diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
index 78946c93d35c5bb5e8d461219429fadf45dd4368..4d059ffe90bbe4644f6e1c1c52249ae2b6a4f905 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverterParams.java
@@ -1,14 +1,19 @@
package lcsb.mapviewer.converter;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.zip.ZipFile;
+import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
/**
* Class that contains information about input data used for creation of the
@@ -52,6 +57,12 @@ public class ComplexZipConverterParams {
return this;
}
+ public ComplexZipConverterParams zipFile(UploadedFileEntry file) throws IOException {
+ File temp = File.createTempFile("model", ".xml");
+ IOUtils.copy(new ByteArrayInputStream(file.getFileContent()), new FileOutputStream(temp));
+ return zipFile(temp.getAbsolutePath());
+ }
+
/**
* Sets {@link #zipFile}.
*
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 325645b14f40c7e8f4e17aa9a9b48f9d1c1bcbc2..e13408a974fc63ff5a03a97e5969f9f2f68903da 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
@@ -372,7 +372,7 @@ 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(file.getFileContent()));
+ params.projectFile(file);
params.projectId(projectId);
params.projectName(getFirstValue(data.get("name")));
params.projectOrganism(getFirstValue(data.get("organism")));
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 013ec3131eefab498b9e142983794da2ca2ed140..d73022892d9183f7742b3ca389118c38be6caff3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1,9 +1,9 @@
package lcsb.mapviewer.services.impl;
+import java.io.ByteArrayInputStream;
import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
import java.io.IOException;
+import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -18,8 +18,6 @@ import java.util.concurrent.CountDownLatch;
import javax.mail.MessagingException;
import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
import org.apache.log4j.Logger;
import org.hibernate.HibernateException;
import org.primefaces.model.DefaultTreeNode;
@@ -54,7 +52,6 @@ import lcsb.mapviewer.converter.graphics.DrawingException;
import lcsb.mapviewer.converter.graphics.MapGenerator;
import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.model.sbgnml.SbgnmlXmlConverter;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
@@ -557,22 +554,16 @@ public class ProjectService implements IProjectService {
throw new InvalidInputDataExecption(e);
}
} else {
- IConverter parser;
- if (params.getParser() != null) {
- parser = params.getParser();
- } else if (params.getProjectFile().endsWith("sbgn")) {
- parser = new SbgnmlXmlConverter();
- } else {
- parser = new CellDesignerXmlParser();
- }
- try {
- Model model = parser.createModel(new ConverterParams().filename(params.getProjectFile())
- .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
- model.setName(params.getProjectName());
- project.addModel(model);
- } catch (FileNotFoundException ex) {
- throw new InvalidInputDataExecption(ex);
+ IConverter parser = params.getParser();
+ if (parser == null) {
+ throw new InvalidArgumentException("Parser is undefined");
}
+ InputStream input = new ByteArrayInputStream(params.getProjectFile().getFileContent());
+ Model model = parser
+ .createModel(new ConverterParams().inputStream(input, params.getProjectFile().getOriginalFileName())
+ .sizeAutoAdjust(params.isAutoResize()).sbgnFormat(params.isSbgnFormat()));
+ model.setName(params.getProjectName());
+ project.addModel(model);
}
Model topModel = project.getModels().iterator().next().getModel();
topModel.setZoomLevels(generator.computeZoomLevels(topModel));
@@ -736,16 +727,8 @@ public class ProjectService implements IProjectService {
outOfMemoryBuffer[i] = Math.random() * OUT_OF_MEMORY_BACKUP_BUFFER_SIZE;
}
- File inputFile = new File(params.getProjectFile());
- if (inputFile.exists()) {
- UploadedFileEntry file = new UploadedFileEntry();
- file.setFileContent(IOUtils.toByteArray(new FileInputStream(inputFile)));
- file.setOriginalFileName(FilenameUtils.getName(params.getProjectFile()));
- file.setLength(file.getFileContent().length);
- User owner = userService.getUserByToken(params.getAuthenticationToken());
- file.setOwner(owner);
- project.setInputData(file);
- }
+ UploadedFileEntry file = params.getProjectFile();
+ project.setInputData(file);
createModel(params, project);
Model originalModel = project.getModels().iterator().next().getModel();
diff --git a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
index 569c725ca466034a3f075446f23ada949c6a2ef9..01c52b7743c3aee3f6d6e2dd6a5469f4eb1fd2fa 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.services.utils;
-import java.io.File;
-import java.io.FileOutputStream;
import java.io.IOException;
-import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
@@ -13,11 +10,11 @@ import java.util.Map;
import java.util.Queue;
import java.util.Set;
-import org.apache.commons.io.IOUtils;
import org.primefaces.model.TreeNode;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.MapCanvasType;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
@@ -55,7 +52,7 @@ public class CreateProjectParams {
/**
* Path to a file used as a model.
*/
- private String projectFile;
+ private UploadedFileEntry projectFile;
private IConverter parser;
@@ -191,17 +188,6 @@ public class CreateProjectParams {
return this;
}
- /**
- * @param projectFile
- * the projectFile to set
- * @return object with all parameters
- * @see #projectFile
- */
- public CreateProjectParams projectFile(String projectFile) {
- this.projectFile = projectFile;
- return this;
- }
-
/**
* @param autoResize
* the autoResize to set
@@ -220,28 +206,14 @@ public class CreateProjectParams {
/**
* Sets input stream from which projects should be generated.
*
- * @param is
- * inputstream with the data of the project to be generated
+ * @param fileEntry
+ * uploaded file that should be used to create a project
* @return object with all parameters
* @throws IOException
* thrown if there are some problem with the stream
*/
- public CreateProjectParams projectFile(InputStream is) throws IOException {
- File temp = File.createTempFile("model", ".xml");
- IOUtils.copy(is, new FileOutputStream(temp));
- this.projectFile = temp.getAbsolutePath();
- return this;
- }
-
- /**
- * Sets file from which projects should be generated.
- *
- * @param file
- * file with the data of the project to be generated
- * @return object with all parameters
- */
- public CreateProjectParams projectFile(File file) {
- this.projectFile = file.getAbsolutePath();
+ public CreateProjectParams projectFile(UploadedFileEntry fileEntry) throws IOException {
+ this.projectFile = fileEntry;
return this;
}
@@ -379,7 +351,7 @@ public class CreateProjectParams {
* @return the projectFile
* @see #projectFile
*/
- public String getProjectFile() {
+ public UploadedFileEntry getProjectFile() {
return projectFile;
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
index 0a58875c94372072436b680d85def08a31f349b9..136ab291acb93a5d0d2e6c65f902d9d1a2a17802 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -7,6 +7,8 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashSet;
@@ -18,6 +20,7 @@ import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
import org.apache.log4j.Logger;
+import org.apache.poi.util.IOUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -35,6 +38,7 @@ import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.OverviewImage;
@@ -134,11 +138,9 @@ public class ProjectServiceTest extends ServiceTestFunctions {
@Test
public void testUpdater() throws Exception {
try {
- String project_id = "test_id";
- projectService.createProject(new CreateProjectParams().authenticationToken(adminToken).projectId(project_id)
- .version("").projectFile("testFiles/centeredAnchorInModifier.xml").annotations(true).images(true).async(false)
- .projectDir(tmpResultDir).analyzeAnnotations(true));
- Project project = projectService.getProjectByProjectId(project_id, adminToken);
+ projectService.createProject(createProjectParams("testFiles/centeredAnchorInModifier.xml").analyzeAnnotations(true));
+ Project project = projectService.getProjectByProjectId(projectId, adminToken);
+ assertNotNull(project);
assertEquals(ProjectStatus.DONE, project.getStatus());
projectService.removeProject(project, null, false, adminToken);
} catch (Exception e) {
@@ -149,18 +151,20 @@ public class ProjectServiceTest extends ServiceTestFunctions {
@Test
public void testCreateComplex() throws Exception {
- String projectId = "test_id";
try {
ZipEntryFile entry1 = new ModelZipEntryFile("main.xml", "main", true, false, SubmodelType.UNKNOWN);
ZipEntryFile entry2 = new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry3 = new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- projectService.createProject(new CreateProjectParams().authenticationToken(adminToken).projectId(projectId)
- .version("").complex(true).projectFile("testFiles/complexModel/complex_model.zip").addZipEntry(entry1)
- .addZipEntry(entry2).addZipEntry(entry3).addZipEntry(entry4).addZipEntry(entry5).annotations(true)
- .semanticZoomContainsMultipleLayouts(true).images(true).async(false).projectDir(tmpResultDir)
- .analyzeAnnotations(true));
+ projectService.createProject(createProjectParams("testFiles/complexModel/complex_model.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ semanticZoomContainsMultipleLayouts(true).
+ images(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
Model model = modelService.getLastModelByProjectId(projectId, adminToken);
@@ -257,7 +261,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
layout.addDataOverlayImageLayer(new DataOverlayImageLayer(model, path + "/nested"));
project.addLayout(layout);
- CreateProjectParams params = new CreateProjectParams().images(true).projectDir(tmpResultDir);
+ CreateProjectParams params = createProjectParams("testFiles/sample.xml").images(true).projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
pService.setProjectDao(Mockito.mock(ProjectDao.class));
@@ -301,7 +305,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "name"));
- CreateProjectParams params = new CreateProjectParams().images(true).projectDir(tmpResultDir);
+ CreateProjectParams params = createProjectParams("testFiles/sample.xml").images(true).projectDir(tmpResultDir);
ProjectService pService = new ProjectService();
pService.setProjectDao(Mockito.mock(ProjectDao.class));
@@ -332,14 +336,16 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ZipEntryFile entry4 = new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN);
ZipEntryFile entry5 = new ModelZipEntryFile("mapping.xml", "mapping", false, true, SubmodelType.UNKNOWN);
- CreateProjectParams params = new CreateProjectParams().projectId(projectId).version("").complex(true)
- .projectFile("testFiles/complexModel/complex_model_with_compartment.zip").addZipEntry(entry1)
- .addZipEntry(entry2).addZipEntry(entry3).addZipEntry(entry4).addZipEntry(entry5).annotations(false)
- .images(false).async(false).projectDir(tmpResultDir).analyzeAnnotations(false);
+ CreateProjectParams params = createProjectParams("testFiles/complexModel/complex_model_with_compartment.zip").
+ addZipEntry(entry1).
+ addZipEntry(entry2).
+ addZipEntry(entry3).
+ addZipEntry(entry4).
+ addZipEntry(entry5).
+ analyzeAnnotations(false);
ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
+ ComplexZipConverterParams complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
for (ZipEntryFile entry : params.getZipEntries()) {
complexParams.entry(entry);
}
@@ -558,7 +564,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
protected Project createComplexProject(String projectId, String filename) throws IOException, SecurityException {
- CreateProjectParams params = new CreateProjectParams();
+ CreateProjectParams params = createProjectParams(filename);
ZipFile zipFile = new ZipFile(filename);
Enumeration<? extends ZipEntry> entries = zipFile.entries();
@@ -569,9 +575,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.authenticationToken(adminToken).projectId(projectId).version("").complex(true)
- .projectFile(filename).annotations(true).images(false).async(false).projectDir(tmpResultDir)
- .analyzeAnnotations(true));
+ projectService.createProject(params);
Project project = projectService.getProjectByProjectId(projectId, adminToken);
return project;
}
@@ -601,7 +605,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
public void testCreateComplexWithLayoutOrder() throws Exception {
try {
String filename = "testFiles/complexModel/complex_model_with_images.zip";
- CreateProjectParams params = new CreateProjectParams();
+ CreateProjectParams params = createProjectParams(filename);
ZipFile zipFile = new ZipFile(filename);
Enumeration<? extends ZipEntry> entries = zipFile.entries();
@@ -611,9 +615,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
zipFile.close();
- projectService.createProject(params.authenticationToken(adminToken).projectId(projectId).version("").complex(true)
- .projectFile(filename).annotations(true).images(false).async(false).networkLayoutAsDefault(true)
- .projectDir(tmpResultDir).analyzeAnnotations(true));
+ projectService.createProject(params.networkLayoutAsDefault(true));
Project project = projectService.getProjectByProjectId(projectId, adminToken);
Model model = modelService.getLastModelByProjectId(projectId, adminToken);
@@ -638,6 +640,19 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
}
+ private CreateProjectParams createProjectParams(String filename) throws FileNotFoundException, IOException {
+ logger.debug(filename);
+ UploadedFileEntry fileEntry = new UploadedFileEntry();
+ fileEntry.setLocalPath(filename);
+ byte[] data = IOUtils.toByteArray(new FileInputStream(filename));
+ fileEntry.setLength(data.length);
+ fileEntry.setFileContent(data);
+
+ return new CreateProjectParams().authenticationToken(adminToken).projectId(projectId).version("").complex(filename.endsWith("zip"))
+ .projectFile(fileEntry).annotations(true).images(false).async(false).projectDir(tmpResultDir)
+ .analyzeAnnotations(true).parser(new CellDesignerXmlParser());
+ }
+
@Test(timeout = 15000)
public void testCreateComplexWithLayouts() throws Exception {
try {