- });
- });
- });
- });
-
it('addOverlay', function() {
var dialog;
return ServerConnector.getProject().then(function(project) {
@@ -43,22 +26,4 @@ describe('AddOverlayDialog', function() {
});
});
-
- it('parse overlay file', function() {
- return ServerConnector.getProject().then(function(project) {
- var dialog = new AddOverlayDialog({
- element : testDiv,
- project : project,
- customMap : null
- });
-
- return ServerConnector.sendGetRequest("testFiles/overlay/good.txt").then(function(fileContent) {
- var obj = dialog.parseFile(fileContent);
- assert.equal(obj.name, "example name");
- assert.equal(obj.description, "layout description");
- assert.equal(obj.type, "GENERIC");
- });
- });
- });
-
});
diff --git a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
index 50d53689717e43f64af90a583f190e09f7f2ba0d..219804ccf82bbf0ebbaabdd3a1e6310c06c6a63f 100644
--- a/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js
@@ -7,6 +7,7 @@ require("../../mocha-config");
var AddProjectDialog = require('../../../../main/js/gui/admin/AddProjectDialog');
var logger = require('../../logger');
+var fs = require("fs");
var chai = require('chai');
var assert = chai.assert;
@@ -20,6 +21,7 @@ describe('AddProjectDialog', function () {
return dialog.init();
}).then(function () {
assert.ok(dialog.getNotifyEmail() !== "");
+ return dialog.destroy();
});
});
@@ -35,6 +37,7 @@ describe('AddProjectDialog', function () {
assert.notOk(dialog.isCache());
dialog.setCache(true);
assert.ok(dialog.isCache());
+ return dialog.destroy();
});
});
@@ -55,6 +58,41 @@ describe('AddProjectDialog', function () {
return dialog.getConverter();
}).then(function (converter) {
assert.equal("xml", converter.extension);
+ return dialog.destroy();
+ });
+ });
+ });
+
+ describe('setZipFileContent', function () {
+ it('submaps', function () {
+ var dialog = new AddProjectDialog({
+ element: testDiv,
+ customMap: null
+ });
+ var buf = fs.readFileSync("testFiles/map/complex_model_with_submaps.zip");
+ buf.name = "complex_model_with_submaps.zip";
+ return dialog.init().then(function () {
+ return dialog.setZipFileContent(buf);
+ }).then(function () {
+ assert.equal(5, dialog.getZipEntries().length);
+ return dialog.destroy();
+ });
+ });
+ it('overlays', function () {
+ var dialog = new AddProjectDialog({
+ element: testDiv,
+ customMap: null
+ });
+ var buf = fs.readFileSync("testFiles/map/complex_model_with_overlays.zip");
+ buf.name = "complex_model_with_overlays.zip";
+ return dialog.init().then(function () {
+ var dataTable = $($("[name='overlaysTable']", testDiv)[0]).DataTable();
+ assert.equal(0, dataTable.data().count());
+ return dialog.setZipFileContent(buf);
+ }).then(function () {
+ var dataTable = $($("[name='overlaysTable']", testDiv)[0]).DataTable();
+ assert.ok(dataTable.data().count() > 0);
+ return dialog.destroy();
});
});
});
@@ -67,7 +105,7 @@ describe('AddProjectDialog', function () {
});
return dialog.showAnnotatorsDialog().then(function () {
- dialog.destroy();
+ return dialog.destroy();
});
});
});
@@ -110,6 +148,7 @@ describe('AddProjectDialog', function () {
assert.ok(options["organism"] !== undefined);
assert.ok(options["sbgn"] !== undefined);
assert.ok(options["semantic-zoom"] !== undefined);
+ return dialog.destroy();
});
});
});
diff --git a/frontend-js/src/test/js/map/OverlayParser-test.js b/frontend-js/src/test/js/map/OverlayParser-test.js
new file mode 100644
index 0000000000000000000000000000000000000000..b3a0f0ae080204da617af2e331435a316882c07a
--- /dev/null
+++ b/frontend-js/src/test/js/map/OverlayParser-test.js
@@ -0,0 +1,33 @@
+"use strict";
+
+require("../mocha-config.js");
+
+var OverlayParser = require('../../../main/js/map/OverlayParser');
+var chai = require('chai');
+var assert = chai.assert;
+
+describe('OverlayParser', function () {
+ describe('parse', function () {
+ it('simple', function () {
+ var parser = new OverlayParser();
+ var fileContent = "#NAME=some Name\n#DESCRIPTION=xxx\nname\tvalue\ns1\t1";
+
+ var overlay = parser.parse(fileContent);
+ assert.ok(overlay);
+ assert.equal(overlay.getDescription(), "xxx");
+ assert.equal(overlay.getName(), "some Name");
+ assert.ok(overlay.getContent());
+ });
+ it('with type', function () {
+
+ return ServerConnector.sendGetRequest("testFiles/overlay/good.txt").then(function (fileContent) {
+ var parser = new OverlayParser();
+ var overlay = parser.parse(fileContent);
+ assert.equal(overlay.getName(), "example name");
+ assert.equal(overlay.getDescription(), "layout description");
+ assert.equal(overlay.getType(), "GENERIC");
+ });
+ });
+ });
+
+});
diff --git a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
index 87bada811f18fa43905db6a71d4b83047d186854..38618b8344d16fc18518b9dfd5cda7551f015063 100644
--- a/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
+++ b/frontend-js/testFiles/apiCalls/configuration/token=MOCK_TOKEN_ID&
@@ -1 +1 @@
-{"modelFormats":[{"handler":"lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser","extension":"xml","name":"CellDesigner SBML"},{"handler":"lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter","extension":"sbgn","name":"SBGN-ML"}],"elementTypes":[{"name":"Degraded","className":"lcsb.mapviewer.model.map.species.Degraded","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.IonChannelProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.TopSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Ion","className":"lcsb.mapviewer.model.map.species.Ion","parentClass":"lcsb.mapviewer.model.map.species.Chemical"},{"name":"Species","className":"lcsb.mapviewer.model.map.species.Species","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.RightSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Drug","className":"lcsb.mapviewer.model.map.species.Drug","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.Protein","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Protein","className":"lcsb.mapviewer.model.map.species.TruncatedProtein","parentClass":"lcsb.mapviewer.model.map.species.Protein"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.PathwayCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"RNA","className":"lcsb.mapviewer.model.map.species.Rna","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Chemical","className":"lcsb.mapviewer.model.map.species.Chemical","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.Compartment","parentClass":"lcsb.mapviewer.model.map.species.Element"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.OvalCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Compartment","className":"lcsb.mapviewer.model.map.compartment.SquareCompartment","parentClass":"lcsb.mapviewer.model.map.compartment.Compartment"},{"name":"Unknown","className":"lcsb.mapviewer.model.map.species.Unknown","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Element","className":"lcsb.mapviewer.model.map.species.Element","parentClass":"lcsb.mapviewer.model.map.BioEntity"},{"name":"Phenotype","className":"lcsb.mapviewer.model.map.species.Phenotype","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Complex","className":"lcsb.mapviewer.model.map.species.Complex","parentClass":"lcsb.mapviewer.model.map.species.Species"},{"name":"Antisense 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management","valueType":"boolean","objectType":null},"CUSTOM_LAYOUTS":{"commonName":"Custom layouts","valueType":"int","objectType":null},"ADD_MAP":{"commonName":"Add project","valueType":"boolean","objectType":null},"LAYOUT_VIEW":{"commonName":"View layout","valueType":"boolean","objectType":"Layout"},"MANAGE_GENOMES":{"commonName":"Manage genomes","valueType":"boolean","objectType":null},"EDIT_COMMENTS_PROJECT":{"commonName":"Manage comments","valueType":"boolean","objectType":"Project"},"CONFIGURATION_MANAGE":{"commonName":"Manage configuration","valueType":"boolean","objectType":null},"USER_MANAGEMENT":{"commonName":"User management","valueType":"boolean","objectType":null}},"overlayTypes":[{"name":"GENERIC"},{"name":"GENETIC_VARIANT"}]}
\ No newline at end of file
diff --git a/frontend-js/testFiles/map/complex_model_with_overlays.zip b/frontend-js/testFiles/map/complex_model_with_overlays.zip
new file mode 100644
index 0000000000000000000000000000000000000000..0aa92bc0ab6aa5a047d64677c3520d45de75e878
Binary files /dev/null and b/frontend-js/testFiles/map/complex_model_with_overlays.zip differ
diff --git a/frontend-js/testFiles/map/complex_model_with_submaps.zip b/frontend-js/testFiles/map/complex_model_with_submaps.zip
new file mode 100644
index 0000000000000000000000000000000000000000..5985c849bbeff096451d99b43a430ec6c266cf5b
Binary files /dev/null and b/frontend-js/testFiles/map/complex_model_with_submaps.zip differ
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
index e1ca1c0399715a380efb489f415821ebd4835974..52d86daa0f012301a2d1813ef17b167af9d1be65 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationController.java
@@ -19,68 +19,71 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
@RestController
public class ConfigurationController extends BaseController {
- @Autowired
- private ConfigurationRestImpl configurationController;
+ @Autowired
+ private ConfigurationRestImpl configurationController;
- @Autowired
- private IConfigurationService configurationService;
+ @Autowired
+ private IConfigurationService configurationService;
- /**
- * Context used to determine deployment path.
- */
- @Autowired
- private ServletContext context;
+ /**
+ * Context used to determine deployment path.
+ */
+ @Autowired
+ private ServletContext context;
- @RequestMapping(value = "/configuration/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, Object> getOverlayTypes(@CookieValue(value = Configuration.AUTH_TOKEN) String token) throws SecurityException {
- Map<String, Object> result = new HashMap<>();
- result.put("options", configurationController.getAllValues(token));
- result.put("imageFormats", configurationController.getImageFormats(token));
- result.put("modelFormats", configurationController.getModelFormats(token));
- result.put("overlayTypes", configurationController.getOverlayTypes(token));
- result.put("elementTypes", configurationController.getElementTypes(token));
- result.put("reactionTypes", configurationController.getReactionTypes(token));
- result.put("miriamTypes", configurationController.getMiriamTypes(token));
- result.put("modificationStateTypes", configurationController.getModificationStateTypes(token));
- result.put("privilegeTypes", configurationController.getPrivilegeTypes(token));
- result.put("version", configurationService.getSystemSvnVersion(context.getRealPath("/")));
- result.put("buildDate", configurationService.getSystemBuild(context.getRealPath("/")));
- result.put("annotators", configurationController.getAnnotators(token));
- return result;
- }
+ @RequestMapping(value = "/configuration/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Map<String, Object> getOverlayTypes(@CookieValue(value = Configuration.AUTH_TOKEN) String token)
+ throws SecurityException {
+ Map<String, Object> result = new HashMap<>();
+ result.put("options", configurationController.getAllValues(token));
+ result.put("imageFormats", configurationController.getImageFormats(token));
+ result.put("modelFormats", configurationController.getModelFormats(token));
+ result.put("overlayTypes", configurationController.getOverlayTypes(token));
+ result.put("elementTypes", configurationController.getElementTypes(token));
+ result.put("reactionTypes", configurationController.getReactionTypes(token));
+ result.put("miriamTypes", configurationController.getMiriamTypes(token));
+ result.put("mapTypes", configurationController.getMapTypes(token));
+ result.put("modificationStateTypes", configurationController.getModificationStateTypes(token));
+ result.put("privilegeTypes", configurationController.getPrivilegeTypes(token));
+ result.put("version", configurationService.getSystemSvnVersion(context.getRealPath("/")));
+ result.put("buildDate", configurationService.getSystemBuild(context.getRealPath("/")));
+ result.put("annotators", configurationController.getAnnotators(token));
+ return result;
+ }
- /**
- * @return the configurationController
- * @see #configurationController
- */
- public ConfigurationRestImpl getConfigurationController() {
- return configurationController;
- }
+ /**
+ * @return the configurationController
+ * @see #configurationController
+ */
+ public ConfigurationRestImpl getConfigurationController() {
+ return configurationController;
+ }
- /**
- * @param configurationController
- * the configurationController to set
- * @see #configurationController
- */
- public void setConfigurationController(ConfigurationRestImpl configurationController) {
- this.configurationController = configurationController;
- }
+ /**
+ * @param configurationController
+ * the configurationController to set
+ * @see #configurationController
+ */
+ public void setConfigurationController(ConfigurationRestImpl configurationController) {
+ this.configurationController = configurationController;
+ }
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 6eb4066d9b08d66ee6a655414166bef47565e3bf..effd2cb87d76612dfeb95ec991946e8d0c174de3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -25,6 +25,8 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.field.ModificationState;
@@ -39,216 +41,228 @@ import lcsb.mapviewer.services.view.ConfigurationView;
@Transactional(value = "txManager")
public class ConfigurationRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ConfigurationRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IConfigurationService configurationService;
-
- @Autowired
- private ModelAnnotator modelAnnotator;
-
- public List<ConfigurationView> getAllValues(String token) throws SecurityException {
- userService.getToken(token);
- return configurationService.getAllValues();
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- public List<Map<String, Object>> getImageFormats(String token) throws SecurityException {
- userService.getToken(token);
-
- List<Map<String, Object>> result = new ArrayList<>();
- ImageGenerators imageGenerators = new ImageGenerators();
- List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGeneratorList = imageGenerators.getAvailableImageGenerators();
-
- for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
- Map<String, Object> row = new HashMap<>();
- row.put("name", element.getLeft());
- row.put("handler", element.getRight().getCanonicalName());
- row.put("extension", imageGenerators.getExtension(element.getRight()));
- result.add(row);
- }
- return result;
- }
-
- public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
- userService.getToken(token);
- List<IConverter> converters = new ArrayList<>();
- converters.add(new CellDesignerXmlParser());
- converters.add(new SbgnmlXmlConverter());
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- for (IConverter converter : converters) {
- Map<String, Object> row = new HashMap<>();
- row.put("name", converter.getCommonName());
- row.put("handler", converter.getClass().getCanonicalName());
- row.put("extension", converter.getFileExtension());
- result.add(row);
- }
- return result;
- }
-
- public List<Map<String, Object>> getOverlayTypes(String token) throws SecurityException {
- userService.getToken(token);
- List<Map<String, Object>> result = new ArrayList<>();
- for (ColorSchemaType type : ColorSchemaType.values()) {
- Map<String, Object> map = new HashMap<>();
- map.put("name", type.name());
- result.add(map);
- }
- return result;
- }
-
- public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
- userService.getToken(token);
-
- return getClassStringTypesList(Element.class);
- }
-
- private Set<Map<String, String>> getClassStringTypesList(Class<?> elementClass) {
- Set<Map<String, String>> result = new HashSet<>();
- ElementUtils elementUtils = new ElementUtils();
- ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
- Queue<ClassTreeNode> queue = new LinkedList<>();
- queue.add(top);
- while (!queue.isEmpty()) {
- ClassTreeNode clazz = queue.poll();
- for (ClassTreeNode child : clazz.getChildren()) {
- queue.add(child);
- }
- if (elementClass.isAssignableFrom(clazz.getClazz())) {
- Map<String, String> row = new HashMap<>();
- row.put("className", clazz.getClazz().getName());
- row.put("name", clazz.getCommonName());
- if (clazz.getParent() == null) {
- row.put("parentClass", null);
- } else {
- row.put("parentClass", clazz.getParent().getClazz().getName());
- }
- result.add(row);
- }
- }
- return result;
- }
-
- public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
- userService.getToken(token);
-
- return getClassStringTypesList(Reaction.class);
- }
-
- public Map<String, Object> getMiriamTypes(String id) {
- Map<String, Object> result = new HashMap<>();
- for (MiriamType type : MiriamType.values()) {
- result.put(type.name(), createMiriamTypeResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
- Map<String, Object> result = new HashMap<>();
- result.put("commonName", type.getCommonName());
- result.put("homepage", type.getDbHomepage());
- result.put("registryIdentifier", type.getRegistryIdentifier());
- result.put("uris", type.getUris());
-
- return result;
- }
-
- public Object getModificationStateTypes(String token) {
- Map<String, Object> result = new HashMap<>();
- for (ModificationState type : ModificationState.values()) {
- result.put(type.name(), createModificationStateResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createModificationStateResponse(ModificationState type) {
- Map<String, Object> result = new HashMap<>();
- result.put("commonName", type.getFullName());
- result.put("abbreviation", type.getAbbreviation());
- return result;
- }
-
- public Map<String, Object> getPrivilegeTypes(String id) {
- Map<String, Object> result = new HashMap<>();
- for (PrivilegeType type : PrivilegeType.values()) {
- result.put(type.name(), createPrivilegeTypeResponse(type));
- }
- return result;
- }
-
- private Map<String, Object> createPrivilegeTypeResponse(PrivilegeType type) {
- Map<String, Object> result = new HashMap<>();
- result.put("commonName", type.getCommonName());
- if (type.getPrivilegeObjectType() != null) {
- result.put("objectType", type.getPrivilegeObjectType().getSimpleName());
- } else {
- result.put("objectType", null);
- }
- if (type.isNumeric()) {
- result.put("valueType", "int");
- } else {
- result.put("valueType", "boolean");
- }
- return result;
- }
-
- public List<Map<String, Object>> getAnnotators(String token) {
- List<Map<String, Object>> result = new ArrayList<>();
- for (ElementAnnotator annotator : modelAnnotator.getAvailableAnnotators()) {
- result.add(prepareAnnotator(annotator));
- }
- return result;
- }
-
- private Map<String, Object> prepareAnnotator(ElementAnnotator annotator) {
- Map<String, Object> result = new HashMap<>();
- result.put("className", annotator.getClass().getName());
- result.put("name", annotator.getCommonName());
- result.put("url", annotator.getUrl());
- result.put("elementClassNames", annotator.getValidClasses());
- return result;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ConfigurationRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IConfigurationService configurationService;
+
+ @Autowired
+ private ModelAnnotator modelAnnotator;
+
+ public List<ConfigurationView> getAllValues(String token) throws SecurityException {
+ userService.getToken(token);
+ return configurationService.getAllValues();
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ public List<Map<String, Object>> getImageFormats(String token) throws SecurityException {
+ userService.getToken(token);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+ ImageGenerators imageGenerators = new ImageGenerators();
+ List<Pair<String, Class<? extends AbstractImageGenerator>>> imageGeneratorList = imageGenerators
+ .getAvailableImageGenerators();
+
+ for (Pair<String, Class<? extends AbstractImageGenerator>> element : imageGeneratorList) {
+ Map<String, Object> row = new HashMap<>();
+ row.put("name", element.getLeft());
+ row.put("handler", element.getRight().getCanonicalName());
+ row.put("extension", imageGenerators.getExtension(element.getRight()));
+ result.add(row);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
+ userService.getToken(token);
+ List<IConverter> converters = new ArrayList<>();
+ converters.add(new CellDesignerXmlParser());
+ converters.add(new SbgnmlXmlConverter());
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (IConverter converter : converters) {
+ Map<String, Object> row = new HashMap<>();
+ row.put("name", converter.getCommonName());
+ row.put("handler", converter.getClass().getCanonicalName());
+ row.put("extension", converter.getFileExtension());
+ result.add(row);
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getOverlayTypes(String token) throws SecurityException {
+ userService.getToken(token);
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ColorSchemaType type : ColorSchemaType.values()) {
+ Map<String, Object> map = new HashMap<>();
+ map.put("name", type.name());
+ result.add(map);
+ }
+ return result;
+ }
+
+ public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
+ userService.getToken(token);
+
+ return getClassStringTypesList(Element.class);
+ }
+
+ private Set<Map<String, String>> getClassStringTypesList(Class<?> elementClass) {
+ Set<Map<String, String>> result = new HashSet<>();
+ ElementUtils elementUtils = new ElementUtils();
+ ClassTreeNode top = elementUtils.getAnnotatedElementClassTree();
+ Queue<ClassTreeNode> queue = new LinkedList<>();
+ queue.add(top);
+ while (!queue.isEmpty()) {
+ ClassTreeNode clazz = queue.poll();
+ for (ClassTreeNode child : clazz.getChildren()) {
+ queue.add(child);
+ }
+ if (elementClass.isAssignableFrom(clazz.getClazz())) {
+ Map<String, String> row = new HashMap<>();
+ row.put("className", clazz.getClazz().getName());
+ row.put("name", clazz.getCommonName());
+ if (clazz.getParent() == null) {
+ row.put("parentClass", null);
+ } else {
+ row.put("parentClass", clazz.getParent().getClazz().getName());
+ }
+ result.add(row);
+ }
+ }
+ return result;
+ }
+
+ public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
+ userService.getToken(token);
+
+ return getClassStringTypesList(Reaction.class);
+ }
+
+ public Map<String, Object> getMiriamTypes(String id) {
+ Map<String, Object> result = new HashMap<>();
+ for (MiriamType type : MiriamType.values()) {
+ result.put(type.name(), createMiriamTypeResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createMiriamTypeResponse(MiriamType type) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("commonName", type.getCommonName());
+ result.put("homepage", type.getDbHomepage());
+ result.put("registryIdentifier", type.getRegistryIdentifier());
+ result.put("uris", type.getUris());
+
+ return result;
+ }
+
+ public Object getModificationStateTypes(String token) {
+ Map<String, Object> result = new HashMap<>();
+ for (ModificationState type : ModificationState.values()) {
+ result.put(type.name(), createModificationStateResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createModificationStateResponse(ModificationState type) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("commonName", type.getFullName());
+ result.put("abbreviation", type.getAbbreviation());
+ return result;
+ }
+
+ public Map<String, Object> getPrivilegeTypes(String id) {
+ Map<String, Object> result = new HashMap<>();
+ for (PrivilegeType type : PrivilegeType.values()) {
+ result.put(type.name(), createPrivilegeTypeResponse(type));
+ }
+ return result;
+ }
+
+ private Map<String, Object> createPrivilegeTypeResponse(PrivilegeType type) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("commonName", type.getCommonName());
+ if (type.getPrivilegeObjectType() != null) {
+ result.put("objectType", type.getPrivilegeObjectType().getSimpleName());
+ } else {
+ result.put("objectType", null);
+ }
+ if (type.isNumeric()) {
+ result.put("valueType", "int");
+ } else {
+ result.put("valueType", "boolean");
+ }
+ return result;
+ }
+
+ public List<Map<String, Object>> getAnnotators(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (ElementAnnotator annotator : modelAnnotator.getAvailableAnnotators()) {
+ result.add(prepareAnnotator(annotator));
+ }
+ return result;
+ }
+
+ private Map<String, Object> prepareAnnotator(ElementAnnotator annotator) {
+ Map<String, Object> result = new HashMap<>();
+ result.put("className", annotator.getClass().getName());
+ result.put("name", annotator.getCommonName());
+ result.put("url", annotator.getUrl());
+ result.put("elementClassNames", annotator.getValidClasses());
+ return result;
+ }
+
+ public List<Map<String, Object>> getMapTypes(String token) {
+ List<Map<String, Object>> result = new ArrayList<>();
+ for (SubmodelType type : SubmodelType.values()) {
+ Map<String, Object> row = new HashMap<>();
+ row.put("id", type.name());
+ row.put("name", type.getCommonName());
+ result.add(row);
+ }
+ return result;
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
index 793084e98a0c168646a689fe89ae948158d3c591..3c2db6e9d4f9186d3ddc9b1c29cadf0ef368f9c3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectController.java
@@ -33,141 +33,152 @@ import lcsb.mapviewer.services.SecurityException;
@RestController
public class ProjectController extends BaseController {
- private Logger logger = Logger.getLogger(ProjectController.class);
-
- @Autowired
- private ServletContext context;
-
- @Autowired
- private ProjectRestImpl projectController;
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ProjectMetaData getProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getProject(projectId, token);
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.PATCH }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ProjectMetaData updateProject(//
- @RequestBody String body, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- Map<String, Object> node = parseBody(body);
- Map<String, Object> data = getData(node, "project");
- return projectController.updateProject(token, projectId, data);
-
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ProjectMetaData addProject(//
- @RequestBody MultiValueMap<String,String> formData, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- return projectController.addProject(token, projectId, formData, context.getRealPath("/"));
-
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.DELETE }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ProjectMetaData removeProject(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, IOException, QueryException {
- return projectController.removeProject(token, projectId, context.getRealPath("/"));
-
- }
-
- @RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<ProjectMetaData> getProjects(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getProjects(token);
- }
-
- @RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Object getStatistics(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return projectController.getStatistics(projectId, token);
- }
-
- @RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getProjectSource(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId //
- ) throws SecurityException, QueryException {
-
- FileEntry file = projectController.getSource(token, projectId);
- MediaType type = MediaType.TEXT_PLAIN;
- if (file.getOriginalFileName().endsWith("xml")) {
- type = MediaType.APPLICATION_XML;
- } else if (file.getOriginalFileName().endsWith("zip")) {
- type = MediaType.APPLICATION_OCTET_STREAM;
- }
- return ResponseEntity
- .ok().contentLength(file.getFileContent().length).contentType(type).header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = { RequestMethod.GET },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsImage(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
-
- FileEntry file = projectController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId, overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity
- .ok().contentLength(file.getFileContent().length).contentType(type).header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = { RequestMethod.GET },
- produces = { MediaType.APPLICATION_JSON_VALUE })
- public ResponseEntity<byte[]> getModelAsModelFile(//
- @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
- @PathVariable(value = "projectId") String projectId, //
- @PathVariable(value = "modelId") String modelId, //
- @RequestParam(value = "handlerClass") String handlerClass, //
- @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
- @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
- @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
- @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
- ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, ConverterException,
- InconsistentModelException {
-
- FileEntry file = projectController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId, overlayIds, zoomLevel, polygonString);
- MediaType type = MediaType.APPLICATION_OCTET_STREAM;
- return ResponseEntity
- .ok().contentLength(file.getFileContent().length).contentType(type).header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
- .body(file.getFileContent());
- }
-
- /**
- * @return the context
- * @see #context
- */
- public ServletContext getContext() {
- return context;
- }
-
- /**
- * @param context the context to set
- * @see #context
- */
- public void setContext(ServletContext context) {
- this.context = context;
- }
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ProjectController.class);
+
+ @Autowired
+ private ServletContext context;
+
+ @Autowired
+ private ProjectRestImpl projectController;
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ProjectMetaData getProject(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getProject(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ProjectMetaData updateProject(//
+ @RequestBody String body, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "project");
+ return projectController.updateProject(token, projectId, data);
+
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.POST }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ProjectMetaData addProject(//
+ @RequestBody MultiValueMap<String, Object> formData, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ return projectController.addProject(token, projectId, formData, context.getRealPath("/"));
+
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}", method = { RequestMethod.DELETE }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ProjectMetaData removeProject(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, IOException, QueryException {
+ return projectController.removeProject(token, projectId, context.getRealPath("/"));
+
+ }
+
+ @RequestMapping(value = "/projects/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<ProjectMetaData> getProjects(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getProjects(token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/statistics", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Object getStatistics(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return projectController.getStatistics(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId}:downloadSource", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getProjectSource(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId //
+ ) throws SecurityException, QueryException {
+
+ FileEntry file = projectController.getSource(token, projectId);
+ MediaType type = MediaType.TEXT_PLAIN;
+ if (file.getOriginalFileName().endsWith("xml")) {
+ type = MediaType.APPLICATION_XML;
+ } else if (file.getOriginalFileName().endsWith("zip")) {
+ type = MediaType.APPLICATION_OCTET_STREAM;
+ }
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadImage", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsImage(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ DrawingException {
+
+ FileEntry file = projectController.getModelAsImage(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ @RequestMapping(value = "/projects/{projectId}/models/{modelId}:downloadModel", method = {
+ RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public ResponseEntity<byte[]> getModelAsModelFile(//
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token, //
+ @PathVariable(value = "projectId") String projectId, //
+ @PathVariable(value = "modelId") String modelId, //
+ @RequestParam(value = "handlerClass") String handlerClass, //
+ @RequestParam(value = "backgroundOverlayId", defaultValue = "") String backgroundOverlayId, //
+ @RequestParam(value = "overlayIds", defaultValue = "") String overlayIds, //
+ @RequestParam(value = "zoomLevel", defaultValue = "") String zoomLevel, //
+ @RequestParam(value = "polygonString", defaultValue = "") String polygonString//
+ ) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ ConverterException, InconsistentModelException {
+
+ FileEntry file = projectController.getModelAsModelFile(token, projectId, modelId, handlerClass, backgroundOverlayId,
+ overlayIds, zoomLevel, polygonString);
+ MediaType type = MediaType.APPLICATION_OCTET_STREAM;
+ return ResponseEntity.ok().contentLength(file.getFileContent().length).contentType(type)
+ .header("Content-Disposition", "attachment; filename=" + file.getOriginalFileName())
+ .body(file.getFileContent());
+ }
+
+ /**
+ * @return the context
+ * @see #context
+ */
+ public ServletContext getContext() {
+ return context;
+ }
+
+ /**
+ * @param context
+ * the context to set
+ * @see #context
+ */
+ public void setContext(ServletContext context) {
+ this.context = context;
+ }
}
\ No newline at end of file
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 b788a8feb8c46cccf085cc3aacc6986f40341f21..6a50de4c1f70aa97abae624754c51e4b116e9f6a 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
@@ -38,9 +38,14 @@ import lcsb.mapviewer.commands.SetFixedHierarchyLevelCommand;
import lcsb.mapviewer.commands.SubModelCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.ImageGenerators;
import lcsb.mapviewer.model.Project;
@@ -56,6 +61,7 @@ import lcsb.mapviewer.model.map.layout.ColorSchema;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
@@ -75,7 +81,7 @@ public class ProjectRestImpl extends BaseRestImpl {
/**
* Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More nformation can be
+ * {@link PathIterator#currentSegment(double[])} method. More information can be
* found <a href=
* "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
* >here</a>
@@ -473,8 +479,9 @@ public class ProjectRestImpl extends BaseRestImpl {
}
}
- public ProjectMetaData addProject(String token, String projectId, MultiValueMap<String, String> data, String path)
+ public ProjectMetaData addProject(String token, String projectId, MultiValueMap<String, Object> data, String path)
throws SecurityException, QueryException, IOException {
+ logger.info(data);
AuthenticationToken authenticationToken = getUserService().getToken(token);
User user = getUserService().getUserByToken(authenticationToken);
Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
@@ -493,6 +500,12 @@ public class ProjectRestImpl extends BaseRestImpl {
}
IConverter parser = getModelParser(parserClass);
+ List<ZipEntryFile> zipEntries = extractZipEntries(data);
+ params.complex(zipEntries.size() > 0);
+ for (ZipEntryFile entry : zipEntries) {
+ params.addZipEntry(entry);
+ }
+
params.addUser(user.getLogin(), null);
params.async(true);
params.parser(parser);
@@ -504,7 +517,7 @@ public class ProjectRestImpl extends BaseRestImpl {
params.notifyEmail(getFirstValue(data.get("notify-email")));
params.projectDir(directory);
params.projectDisease(getFirstValue(data.get("disease")));
- params.projectFile(new ByteArrayInputStream(fileContent.getBytes(StandardCharsets.UTF_8)));
+ params.projectFile(new ByteArrayInputStream(fileContent.getBytes()));
params.projectId(projectId);
params.projectName(getFirstValue(data.get("name")));
params.projectOrganism(getFirstValue(data.get("organism")));
@@ -525,12 +538,57 @@ public class ProjectRestImpl extends BaseRestImpl {
return getProject(projectId, token);
}
- private String getFirstValue(List<String> list) {
+ protected List<ZipEntryFile> extractZipEntries(MultiValueMap<String, Object> data) {
+ int fileIndex = 0;
+ List<ZipEntryFile> result = new ArrayList<>();
+ while (data.get("zip-entries[" + fileIndex + "][_filename]") != null) {
+ ZipEntryFile entry = null;
+ String entryType = (String) data.get("zip-entries[" + fileIndex + "][_type]").get(0);
+ String filename = (String) data.get("zip-entries[" + fileIndex + "][_filename]").get(0);
+ if ("MAP".equalsIgnoreCase(entryType)) {
+ String submodelTypeKey = "zip-entries[" + fileIndex + "][_data][type][id]";
+ String rootKey = "zip-entries[" + fileIndex + "][_data][root]";
+ String mappingKey = "zip-entries[" + fileIndex + "][_data][mapping]";
+ SubmodelType mapType = SubmodelType.valueOf((String) data.get(submodelTypeKey).get(0));
+ String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
+ Boolean root = getBoolValue(data.get(rootKey), false);
+ Boolean mapping = getBoolValue(data.get(mappingKey), false);
+
+ entry = new ModelZipEntryFile(filename, name, root, mapping, mapType);
+ } else if ("OVERLAY".equalsIgnoreCase(entryType)) {
+ String name = (String) data.get("zip-entries[" + fileIndex + "][_data][name]").get(0);
+ String description = (String) data.get("zip-entries[" + fileIndex + "][_data][description]").get(0);
+ entry = new LayoutZipEntryFile(filename, name, description);
+ } else if ("IMAGE".equalsIgnoreCase(entryType)) {
+ entry = new ImageZipEntryFile(filename);
+ } else {
+ throw new Error("Unknown entry type: " + entryType);
+ }
+ fileIndex++;
+ result.add(entry);
+
+ }
+ return result;
+ }
+
+ private Boolean getBoolValue(List<Object> list, boolean defaultValue) {
+ if (list == null) {
+ return defaultValue;
+ }
+ Object obj = list.get(0);
+ if (obj instanceof Boolean) {
+ return (Boolean) list.get(0);
+ } else {
+ return "true".equalsIgnoreCase((String) obj);
+ }
+ }
+
+ private String getFirstValue(List<Object> list) {
if (list == null) {
return null;
}
if (list.size() > 0) {
- return list.get(0);
+ return (String) list.get(0);
}
return null;
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 97482c221658f95a21ec2112e04bc8b5b9f06757..f7bfb87b87c29fba1c290f12b0373a8bcb152a45 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.api.projects;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyString;
@@ -9,6 +10,7 @@ import static org.mockito.Mockito.times;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@@ -19,6 +21,8 @@ import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.util.LinkedMultiValueMap;
+import org.springframework.util.MultiValueMap;
import com.google.gson.Gson;
@@ -28,6 +32,10 @@ import lcsb.mapviewer.api.RestTestFunctions;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.graphics.PdfImageGenerator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.FileEntry;
import lcsb.mapviewer.model.map.MiriamType;
@@ -36,222 +44,260 @@ import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectService;
public class ProjectRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(ProjectRestImplTest.class);
-
- @Autowired
- ProjectRestImpl _projectRestImpl;
-
- @Autowired
- IModelService modelService;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetModelAsImageForInvalidConverter() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token.getId(), "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsImage() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- FileEntry result = projectRest.getModelAsImage(token.getId(), "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
- assertNotNull(result);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelDataDependencies() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- Mockito.verify(projectRest.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(expected = ObjectNotFoundException.class)
- public void testGetInvalidMetaData() throws Exception {
- ProjectRestImpl projectRest = createMockProjectRest(null);
- projectRest.getProject("unknown_model_id", token.getId());
- }
-
- @Test
- public void testGetModelAsImage2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token.getId(), "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel2() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "", "0,0;90,0;90,90;90,0");
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetModelAsFileModel3() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProject() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateProject() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String,String> disease = new HashMap<>();
- disease.put("type",MiriamType.MESH_2012.name());
- disease.put("resource", "D010300");
- Map<String, Object> data = new HashMap<>();
- data.put("version", "1");
- data.put("name", "test");
- data.put("organism", null);
- data.put("disease", disease);
- data.put("projectId", "sample");
- data.put("id", "0");
- projectRest.updateProject(adminToken.getId(), "sample", data);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProjects() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- List<ProjectMetaData> result = projectRest.getProjects(token.getId());
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetStatistics() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getStatistics("sample", token.getId());
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
-
- Map<?, ?> elementAnnotations = (Map<?, ?>) result.get("elementAnnotations");
- assertEquals(elementAnnotations.get(MiriamType.CAS), 0);
- assertEquals(elementAnnotations.get(MiriamType.ENTREZ), 1);
-
- Map<?, ?> reactionAnnotations = (Map<?, ?>) result.get("reactionAnnotations");
- assertEquals(reactionAnnotations.get(MiriamType.ENTREZ), 0);
- assertEquals(reactionAnnotations.get(MiriamType.PUBMED), 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMetaDataForComplexWithImages() throws Exception {
- try {
- ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/complex_model_with_submaps.zip");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
- Gson gson = new Gson();
- assertNotNull(gson.toJson(result));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private ProjectRestImpl createMockProjectRest(String string) throws Exception {
- Model model = null;
- Project project = null;
- if (string != null) {
- project = new Project();
- model = super.getModelForFile(string, true);
- project.addModel(model);
- project.setProjectId(model.getName());
- }
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _projectRestImpl.setModelService(mockModelService);
-
- IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
- Mockito.when(projectServiceMock.getProjectByProjectId(anyString(), any())).thenReturn(project);
- List<Project> projects = new ArrayList<>();
- projects.add(project);
- Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
- _projectRestImpl.setProjectService(projectServiceMock);
-
- return _projectRestImpl;
- }
+ Logger logger = Logger.getLogger(ProjectRestImplTest.class);
+
+ @Autowired
+ ProjectRestImpl _projectRestImpl;
+
+ @Autowired
+ IModelService modelService;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetModelAsImageForInvalidConverter() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsImage(token.getId(), "sample", "0", "", "", "", "", "");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsImage() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ FileEntry result = projectRest.getModelAsImage(token.getId(), "sample", "0",
+ PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
+ assertNotNull(result);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelDataDependencies() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ Mockito.verify(projectRest.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(expected = ObjectNotFoundException.class)
+ public void testGetInvalidMetaData() throws Exception {
+ ProjectRestImpl projectRest = createMockProjectRest(null);
+ projectRest.getProject("unknown_model_id", token.getId());
+ }
+
+ @Test
+ public void testGetModelAsImage2() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsImage(token.getId(), "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "",
+ "");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel2() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token.getId(), "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "",
+ "", "", "0,0;90,0;90,90;90,0");
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetModelAsFileModel3() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProject() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateProject() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, String> disease = new HashMap<>();
+ disease.put("type", MiriamType.MESH_2012.name());
+ disease.put("resource", "D010300");
+ Map<String, Object> data = new HashMap<>();
+ data.put("version", "1");
+ data.put("name", "test");
+ data.put("organism", null);
+ data.put("disease", disease);
+ data.put("projectId", "sample");
+ data.put("id", "0");
+ projectRest.updateProject(adminToken.getId(), "sample", data);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProjects() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ List<ProjectMetaData> result = projectRest.getProjects(token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetStatistics() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getStatistics("sample", token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+
+ Map<?, ?> elementAnnotations = (Map<?, ?>) result.get("elementAnnotations");
+ assertEquals(elementAnnotations.get(MiriamType.CAS), 0);
+ assertEquals(elementAnnotations.get(MiriamType.ENTREZ), 1);
+
+ Map<?, ?> reactionAnnotations = (Map<?, ?>) result.get("reactionAnnotations");
+ assertEquals(reactionAnnotations.get(MiriamType.ENTREZ), 0);
+ assertEquals(reactionAnnotations.get(MiriamType.PUBMED), 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMetaDataForComplexWithImages() throws Exception {
+ try {
+ ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/complex_model_with_submaps.zip");
+ ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ Gson gson = new Gson();
+ assertNotNull(gson.toJson(result));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExtractZipEntries() throws Exception {
+ try {
+ MultiValueMap<String, Object> data = new LinkedMultiValueMap<>();
+ data.put("zip-entries[0][_type]",createLinkedList("MAP"));
+ data.put("zip-entries[0][_filename]",createLinkedList("main.xml"));
+ data.put("zip-entries[0][_data][root]",createLinkedList("true"));
+ data.put("zip-entries[0][_data][name]",createLinkedList("main"));
+ data.put("zip-entries[0][_data][type][id]",createLinkedList("UNKNOWN"));
+ data.put("zip-entries[0][_data][type][name]",createLinkedList("Unknown"));
+ data.put("zip-entries[1][_type]",createLinkedList("OVERLAY"));
+ data.put("zip-entries[1][_filename]",createLinkedList("layouts/goodschema.txt"));
+ data.put("zip-entries[1][_data][name]",createLinkedList("example name"));
+ data.put("zip-entries[1][_data][description]",createLinkedList("layout description"));
+ data.put("zip-entries[2][_type]",createLinkedList("IMAGE"));
+ data.put("zip-entries[2][_filename]",createLinkedList("images/test.png"));
+ List<ZipEntryFile> result = _projectRestImpl.extractZipEntries(data);
+ assertNotNull(result);
+ assertEquals(3, result.size());
+ assertTrue(result.get(0) instanceof ModelZipEntryFile);
+ assertTrue(result.get(1) instanceof LayoutZipEntryFile);
+ assertTrue(result.get(2) instanceof ImageZipEntryFile);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private LinkedList<Object> createLinkedList(Object string) {
+ LinkedList<Object> result = new LinkedList<>();
+ result.add(string);
+ return result;
+ }
+
+ private ProjectRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = null;
+ Project project = null;
+ if (string != null) {
+ project = new Project();
+ model = super.getModelForFile(string, true);
+ project.addModel(model);
+ project.setProjectId(model.getName());
+ }
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _projectRestImpl.setModelService(mockModelService);
+
+ IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
+ Mockito.when(projectServiceMock.getProjectByProjectId(anyString(), any())).thenReturn(project);
+ List<Project> projects = new ArrayList<>();
+ projects.add(project);
+ Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
+ _projectRestImpl.setProjectService(projectServiceMock);
+
+ return _projectRestImpl;
+ }
}