diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 5811bd86c8e30480f3682a6b2c5893a37006d79b..26dea5dfd6dd9bdc3a4793fc5dead2f571d1f640 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -590,7 +590,10 @@ AddProjectDialog.prototype.onSaveClicked = function () {
"disease": self.getDisease(),
"organism": self.getOrganism(),
"sbgn": self.isSbgn(),
- "semantic-zoom": self.isSemanticZooming()
+ "semantic-zoom": self.isSemanticZooming(),
+ "annotate": self.isAnnotateAutomatically(),
+ "verify-annotations": self.isVerifyAnnotations(),
+
};
return ServerConnector.addProject(options);
});
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 652a49ce9eec5e368d1d683c4a2fc983172d534c..b788a8feb8c46cccf085cc3aacc6986f40341f21 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
@@ -62,6 +62,7 @@ import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
@@ -72,483 +73,500 @@ import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
public class ProjectRestImpl extends BaseRestImpl {
- /**
- * Constant defining size of the array returned by
- * {@link PathIterator#currentSegment(double[])} method. More nformation can
- * be found <a href=
- * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
- * >here</a>
- */
- private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ProjectRestImpl.class);
-
- @Autowired
- private PublicationsRestImpl publicationsRestImpl;
-
- @Autowired
- private ILayoutService layoutService;
-
- @Autowired
- private OverviewImageViewFactory factory;
-
- public ProjectMetaData getProject(String projectId, String token) throws SecurityException, ObjectNotFoundException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- ProjectMetaData result = createData(project);
- return result;
- }
-
- private ProjectMetaData createData(Project project) {
- ProjectMetaData result = new ProjectMetaData();
-
- result.setName(project.getName());
- result.setProjectId(project.getProjectId());
- result.setIdObject(project.getId());
- result.setVersion(project.getVersion());
- result.setNotifyEmail(project.getNotifyEmail());
- if (project.getStatus() != null) {
- result.setStatus(project.getStatus().toString());
- }
- result.setProgress(project.getProgress());
-
- result.setOverviewImageViews(factory.createList(project.getOverviewImages()));
-
- Set<OverviewImage> set = new HashSet<>();
- set.addAll(project.getOverviewImages());
- for (OverviewImage image : project.getOverviewImages()) {
- for (OverviewLink ol : image.getLinks()) {
- if (ol instanceof OverviewImageLink) {
- set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
- }
- }
- }
- if (set.size() > 0) {
- result.setTopOverviewImage(factory.create(set.iterator().next()));
- } else if (project.getOverviewImages().size() > 0) {
- logger.warn("Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
- result.setTopOverviewImage(factory.create(project.getOverviewImages().get(0)));
- }
-
- if (project.getOrganism() != null) {
- result.setOrganism(createAnnotation(project.getOrganism()));
- }
- if (project.getDisease() != null) {
- result.setDisease(createAnnotation(project.getDisease()));
- }
-
- return result;
- }
-
- /**
- * @return the factory
- * @see #factory
- */
- public OverviewImageViewFactory getFactory() {
- return factory;
- }
-
- /**
- * @param factory
- * the factory to set
- * @see #factory
- */
- public void setFactory(OverviewImageViewFactory factory) {
- this.factory = factory;
- }
-
- public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- return project.getInputData();
- }
-
- public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass, String backgroundOverlayId, String overlayIds,
- String zoomLevel, String polygonString)
- throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- User user = getUserService().getUserByToken(authenticationToken);
-
- Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- Layout overlay = null;
- if (!backgroundOverlayId.equals("")) {
- overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
-
- if (overlay == null) {
- throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
- }
- } else {
- if (topModel.getLayouts().size() > 0) {
- overlay = topModel.getLayouts().get(0);
- }
- }
-
- Model colorModel = new CopyCommand(originalModel).execute();
- if (overlay != null) {
- if (overlay.getInputData() != null) {
- ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
-
- new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
- } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
- // this might not return true if we change CLEAN.title in future...
-
- // if it's clean then remove coloring
- new ClearColorModelCommand(colorModel).execute();
- } else if (overlay.isHierarchicalView()) {
- new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
- }
- }
-
- Integer level = Configuration.MIN_ZOOM_LEVEL;
- if (!zoomLevel.equals("")) {
- level = Integer.valueOf(zoomLevel);
- }
-
- // transform polygon
- CoordinationConverter cc = new CoordinationConverter(colorModel);
- Double minX = originalModel.getWidth();
- Double minY = originalModel.getHeight();
- Double maxX = 0.0;
- Double maxY = 0.0;
- Path2D polygon = cc.latLngToPolygon(polygonString);
-
- PathIterator pathIter = polygon.getPathIterator(null);
- while (!pathIter.isDone()) {
- final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
- if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
- minX = Math.min(minX, segment[0]);
- maxX = Math.max(maxX, segment[0]);
- minY = Math.min(minY, segment[1]);
- maxY = Math.max(maxY, segment[1]);
- }
- pathIter.next();
- }
-
- maxX = Math.min(originalModel.getWidth(), maxX);
- maxY = Math.min(originalModel.getHeight(), maxY);
- minX = Math.max(0.0, minX);
- minY = Math.max(0.0, minY);
-
- Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
-
- for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
- scale /= 2;
- }
-
- ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
-
- Params params = new Params().//
- x(minX).//
- y(minY).//
- height((maxY - minY) / scale).//
- width((maxX - minX) / scale).//
- level(level - Configuration.MIN_ZOOM_LEVEL).//
- nested(false).// automatically set nested view as invalid
- scale(scale).//
- colorExtractor(colorExtractor).//
- sbgn(topModel.getProject().isSbgnFormat()).//
- model(colorModel);
- if (overlay != null) {
- params.nested(overlay.isHierarchicalView());
- }
- List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
- for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, authenticationToken);
- params.addVisibleLayout(map);
- }
-
- ImageGenerators imageGenerator = new ImageGenerators();
- String extension = imageGenerator.getExtension(handlerClass);
- File file = File.createTempFile("map", "." + extension);
-
- imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
-
- FileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("map." + extension);
- entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
- file.delete();
- return entry;
-
- }
-
- private List<Integer> deserializeIdList(String overlayIds) {
- List<Integer> result = new ArrayList<>();
- String[] tmp = overlayIds.split(",");
- for (String string : tmp) {
- if (!string.equals("")) {
- result.add(Integer.valueOf(string));
- }
- }
- return result;
- }
-
- public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass, String backgroundOverlayId, String overlayIds,
- String zoomLevel, String polygonString) throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
- ConverterException, InconsistentModelException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
-
- Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
- if (topModel == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Model originalModel = topModel.getSubmodelById(modelId);
-
- if (originalModel == null) {
- throw new ObjectNotFoundException("Model with given id doesn't exist");
- }
-
- CoordinationConverter cc = new CoordinationConverter(originalModel);
- Path2D polygon = cc.latLngToPolygon(polygonString);
-
- // create model bounded by the polygon
- SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
- Model part = subModelCommand.execute();
-
- IConverter parser = getModelParser(handlerClass);
- InputStream is = parser.exportModelToInputStream(part);
-
- String fileExtension = parser.getFileExtension();
-
- FileEntry entry = new UploadedFileEntry();
- entry.setOriginalFileName("model." + fileExtension);
- entry.setFileContent(IOUtils.toByteArray(is));
- return entry;
-
- }
-
- public Map<String, Object> getStatistics(String projectId, String token) throws SecurityException, ObjectNotFoundException {
- Map<String, Object> result = new HashMap<String, Object>();
- AuthenticationToken authenticationToken = getUserService().getToken(token);
-
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
- if (model == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
-
- Map<MiriamType, Integer> elementAnnotations = new HashMap<>();
- for (MiriamType mt : MiriamType.values()) {
- elementAnnotations.put(mt, 0);
- }
- Set<Model> models = new HashSet<>();
- models.add(model);
- models.addAll(model.getSubmodels());
-
- for (Model model2 : models) {
- for (Element alias : model2.getElements()) {
- for (MiriamData md : alias.getMiriamData()) {
- Integer amount = elementAnnotations.get(md.getDataType());
- amount += 1;
- elementAnnotations.put(md.getDataType(), amount);
- }
- }
- }
- result.put("elementAnnotations", elementAnnotations);
-
- Map<MiriamType, Integer> reactionAnnotations = new HashMap<>();
- for (MiriamType mt : MiriamType.values()) {
- reactionAnnotations.put(mt, 0);
- }
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- Integer amount = reactionAnnotations.get(md.getDataType());
- amount += 1;
- reactionAnnotations.put(md.getDataType(), amount);
- }
- }
- }
-
- result.put("reactionAnnotations", reactionAnnotations);
-
- result.put("publications", publicationsRestImpl.getPublications(models).size());
-
- return result;
- }
-
- public List<ProjectMetaData> getProjects(String token) throws SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- List<Project> projects = getProjectService().getAllProjects(authenticationToken);
- List<ProjectMetaData> result = new ArrayList<>();
- for (Project project : projects) {
- result.add(createData(project));
- }
- return result;
- }
-
- public ProjectMetaData updateProject(String token, String projectId, Map<String, Object> data) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
- if (project == null) {
- throw new ObjectNotFoundException("Project with given id doesn't exist");
- }
- boolean canModify = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.ADD_MAP);
- if (!canModify) {
- throw new SecurityException("You cannot update projects");
- }
- Set<String> fields = data.keySet();
- for (String fieldName : fields) {
- Object value = data.get(fieldName);
- String stringValue = null;
- if (value instanceof String) {
- stringValue = (String) value;
- }
- if (fieldName.equalsIgnoreCase("version")) {
- project.setVersion((String) value);
- } else if (fieldName.equalsIgnoreCase("id")) {
- try {
- int id = Integer.parseInt(stringValue);
- if (id != project.getId()) {
- throw new QueryException("Invalid id: " + stringValue);
- }
- } catch (NumberFormatException e) {
- throw new QueryException("Invalid id: " + stringValue);
- }
- } else if (fieldName.equalsIgnoreCase("projectId")) {
- if (!project.getProjectId().equalsIgnoreCase(stringValue)) {
- throw new QueryException("You cannot modify projectId");
- }
- } else if (fieldName.equalsIgnoreCase("name")) {
- project.setName((String) value);
- } else if (fieldName.equalsIgnoreCase("notifyEmail")) {
- project.setNotifyEmail(stringValue);
- } else if (fieldName.equalsIgnoreCase("organism")) {
- MiriamData organism = updateMiriamData(project.getOrganism(), value);
- project.setOrganism(organism);
- } else if (fieldName.equalsIgnoreCase("disease")) {
- MiriamData disease = updateMiriamData(project.getDisease(), value);
- project.setDisease(disease);
- } else {
- throw new QueryException("Unknown field: " + fieldName);
- }
- }
- getProjectService().updateProject(project);
- return getProject(projectId, token);
- }
-
- private MiriamData updateMiriamData(MiriamData organism, Object res) {
- if (res == null) {
- return null;
- }
- if (organism == null) {
- organism = new MiriamData();
- }
-
- if (res instanceof Map) {
- @SuppressWarnings("unchecked")
- Map<String, Object> map = (Map<String, Object>) res;
- organism.setDataType(MiriamType.valueOf((String) map.get("type")));
- organism.setResource((String) map.get("resource"));
- return organism;
- } else {
- throw new InvalidArgumentException("invalid miriamdData: " + res);
- }
- }
-
- public ProjectMetaData addProject(String token, String projectId, MultiValueMap<String, String> data, String path)
- throws SecurityException, QueryException, IOException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- User user = getUserService().getUserByToken(authenticationToken);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
- if (project != null) {
- throw new ObjectExistsException("Project with given id already exists");
- }
- CreateProjectParams params = new CreateProjectParams();
- String directory = path + "/../map_images/" + md5(projectId) + "/";
- String fileContent = getFirstValue(data.get("file-content"));
- if (fileContent == null) {
- throw new QueryException("file-content is obligatory");
- }
- String parserClass = getFirstValue(data.get("parser"));
- if (parserClass == null) {
- throw new QueryException("parser is obligatory");
- }
- IConverter parser = getModelParser(parserClass);
-
- params.addUser(user.getLogin(), null);
- params.async(true);
- params.parser(parser);
- params.authenticationToken(authenticationToken);
- params.autoResize(getFirstValue(data.get("auto-resize")));
- params.cacheModel(getFirstValue(data.get("cache")));
- params.description(getFirstValue(data.get("description")));
- params.images(true);
- 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.projectId(projectId);
- params.projectName(getFirstValue(data.get("name")));
- params.projectOrganism(getFirstValue(data.get("organism")));
- params.sbgnFormat(getFirstValue(data.get("sbgn")));
- params.semanticZoom(getFirstValue(data.get("semantic-zoom")));
- params.version(getFirstValue(data.get("version")));
-
- getProjectService().createProject(params);
- return getProject(projectId, token);
- }
-
- private String getFirstValue(List<String> list) {
- if (list == null) {
- return null;
- }
- if (list.size() > 0) {
- return list.get(0);
- }
- return null;
- }
-
- /**
- * Method that computes md5 hash for a given {@link String}.
- *
- * @param data
- * input string
- * @return md5 hash for input string
- */
- private String md5(String data) {
- try {
- MessageDigest md = MessageDigest.getInstance("MD5");
- byte[] mdbytes = md.digest(data.getBytes());
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mdbytes.length; i++) {
- // CHECKSTYLE:OFF
- // this magic formula transforms int into hex value
- sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
- // CHECKSTYLE:ON
- }
- return sb.toString();
- } catch (NoSuchAlgorithmException e) {
- logger.fatal("Problem with instance of MD5 encoder", e);
- }
-
- return null;
- }
-
- public ProjectMetaData removeProject(String token, String projectId, String path) throws ObjectNotFoundException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
- getProjectService().removeProject(project, path, true, authenticationToken);
- return getProject(projectId, token);
- }
+ /**
+ * Constant defining size of the array returned by
+ * {@link PathIterator#currentSegment(double[])} method. More nformation can be
+ * found <a href=
+ * "http://docs.oracle.com/javase/7/docs/api/java/awt/geom/PathIterator.html#currentSegment(double[])"
+ * >here</a>
+ */
+ private static final int PATH_ITERATOR_SEGMENT_SIZE = 6;
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ProjectRestImpl.class);
+
+ @Autowired
+ private PublicationsRestImpl publicationsRestImpl;
+
+ @Autowired
+ private ILayoutService layoutService;
+
+ @Autowired
+ private IProjectService projectService;
+
+ @Autowired
+ private OverviewImageViewFactory factory;
+
+ public ProjectMetaData getProject(String projectId, String token) throws SecurityException, ObjectNotFoundException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ ProjectMetaData result = createData(project);
+ return result;
+ }
+
+ private ProjectMetaData createData(Project project) {
+ ProjectMetaData result = new ProjectMetaData();
+
+ result.setName(project.getName());
+ result.setProjectId(project.getProjectId());
+ result.setIdObject(project.getId());
+ result.setVersion(project.getVersion());
+ result.setNotifyEmail(project.getNotifyEmail());
+ if (project.getStatus() != null) {
+ result.setStatus(project.getStatus().toString());
+ }
+ result.setProgress(project.getProgress());
+
+ result.setOverviewImageViews(factory.createList(project.getOverviewImages()));
+
+ Set<OverviewImage> set = new HashSet<>();
+ set.addAll(project.getOverviewImages());
+ for (OverviewImage image : project.getOverviewImages()) {
+ for (OverviewLink ol : image.getLinks()) {
+ if (ol instanceof OverviewImageLink) {
+ set.remove(((OverviewImageLink) ol).getLinkedOverviewImage());
+ }
+ }
+ }
+ if (set.size() > 0) {
+ result.setTopOverviewImage(factory.create(set.iterator().next()));
+ } else if (project.getOverviewImages().size() > 0) {
+ logger.warn(
+ "Cannot determine top level image. Taking first one. " + project.getOverviewImages().get(0).getFilename());
+ result.setTopOverviewImage(factory.create(project.getOverviewImages().get(0)));
+ }
+
+ if (project.getOrganism() != null) {
+ result.setOrganism(createAnnotation(project.getOrganism()));
+ }
+ if (project.getDisease() != null) {
+ result.setDisease(createAnnotation(project.getDisease()));
+ }
+
+ return result;
+ }
+
+ /**
+ * @return the factory
+ * @see #factory
+ */
+ public OverviewImageViewFactory getFactory() {
+ return factory;
+ }
+
+ /**
+ * @param factory
+ * the factory to set
+ * @see #factory
+ */
+ public void setFactory(OverviewImageViewFactory factory) {
+ this.factory = factory;
+ }
+
+ public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ return project.getInputData();
+ }
+
+ public FileEntry getModelAsImage(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString) throws SecurityException,
+ QueryException, IOException, InvalidColorSchemaException, CommandExecutionException, DrawingException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ User user = getUserService().getUserByToken(authenticationToken);
+
+ Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ Layout overlay = null;
+ if (!backgroundOverlayId.equals("")) {
+ overlay = topModel.getLayoutByIdentifier(Integer.valueOf(backgroundOverlayId));
+
+ if (overlay == null) {
+ throw new ObjectNotFoundException("Unknown overlay in model. Layout.id=" + backgroundOverlayId);
+ }
+ } else {
+ if (topModel.getLayouts().size() > 0) {
+ overlay = topModel.getLayouts().get(0);
+ }
+ }
+
+ Model colorModel = new CopyCommand(originalModel).execute();
+ if (overlay != null) {
+ if (overlay.getInputData() != null) {
+ ColorSchemaReader reader = new ColorSchemaReader();
+ Collection<ColorSchema> schemas = reader.readColorSchema(overlay.getInputData().getFileContent());
+
+ new ColorModelCommand(colorModel, schemas, getUserService().getColorExtractorForUser(user)).execute();
+ } else if (overlay.getTitle().equals(BuildInLayout.CLEAN.getTitle())) {
+ // this might not return true if we change CLEAN.title in future...
+
+ // if it's clean then remove coloring
+ new ClearColorModelCommand(colorModel).execute();
+ } else if (overlay.isHierarchicalView()) {
+ new SetFixedHierarchyLevelCommand(colorModel, overlay.getHierarchyViewLevel()).execute();
+ }
+ }
+
+ Integer level = Configuration.MIN_ZOOM_LEVEL;
+ if (!zoomLevel.equals("")) {
+ level = Integer.valueOf(zoomLevel);
+ }
+
+ // transform polygon
+ CoordinationConverter cc = new CoordinationConverter(colorModel);
+ Double minX = originalModel.getWidth();
+ Double minY = originalModel.getHeight();
+ Double maxX = 0.0;
+ Double maxY = 0.0;
+ Path2D polygon = cc.latLngToPolygon(polygonString);
+
+ PathIterator pathIter = polygon.getPathIterator(null);
+ while (!pathIter.isDone()) {
+ final double[] segment = new double[PATH_ITERATOR_SEGMENT_SIZE];
+ if (pathIter.currentSegment(segment) != PathIterator.SEG_CLOSE) {
+ minX = Math.min(minX, segment[0]);
+ maxX = Math.max(maxX, segment[0]);
+ minY = Math.min(minY, segment[1]);
+ maxY = Math.max(maxY, segment[1]);
+ }
+ pathIter.next();
+ }
+
+ maxX = Math.min(originalModel.getWidth(), maxX);
+ maxY = Math.min(originalModel.getHeight(), maxY);
+ minX = Math.max(0.0, minX);
+ minY = Math.max(0.0, minY);
+
+ Double scale = Math.max(originalModel.getHeight(), originalModel.getWidth()) / (originalModel.getTileSize());
+
+ for (int i = level; i > Configuration.MIN_ZOOM_LEVEL; i--) {
+ scale /= 2;
+ }
+
+ ColorExtractor colorExtractor = getUserService().getColorExtractorForUser(user);
+
+ Params params = new Params().//
+ x(minX).//
+ y(minY).//
+ height((maxY - minY) / scale).//
+ width((maxX - minX) / scale).//
+ level(level - Configuration.MIN_ZOOM_LEVEL).//
+ nested(false).// automatically set nested view as invalid
+ scale(scale).//
+ colorExtractor(colorExtractor).//
+ sbgn(topModel.getProject().isSbgnFormat()).//
+ model(colorModel);
+ if (overlay != null) {
+ params.nested(overlay.isHierarchicalView());
+ }
+ List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
+ for (Integer integer : visibleLayoutIds) {
+ Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, authenticationToken);
+ params.addVisibleLayout(map);
+ }
+
+ ImageGenerators imageGenerator = new ImageGenerators();
+ String extension = imageGenerator.getExtension(handlerClass);
+ File file = File.createTempFile("map", "." + extension);
+
+ imageGenerator.generate(handlerClass, params, file.getAbsolutePath());
+
+ FileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("map." + extension);
+ entry.setFileContent(IOUtils.toByteArray(new FileInputStream(file)));
+ file.delete();
+ return entry;
+
+ }
+
+ private List<Integer> deserializeIdList(String overlayIds) {
+ List<Integer> result = new ArrayList<>();
+ String[] tmp = overlayIds.split(",");
+ for (String string : tmp) {
+ if (!string.equals("")) {
+ result.add(Integer.valueOf(string));
+ }
+ }
+ return result;
+ }
+
+ public FileEntry getModelAsModelFile(String token, String projectId, String modelId, String handlerClass,
+ String backgroundOverlayId, String overlayIds, String zoomLevel, String polygonString)
+ throws SecurityException, QueryException, IOException, InvalidColorSchemaException, CommandExecutionException,
+ ConverterException, InconsistentModelException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+
+ Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ if (topModel == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Model originalModel = topModel.getSubmodelById(modelId);
+
+ if (originalModel == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ CoordinationConverter cc = new CoordinationConverter(originalModel);
+ Path2D polygon = cc.latLngToPolygon(polygonString);
+
+ // create model bounded by the polygon
+ SubModelCommand subModelCommand = new SubModelCommand(originalModel, polygon);
+ Model part = subModelCommand.execute();
+
+ IConverter parser = getModelParser(handlerClass);
+ InputStream is = parser.exportModelToInputStream(part);
+
+ String fileExtension = parser.getFileExtension();
+
+ FileEntry entry = new UploadedFileEntry();
+ entry.setOriginalFileName("model." + fileExtension);
+ entry.setFileContent(IOUtils.toByteArray(is));
+ return entry;
+
+ }
+
+ public Map<String, Object> getStatistics(String projectId, String token)
+ throws SecurityException, ObjectNotFoundException {
+ Map<String, Object> result = new HashMap<String, Object>();
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+
+ Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+
+ Map<MiriamType, Integer> elementAnnotations = new HashMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ elementAnnotations.put(mt, 0);
+ }
+ Set<Model> models = new HashSet<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+
+ for (Model model2 : models) {
+ for (Element alias : model2.getElements()) {
+ for (MiriamData md : alias.getMiriamData()) {
+ Integer amount = elementAnnotations.get(md.getDataType());
+ amount += 1;
+ elementAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+ result.put("elementAnnotations", elementAnnotations);
+
+ Map<MiriamType, Integer> reactionAnnotations = new HashMap<>();
+ for (MiriamType mt : MiriamType.values()) {
+ reactionAnnotations.put(mt, 0);
+ }
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ Integer amount = reactionAnnotations.get(md.getDataType());
+ amount += 1;
+ reactionAnnotations.put(md.getDataType(), amount);
+ }
+ }
+ }
+
+ result.put("reactionAnnotations", reactionAnnotations);
+
+ result.put("publications", publicationsRestImpl.getPublications(models).size());
+
+ return result;
+ }
+
+ public List<ProjectMetaData> getProjects(String token) throws SecurityException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ List<Project> projects = getProjectService().getAllProjects(authenticationToken);
+ List<ProjectMetaData> result = new ArrayList<>();
+ for (Project project : projects) {
+ result.add(createData(project));
+ }
+ return result;
+ }
+
+ public ProjectMetaData updateProject(String token, String projectId, Map<String, Object> data)
+ throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ boolean canModify = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.ADD_MAP);
+ if (!canModify) {
+ throw new SecurityException("You cannot update projects");
+ }
+ Set<String> fields = data.keySet();
+ for (String fieldName : fields) {
+ Object value = data.get(fieldName);
+ String stringValue = null;
+ if (value instanceof String) {
+ stringValue = (String) value;
+ }
+ if (fieldName.equalsIgnoreCase("version")) {
+ project.setVersion((String) value);
+ } else if (fieldName.equalsIgnoreCase("id")) {
+ try {
+ int id = Integer.parseInt(stringValue);
+ if (id != project.getId()) {
+ throw new QueryException("Invalid id: " + stringValue);
+ }
+ } catch (NumberFormatException e) {
+ throw new QueryException("Invalid id: " + stringValue);
+ }
+ } else if (fieldName.equalsIgnoreCase("projectId")) {
+ if (!project.getProjectId().equalsIgnoreCase(stringValue)) {
+ throw new QueryException("You cannot modify projectId");
+ }
+ } else if (fieldName.equalsIgnoreCase("name")) {
+ project.setName((String) value);
+ } else if (fieldName.equalsIgnoreCase("notifyEmail")) {
+ project.setNotifyEmail(stringValue);
+ } else if (fieldName.equalsIgnoreCase("organism")) {
+ MiriamData organism = updateMiriamData(project.getOrganism(), value);
+ project.setOrganism(organism);
+ } else if (fieldName.equalsIgnoreCase("disease")) {
+ MiriamData disease = updateMiriamData(project.getDisease(), value);
+ project.setDisease(disease);
+ } else {
+ throw new QueryException("Unknown field: " + fieldName);
+ }
+ }
+ getProjectService().updateProject(project);
+ return getProject(projectId, token);
+ }
+
+ private MiriamData updateMiriamData(MiriamData organism, Object res) {
+ if (res == null) {
+ return null;
+ }
+ if (organism == null) {
+ organism = new MiriamData();
+ }
+
+ if (res instanceof Map) {
+ @SuppressWarnings("unchecked")
+ Map<String, Object> map = (Map<String, Object>) res;
+ organism.setDataType(MiriamType.valueOf((String) map.get("type")));
+ organism.setResource((String) map.get("resource"));
+ return organism;
+ } else {
+ throw new InvalidArgumentException("invalid miriamdData: " + res);
+ }
+ }
+
+ public ProjectMetaData addProject(String token, String projectId, MultiValueMap<String, String> data, String path)
+ throws SecurityException, QueryException, IOException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ User user = getUserService().getUserByToken(authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project != null) {
+ throw new ObjectExistsException("Project with given id already exists");
+ }
+ CreateProjectParams params = new CreateProjectParams();
+ String directory = path + "/../map_images/" + md5(projectId) + "/";
+ String fileContent = getFirstValue(data.get("file-content"));
+ if (fileContent == null) {
+ throw new QueryException("file-content is obligatory");
+ }
+ String parserClass = getFirstValue(data.get("parser"));
+ if (parserClass == null) {
+ throw new QueryException("parser is obligatory");
+ }
+ IConverter parser = getModelParser(parserClass);
+
+ params.addUser(user.getLogin(), null);
+ params.async(true);
+ params.parser(parser);
+ params.authenticationToken(authenticationToken);
+ params.autoResize(getFirstValue(data.get("auto-resize")));
+ params.cacheModel(getFirstValue(data.get("cache")));
+ params.description(getFirstValue(data.get("description")));
+ params.images(true);
+ 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.projectId(projectId);
+ params.projectName(getFirstValue(data.get("name")));
+ params.projectOrganism(getFirstValue(data.get("organism")));
+ params.sbgnFormat(getFirstValue(data.get("sbgn")));
+ params.semanticZoom(getFirstValue(data.get("semantic-zoom")));
+ params.version(getFirstValue(data.get("version")));
+ params.annotations(getFirstValue(data.get("annotate")));
+ if (params.isUpdateAnnotations()) {
+ params.annotatorsMap(projectService.createClassAnnotatorTree(user));
+ }
+ params.analyzeAnnotations(getFirstValue(data.get("verify-annotations")));
+ if (params.isAnalyzeAnnotations()) {
+ params.requiredAnnotations(projectService.createClassAnnotatorTree(user));
+ params.validAnnotations(projectService.createClassAnnotatorTree(user));
+ }
+
+ getProjectService().createProject(params);
+ return getProject(projectId, token);
+ }
+
+ private String getFirstValue(List<String> list) {
+ if (list == null) {
+ return null;
+ }
+ if (list.size() > 0) {
+ return list.get(0);
+ }
+ return null;
+ }
+
+ /**
+ * Method that computes md5 hash for a given {@link String}.
+ *
+ * @param data
+ * input string
+ * @return md5 hash for input string
+ */
+ private String md5(String data) {
+ try {
+ MessageDigest md = MessageDigest.getInstance("MD5");
+ byte[] mdbytes = md.digest(data.getBytes());
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < mdbytes.length; i++) {
+ // CHECKSTYLE:OFF
+ // this magic formula transforms int into hex value
+ sb.append(Integer.toString((mdbytes[i] & 0xff) + 0x100, 16).substring(1));
+ // CHECKSTYLE:ON
+ }
+ return sb.toString();
+ } catch (NoSuchAlgorithmException e) {
+ logger.fatal("Problem with instance of MD5 encoder", e);
+ }
+
+ return null;
+ }
+
+ public ProjectMetaData removeProject(String token, String projectId, String path)
+ throws ObjectNotFoundException, SecurityException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ getProjectService().removeProject(project, path, true, authenticationToken);
+ return getProject(projectId, token);
+ }
}
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 69b792a9bb8d1ed9d4a8e1641c76927df4afb7a6..a1f3ab33bcb611c39b4a409d0dbcec2429ec1a0e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -31,737 +31,740 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
*/
public class CreateProjectParams {
- /**
- * User defined project identifier.
- */
- private String projectId;
-
- /**
- * Name of the project.
- */
- private String projectName;
-
- /**
- * Disease associated to the project.
- */
- private String disease;
-
- /**
- * Organism associated to the project.
- */
- private String organism;
-
- /**
- * Path to a file used as a model.
- */
- private String projectFile;
-
- private IConverter parser;
-
- /**
- * Is the project a complex multi-file project.
- */
- private boolean complex;
- private boolean semanticZoom;
-
- /**
- * List of zip entries in the complex model definition.
- */
- private List<ZipEntryFile> zipEntries = new ArrayList<ZipEntryFile>();
-
- /**
- * Should the elements be annotated by the external resources.
- */
- private boolean updateAnnotations = false;
-
- /**
- * Do we want to generate images for all available layers.
- */
- private boolean images = false;
-
- /**
- * Should the map be autoresized after processing (to trim unnecessary
- * margins).
- */
- private boolean autoResize = true;
-
- /**
- * Should the data from external resources but linked to model be cached.
- */
- private boolean cacheModel = true;
-
- /**
- * Should the process of creation of the project be asynchronous (in separate
- * thread).
- */
- private boolean async = false;
-
- /**
- * Should the map be displayed in SBGN format.
- */
- private boolean sbgnFormat = false;
-
- /**
- * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
- * default {@link lcsb.mapviewer.model.map.layout.Layout Layout} when
- * generating new project.
- */
- private boolean networkLayoutAsDefault = false;
-
- /**
- * Do we want to analyze annotations after processing of the map. If yes then
- * in the email with summary of the generation process information about
- * improper annotations will be sent.
- */
- private boolean analyzeAnnotations = false;
-
- /**
- * Email address that should be notified after everything is done.
- */
- private String notifyEmail = null;
-
- /**
- * Description of the project.
- */
- private String description = "";
-
- /**
- * Version of the map.
- */
- private String version = "0";
-
- /**
- * Users that should have access to the map.
- */
- private List<String[]> users = new ArrayList<String[]>();
-
- /**
- * Directory with the static images that will be stored on server. This
- * directory is relative and it's a simple uniqe name within folder with
- * images.
- */
- private String projectDir;
-
- private AuthenticationToken authenticationToken;
-
- /**
- * Map that contains informnation what kind of annotators should be used for
- * specific class.
- */
- private Map<Class<?>, List<String>> annotatorsMap = null;
-
- /**
- * Map that contains information which {@link MiriamType miriam types} are
- * valid for which class.
- */
- private Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations = null;
-
- /**
- * Map that contains information which {@link MiriamType miriam types} are
- * obigatory for which class.
- */
- private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
-
- /**
- * @param projectId
- * the projectId to set
- * @return object with all parameters
- * @see #projectId
- */
- public CreateProjectParams projectId(String projectId) {
- this.projectId = projectId;
- return this;
- }
-
- public CreateProjectParams parser(IConverter parser) {
- this.parser = parser;
- return this;
- }
-
-
-
-
- /**
- * @param notifyEmail
- * the notifyEmail to set
- * @return object with all parameters
- * @see #notifyEmail
- */
- public CreateProjectParams notifyEmail(String notifyEmail) {
- this.notifyEmail = notifyEmail;
- 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
- * @return object with all parameters
- * @see #autoResize
- */
- public CreateProjectParams autoResize(boolean autoResize) {
- this.autoResize = autoResize;
- return this;
- }
-
- public CreateProjectParams autoResize(String value) {
- return this.autoResize("true".equalsIgnoreCase(value));
- }
-
- /**
- * Sets input stream from which projects should be generated.
- *
- * @param is
- * inputstream with the data of the project to be generated
- * @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();
- return this;
- }
-
- /**
- * @param async
- * the async to set
- * @return object with all parameters
- * @see #async
- */
- public CreateProjectParams async(boolean async) {
- this.async = async;
- return this;
- }
-
- /**
- * @param analyzeAnnotations
- * the analyzeAnnotations to set
- * @return object with all parameters
- * @see #analyzeAnnotations
- */
- public CreateProjectParams analyzeAnnotations(boolean analyzeAnnotations) {
- this.analyzeAnnotations = analyzeAnnotations;
- return this;
- }
-
- /**
- * @param updateAnnotations
- * the updateAnnotations to set
- * @return object with all parameters
- * @see #updateAnnotations
- */
- public CreateProjectParams annotations(boolean updateAnnotations) {
- this.updateAnnotations = updateAnnotations;
- return this;
- }
-
- /**
- * @param images
- * the images to set
- * @return object with all parameters
- * @see #images
- */
- public CreateProjectParams images(boolean images) {
- this.images = images;
- return this;
- }
-
- /**
- * @param description
- * the description to set
- * @return object with all parameters
- * @see #description
- */
- public CreateProjectParams description(String description) {
- this.description = description;
- return this;
- }
-
- /**
- * @param version
- * the version to set
- * @return object with all parameters
- * @see #version
- */
- public CreateProjectParams version(String version) {
- this.version = version;
- return this;
- }
-
- /**
- * Adds a user to the list of users that should have access to the project
- * from the beginning.
- *
- * @param login
- * login of the user
- * @param password
- * password (in case user doesn't exist yet)
- * @return object with all parameters
- * @return
- */
- public CreateProjectParams addUser(String login, String password) {
- this.users.add(new String[] { login, password });
- return this;
- }
-
- /**
- * @return the users
- * @see #users
- */
- public List<String[]> getUsers() {
- return users;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @return the notifyEmail
- * @see #notifyEmail
- */
- public String getNotifyEmail() {
- return notifyEmail;
- }
-
- /**
- * @return the analyzeAnnotations
- * @see #analyzeAnnotations
- */
- public boolean isAnalyzeAnnotations() {
- return analyzeAnnotations;
- }
-
- /**
- * @return the async
- * @see #async
- */
- public boolean isAsync() {
- return async;
- }
-
- /**
- * @return the autoResize
- * @see #autoResize
- */
- public boolean isAutoResize() {
- return autoResize;
- }
-
- /**
- * @return the images
- * @see #images
- */
- public boolean isImages() {
- return images;
- }
-
- /**
- * @return the updateAnnotations
- * @see #updateAnnotations
- */
- public boolean isUpdateAnnotations() {
- return updateAnnotations;
- }
-
- /**
- * @return the projectFile
- * @see #projectFile
- */
- public String getProjectFile() {
- return projectFile;
- }
-
- /**
- * @return the projectId
- * @see #projectId
- */
- public String getProjectId() {
- return projectId;
- }
-
- /**
- * @return the cacheModel
- * @see #cacheModel
- */
- public boolean isCacheModel() {
- return cacheModel;
- }
-
- /**
- * @param cacheModel
- * the cacheModel to set
- * @see #cacheModel
- * @return object with all parameters
- */
- public CreateProjectParams cacheModel(boolean cacheModel) {
- this.cacheModel = cacheModel;
- return this;
- }
-
- public CreateProjectParams cacheModel(String value) {
- return this.cacheModel("true".equalsIgnoreCase(value));
- }
-
- /**
- * @return the submodels
- * @see #zipEntries
- */
- public List<ZipEntryFile> getZipEntries() {
- return zipEntries;
- }
-
- /**
- * @param entry
- * the submodel to add
- * @see #zipEntries
- * @return object with all parameters
- */
- public CreateProjectParams addZipEntry(ZipEntryFile entry) {
- if (entry != null) {
- this.zipEntries.add(entry);
- }
- return this;
- }
-
- /**
- * @return the complex
- * @see #complex
- */
- public boolean isComplex() {
- return complex;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public boolean isSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public CreateProjectParams sbgnFormat(boolean sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- return this;
- }
-
- public CreateProjectParams sbgnFormat(String value) {
- return this.sbgnFormat("true".equalsIgnoreCase(value));
- }
-
- /**
- * @param complex
- * the complex to set
- * @see #complex
- * @return object with all parameters
- */
- public CreateProjectParams complex(boolean complex) {
- this.complex = complex;
- return this;
- }
-
- /**
- * Creates {@link #annotatorsMap}.
- *
- * @param annotatorsTree
- * tree containing information about annotators for given classes
- */
- public void annotatorsMap(TreeNode annotatorsTree) {
- Map<Class<?>, List<String>> map = new HashMap<Class<?>, List<String>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
-
- Set<String> set = new HashSet<String>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getUsedAnnotators());
- parent = parent.getParent();
- }
- List<String> list = new ArrayList<String>();
- list.addAll(set);
- map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(), list);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- annotatorsMap = map;
- }
-
- /**
- * @return the annotatorsMap
- * @see #annotatorsMap
- */
- public Map<Class<?>, List<String>> getAnnotatorsMap() {
- return annotatorsMap;
- }
-
- /**
- * @param annotatorsMap
- * the annotatorsMap to set
- * @see #annotatorsMap
- */
- public void setAnnotatorsMap(Map<Class<?>, List<String>> annotatorsMap) {
- this.annotatorsMap = annotatorsMap;
- }
-
- /**
- * Creates {@link #validAnnotations}.
- *
- * @param annotatorsTree
- * tree containing information about valid {@link MiriamType miriam
- * types}
- */
- @SuppressWarnings("unchecked")
- public void validAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- Set<MiriamType> set = new HashSet<MiriamType>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getValidAnnotations());
- parent = parent.getParent();
- }
- map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- validAnnotations = map;
- }
-
- /**
- * Creates {@link #requiredAnnotations}.
- *
- * @param annotatorsTree
- * tree containing information about required {@link MiriamType
- * miriam types}
- */
- @SuppressWarnings("unchecked")
- public void requiredAnnotations(TreeNode annotatorsTree) {
- Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
- Queue<TreeNode> queue = new LinkedList<TreeNode>();
- queue.add(annotatorsTree);
- while (!queue.isEmpty()) {
- TreeNode node = queue.poll();
- boolean valid = ((AnnotatedObjectTreeRow) node.getData()).getRequire();
- Set<MiriamType> set = new HashSet<MiriamType>();
-
- TreeNode parent = node;
- while (parent != null) {
- set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getRequiredAnnotations());
- if (((AnnotatedObjectTreeRow) parent.getData()).getRequire()) {
- valid = true;
- }
- parent = parent.getParent();
- }
- if (!valid) {
- set = null;
- }
- map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
-
- for (TreeNode node2 : node.getChildren()) {
- queue.add(node2);
- }
- }
- requiredAnnotations = map;
- }
-
- /**
- * Returns {@link #validAnnotations}.
- *
- * @return {@link #validAnnotations}.
- */
- public Map<Class<? extends BioEntity>, Set<MiriamType>> getValidAnnotations() {
- return validAnnotations;
- }
-
- /**
- * Returns {@link #requiredAnnotations}.
- *
- * @return {@link #requiredAnnotations}.
- */
- public Map<Class<? extends BioEntity>, Set<MiriamType>> getRequiredAnnotations() {
- return requiredAnnotations;
- }
-
- /**
- * Sets {@link #projectDir}.
- *
- * @param directory
- * new {@link #projectDir} value
- * @return instance of this class with new value set
- */
- public CreateProjectParams projectDir(String directory) {
- this.projectDir = directory;
- return this;
- }
-
- /**
- * @return the projectDir
- * @see #projectDir
- */
- public String getProjectDir() {
- return projectDir;
- }
-
- /**
- *
- * @param projectName
- * new {@link #projectName}
- * @return instance of this class with new value set
- */
- public CreateProjectParams projectName(String projectName) {
- this.projectName = projectName;
- return this;
- }
-
- /**
- * @return the projectName
- * @see #projectName
- */
- public String getProjectName() {
- return projectName;
- }
-
- /**
- * @param value
- * the networkLayoutAsDefault to set
- * @see #networkLayoutAsDefault
- * @return instance of this class with new value set
- */
- public CreateProjectParams networkLayoutAsDefault(boolean value) {
- this.networkLayoutAsDefault = value;
- return this;
-
- }
-
- /**
- * @return the networkLayoutAsDefault
- * @see #networkLayoutAsDefault
- */
- public boolean isNetworkLayoutAsDefault() {
- return networkLayoutAsDefault;
- }
-
- /**
- * @return disease MESH code.
- */
- public String getDisease() {
- return disease;
- }
-
- /**
- * @param disease
- * the code of the disease.
- * @return updated params object.
- */
- public CreateProjectParams projectDisease(String disease) {
- this.disease = disease;
- return this;
- }
-
- /**
- * @return the organism
- * @see #organism
- */
- public String getOrganism() {
- return organism;
- }
-
- /**
- * @param organism
- * the organism to set
- * @return updated params object.
- */
- public CreateProjectParams projectOrganism(String organism) {
- this.organism = organism;
- return this;
- }
-
- /**
- * @return the authenticationToken
- * @see #authenticationToken
- */
- public AuthenticationToken getAuthenticationToken() {
- return authenticationToken;
- }
-
- /**
- * @param authenticationToken
- * the authenticationToken to set
- * @see #authenticationToken
- */
- public CreateProjectParams authenticationToken(AuthenticationToken authenticationToken) {
- this.authenticationToken = authenticationToken;
-
- return this;
- }
-
- public CreateProjectParams semanticZoom(boolean semanticZoom) {
- this.semanticZoom = semanticZoom;
- return this;
- }
-
- public CreateProjectParams semanticZoom(String value) {
- return this.semanticZoom("true".equals(value));
- }
-
- public boolean isSemanticZoom() {
- return this.semanticZoom;
- }
-
- public IConverter getParser() {
- return this.parser ;
- }
+ /**
+ * User defined project identifier.
+ */
+ private String projectId;
+
+ /**
+ * Name of the project.
+ */
+ private String projectName;
+
+ /**
+ * Disease associated to the project.
+ */
+ private String disease;
+
+ /**
+ * Organism associated to the project.
+ */
+ private String organism;
+
+ /**
+ * Path to a file used as a model.
+ */
+ private String projectFile;
+
+ private IConverter parser;
+
+ /**
+ * Is the project a complex multi-file project.
+ */
+ private boolean complex;
+ private boolean semanticZoom;
+
+ /**
+ * List of zip entries in the complex model definition.
+ */
+ private List<ZipEntryFile> zipEntries = new ArrayList<ZipEntryFile>();
+
+ /**
+ * Should the elements be annotated by the external resources.
+ */
+ private boolean updateAnnotations = false;
+
+ /**
+ * Do we want to generate images for all available layers.
+ */
+ private boolean images = false;
+
+ /**
+ * Should the map be autoresized after processing (to trim unnecessary margins).
+ */
+ private boolean autoResize = true;
+
+ /**
+ * Should the data from external resources but linked to model be cached.
+ */
+ private boolean cacheModel = true;
+
+ /**
+ * Should the process of creation of the project be asynchronous (in separate
+ * thread).
+ */
+ private boolean async = false;
+
+ /**
+ * Should the map be displayed in SBGN format.
+ */
+ private boolean sbgnFormat = false;
+
+ /**
+ * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
+ * default {@link lcsb.mapviewer.model.map.layout.Layout Layout} when generating
+ * new project.
+ */
+ private boolean networkLayoutAsDefault = false;
+
+ /**
+ * Do we want to analyze annotations after processing of the map. If yes then in
+ * the email with summary of the generation process information about improper
+ * annotations will be sent.
+ */
+ private boolean analyzeAnnotations = false;
+
+ /**
+ * Email address that should be notified after everything is done.
+ */
+ private String notifyEmail = null;
+
+ /**
+ * Description of the project.
+ */
+ private String description = "";
+
+ /**
+ * Version of the map.
+ */
+ private String version = "0";
+
+ /**
+ * Users that should have access to the map.
+ */
+ private List<String[]> users = new ArrayList<String[]>();
+
+ /**
+ * Directory with the static images that will be stored on server. This
+ * directory is relative and it's a simple uniqe name within folder with images.
+ */
+ private String projectDir;
+
+ private AuthenticationToken authenticationToken;
+
+ /**
+ * Map that contains informnation what kind of annotators should be used for
+ * specific class.
+ */
+ private Map<Class<?>, List<String>> annotatorsMap = null;
+
+ /**
+ * Map that contains information which {@link MiriamType miriam types} are valid
+ * for which class.
+ */
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> validAnnotations = null;
+
+ /**
+ * Map that contains information which {@link MiriamType miriam types} are
+ * obigatory for which class.
+ */
+ private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
+
+ /**
+ * @param projectId
+ * the projectId to set
+ * @return object with all parameters
+ * @see #projectId
+ */
+ public CreateProjectParams projectId(String projectId) {
+ this.projectId = projectId;
+ return this;
+ }
+
+ public CreateProjectParams parser(IConverter parser) {
+ this.parser = parser;
+ return this;
+ }
+
+ /**
+ * @param notifyEmail
+ * the notifyEmail to set
+ * @return object with all parameters
+ * @see #notifyEmail
+ */
+ public CreateProjectParams notifyEmail(String notifyEmail) {
+ this.notifyEmail = notifyEmail;
+ 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
+ * @return object with all parameters
+ * @see #autoResize
+ */
+ public CreateProjectParams autoResize(boolean autoResize) {
+ this.autoResize = autoResize;
+ return this;
+ }
+
+ public CreateProjectParams autoResize(String value) {
+ return this.autoResize("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * Sets input stream from which projects should be generated.
+ *
+ * @param is
+ * inputstream with the data of the project to be generated
+ * @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();
+ return this;
+ }
+
+ /**
+ * @param async
+ * the async to set
+ * @return object with all parameters
+ * @see #async
+ */
+ public CreateProjectParams async(boolean async) {
+ this.async = async;
+ return this;
+ }
+
+ /**
+ * @param analyzeAnnotations
+ * the analyzeAnnotations to set
+ * @return object with all parameters
+ * @see #analyzeAnnotations
+ */
+ public CreateProjectParams analyzeAnnotations(boolean analyzeAnnotations) {
+ this.analyzeAnnotations = analyzeAnnotations;
+ return this;
+ }
+
+ /**
+ * @param updateAnnotations
+ * the updateAnnotations to set
+ * @return object with all parameters
+ * @see #updateAnnotations
+ */
+ public CreateProjectParams annotations(boolean updateAnnotations) {
+ this.updateAnnotations = updateAnnotations;
+ return this;
+ }
+
+ /**
+ * @param images
+ * the images to set
+ * @return object with all parameters
+ * @see #images
+ */
+ public CreateProjectParams images(boolean images) {
+ this.images = images;
+ return this;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @return object with all parameters
+ * @see #description
+ */
+ public CreateProjectParams description(String description) {
+ this.description = description;
+ return this;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @return object with all parameters
+ * @see #version
+ */
+ public CreateProjectParams version(String version) {
+ this.version = version;
+ return this;
+ }
+
+ /**
+ * Adds a user to the list of users that should have access to the project from
+ * the beginning.
+ *
+ * @param login
+ * login of the user
+ * @param password
+ * password (in case user doesn't exist yet)
+ * @return object with all parameters
+ * @return
+ */
+ public CreateProjectParams addUser(String login, String password) {
+ this.users.add(new String[] { login, password });
+ return this;
+ }
+
+ /**
+ * @return the users
+ * @see #users
+ */
+ public List<String[]> getUsers() {
+ return users;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @return the notifyEmail
+ * @see #notifyEmail
+ */
+ public String getNotifyEmail() {
+ return notifyEmail;
+ }
+
+ /**
+ * @return the analyzeAnnotations
+ * @see #analyzeAnnotations
+ */
+ public boolean isAnalyzeAnnotations() {
+ return analyzeAnnotations;
+ }
+
+ /**
+ * @return the async
+ * @see #async
+ */
+ public boolean isAsync() {
+ return async;
+ }
+
+ /**
+ * @return the autoResize
+ * @see #autoResize
+ */
+ public boolean isAutoResize() {
+ return autoResize;
+ }
+
+ /**
+ * @return the images
+ * @see #images
+ */
+ public boolean isImages() {
+ return images;
+ }
+
+ /**
+ * @return the updateAnnotations
+ * @see #updateAnnotations
+ */
+ public boolean isUpdateAnnotations() {
+ return updateAnnotations;
+ }
+
+ /**
+ * @return the projectFile
+ * @see #projectFile
+ */
+ public String getProjectFile() {
+ return projectFile;
+ }
+
+ /**
+ * @return the projectId
+ * @see #projectId
+ */
+ public String getProjectId() {
+ return projectId;
+ }
+
+ /**
+ * @return the cacheModel
+ * @see #cacheModel
+ */
+ public boolean isCacheModel() {
+ return cacheModel;
+ }
+
+ /**
+ * @param cacheModel
+ * the cacheModel to set
+ * @see #cacheModel
+ * @return object with all parameters
+ */
+ public CreateProjectParams cacheModel(boolean cacheModel) {
+ this.cacheModel = cacheModel;
+ return this;
+ }
+
+ public CreateProjectParams cacheModel(String value) {
+ return this.cacheModel("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * @return the submodels
+ * @see #zipEntries
+ */
+ public List<ZipEntryFile> getZipEntries() {
+ return zipEntries;
+ }
+
+ /**
+ * @param entry
+ * the submodel to add
+ * @see #zipEntries
+ * @return object with all parameters
+ */
+ public CreateProjectParams addZipEntry(ZipEntryFile entry) {
+ if (entry != null) {
+ this.zipEntries.add(entry);
+ }
+ return this;
+ }
+
+ /**
+ * @return the complex
+ * @see #complex
+ */
+ public boolean isComplex() {
+ return complex;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public boolean isSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @see #sbgnFormat
+ */
+ public CreateProjectParams sbgnFormat(boolean sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ return this;
+ }
+
+ public CreateProjectParams sbgnFormat(String value) {
+ return this.sbgnFormat("true".equalsIgnoreCase(value));
+ }
+
+ /**
+ * @param complex
+ * the complex to set
+ * @see #complex
+ * @return object with all parameters
+ */
+ public CreateProjectParams complex(boolean complex) {
+ this.complex = complex;
+ return this;
+ }
+
+ /**
+ * Creates {@link #annotatorsMap}.
+ *
+ * @param annotatorsTree
+ * tree containing information about annotators for given classes
+ */
+ public void annotatorsMap(TreeNode annotatorsTree) {
+ Map<Class<?>, List<String>> map = new HashMap<Class<?>, List<String>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+
+ Set<String> set = new HashSet<String>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getUsedAnnotators());
+ parent = parent.getParent();
+ }
+ List<String> list = new ArrayList<String>();
+ list.addAll(set);
+ map.put(((AnnotatedObjectTreeRow) node.getData()).getClazz(), list);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ annotatorsMap = map;
+ }
+
+ /**
+ * @return the annotatorsMap
+ * @see #annotatorsMap
+ */
+ public Map<Class<?>, List<String>> getAnnotatorsMap() {
+ return annotatorsMap;
+ }
+
+ /**
+ * @param annotatorsMap
+ * the annotatorsMap to set
+ * @see #annotatorsMap
+ */
+ public void setAnnotatorsMap(Map<Class<?>, List<String>> annotatorsMap) {
+ this.annotatorsMap = annotatorsMap;
+ }
+
+ /**
+ * Creates {@link #validAnnotations}.
+ *
+ * @param annotatorsTree
+ * tree containing information about valid {@link MiriamType miriam
+ * types}
+ */
+ @SuppressWarnings("unchecked")
+ public void validAnnotations(TreeNode annotatorsTree) {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ Set<MiriamType> set = new HashSet<MiriamType>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getValidAnnotations());
+ parent = parent.getParent();
+ }
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ validAnnotations = map;
+ }
+
+ /**
+ * Creates {@link #requiredAnnotations}.
+ *
+ * @param annotatorsTree
+ * tree containing information about required {@link MiriamType miriam
+ * types}
+ */
+ @SuppressWarnings("unchecked")
+ public void requiredAnnotations(TreeNode annotatorsTree) {
+ Map<Class<? extends BioEntity>, Set<MiriamType>> map = new HashMap<Class<? extends BioEntity>, Set<MiriamType>>();
+ Queue<TreeNode> queue = new LinkedList<TreeNode>();
+ queue.add(annotatorsTree);
+ while (!queue.isEmpty()) {
+ TreeNode node = queue.poll();
+ boolean valid = ((AnnotatedObjectTreeRow) node.getData()).getRequire();
+ Set<MiriamType> set = new HashSet<MiriamType>();
+
+ TreeNode parent = node;
+ while (parent != null) {
+ set.addAll(((AnnotatedObjectTreeRow) parent.getData()).getRequiredAnnotations());
+ if (((AnnotatedObjectTreeRow) parent.getData()).getRequire()) {
+ valid = true;
+ }
+ parent = parent.getParent();
+ }
+ if (!valid) {
+ set = null;
+ }
+ map.put((Class<? extends BioEntity>) ((AnnotatedObjectTreeRow) node.getData()).getClazz(), set);
+
+ for (TreeNode node2 : node.getChildren()) {
+ queue.add(node2);
+ }
+ }
+ requiredAnnotations = map;
+ }
+
+ /**
+ * Returns {@link #validAnnotations}.
+ *
+ * @return {@link #validAnnotations}.
+ */
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getValidAnnotations() {
+ return validAnnotations;
+ }
+
+ /**
+ * Returns {@link #requiredAnnotations}.
+ *
+ * @return {@link #requiredAnnotations}.
+ */
+ public Map<Class<? extends BioEntity>, Set<MiriamType>> getRequiredAnnotations() {
+ return requiredAnnotations;
+ }
+
+ /**
+ * Sets {@link #projectDir}.
+ *
+ * @param directory
+ * new {@link #projectDir} value
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams projectDir(String directory) {
+ this.projectDir = directory;
+ return this;
+ }
+
+ /**
+ * @return the projectDir
+ * @see #projectDir
+ */
+ public String getProjectDir() {
+ return projectDir;
+ }
+
+ /**
+ *
+ * @param projectName
+ * new {@link #projectName}
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams projectName(String projectName) {
+ this.projectName = projectName;
+ return this;
+ }
+
+ /**
+ * @return the projectName
+ * @see #projectName
+ */
+ public String getProjectName() {
+ return projectName;
+ }
+
+ /**
+ * @param value
+ * the networkLayoutAsDefault to set
+ * @see #networkLayoutAsDefault
+ * @return instance of this class with new value set
+ */
+ public CreateProjectParams networkLayoutAsDefault(boolean value) {
+ this.networkLayoutAsDefault = value;
+ return this;
+
+ }
+
+ /**
+ * @return the networkLayoutAsDefault
+ * @see #networkLayoutAsDefault
+ */
+ public boolean isNetworkLayoutAsDefault() {
+ return networkLayoutAsDefault;
+ }
+
+ /**
+ * @return disease MESH code.
+ */
+ public String getDisease() {
+ return disease;
+ }
+
+ /**
+ * @param disease
+ * the code of the disease.
+ * @return updated params object.
+ */
+ public CreateProjectParams projectDisease(String disease) {
+ this.disease = disease;
+ return this;
+ }
+
+ /**
+ * @return the organism
+ * @see #organism
+ */
+ public String getOrganism() {
+ return organism;
+ }
+
+ /**
+ * @param organism
+ * the organism to set
+ * @return updated params object.
+ */
+ public CreateProjectParams projectOrganism(String organism) {
+ this.organism = organism;
+ return this;
+ }
+
+ /**
+ * @return the authenticationToken
+ * @see #authenticationToken
+ */
+ public AuthenticationToken getAuthenticationToken() {
+ return authenticationToken;
+ }
+
+ /**
+ * @param authenticationToken
+ * the authenticationToken to set
+ * @see #authenticationToken
+ */
+ public CreateProjectParams authenticationToken(AuthenticationToken authenticationToken) {
+ this.authenticationToken = authenticationToken;
+
+ return this;
+ }
+
+ public CreateProjectParams semanticZoom(boolean semanticZoom) {
+ this.semanticZoom = semanticZoom;
+ return this;
+ }
+
+ public CreateProjectParams semanticZoom(String value) {
+ return this.semanticZoom("true".equals(value));
+ }
+
+ public boolean isSemanticZoom() {
+ return this.semanticZoom;
+ }
+
+ public IConverter getParser() {
+ return this.parser;
+ }
+
+ public CreateProjectParams annotations(String value) {
+ return this.annotations("true".equalsIgnoreCase(value));
+ }
+
+ public CreateProjectParams analyzeAnnotations(String value) {
+ return this.analyzeAnnotations("true".equalsIgnoreCase(value));
+ }
}