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Commit f47be7d8 authored by Piotr Gawron's avatar Piotr Gawron
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frontend for add zip projects

parent d074a0b8
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.idea/modules.xml
View file @ f47be7d8
......@@ -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
converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
View file @ f47be7d8
......@@ -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));
}
......
converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
View file @ f47be7d8
......@@ -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;
}
......
converter/src/main/java/lcsb/mapviewer/converter/zip/ImageZipEntryFile.java
View file @ f47be7d8
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();
}
}
converter/src/main/java/lcsb/mapviewer/converter/zip/LayoutZipEntryFile.java
View file @ f47be7d8
......@@ -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;
}
}
converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
View file @ f47be7d8
......@@ -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));
......
converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
View file @ f47be7d8
......@@ -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) {