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 173b6102c26150c9d7dab9af764d11a6b30d3afb..40d94a3fc6a3ef5a24ce2282fb0d9dd4020db7a2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -1,890 +1,896 @@
-package lcsb.mapviewer.services.impl;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Queue;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.primefaces.model.TreeNode;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.converter.ComplexZipConverter;
-import lcsb.mapviewer.converter.ComplexZipConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.user.ObjectPrivilege;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.model.user.UserAnnotationSchema;
-import lcsb.mapviewer.model.user.UserClassAnnotators;
-import lcsb.mapviewer.model.user.UserClassValidAnnotations;
-import lcsb.mapviewer.persist.dao.map.species.ElementDao;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.ServiceTestFunctions;
-import lcsb.mapviewer.services.UserAccessException;
-import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
-import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.utils.data.BuildInLayout;
-import lcsb.mapviewer.services.view.AuthenticationToken;
-import lcsb.mapviewer.services.view.ProjectView;
-
-@Rollback(true)
-public class ProjectServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(ProjectServiceTest.class);
-
- ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
-
- private final String tmpResultDir = "tmp/";
- String projectId = "Some_id";
-
- @Autowired
- ElementDao aliasDao;
-
- // assume that we have admin account with all the privileges
- AuthenticationToken adminToken;
-
- @Before
- public void setUp() throws Exception {
- adminToken = userService.login("admin", "admin");
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetProjectWithoutAccessToEverything() {
- try {
- createUser();
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
- List<Project> projects = projectService.getAllProjects(token);
- assertNotNull(projects);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void test() {
- try {
- List<Project> projects = projectService.getAllProjects(adminToken);
-
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.evict(project);
-
- List<Project> projects2 = projectService.getAllProjects(adminToken);
-
- assertEquals(projects.size() + 1, projects2.size());
-
- for (Project tmpProject : projects2) {
- if (!projects.contains(tmpProject)) {
- assertEquals(projectId, tmpProject.getProjectId());
- }
- }
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- projectDao.delete(project2);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemove() throws Exception {
-
- try {
- String project_id = "Some_id";
- Project project = new Project();
- project.setProjectId(project_id);
- projectDao.add(project);
-
- List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
- ProjectView row = null;
- for (ProjectView projectRow : projects2) {
- if (projectRow.getIdObject() == project.getId()) {
- row = projectRow;
- }
- }
- assertNotNull(row);
-
- User user = new User();
- user.setLogin("x");
- userDao.add(user);
- userDao.evict(user);
-
- int userId = user.getId();
-
- user = userService.getUserById(userId);
-
- userDao.evict(user);
-
- userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
-
- user = userService.getUserById(userId);
- int newAmount = user.getPrivileges().size();
-
- userDao.evict(user);
-
- projectService.removeProject(row, tmpResultDir, false, adminToken);
-
- user = userService.getUserById(userId);
-
- assertEquals("After removing project number of privileges didn't drop down", newAmount - 1, user.getPrivileges().size());
-
- userDao.delete(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRemoveUserAfterRemoveProject() throws Exception {
-
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
- ProjectView row = null;
- for (ProjectView projectRow : projects2) {
- if (projectRow.getIdObject() == project.getId()) {
- row = projectRow;
- }
- }
- assertNotNull(row);
-
- User user = new User();
- user.setLogin("x");
- userDao.add(user);
- userDao.evict(user);
-
- int userId = user.getId();
-
- userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
-
- user = userService.getUserById(userId);
-
- long counter = logDao.getCount();
- projectService.removeProject(row, tmpResultDir, false, adminToken);
- long counter2 = logDao.getCount();
- assertTrue("Logs didn't appear after removing project", counter < counter2);
-
- user = userService.getUserById(userId);
- userDao.delete(user);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdater() throws Exception {
- try {
- String project_id = "test_id";
- projectService.createProject(new CreateProjectParams().//
- projectId(project_id).//
- version("").//
- projectFile("testFiles/centeredAnchorInModifier.xml").//
- annotations(true).//
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("gawi", "gawi").//
- analyzeAnnotations(true));
- AuthenticationToken token = userService.login("gawi", "gawi");
- Project project = projectService.getProjectByProjectId(project_id, token);
- assertEquals(ProjectStatus.DONE, project.getStatus());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @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().//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile("testFiles/complexModel/complex_model.zip").//
- addZipEntry(entry1).//
- addZipEntry(entry2).//
- addZipEntry(entry3).//
- addZipEntry(entry4).//
- addZipEntry(entry5).//
- annotations(true).//
- semanticZoom(true).//
- images(true).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("gawi", "gawi").//
- analyzeAnnotations(true));
- AuthenticationToken token = userService.login("gawi", "gawi");
- Project project = projectService.getProjectByProjectId(projectId, token);
-
- Model model = modelService.getLastModelByProjectId(projectId, token);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- Model s1Model = null;
- Model s2Model = null;
- Model s3Model = null;
-
- for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
- if (submodel.getName().equals("s1")) {
- s1Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s2")) {
- s2Model = submodel.getSubmodel().getModel();
- }
- if (submodel.getName().equals("s3")) {
- s3Model = submodel.getSubmodel().getModel();
- }
- }
- assertNotNull(s1Model);
- assertNotNull(s2Model);
- assertNotNull(s3Model);
-
- Element al1 = model.getElementByElementId("sa1");
- assertNotNull(al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
- assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
-
- Element al2 = model.getElementByElementId("sa2");
- assertNull(al2.getSubmodel());
-
- Element al4 = model.getElementByElementId("sa4");
- assertNotNull(al4.getSubmodel());
- assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
- assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
-
- Element s1_al1 = s1Model.getElementByElementId("sa1");
- assertNotNull(s1_al1.getSubmodel());
- assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
- assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
-
- assertEquals(ProjectStatus.DONE, project.getStatus());
-
- // now check layouts
- for (Layout l : s2Model.getLayouts()) {
- assertNotNull(l.getParentLayout());
- }
-
- projectService.removeProject(project, null, false, adminToken);
-
- // and now check layouts (check if every submodel have them, and point
- // into different directory)
-
- // there are 2 levels
- int semanticOverlays = 2;
- // -1 is due to pathways and compartments that is not there
- int overlays = BuildInLayout.values().length + semanticOverlays - 1;
- assertEquals(overlays, model.getLayouts().size());
- assertEquals(overlays, s1Model.getLayouts().size());
- assertEquals(overlays, s2Model.getLayouts().size());
- assertEquals(overlays, s3Model.getLayouts().size());
- Set<String> directories = new HashSet<String>();
- directories.add(model.getLayouts().get(0).getDirectory());
- directories.add(s1Model.getLayouts().get(0).getDirectory());
- directories.add(s2Model.getLayouts().get(0).getDirectory());
- directories.add(s3Model.getLayouts().get(0).getDirectory());
- assertEquals(4, directories.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- Project project = projectService.getProjectByProjectId(projectId, adminToken);
- if (project != null) {
- projectService.removeProject(project, null, false, adminToken);
- }
- }
- }
-
- @Test
- public void testGenerateImages() throws Exception {
- File f = createTempDirectory();
- String path = f.getAbsolutePath() + "/" + tmpResultDir;
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
-
- model.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal", false));
- model.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested", false));
-
- CreateProjectParams params = new CreateProjectParams().images(true).//
- projectDir(tmpResultDir);
-
- ProjectService pService = new ProjectService();
-
- pService.createImages(model, params);
-
- File tmp = new File(path + "/normal");
- assertTrue(tmp.exists());
-
- tmp = new File(path + "/nested");
- assertTrue(tmp.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- f.delete();
- }
-
- }
-
- @Test
- public void testGenerateImagesInSubmodels() throws Exception {
- File f = createTempDirectory();
- String path = f.getAbsolutePath() + "/" + tmpResultDir;
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
-
- Model model2 = getModelForFile("testFiles/sample.xml", false);
-
- model2.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal_A", false));
- model2.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested_B", false));
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "name"));
-
- CreateProjectParams params = new CreateProjectParams().images(true).//
- projectDir(tmpResultDir);
-
- ProjectService pService = new ProjectService();
-
- pService.createImages(model, params);
-
- File tmp = new File(path + "/normal_A");
- assertTrue(tmp.exists());
-
- tmp = new File(path + "/nested_B");
- assertTrue(tmp.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- f.delete();
- }
-
- }
-
- @Test
- public void testCopyComplexWithCompartments() throws Exception {
- try {
- String projectId = "Some_id";
- 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);
-
- 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);
-
- ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
- ComplexZipConverterParams complexParams;
- complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
- for (ZipEntryFile entry : params.getZipEntries()) {
- complexParams.entry(entry);
- }
- Model model = parser.createModel(complexParams);
-
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(3, model.getSubmodelConnections().size());
-
- int oldSize = 0;
- for (Model m : model.getSubmodels()) {
- oldSize += m.getParentModels().size();
- }
-
- new CopyCommand(model).execute();
-
- int newSize = 0;
- for (Model m : model.getSubmodels()) {
- newSize += m.getParentModels().size();
- }
- assertEquals("Submodels doesn't match after copying", oldSize, newSize);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotatorTree() throws Exception {
- try {
- TreeNode tree = projectService.createClassAnnotatorTree(null);
- assertNotNull(tree);
-
- AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
-
- assertEquals(BioEntity.class, dataNode.getClazz());
-
- Queue<TreeNode> nodes = new LinkedList<TreeNode>();
- nodes.add(tree);
- boolean annotatorsFound = false;
- while (!nodes.isEmpty()) {
- TreeNode node = nodes.poll();
- dataNode = (AnnotatedObjectTreeRow) node.getData();
- if (dataNode.getValidAnnotators().size() > 0) {
- annotatorsFound = true;
- }
- for (TreeNode n : node.getChildren()) {
- nodes.add(n);
- }
- }
- assertTrue(annotatorsFound);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyAnnotatorTreeForUser() throws Exception {
- try {
- super.createUser();
- UserAnnotationSchema schema = new UserAnnotationSchema();
- user.setAnnotationSchema(schema);
- userDao.update(user);
-
- TreeNode tree = projectService.createClassAnnotatorTree(user);
- assertNotNull(tree);
-
- AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
-
- assertEquals(BioEntity.class, dataNode.getClazz());
-
- Queue<TreeNode> nodes = new LinkedList<TreeNode>();
- nodes.add(tree);
- boolean annotatorsFound = false;
- while (!nodes.isEmpty()) {
- TreeNode node = nodes.poll();
- dataNode = (AnnotatedObjectTreeRow) node.getData();
- assertEquals("Annotators found for class: " + dataNode.getClazz(), 0, dataNode.getUsedAnnotators().size());
- if (dataNode.getValidAnnotators().size() > 0) {
- annotatorsFound = true;
- }
- for (TreeNode n : node.getChildren()) {
- nodes.add(n);
- }
- }
- assertTrue(annotatorsFound);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotatorTreeForUser() throws Exception {
- try {
- super.createUser();
- UserAnnotationSchema schema = new UserAnnotationSchema();
- schema.addClassAnnotator(new UserClassAnnotators(Protein.class, modelAnnotator.getAvailableAnnotatorNames(Protein.class)));
- user.setAnnotationSchema(schema);
- userDao.update(user);
-
- TreeNode tree = projectService.createClassAnnotatorTree(user);
- assertNotNull(tree);
-
- AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
-
- assertEquals(BioEntity.class, dataNode.getClazz());
-
- Queue<TreeNode> nodes = new LinkedList<>();
- nodes.add(tree);
- boolean annotatorsFound = false;
- while (!nodes.isEmpty()) {
- TreeNode node = nodes.poll();
- dataNode = (AnnotatedObjectTreeRow) node.getData();
- if (dataNode.getUsedAnnotators().size() > 0) {
- annotatorsFound = true;
- }
- for (TreeNode n : node.getChildren()) {
- nodes.add(n);
- }
- }
- assertTrue(annotatorsFound);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testEmptyValidMiriamTreeForUser() throws Exception {
- try {
- super.createUser();
- UserAnnotationSchema schema = new UserAnnotationSchema();
- user.setAnnotationSchema(schema);
- userDao.update(user);
-
- TreeNode tree = projectService.createClassAnnotatorTree(user);
- assertNotNull(tree);
-
- AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
-
- assertEquals(BioEntity.class, dataNode.getClazz());
-
- Queue<TreeNode> nodes = new LinkedList<TreeNode>();
- nodes.add(tree);
- boolean annotatorsFound = false;
- while (!nodes.isEmpty()) {
- TreeNode node = nodes.poll();
- dataNode = (AnnotatedObjectTreeRow) node.getData();
- assertEquals("Valid miriam found for class: " + dataNode.getClazz(), 0, dataNode.getValidAnnotations().size());
- assertEquals("Required miriam found for class: " + dataNode.getClazz(), 0, dataNode.getRequiredAnnotations().size());
- if (dataNode.getMissingValidAnnotations().size() > 0 && dataNode.getMissingRequiredAnnotations().size() > 0) {
- annotatorsFound = true;
- }
- for (TreeNode n : node.getChildren()) {
- nodes.add(n);
- }
- }
- assertTrue(annotatorsFound);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testValidMiriamTreeForUser() throws Exception {
- try {
- super.createUser();
- UserAnnotationSchema schema = new UserAnnotationSchema();
- schema.addClassValidAnnotations(new UserClassValidAnnotations(Protein.class, MiriamType.values()));
- user.setAnnotationSchema(schema);
- userDao.update(user);
- userDao.flush();
-
- TreeNode tree = projectService.createClassAnnotatorTree(user);
- assertNotNull(tree);
-
- AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
-
- assertEquals(BioEntity.class, dataNode.getClazz());
-
- Queue<TreeNode> nodes = new LinkedList<>();
- nodes.add(tree);
- boolean annotatorsFound = false;
- while (!nodes.isEmpty()) {
- TreeNode node = nodes.poll();
- dataNode = (AnnotatedObjectTreeRow) node.getData();
- if (dataNode.getValidAnnotations().size() > 0) {
- annotatorsFound = true;
- }
- for (TreeNode n : node.getChildren()) {
- nodes.add(n);
- }
- }
- assertTrue(annotatorsFound);
-
- userDao.delete(user);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testCreateComplexWithDataMining() throws Exception {
- String name = "Some_id";
- try {
- String filename = "testFiles/complexModel/complex_model_with_data_mining.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- boolean dmFound = false;
- for (Element element : model.getElements()) {
- if (element.getDataMining().size() > 0) {
- dmFound = true;
- }
- }
- assertTrue("Cannot find data mining information for the model", dmFound);
- projectService.removeProject(project, null, false, adminToken);
- AuthenticationToken token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
- assertNull(projectService.getProjectByProjectId(name, token));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- protected Project createComplexProject(String projectId, String filename) throws IOException, SecurityException {
- CreateProjectParams params = new CreateProjectParams();
-
- ZipFile zipFile = new ZipFile(filename);
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- ZipEntryFile e = zefFactory.createZipEntryFile(entry, zipFile);
- params.addZipEntry(e);
- }
- zipFile.close();
-
- projectService.createProject(params.//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
- analyzeAnnotations(true));
- AuthenticationToken token = userService.login("admin", "admin");
- Project project = projectService.getProjectByProjectId(projectId, token);
- return project;
- }
-
- @Test
- public void testCreateComplexWithImages() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/complex_model_with_images.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
- assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(0).getTitle());
- assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(1).getTitle());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComplexWithLayoutOrder() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/complex_model_with_images.zip";
- CreateProjectParams params = new CreateProjectParams();
-
- ZipFile zipFile = new ZipFile(filename);
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- params.addZipEntry(zefFactory.createZipEntryFile(entry, zipFile));
- }
- zipFile.close();
-
- projectService.createProject(params.//
- projectId(projectId).//
- version("").//
- complex(true).//
- projectFile(filename).//
- annotations(true).//
- images(false).//
- async(false).//
- networkLayoutAsDefault(true).//
- projectDir(tmpResultDir).//
- addUser("admin", "admin").//
- analyzeAnnotations(true));
- Project project = projectService.getProjectByProjectId(projectId, adminToken);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
- assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(1).getTitle());
- assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(0).getTitle());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCreateComplexWithLayouts() throws Exception {
- String projectId = "Some_id";
- try {
- String filename = "testFiles/complexModel/complex_model_with_layouts.zip";
- Project project = createComplexProject(projectId, filename);
-
- Model model = modelService.getLastModelByProjectId(projectId, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length, model.getLayouts().size());
- boolean additionalFound = false;
-
- for (Layout layout : model.getLayouts()) {
- if ("example name".equals(layout.getTitle())) {
- additionalFound = true;
- assertEquals("layout description", layout.getDescription());
- assertTrue(layout.getDirectory().contains("example"));
- }
- }
- assertTrue("Cannot find layout with predefined name from file", additionalFound);
- projectService.removeProject(project, null, false, adminToken);
- assertNull(projectService.getProjectByProjectId(projectId, adminToken));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateComplexWithSumbaps() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/complex_model_with_submaps.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals("main", model.getName());
- assertEquals(ProjectStatus.DONE, project.getStatus());
- assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateEmptyComplex() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/empty_complex_model.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals(ProjectStatus.DONE, project.getStatus());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateEmptyComplex2() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/empty_complex_model2.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals(ProjectStatus.DONE, project.getStatus());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCreateEmptyComplex3() throws Exception {
- try {
- String name = "Some_id";
- String filename = "testFiles/complexModel/empty_complex_model3.zip";
- Project project = createComplexProject(name, filename);
-
- Model model = modelService.getLastModelByProjectId(name, adminToken);
- assertNotNull(model);
- assertEquals(ProjectStatus.DONE, project.getStatus());
- projectService.removeProject(project, null, false, adminToken);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.primefaces.model.TreeNode;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.annotation.Rollback;
+
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.converter.ComplexZipConverter;
+import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.user.ObjectPrivilege;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.model.user.UserAnnotationSchema;
+import lcsb.mapviewer.model.user.UserClassAnnotators;
+import lcsb.mapviewer.model.user.UserClassValidAnnotations;
+import lcsb.mapviewer.persist.dao.map.species.ElementDao;
+import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.ServiceTestFunctions;
+import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
+import lcsb.mapviewer.services.utils.CreateProjectParams;
+import lcsb.mapviewer.services.utils.data.BuildInLayout;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+import lcsb.mapviewer.services.view.ProjectView;
+
+@Rollback(true)
+public class ProjectServiceTest extends ServiceTestFunctions {
+ Logger logger = Logger.getLogger(ProjectServiceTest.class);
+
+ ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
+
+ private final String tmpResultDir = "tmp/";
+ String projectId = "Some_id";
+
+ @Autowired
+ ElementDao aliasDao;
+
+ // assume that we have admin account with all the privileges
+ AuthenticationToken adminToken;
+
+ @Before
+ public void setUp() throws Exception {
+ adminToken = userService.login("admin", "admin");
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetProjectWithoutAccessToEverything() {
+ try {
+ createUser();
+ AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+ List<Project> projects = projectService.getAllProjects(token);
+ assertNotNull(projects);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void test() {
+ try {
+ List<Project> projects = projectService.getAllProjects(adminToken);
+
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ List<Project> projects2 = projectService.getAllProjects(adminToken);
+
+ assertEquals(projects.size() + 1, projects2.size());
+
+ for (Project tmpProject : projects2) {
+ if (!projects.contains(tmpProject)) {
+ assertEquals(projectId, tmpProject.getProjectId());
+ }
+ }
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ projectDao.delete(project2);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemove() throws Exception {
+
+ try {
+ String project_id = "Some_id";
+ Project project = new Project();
+ project.setProjectId(project_id);
+ projectDao.add(project);
+
+ List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
+ ProjectView row = null;
+ for (ProjectView projectRow : projects2) {
+ if (projectRow.getIdObject() == project.getId()) {
+ row = projectRow;
+ }
+ }
+ assertNotNull(row);
+
+ User user = new User();
+ user.setLogin("x");
+ userDao.add(user);
+ userDao.evict(user);
+
+ int userId = user.getId();
+
+ user = userService.getUserById(userId);
+
+ userDao.evict(user);
+
+ userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
+
+ user = userService.getUserById(userId);
+ int newAmount = user.getPrivileges().size();
+
+ userDao.evict(user);
+
+ projectService.removeProject(row, tmpResultDir, false, adminToken);
+
+ user = userService.getUserById(userId);
+
+ assertEquals("After removing project number of privileges didn't drop down", newAmount - 1,
+ user.getPrivileges().size());
+
+ userDao.delete(user);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRemoveUserAfterRemoveProject() throws Exception {
+
+ try {
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+
+ List<ProjectView> projects2 = projectService.getAllProjectViews(adminToken);
+ ProjectView row = null;
+ for (ProjectView projectRow : projects2) {
+ if (projectRow.getIdObject() == project.getId()) {
+ row = projectRow;
+ }
+ }
+ assertNotNull(row);
+
+ User user = new User();
+ user.setLogin("x");
+ userDao.add(user);
+ userDao.evict(user);
+
+ int userId = user.getId();
+
+ userService.setUserPrivilege(user, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, user));
+
+ user = userService.getUserById(userId);
+
+ long counter = logDao.getCount();
+ projectService.removeProject(row, tmpResultDir, false, adminToken);
+ long counter2 = logDao.getCount();
+ assertTrue("Logs didn't appear after removing project", counter < counter2);
+
+ user = userService.getUserById(userId);
+ userDao.delete(user);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @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).//
+ addUser("gawi", "gawi").//
+ analyzeAnnotations(true));
+ AuthenticationToken token = userService.login("gawi", "gawi");
+ Project project = projectService.getProjectByProjectId(project_id, token);
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @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).//
+ semanticZoom(true).//
+ images(true).//
+ async(false).//
+ projectDir(tmpResultDir).//
+ addUser("gawi", "gawi").//
+ analyzeAnnotations(true));
+ AuthenticationToken token = userService.login("gawi", "gawi");
+ Project project = projectService.getProjectByProjectId(projectId, token);
+
+ Model model = modelService.getLastModelByProjectId(projectId, token);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ Model s1Model = null;
+ Model s2Model = null;
+ Model s3Model = null;
+
+ for (ModelSubmodelConnection submodel : model.getSubmodelConnections()) {
+ if (submodel.getName().equals("s1")) {
+ s1Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s2")) {
+ s2Model = submodel.getSubmodel().getModel();
+ }
+ if (submodel.getName().equals("s3")) {
+ s3Model = submodel.getSubmodel().getModel();
+ }
+ }
+ assertNotNull(s1Model);
+ assertNotNull(s2Model);
+ assertNotNull(s3Model);
+
+ Element al1 = model.getElementByElementId("sa1");
+ assertNotNull(al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, al1.getSubmodel().getType());
+ assertEquals(s1Model, al1.getSubmodel().getSubmodel().getModel());
+
+ Element al2 = model.getElementByElementId("sa2");
+ assertNull(al2.getSubmodel());
+
+ Element al4 = model.getElementByElementId("sa4");
+ assertNotNull(al4.getSubmodel());
+ assertEquals(SubmodelType.PATHWAY, al4.getSubmodel().getType());
+ assertEquals(s2Model, al4.getSubmodel().getSubmodel().getModel());
+
+ Element s1_al1 = s1Model.getElementByElementId("sa1");
+ assertNotNull(s1_al1.getSubmodel());
+ assertEquals(SubmodelType.DOWNSTREAM_TARGETS, s1_al1.getSubmodel().getType());
+ assertEquals(s3Model, s1_al1.getSubmodel().getSubmodel().getModel());
+
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+
+ // now check layouts
+ for (Layout l : s2Model.getLayouts()) {
+ assertNotNull(l.getParentLayout());
+ }
+
+ projectService.removeProject(project, null, false, adminToken);
+
+ // and now check layouts (check if every submodel have them, and point
+ // into different directory)
+
+ // there are 2 levels
+ int semanticOverlays = 2;
+ // -1 is due to pathways and compartments that is not there
+ int overlays = BuildInLayout.values().length + semanticOverlays - 1;
+ assertEquals(overlays, model.getLayouts().size());
+ assertEquals(overlays, s1Model.getLayouts().size());
+ assertEquals(overlays, s2Model.getLayouts().size());
+ assertEquals(overlays, s3Model.getLayouts().size());
+ Set<String> directories = new HashSet<String>();
+ directories.add(model.getLayouts().get(0).getDirectory());
+ directories.add(s1Model.getLayouts().get(0).getDirectory());
+ directories.add(s2Model.getLayouts().get(0).getDirectory());
+ directories.add(s3Model.getLayouts().get(0).getDirectory());
+ assertEquals(4, directories.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ Project project = projectService.getProjectByProjectId(projectId, adminToken);
+ if (project != null) {
+ projectService.removeProject(project, null, false, adminToken);
+ }
+ }
+ }
+
+ @Test
+ public void testGenerateImages() throws Exception {
+ File f = createTempDirectory();
+ String path = f.getAbsolutePath() + "/" + tmpResultDir;
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+
+ model.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal", false));
+ model.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested", false));
+
+ CreateProjectParams params = new CreateProjectParams().images(true).//
+ projectDir(tmpResultDir);
+
+ ProjectService pService = new ProjectService();
+
+ pService.createImages(model, params);
+
+ File tmp = new File(path + "/normal");
+ assertTrue(tmp.exists());
+
+ tmp = new File(path + "/nested");
+ assertTrue(tmp.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ f.delete();
+ }
+
+ }
+
+ @Test
+ public void testGenerateImagesInSubmodels() throws Exception {
+ File f = createTempDirectory();
+ String path = f.getAbsolutePath() + "/" + tmpResultDir;
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+
+ Model model2 = getModelForFile("testFiles/sample.xml", false);
+
+ model2.addLayout(new Layout(BuildInLayout.NORMAL.getTitle(), path + "/normal_A", false));
+ model2.addLayout(new Layout(BuildInLayout.NESTED.getTitle(), path + "/nested_B", false));
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "name"));
+
+ CreateProjectParams params = new CreateProjectParams().images(true).//
+ projectDir(tmpResultDir);
+
+ ProjectService pService = new ProjectService();
+
+ pService.createImages(model, params);
+
+ File tmp = new File(path + "/normal_A");
+ assertTrue(tmp.exists());
+
+ tmp = new File(path + "/nested_B");
+ assertTrue(tmp.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ f.delete();
+ }
+
+ }
+
+ @Test
+ public void testCopyComplexWithCompartments() throws Exception {
+ try {
+ String projectId = "Some_id";
+ 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);
+
+ 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);
+
+ ComplexZipConverter parser = new ComplexZipConverter(CellDesignerXmlParser.class);
+ ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(params.getProjectFile());
+ for (ZipEntryFile entry : params.getZipEntries()) {
+ complexParams.entry(entry);
+ }
+ Model model = parser.createModel(complexParams);
+
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(3, model.getSubmodelConnections().size());
+
+ int oldSize = 0;
+ for (Model m : model.getSubmodels()) {
+ oldSize += m.getParentModels().size();
+ }
+
+ new CopyCommand(model).execute();
+
+ int newSize = 0;
+ for (Model m : model.getSubmodels()) {
+ newSize += m.getParentModels().size();
+ }
+ assertEquals("Submodels doesn't match after copying", oldSize, newSize);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotatorTree() throws Exception {
+ try {
+ TreeNode tree = projectService.createClassAnnotatorTree(null);
+ assertNotNull(tree);
+
+ AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
+
+ assertEquals(BioEntity.class, dataNode.getClazz());
+
+ Queue<TreeNode> nodes = new LinkedList<TreeNode>();
+ nodes.add(tree);
+ boolean annotatorsFound = false;
+ while (!nodes.isEmpty()) {
+ TreeNode node = nodes.poll();
+ dataNode = (AnnotatedObjectTreeRow) node.getData();
+ if (dataNode.getValidAnnotators().size() > 0) {
+ annotatorsFound = true;
+ }
+ for (TreeNode n : node.getChildren()) {
+ nodes.add(n);
+ }
+ }
+ assertTrue(annotatorsFound);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyAnnotatorTreeForUser() throws Exception {
+ try {
+ super.createUser();
+ UserAnnotationSchema schema = new UserAnnotationSchema();
+ user.setAnnotationSchema(schema);
+ userDao.update(user);
+
+ TreeNode tree = projectService.createClassAnnotatorTree(user);
+ assertNotNull(tree);
+
+ AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
+
+ assertEquals(BioEntity.class, dataNode.getClazz());
+
+ Queue<TreeNode> nodes = new LinkedList<TreeNode>();
+ nodes.add(tree);
+ boolean annotatorsFound = false;
+ while (!nodes.isEmpty()) {
+ TreeNode node = nodes.poll();
+ dataNode = (AnnotatedObjectTreeRow) node.getData();
+ assertEquals("Annotators found for class: " + dataNode.getClazz(), 0, dataNode.getUsedAnnotators().size());
+ if (dataNode.getValidAnnotators().size() > 0) {
+ annotatorsFound = true;
+ }
+ for (TreeNode n : node.getChildren()) {
+ nodes.add(n);
+ }
+ }
+ assertTrue(annotatorsFound);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotatorTreeForUser() throws Exception {
+ try {
+ super.createUser();
+ UserAnnotationSchema schema = new UserAnnotationSchema();
+ schema.addClassAnnotator(
+ new UserClassAnnotators(Protein.class, modelAnnotator.getAvailableAnnotatorNames(Protein.class)));
+ user.setAnnotationSchema(schema);
+ userDao.update(user);
+
+ TreeNode tree = projectService.createClassAnnotatorTree(user);
+ assertNotNull(tree);
+
+ AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
+
+ assertEquals(BioEntity.class, dataNode.getClazz());
+
+ Queue<TreeNode> nodes = new LinkedList<>();
+ nodes.add(tree);
+ boolean annotatorsFound = false;
+ while (!nodes.isEmpty()) {
+ TreeNode node = nodes.poll();
+ dataNode = (AnnotatedObjectTreeRow) node.getData();
+ if (dataNode.getUsedAnnotators().size() > 0) {
+ annotatorsFound = true;
+ }
+ for (TreeNode n : node.getChildren()) {
+ nodes.add(n);
+ }
+ }
+ assertTrue(annotatorsFound);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testEmptyValidMiriamTreeForUser() throws Exception {
+ try {
+ super.createUser();
+ UserAnnotationSchema schema = new UserAnnotationSchema();
+ user.setAnnotationSchema(schema);
+ userDao.update(user);
+
+ TreeNode tree = projectService.createClassAnnotatorTree(user);
+ assertNotNull(tree);
+
+ AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
+
+ assertEquals(BioEntity.class, dataNode.getClazz());
+
+ Queue<TreeNode> nodes = new LinkedList<TreeNode>();
+ nodes.add(tree);
+ boolean annotatorsFound = false;
+ while (!nodes.isEmpty()) {
+ TreeNode node = nodes.poll();
+ dataNode = (AnnotatedObjectTreeRow) node.getData();
+ assertEquals("Valid miriam found for class: " + dataNode.getClazz(), 0, dataNode.getValidAnnotations().size());
+ assertEquals("Required miriam found for class: " + dataNode.getClazz(), 0,
+ dataNode.getRequiredAnnotations().size());
+ if (dataNode.getMissingValidAnnotations().size() > 0 && dataNode.getMissingRequiredAnnotations().size() > 0) {
+ annotatorsFound = true;
+ }
+ for (TreeNode n : node.getChildren()) {
+ nodes.add(n);
+ }
+ }
+ assertTrue(annotatorsFound);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testValidMiriamTreeForUser() throws Exception {
+ try {
+ super.createUser();
+ UserAnnotationSchema schema = new UserAnnotationSchema();
+ schema.addClassValidAnnotations(new UserClassValidAnnotations(Protein.class, MiriamType.values()));
+ user.setAnnotationSchema(schema);
+ userDao.update(user);
+ userDao.flush();
+
+ TreeNode tree = projectService.createClassAnnotatorTree(user);
+ assertNotNull(tree);
+
+ AnnotatedObjectTreeRow dataNode = (AnnotatedObjectTreeRow) tree.getData();
+
+ assertEquals(BioEntity.class, dataNode.getClazz());
+
+ Queue<TreeNode> nodes = new LinkedList<>();
+ nodes.add(tree);
+ boolean annotatorsFound = false;
+ while (!nodes.isEmpty()) {
+ TreeNode node = nodes.poll();
+ dataNode = (AnnotatedObjectTreeRow) node.getData();
+ if (dataNode.getValidAnnotations().size() > 0) {
+ annotatorsFound = true;
+ }
+ for (TreeNode n : node.getChildren()) {
+ nodes.add(n);
+ }
+ }
+ assertTrue(annotatorsFound);
+
+ userDao.delete(user);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testCreateComplexWithDataMining() throws Exception {
+ String name = "Some_id";
+ try {
+ String filename = "testFiles/complexModel/complex_model_with_data_mining.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ boolean dmFound = false;
+ for (Element element : model.getElements()) {
+ if (element.getDataMining().size() > 0) {
+ dmFound = true;
+ }
+ }
+ assertTrue("Cannot find data mining information for the model", dmFound);
+ projectService.removeProject(project, null, false, adminToken);
+ AuthenticationToken token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
+ assertNull(projectService.getProjectByProjectId(name, token));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ protected Project createComplexProject(String projectId, String filename) throws IOException, SecurityException {
+ CreateProjectParams params = new CreateProjectParams();
+
+ ZipFile zipFile = new ZipFile(filename);
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ ZipEntryFile e = zefFactory.createZipEntryFile(entry, zipFile);
+ params.addZipEntry(e);
+ }
+ zipFile.close();
+
+ projectService.createProject(params.//
+ authenticationToken(adminToken).//
+ projectId(projectId).//
+ version("").//
+ complex(true).//
+ projectFile(filename).//
+ annotations(true).//
+ images(false).//
+ async(false).//
+ projectDir(tmpResultDir).//
+ addUser("admin", "admin").//
+ analyzeAnnotations(true));
+ AuthenticationToken token = userService.login("admin", "admin");
+ Project project = projectService.getProjectByProjectId(projectId, token);
+ return project;
+ }
+
+ @Test
+ public void testCreateComplexWithImages() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/complex_model_with_images.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
+ assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(0).getTitle());
+ assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(1).getTitle());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComplexWithLayoutOrder() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/complex_model_with_images.zip";
+ CreateProjectParams params = new CreateProjectParams();
+
+ ZipFile zipFile = new ZipFile(filename);
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ params.addZipEntry(zefFactory.createZipEntryFile(entry, zipFile));
+ }
+ zipFile.close();
+
+ projectService.createProject(params.//
+ authenticationToken(adminToken).//
+ projectId(projectId).//
+ version("").//
+ complex(true).//
+ projectFile(filename).//
+ annotations(true).//
+ images(false).//
+ async(false).//
+ networkLayoutAsDefault(true).//
+ projectDir(tmpResultDir).//
+ addUser("admin", "admin").//
+ analyzeAnnotations(true));
+ Project project = projectService.getProjectByProjectId(projectId, adminToken);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ assertEquals("Cannot find overview images the model", 2, project.getOverviewImages().size());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
+ assertEquals(BuildInLayout.NESTED.getTitle(), model.getLayouts().get(1).getTitle());
+ assertEquals(BuildInLayout.NORMAL.getTitle(), model.getLayouts().get(0).getTitle());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCreateComplexWithLayouts() throws Exception {
+ String projectId = "Some_id";
+ try {
+ String filename = "testFiles/complexModel/complex_model_with_layouts.zip";
+ Project project = createComplexProject(projectId, filename);
+
+ Model model = modelService.getLastModelByProjectId(projectId, adminToken);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length, model.getLayouts().size());
+ boolean additionalFound = false;
+
+ for (Layout layout : model.getLayouts()) {
+ if ("example name".equals(layout.getTitle())) {
+ additionalFound = true;
+ assertEquals("layout description", layout.getDescription());
+ assertTrue(layout.getDirectory().contains("example"));
+ }
+ }
+ assertTrue("Cannot find layout with predefined name from file", additionalFound);
+ projectService.removeProject(project, null, false, adminToken);
+ assertNull(projectService.getProjectByProjectId(projectId, adminToken));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateComplexWithSumbaps() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/complex_model_with_submaps.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals("main", model.getName());
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ assertEquals("Number of layouts doesn't match", BuildInLayout.values().length - 1, model.getLayouts().size());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateEmptyComplex() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/empty_complex_model.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateEmptyComplex2() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/empty_complex_model2.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCreateEmptyComplex3() throws Exception {
+ try {
+ String name = "Some_id";
+ String filename = "testFiles/complexModel/empty_complex_model3.zip";
+ Project project = createComplexProject(name, filename);
+
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
+ assertNotNull(model);
+ assertEquals(ProjectStatus.DONE, project.getStatus());
+ projectService.removeProject(project, null, false, adminToken);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}