diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 88bbff2177235ea9d63129360e3fed75396b1b6a..54e58c6f1d6400437ede3acb2d959bc5bcc07ead 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.api;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
-import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
@@ -126,31 +125,28 @@ public abstract class BaseRestImpl {
result.put("type", annotation.getDataType().name());
result.put("resource", annotation.getResource());
result.put("id", annotation.getId());
-
- if (annotation.getAnnotator() != null) {
- try {
- result.put("annotatorClassName", annotation.getAnnotator().getName());
- result.put("descriptionByType",
- ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance()).getDescription( annotation.getDataType())
- );
- result.put("descriptionByTypeRelation",
- ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance()).getDescription(
- annotation.getDataType(),
- annotation.getRelationType())
- );
-
- }catch(Exception e) {
- logger.error("Problem with retrieving description from annotator", e);
- result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
- }
+
+ if (annotation.getAnnotator() != null) {
+ try {
+ result.put("annotatorClassName", annotation.getAnnotator().getName());
+ result.put("descriptionByType", ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
+ .getDescription(annotation.getDataType()));
+ result.put("descriptionByTypeRelation",
+ ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance())
+ .getDescription(annotation.getDataType(), annotation.getRelationType()));
+
+ } catch (Exception e) {
+ logger.error("Problem with retrieving description from annotator", e);
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
+ }
} else {
- result.put("annotatorClassName", "");
- result.put("descriptionByType", "");
- result.put("descriptionByTypeRelation", "");
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
}
-
+
return result;
} else {
throw new InvalidArgumentException("invalid miriam data: " + annotation);
@@ -206,7 +202,7 @@ public abstract class BaseRestImpl {
}
protected List<Model> getModels(String projectId, String modelId, String token) throws SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ Model model = modelService.getLastModelByProjectId(projectId, token);
List<Model> models = new ArrayList<>();
if (!modelId.equals("*")) {
@@ -384,4 +380,11 @@ public abstract class BaseRestImpl {
}
return this.mathMlTransformer;
}
+
+ protected void verifyToken(String token) throws SecurityException {
+ if (getUserService().getUserByToken(token) == null) {
+ throw new SecurityException("Invalid token");
+ }
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 3dc7786f2089db07d14fa75b3471fd0a6b7449d7..fcdc73a49ad371a720df56aec65cf62678d77c4e 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -55,7 +55,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
private ModelAnnotator modelAnnotator;
public List<ConfigurationView> getAllValues(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
return configurationService.getAllValues();
}
@@ -94,7 +94,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getImageFormats(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
List<Map<String, Object>> result = new ArrayList<>();
ImageGenerators imageGenerators = new ImageGenerators();
@@ -112,7 +112,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getModelFormats(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
List<IConverter> converters = getModelConverters();
List<Map<String, Object>> result = new ArrayList<>();
@@ -128,7 +128,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getOverlayTypes(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
List<Map<String, Object>> result = new ArrayList<>();
for (ColorSchemaType type : ColorSchemaType.values()) {
Map<String, Object> map = new HashMap<>();
@@ -139,7 +139,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
}
public Set<Map<String, String>> getElementTypes(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
return getClassStringTypesList(Element.class);
}
@@ -171,7 +171,7 @@ public class ConfigurationRestImpl extends BaseRestImpl {
}
public Set<Map<String, String>> getReactionTypes(String token) throws SecurityException {
- userService.getToken(token);
+ verifyToken(token);
return getClassStringTypesList(Reaction.class);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
index fc7c4f7ab211e029e9a3573021b9e39976fd238d..e517c1eaad75d97c2ad20b2b68dc7d7e83037ecd 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java
@@ -10,49 +10,43 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ReferenceGenomeView;
@Transactional(value = "txManager")
public class ReferenceGenomeRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReferenceGenomeRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- /**
- * Service that manages reference genomes.
- */
- @Autowired
- private IReferenceGenomeService referenceGenomeService;
-
- public ReferenceGenomeView getReferenceGenome(String token, String organismId, String type, String version) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
-
- MiriamData organism = null;
- if (organismId != null && !organismId.isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, organismId);
- } else {
- throw new QueryException("Unknown taxonomy organism: " + organismId);
- }
- ReferenceGenomeView result = null;
- try {
- ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
- version = version.replaceAll("\\*", "");
- result = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version, authenticationToken);
- if (result == null) {
- throw new QueryException("Cannot find requested reference genome");
- }
- } catch (IllegalArgumentException e) {
- throw new QueryException("Cannot find type: " + type);
- }
- return result;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReferenceGenomeRestImpl.class);
+
+ /**
+ * Service that manages reference genomes.
+ */
+ @Autowired
+ private IReferenceGenomeService referenceGenomeService;
+
+ public ReferenceGenomeView getReferenceGenome(String token, String organismId, String type, String version)
+ throws SecurityException, QueryException {
+ MiriamData organism = null;
+ if (organismId != null && !organismId.isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, organismId);
+ } else {
+ throw new QueryException("Unknown taxonomy organism: " + organismId);
+ }
+ ReferenceGenomeView result = null;
+ try {
+ ReferenceGenomeType genomeType = ReferenceGenomeType.valueOf(type);
+ version = version.replaceAll("\\*", "");
+ result = referenceGenomeService.getReferenceGenomeViewByParams(organism, genomeType, version, token);
+ if (result == null) {
+ throw new QueryException("Cannot find requested reference genome");
+ }
+ } catch (IllegalArgumentException e) {
+ throw new QueryException("Cannot find type: " + type);
+ }
+ return result;
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
index 82d645cb8972bf78ff6ad3934872ba7999c007eb..378fc0ac2994aa633ae36b6ed472f6d5ae749b58 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/mesh/MeshController.java
@@ -1,40 +1,18 @@
package lcsb.mapviewer.api.mesh;
-import java.io.IOException;
-import java.util.Calendar;
-import java.util.HashMap;
-import java.util.List;
import java.util.Map;
-import javax.servlet.http.Cookie;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.security.web.authentication.logout.SecurityContextLogoutHandler;
-import org.springframework.util.MultiValueMap;
import org.springframework.web.bind.annotation.CookieValue;
import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;
-import com.fasterxml.jackson.core.JsonParseException;
-import com.fasterxml.jackson.databind.JsonMappingException;
-
import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@RestController
public class MeshController extends BaseController {
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 19612ef9238b6ac1ff622c8bd71d2e20135b9b7a..69fb7e38daafb097c0caac1ea35f33f2691762fc 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
@@ -75,7 +75,6 @@ import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
import lcsb.mapviewer.services.utils.gmap.CoordinationConverter;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.OverviewImageViewFactory;
@Transactional(value = "txManager")
@@ -114,8 +113,7 @@ public class ProjectRestImpl extends BaseRestImpl {
private UploadedFileEntryDao uploadedFileEntryDao;
public ProjectMetaData getProject(String projectId, String token) throws SecurityException, ObjectNotFoundException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -185,8 +183,7 @@ public class ProjectRestImpl extends BaseRestImpl {
}
public FileEntry getSource(String token, String projectId) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -200,10 +197,9 @@ public class ProjectRestImpl extends BaseRestImpl {
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);
+ User user = getUserService().getUserByToken(token);
- Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
if (topModel == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -298,7 +294,7 @@ public class ProjectRestImpl extends BaseRestImpl {
}
List<Integer> visibleLayoutIds = deserializeIdList(overlayIds);
for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, authenticationToken);
+ Map<Object, ColorSchema> map = layoutService.getElementsForLayout(colorModel, integer, token);
params.addVisibleLayout(map);
}
@@ -332,9 +328,7 @@ public class ProjectRestImpl extends BaseRestImpl {
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);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
if (topModel == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -367,10 +361,8 @@ public class ProjectRestImpl extends BaseRestImpl {
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);
+ Map<String, Object> result = new HashMap<>();
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -416,8 +408,7 @@ public class ProjectRestImpl extends BaseRestImpl {
}
public List<ProjectMetaData> getProjects(String token) throws SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- List<Project> projects = getProjectService().getAllProjects(authenticationToken);
+ List<Project> projects = getProjectService().getAllProjects(token);
List<ProjectMetaData> result = new ArrayList<>();
for (Project project : projects) {
result.add(createData(project));
@@ -427,12 +418,11 @@ public class ProjectRestImpl extends BaseRestImpl {
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);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
- boolean canModify = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.ADD_MAP);
+ boolean canModify = getUserService().userHasPrivilege(token, PrivilegeType.ADD_MAP);
if (!canModify) {
throw new SecurityException("You cannot update projects");
}
@@ -497,9 +487,8 @@ public class ProjectRestImpl extends BaseRestImpl {
public ProjectMetaData addProject(String token, String projectId, MultiValueMap<String, Object> data, String path)
throws SecurityException, QueryException, IOException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- User user = getUserService().getUserByToken(authenticationToken);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ User user = getUserService().getUserByToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project != null) {
logger.debug(project.getProjectId());
throw new ObjectExistsException("Project with given id already exists");
@@ -532,7 +521,7 @@ public class ProjectRestImpl extends BaseRestImpl {
params.addUser(user.getLogin(), null);
params.async(true);
params.parser(parser);
- params.authenticationToken(authenticationToken);
+ params.authenticationToken(token);
params.autoResize(getFirstValue(data.get("auto-resize")));
params.cacheModel(getFirstValue(data.get("cache")));
params.description(getFirstValue(data.get("description")));
@@ -640,9 +629,8 @@ public class ProjectRestImpl extends BaseRestImpl {
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);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
+ getProjectService().removeProject(project, path, true, token);
return getProject(projectId, token);
}
@@ -684,8 +672,7 @@ public class ProjectRestImpl extends BaseRestImpl {
public Map<String, Object> getLogs(String projectId, String level, String token, String startString, Integer length,
String sortColumn, String sortOrder, String search) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
index 47792473aa7c4192fc605c36963ba95374bfa618..2c8427aaa976c26adb592932767ee679ba4ffec9 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/chemicals/ChemicalRestImpl.java
@@ -25,12 +25,9 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
public class ChemicalRestImpl extends BaseRestImpl {
@@ -51,8 +48,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getChemicalsByQuery(String token, String projectId, String columns, String query)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -172,8 +168,7 @@ public class ChemicalRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getChemicalsByTarget(String token, String projectId, String targetType,
String targetId, String columns) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -220,9 +215,9 @@ public class ChemicalRestImpl extends BaseRestImpl {
return result;
}
- public List<String> getSuggestedQueryList(String projectId, String token) throws SecurityException, ChemicalSearchException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ public List<String> getSuggestedQueryList(String projectId, String token)
+ throws SecurityException, ChemicalSearchException {
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
return chemicalParser.getSuggestedQueryList(project, project.getDisease());
}
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
index b42991f0670f18b6f45e501f06c83c25ea39ec5a..4b777b9bc7d8de831338e922d0aac9d8c00a6635 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/comments/CommentRestImpl.java
@@ -25,11 +25,8 @@ import lcsb.mapviewer.persist.dao.map.ReactionDao;
import lcsb.mapviewer.persist.dao.map.species.ElementDao;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ICommentService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.overlay.IconManager;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
public class CommentRestImpl extends BaseRestImpl {
@@ -50,18 +47,16 @@ public class CommentRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getCommentList(String token, String projectId, String columns, String elementId,
String elementType, String removed) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
- boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.EDIT_COMMENTS_PROJECT,
- project);
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
Set<String> columnsSet = createCommentColumnSet(columns, isAdmin);
List<Map<String, Object>> result = new ArrayList<>();
- List<Comment> comments = commentService.getCommentsByProject(project, authenticationToken);
+ List<Comment> comments = commentService.getCommentsByProject(project, token);
for (Comment comment : comments) {
boolean reject = false;
if (!"".equals(elementType)) {
@@ -291,8 +286,7 @@ public class CommentRestImpl extends BaseRestImpl {
public Map<String, Object> addComment(String token, String projectId, String elementType, String elementId,
String name, String email, String content, boolean pinned, Point2D pointCoordinates, String submodelId)
throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -328,15 +322,13 @@ public class CommentRestImpl extends BaseRestImpl {
submodel);
Project project = model.getProject();
- boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.EDIT_COMMENTS_PROJECT,
- project);
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
return preparedComment(comment, createCommentColumnSet("", isAdmin), isAdmin);
}
public Map<String, Object> removeComment(String token, String projectId, String commentId, String reason)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
@@ -345,7 +337,7 @@ public class CommentRestImpl extends BaseRestImpl {
throw new ObjectNotFoundException("Comment with given id doesn't exist");
}
- commentService.deleteComment(comment, authenticationToken, reason);
+ commentService.deleteComment(comment, token, reason);
return okStatus();
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
index a16f3c4565c4bcd939d696248fdb8a2f8e7c251d..af6ef3756fa328319b93fab712a33bee255ebbe4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/drugs/DrugRestImpl.java
@@ -26,7 +26,6 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.drug.IDrugService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
public class DrugRestImpl extends BaseRestImpl {
@@ -48,8 +47,7 @@ public class DrugRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getDrugsByQuery(String token, String projectId, String columns, String query)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = modelService.getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -180,8 +178,7 @@ public class DrugRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getDrugsByTarget(String token, String projectId, String targetType, String targetId,
String columns) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ Model model = modelService.getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -225,8 +222,7 @@ public class DrugRestImpl extends BaseRestImpl {
public List<String> getSuggestedQueryList(String projectId, String token)
throws SecurityException, DrugSearchException {
- AuthenticationToken authenticationToken = userService.getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
return drugService.getSuggestedQueryList(project, project.getOrganism());
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
index 4037cda6cb8d9af3dd88ba0d440a76908f42b68e..a292ef60b5695421607ab7bf498654939303c891 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImpl.java
@@ -25,7 +25,6 @@ import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.search.db.DbSearchCriteria;
import lcsb.mapviewer.services.search.db.mirna.IMiRNAService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
public class MiRnaRestImpl extends BaseRestImpl {
@@ -44,8 +43,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getMiRnasByQuery(String token, String projectId, String columns, String query)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -127,8 +125,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getMiRnasByTarget(String token, String projectId, String targetType, String targetId,
String columns) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -172,8 +169,7 @@ public class MiRnaRestImpl extends BaseRestImpl {
public List<String> getSuggestedQueryList(String projectId, String token)
throws SecurityException, MiRNASearchException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
return miRNAParser.getSuggestedQueryList(project);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index 7c58d07ffa1272781cacdb2bb5511cf1397ec2ea..b39b48d148e0327efe16cfbbfec66336cae7f0fd 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -19,7 +19,6 @@ import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
public class ModelRestImpl extends BaseRestImpl {
@@ -35,18 +34,16 @@ public class ModelRestImpl extends BaseRestImpl {
public List<ModelMetaData> getModels(String projectId, String token)
throws SecurityException, ObjectNotFoundException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
- List<ModelMetaData> result = createData(project, authenticationToken);
+ List<ModelMetaData> result = createData(project, token);
return result;
}
public ModelMetaData getModel(String projectId, String modelId, String token) throws SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
Model submodel = model.getSubmodelById(modelId);
if (submodel == null) {
return null;
@@ -58,13 +55,12 @@ public class ModelRestImpl extends BaseRestImpl {
metaDataToProcess.addAll(result.getSubmodels());
for (ModelMetaData submodelData : metaDataToProcess) {
submodelData.setLayouts(layoutService.getGeneralLayouts(model.getSubmodelById(submodelData.getIdObject())));
- logger.debug(submodelData.getLayouts());
}
return result;
}
}
- private List<ModelMetaData> createData(Project project, AuthenticationToken token) throws SecurityException {
+ private List<ModelMetaData> createData(Project project, String token) throws SecurityException {
List<ModelMetaData> result = new ArrayList<>();
Model model = getModelService().getLastModelByProjectId(project.getProjectId(), token);
if (model != null) {
@@ -73,7 +69,7 @@ public class ModelRestImpl extends BaseRestImpl {
models.add(model);
models.addAll(model.getSubmodels());
for (Model model2 : models) {
- result.add(getModel(project.getProjectId(), model2.getId() + "", token.getId()));
+ result.add(getModel(project.getProjectId(), model2.getId() + "", token));
}
}
return result;
@@ -81,12 +77,11 @@ public class ModelRestImpl extends BaseRestImpl {
public ModelMetaData updateModel(String projectId, String modelId, Map<String, Object> data, String token)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ Project project = getProjectService().getProjectByProjectId(projectId, token);
if (project == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
- boolean canModify = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.ADD_MAP);
+ boolean canModify = getUserService().userHasPrivilege(token, PrivilegeType.ADD_MAP);
if (!canModify) {
throw new SecurityException("You cannot update projects");
}
@@ -118,7 +113,7 @@ public class ModelRestImpl extends BaseRestImpl {
throw new QueryException("Unknown field: " + fieldName);
}
}
- getModelService().updateModel(model, authenticationToken);
+ getModelService().updateModel(model, token);
return getModel(projectId, modelId, token);
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
index b2b1dd3884d242331786a8c1349ff2f8cf9142f6..9e79f1a7f475dd8bdd07c81672da8341e4a3e8f3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesRestImpl.java
@@ -21,107 +21,108 @@ import lcsb.mapviewer.services.interfaces.IUserService;
@Transactional(value = "txManager")
public class BioEntitiesRestImpl extends BaseRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
-
- @Autowired
- private ISearchService searchService;
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token, Point2D coordinates, Integer count,
- String perfectMatch) throws UserAccessException, SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
-
- Model submodel = model.getSubmodelById(modelId);
-
- List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count, perfectMatch.equalsIgnoreCase("true"));
- for (Object object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the searchService
- * @see #searchService
- */
- public ISearchService getSearchService() {
- return searchService;
- }
-
- /**
- * @param searchService
- * the searchService to set
- * @see #searchService
- */
- public void setSearchService(ISearchService searchService) {
- this.searchService = searchService;
- }
-
- public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String modelId, String query, Integer maxElements, String perfectMatch)
- throws SecurityException {
- List<Map<String, Object>> resultMap = new ArrayList<>();
-
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
-
- Integer limit = Integer.valueOf(maxElements);
- boolean match = perfectMatch.equals("true");
- List<Object> elements = searchService.searchByQuery(model, query, limit, match);
- for (Object object : elements) {
- Map<String, Object> result = createMinifiedSearchResult(object);
- resultMap.add(result);
- }
- return resultMap;
- }
-
- public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
- Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
- return searchService.getSuggestedQueryList(model);
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(BioEntitiesRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ @Autowired
+ private ISearchService searchService;
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ public List<Map<String, Object>> getClosestElementsByCoordinates(String projectId, String modelId, String token,
+ Point2D coordinates, Integer count, String perfectMatch) throws UserAccessException, SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = modelService.getLastModelByProjectId(projectId, token);
+
+ Model submodel = model.getSubmodelById(modelId);
+
+ List<BioEntity> elements = searchService.getClosestElements(submodel, coordinates, count,
+ perfectMatch.equalsIgnoreCase("true"));
+ for (Object object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the searchService
+ * @see #searchService
+ */
+ public ISearchService getSearchService() {
+ return searchService;
+ }
+
+ /**
+ * @param searchService
+ * the searchService to set
+ * @see #searchService
+ */
+ public void setSearchService(ISearchService searchService) {
+ this.searchService = searchService;
+ }
+
+ public List<Map<String, Object>> getElementsByQuery(String projectId, String token, String modelId, String query,
+ Integer maxElements, String perfectMatch) throws SecurityException {
+ List<Map<String, Object>> resultMap = new ArrayList<>();
+
+ Model model = modelService.getLastModelByProjectId(projectId, token);
+
+ Integer limit = Integer.valueOf(maxElements);
+ boolean match = perfectMatch.equals("true");
+ List<Object> elements = searchService.searchByQuery(model, query, limit, match);
+ for (Object object : elements) {
+ Map<String, Object> result = createMinifiedSearchResult(object);
+ resultMap.add(result);
+ }
+ return resultMap;
+ }
+
+ public String[] getSuggestedQueryList(String projectId, String token) throws SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, token);
+ return searchService.getSuggestedQueryList(model);
+ }
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
index 0b0d3f1137ae9570e1aa2b87ab4151587b215eeb..4bc6766e04aedad0718514f325159aaa875a89d7 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java
@@ -35,7 +35,6 @@ import lcsb.mapviewer.services.search.layout.FullLayoutReactionView;
import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
@Transactional(value = "txManager")
@@ -58,8 +57,7 @@ public class OverlayRestImpl extends BaseRestImpl {
public List<LayoutView> getOverlayList(String token, String projectId, String creatorLogin, String publicOverlay)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
return new ArrayList<>();
}
@@ -97,13 +95,12 @@ public class OverlayRestImpl extends BaseRestImpl {
public List<Map<String, Object>> getOverlayElements(String token, String projectId, int overlayId, String columns)
throws QueryException, SecurityException {
List<Map<String, Object>> result = new ArrayList<>();
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
- List<LightLayoutAliasView> speciesList = layoutService.getAliasesForLayout(model, overlayId, authenticationToken);
+ List<LightLayoutAliasView> speciesList = layoutService.getAliasesForLayout(model, overlayId, token);
for (LightLayoutAliasView lightLayoutAliasView : speciesList) {
Map<String, Object> element = new HashMap<>();
element.put("type", ElementIdentifierType.ALIAS);
@@ -111,8 +108,7 @@ public class OverlayRestImpl extends BaseRestImpl {
result.add(element);
}
- List<LightLayoutReactionView> reactions = layoutService.getReactionsForLayout(model, overlayId,
- authenticationToken);
+ List<LightLayoutReactionView> reactions = layoutService.getReactionsForLayout(model, overlayId, token);
for (LightLayoutReactionView lightReactionView : reactions) {
Map<String, Object> element = new HashMap<>();
element.put("type", ElementIdentifierType.REACTION);
@@ -124,24 +120,22 @@ public class OverlayRestImpl extends BaseRestImpl {
public LayoutView getOverlayById(String token, String projectId, String overlayId)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
- return layoutService.getLayoutById(Integer.valueOf(overlayId), authenticationToken);
+ return layoutService.getLayoutById(Integer.valueOf(overlayId), token);
}
public FileEntry getOverlaySource(String token, String projectId, String overlayId)
throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
try {
Integer id = Integer.valueOf(overlayId);
- Layout layout = layoutService.getLayoutDataById(id, authenticationToken);
+ Layout layout = layoutService.getLayoutDataById(id, token);
if (layout == null) {
throw new QueryException("Invalid overlay id");
}
@@ -155,17 +149,16 @@ public class OverlayRestImpl extends BaseRestImpl {
public LayoutView updateOverlay(String token, String projectId, String overlayId, Map<String, Object> overlayData)
throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
if (overlayData == null) {
throw new QueryException("overlay field cannot be undefined");
}
try {
Integer id = Integer.valueOf(overlayId);
- Layout layout = layoutService.getLayoutDataById(id, authenticationToken);
+ Layout layout = layoutService.getLayoutDataById(id, token);
if (layout == null) {
throw new ObjectNotFoundException("overlay doesn't exist");
}
- boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.LAYOUT_MANAGEMENT,
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.LAYOUT_MANAGEMENT,
layout.getModel().getProject());
if (layout.isPublicLayout() && !isAdmin) {
throw new SecurityException("You cannot modify given overlay");
@@ -191,7 +184,7 @@ public class OverlayRestImpl extends BaseRestImpl {
}
}
layoutDao.update(layout);
- return layoutService.getLayoutById(Integer.valueOf(overlayId), authenticationToken);
+ return layoutService.getLayoutById(Integer.valueOf(overlayId), token);
} catch (NumberFormatException e) {
throw new ObjectNotFoundException("overlay doesn't exist");
}
@@ -207,18 +200,17 @@ public class OverlayRestImpl extends BaseRestImpl {
public Map<String, Object> removeOverlay(String token, String projectId, String overlayId)
throws QueryException, SecurityException, IOException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new ObjectNotFoundException("Project with given id doesn't exist");
}
try {
Integer id = Integer.valueOf(overlayId);
- LayoutView layout = layoutService.getLayoutById(id, authenticationToken);
+ LayoutView layout = layoutService.getLayoutById(id, token);
if (layout == null) {
throw new ObjectNotFoundException("Overlay doesn't exist");
}
- if (layoutService.userCanRemoveLayout(layout, authenticationToken)) {
+ if (layoutService.userCanRemoveLayout(layout, token)) {
layoutService.removeLayout(layout, null);
return okStatus();
} else {
@@ -248,12 +240,11 @@ public class OverlayRestImpl extends BaseRestImpl {
public LayoutView addOverlay(String token, String projectId, String name, String description, String content,
String fileId, String filename, String type) throws SecurityException, QueryException, IOException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
User user = getUserService().getUserByToken(token);
if (Configuration.ANONYMOUS_LOGIN.equals(user.getLogin())) {
throw new SecurityException("You have no privileges to add overlay");
}
- Model model = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model model = getModelService().getLastModelByProjectId(projectId, token);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -292,7 +283,7 @@ public class OverlayRestImpl extends BaseRestImpl {
LayoutView layout = layoutService.createLayout(new CreateLayoutParams().async(false).colorInputStream(stream)
.description(description).layoutFileName(filename).model(model).name(name).user(user)
.colorSchemaType(colorSchemaType).directory("."));
- return layoutService.getLayoutById(Integer.valueOf(layout.getIdObject()), authenticationToken);
+ return layoutService.getLayoutById(Integer.valueOf(layout.getIdObject()), token);
} catch (InvalidColorSchemaException e) {
throw new QueryException(e.getMessage(), e);
}
@@ -301,9 +292,7 @@ public class OverlayRestImpl extends BaseRestImpl {
public Map<String, Object> getOverlayElement(String token, String projectId, Integer modelId, Integer overlayId,
Integer elementId, String elementType, String columns) throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
-
- Model topModel = getModelService().getLastModelByProjectId(projectId, authenticationToken);
+ Model topModel = getModelService().getLastModelByProjectId(projectId, token);
if (topModel == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -311,14 +300,13 @@ public class OverlayRestImpl extends BaseRestImpl {
Map<String, Object> result = new HashMap<>();
if (ElementIdentifierType.ALIAS.getJsName().equals(elementType)) {
- FullLayoutAliasView layoutAliasView = layoutService.getFullAliasForLayout(model, elementId, overlayId,
- authenticationToken);
+ FullLayoutAliasView layoutAliasView = layoutService.getFullAliasForLayout(model, elementId, overlayId, token);
result.put("type", ElementIdentifierType.ALIAS);
result.put("overlayContent", layoutAliasView);
return result;
} else if (ElementIdentifierType.REACTION.getJsName().equals(elementType)) {
FullLayoutReactionView layoutAliasView = layoutService.getFullReactionForLayout(model, elementId, overlayId,
- authenticationToken);
+ token);
result.put("type", ElementIdentifierType.REACTION);
result.put("overlayContent", layoutAliasView);
return result;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
index 508fa68941203ef756725bd3ee94aaad53328d9a..4312f60b41c64c6d0fb56574f46b35f43e9a38ca 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserController.java
@@ -15,6 +15,7 @@ import org.springframework.http.MediaType;
import org.springframework.security.authentication.AuthenticationProvider;
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
import org.springframework.security.core.Authentication;
+import org.springframework.security.core.AuthenticationException;
import org.springframework.security.core.context.SecurityContextHolder;
import org.springframework.security.core.session.SessionRegistry;
import org.springframework.security.web.authentication.WebAuthenticationDetails;
@@ -37,7 +38,6 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@RestController
public class UserController extends BaseController {
@@ -56,9 +56,6 @@ public class UserController extends BaseController {
@Autowired
private AuthenticationProvider authenticationProvider;
- @Autowired
- private SessionRegistry sessionRegistry;
-
@RequestMapping(value = "/doLogin", method = { RequestMethod.GET, RequestMethod.POST }, produces = {
MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> login(//
@@ -67,20 +64,20 @@ public class UserController extends BaseController {
HttpServletResponse response, //
HttpServletRequest request//
) throws SecurityException, IOException {
- AuthenticationToken token = userService.login(login, password, request.getSession().getId());
- if (token == null) {
- throw new SecurityException("Invalid credentials");
- } else {
+ try {
UsernamePasswordAuthenticationToken springToken = new UsernamePasswordAuthenticationToken(login, password);
springToken.setDetails(new WebAuthenticationDetails(request));
Authentication authentication = this.authenticationProvider.authenticate(springToken);
SecurityContextHolder.getContext().setAuthentication(authentication);
- sessionRegistry.registerNewSession(request.getSession().getId(), authentication.getPrincipal());
-
+
+ userService.login(login, password, request.getSession().getId());
+
Map<String, Object> result = new HashMap<>();
result.put("info", "Login successful. TOKEN returned as a cookie");
return result;
+ } catch (AuthenticationException e) {
+ throw new SecurityException("Invalid credentials");
}
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 4b60023f4fce4065c34ad9a81b954bfbda639f80..5044560529757522224586fa0e534709a195bfec 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -30,7 +30,6 @@ import lcsb.mapviewer.model.user.UserClassValidAnnotations;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ConfigurationView;
@Transactional(value = "txManager")
@@ -137,25 +136,26 @@ public class UserRestImpl extends BaseRestImpl {
result.put("annotators-parameters", prepareAnnotatorsParams(schema.getAnnotatorsParams()));
return result;
}
-
+
/**
- * Prepares annotator parameters in the form of a map having annotators
- * class names as keys and map of name:value pairs of given annotator as values.
+ * Prepares annotator parameters in the form of a map having annotators class
+ * names as keys and map of name:value pairs of given annotator as values.
+ *
* @param annotatorsParams
* @return
*/
private Map<String, Object> prepareAnnotatorsParams(List<UserAnnotatorsParam> annotatorsParams) {
- Map<String, Object> result = new HashMap<>();
- for (UserAnnotatorsParam param : annotatorsParams) {
- String className = param.getAnnotatorClassName().getName();
- Map<String, String> annotatorParams = (Map<String, String>)result.get(className);
- if (annotatorParams == null) {
- annotatorParams = new HashMap<>();
- result.put(className, annotatorParams);
- }
- annotatorParams.put(param.getParamName(), param.getParamValue());
- }
- return result;
+ Map<String, Object> result = new HashMap<>();
+ for (UserAnnotatorsParam param : annotatorsParams) {
+ String className = param.getAnnotatorClassName().getName();
+ Map<String, String> annotatorParams = (Map<String, String>) result.get(className);
+ if (annotatorParams == null) {
+ annotatorParams = new HashMap<>();
+ result.put(className, annotatorParams);
+ }
+ annotatorParams.put(param.getParamName(), param.getParamValue());
+ }
+ return result;
}
private Map<String, Object> prepareValidAnnotations(List<UserClassValidAnnotations> classValidAnnotators) {
@@ -185,20 +185,20 @@ public class UserRestImpl extends BaseRestImpl {
}
}
}
-
- private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
- for (String annotatorClassname : data.keySet()) {
- Map<String, Object> nameValueS = (Map<String, Object>)data.get(annotatorClassname);
- for (String name: nameValueS.keySet()) {
- String value = (String)nameValueS.get(name);
- try {
- UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), name, value);
- schema.addAnnotatorParam(param);
- } catch (ClassNotFoundException e) {
- throw new QueryException("Unknown annotator class name: " + annotatorClassname);
- }
- }
- }
+
+ private void updateAnnotatorsParams(UserAnnotationSchema schema, Map<String, Object> data) throws QueryException {
+ for (String annotatorClassname : data.keySet()) {
+ Map<String, Object> nameValueS = (Map<String, Object>) data.get(annotatorClassname);
+ for (String name : nameValueS.keySet()) {
+ String value = (String) nameValueS.get(name);
+ try {
+ UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), name, value);
+ schema.addAnnotatorParam(param);
+ } catch (ClassNotFoundException e) {
+ throw new QueryException("Unknown annotator class name: " + annotatorClassname);
+ }
+ }
+ }
}
private Map<String, Object> prepareRequiredAnnotations(List<UserClassRequiredAnnotations> classRequiredAnnotators) {
@@ -368,14 +368,13 @@ public class UserRestImpl extends BaseRestImpl {
}
public List<Map<String, Object>> getUsers(String token, String columns) throws SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
User ownUserData = getUserService().getUserByToken(token);
boolean isAdmin = getUserService().userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
Set<String> columnSet = createUserColumnSet(columns);
List<Map<String, Object>> result = new ArrayList<>();
- for (User user : getUserService().getUsers(authenticationToken)) {
+ for (User user : getUserService().getUsers(token)) {
result.add(prepareUse(user, columnSet, isAdmin));
}
return result;
@@ -387,7 +386,6 @@ public class UserRestImpl extends BaseRestImpl {
throw new QueryException("Privileges not defined");
}
try {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
User modifiedUser = getUserService().getUserByLogin(login);
for (String key : privilegesData.keySet()) {
@@ -396,7 +394,7 @@ public class UserRestImpl extends BaseRestImpl {
PrivilegeType type = PrivilegeType.valueOf(key);
if (type.getPrivilegeClassType().equals(BasicPrivilege.class)) {
- getUserService().setUserPrivilege(modifiedUser, type, value, authenticationToken);
+ getUserService().setUserPrivilege(modifiedUser, type, value, token);
} else if (type.getPrivilegeClassType().equals(ObjectPrivilege.class)) {
if (value instanceof Map) {
Map<?, ?> objects = (Map<?, ?>) value;
@@ -405,8 +403,7 @@ public class UserRestImpl extends BaseRestImpl {
if (!objectId.equals("null")) {
objectIdAsInteger = Integer.valueOf((String) objectId);
}
- getUserService().setUserPrivilege(modifiedUser, type, objects.get(objectId), objectIdAsInteger,
- authenticationToken);
+ getUserService().setUserPrivilege(modifiedUser, type, objects.get(objectId), objectIdAsInteger, token);
}
} else {
throw new QueryException("Invalid value for privilege: " + key);
@@ -428,7 +425,6 @@ public class UserRestImpl extends BaseRestImpl {
throw new QueryException("Preferences not defined");
}
try {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
User modifiedUser = getUserService().getUserByLogin(login);
if (modifiedUser == null) {
throw new ObjectNotFoundException("User doesn't exist");
@@ -438,7 +434,7 @@ public class UserRestImpl extends BaseRestImpl {
for (String key : preferencesData.keySet()) {
Map<String, Object> value = (Map<String, Object>) preferencesData.get(key);
-
+
if (key.equals("project-upload")) {
updateUploadPreferences(schema, value);
} else if (key.equals("element-annotators")) {
@@ -447,14 +443,14 @@ public class UserRestImpl extends BaseRestImpl {
updateRequiredAnnotations(schema, value);
} else if (key.equals("element-valid-annotations")) {
updateValidAnnotations(schema, value);
- } else if (key.equals("annotators-parameters")) {
- updateAnnotatorsParams(schema, value);
+ } else if (key.equals("annotators-parameters")) {
+ updateAnnotatorsParams(schema, value);
} else {
throw new QueryException("Unknown preferences field: " + key);
}
}
modifiedUser.setAnnotationSchema(schema);
- getUserService().updateUser(modifiedUser, authenticationToken);
+ getUserService().updateUser(modifiedUser, token);
return getUser(token, login, "");
} catch (IllegalArgumentException e) {
throw new QueryException("Invalid input", e);
@@ -487,7 +483,6 @@ public class UserRestImpl extends BaseRestImpl {
public Map<String, Object> updateUser(String token, String login, Map<String, Object> userData)
throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
if (userData == null) {
throw new QueryException("user field cannot be undefined");
}
@@ -495,7 +490,7 @@ public class UserRestImpl extends BaseRestImpl {
if (user == null) {
throw new ObjectNotFoundException("user doesn't exist");
}
- boolean isAdmin = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.USER_MANAGEMENT);
+ boolean isAdmin = getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
if (!isAdmin && !login.equalsIgnoreCase(getUserService().getUserByToken(token).getLogin())) {
throw new SecurityException("Access denied");
}
@@ -529,8 +524,7 @@ public class UserRestImpl extends BaseRestImpl {
public Map<String, Object> addProject(String token, String login, MultiValueMap<String, Object> userData)
throws QueryException, SecurityException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
- if (!getUserService().userHasPrivilege(authenticationToken, PrivilegeType.USER_MANAGEMENT)) {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
throw new SecurityException("Access denied");
}
@@ -565,9 +559,8 @@ public class UserRestImpl extends BaseRestImpl {
}
public Map<String, Object> removeUser(String token, String login) throws SecurityException, QueryException {
- AuthenticationToken authenticationToken = getUserService().getToken(token);
User user = getUserService().getUserByLogin(login);
- if (!getUserService().userHasPrivilege(authenticationToken, PrivilegeType.USER_MANAGEMENT)) {
+ if (!getUserService().userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
throw new SecurityException("Access denied");
}
if (user == null) {
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
index a8ff54bc1afba24c6823953e5d13fdccd88f1d6e..37c0ec02045d5b2fc12481aa2917a9c2c2acd91b 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/RestTestFunctions.java
@@ -59,15 +59,15 @@ import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.persist.DbUtils;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
@Transactional(value = "txManager")
@Rollback(true)
@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/applicationContext-annotation.xml", //
- "/applicationContext-service.xml", //
- "/applicationContext-rest.xml", //
- "/dataSource.xml", //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-service.xml", //
+ "/applicationContext-rest.xml", //
+ "/test-applicationContext.xml", //
+ "/dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class RestTestFunctions {
@@ -84,15 +84,15 @@ public abstract class RestTestFunctions {
@Autowired
protected DbUtils dbUtils;
- protected AuthenticationToken token;
+ protected String token;
- protected AuthenticationToken adminToken;
+ protected String adminToken;
@Before
public void generalSetUp() {
dbUtils.setAutoFlush(false);
- token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
+ token = userService.login(Configuration.ANONYMOUS_LOGIN, "");
// assume that we have admin account with all the privileges
adminToken = userService.login("admin", "admin");
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
index fe90900409938f0ecef9997959c126b825a84572..61a8f65f47bf0fd421af0af04528eb385eb7672f 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/configuration/ConfigurationRestImplTest.java
@@ -22,98 +22,98 @@ import lcsb.mapviewer.services.view.ConfigurationView;
public class ConfigurationRestImplTest extends RestTestFunctions {
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ConfigurationRestImplTest.class);
-
- @Autowired
- public ConfigurationRestImpl configurationRestImpl;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetAllParams() throws Exception {
- try {
- List<ConfigurationView> list = configurationRestImpl.getAllValues(token.getId());
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testImageFormats() throws Exception {
- try {
- List<Map<String, Object>> list = configurationRestImpl.getImageFormats(token.getId());
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testModelFormats() throws Exception {
- try {
- List<Map<String, Object>> list = configurationRestImpl.getModelFormats(token.getId());
- assertTrue(list.size() > 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetElementTypes() throws Exception {
- try {
- Set<Map<String, String>> list = configurationRestImpl.getElementTypes(token.getId());
- GenericProtein protein = new GenericProtein("id");
- boolean contains = false;
- for (Map<String, String> object : list) {
- contains |= (object.get("name").equals(protein.getStringType()));
- }
- assertTrue(contains);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetReactionTypes() throws Exception {
- try {
- Set<Map<String, String>> list = configurationRestImpl.getReactionTypes(token.getId());
- StateTransitionReaction reaction = new StateTransitionReaction();
- boolean contains = false;
- for (Map<String, String> object : list) {
- contains |= (object.get("name").equals(reaction.getStringType()));
- }
- assertTrue(contains);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetMiriamTypes() throws Exception {
- try {
- Map<?, ?> list = configurationRestImpl.getMiriamTypes(token.getId());
- assertNotNull(list.get(MiriamType.PUBMED.name()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ConfigurationRestImplTest.class);
+
+ @Autowired
+ public ConfigurationRestImpl configurationRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetAllParams() throws Exception {
+ try {
+ List<ConfigurationView> list = configurationRestImpl.getAllValues(token);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testImageFormats() throws Exception {
+ try {
+ List<Map<String, Object>> list = configurationRestImpl.getImageFormats(token);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModelFormats() throws Exception {
+ try {
+ List<Map<String, Object>> list = configurationRestImpl.getModelFormats(token);
+ assertTrue(list.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetElementTypes() throws Exception {
+ try {
+ Set<Map<String, String>> list = configurationRestImpl.getElementTypes(token);
+ GenericProtein protein = new GenericProtein("id");
+ boolean contains = false;
+ for (Map<String, String> object : list) {
+ contains |= (object.get("name").equals(protein.getStringType()));
+ }
+ assertTrue(contains);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetReactionTypes() throws Exception {
+ try {
+ Set<Map<String, String>> list = configurationRestImpl.getReactionTypes(token);
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ boolean contains = false;
+ for (Map<String, String> object : list) {
+ contains |= (object.get("name").equals(reaction.getStringType()));
+ }
+ assertTrue(contains);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetMiriamTypes() throws Exception {
+ try {
+ Map<?, ?> list = configurationRestImpl.getMiriamTypes(token);
+ assertNotNull(list.get(MiriamType.PUBMED.name()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
index 69ef990fdfc1f6cef0698f94e0b37d4e38a48de1..28ad0cf7b0e155f53bd693234641bb23d2ddaca1 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/files/FileRestImplTest.java
@@ -24,12 +24,12 @@ public class FileRestImplTest extends RestTestFunctions {
@Test(expected = lcsb.mapviewer.services.SecurityException.class)
public void testCreateFileWithoutPrivilege() throws Exception {
- fileRestImpl.createFile(token.getId(), "test.txt", "100");
+ fileRestImpl.createFile(token, "test.txt", "100");
}
@Test
public void testCreateFile() throws Exception {
- Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ Map<String, Object> result = fileRestImpl.createFile(adminToken, "test.txt", "100");
assertNotNull(result);
int id = (Integer) result.get("id");
UploadedFileEntry file = uploadedFileEntryDao.getById(id);
@@ -44,16 +44,16 @@ public class FileRestImplTest extends RestTestFunctions {
byte[] dataChunk = new byte[] { 105, 103 };
byte[] dataChunk2 = new byte[] { 32, 73 };
byte[] dataChunkMerged = ArrayUtils.addAll(dataChunk, dataChunk2);
- Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ Map<String, Object> result = fileRestImpl.createFile(adminToken, "test.txt", "100");
int id = (Integer) result.get("id");
- fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk);
+ fileRestImpl.uploadContent(adminToken, id + "", dataChunk);
UploadedFileEntry file = uploadedFileEntryDao.getById(id);
assertEquals(100, file.getLength());
assertEquals(2, file.getFileContent().length);
assertArrayEquals(dataChunk, file.getFileContent());
- fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk2);
+ fileRestImpl.uploadContent(adminToken, id + "", dataChunk2);
assertEquals(100, file.getLength());
assertEquals(4, file.getFileContent().length);
@@ -65,11 +65,11 @@ public class FileRestImplTest extends RestTestFunctions {
@Test
public void testUploadInvalidContent() throws Exception {
byte[] dataChunk = new byte[100];
- Map<String, Object> result = fileRestImpl.createFile(adminToken.getId(), "test.txt", "100");
+ Map<String, Object> result = fileRestImpl.createFile(adminToken, "test.txt", "100");
int id = (Integer) result.get("id");
try {
- fileRestImpl.uploadContent(adminToken.getId(), id + "", dataChunk);
+ fileRestImpl.uploadContent(adminToken, id + "", dataChunk);
} finally {
uploadedFileEntryDao.getById(id);
UploadedFileEntry file = uploadedFileEntryDao.getById(id);
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
index b1a2c84e9b467b750f25e6bcb8390f72e4d38d41..cc820e078009074692d9783239bfe63a569af60a 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/genomics/ReferenceGenomeControllerTest.java
@@ -14,47 +14,47 @@ import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.RestTestFunctions;
public class ReferenceGenomeControllerTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(ReferenceGenomeControllerTest.class);
-
- @Autowired
- public ReferenceGenomeRestImpl referenceGenomeRestImpl;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetForNonExistingType() throws Exception {
- try {
- referenceGenomeRestImpl.getReferenceGenome(token.getId(), "9606", "type", "ver");
- fail("Exception expected");
- } catch (QueryException e2) {
- assertTrue(e2.getMessage().contains("Cannot find type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetForNonExistingOrganism() throws Exception {
- try {
- referenceGenomeRestImpl.getReferenceGenome(token.getId(), "960000", "UCSC", "ver");
- fail("Exception expected");
- } catch (QueryException e2) {
- assertTrue(e2.getMessage().contains("Cannot find requested reference genome"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ReferenceGenomeControllerTest.class);
+
+ @Autowired
+ public ReferenceGenomeRestImpl referenceGenomeRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetForNonExistingType() throws Exception {
+ try {
+ referenceGenomeRestImpl.getReferenceGenome(token, "9606", "type", "ver");
+ fail("Exception expected");
+ } catch (QueryException e2) {
+ assertTrue(e2.getMessage().contains("Cannot find type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetForNonExistingOrganism() throws Exception {
+ try {
+ referenceGenomeRestImpl.getReferenceGenome(token, "960000", "UCSC", "ver");
+ fail("Exception expected");
+ } catch (QueryException e2) {
+ assertTrue(e2.getMessage().contains("Cannot find requested reference genome"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
index 93e6211849e467387830251cf12dac5e0343ed25..dcc0aabb4cac149edc49e3e4fd714c939331b008 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/mesh/MeshRestImplTest.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.mesh;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
import java.util.Map;
@@ -20,9 +21,9 @@ public class MeshRestImplTest extends RestTestFunctions {
@Test
public void test() throws ObjectNotFoundException, AnnotatorException {
- Map<String, Object> result = meshRestImpl.getMesh(token.getId(), "D010300");
+ Map<String, Object> result = meshRestImpl.getMesh(token, "D010300");
assertNotNull(result);
- String name =(String) result.get("name");
+ String name = (String) result.get("name");
assertTrue(name.toLowerCase().contains("parkinson"));
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
index 074b22ed0a0e2d07e93c18b83aa4e126be46b14f..872eec22049face74dd5dd2d78263a4b79e73144 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java
@@ -75,7 +75,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelAsImageForInvalidConverter() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token.getId(), "sample", "0", "", "", "", "", "");
+ projectRest.getModelAsImage(token, "sample", "0", "", "", "", "", "");
fail("Exception expected");
} catch (InvalidArgumentException e) {
} catch (Exception e) {
@@ -88,8 +88,8 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelAsImage() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- FileEntry result = projectRest.getModelAsImage(token.getId(), "sample", "0",
- PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
+ FileEntry result = projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(),
+ "", "", "", "");
assertNotNull(result);
} catch (Exception e) {
e.printStackTrace();
@@ -101,7 +101,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelDataDependencies() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ ProjectMetaData result = projectRest.getProject("sample", token);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
Mockito.verify(projectRest.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
@@ -114,15 +114,14 @@ public class ProjectRestImplTest extends RestTestFunctions {
@Test(expected = ObjectNotFoundException.class)
public void testGetInvalidMetaData() throws Exception {
ProjectRestImpl projectRest = createMockProjectRest(null);
- projectRest.getProject("unknown_model_id", token.getId());
+ projectRest.getProject("unknown_model_id", token);
}
@Test
public void testGetModelAsImage2() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsImage(token.getId(), "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "",
- "");
+ projectRest.getModelAsImage(token, "sample", "0", PdfImageGenerator.class.getCanonicalName(), "", "", "", "");
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -133,7 +132,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelAsFileModel() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "");
+ projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "");
fail("Exception expected");
} catch (QueryException e) {
} catch (Exception e) {
@@ -146,8 +145,8 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelAsFileModel2() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "",
- "", "", "0,0;90,0;90,90;90,0");
+ projectRest.getModelAsModelFile(token, "sample", "0", CellDesignerXmlParser.class.getCanonicalName(), "", "", "",
+ "0,0;90,0;90,90;90,0");
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -158,7 +157,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetModelAsFileModel3() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getModelAsModelFile(token.getId(), "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
+ projectRest.getModelAsModelFile(token, "sample", "0", "", "", "", "", "0,0;90,0;90,90;90,0");
fail("Exception expected");
} catch (QueryException e) {
} catch (Exception e) {
@@ -171,7 +170,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetProject() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ ProjectMetaData result = projectRest.getProject("sample", token);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
} catch (Exception e) {
@@ -194,7 +193,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
data.put("disease", disease);
data.put("projectId", "sample");
data.put("id", "0");
- projectRest.updateProject(adminToken.getId(), "sample", data);
+ projectRest.updateProject(adminToken, "sample", data);
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -224,7 +223,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetProjects() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- List<ProjectMetaData> result = projectRest.getProjects(token.getId());
+ List<ProjectMetaData> result = projectRest.getProjects(token);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
} catch (Exception e) {
@@ -237,7 +236,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetStatistics() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getStatistics("sample", token.getId());
+ Map<String, Object> result = projectRest.getStatistics("sample", token);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
@@ -259,7 +258,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetMetaDataForComplexWithImages() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/complex_model_with_submaps.zip");
- ProjectMetaData result = projectRest.getProject("sample", token.getId());
+ ProjectMetaData result = projectRest.getProject("sample", token);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
} catch (Exception e) {
@@ -331,7 +330,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
public void testGetLogs() throws Exception {
try {
ProjectRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getLogs("sample", "", token.getId(), "0", 10, "id", "asc", "");
+ Map<String, Object> result = projectRest.getLogs("sample", "", token, "0", 10, "id", "asc", "");
assertNotNull(result);
Gson gson = new Gson();
assertNotNull(gson.toJson(result));
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
index 58213ce5c9cff44adc2e93f05a1952bd0fabf389..75b9c48eb49fac8bf7e0760b3af5b8996c97add2 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/comments/CommentRestImplTest.java
@@ -26,68 +26,68 @@ import lcsb.mapviewer.services.interfaces.IProjectService;
public class CommentRestImplTest extends RestTestFunctions {
- @Autowired
- public CommentRestImpl _commentRestImpl;
+ @Autowired
+ public CommentRestImpl _commentRestImpl;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetForNonExisting() throws Exception {
- try {
- _commentRestImpl.getCommentList(token.getId(), "unk", "", "", "", "");
- fail("Exception expected");
- } catch (QueryException e2) {
- assertTrue(e2.getMessage().contains("Project with given id doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testGetForNonExisting() throws Exception {
+ try {
+ _commentRestImpl.getCommentList(token, "unk", "", "", "", "");
+ fail("Exception expected");
+ } catch (QueryException e2) {
+ assertTrue(e2.getMessage().contains("Project with given id doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testGetCommentsDependencies() throws Exception {
- try {
- CommentRestImpl commentRestImpl = createMockProjectRest("testFiles/model/sample.xml");
- commentRestImpl.getCommentList(adminToken.getId(), "sample", "", "", "", "");
- Mockito.verify(commentRestImpl.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testGetCommentsDependencies() throws Exception {
+ try {
+ CommentRestImpl commentRestImpl = createMockProjectRest("testFiles/model/sample.xml");
+ commentRestImpl.getCommentList(adminToken, "sample", "", "", "", "");
+ Mockito.verify(commentRestImpl.getModelService(), times(0)).getLastModelByProjectId(anyString(), any());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private CommentRestImpl createMockProjectRest(String string) throws Exception {
- Model model = null;
- Project project = null;
- String modelName = "";
- if (string != null) {
- project = new Project();
- model = super.getModelForFile(string, true);
- project.addModel(model);
- modelName = model.getName();
- }
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(eq(modelName), any())).thenReturn(model);
- _commentRestImpl.setModelService(mockModelService);
+ private CommentRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = null;
+ Project project = null;
+ String modelName = "";
+ if (string != null) {
+ project = new Project();
+ model = super.getModelForFile(string, true);
+ project.addModel(model);
+ modelName = model.getName();
+ }
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(eq(modelName), any())).thenReturn(model);
+ _commentRestImpl.setModelService(mockModelService);
- IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
- Mockito.when(projectServiceMock.getProjectByProjectId(eq(modelName), any())).thenReturn(project);
- List<Project> projects = new ArrayList<>();
- projects.add(project);
- Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
- _commentRestImpl.setProjectService(projectServiceMock);
+ IProjectService projectServiceMock = Mockito.mock(IProjectService.class);
+ Mockito.when(projectServiceMock.getProjectByProjectId(eq(modelName), any())).thenReturn(project);
+ List<Project> projects = new ArrayList<>();
+ projects.add(project);
+ Mockito.when(projectServiceMock.getAllProjects(any())).thenReturn(projects);
+ _commentRestImpl.setProjectService(projectServiceMock);
- return _commentRestImpl;
- }
+ return _commentRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
index 880479f85b67aba56a6e8497d0967e9453089d1d..89e6026906bae288de75b8592cb26850ce9b6a03 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/drugs/DrugRestImplTest.java
@@ -20,46 +20,46 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
public class DrugRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(DrugRestImplTest.class);
+ Logger logger = Logger.getLogger(DrugRestImplTest.class);
- @Autowired
+ @Autowired
- private DrugRestImpl _drugRestImpl;
+ private DrugRestImpl _drugRestImpl;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- @SuppressWarnings("unchecked")
- public void testGetDrugsByQuery() throws Exception {
- try {
- DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = drugRestImpl.getDrugsByQuery(token.getId(), "sample", "", "nadh").get(0);
- List<Map<String, Object>> references = (List<Map<String, Object>>) result.get("references");
- Map<String, Object> reference = references.get(0);
- assertNotNull(reference.get("type"));
+ @Test
+ @SuppressWarnings("unchecked")
+ public void testGetDrugsByQuery() throws Exception {
+ try {
+ DrugRestImpl drugRestImpl = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = drugRestImpl.getDrugsByQuery(token, "sample", "", "nadh").get(0);
+ List<Map<String, Object>> references = (List<Map<String, Object>>) result.get("references");
+ Map<String, Object> reference = references.get(0);
+ assertNotNull(reference.get("type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private DrugRestImpl createMockProjectRest(String string) throws Exception {
- Model model = super.getModelForFile(string, true);
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _drugRestImpl.setModelService(mockModelService);
- return _drugRestImpl;
- }
+ private DrugRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _drugRestImpl.setModelService(mockModelService);
+ return _drugRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
index fb9da16bb839051db9619b5f3242fe6f008a78d7..25456e10a7a726ce6e63d246472cce55feb8eb41 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/mirnas/MiRnaRestImplTest.java
@@ -22,46 +22,47 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
public class MiRnaRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(MiRnaRestImplTest.class);
+ Logger logger = Logger.getLogger(MiRnaRestImplTest.class);
- @Autowired
- MiRnaRestImpl _miRnaRestImpl;
+ @Autowired
+ MiRnaRestImpl _miRnaRestImpl;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetMiRnasByTarget() throws Exception {
- try {
- MiRnaRestImpl miRnaRestImpl = createMockProjectRest("testFiles/model/mi_rna_target.xml");
- List<Map<String, Object>> result = miRnaRestImpl.getMiRnasByTarget(token.getId(), "mi_rna_target", "ALIAS", "0", "");
- Set<String> names = new HashSet<>();
- for (Map<String, Object> miRna : result) {
- assertFalse("Duplicate miRna found: " + miRna.get("name"), names.contains(miRna.get("name")));
- names.add((String)miRna.get("name"));
- }
+ @Test
+ public void testGetMiRnasByTarget() throws Exception {
+ try {
+ MiRnaRestImpl miRnaRestImpl = createMockProjectRest("testFiles/model/mi_rna_target.xml");
+ List<Map<String, Object>> result = miRnaRestImpl.getMiRnasByTarget(token, "mi_rna_target", "ALIAS", "0",
+ "");
+ Set<String> names = new HashSet<>();
+ for (Map<String, Object> miRna : result) {
+ assertFalse("Duplicate miRna found: " + miRna.get("name"), names.contains(miRna.get("name")));
+ names.add((String) miRna.get("name"));
+ }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private MiRnaRestImpl createMockProjectRest(String string) throws Exception {
- Model model = super.getModelForFile(string, true);
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _miRnaRestImpl.setModelService(mockModelService);
- return _miRnaRestImpl;
- }
+ private MiRnaRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _miRnaRestImpl.setModelService(mockModelService);
+ return _miRnaRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
index 658733631c3cc430d40f9f1f0e4b43ba0539c3ab..0b7b40b3abb5c454973195b69f647d73fab0bcde 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/ModelRestImplTest.java
@@ -8,27 +8,33 @@ import static org.mockito.Matchers.refEq;
import java.util.List;
import org.junit.After;
-import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IProjectService;
public class ModelRestImplTest extends RestTestFunctions {
@Autowired
- ModelRestImpl _projectRestImpl;
+ ModelRestImpl _modelRestImpl;
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @Autowired
+ IModelService modelService;
+
+ @Autowired
+ IProjectService projectService;
@Before
public void setUp() throws Exception {
+ _modelRestImpl.setModelService(modelService);
+ _modelRestImpl.setProjectService(projectService);
}
@After
@@ -39,19 +45,19 @@ public class ModelRestImplTest extends RestTestFunctions {
public void testModels() throws Exception {
try {
ModelRestImpl modelRest = createMockProjectRest("testFiles/model/sample.xml");
- List<ModelMetaData> result = modelRest.getModels("sample", token.getId());
+ List<ModelMetaData> result = modelRest.getModels("sample", token);
assertEquals(1, result.size());
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
-
+
@Test
public void testGetEmptyModels() throws Exception {
try {
ModelRestImpl modelRest = createEmptyProjectRest("test");
- List<ModelMetaData> result = modelRest.getModels("test", token.getId());
+ List<ModelMetaData> result = modelRest.getModels("test", token);
assertEquals(0, result.size());
} catch (Exception e) {
e.printStackTrace();
@@ -59,19 +65,24 @@ public class ModelRestImplTest extends RestTestFunctions {
}
}
- private ModelRestImpl createEmptyProjectRest(String string) {
+ private ModelRestImpl createEmptyProjectRest(String string) throws Exception {
IModelService mockModelService = Mockito.mock(IModelService.class);
Mockito.when(mockModelService.getLastModelByProjectId(refEq(string), any())).thenReturn(null);
- _projectRestImpl.setModelService(mockModelService);
- return _projectRestImpl;
+
+ IProjectService mockProjectService = Mockito.mock(IProjectService.class);
+ Mockito.when(mockProjectService.getProjectByProjectId(refEq(string), any())).thenReturn(new Project());
+
+ _modelRestImpl.setModelService(mockModelService);
+ _modelRestImpl.setProjectService(mockProjectService);
+ return _modelRestImpl;
}
private ModelRestImpl createMockProjectRest(String string) throws Exception {
Model model = super.getModelForFile(string, true);
IModelService mockModelService = Mockito.mock(IModelService.class);
Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _projectRestImpl.setModelService(mockModelService);
- return _projectRestImpl;
+ _modelRestImpl.setModelService(mockModelService);
+ return _modelRestImpl;
}
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
index 50bec236b39243a7a2ca3bfcad34e76447051193..04822ae7148dd5342655ce8bc49f88443a64fa0f 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/BioEntitiesControllerTest.java
@@ -24,47 +24,48 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
public class BioEntitiesControllerTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(BioEntitiesControllerTest.class);
+ Logger logger = Logger.getLogger(BioEntitiesControllerTest.class);
- @Autowired
- BioEntitiesRestImpl _bioEntitiesRestImpl;
+ @Autowired
+ BioEntitiesRestImpl _bioEntitiesRestImpl;
- ObjectMapper mapper = new ObjectMapper();
+ ObjectMapper mapper = new ObjectMapper();
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testGetClosestElementsByCoordinates() throws Exception {
- try {
- BioEntitiesRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- int count = 3;
- List<Map<String, Object>> result = projectRest.getClosestElementsByCoordinates("sample", "0", token.getId(), new Point2D.Double(1, 2), count, "false");
- assertEquals(count, result.size());
-
- String json = mapper.writeValueAsString(result);
- assertNotNull(json);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testGetClosestElementsByCoordinates() throws Exception {
+ try {
+ BioEntitiesRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ int count = 3;
+ List<Map<String, Object>> result = projectRest.getClosestElementsByCoordinates("sample", "0", token,
+ new Point2D.Double(1, 2), count, "false");
+ assertEquals(count, result.size());
- private BioEntitiesRestImpl createMockProjectRest(String string) throws Exception {
- Model model = super.getModelForFile(string, true);
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _bioEntitiesRestImpl.setModelService(mockModelService);
- return _bioEntitiesRestImpl;
- }
+ String json = mapper.writeValueAsString(result);
+ assertNotNull(json);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private BioEntitiesRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _bioEntitiesRestImpl.setModelService(mockModelService);
+ return _bioEntitiesRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
index 5e9ac8b9f8f0e4e1e4a24acb50d8d0e0ba538c7d..a5a06edbcebc117f303da8876033620b17043439 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/bioEntities/elements/ElementRestImplTest.java
@@ -34,165 +34,165 @@ import lcsb.mapviewer.model.map.species.field.RnaRegion;
import lcsb.mapviewer.services.interfaces.IModelService;
public class ElementRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(RestTestFunctions.class);
-
- @Autowired
- ElementsRestImpl _elementsRestImpl;
-
- @Autowired
- PdbAnnotator pdbAnnotator;
-
- ObjectMapper mapper = new ObjectMapper();
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetElementsProcessAllColumns() throws Exception {
- try {
- ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", true);
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
- for (Map<String, Object> element : result) {
- for (String paramName : element.keySet()) {
- Object val = element.get(paramName);
- String paramValue = "";
- if (val != null) {
- paramValue = val.toString();
- }
- assertFalse("Improper handler for column name: " + paramName, paramValue.contains("Unknown column"));
- }
- }
- String json = mapper.writeValueAsString(result);
- assertNotNull(json);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetElementsByType() throws Exception {
- try {
- String proteinType = new GenericProtein("1").getStringType();
- ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", false);
- List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token.getId(), proteinType, "", "");
- assertEquals(12, result.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetElementsVisibility() throws Exception {
- try {
- ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
- List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token.getId(), "", "", "");
- for (Map<String, Object> map : result) {
- assertTrue(map.get("hierarchyVisibilityLevel") instanceof String);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @SuppressWarnings("unchecked")
- @Test
- public void testGetModificationsForProtein() throws Exception {
- try {
- String state = "asd";
- GenericProtein protein = new GenericProtein("s1");
- ModificationResidue mr = new ModificationResidue();
- mr.setState(ModificationState.ACETYLATED);
- mr.setName("S250");
- protein.addModificationResidue(mr);
- protein.setStructuralState(state);
- Map<String, Object> result = _elementsRestImpl.getOthersForElement(protein);
- assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
- List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
- assertEquals(1, modifications.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @SuppressWarnings("unchecked")
- @Test
- public void testGetModificationsForRna() throws Exception {
- try {
- String state = "asd";
- Rna rna = new Rna("s1");
- RnaRegion mr = new RnaRegion();
- mr.setState(ModificationState.ACETYLATED);
- mr.setName("S250");
- rna.addRegion(mr);
- rna.setState(state);
- Map<String, Object> result = _elementsRestImpl.getOthersForElement(rna);
- assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
- List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
- assertEquals(1, modifications.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @SuppressWarnings("unchecked")
- @Test
- public void testGetModificationsForAntisenseRna() throws Exception {
- try {
- String state = "asd";
- AntisenseRna antisenseRna = new AntisenseRna("s1");
- AntisenseRnaRegion mr = new AntisenseRnaRegion();
- mr.setState(ModificationState.ACETYLATED);
- mr.setName("S250");
- antisenseRna.addRegion(mr);
- antisenseRna.setState(state);
- Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
- assertNotNull(result.get("modifications"));
- assertEquals(state, result.get("structuralState"));
- List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
- assertEquals(1, modifications.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private ElementsRestImpl createMockElementRest(String string) throws Exception {
- return createMockElementRest(string, false);
- }
-
- private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
- Model model = super.getModelForFile(string, true);
- if (annotate) {
- try {
- Protein protein = new GenericProtein("SNCA");
- protein.setElementId("SNCA");
- pdbAnnotator.annotateElement(protein);
- model.addElement(protein);
- } catch (Exception e) {
- }
- }
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _elementsRestImpl.setModelService(mockModelService);
- return _elementsRestImpl;
- }
+ Logger logger = Logger.getLogger(RestTestFunctions.class);
+
+ @Autowired
+ ElementsRestImpl _elementsRestImpl;
+
+ @Autowired
+ PdbAnnotator pdbAnnotator;
+
+ ObjectMapper mapper = new ObjectMapper();
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetElementsProcessAllColumns() throws Exception {
+ try {
+ ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", true);
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token, "", "", "");
+ for (Map<String, Object> element : result) {
+ for (String paramName : element.keySet()) {
+ Object val = element.get(paramName);
+ String paramValue = "";
+ if (val != null) {
+ paramValue = val.toString();
+ }
+ assertFalse("Improper handler for column name: " + paramName, paramValue.contains("Unknown column"));
+ }
+ }
+ String json = mapper.writeValueAsString(result);
+ assertNotNull(json);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetElementsByType() throws Exception {
+ try {
+ String proteinType = new GenericProtein("1").getStringType();
+ ElementsRestImpl projectRest = createMockElementRest("testFiles/model/sample.xml", false);
+ List<Map<String, Object>> result = projectRest.getElements("sample", "", "", "*", token, proteinType, "", "");
+ assertEquals(12, result.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetElementsVisibility() throws Exception {
+ try {
+ ElementsRestImpl elementRest = createMockElementRest("testFiles/model/sample.xml");
+ List<Map<String, Object>> result = elementRest.getElements("sample", "", "", "*", token, "", "", "");
+ for (Map<String, Object> map : result) {
+ assertTrue(map.get("hierarchyVisibilityLevel") instanceof String);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testGetModificationsForProtein() throws Exception {
+ try {
+ String state = "asd";
+ GenericProtein protein = new GenericProtein("s1");
+ ModificationResidue mr = new ModificationResidue();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ protein.addModificationResidue(mr);
+ protein.setStructuralState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(protein);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testGetModificationsForRna() throws Exception {
+ try {
+ String state = "asd";
+ Rna rna = new Rna("s1");
+ RnaRegion mr = new RnaRegion();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ rna.addRegion(mr);
+ rna.setState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(rna);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ @Test
+ public void testGetModificationsForAntisenseRna() throws Exception {
+ try {
+ String state = "asd";
+ AntisenseRna antisenseRna = new AntisenseRna("s1");
+ AntisenseRnaRegion mr = new AntisenseRnaRegion();
+ mr.setState(ModificationState.ACETYLATED);
+ mr.setName("S250");
+ antisenseRna.addRegion(mr);
+ antisenseRna.setState(state);
+ Map<String, Object> result = _elementsRestImpl.getOthersForElement(antisenseRna);
+ assertNotNull(result.get("modifications"));
+ assertEquals(state, result.get("structuralState"));
+ List<Map<String, Object>> modifications = (List<Map<String, Object>>) result.get("modifications");
+ assertEquals(1, modifications.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ElementsRestImpl createMockElementRest(String string) throws Exception {
+ return createMockElementRest(string, false);
+ }
+
+ private ElementsRestImpl createMockElementRest(String string, Boolean annotate) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ if (annotate) {
+ try {
+ Protein protein = new GenericProtein("SNCA");
+ protein.setElementId("SNCA");
+ pdbAnnotator.annotateElement(protein);
+ model.addElement(protein);
+ } catch (Exception e) {
+ }
+ }
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _elementsRestImpl.setModelService(mockModelService);
+ return _elementsRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
index 551214008055f3656e88524ddf4c7bf85eb18914..3aee7fc3105936353401d1d021d8e9ae44d8616c 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/projects/models/publications/PublicationsRestImplTest.java
@@ -22,85 +22,85 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.interfaces.IModelService;
public class PublicationsRestImplTest extends RestTestFunctions {
- Logger logger = Logger.getLogger(PublicationsRestImplTest.class);
-
- @Autowired
- PublicationsRestImpl _projectRestImpl;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testPublications() throws Exception {
- try {
- PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getPublications("sample", "*", token.getId(), "0", 20, "", "", "");
- assertEquals(1, result.get("totalSize"));
- assertEquals(0, result.get("start"));
- assertEquals(1, ((List<?>) result.get("data")).size());
-
- result = projectRest.getPublications("sample", "*", token.getId(), "1", 20, "", "", "");
- assertEquals(1, result.get("totalSize"));
- assertEquals(1, result.get("start"));
- assertEquals(0, ((List<?>) result.get("data")).size());
-
- result = projectRest.getPublications("sample", "*", token.getId(), "0", 00, "", "", "");
- assertEquals(1, result.get("totalSize"));
- assertEquals(0, result.get("start"));
- assertEquals(0, ((List<?>) result.get("data")).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPublicationsFiltering() throws Exception {
- try {
- PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- Map<String, Object> result = projectRest.getPublications("sample", "*", token.getId(), "0", 20, "pubmedId", "asc", "123");
- assertEquals(1, result.get("totalSize"));
- assertEquals(0, result.get("start"));
- assertEquals(1, ((List<?>) result.get("data")).size());
-
- result = projectRest.getPublications("sample", "*", token.getId(), "0", 20, "pubmedId", "asc", "1234");
- assertEquals(1, result.get("totalSize"));
- assertEquals(0, result.get("start"));
- assertEquals(0, ((List<?>) result.get("data")).size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPublicationsInvalidSortingFiltering() throws Exception {
- try {
- PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
- projectRest.getPublications("sample", "*", token.getId(), "0", 20, "xxx", "asc", "123");
- fail("Exception expected");
- } catch (QueryException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private PublicationsRestImpl createMockProjectRest(String string) throws Exception {
- Model model = super.getModelForFile(string, true);
- IModelService mockModelService = Mockito.mock(IModelService.class);
- Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
- _projectRestImpl.setModelService(mockModelService);
- return _projectRestImpl;
- }
+ Logger logger = Logger.getLogger(PublicationsRestImplTest.class);
+
+ @Autowired
+ PublicationsRestImpl _projectRestImpl;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testPublications() throws Exception {
+ try {
+ PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getPublications("sample", "*", token, "0", 20, "", "", "");
+ assertEquals(1, result.get("totalSize"));
+ assertEquals(0, result.get("start"));
+ assertEquals(1, ((List<?>) result.get("data")).size());
+
+ result = projectRest.getPublications("sample", "*", token, "1", 20, "", "", "");
+ assertEquals(1, result.get("totalSize"));
+ assertEquals(1, result.get("start"));
+ assertEquals(0, ((List<?>) result.get("data")).size());
+
+ result = projectRest.getPublications("sample", "*", token, "0", 00, "", "", "");
+ assertEquals(1, result.get("totalSize"));
+ assertEquals(0, result.get("start"));
+ assertEquals(0, ((List<?>) result.get("data")).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPublicationsFiltering() throws Exception {
+ try {
+ PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ Map<String, Object> result = projectRest.getPublications("sample", "*", token, "0", 20, "pubmedId", "asc", "123");
+ assertEquals(1, result.get("totalSize"));
+ assertEquals(0, result.get("start"));
+ assertEquals(1, ((List<?>) result.get("data")).size());
+
+ result = projectRest.getPublications("sample", "*", token, "0", 20, "pubmedId", "asc", "1234");
+ assertEquals(1, result.get("totalSize"));
+ assertEquals(0, result.get("start"));
+ assertEquals(0, ((List<?>) result.get("data")).size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPublicationsInvalidSortingFiltering() throws Exception {
+ try {
+ PublicationsRestImpl projectRest = createMockProjectRest("testFiles/model/sample.xml");
+ projectRest.getPublications("sample", "*", token, "0", 20, "xxx", "asc", "123");
+ fail("Exception expected");
+ } catch (QueryException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private PublicationsRestImpl createMockProjectRest(String string) throws Exception {
+ Model model = super.getModelForFile(string, true);
+ IModelService mockModelService = Mockito.mock(IModelService.class);
+ Mockito.when(mockModelService.getLastModelByProjectId(anyString(), any())).thenReturn(model);
+ _projectRestImpl.setModelService(mockModelService);
+ return _projectRestImpl;
+ }
}
diff --git a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
index 07d064945bcb49597c5b02b0f4e7bb11546163e7..dff753719ffc90d4760a1e1b7a5c1a5e31b9fd0d 100644
--- a/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
+++ b/rest-api/src/test/java/lcsb/mapviewer/api/users/UserRestImplTest.java
@@ -46,7 +46,7 @@ public class UserRestImplTest extends RestTestFunctions {
@Test
public void testGetUser() throws Exception {
try {
- Object response = userRestImpl.getUser(token.getId(), Configuration.ANONYMOUS_LOGIN, "");
+ Object response = userRestImpl.getUser(token, Configuration.ANONYMOUS_LOGIN, "");
assertNotNull(response);
} catch (Exception e) {
e.printStackTrace();
@@ -59,12 +59,12 @@ public class UserRestImplTest extends RestTestFunctions {
try {
Map<String, Object> data = new HashMap<>();
data.put(PrivilegeType.ADD_MAP.name(), 1);
- userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
+ userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
assertTrue(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
PrivilegeType.ADD_MAP));
data.put(PrivilegeType.ADD_MAP.name(), 0);
- userRestImpl.updatePrivileges(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, data);
+ userRestImpl.updatePrivileges(adminToken, Configuration.ANONYMOUS_LOGIN, data);
assertFalse(userService.userHasPrivilege(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN),
PrivilegeType.ADD_MAP));
@@ -77,9 +77,8 @@ public class UserRestImplTest extends RestTestFunctions {
@Test
public void testUpdatePreferences() throws Exception {
try {
- Map<String, Object> data = deserialize(
- userRestImpl.getUser(adminToken.getId(), Configuration.ANONYMOUS_LOGIN, ""));
- userRestImpl.updatePreferences(adminToken.getId(), Configuration.ANONYMOUS_LOGIN,
+ Map<String, Object> data = deserialize(userRestImpl.getUser(adminToken, Configuration.ANONYMOUS_LOGIN, ""));
+ userRestImpl.updatePreferences(adminToken, Configuration.ANONYMOUS_LOGIN,
(Map<String, Object>) data.get("preferences"));
} catch (Exception e) {
@@ -99,7 +98,7 @@ public class UserRestImplTest extends RestTestFunctions {
@Test
public void testGetUsers() throws Exception {
try {
- Object response = userRestImpl.getUsers(adminToken.getId(), "");
+ Object response = userRestImpl.getUsers(adminToken, "");
assertNotNull(response);
} catch (Exception e) {
e.printStackTrace();
diff --git a/rest-api/src/test/resources/test-applicationContext.xml b/rest-api/src/test/resources/test-applicationContext.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9bd238746219dfb4bf7a443451209c5d8ecb9116
--- /dev/null
+++ b/rest-api/src/test/resources/test-applicationContext.xml
@@ -0,0 +1,14 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+ <bean id="SessionRegistry" class="org.springframework.security.core.session.SessionRegistryImpl"/>
+
+</beans>
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
index faf8f766ae94a39b5accd4f67f10098b8d555708..1e928dd14e09bad74c4f6dc8786f13c9256af80c 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -25,6 +25,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.CommentDao;
+import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.interfaces.ICommentService;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
@@ -37,7 +38,6 @@ import lcsb.mapviewer.services.search.comment.FullCommentViewFactory;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
import lcsb.mapviewer.services.search.data.ElementIdentifier.ElementIdentifierType;
import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.CommentView;
import lcsb.mapviewer.services.view.CommentViewFactory;
@@ -54,7 +54,7 @@ public class CommentService implements ICommentService {
/**
* Max distance between two points on map for which two comments should be
- * considered as refereing to the same point.
+ * considered as referring to the same point.
*/
private static final double COMMENT_POINT_DISTANCE_EPSILON = 0.02;
@@ -189,7 +189,7 @@ public class CommentService implements ICommentService {
}
@Override
- public List<CommentView> getCommentsByMap(Model model, AuthenticationToken token) throws UserAccessException {
+ public List<CommentView> getCommentsByMap(Model model, String token) throws SecurityException {
boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, model.getProject());
boolean viewProject = userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject());
if (!editComments && !viewProject) {
@@ -409,7 +409,7 @@ public class CommentService implements ICommentService {
}
@Override
- public List<Comment> getCommentsByProject(Project project, AuthenticationToken token) throws UserAccessException {
+ public List<Comment> getCommentsByProject(Project project, String token) throws SecurityException {
boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
boolean viewProject = userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project);
boolean manageProjects = userService.userHasPrivilege(token, PrivilegeType.PROJECT_MANAGEMENT);
@@ -426,10 +426,11 @@ public class CommentService implements ICommentService {
}
@Override
- public void deleteComment(Comment comment, AuthenticationToken token, String reason) throws UserAccessException {
+ public void deleteComment(Comment comment, String token, String reason) throws SecurityException {
Project project = comment.getModelData().getProject();
boolean editComments = userService.userHasPrivilege(token, PrivilegeType.EDIT_COMMENTS_PROJECT, project);
- if (editComments || userService.getUserByToken(token).equals(comment.getUser())) {
+ User user = userService.getUserByToken(token);
+ if (editComments || user.equals(comment.getUser())) {
comment.setDeleted(true);
comment.setRemoveReason(reason);
commentDao.update(comment);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
index 753d7999db145c31b109185974aa7ce94fd95533..85f04b62e41bdb7de6b929aab92502a586d929d2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -68,7 +68,6 @@ import lcsb.mapviewer.services.search.layout.LightLayoutReactionViewFactory;
import lcsb.mapviewer.services.utils.ColorSchemaReader;
import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.data.ColorSchemaColumn;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
import lcsb.mapviewer.services.view.LayoutViewFactory;
@@ -897,7 +896,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public byte[] getInputDataForLayout(LayoutView layoutView, AuthenticationToken token) throws SecurityException {
+ public byte[] getInputDataForLayout(LayoutView layoutView, String token) throws SecurityException {
return getInputDataForLayout(layoutView.getIdObject(), token);
}
@@ -912,7 +911,7 @@ public class LayoutService implements ILayoutService {
* database (compatibility reasons) then null is returned
* @throws SecurityException
*/
- private byte[] getInputDataForLayout(int layoutId, AuthenticationToken token) throws SecurityException {
+ private byte[] getInputDataForLayout(int layoutId, String token) throws SecurityException {
Layout layout = getLayoutDataById(layoutId, token);
if (layout == null) {
return null;
@@ -926,7 +925,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, AuthenticationToken token)
+ public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, String token)
throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
@@ -950,7 +949,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, AuthenticationToken token)
+ public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, String token)
throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
@@ -974,7 +973,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, AuthenticationToken token)
+ public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token)
throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
@@ -993,7 +992,7 @@ public class LayoutService implements ILayoutService {
@Override
public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers,
- int layoutId, AuthenticationToken token) throws SecurityException {
+ int layoutId, String token) throws SecurityException {
try {
Set<Integer> ids = new HashSet<>();
for (Pair<Integer, Integer> pair : identifiers) {
@@ -1043,7 +1042,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public LayoutView getLayoutById(int overlayId, AuthenticationToken token) throws SecurityException {
+ public LayoutView getLayoutById(int overlayId, String token) throws SecurityException {
Layout layout = getLayoutDataById(overlayId, token);
if (layout == null) {
return null;
@@ -1052,7 +1051,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public Layout getLayoutDataById(int overlayId, AuthenticationToken token) throws SecurityException {
+ public Layout getLayoutDataById(int overlayId, String token) throws SecurityException {
Layout layout = layoutDao.getById(overlayId);
if (layout == null) {
return null;
@@ -1065,7 +1064,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, AuthenticationToken token)
+ public FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
@@ -1093,8 +1092,8 @@ public class LayoutService implements ILayoutService {
}
@Override
- public FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId,
- AuthenticationToken token) throws SecurityException {
+ public FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas;
@@ -1121,7 +1120,7 @@ public class LayoutService implements ILayoutService {
}
@Override
- public boolean userCanRemoveLayout(LayoutView layout, AuthenticationToken authenticationToken) {
+ public boolean userCanRemoveLayout(LayoutView layout, String authenticationToken) throws SecurityException {
User user = userService.getUserByToken(authenticationToken);
return userCanRemoveLayout(layout, user);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index d3634f6b8db02c1ef0494eb7d8ee3187ed9d9e1c..9f8111197fd2cd33ea13978d6f9c2592cb258bd4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -41,7 +41,6 @@ import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
import lcsb.mapviewer.services.view.ModelView;
import lcsb.mapviewer.services.view.ModelViewFactory;
@@ -123,7 +122,7 @@ public class ModelService implements IModelService {
private TaxonomyBackend taxonomyBackend;
@Override
- public Model getLastModelByProjectId(String projectName, AuthenticationToken token) {
+ public Model getLastModelByProjectId(String projectName, String token) throws lcsb.mapviewer.services.SecurityException {
if (projectName == null) {
return null;
}
@@ -561,7 +560,7 @@ public class ModelService implements IModelService {
}
@Override
- public void updateModel(ModelData model, AuthenticationToken token) {
+ public void updateModel(ModelData model, String token) throws lcsb.mapviewer.services.SecurityException {
Model topCachedData = getLastModelByProjectId(model.getProject().getProjectId(), token);
Model cachedData = topCachedData.getSubmodelById(model.getId());
cachedData.setDefaultCenterX(model.getDefaultCenterX());
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 4e1cb28e8895f1d23f26ea4d39cace0a6aace908..a6713e8be40dbf351ce845634fe18fc958ca44f8 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -106,7 +106,6 @@ import lcsb.mapviewer.services.utils.CreateProjectParams;
import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.InvalidDataMiningInputFile;
import lcsb.mapviewer.services.utils.data.BuildInLayout;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ProjectView;
import lcsb.mapviewer.services.view.ProjectViewFactory;
@@ -265,7 +264,7 @@ public class ProjectService implements IProjectService {
private MapGenerator generator = new MapGenerator();
@Override
- public Project getProjectByProjectId(String name, AuthenticationToken token) throws UserAccessException {
+ public Project getProjectByProjectId(String name, String token) throws SecurityException {
Project result = projectDao.getProjectByProjectId(name);
if (result == null) {
return result;
@@ -287,7 +286,7 @@ public class ProjectService implements IProjectService {
}
@Override
- public List<Project> getAllProjects(AuthenticationToken token) {
+ public List<Project> getAllProjects(String token) throws SecurityException {
List<Project> projects = projectDao.getAll();
if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
return projects;
@@ -302,7 +301,7 @@ public class ProjectService implements IProjectService {
}
@Override
- public List<ProjectView> getAllProjectViews(AuthenticationToken token) {
+ public List<ProjectView> getAllProjectViews(String token) throws SecurityException {
List<ProjectView> result = new ArrayList<>();
List<Project> projects = getAllProjects(token);
for (Project project : projects) {
@@ -359,8 +358,8 @@ public class ProjectService implements IProjectService {
}
@Override
- public void removeProject(ProjectView selectedProject, String homeDir, boolean async, AuthenticationToken token)
- throws UserAccessException {
+ public void removeProject(ProjectView selectedProject, String homeDir, boolean async, String token)
+ throws SecurityException {
Project project = projectDao.getById(selectedProject.getIdObject());
removeProject(project, homeDir, async, token);
}
@@ -381,14 +380,14 @@ public class ProjectService implements IProjectService {
}
@Override
- public ProjectView getProjectViewByProjectId(String name, AuthenticationToken token) throws UserAccessException {
+ public ProjectView getProjectViewByProjectId(String name, String token) throws SecurityException {
Project project = getProjectByProjectId(name, token);
return projectViewFactory.create(project);
}
@Override
- public void removeProject(final Project p, final String dir, final boolean async, AuthenticationToken token)
- throws UserAccessException {
+ public void removeProject(final Project p, final String dir, final boolean async, String token)
+ throws SecurityException {
if (!userService.userHasPrivilege(userService.getUserByToken(token), PrivilegeType.PROJECT_MANAGEMENT)) {
throw new UserAccessException("User cannot remove project");
}
@@ -497,17 +496,17 @@ public class ProjectService implements IProjectService {
/**
* When we encountered hibernate exception we need to handle error reporting
* differently (hibernate session is broken). This method handles such case when
- * hibernate excedption occured when removing project.
+ * hibernate exception occurred when removing project.
*
* @param originalProject
- * project that was beining removed
+ * project that was being removed
* @param exception
* hibernate exception that caused problems
*/
protected void handleHibernateExceptionRemovingReporting(Project originalProject, HibernateException exception,
- AuthenticationToken token) {
+ String token) {
// we need to open separate thread because current one thrown db exception
- // and transaction is corrupetd and will be rolledback
+ // and transaction is corrupted and will be rolledback
Thread reportInSeparateThread = new Thread(new Runnable() {
@Override
@@ -522,7 +521,7 @@ public class ProjectService implements IProjectService {
project.setErrors(errorMessage + "\n" + project.getErrors());
project.setStatus(ProjectStatus.FAIL);
projectDao.update(project);
- } catch (UserAccessException e) {
+ } catch (SecurityException e) {
logger.error(e, e);
} finally {
dbUtils.closeSessionForCurrentThread();
@@ -540,7 +539,7 @@ public class ProjectService implements IProjectService {
}
@Override
- public ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException {
+ public ProjectView getProjectViewById(Integer id, String token) throws SecurityException {
Project project = projectDao.getById(id);
if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, project)) {
return projectViewFactory.create(project);
@@ -1529,11 +1528,11 @@ public class ProjectService implements IProjectService {
* @param params
* parameters used to create project
* @param e
- * exception that occured during uploading of the project
+ * exception that occurred during uploading of the project
*/
private void handleHibernateExceptionReporting(CreateProjectParams params, HibernateException e) {
// we need to open separate thread because current one thrown db exception
- // and transaction is corrupetd and will be rolledback
+ // and transaction is corrupted and will be rolledback
Thread reportInSeparateThread = new Thread(new Runnable() {
@Override
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
index 13fd8dc9e217d4ae68f0955a58cec0e3700af48b..07fc7be059671037a6e84c5f560d07f9e1fe8bf7 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ReferenceGenomeService.java
@@ -21,7 +21,6 @@ import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
import lcsb.mapviewer.persist.dao.map.layout.ReferenceGenomeDao;
import lcsb.mapviewer.services.interfaces.IReferenceGenomeService;
import lcsb.mapviewer.services.utils.ReferenceGenomeExistsException;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ReferenceGenomeView;
import lcsb.mapviewer.services.view.ReferenceGenomeViewFactory;
@@ -34,123 +33,128 @@ import lcsb.mapviewer.services.view.ReferenceGenomeViewFactory;
@Transactional(value = "txManager")
public class ReferenceGenomeService implements IReferenceGenomeService {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReferenceGenomeService.class);
-
- /**
- * Class responsible for connection to {@link ReferenceGenomeType#UCSC}
- * database.
- */
- @Autowired
- private UcscReferenceGenomeConnector ucscReferenceGenomeConnector;
-
- /**
- * Data access object for {@link ReferenceGenome} objects.
- */
- @Autowired
- private ReferenceGenomeDao referenceGenomeDao;
-
- /**
- * Factory that creates {@link ReferenceGenomeView}.
- */
- @Autowired
- private ReferenceGenomeViewFactory factory;
-
- @Override
- public void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- for (ReferenceGenome genome : getDownloadedGenomes()) {
- if (genome.getType().equals(type) && genome.getOrganism().equals(organism) && genome.getVersion().equals(version)) {
- throw new ReferenceGenomeExistsException("Selected reference genome already downloaded");
- }
- }
- getReferenceGenomeConnector(type).downloadGenomeVersion(organism, version, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, customUrl);
- }
-
- /**
- * Return {@link ReferenceGenomeConnector} implementation for given reference
- * genome type.
- *
- * @param type
- * type of reference genome
- * @return {@link ReferenceGenomeConnector} implementation for given reference
- * genome type
- */
- private ReferenceGenomeConnector getReferenceGenomeConnector(ReferenceGenomeType type) {
- if (type == ReferenceGenomeType.UCSC) {
- return ucscReferenceGenomeConnector;
- } else {
- throw new InvalidArgumentException("Unknown reference genome type: " + type);
- }
- }
-
- @Override
- public List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException {
- return getReferenceGenomeConnector(type).getAvailableOrganisms();
- }
-
- @Override
- public List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism) throws ReferenceGenomeConnectorException {
- return getReferenceGenomeConnector(type).getAvailableGenomeVersion(organism);
- }
-
- @Override
- public String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version) {
- try {
- return getReferenceGenomeConnector(type).getGenomeVersionFile(organism, version);
- } catch (FileNotAvailableException e) {
- return null;
- }
- }
-
- @Override
- public List<ReferenceGenome> getDownloadedGenomes() {
- return referenceGenomeDao.getAll();
- }
-
- @Override
- public void removeGenome(ReferenceGenome genome) throws IOException {
- getReferenceGenomeConnector(genome.getType()).removeGenomeVersion(genome.getOrganism(), genome.getVersion());
- }
-
- @Override
- public void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
- getReferenceGenomeConnector(referenceGenome.getType()).downloadGeneMappingGenomeVersion(referenceGenome, name, new IProgressUpdater() {
- @Override
- public void setProgress(double progress) {
- }
- }, true, url);
-
- }
-
- @Override
- public void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping genome) throws IOException {
- getReferenceGenomeConnector(genome.getReferenceGenome().getType()).removeGeneMapping(genome);
- }
-
- @Override
- public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType, String version) {
- List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
- for (ReferenceGenome referenceGenome : list) {
- if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
- return factory.create(referenceGenome);
- }
- }
- return null;
- }
-
- @Override
- public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
- AuthenticationToken authenticationToken) {
- return this.getReferenceGenomeViewByParams(organism, genomeType, version);
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReferenceGenomeService.class);
+
+ /**
+ * Class responsible for connection to {@link ReferenceGenomeType#UCSC}
+ * database.
+ */
+ @Autowired
+ private UcscReferenceGenomeConnector ucscReferenceGenomeConnector;
+
+ /**
+ * Data access object for {@link ReferenceGenome} objects.
+ */
+ @Autowired
+ private ReferenceGenomeDao referenceGenomeDao;
+
+ /**
+ * Factory that creates {@link ReferenceGenomeView}.
+ */
+ @Autowired
+ private ReferenceGenomeViewFactory factory;
+
+ @Override
+ public void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ for (ReferenceGenome genome : getDownloadedGenomes()) {
+ if (genome.getType().equals(type) && genome.getOrganism().equals(organism)
+ && genome.getVersion().equals(version)) {
+ throw new ReferenceGenomeExistsException("Selected reference genome already downloaded");
+ }
+ }
+ getReferenceGenomeConnector(type).downloadGenomeVersion(organism, version, new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, customUrl);
+ }
+
+ /**
+ * Return {@link ReferenceGenomeConnector} implementation for given reference
+ * genome type.
+ *
+ * @param type
+ * type of reference genome
+ * @return {@link ReferenceGenomeConnector} implementation for given reference
+ * genome type
+ */
+ private ReferenceGenomeConnector getReferenceGenomeConnector(ReferenceGenomeType type) {
+ if (type == ReferenceGenomeType.UCSC) {
+ return ucscReferenceGenomeConnector;
+ } else {
+ throw new InvalidArgumentException("Unknown reference genome type: " + type);
+ }
+ }
+
+ @Override
+ public List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type)
+ throws ReferenceGenomeConnectorException {
+ return getReferenceGenomeConnector(type).getAvailableOrganisms();
+ }
+
+ @Override
+ public List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
+ throws ReferenceGenomeConnectorException {
+ return getReferenceGenomeConnector(type).getAvailableGenomeVersion(organism);
+ }
+
+ @Override
+ public String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version) {
+ try {
+ return getReferenceGenomeConnector(type).getGenomeVersionFile(organism, version);
+ } catch (FileNotAvailableException e) {
+ return null;
+ }
+ }
+
+ @Override
+ public List<ReferenceGenome> getDownloadedGenomes() {
+ return referenceGenomeDao.getAll();
+ }
+
+ @Override
+ public void removeGenome(ReferenceGenome genome) throws IOException {
+ getReferenceGenomeConnector(genome.getType()).removeGenomeVersion(genome.getOrganism(), genome.getVersion());
+ }
+
+ @Override
+ public void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException {
+ getReferenceGenomeConnector(referenceGenome.getType()).downloadGeneMappingGenomeVersion(referenceGenome, name,
+ new IProgressUpdater() {
+ @Override
+ public void setProgress(double progress) {
+ }
+ }, true, url);
+
+ }
+
+ @Override
+ public void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping genome) throws IOException {
+ getReferenceGenomeConnector(genome.getReferenceGenome().getType()).removeGeneMapping(genome);
+ }
+
+ @Override
+ public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData miriamData, ReferenceGenomeType genomeType,
+ String version) {
+ List<ReferenceGenome> list = referenceGenomeDao.getByType(genomeType);
+ for (ReferenceGenome referenceGenome : list) {
+ if (referenceGenome.getOrganism().equals(miriamData) && referenceGenome.getVersion().equals(version)) {
+ return factory.create(referenceGenome);
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
+ String version, String authenticationToken) {
+ return this.getReferenceGenomeViewByParams(organism, genomeType, version);
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
index 5a72274aa34818ccc17610d7d171d4d5a4aa8085..bac9ff234a7609bc95bcea60948f7bbac381db5a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/UserService.java
@@ -5,14 +5,12 @@ import java.math.BigInteger;
import java.security.SecureRandom;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
import java.util.Random;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.security.core.authority.AuthorityUtils;
import org.springframework.security.core.session.SessionInformation;
import org.springframework.security.core.session.SessionRegistry;
import org.springframework.security.crypto.password.PasswordEncoder;
@@ -34,14 +32,11 @@ import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.user.PrivilegeDao;
import lcsb.mapviewer.persist.dao.user.UserDao;
-import lcsb.mapviewer.services.AuthenticationTokenExpireException;
-import lcsb.mapviewer.services.InvalidTokenException;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.ILogService;
import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.PrivilegeView;
import lcsb.mapviewer.services.view.UserView;
import lcsb.mapviewer.services.view.UserView.UserProjectPrivilegeView;
@@ -56,10 +51,6 @@ import lcsb.mapviewer.services.view.UserViewFactory;
@Transactional(value = "txManager")
public class UserService implements IUserService {
- private static Map<String, AuthenticationToken> authenticationTokens = new HashMap<>();
-
- private static Map<AuthenticationToken, User> authenticatedUsers = new HashMap<>();
-
/**
* Default class logger.
*/
@@ -111,23 +102,12 @@ public class UserService implements IUserService {
private IConfigurationService configurationService;
@Override
- public AuthenticationToken login(String login, String password) {
+ public String login(String login, String password) {
Random random = new SecureRandom();
String id = new BigInteger(130, random).toString(32);
return this.login(login, password, id);
}
- private void clearAuthenticationTokens() {
- synchronized (authenticationTokens) {
- List<String> toRemove = new ArrayList<>();
- for (AuthenticationToken token : authenticationTokens.values()) {
- if (isSessionExpired(token)) {
- toRemove.add(token.getId());
- }
- }
- }
- }
-
@Override
public boolean userHasPrivilege(User user, PrivilegeType type) {
return getUserPrivilegeLevel(user, type) > 0;
@@ -509,72 +489,39 @@ public class UserService implements IUserService {
}
@Override
- public User getUserByToken(AuthenticationToken token) {
- User result = null;
+ public User getUserByToken(String token) throws SecurityException {
if (!isSessionExpired(token)) {
- synchronized (authenticationTokens) {
- result = authenticatedUsers.get(token);
- }
- }
- return result;
- }
-
- @Override
- public User getUserByToken(String tokenString) throws SecurityException {
- return getUserByToken(getToken(tokenString));
- }
-
- @Override
- public AuthenticationToken getToken(String tokenString) throws SecurityException {
- AuthenticationToken result = null;
- synchronized (authenticationTokens) {
- result = authenticationTokens.get(tokenString);
- }
- if (result == null) {
- throw new InvalidTokenException("Token string is invalid");
- }
- if (isSessionExpired(result)) {
- logout(result);
- throw new AuthenticationTokenExpireException("Token validity expired");
+ String login = ((org.springframework.security.core.userdetails.User) (sessionRegistry.getSessionInformation(token)
+ .getPrincipal())).getUsername();
+ return userDao.getUserByLogin(login);
+ } else {
+ throw new SecurityException("Invalid token");
}
- return result;
}
- private boolean isSessionExpired(AuthenticationToken result) {
- SessionInformation sessionData = sessionRegistry.getSessionInformation(result.getId());
+ private boolean isSessionExpired(String token) {
+ SessionInformation sessionData = sessionRegistry.getSessionInformation(token);
if (sessionData == null) {
- logger.debug("No session data for token id: " + result.getId());
+ logger.debug("No session data for token id: " + token);
return true;
}
return sessionData.isExpired();
}
@Override
- public void logout(AuthenticationToken token) {
- synchronized (authenticationTokens) {
- authenticationTokens.remove(token.getId());
- authenticatedUsers.remove(token);
- }
- }
-
- @Override
- public boolean userHasPrivilege(AuthenticationToken token, PrivilegeType type, Object object) {
+ public boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException {
return userHasPrivilege(getUserByToken(token), type, object);
}
@Override
- public void logout(String tokenString) throws SecurityException {
- AuthenticationToken token = getToken(tokenString);
- logout(token);
- }
-
- @Override
- public boolean userHasPrivilege(AuthenticationToken token, PrivilegeType type) {
- return userHasPrivilege(getUserByToken(token), type);
+ public void logout(String tokenString) {
+ if (!isSessionExpired(tokenString)) {
+ sessionRegistry.removeSessionInformation(tokenString);
+ }
}
@Override
- public User getUserById(String creatorId, AuthenticationToken authenticationToken) throws SecurityException {
+ public User getUserById(String creatorId, String authenticationToken) throws SecurityException {
User user = getUserByToken(authenticationToken);
Integer id = Integer.parseInt(creatorId);
if (user.getId().equals(id)) {
@@ -587,7 +534,7 @@ public class UserService implements IUserService {
}
@Override
- public List<User> getUsers(AuthenticationToken token) throws SecurityException {
+ public List<User> getUsers(String token) throws SecurityException {
if (userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
return userDao.getAll();
} else {
@@ -596,8 +543,7 @@ public class UserService implements IUserService {
}
@Override
- public void setUserPrivilege(User user, PrivilegeType type, Object value, AuthenticationToken token)
- throws SecurityException {
+ public void setUserPrivilege(User user, PrivilegeType type, Object value, String token) throws SecurityException {
if (!userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
throw new SecurityException("You cannot modify user privileges");
}
@@ -615,7 +561,7 @@ public class UserService implements IUserService {
}
@Override
- public void setUserPrivilege(User user, PrivilegeType type, Object value, Integer objectId, AuthenticationToken token)
+ public void setUserPrivilege(User user, PrivilegeType type, Object value, Integer objectId, String token)
throws SecurityException {
boolean canModify = userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT);
if (!canModify) {
@@ -647,7 +593,7 @@ public class UserService implements IUserService {
}
@Override
- public void updateUser(User modifiedUser, AuthenticationToken token) throws SecurityException {
+ public void updateUser(User modifiedUser, String token) throws SecurityException {
User user = getUserByToken(token);
if (user.getLogin().equals(modifiedUser.getLogin()) || userHasPrivilege(token, PrivilegeType.USER_MANAGEMENT)) {
updateUser(modifiedUser);
@@ -663,26 +609,15 @@ public class UserService implements IUserService {
}
@Override
- public AuthenticationToken login(String login, String password, String id) {
+ public String login(String login, String password, String token) {
User user = userDao.getUserByLoginAndPassword(login, password);
if (user == null && Configuration.ANONYMOUS_LOGIN.equals(login) && "".equals(password)) {
user = getUserByLogin(Configuration.ANONYMOUS_LOGIN);
}
if (user != null) {
- int count = 0;
- synchronized (authenticationTokens) {
- count = authenticationTokens.size();
- }
-
- if (count > 1000) {
- clearAuthenticationTokens();
- }
- AuthenticationToken authenticationToken = new AuthenticationToken(id);
- synchronized (authenticationTokens) {
- authenticationTokens.put(authenticationToken.getId(), authenticationToken);
- authenticatedUsers.put(authenticationToken, user);
- }
- return authenticationToken;
+ sessionRegistry.registerNewSession(token, new org.springframework.security.core.userdetails.User(login,
+ passwordEncoder.encode(password), AuthorityUtils.commaSeparatedStringToAuthorityList("")));
+ return token;
} else {
return null;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
index dd3db2c6beb22011de2f1a352a919a8893a903f5..048f9249b28823e55e698b2c9d61fcdd6a770506 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
@@ -8,11 +8,11 @@ import lcsb.mapviewer.model.map.Comment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.search.ElementIdentifierDetails;
import lcsb.mapviewer.services.search.comment.FullCommentView;
import lcsb.mapviewer.services.search.data.ElementIdentifier;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.CommentView;
/**
@@ -22,101 +22,103 @@ import lcsb.mapviewer.services.view.CommentView;
*
*/
public interface ICommentService {
- /**
- * Adds comment to the map.
- *
- * @param pinned
- * parameter that defines if comment should be visible on the map.
- * @param object
- * determines which object is commented - it could be null; in this
- * case it means that a comment is general one.
- * @param name
- * name of person that comments
- * @param email
- * email of the person that comments
- * @param content
- * content of the comment
- * @param model
- * which map we comment on
- * @param submodel
- * on which submodel we comment on
- * @param coordinates
- * where exactly the comment should be placed on
- *
- * @return comment object created based on the data provided as parameters
- */
- Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object, boolean pinned, Model submodel);
+ /**
+ * Adds comment to the map.
+ *
+ * @param pinned
+ * parameter that defines if comment should be visible on the map.
+ * @param object
+ * determines which object is commented - it could be null; in this
+ * case it means that a comment is general one.
+ * @param name
+ * name of person that comments
+ * @param email
+ * email of the person that comments
+ * @param content
+ * content of the comment
+ * @param model
+ * which map we comment on
+ * @param submodel
+ * on which submodel we comment on
+ * @param coordinates
+ * where exactly the comment should be placed on
+ *
+ * @return comment object created based on the data provided as parameters
+ */
+ Comment addComment(String name, String email, String content, Model model, Point2D coordinates, Object object,
+ boolean pinned, Model submodel);
- /**
- * This method remove comment. Comment is not removed from the system, only
- * 'deleted' flag is set.
- *
- * @param loggedUser
- * user that wants to remove the comment
- * @param commentId
- * identifier of the comment that user wants to remove
- * @param reason
- * why user wants to remove the comment
- */
- void deleteComment(User loggedUser, String commentId, String reason);
-
- void deleteComment(Comment comment, AuthenticationToken token, String reason) throws UserAccessException;
+ /**
+ * This method remove comment. Comment is not removed from the system, only
+ * 'deleted' flag is set.
+ *
+ * @param loggedUser
+ * user that wants to remove the comment
+ * @param commentId
+ * identifier of the comment that user wants to remove
+ * @param reason
+ * why user wants to remove the comment
+ */
+ void deleteComment(User loggedUser, String commentId, String reason);
- /**
- * Method returns all comments for a given map.
- *
- * @param model
- * given map
- * @return list of the comments to the map
- * @throws UserAccessException
- */
- List<CommentView> getCommentsByMap(Model model, AuthenticationToken token) throws UserAccessException;
-
- List<Comment> getCommentsByProject(Project project, AuthenticationToken token) throws UserAccessException;
+ void deleteComment(Comment comment, String token, String reason) throws UserAccessException, SecurityException;
- /**
- * Returns number of comments in the system.
- *
- * @return number of comments in the system
- */
- long getCommentCount();
+ /**
+ * Method returns all comments for a given map.
+ *
+ * @param model
+ * given map
+ * @return list of the comments to the map
+ * @throws UserAccessException
+ * @throws SecurityException
+ */
+ List<CommentView> getCommentsByMap(Model model, String token) throws UserAccessException, SecurityException;
- /**
- * Removes comments from the model.
- *
- * @param model
- * from which model we want to remove comments
- */
- void removeCommentsForModel(Model model);
+ List<Comment> getCommentsByProject(Project project, String token) throws UserAccessException, SecurityException;
- /**
- * This method returns marker for all comments in a model.
- *
- * @param model
- * object to which we are looking for comments
- * @return list of markers for comments
- */
- List<FullCommentView> getCommentMarkers(Model model);
+ /**
+ * Returns number of comments in the system.
+ *
+ * @return number of comments in the system
+ */
+ long getCommentCount();
- /**
- * Removes comments from the model.
- *
- * @param model
- * from which model we want to remove comments
- */
- void removeCommentsForModel(ModelData model);
+ /**
+ * Removes comments from the model.
+ *
+ * @param model
+ * from which model we want to remove comments
+ */
+ void removeCommentsForModel(Model model);
- /**
- * Returns detailed comment information about element.
- *
- * @param element
- * element for which we are looking for comments
- * @param model
- * model where we are looking for comments
- * @return detailed comment information about element
- */
- List<ElementIdentifierDetails> getElementInformationForResult(ElementIdentifier element, Model model);
+ /**
+ * This method returns marker for all comments in a model.
+ *
+ * @param model
+ * object to which we are looking for comments
+ * @return list of markers for comments
+ */
+ List<FullCommentView> getCommentMarkers(Model model);
- Comment getCommentById(String commentId);
+ /**
+ * Removes comments from the model.
+ *
+ * @param model
+ * from which model we want to remove comments
+ */
+ void removeCommentsForModel(ModelData model);
+
+ /**
+ * Returns detailed comment information about element.
+ *
+ * @param element
+ * element for which we are looking for comments
+ * @param model
+ * model where we are looking for comments
+ * @return detailed comment information about element
+ */
+ List<ElementIdentifierDetails> getElementInformationForResult(ElementIdentifier element, Model model);
+
+ Comment getCommentById(String commentId);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
index a95d2623c9c82080e0887c71356fd143e28edae5..4b2c24e810b38875a9664fb7ab77e940bb73f53b 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -21,7 +21,6 @@ import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
import lcsb.mapviewer.services.utils.EmailSender;
import lcsb.mapviewer.services.utils.data.ColorSchemaType;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
/**
@@ -32,501 +31,502 @@ import lcsb.mapviewer.services.view.LayoutView;
*/
public interface ILayoutService {
- /**
- * Parameters used for creation of the layout.
- *
- * @author Piotr Gawron
- *
- */
- class CreateLayoutParams {
-
- /**
- * Size of the buffer used to copy stream data.
- */
- private static final int BUFFER_SIZE = 1024;
-
- /**
- * Name of the layout.
- *
- */
- private String name;
-
- /**
- * Description of the layout.
- *
- */
- private String description;
-
- /**
- * Where the graphic files should be saved.
- *
- */
- private String directory;
-
- /**
- *
- * {@link Model} for which the layout is created.
- */
- private Model model;
-
- /**
- * Who creates the layout.
- *
- */
- private User user;
-
- /**
- *
- * Input stream with coloring information data in the stream should
- * correspond to a file that can be parsed by
- * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader
- * ColorSchemaReader} . This is a copy of original input stream, so we can
- * read this input stream multiple times.
- */
- private ByteArrayOutputStream colorInputStreamCopy;
-
- /**
- * Name of the file used as input (if available).
- */
- private String layoutFileName;
-
- /**
- * Determines if creation of the output files should be done asynchronously
- * who creates the layout.
- *
- */
- private boolean async = false;
-
- /**
- * Type of the uploaded file.
- */
- private ColorSchemaType colorSchemaType;
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams name(String name) {
- this.name = name;
- return this;
- }
-
- /**
- * @return the directory
- * @see #directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param directory
- * the directory to set
- * @see #directory
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams directory(String directory) {
- this.directory = directory;
- return this;
- }
-
- /**
- * @return the model
- * @see #model
- */
- public Model getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams model(Model model) {
- this.model = model;
- return this;
- }
-
- /**
- * @return the user
- * @see #user
- */
- public User getUser() {
- return user;
- }
-
- /**
- * @param user
- * the user to set
- * @see #user
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams user(User user) {
- this.user = user;
- return this;
- }
-
- /**
- * @return the colorInputStream
- * @see #colorInputStream
- */
- public InputStream getColorInputStream() {
- return new ByteArrayInputStream(colorInputStreamCopy.toByteArray());
- }
-
- /**
- * @param colorInputStream
- * the colorInputStream to set
- * @see #colorInputStream
- * @return {@link CreateLayoutParams} object
- * @throws IOException
- * thrown when there is a problem with accessing input stream
- */
- public CreateLayoutParams colorInputStream(InputStream colorInputStream) throws IOException {
- if (colorInputStream == null) {
- this.colorInputStreamCopy = null;
- } else {
- this.colorInputStreamCopy = new ByteArrayOutputStream();
-
- byte[] buffer = new byte[BUFFER_SIZE];
- int len;
- while ((len = colorInputStream.read(buffer)) > -1) {
- this.colorInputStreamCopy.write(buffer, 0, len);
- }
- this.colorInputStreamCopy.flush();
- }
- return this;
- }
-
- /**
- * @return the async
- * @see #async
- */
- public boolean isAsync() {
- return async;
- }
-
- /**
- * @param async
- * the async to set
- * @see #async
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams async(boolean async) {
- this.async = async;
- return this;
- }
-
- /**
- * @return the description
- * @see #description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param description
- * the description to set
- * @see #description
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams description(String description) {
- this.description = description;
- return this;
- }
-
- /**
- *
- * @return {@link #colorSchemaType}
- */
- public ColorSchemaType getColorSchemaType() {
- return colorSchemaType;
- }
-
- /**
- * @param colorSchemaType
- * the colorSchemaType to set
- * @see #colorSchemaType
- * @return {@link CreateLayoutParams} object
- */
- public CreateLayoutParams colorSchemaType(ColorSchemaType colorSchemaType) {
- this.colorSchemaType = colorSchemaType;
- return this;
- }
-
- /**
- * @return the layoutFileName
- * @see #layoutFileName
- */
- public String getLayoutFileName() {
- return layoutFileName;
- }
-
- /**
- * @param layoutFileName
- * the layoutFileName to set
- * @return {@link CreateLayoutParams} object
- * @see #layoutFileName
- */
- public CreateLayoutParams layoutFileName(String layoutFileName) {
- this.layoutFileName = layoutFileName;
- return this;
- }
- }
-
- /**
- * Returns true if user can add layout to the model.
- *
- * @param model
- * to which model user wants to add layout
- * @param user
- * who wants to add layout
- * @return <code>true</code> if user can add layout, <code>false</code>
- * otherwise
- */
- boolean userCanAddLayout(Model model, User user);
-
- /**
- * Returns true if user can remove layout from the model.
- *
- * @param layout
- * which layout user want to remove
- * @param user
- * who wants to remove layout
- * @return <code>true</code> if user can remove layout, <code>false</code>
- * otherwise
- */
- boolean userCanRemoveLayout(LayoutView layout, User user);
-
- /**
- * Returns list of custom layouts.
- *
- * @param model
- * model where the layouts lay on
- * @param user
- * user who asks for the layouts
- * @return list of custom layouts
- */
- List<LayoutView> getCustomLayouts(Model model, User user, Boolean publicOverlay, User creator);
-
- /**
- * Returns list of general publicly available layouts.
- *
- * @param model
- * model where the layouts lay on
- * @return list of custom layouts
- */
- List<LayoutView> getGeneralLayouts(Model model);
-
- /**
- * Removes layout from the system.
- *
- * @param layout
- * layout to remove
- * @param homeDir
- * directory where the system is deployed
- * @throws IOException
- * thrown when there are problems with removing layout files
- */
- void removeLayout(LayoutView layout, String homeDir) throws IOException;
-
- /**
- * Updates data about the layout.
- *
- * @param layout
- * layout to update
- */
- void updateLayout(LayoutView layout);
-
- /**
- * Adds view privilege to the layout for the user.
- *
- * @param layout
- * layout for privilege
- * @param user
- * who should own the privilege
- */
- void addViewPrivilegeToLayout(LayoutView layout, User user);
-
- /**
- * Removes view privilege to the layout from the user.
- *
- * @param layout
- * layout for privilege remove
- * @param user
- * who shouldn't have the privilege
- */
- void dropViewPrivilegeFromLayout(LayoutView layout, User user);
-
- /**
- * Create layout based on the data in the parameter.
- *
- * @param params
- * list of {@link CreateLayoutParams params} necessary to create
- * layout
- * @return object that refers to created layout
- * @throws IOException
- * thrown when there are problems with files
- * @throws InvalidColorSchemaException
- * if the coloring source is invalid
- * @throws CommandExecutionException
- */
- LayoutView createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
-
- /**
- * Create layout based on the data in the parameter. Layout will contain set
- * of images that can be further visualized in goolge maps api.
- *
- * @param params
- * list of {@link CreateLayoutParams params} necessary to create
- * layout
- * @return object that refers to created layout
- * @throws IOException
- * thrown when there are problems with files
- * @throws CommandExecutionException
- * if the coloring source is invalid
- * @throws InvalidColorSchemaException
- * if the coloring source is invalid
- */
- LayoutView createLayoutWithImages(CreateLayoutParams params) throws IOException, CommandExecutionException, InvalidColorSchemaException;
-
- /**
- * Returns number of still available custom layouts for the user.
- *
- * @param user
- * user for which the number of available custom layouts will be
- * returned
- * @return number of available custom layouts
- */
- long getAvailableCustomLayoutsNumber(User user);
-
- /**
- * Returns layout identified by name and model.
- *
- * @param model
- * model where the layouts lay on
- * @param name
- * name of the layout
- * @return layout
- */
- LayoutView getLayoutByName(Model model, String name);
-
- /**
- * Returns byte array containing data from original input file that was used
- * to generate the layout.
- *
- * @param layout
- * layout for which we want to retrieve original file data
- * @return original data file for given layout, if such file is not stored in
- * database (compatibility reasons) then null is returned
- * @throws SecurityException
- */
- byte[] getInputDataForLayout(LayoutView layout, AuthenticationToken token) throws SecurityException;
-
- /**
- * Returns a list of {@link LightLayoutAliasView aliases} that are visualized
- * in a {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @param model
- * model where data is located
- * @param layoutId
- * identifier of the layout
- * @return a list of {@link LightLayoutAliasView aliases} that are visualized
- * in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException;
-
- /**
- * Returns a list of {@link LightLayoutReactionView reactions} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}.
- *
- * @param model
- * model where data is located
- * @param layoutId
- * identifier of the layout
- * @return a list of {@link LightLayoutReactionView reactions} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException;
-
- /**
- * Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
- * Alias}/ {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} and
- * {@link ColorSchema} used for coloring object in the layout given in the
- * parameter.
- *
- * @param model
- * model where data is lcoated
- * @param layoutId
- * identifier of the layout
- * @return a list of {@link LightLayoutReactionView reactions} that are
- * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, AuthenticationToken token) throws SecurityException;
-
- /**
- * Returns a list of {@link FullLayoutAliasView aliases} that are visualized
- * in a {@link lcsb.mapviewer.model.map.layout.Layout} and have given
- * identifiers.
- *
- * @param model
- * model where data is lcoated
- * @param layoutId
- * identifier of the layout
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return a list of {@link LightLayoutAliasView aliases} that are visualized
- * in a {@link lcsb.mapviewer.model.map.layout.Layout}
- * @throws SecurityException
- */
- List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId, AuthenticationToken token)
- throws SecurityException;
-
- FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, AuthenticationToken token) throws SecurityException;
-
- FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId, AuthenticationToken token) throws SecurityException;
-
- /**
- * Returns {@link EmailSender} used by the service.
- *
- * @return {@link EmailSender} used by the service
- */
- EmailSender getEmailSender();
-
- /**
- * Sets {@link EmailSender} used by the service.
- *
- * @param emailSender
- * {@link EmailSender} used by the service
- */
- void setEmailSender(EmailSender emailSender);
-
- List<LayoutView> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator) throws SecurityException;
-
- LayoutView getLayoutById(int overlayId, AuthenticationToken token) throws SecurityException;
-
- Layout getLayoutDataById(int overlayId, AuthenticationToken authenticationToken) throws SecurityException;
-
- boolean userCanRemoveLayout(LayoutView layout, AuthenticationToken authenticationToken);
+ /**
+ * Parameters used for creation of the layout.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ class CreateLayoutParams {
+
+ /**
+ * Size of the buffer used to copy stream data.
+ */
+ private static final int BUFFER_SIZE = 1024;
+
+ /**
+ * Name of the layout.
+ *
+ */
+ private String name;
+
+ /**
+ * Description of the layout.
+ *
+ */
+ private String description;
+
+ /**
+ * Where the graphic files should be saved.
+ *
+ */
+ private String directory;
+
+ /**
+ *
+ * {@link Model} for which the layout is created.
+ */
+ private Model model;
+
+ /**
+ * Who creates the layout.
+ *
+ */
+ private User user;
+
+ /**
+ *
+ * Input stream with coloring information data in the stream should correspond
+ * to a file that can be parsed by
+ * {@link lcsb.mapviewer.services.utils.ColorSchemaXlsxReader ColorSchemaReader}
+ * . This is a copy of original input stream, so we can read this input stream
+ * multiple times.
+ */
+ private ByteArrayOutputStream colorInputStreamCopy;
+
+ /**
+ * Name of the file used as input (if available).
+ */
+ private String layoutFileName;
+
+ /**
+ * Determines if creation of the output files should be done asynchronously who
+ * creates the layout.
+ *
+ */
+ private boolean async = false;
+
+ /**
+ * Type of the uploaded file.
+ */
+ private ColorSchemaType colorSchemaType;
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams name(String name) {
+ this.name = name;
+ return this;
+ }
+
+ /**
+ * @return the directory
+ * @see #directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param directory
+ * the directory to set
+ * @see #directory
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams directory(String directory) {
+ this.directory = directory;
+ return this;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public Model getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams model(Model model) {
+ this.model = model;
+ return this;
+ }
+
+ /**
+ * @return the user
+ * @see #user
+ */
+ public User getUser() {
+ return user;
+ }
+
+ /**
+ * @param user
+ * the user to set
+ * @see #user
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams user(User user) {
+ this.user = user;
+ return this;
+ }
+
+ /**
+ * @return the colorInputStream
+ * @see #colorInputStream
+ */
+ public InputStream getColorInputStream() {
+ return new ByteArrayInputStream(colorInputStreamCopy.toByteArray());
+ }
+
+ /**
+ * @param colorInputStream
+ * the colorInputStream to set
+ * @see #colorInputStream
+ * @return {@link CreateLayoutParams} object
+ * @throws IOException
+ * thrown when there is a problem with accessing input stream
+ */
+ public CreateLayoutParams colorInputStream(InputStream colorInputStream) throws IOException {
+ if (colorInputStream == null) {
+ this.colorInputStreamCopy = null;
+ } else {
+ this.colorInputStreamCopy = new ByteArrayOutputStream();
+
+ byte[] buffer = new byte[BUFFER_SIZE];
+ int len;
+ while ((len = colorInputStream.read(buffer)) > -1) {
+ this.colorInputStreamCopy.write(buffer, 0, len);
+ }
+ this.colorInputStreamCopy.flush();
+ }
+ return this;
+ }
+
+ /**
+ * @return the async
+ * @see #async
+ */
+ public boolean isAsync() {
+ return async;
+ }
+
+ /**
+ * @param async
+ * the async to set
+ * @see #async
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams async(boolean async) {
+ this.async = async;
+ return this;
+ }
+
+ /**
+ * @return the description
+ * @see #description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description
+ * the description to set
+ * @see #description
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams description(String description) {
+ this.description = description;
+ return this;
+ }
+
+ /**
+ *
+ * @return {@link #colorSchemaType}
+ */
+ public ColorSchemaType getColorSchemaType() {
+ return colorSchemaType;
+ }
+
+ /**
+ * @param colorSchemaType
+ * the colorSchemaType to set
+ * @see #colorSchemaType
+ * @return {@link CreateLayoutParams} object
+ */
+ public CreateLayoutParams colorSchemaType(ColorSchemaType colorSchemaType) {
+ this.colorSchemaType = colorSchemaType;
+ return this;
+ }
+
+ /**
+ * @return the layoutFileName
+ * @see #layoutFileName
+ */
+ public String getLayoutFileName() {
+ return layoutFileName;
+ }
+
+ /**
+ * @param layoutFileName
+ * the layoutFileName to set
+ * @return {@link CreateLayoutParams} object
+ * @see #layoutFileName
+ */
+ public CreateLayoutParams layoutFileName(String layoutFileName) {
+ this.layoutFileName = layoutFileName;
+ return this;
+ }
+ }
+
+ /**
+ * Returns true if user can add layout to the model.
+ *
+ * @param model
+ * to which model user wants to add layout
+ * @param user
+ * who wants to add layout
+ * @return <code>true</code> if user can add layout, <code>false</code>
+ * otherwise
+ */
+ boolean userCanAddLayout(Model model, User user);
+
+ /**
+ * Returns true if user can remove layout from the model.
+ *
+ * @param layout
+ * which layout user want to remove
+ * @param user
+ * who wants to remove layout
+ * @return <code>true</code> if user can remove layout, <code>false</code>
+ * otherwise
+ */
+ boolean userCanRemoveLayout(LayoutView layout, User user);
+
+ /**
+ * Returns list of custom layouts.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @param user
+ * user who asks for the layouts
+ * @return list of custom layouts
+ */
+ List<LayoutView> getCustomLayouts(Model model, User user, Boolean publicOverlay, User creator);
+
+ /**
+ * Returns list of general publicly available layouts.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @return list of custom layouts
+ */
+ List<LayoutView> getGeneralLayouts(Model model);
+
+ /**
+ * Removes layout from the system.
+ *
+ * @param layout
+ * layout to remove
+ * @param homeDir
+ * directory where the system is deployed
+ * @throws IOException
+ * thrown when there are problems with removing layout files
+ */
+ void removeLayout(LayoutView layout, String homeDir) throws IOException;
+
+ /**
+ * Updates data about the layout.
+ *
+ * @param layout
+ * layout to update
+ */
+ void updateLayout(LayoutView layout);
+
+ /**
+ * Adds view privilege to the layout for the user.
+ *
+ * @param layout
+ * layout for privilege
+ * @param user
+ * who should own the privilege
+ */
+ void addViewPrivilegeToLayout(LayoutView layout, User user);
+
+ /**
+ * Removes view privilege to the layout from the user.
+ *
+ * @param layout
+ * layout for privilege remove
+ * @param user
+ * who shouldn't have the privilege
+ */
+ void dropViewPrivilegeFromLayout(LayoutView layout, User user);
+
+ /**
+ * Create layout based on the data in the parameter.
+ *
+ * @param params
+ * list of {@link CreateLayoutParams params} necessary to create layout
+ * @return object that refers to created layout
+ * @throws IOException
+ * thrown when there are problems with files
+ * @throws InvalidColorSchemaException
+ * if the coloring source is invalid
+ * @throws CommandExecutionException
+ */
+ LayoutView createLayout(CreateLayoutParams params) throws IOException, InvalidColorSchemaException;
+
+ /**
+ * Create layout based on the data in the parameter. Layout will contain set of
+ * images that can be further visualized in goolge maps api.
+ *
+ * @param params
+ * list of {@link CreateLayoutParams params} necessary to create layout
+ * @return object that refers to created layout
+ * @throws IOException
+ * thrown when there are problems with files
+ * @throws CommandExecutionException
+ * if the coloring source is invalid
+ * @throws InvalidColorSchemaException
+ * if the coloring source is invalid
+ */
+ LayoutView createLayoutWithImages(CreateLayoutParams params)
+ throws IOException, CommandExecutionException, InvalidColorSchemaException;
+
+ /**
+ * Returns number of still available custom layouts for the user.
+ *
+ * @param user
+ * user for which the number of available custom layouts will be
+ * returned
+ * @return number of available custom layouts
+ */
+ long getAvailableCustomLayoutsNumber(User user);
+
+ /**
+ * Returns layout identified by name and model.
+ *
+ * @param model
+ * model where the layouts lay on
+ * @param name
+ * name of the layout
+ * @return layout
+ */
+ LayoutView getLayoutByName(Model model, String name);
+
+ /**
+ * Returns byte array containing data from original input file that was used to
+ * generate the layout.
+ *
+ * @param layout
+ * layout for which we want to retrieve original file data
+ * @return original data file for given layout, if such file is not stored in
+ * database (compatibility reasons) then null is returned
+ * @throws SecurityException
+ */
+ byte[] getInputDataForLayout(LayoutView layout, String token) throws SecurityException;
+
+ /**
+ * Returns a list of {@link LightLayoutAliasView aliases} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of {@link LightLayoutAliasView aliases} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, String token) throws SecurityException;
+
+ /**
+ * Returns a list of {@link LightLayoutReactionView reactions} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of {@link LightLayoutReactionView reactions} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, String token) throws SecurityException;
+
+ /**
+ * Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
+ * Alias}/ {@link lcsb.mapviewer.model.map.reaction.Reaction Reaction} and
+ * {@link ColorSchema} used for coloring object in the layout given in the
+ * parameter.
+ *
+ * @param model
+ * model where data is lcoated
+ * @param layoutId
+ * identifier of the layout
+ * @return a list of {@link LightLayoutReactionView reactions} that are
+ * visualized in a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, String token) throws SecurityException;
+
+ /**
+ * Returns a list of {@link FullLayoutAliasView aliases} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout} and have given identifiers.
+ *
+ * @param model
+ * model where data is located
+ * @param layoutId
+ * identifier of the layout
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return a list of {@link LightLayoutAliasView aliases} that are visualized in
+ * a {@link lcsb.mapviewer.model.map.layout.Layout}
+ * @throws SecurityException
+ */
+ List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers,
+ int layoutId, String token) throws SecurityException;
+
+ FullLayoutAliasView getFullAliasForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException;
+
+ FullLayoutReactionView getFullReactionForLayout(Model model, Integer id, int layoutId, String token)
+ throws SecurityException;
+
+ /**
+ * Returns {@link EmailSender} used by the service.
+ *
+ * @return {@link EmailSender} used by the service
+ */
+ EmailSender getEmailSender();
+
+ /**
+ * Sets {@link EmailSender} used by the service.
+ *
+ * @param emailSender
+ * {@link EmailSender} used by the service
+ */
+ void setEmailSender(EmailSender emailSender);
+
+ List<LayoutView> getCustomLayouts(Model model, String token, Boolean publicOverlay, User creator)
+ throws SecurityException;
+
+ LayoutView getLayoutById(int overlayId, String token) throws SecurityException;
+
+ Layout getLayoutDataById(int overlayId, String authenticationToken) throws SecurityException;
+
+ boolean userCanRemoveLayout(LayoutView layout, String authenticationToken) throws SecurityException;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index 53fda094d003d47b8f2d2a0f95531517194f9227..57495869e7ca7959078d9ee7cc9ba1d7148c1ab4 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -7,9 +7,9 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.search.data.LightAliasView;
import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ModelView;
import lcsb.mapviewer.services.view.ProjectView;
@@ -28,8 +28,9 @@ public interface IModelService {
* @param projectId
* {@link lcsb.mapviewer.model.Project#projectId project identifier}
* @return the newest model for the project
+ * @throws SecurityException
*/
- Model getLastModelByProjectId(String projectId, AuthenticationToken token);
+ Model getLastModelByProjectId(String projectId, String token) throws SecurityException;
/**
* Caches information about all pubmed articles for the given model.
@@ -126,5 +127,5 @@ public interface IModelService {
*/
List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers);
- void updateModel(ModelData model, AuthenticationToken token);
+ void updateModel(ModelData model, String token) throws SecurityException;
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index b802cfe8897af65cc9a6d99b1b2af672d19c5806..aaf3bbf5d8a6a7a3a0e14a322ab9fe79a526c020 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -11,7 +11,6 @@ import lcsb.mapviewer.model.user.UserAnnotatorsParam;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.utils.CreateProjectParams;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ProjectView;
/**
@@ -29,8 +28,9 @@ public interface IProjectService {
* {@link Project#projectId project identifier}
* @return project with an identifier given as parameter. Null if such project
* doesn't exist.
+ * @throws SecurityException
*/
- Project getProjectByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
+ Project getProjectByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
/**
* Checks if project with a given {@link Project#projectId identifier} exists.
@@ -46,15 +46,17 @@ public interface IProjectService {
* Returns list of all projects.
*
* @return list of all projects.
+ * @throws SecurityException
*/
- List<Project> getAllProjects(AuthenticationToken token);
+ List<Project> getAllProjects(String token) throws SecurityException;
/**
* Returns a list of Project views for all projects.
*
* @return list of Project views for all projects
+ * @throws SecurityException
*/
- List<ProjectView> getAllProjectViews(AuthenticationToken token);
+ List<ProjectView> getAllProjectViews(String token) throws SecurityException;
/**
* Updates project.
@@ -74,10 +76,9 @@ public interface IProjectService {
* information about project to remove
* @param async
* should the operation be done asynchronously
- * @throws UserAccessException
+ * @throws SecurityException
*/
- void removeProject(ProjectView projectView, String homeDir, boolean async, AuthenticationToken token)
- throws UserAccessException;
+ void removeProject(ProjectView projectView, String homeDir, boolean async, String token) throws SecurityException;
/**
* Removes project from the system.
@@ -88,10 +89,9 @@ public interface IProjectService {
* object to remove
* @param async
* should the operation be done asynchronously
- * @throws UserAccessException
+ * @throws SecurityException
*/
- void removeProject(Project project, String homeDir, boolean async, AuthenticationToken token)
- throws UserAccessException;
+ void removeProject(Project project, String homeDir, boolean async, String token) throws SecurityException;
/**
* Gets view of the project by the {@link Project#projectId project identifier}.
@@ -100,8 +100,9 @@ public interface IProjectService {
* {@link Project#projectId project identifier}
* @return view of the project
* @throws UserAccessException
+ * @throws SecurityException
*/
- ProjectView getProjectViewByProjectId(String projectId, AuthenticationToken token) throws UserAccessException;
+ ProjectView getProjectViewByProjectId(String projectId, String token) throws UserAccessException, SecurityException;
/**
* Adds project to the system.
@@ -118,8 +119,9 @@ public interface IProjectService {
* database identifier of the project
* @return project view
* @throws UserAccessException
+ * @throws SecurityException
*/
- ProjectView getProjectViewById(Integer id, AuthenticationToken token) throws UserAccessException;
+ ProjectView getProjectViewById(Integer id, String token) throws UserAccessException, SecurityException;
/**
* Creates project using give parameters. See {@link CreateProjectParams}.
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
index a588d82b4373573a0d96437013b223ea6148aad1..1857baf300e4fd52b8de9b59794c78b985c5c244 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IReferenceGenomeService.java
@@ -9,7 +9,6 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.layout.ReferenceGenome;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeGeneMapping;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ReferenceGenomeView;
/**
@@ -20,129 +19,131 @@ import lcsb.mapviewer.services.view.ReferenceGenomeView;
*/
public interface IReferenceGenomeService {
- /**
- * Adds reference genome to the system.
- *
- * @param type
- * {@link ReferenceGenomeType type} of reference genome
- * @param organism
- * organism for which renference genome is added
- * @param version
- * version of the reference genome
- * @param customUrl
- * url from which reference genome should be downloaded
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when reference genome already exists or there is problem
- * wirh adding genome
- */
- void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+ /**
+ * Adds reference genome to the system.
+ *
+ * @param type
+ * {@link ReferenceGenomeType type} of reference genome
+ * @param organism
+ * organism for which renference genome is added
+ * @param version
+ * version of the reference genome
+ * @param customUrl
+ * url from which reference genome should be downloaded
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when reference genome already exists or there is problem
+ * wirh adding genome
+ */
+ void addReferenceGenome(ReferenceGenomeType type, MiriamData organism, String version, String customUrl)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
- /**
- * Returns list of organisms available for {@link ReferenceGenomeType
- * reference genome type}.
- *
- * @param type
- * type of reference genome
- * @return list of available organisms
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing information about
- * reference genoems
- */
- List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
+ /**
+ * Returns list of organisms available for {@link ReferenceGenomeType reference
+ * genome type}.
+ *
+ * @param type
+ * type of reference genome
+ * @return list of available organisms
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing information about
+ * reference genoems
+ */
+ List<MiriamData> getOrganismsByReferenceGenomeType(ReferenceGenomeType type) throws ReferenceGenomeConnectorException;
- /**
- * Returns list of genome versions available for organism of specific
- * {@link ReferenceGenomeType reference genome type}.
- *
- * @param type
- * type of reference genome
- * @param organism
- * organism for which we check genome versions
- * @return list of available organisms
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with accessing information about
- * reference genoems
- */
- List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism) throws ReferenceGenomeConnectorException;
+ /**
+ * Returns list of genome versions available for organism of specific
+ * {@link ReferenceGenomeType reference genome type}.
+ *
+ * @param type
+ * type of reference genome
+ * @param organism
+ * organism for which we check genome versions
+ * @return list of available organisms
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with accessing information about
+ * reference genoems
+ */
+ List<String> getAvailableGenomeVersions(ReferenceGenomeType type, MiriamData organism)
+ throws ReferenceGenomeConnectorException;
- /**
- * Returns url to the file that describes genome.
- *
- * @param type
- * type of reference genome
- * @param organism
- * organism of reference genome
- * @param version
- * version of reference genome
- * @return url to the file that describes genome
- */
- String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
+ /**
+ * Returns url to the file that describes genome.
+ *
+ * @param type
+ * type of reference genome
+ * @param organism
+ * organism of reference genome
+ * @param version
+ * version of reference genome
+ * @return url to the file that describes genome
+ */
+ String getUrlForGenomeVersion(ReferenceGenomeType type, MiriamData organism, String version);
- /**
- * Returns list of all downladed reference genomes.
- *
- * @return list of all downladed reference genomes
- */
- List<ReferenceGenome> getDownloadedGenomes();
+ /**
+ * Returns list of all downladed reference genomes.
+ *
+ * @return list of all downladed reference genomes
+ */
+ List<ReferenceGenome> getDownloadedGenomes();
- /**
- * Removes reference genome from the system.
- *
- * @param genome
- * genome to be removed
- * @throws IOException
- * thrown when there is a problem with removing genome
- */
- void removeGenome(ReferenceGenome genome) throws IOException;
+ /**
+ * Removes reference genome from the system.
+ *
+ * @param genome
+ * genome to be removed
+ * @throws IOException
+ * thrown when there is a problem with removing genome
+ */
+ void removeGenome(ReferenceGenome genome) throws IOException;
- /**
- * Adds gene mapping to refernce genome.
- *
- * @param referenceGenome
- * reference genome where we add mapping
- * @param name
- * name of the mapping
- * @param url
- * url to the file that describes mapping
- * @throws IOException
- * thrown when there is a problem with downloading file
- * @throws URISyntaxException
- * thrown when url is invalid
- * @throws ReferenceGenomeConnectorException
- * thrown when there is a problem with manipulatinf information
- * about reference genome
- */
- void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
- throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
+ /**
+ * Adds gene mapping to refernce genome.
+ *
+ * @param referenceGenome
+ * reference genome where we add mapping
+ * @param name
+ * name of the mapping
+ * @param url
+ * url to the file that describes mapping
+ * @throws IOException
+ * thrown when there is a problem with downloading file
+ * @throws URISyntaxException
+ * thrown when url is invalid
+ * @throws ReferenceGenomeConnectorException
+ * thrown when there is a problem with manipulatinf information about
+ * reference genome
+ */
+ void addReferenceGenomeGeneMapping(ReferenceGenome referenceGenome, String name, String url)
+ throws IOException, URISyntaxException, ReferenceGenomeConnectorException;
- /**
- * Removes gene mapping for reference genome.
- *
- * @param mapping
- * mapping to be removed
- * @throws IOException
- * thrown when there is a problem with removing file
- */
- void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
+ /**
+ * Removes gene mapping for reference genome.
+ *
+ * @param mapping
+ * mapping to be removed
+ * @throws IOException
+ * thrown when there is a problem with removing file
+ */
+ void removeReferenceGenomeGeneMapping(ReferenceGenomeGeneMapping mapping) throws IOException;
- /**
- * Returns {@link ReferenceGenomeView} for specific reference genome.
- *
- * @param organism
- * organism of reference genome
- * @param genomeType
- * reference genome type
- * @param version
- * version of the reference genome
- * @return {@link ReferenceGenomeView} for specific reference genome
- */
- ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version);
+ /**
+ * Returns {@link ReferenceGenomeView} for specific reference genome.
+ *
+ * @param organism
+ * organism of reference genome
+ * @param genomeType
+ * reference genome type
+ * @param version
+ * version of the reference genome
+ * @return {@link ReferenceGenomeView} for specific reference genome
+ */
+ ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
+ String version);
- ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType, String version,
- AuthenticationToken authenticationToken);
+ ReferenceGenomeView getReferenceGenomeViewByParams(MiriamData organism, ReferenceGenomeType genomeType,
+ String version, String authenticationToken);
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
index 5cc8b181b26587cdb38e4360d3edae6343d669a9..b0078cba8cceb46ada46588a90b7eb7e046bddb2 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IUserService.java
@@ -8,7 +8,6 @@ import lcsb.mapviewer.model.user.BasicPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.UserView;
/**
@@ -25,10 +24,10 @@ public interface IUserService {
* user login
* @param password
* plan password
- * @return {@link AuthenticationToken} if credentials are valid,
+ * @return {@link String} containing session id if credentials are valid,
* <code>null</code> otherwise
*/
- AuthenticationToken login(String login, String password);
+ String login(String login, String password);
/**
* Returns user by login.
@@ -50,8 +49,6 @@ public interface IUserService {
*/
boolean userHasPrivilege(User user, PrivilegeType type);
- boolean userHasPrivilege(String token, PrivilegeType type) throws SecurityException;
-
/**
* Returns level of the user privilege.
*
@@ -241,32 +238,26 @@ public interface IUserService {
*/
ColorExtractor getColorExtractorForUser(User user);
- User getUserByToken(AuthenticationToken token);
-
User getUserByToken(String token) throws SecurityException;
- AuthenticationToken getToken(String token) throws SecurityException;
-
- boolean userHasPrivilege(AuthenticationToken token, PrivilegeType type, Object object);
+ boolean userHasPrivilege(String token, PrivilegeType type, Object object) throws SecurityException;
void logout(String tokenString) throws SecurityException;
- void logout(AuthenticationToken token);
-
- boolean userHasPrivilege(AuthenticationToken token, PrivilegeType addMap);
+ boolean userHasPrivilege(String token, PrivilegeType addMap) throws SecurityException;
- User getUserById(String creatorId, AuthenticationToken authenticationToken) throws SecurityException;
+ User getUserById(String creatorId, String token) throws SecurityException;
- List<User> getUsers(AuthenticationToken token) throws SecurityException;
+ List<User> getUsers(String token) throws SecurityException;
- void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet,
- AuthenticationToken authenticationToken) throws SecurityException;
+ void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, String authenticationToken)
+ throws SecurityException;
void setUserPrivilege(User modifiedUser, PrivilegeType type, Object privilegeToSet, Integer objectId,
- AuthenticationToken authenticationToken) throws SecurityException;
+ String authenticationToken) throws SecurityException;
- void updateUser(User modifiedUser, AuthenticationToken authenticationToken) throws SecurityException;
+ void updateUser(User modifiedUser, String authenticationToken) throws SecurityException;
- AuthenticationToken login(String login, String password, String id);
+ String login(String login, String password, String id);
}
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 8a253f27423751210ba30cb81ff757af5577968c..451ed2a5d46f8fef5f6759eaa58b6a28df3ab193 100644
--- a/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
+++ b/service/src/main/java/lcsb/mapviewer/services/utils/CreateProjectParams.java
@@ -16,14 +16,12 @@ import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.primefaces.model.TreeNode;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorParamDefinition;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.user.UserAnnotatorsParam;
import lcsb.mapviewer.services.overlay.AnnotatedObjectTreeRow;
-import lcsb.mapviewer.services.view.AuthenticationToken;
/**
* Set of parameters used during creation of new project.
@@ -143,7 +141,7 @@ public class CreateProjectParams {
*/
private String projectDir;
- private AuthenticationToken authenticationToken;
+ private String authenticationToken;
/**
* Map that contains information what kind of annotators should be used for
@@ -162,11 +160,11 @@ public class CreateProjectParams {
* obligatory for which class.
*/
private Map<Class<? extends BioEntity>, Set<MiriamType>> requiredAnnotations = null;
-
+
/**
* List with annotators parameters.
*/
- private List<UserAnnotatorsParam> annotatorsParams = null;
+ private List<UserAnnotatorsParam> annotatorsParams = new ArrayList<>();
/**
* @param projectId
@@ -551,27 +549,27 @@ public class CreateProjectParams {
public void setAnnotatorsMap(Map<Class<?>, List<String>> annotatorsMap) {
this.annotatorsMap = annotatorsMap;
}
-
+
/**
* @return the annotators params
*/
public List<UserAnnotatorsParam> getAnnotatorsParams() {
return annotatorsParams;
}
-
- public Map<Class<?>, List<UserAnnotatorsParam>> getAnnotatorsParamsAsMap(){
-
- Map<Class<?>, List<UserAnnotatorsParam>> paramsMap = new HashMap<>();
-
- for (UserAnnotatorsParam param: getAnnotatorsParams()){
- Class<?> annotatorClassName = param.getAnnotatorClassName();
- if (!paramsMap.containsKey(annotatorClassName)) {
- paramsMap.put(annotatorClassName, new ArrayList<>());
- }
- paramsMap.get(annotatorClassName).add(param);
- }
-
- return paramsMap;
+
+ public Map<Class<?>, List<UserAnnotatorsParam>> getAnnotatorsParamsAsMap() {
+
+ Map<Class<?>, List<UserAnnotatorsParam>> paramsMap = new HashMap<>();
+
+ for (UserAnnotatorsParam param : getAnnotatorsParams()) {
+ Class<?> annotatorClassName = param.getAnnotatorClassName();
+ if (!paramsMap.containsKey(annotatorClassName)) {
+ paramsMap.put(annotatorClassName, new ArrayList<>());
+ }
+ paramsMap.get(annotatorClassName).add(param);
+ }
+
+ return paramsMap;
}
/**
@@ -765,7 +763,7 @@ public class CreateProjectParams {
* @return the authenticationToken
* @see #authenticationToken
*/
- public AuthenticationToken getAuthenticationToken() {
+ public String getAuthenticationToken() {
return authenticationToken;
}
@@ -774,7 +772,7 @@ public class CreateProjectParams {
* the authenticationToken to set
* @see #authenticationToken
*/
- public CreateProjectParams authenticationToken(AuthenticationToken authenticationToken) {
+ public CreateProjectParams authenticationToken(String authenticationToken) {
this.authenticationToken = authenticationToken;
return this;
diff --git a/service/src/main/java/lcsb/mapviewer/services/view/AuthenticationToken.java b/service/src/main/java/lcsb/mapviewer/services/view/AuthenticationToken.java
deleted file mode 100644
index 0c826590405fd40e0e271632fe60303855c13090..0000000000000000000000000000000000000000
--- a/service/src/main/java/lcsb/mapviewer/services/view/AuthenticationToken.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package lcsb.mapviewer.services.view;
-
-import java.math.BigInteger;
-import java.security.SecureRandom;
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-
-public class AuthenticationToken {
- private String id;
-// private Calendar expires;
-
- public AuthenticationToken() {
- this(new BigInteger(130, new SecureRandom()).toString(32));
- }
-
- public AuthenticationToken(String id) {
- this.id = id;
-// expires = Calendar.getInstance();
-// expires.add(Calendar.HOUR, 2);
- }
-
- /**
- * @return the id
- * @see #id
- */
- public String getId() {
- return id;
- }
-
-// /**
-// * @return the expires
-// * @see #expires
-// */
-// public Calendar getExpires() {
-// return expires;
-// }
-//
-// @Override
-// public String toString() {
-// return getId() + ", expirese: " + new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSSXXX").format(expires.getTime());
-// }
-//
-}
diff --git a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
index b7eaa4225800da8e01abf213f9944b4b7d6705b5..118a8d67e51e24e700449ceab05c1d1f4e9feabf 100644
--- a/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
+++ b/service/src/test/java/lcsb/mapviewer/services/ServiceTestFunctions.java
@@ -86,6 +86,7 @@ import lcsb.mapviewer.services.search.db.drug.IDrugService;
@ContextConfiguration(locations = { "/applicationContext-annotation.xml", //
"/applicationContext-persist.xml", //
"/applicationContext-service.xml", //
+ "/test-applicationContext.xml", //
"/dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
index ef435d1a1c393df4a69a7597a60ff845caab5dd9..4f8644c3d0fc39cf56a41712bda473bd3bcbe6e2 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -26,223 +26,232 @@ import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.search.comment.FullCommentView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.CommentView;
@Rollback(true)
public class CommentServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(CommentServiceTest.class);
- Model model;
- Project project;
- Element alias;
- Element alias2;
- private String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- try {
- dbUtils.setAutoFlush(true);
- project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- project = new Project();
- project.setProjectId(projectId);
- model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
- model.setTileSize(128);
- Set<Element> aliases = model.getElements();
- alias = null;
- alias2 = null;
- for (Element nAlias : aliases) {
- alias2 = alias;
- alias = nAlias;
- }
- project.addModel(model);
- projectDao.add(project);
-
-
- projectDao.evict(project);
- modelDao.evict(model);
-
- project = projectDao.getById(project.getId());
- model = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(project.getProjectId(), false));
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @After
- public void tearDown() throws Exception {
- try {
- projectDao.delete(project);
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
- @Test
- public void testGetAgregatedComments() throws Exception {
- try {
- commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false, model);
- CommentService service = new CommentService();
- service.setCommentDao(commentDao);
- List<List<Comment>> comments = service.getAgregatedComments(model, null);
- assertEquals(4, comments.size());
- int size = 0;
- for (List<Comment> list : comments) {
- size += list.size();
- }
- assertEquals(5, size);
-
- List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
- assertEquals(5, allComments.size());
- for (Comment comment : allComments) {
- commentDao.delete(comment);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAgregatedCommentsIntoMarker() throws Exception {
- try {
- commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false, model);
- commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false, model);
- CommentService service = new CommentService();
- service.setCommentDao(commentDao);
- List<List<Comment>> comments = service.getAgregatedComments(model, null);
- assertEquals(4, comments.size());
-
- List<FullCommentView> markers = service.agregatedCommentsIntoMarker(comments, model);
- assertNotNull(markers);
- assertEquals(4, markers.size());
-
- assertEquals(2, markers.get(0).getComments().size());
- assertEquals("Conteneta 1", markers.get(0).getComments().get(0).getRight());
- assertEquals(1, markers.get(1).getComments().size());
-
- List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
- assertEquals(5, allComments.size());
- for (Comment comment : allComments) {
- commentDao.delete(comment);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddComment() throws Exception {
- try {
-
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), null, false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCommentForReaction() throws Exception {
- try {
-
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), model.getReactions().iterator().next(), false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAddCommentForAlias() throws Exception {
- try {
- Element alias = model.getElementByElementId("sa1");
- long counter = commentService.getCommentCount();
- Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
- long counter2 = commentService.getCommentCount();
- assertEquals(counter + 1, counter2);
- commentDao.delete(feedback);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionComment() throws Exception {
- try {
- User admin = userService.getUserByLogin("admin");
- userService.setUserPrivilege(admin, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, admin));
-
- Reaction reaction = model.getReactionByReactionId("re3");
- Comment comment = commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), reaction, false, model);
-
- AuthenticationToken adminToken;
- // assume that we have admin account with all the privileges
- adminToken = userService.login("admin", "admin");
-
- List<CommentView> views = commentService.getCommentsByMap(model, adminToken);
- assertNotNull(views.get(0).getTitle());
- commentDao.delete(comment);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertTrue(cs.equalPoints("Point2D.Double[117.685546875, 204.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId2() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertFalse(cs.equalPoints("Point2D.Double[118.685546875, 204.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComparePointCommentId3() throws Exception {
- try {
- CommentService cs = new CommentService();
- assertFalse(cs.equalPoints("Point2D.Double[117.685546875, 205.6923828125001]", "(117.69, 204.69)"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ static Logger logger = Logger.getLogger(CommentServiceTest.class);
+ Model model;
+ Project project;
+ Element alias;
+ Element alias2;
+ private String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ try {
+ dbUtils.setAutoFlush(true);
+ project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ project = new Project();
+ project.setProjectId(projectId);
+ model = getModelForFile("testFiles/centeredAnchorInModifier.xml", false);
+ model.setTileSize(128);
+ Set<Element> aliases = model.getElements();
+ alias = null;
+ alias2 = null;
+ for (Element nAlias : aliases) {
+ alias2 = alias;
+ alias = nAlias;
+ }
+ project.addModel(model);
+ projectDao.add(project);
+
+ projectDao.evict(project);
+ modelDao.evict(model);
+
+ project = projectDao.getById(project.getId());
+ model = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(project.getProjectId(), false));
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ try {
+ projectDao.delete(project);
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ @Test
+ public void testGetAgregatedComments() throws Exception {
+ try {
+ commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false,
+ model);
+ CommentService service = new CommentService();
+ service.setCommentDao(commentDao);
+ List<List<Comment>> comments = service.getAgregatedComments(model, null);
+ assertEquals(4, comments.size());
+ int size = 0;
+ for (List<Comment> list : comments) {
+ size += list.size();
+ }
+ assertEquals(5, size);
+
+ List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
+ assertEquals(5, allComments.size());
+ for (Comment comment : allComments) {
+ commentDao.delete(comment);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAgregatedCommentsIntoMarker() throws Exception {
+ try {
+ commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetb 2", model, new Point2D.Double(0, 2), alias, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 3", model, new Point2D.Double(0, 3), alias2, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 4", model, new Point2D.Double(0, 4), null, false,
+ model);
+ commentService.addComment("John Doe", "a@a.pl", "Contenetc 5", model, new Point2D.Double(0, 5), null, false,
+ model);
+ CommentService service = new CommentService();
+ service.setCommentDao(commentDao);
+ List<List<Comment>> comments = service.getAgregatedComments(model, null);
+ assertEquals(4, comments.size());
+
+ List<FullCommentView> markers = service.agregatedCommentsIntoMarker(comments, model);
+ assertNotNull(markers);
+ assertEquals(4, markers.size());
+
+ assertEquals(2, markers.get(0).getComments().size());
+ assertEquals("Conteneta 1", markers.get(0).getComments().get(0).getRight());
+ assertEquals(1, markers.get(1).getComments().size());
+
+ List<Comment> allComments = commentDao.getCommentByModel(model, null, null);
+ assertEquals(5, allComments.size());
+ for (Comment comment : allComments) {
+ commentDao.delete(comment);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddComment() throws Exception {
+ try {
+
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), null, false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCommentForReaction() throws Exception {
+ try {
+
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0),
+ model.getReactions().iterator().next(), false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAddCommentForAlias() throws Exception {
+ try {
+ Element alias = model.getElementByElementId("sa1");
+ long counter = commentService.getCommentCount();
+ Comment feedback = commentService.addComment("a", "b", "c", model, new Point2D.Double(0, 0), alias, false, model);
+ long counter2 = commentService.getCommentCount();
+ assertEquals(counter + 1, counter2);
+ commentDao.delete(feedback);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionComment() throws Exception {
+ try {
+ User admin = userService.getUserByLogin("admin");
+ userService.setUserPrivilege(admin, new ObjectPrivilege(project, 1, PrivilegeType.VIEW_PROJECT, admin));
+
+ Reaction reaction = model.getReactionByReactionId("re3");
+ Comment comment = commentService.addComment("John Doe", "a@a.pl", "Conteneta 1", model, new Point2D.Double(0, 1),
+ reaction, false, model);
+
+ // assume that we have admin account with all the privileges
+ String adminToken = userService.login("admin", "admin");
+
+ List<CommentView> views = commentService.getCommentsByMap(model, adminToken);
+ assertNotNull(views.get(0).getTitle());
+ commentDao.delete(comment);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertTrue(cs.equalPoints("Point2D.Double[117.685546875, 204.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId2() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertFalse(cs.equalPoints("Point2D.Double[118.685546875, 204.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComparePointCommentId3() throws Exception {
+ try {
+ CommentService cs = new CommentService();
+ assertFalse(cs.equalPoints("Point2D.Double[117.685546875, 205.6923828125001]", "(117.69, 204.69)"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
index ca85d27c3a208e4abbd7c949575e776baaa96e46..3e3cc18f68168b3cebf88b489fd261cb3ef847d6 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -39,7 +39,6 @@ import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
import lcsb.mapviewer.services.utils.EmailSender;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
public class LayoutServiceTest extends ServiceTestFunctions {
@@ -60,7 +59,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
ILayoutService layoutService;
// assume that we have admin account with all the privileges
- AuthenticationToken adminToken;
+ String adminToken;
@Before
public void setUp() throws Exception {
@@ -362,7 +361,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
layoutService.createLayout(params);
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+ String token = userService.login(user.getLogin(), "passwd");
Project pr2 = projectService.getProjectByProjectId(localProject.getProjectId(), token);
Model fromDbModel = pr2.getModels().iterator().next().getModel();
@@ -402,7 +401,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
LayoutView row = layoutService.createLayout(params);
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+ String token = userService.login(user.getLogin(), "passwd");
assertNotNull(row);
assertNotNull(row.getIdObject());
@@ -440,7 +439,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
LayoutView row = layoutService.createLayout(params);
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+ String token = userService.login(user.getLogin(), "passwd");
List<LightLayoutAliasView> result = layoutService.getAliasesForLayout(model, row.getIdObject(), token);
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
index 8ba0310fdeb3adec3616b12484db01e264cc3f3d..11cc1b98006d3ffbf892157e35d3f2b6fef8575d 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ModelServiceTest.java
@@ -27,140 +27,139 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.ServiceTestFunctions;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ProjectView;
@Rollback(true)
public class ModelServiceTest extends ServiceTestFunctions {
- static Logger logger = Logger.getLogger(ModelServiceTest.class);
- @Autowired
- IModelService modelService;
-
- @Autowired
- PubmedParser backend;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testRemoveModel() throws Exception {
- try {
- String directory = "test_directory";
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/sample.xml", false);
- model.addLayout(new Layout("test", directory, false));
-
- project.addModel(model);
- projectDao.update(project);
-
- MapGenerator generator = new MapGenerator();
- MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(directory);
- generator.generateMapImages(params);
-
- AuthenticationToken adminToken = userService.login("admin", "admin");
- ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
- projectService.removeProject(row, null, false, adminToken);
-
- File file = new File(directory);
- assertFalse(file.exists());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetAliasByIds() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- int counter = 0;
- Element alias0 = null;
- for (Element alias : model.getElements()) {
- if (counter == 0) {
- alias0 = alias;
- }
- alias.setId(counter++);
- }
- List<Pair<Integer, Integer>> identifiers = new ArrayList<>();
- identifiers.add(new Pair<Integer, Integer>(0, 0));
- List<LightAliasView> list = modelService.getLightAliasesByIds(model, identifiers);
- assertEquals(1, list.size());
- assertEquals(alias0.getX(), list.get(0).getBounds().getX(), EPSILON);
- assertEquals(alias0.getY(), list.get(0).getBounds().getY(), EPSILON);
- assertEquals(alias0.getWidth(), list.get(0).getBounds().getWidth(), EPSILON);
- assertEquals(alias0.getHeight(), list.get(0).getBounds().getHeight(), EPSILON);
- identifiers.add(new Pair<Integer, Integer>(0, 5));
- list = modelService.getLightAliasesByIds(model, identifiers);
- assertEquals(2, list.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testGetAliasByInvalidIds() throws Exception {
- try {
- Model model = getModelForFile("testFiles/db_problem_model.xml", false);
- List<Pair<Integer, Integer>> identifiers = new ArrayList<>();
- // check with wrong alias id
- identifiers.add(new Pair<Integer, Integer>(0, 1));
- try {
- modelService.getLightAliasesByIds(model, identifiers);
- fail(InvalidArgumentException.class + " expected");
- } catch (InvalidArgumentException e) {
-
- }
- identifiers = new ArrayList<>();
- // check with wrong model id
- identifiers.add(new Pair<Integer, Integer>(1, 0));
- try {
- modelService.getLightAliasesByIds(model, identifiers);
- fail(InvalidArgumentException.class + " expected");
- } catch (InvalidArgumentException e) {
-
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testAddModel() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
-
- Model model = getModelForFile("testFiles/db_problem_model.xml", false);
-
- project.addModel(model);
- projectDao.update(project);
-
- AuthenticationToken adminToken = userService.login("admin", "admin");
- ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
- projectService.removeProject(row, null, false, adminToken);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
+ static Logger logger = Logger.getLogger(ModelServiceTest.class);
+ @Autowired
+ IModelService modelService;
+
+ @Autowired
+ PubmedParser backend;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testRemoveModel() throws Exception {
+ try {
+ String directory = "test_directory";
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ model.addLayout(new Layout("test", directory, false));
+
+ project.addModel(model);
+ projectDao.update(project);
+
+ MapGenerator generator = new MapGenerator();
+ MapGeneratorParams params = generator.new MapGeneratorParams().model(model).directory(directory);
+ generator.generateMapImages(params);
+
+ String adminToken = userService.login("admin", "admin");
+ ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
+ projectService.removeProject(row, null, false, adminToken);
+
+ File file = new File(directory);
+ assertFalse(file.exists());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetAliasByIds() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ int counter = 0;
+ Element alias0 = null;
+ for (Element alias : model.getElements()) {
+ if (counter == 0) {
+ alias0 = alias;
+ }
+ alias.setId(counter++);
+ }
+ List<Pair<Integer, Integer>> identifiers = new ArrayList<>();
+ identifiers.add(new Pair<Integer, Integer>(0, 0));
+ List<LightAliasView> list = modelService.getLightAliasesByIds(model, identifiers);
+ assertEquals(1, list.size());
+ assertEquals(alias0.getX(), list.get(0).getBounds().getX(), EPSILON);
+ assertEquals(alias0.getY(), list.get(0).getBounds().getY(), EPSILON);
+ assertEquals(alias0.getWidth(), list.get(0).getBounds().getWidth(), EPSILON);
+ assertEquals(alias0.getHeight(), list.get(0).getBounds().getHeight(), EPSILON);
+ identifiers.add(new Pair<Integer, Integer>(0, 5));
+ list = modelService.getLightAliasesByIds(model, identifiers);
+ assertEquals(2, list.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testGetAliasByInvalidIds() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/db_problem_model.xml", false);
+ List<Pair<Integer, Integer>> identifiers = new ArrayList<>();
+ // check with wrong alias id
+ identifiers.add(new Pair<Integer, Integer>(0, 1));
+ try {
+ modelService.getLightAliasesByIds(model, identifiers);
+ fail(InvalidArgumentException.class + " expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ identifiers = new ArrayList<>();
+ // check with wrong model id
+ identifiers.add(new Pair<Integer, Integer>(1, 0));
+ try {
+ modelService.getLightAliasesByIds(model, identifiers);
+ fail(InvalidArgumentException.class + " expected");
+ } catch (InvalidArgumentException e) {
+
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testAddModel() throws Exception {
+ try {
+ String projectId = "Some_id";
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+
+ Model model = getModelForFile("testFiles/db_problem_model.xml", false);
+
+ project.addModel(model);
+ projectDao.update(project);
+
+ String adminToken = userService.login("admin", "admin");
+ ProjectView row = projectService.getProjectViewByProjectId(project.getProjectId(), adminToken);
+ projectService.removeProject(row, null, false, adminToken);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
}
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 67a3fcdfd6b2136bcbcbb6f580c2402ae194855d..de1196579ef6b56fe915a0cab70fa3b7d88b069a 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -55,7 +55,6 @@ 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.ConfigurationView;
import lcsb.mapviewer.services.view.ProjectView;
@@ -72,7 +71,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
ElementDao aliasDao;
// assume that we have admin account with all the privileges
- AuthenticationToken adminToken;
+ String adminToken;
@Before
public void setUp() throws Exception {
@@ -84,10 +83,10 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
@Test
- public void testGetProjectWithoutAccessToEverything() {
+ public void testGetProjectWithoutAccessToEverything() throws Exception {
try {
createUser();
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+ String token = userService.login(user.getLogin(), "passwd");
List<Project> projects = projectService.getAllProjects(token);
assertNotNull(projects);
} catch (Exception e) {
@@ -97,7 +96,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
@Test
- public void test() {
+ public void test() throws Exception {
try {
List<Project> projects = projectService.getAllProjects(adminToken);
@@ -251,9 +250,6 @@ public class ProjectServiceTest extends ServiceTestFunctions {
public void testCreateComplex() throws Exception {
String projectId = "test_id";
try {
- createUser();
- AuthenticationToken token = userService.login(user.getLogin(), "passwd");
-
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);
@@ -275,11 +271,11 @@ public class ProjectServiceTest extends ServiceTestFunctions {
images(true).//
async(false).//
projectDir(tmpResultDir).//
- addUser(user.getLogin(), "admin").//
+ addUser("admin", "admin").//
analyzeAnnotations(true));
- Project project = projectService.getProjectByProjectId(projectId, token);
+ Project project = projectService.getProjectByProjectId(projectId, adminToken);
- Model model = modelService.getLastModelByProjectId(projectId, token);
+ Model model = modelService.getLastModelByProjectId(projectId, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -691,7 +687,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
}
assertTrue("Cannot find data mining information for the model", dmFound);
projectService.removeProject(project, null, false, adminToken);
- AuthenticationToken token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
+ String token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
assertNull(projectService.getProjectByProjectId(name, token));
} catch (Exception e) {
e.printStackTrace();
@@ -723,8 +719,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
projectDir(tmpResultDir).//
addUser("admin", "admin").//
analyzeAnnotations(true));
- AuthenticationToken token = userService.login("admin", "admin");
- Project project = projectService.getProjectByProjectId(projectId, token);
+ Project project = projectService.getProjectByProjectId(projectId, adminToken);
return project;
}
diff --git a/service/src/test/resources/test-applicationContext.xml b/service/src/test/resources/test-applicationContext.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9bd238746219dfb4bf7a443451209c5d8ecb9116
--- /dev/null
+++ b/service/src/test/resources/test-applicationContext.xml
@@ -0,0 +1,14 @@
+<beans xmlns="http://www.springframework.org/schema/beans"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:tx="http://www.springframework.org/schema/tx"
+ xmlns:context="http://www.springframework.org/schema/context"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-4.0.xsd
+ http://www.springframework.org/schema/tx
+ http://www.springframework.org/schema/tx/spring-tx-4.0.xsd
+ http://www.springframework.org/schema/context
+ http://www.springframework.org/schema/context/spring-context-4.0.xsd">
+
+ <bean id="SessionRegistry" class="org.springframework.security.core.session.SessionRegistryImpl"/>
+
+</beans>
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
index b93fdd83be4beaa8cbf60a0da5a956f6af3e40ac..692c2af511d270b38661eeca476e730ec688d347 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ConfigurationBean.java
@@ -25,7 +25,6 @@ import lcsb.mapviewer.common.FrameworkVersion;
import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.UserAccessException;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
@@ -42,468 +41,470 @@ import lcsb.mapviewer.services.view.ProjectView;
@ViewScoped
public class ConfigurationBean extends AbstractManagedBean implements Serializable {
- /**
- * String representing {@link ConfigurationElementType#DEFAULT_MAP} system
- * property used by {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String DEFAULT_MODEL_PROPERTY = "DEFAULT_MODEL";
-
- /**
- * String representing {@link ConfigurationElementType#X_FRAME_DOMAIN} system
- * property used by {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String X_FRAME_PROPERTY = "X_FRAME";
-
- /**
- * String representing {@link #logoImg} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_IMG_PROPERTY = "LOGO_IMG";
-
- /**
- * String representing {@link #logoLink} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_LINK_PROPERTY = "LOGO_LINK";
-
- /**
- * String representing {@link #logoText} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGO_TEXT_PROPERTY = "LOGO_TEXT";
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ConfigurationBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * List of values for all possible configurable parameters.
- */
- private List<ConfigurationView> values = new ArrayList<>();
-
- /**
- * Release version of the framework.
- */
- private FrameworkVersion version;
-
- /**
- * Configrutaion params value.
- */
- private Map<ConfigurationElementType, String> valueMap = new HashMap<>();
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used to access information about projects.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- @Override
- public final void init() {
- // listener that checks if the new default map exists in the system
- VetoableChangeListener selectedMapVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- if ((DEFAULT_MODEL_PROPERTY).equals(arg0.getPropertyName())) {
- if (!projectService.projectExists((String) arg0.getNewValue())) {
- throw new PropertyVetoException("Project " + arg0.getNewValue() + " doesn't exist", arg0);
- } else {
- ProjectView view;
- try {
- view = projectService.getProjectViewByProjectId((String) arg0.getNewValue(), userBean.getAuthenticationToken());
- } catch (UserAccessException e) {
- throw new PropertyVetoException("You have no privilege to perform this operation", arg0);
- }
- if (!view.getStatus().equalsIgnoreCase("OK")) {
- throw new PropertyVetoException("Project " + arg0.getNewValue() + " is invalid. Project status: " + view.getStatus(), arg0);
- }
- }
- }
- }
- };
- addVetoablePropertyChangeListener(selectedMapVetoChanged);
-
- PropertyChangeListener xFrameChanged = new PropertyChangeListener() {
-
- @Override
- public void propertyChange(PropertyChangeEvent arg0) {
- if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
- Configuration.setxFrameDomain((String) arg0.getNewValue());
- }
- }
- };
- addPropertyChangeListener(xFrameChanged);
-
- // listener that checks if the new x-fram address is valid
- VetoableChangeListener xFrameVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
- String domain = (String) arg0.getNewValue();
- if (!new UrlValidator().isValid(domain) && !(domain != null && domain.contains("localhost"))) {
- throw new PropertyVetoException("Invalid address: " + domain, arg0);
- }
- }
- }
- };
- addVetoablePropertyChangeListener(xFrameVetoChanged);
-
- version = configurationService.getSystemVersion(getProjectDeployPath());
-
- refreshValues(null);
-
- Configuration.setWebAppDir(new File(getPrimefacesUtils().getPath() + "../").getAbsolutePath() + "/");
- }
-
- /**
- * Refresh values from the database.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public final void refreshValues(final ActionEvent actionEvent) {
- values = configurationService.getAllValues();
- for (ConfigurationView view : values) {
- valueMap.put(view.getType(), view.getValue());
- }
- }
-
- /**
- * Save values to the database.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public final void saveValues(final ActionEvent actionEvent) {
- // first check if we have privileges
- if (getUserHasConfigurationView()) {
- setValues(values);
- configurationService.updateConfiguration(values);
- values = configurationService.getAllValues();
- }
- }
-
- /**
- * Checks if logged user can manage the configuration of the system.
- *
- * @return <code>true</code> if logged user can manage the configuration,
- * <code>false</code> otherwise
- */
- public final boolean getUserHasConfigurationView() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.CONFIGURATION_MANAGE);
- return result;
- }
-
- /**
- *
- * @return list of all configuration values
- * @see #values
- */
- public final List<ConfigurationView> getValues() {
- if (getUserHasConfigurationView()) {
- return values;
- } else {
- return new ArrayList<>();
- }
- }
-
- /**
- * Sets the new list of configurable parameters.
- *
- * @param values
- * list of configurable parameters with new values
- */
- public final void setValues(final List<ConfigurationView> values) {
- // when we set new values we should:
- // 1) check if they are correct (vchs listeners)
- // 2) notify apropriate listeners
-
- // for the naming convention of parameters take a look at {@link #vchs}
-
- // remember the old values from the system (!! not from the bean !!)
- List<ConfigurationView> old = configurationService.getAllValues();
- this.values = values;
- for (ConfigurationView el : values) {
- String newVal = el.getValue();
- String oldVal = null;
- for (ConfigurationView oldEl : old) {
- if (oldEl.getType().equals(el.getType())) {
- oldVal = oldEl.getValue();
- }
- }
- try {
- if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
- fireVetoableChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
- }
- } catch (PropertyVetoException e) { // if there was a veto then rollback
- // to system parameters
- this.values = old;
- logger.debug("Rollback because parameter " + el.getType().name() + " contains inproper value: " + newVal);
- sendError(e.getMessage());
- return;
- }
- }
- for (ConfigurationView el : values) {
- String newVal = el.getValue();
- String oldVal = null;
- for (ConfigurationView oldEl : old) {
- if (oldEl.getType().equals(el.getType())) {
- oldVal = oldEl.getValue();
- }
- }
- if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
- firePropertyChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
- } else if (el.getType().equals(ConfigurationElementType.X_FRAME_DOMAIN)) {
- firePropertyChange(X_FRAME_PROPERTY, oldVal, newVal);
- }
-
- }
- }
-
- @Override
- public void clear() {
- setValues(new ArrayList<ConfigurationView>());
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the version
- * @see #version
- */
- public FrameworkVersion getVersion() {
- return version;
- }
-
- /**
- * @param version
- * the version to set
- * @see #version
- */
- public void setVersion(FrameworkVersion version) {
- this.version = version;
- }
-
- /**
- * Returns {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
- * analytics identifier} used for tracking web-service usage.
- *
- * @return {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
- * analytics identifier} used for tracking web-service usage
- */
- public String getGoogleAnalyticsIdentifier() {
- return valueMap.get(ConfigurationElementType.GOOGLE_ANALYTICS_IDENTIFIER);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_IMG logo image}.
- *
- * @return {@link ConfigurationElementType#LOGO_IMG logo image}
- */
- public String getLogoImg() {
- return valueMap.get(ConfigurationElementType.LOGO_IMG);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_LINK logo link}.
- *
- * @return {@link ConfigurationElementType#LOGO_LINK logo link}
- */
- public String getLogoLink() {
- return valueMap.get(ConfigurationElementType.LOGO_LINK);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LOGO_TEXT alt text for logo}.
- *
- * @return {@link ConfigurationElementType#LOGO_TEXT alt text for logo}
- */
- public String getLogoText() {
- return valueMap.get(ConfigurationElementType.LOGO_TEXT);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}
- */
- public String getLegendFile1() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_1);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}
- */
- public String getLegendFile2() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_2);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}
- */
- public String getLegendFile3() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_3);
- }
-
- /**
- * Returns {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}.
- *
- * @return {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}
- */
- public String getLegendFile4() {
- return valueMap.get(ConfigurationElementType.LEGEND_FILE_4);
- }
-
- /**
- * Returns {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}.
- *
- * @return {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}
- */
- public String getUserManual() {
- return valueMap.get(ConfigurationElementType.USER_MANUAL_FILE);
- }
-
- /**
- * Returns {@link String} with estimated current memory usage (in MB).
- *
- * @return estimated current memory usage (in MB)
- */
- public String getMemoryUsage() {
- return NumberFormat.getInstance().format(configurationService.getMemoryUsage()) + " MB";
- }
-
- /**
- * Returns {@link String} with max memory available to JVM (in MB).
- *
- * @return max memory available to JVM (in MB)
- */
- public String getMaxMemory() {
- return NumberFormat.getInstance().format(configurationService.getMaxMemory()) + " MB";
- }
-
- /**
- * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values.
- *
- * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values
- */
- public String getMinColor() {
- return valueMap.get(ConfigurationElementType.MIN_COLOR_VAL);
- }
-
- /**
- * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with negative values.
- *
- * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
- * representing overlay element with positive values
- */
- public String getMaxColor() {
- return valueMap.get(ConfigurationElementType.MAX_COLOR_VAL);
- }
+ /**
+ * String representing {@link ConfigurationElementType#DEFAULT_MAP} system
+ * property used by {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String DEFAULT_MODEL_PROPERTY = "DEFAULT_MODEL";
+
+ /**
+ * String representing {@link ConfigurationElementType#X_FRAME_DOMAIN} system
+ * property used by {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String X_FRAME_PROPERTY = "X_FRAME";
+
+ /**
+ * String representing {@link #logoImg} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LOGO_IMG_PROPERTY = "LOGO_IMG";
+
+ /**
+ * String representing {@link #logoLink} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LOGO_LINK_PROPERTY = "LOGO_LINK";
+
+ /**
+ * String representing {@link #logoText} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LOGO_TEXT_PROPERTY = "LOGO_TEXT";
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ConfigurationBean.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * List of values for all possible configurable parameters.
+ */
+ private List<ConfigurationView> values = new ArrayList<>();
+
+ /**
+ * Release version of the framework.
+ */
+ private FrameworkVersion version;
+
+ /**
+ * Configrutaion params value.
+ */
+ private Map<ConfigurationElementType, String> valueMap = new HashMap<>();
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * users (including information about currently logged user).
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
+ /**
+ * Service used to access configuration parameters.
+ *
+ * @see IConfigurationService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ /**
+ * Service used to access information about users.
+ *
+ * @see IUserService
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Service used to access information about projects.
+ *
+ * @see IProjectService
+ */
+ @ManagedProperty(value = "#{ProjectService}")
+ private transient IProjectService projectService;
+
+ @Override
+ public final void init() {
+ // listener that checks if the new default map exists in the system
+ VetoableChangeListener selectedMapVetoChanged = new VetoableChangeListener() {
+ @Override
+ public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
+ if ((DEFAULT_MODEL_PROPERTY).equals(arg0.getPropertyName())) {
+ if (!projectService.projectExists((String) arg0.getNewValue())) {
+ throw new PropertyVetoException("Project " + arg0.getNewValue() + " doesn't exist", arg0);
+ } else {
+ ProjectView view;
+ try {
+ view = projectService.getProjectViewByProjectId((String) arg0.getNewValue(),
+ userBean.getAuthenticationToken());
+ } catch (lcsb.mapviewer.services.SecurityException e) {
+ throw new PropertyVetoException("You have no privilege to perform this operation", arg0);
+ }
+ if (!view.getStatus().equalsIgnoreCase("OK")) {
+ throw new PropertyVetoException(
+ "Project " + arg0.getNewValue() + " is invalid. Project status: " + view.getStatus(), arg0);
+ }
+ }
+ }
+ }
+ };
+ addVetoablePropertyChangeListener(selectedMapVetoChanged);
+
+ PropertyChangeListener xFrameChanged = new PropertyChangeListener() {
+
+ @Override
+ public void propertyChange(PropertyChangeEvent arg0) {
+ if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
+ Configuration.setxFrameDomain((String) arg0.getNewValue());
+ }
+ }
+ };
+ addPropertyChangeListener(xFrameChanged);
+
+ // listener that checks if the new x-fram address is valid
+ VetoableChangeListener xFrameVetoChanged = new VetoableChangeListener() {
+ @Override
+ public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
+ if ((X_FRAME_PROPERTY).equals(arg0.getPropertyName())) {
+ String domain = (String) arg0.getNewValue();
+ if (!new UrlValidator().isValid(domain) && !(domain != null && domain.contains("localhost"))) {
+ throw new PropertyVetoException("Invalid address: " + domain, arg0);
+ }
+ }
+ }
+ };
+ addVetoablePropertyChangeListener(xFrameVetoChanged);
+
+ version = configurationService.getSystemVersion(getProjectDeployPath());
+
+ refreshValues(null);
+
+ Configuration.setWebAppDir(new File(getPrimefacesUtils().getPath() + "../").getAbsolutePath() + "/");
+ }
+
+ /**
+ * Refresh values from the database.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public final void refreshValues(final ActionEvent actionEvent) {
+ values = configurationService.getAllValues();
+ for (ConfigurationView view : values) {
+ valueMap.put(view.getType(), view.getValue());
+ }
+ }
+
+ /**
+ * Save values to the database.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public final void saveValues(final ActionEvent actionEvent) {
+ // first check if we have privileges
+ if (getUserHasConfigurationView()) {
+ setValues(values);
+ configurationService.updateConfiguration(values);
+ values = configurationService.getAllValues();
+ }
+ }
+
+ /**
+ * Checks if logged user can manage the configuration of the system.
+ *
+ * @return <code>true</code> if logged user can manage the configuration,
+ * <code>false</code> otherwise
+ */
+ public final boolean getUserHasConfigurationView() {
+ User user = userBean.getLoggedUser();
+ boolean result = userService.userHasPrivilege(user, PrivilegeType.CONFIGURATION_MANAGE);
+ return result;
+ }
+
+ /**
+ *
+ * @return list of all configuration values
+ * @see #values
+ */
+ public final List<ConfigurationView> getValues() {
+ if (getUserHasConfigurationView()) {
+ return values;
+ } else {
+ return new ArrayList<>();
+ }
+ }
+
+ /**
+ * Sets the new list of configurable parameters.
+ *
+ * @param values
+ * list of configurable parameters with new values
+ */
+ public final void setValues(final List<ConfigurationView> values) {
+ // when we set new values we should:
+ // 1) check if they are correct (vchs listeners)
+ // 2) notify apropriate listeners
+
+ // for the naming convention of parameters take a look at {@link #vchs}
+
+ // remember the old values from the system (!! not from the bean !!)
+ List<ConfigurationView> old = configurationService.getAllValues();
+ this.values = values;
+ for (ConfigurationView el : values) {
+ String newVal = el.getValue();
+ String oldVal = null;
+ for (ConfigurationView oldEl : old) {
+ if (oldEl.getType().equals(el.getType())) {
+ oldVal = oldEl.getValue();
+ }
+ }
+ try {
+ if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
+ fireVetoableChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
+ }
+ } catch (PropertyVetoException e) { // if there was a veto then rollback
+ // to system parameters
+ this.values = old;
+ logger.debug("Rollback because parameter " + el.getType().name() + " contains inproper value: " + newVal);
+ sendError(e.getMessage());
+ return;
+ }
+ }
+ for (ConfigurationView el : values) {
+ String newVal = el.getValue();
+ String oldVal = null;
+ for (ConfigurationView oldEl : old) {
+ if (oldEl.getType().equals(el.getType())) {
+ oldVal = oldEl.getValue();
+ }
+ }
+ if (el.getType().equals(ConfigurationElementType.DEFAULT_MAP)) {
+ firePropertyChange(DEFAULT_MODEL_PROPERTY, oldVal, newVal);
+ } else if (el.getType().equals(ConfigurationElementType.X_FRAME_DOMAIN)) {
+ firePropertyChange(X_FRAME_PROPERTY, oldVal, newVal);
+ }
+
+ }
+ }
+
+ @Override
+ public void clear() {
+ setValues(new ArrayList<ConfigurationView>());
+ }
+
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService
+ * the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ /**
+ * @return the version
+ * @see #version
+ */
+ public FrameworkVersion getVersion() {
+ return version;
+ }
+
+ /**
+ * @param version
+ * the version to set
+ * @see #version
+ */
+ public void setVersion(FrameworkVersion version) {
+ this.version = version;
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
+ * analytics identifier} used for tracking web-service usage.
+ *
+ * @return {@link ConfigurationElementType#GOOGLE_ANALYTICS_IDENTIFIER google
+ * analytics identifier} used for tracking web-service usage
+ */
+ public String getGoogleAnalyticsIdentifier() {
+ return valueMap.get(ConfigurationElementType.GOOGLE_ANALYTICS_IDENTIFIER);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LOGO_IMG logo image}.
+ *
+ * @return {@link ConfigurationElementType#LOGO_IMG logo image}
+ */
+ public String getLogoImg() {
+ return valueMap.get(ConfigurationElementType.LOGO_IMG);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LOGO_LINK logo link}.
+ *
+ * @return {@link ConfigurationElementType#LOGO_LINK logo link}
+ */
+ public String getLogoLink() {
+ return valueMap.get(ConfigurationElementType.LOGO_LINK);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LOGO_TEXT alt text for logo}.
+ *
+ * @return {@link ConfigurationElementType#LOGO_TEXT alt text for logo}
+ */
+ public String getLogoText() {
+ return valueMap.get(ConfigurationElementType.LOGO_TEXT);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}.
+ *
+ * @return {@link ConfigurationElementType#LEGEND_FILE_1 legend file 1}
+ */
+ public String getLegendFile1() {
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_1);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}.
+ *
+ * @return {@link ConfigurationElementType#LEGEND_FILE_2 legend file 2}
+ */
+ public String getLegendFile2() {
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_2);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}.
+ *
+ * @return {@link ConfigurationElementType#LEGEND_FILE_3 legend file 3}
+ */
+ public String getLegendFile3() {
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_3);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}.
+ *
+ * @return {@link ConfigurationElementType#LEGEND_FILE_4 legend file 4}
+ */
+ public String getLegendFile4() {
+ return valueMap.get(ConfigurationElementType.LEGEND_FILE_4);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}.
+ *
+ * @return {@link ConfigurationElementType#USER_MANUAL_FILE user manual file}
+ */
+ public String getUserManual() {
+ return valueMap.get(ConfigurationElementType.USER_MANUAL_FILE);
+ }
+
+ /**
+ * Returns {@link String} with estimated current memory usage (in MB).
+ *
+ * @return estimated current memory usage (in MB)
+ */
+ public String getMemoryUsage() {
+ return NumberFormat.getInstance().format(configurationService.getMemoryUsage()) + " MB";
+ }
+
+ /**
+ * Returns {@link String} with max memory available to JVM (in MB).
+ *
+ * @return max memory available to JVM (in MB)
+ */
+ public String getMaxMemory() {
+ return NumberFormat.getInstance().format(configurationService.getMaxMemory()) + " MB";
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values.
+ *
+ * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values
+ */
+ public String getMinColor() {
+ return valueMap.get(ConfigurationElementType.MIN_COLOR_VAL);
+ }
+
+ /**
+ * Returns {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with negative values.
+ *
+ * @return {@link ConfigurationElementType#MIN_COLOR_VAL color} used for
+ * representing overlay element with positive values
+ */
+ public String getMaxColor() {
+ return valueMap.get(ConfigurationElementType.MAX_COLOR_VAL);
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java b/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
index b3b6c2e1f3907eacc517e577959233942f258be6..278b5f362fc4403159aaeba007b62b53ea736b26 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
@@ -20,7 +20,6 @@ import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
/**
@@ -32,190 +31,192 @@ import lcsb.mapviewer.services.view.LayoutView;
@ManagedBean(name = "galaxyMB")
@RequestScoped
public class GalaxyBean extends AbstractManagedBean implements Serializable {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(GalaxyBean.class);
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Status of the processed request.
- */
- private String status = null;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used for managing layouts.
- */
- @ManagedProperty(value = "#{LayoutService}")
- private transient ILayoutService layoutService;
-
- @Override
- public void clear() {
- status = null;
- }
-
- /**
- * @return the status
- * @see #status
- */
- public String getStatus() {
- if (status == null) {
- try {
- Map<String, String> requestParams = FacesContext.getCurrentInstance().getExternalContext().getRequestParameterMap();
- String identifier = requestParams.get("identifier");
- String schema = requestParams.get("expression_value");
- String login = requestParams.get("login");
- String password = requestParams.get("password");
- String modelName = requestParams.get("model");
-
- AuthenticationToken token = userService.login(login, password);
- Model model = (Model) modelService.getLastModelByProjectId(modelName, token);
- User user = null;
- if (token != null) {
- user = userService.getUserByToken(token);
- }
- LayoutView layout = layoutService.getLayoutByName(model, identifier);
- if (identifier == null) {
- status = "ERROR. Identifier cannot be null";
- } else if (schema == null) {
- status = "ERROR. Expression values schema cannot be null";
- } else if (user == null) {
- status = "ERROR. Invalid credentials.";
- } else if (modelName == null) {
- status = "ERROR. Model cannot be null.";
- } else if (model == null) {
- status = "ERROR. " + modelName + " model doesn't exist.";
- } else if (layout != null) {
- status = "ERROR. Layout with given identifier (\"" + identifier + "\") already exists.";
- } else {
- createLayout(identifier, schema, model, user);
- }
- if (!status.equals("OK")) {
- logger.warn("Problem in galaxy connector: " + status);
- }
- } catch (Exception e) {
- logger.error(e, e);
- status = "INTERNAL SERVER ERROR";
- }
- } else {
- logger.debug("Status already set...");
- }
- return status;
- }
-
- /**
- * Creates layout from coloring data.
- *
- * @param identifier
- * identifier of layout
- * @param schema
- * coloring schema (in string format)
- * @param model
- * model for which we create layout
- * @param user
- * user who will own the layout
- */
- protected void createLayout(String identifier, String schema, Model model, User user) {
- String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/" + model.getProject().getProjectId() + Math.random();
-
- InputStream stream = new ByteArrayInputStream(schema.getBytes(StandardCharsets.UTF_8));
- // the following call will execute asynchronically
- try {
- CreateLayoutParams params = new CreateLayoutParams().name(identifier).//
- directory(directory).//
- model(model).//
- colorInputStream(stream).//
- user(user).//
- async(true);
- layoutService.createLayout(params);
- status = "OK";
-
- } catch (InvalidColorSchemaException e) {
- status = "Problem with input file: " + e.getMessage();
- } catch (Exception e) {
- logger.error(e, e);
- status = "Internal server error. More details can be found in log file.";
- }
- }
-
- /**
- * @param status
- * the status to set
- * @see #status
- */
- public void setStatus(String status) {
- this.status = status;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- @Override
- public void init() {
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(GalaxyBean.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Status of the processed request.
+ */
+ private String status = null;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @ManagedProperty(value = "#{ModelService}")
+ private transient IModelService modelService;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Service used for managing layouts.
+ */
+ @ManagedProperty(value = "#{LayoutService}")
+ private transient ILayoutService layoutService;
+
+ @Override
+ public void clear() {
+ status = null;
+ }
+
+ /**
+ * @return the status
+ * @see #status
+ */
+ public String getStatus() {
+ if (status == null) {
+ try {
+ Map<String, String> requestParams = FacesContext.getCurrentInstance().getExternalContext()
+ .getRequestParameterMap();
+ String identifier = requestParams.get("identifier");
+ String schema = requestParams.get("expression_value");
+ String login = requestParams.get("login");
+ String password = requestParams.get("password");
+ String modelName = requestParams.get("model");
+
+ String token = userService.login(login, password);
+ Model model = (Model) modelService.getLastModelByProjectId(modelName, token);
+ User user = null;
+ if (token != null) {
+ user = userService.getUserByToken(token);
+ }
+ LayoutView layout = layoutService.getLayoutByName(model, identifier);
+ if (identifier == null) {
+ status = "ERROR. Identifier cannot be null";
+ } else if (schema == null) {
+ status = "ERROR. Expression values schema cannot be null";
+ } else if (user == null) {
+ status = "ERROR. Invalid credentials.";
+ } else if (modelName == null) {
+ status = "ERROR. Model cannot be null.";
+ } else if (model == null) {
+ status = "ERROR. " + modelName + " model doesn't exist.";
+ } else if (layout != null) {
+ status = "ERROR. Layout with given identifier (\"" + identifier + "\") already exists.";
+ } else {
+ createLayout(identifier, schema, model, user);
+ }
+ if (!status.equals("OK")) {
+ logger.warn("Problem in galaxy connector: " + status);
+ }
+ } catch (Exception e) {
+ logger.error(e, e);
+ status = "INTERNAL SERVER ERROR";
+ }
+ } else {
+ logger.debug("Status already set...");
+ }
+ return status;
+ }
+
+ /**
+ * Creates layout from coloring data.
+ *
+ * @param identifier
+ * identifier of layout
+ * @param schema
+ * coloring schema (in string format)
+ * @param model
+ * model for which we create layout
+ * @param user
+ * user who will own the layout
+ */
+ protected void createLayout(String identifier, String schema, Model model, User user) {
+ String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/"
+ + model.getProject().getProjectId() + Math.random();
+
+ InputStream stream = new ByteArrayInputStream(schema.getBytes(StandardCharsets.UTF_8));
+ // the following call will execute asynchronically
+ try {
+ CreateLayoutParams params = new CreateLayoutParams().name(identifier).//
+ directory(directory).//
+ model(model).//
+ colorInputStream(stream).//
+ user(user).//
+ async(true);
+ layoutService.createLayout(params);
+ status = "OK";
+
+ } catch (InvalidColorSchemaException e) {
+ status = "Problem with input file: " + e.getMessage();
+ } catch (Exception e) {
+ logger.error(e, e);
+ status = "Internal server error. More details can be found in log file.";
+ }
+ }
+
+ /**
+ * @param status
+ * the status to set
+ * @see #status
+ */
+ public void setStatus(String status) {
+ this.status = status;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the layoutService
+ * @see #layoutService
+ */
+ public ILayoutService getLayoutService() {
+ return layoutService;
+ }
+
+ /**
+ * @param layoutService
+ * the layoutService to set
+ * @see #layoutService
+ */
+ public void setLayoutService(ILayoutService layoutService) {
+ this.layoutService = layoutService;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ @Override
+ public void init() {
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java b/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
index 2c866c388497b506597d22ffce6ceeb5519128c1..89300005b0100ec6299c0e1aa6142cbbfa376fc5 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
@@ -55,757 +55,760 @@ import lcsb.mapviewer.services.view.ProjectView;
@ViewScoped
public class LayoutBean extends AbstractManagedBean implements Serializable {
- /**
- * String representing {@link #layoutFile} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LAYOUT_FILE_PROPERTY = "LAYOUT_FILE";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(LayoutBean.class);
-
- /**
- * List of custom layouts available for current user.
- */
- private List<LayoutView> customLayouts = null;
-
- /**
- * List of general layouts.
- */
- private List<LayoutView> generalLayouts = null;
-
- /**
- * Layout selected by user for editing.
- */
- private LayoutView selectedLayout = null;
-
- /**
- * Name of currently edited/created layout.
- */
- private String layoutName = "";
-
- /**
- * Description of currently edited/created layout.
- */
- private String layoutDescription = "";
-
- /**
- * Type of uploaded layout.
- */
- private ColorSchemaType layoutType = ColorSchemaType.GENERIC;
-
- /**
- * Bool information if any error during parsing layout occurred.
- */
- private boolean errorOccurred = false;
-
- /**
- * This param should identifie layout currently visualized. However this is
- * not handled properly yet.
- */
- private LayoutView visualizedLayout = new LayoutView();
-
- /**
- * File uploaded by user.
- */
- private transient File layoutFile = null;
-
- /**
- * Service used for managing layouts.
- */
- @ManagedProperty(value = "#{LayoutService}")
- private transient ILayoutService layoutService;
-
- /**
- * Service used for accessing information about maps.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the map currently
- * visualized.
- *
- * @see MapBean
- */
- @ManagedProperty(value = "#{mapMB}")
- private transient MapBean mapBean;
-
- @Override
- public void init() {
- refreshCustomLayouts(null);
-
- PropertyChangeListener uploadedFilePropertyChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LAYOUT_FILE_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- File file = (File) arg0.getNewValue();
- ZipEntryFileFactory zife = new ZipEntryFileFactory();
- LayoutZipEntryFile zif = zife.createLayoutZipEntryFile(layoutName, new FileInputStream(file));
- layoutName = zif.getName();
- layoutDescription = zif.getDescription();
- String typeStr = zif.getHeaderParameter(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
- if (typeStr != null) {
- try {
- layoutType = ColorSchemaType.valueOf(typeStr);
- } catch (IllegalArgumentException e) {
- layoutType = ColorSchemaType.GENERIC;
- sendError("Invalid type of overview: " + typeStr);
- }
- }
- } catch (Exception e) {
- sendError("Internal server error.", e);
- }
- }
- }
- };
- addPropertyChangeListener(uploadedFilePropertyChangeListener);
-
- // after object was added, refresh custom layouts list
- this.registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- logger.debug("Refreshing layouts after add: ");
- Model model = getCurrentTopModel();
- LayoutView layout = (LayoutView) event.getObject();
- if (model != null && model.getId().equals(layout.getModelId())) {
- logger.debug("OK");
- refreshCustomLayouts(null);
- mapBean.updateModelView();
- } else {
- logger.debug("NOT OK");
- }
- }
- });
-
- // after object was removed, refresh custom layouts list
- this.registerListener(new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectRemovedEvent event) {
- Model model = getCurrentTopModel();
- LayoutView layout = (LayoutView) event.getObject();
- if (model != null && model.getId().equals(layout.getModelId())) {
- refreshCustomLayouts(null);
- mapBean.updateModelView();
- }
- }
- });
- }
-
- /**
- * Check if logged user has privilege to add new layout for current map.
- *
- * @return true if logged user has privilege to add new layout for current map
- */
- public boolean getUserHasAddLayoutPrivilege() {
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
- if (model == null) {
- return false;
- }
- return layoutService.userCanAddLayout(model, user);
- }
-
- /**
- * Check if user can remove actually selected layout.
- *
- * @return <i>true</i> if user can remove actually selected layout,<br/>
- * <i>false</i> otherwise
- */
- public boolean getUserHasRemoveLayoutPrivilege() {
- User user = userBean.getLoggedUser();
- return layoutService.userCanRemoveLayout(selectedLayout, user);
- }
-
- /**
- * Refresh list of custom layouts.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshCustomLayouts(final ActionEvent actionEvent) {
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
- customLayouts = layoutService.getCustomLayouts(model, user, true, user);
- generalLayouts = layoutService.getGeneralLayouts(model);
- }
-
- /**
- * This method handle upload of a file.
- *
- * @param event
- * event send by the client with a file reference
- */
- public void handleFileUpload(final FileUploadEvent event) {
- try {
- logger.debug(event.getFile().getFileName() + " is uploaded.");
- UploadedFile uploadedFile = event.getFile();
- String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
- String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
- File file = File.createTempFile(filename + "-layout-", "." + extension);
- file.delete();
- InputStream input = uploadedFile.getInputstream();
- Files.copy(input, file.toPath());
- input.close();
- this.setLayoutFile(file);
- } catch (Exception e) {
- sendError("Problem with uploading...", e);
- }
- }
-
- /**
- * Adds public layout to the project selected in the parameter.
- *
- * @param project
- * where the new layout should be added
- */
- public void addAnonymousLayout(ProjectView project) {
- errorOccurred = false;
- Model model = modelService.getLastModelByProjectId(project.getProjectId(), userBean.getAuthenticationToken());
- addLayout(model, null);
- }
-
- /**
- * This method adds new layout to the model given in parameter.
- *
- *
- * @param model
- * where the new layout should be added
- * @param user
- * who should be the owenr of new layout (if <code>null</code> the
- * layout will be available to everybody)
- */
- private void addLayout(Model model, User user) {
- if (model == null) {
- errorOccurred = true;
- sendError("Unknown model.");
- return;
- }
- try {
- String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/" + model.getProject().getProjectId()
- + Math.random();
-
- // the following call will execute asynchronically
- CreateLayoutParams params = new CreateLayoutParams().name(layoutName).//
- directory(directory).//
- model(model).//
- description(layoutDescription).//
- colorInputStream(new FileInputStream(layoutFile)).//
- layoutFileName(layoutFile.getName()).//
- user(user).//
- colorSchemaType(layoutType).//
- async(true);
- LayoutView view = layoutService.createLayout(params);
- layoutName = "";
- layoutFile = null;
-
- ObjectAddedEvent event = new ObjectAddedEvent(view);
- super.callListeners(event);
-
- sendInfo("File processed successfully. Generating layout.");
- } catch (IOException e) {
- errorOccurred = true;
- logger.error("Problem with uploading layout", e);
- sendError(e.getMessage());
- } catch (InvalidColorSchemaException e) {
- errorOccurred = true;
- logger.error("Problem with uploading layout", e);
- sendError(e.getMessage());
- } catch (Exception e) {
- logger.error("Problem with uploading layout", e);
- sendError("Unknown problem with uploaded file...");
- }
- }
-
- /**
- * This method adds a new custom layout to currently selected map.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void addLayout(final ActionEvent actionEvent) {
- errorOccurred = false;
- User user = userBean.getLoggedUser();
- Model model = getCurrentTopModel();
-
- if (!getUserHasAddLayoutPrivilege()) {
- errorOccurred = true;
- sendError("You cannot add new layout");
- return;
- }
- addLayout(model, user);
- }
-
- /**
- * Removes layout selected by the client.
- *
- * @param actionEvent
- * action event from client side
- */
- public void removeLayout(final ActionEvent actionEvent) {
- removeLayout(selectedLayout);
- }
-
- /**
- * Removes layout given in the parameter.
- *
- * @param layout
- * layout that should be removed
- */
- public void removeLayout(LayoutView layout) {
- errorOccurred = false;
- try {
- User user = userBean.getLoggedUser();
- if (!layoutService.userCanRemoveLayout(layout, user)) {
- errorOccurred = true;
- sendError("You cannot remove this layout");
- return;
- }
- layoutService.removeLayout(layout, getProjectDeployPath());
-
- ObjectRemovedEvent event = new ObjectRemovedEvent(layout);
- super.callListeners(event);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with removing layout", e);
- }
- }
-
- /**
- * Updates selectedLayout in the service layer.
- *
- * @param actionEvent
- * action event from client side
- */
- public void updateLayout(final ActionEvent actionEvent) {
- errorOccurred = false;
- if (!getUserHasRemoveLayoutPrivilege()) {
- errorOccurred = true;
- sendError("You cannot update this layout");
- return;
- }
- try {
- layoutService.updateLayout(selectedLayout);
- refreshCustomLayouts(actionEvent);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with updating layout", e);
- }
- }
-
- /**
- * Updates layout in the service layer.
- *
- * @param layout
- * layout for update
- */
- public void updateLayout(final LayoutView layout) {
- errorOccurred = false;
- User user = userBean.getLoggedUser();
- if (!layoutService.userCanRemoveLayout(layout, user)) {
- errorOccurred = true;
- sendError("You cannot update this layout");
- return;
- }
- try {
- layoutService.updateLayout(layout);
- refreshCustomLayouts(null);
- } catch (Exception e) {
- errorOccurred = true;
- sendError("Problem with updating layout", e);
- }
- }
-
- /**
- * Returns the number of layouts that can be uploaded by the user.
- *
- * @return number of layouts that can still be uploaded by the user
- */
- public int getAvailableCustomLayoutNumber() {
- User user = userBean.getLoggedUser();
- return (int) layoutService.getAvailableCustomLayoutsNumber(user);
- }
-
- @Override
- public void clear() {
- setCustomLayouts(null);
- setSelectedLayout(null);
- setLayoutFile(null);
- setLayoutName(null);
- setErrorOccurred(false);
- setLayoutType(ColorSchemaType.GENERIC);
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- /**
- * @return the mapBean
- * @see #mapBean
- */
- public MapBean getMapBean() {
- return mapBean;
- }
-
- /**
- * @param mapBean
- * the mapBean to set
- * @see #mapBean
- */
- public void setMapBean(MapBean mapBean) {
- this.mapBean = mapBean;
- }
-
- /**
- * @return the selectedLayout
- * @see #selectedLayout
- */
- public LayoutView getSelectedLayout() {
- return selectedLayout;
- }
-
- /**
- * @param selectedLayout
- * the selectedLayout to set
- * @see #selectedLayout
- */
- public void setSelectedLayout(LayoutView selectedLayout) {
- this.selectedLayout = selectedLayout;
- }
-
- /**
- * @return the customLayouts
- * @see #customLayouts
- */
- public List<LayoutView> getCustomLayouts() {
- return customLayouts;
- }
-
- /**
- * @param customLayouts
- * the customLayouts to set
- * @see #customLayouts
- */
- public void setCustomLayouts(List<LayoutView> customLayouts) {
- this.customLayouts = customLayouts;
- }
-
- /**
- * @return the layoutFile
- * @see #layoutFile
- */
- public File getLayoutFile() {
- return layoutFile;
- }
-
- /**
- * @param layoutFile
- * the layoutFile to set
- * @see #layoutFile
- */
- public void setLayoutFile(File layoutFile) {
- File oldFile = this.layoutFile;
- this.layoutFile = layoutFile;
- firePropertyChange(LAYOUT_FILE_PROPERTY, oldFile, layoutFile);
- }
-
- /**
- * @return the layoutName
- * @see #layoutName
- */
- public String getLayoutName() {
- return layoutName;
- }
-
- /**
- * @param layoutName
- * the layoutName to set
- * @see #layoutName
- */
- public void setLayoutName(String layoutName) {
- this.layoutName = layoutName;
- }
-
- /**
- * @return the errorOccurred
- * @see #errorOccurred
- */
- public boolean isErrorOccurred() {
- return errorOccurred;
- }
-
- /**
- * @param errorOccurred
- * the errorOccurred to set
- * @see #errorOccurred
- */
- public void setErrorOccurred(boolean errorOccurred) {
- this.errorOccurred = errorOccurred;
- }
-
- /**
- * @return the visualizedLayout
- * @see #visualizedLayout
- */
- public LayoutView getVisualizedLayout() {
- return visualizedLayout;
- }
-
- /**
- * @param visualizedLayout
- * the visualizedLayout to set
- * @see #visualizedLayout
- */
- public void setVisualizedLayout(LayoutView visualizedLayout) {
- this.visualizedLayout = visualizedLayout;
- }
-
- /**
- * Updates information in {@link #visualizedLayout} object.
- *
- * @param actionEvent
- * action event from client side
- */
- public void getVisualizedLayoutDetails(final ActionEvent actionEvent) {
- if (visualizedLayout.getName() != null && !visualizedLayout.getName().trim().equals("")) {
- visualizedLayout = layoutService.getLayoutByName(getCurrentTopModel(), visualizedLayout.getName());
- if (visualizedLayout == null) {
- visualizedLayout = new LayoutView();
- } else {
- // we have new element to vizualize
- ObjectAddedEvent event = new ObjectAddedEvent(visualizedLayout);
- super.callListeners(event);
- }
- }
- }
-
- /**
- * @return the generalLayouts
- * @see #generalLayouts
- */
- public List<LayoutView> getGeneralLayouts() {
- return generalLayouts;
- }
-
- /**
- * @param generalLayouts
- * the generalLayouts to set
- * @see #generalLayouts
- */
- public void setGeneralLayouts(List<LayoutView> generalLayouts) {
- this.generalLayouts = generalLayouts;
- }
-
- /**
- * Method that allows to donlwoad input data for given layout.
- *
- * @param layout
- * layout for which input data will be downloaded
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- * @throws SecurityException
- */
- public void downloadInputData(LayoutView layout) throws IOException, SecurityException {
- // get input data from database
- byte[] data = layoutService.getInputDataForLayout(layout, userBean.getAuthenticationToken());
- String string = new String(data, StandardCharsets.UTF_8);
-
- sendFileAsResponse(string, "layout_" + layout.getIdObject() + ".txt", MimeType.TEXT);
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the layoutDescription
- * @see #layoutDescription
- */
- public String getLayoutDescription() {
- return layoutDescription;
- }
-
- /**
- * @param layoutDescription
- * the layoutDescription to set
- * @see #layoutDescription
- */
- public void setLayoutDescription(String layoutDescription) {
- this.layoutDescription = layoutDescription;
- }
-
- /**
- * This method sends list of aliases that should be visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveActiveAliasesForLayout() throws IOException {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<LightLayoutAliasView> list = layoutService.getAliasesForLayout(getCurrentTopModel(), layoutId, userBean.getAuthenticationToken());
- LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
- string = factory.createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.addAliasesForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * This method sends full information about aliases that are visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser and
- * identified by list of identifiers.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveFullAliasesForLayout() {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<FullLayoutAliasView> list = layoutService
- .getFullAliasesForLayoutByIds(getCurrentTopModel(), identifiers, layoutId, userBean.getAuthenticationToken());
- string = new FullLayoutAliasViewFactory().createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.updateAliasesForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * This method sends list of reactions that should be visualized in a
- * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
- *
- * @throws IOException
- * thrown when there is a problem with accessing information about
- * layout
- */
- public void retreiveActiveReactionsForLayout() throws IOException {
- int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
- String string = "[]";
- try {
- List<LightLayoutReactionView> list = layoutService.getReactionsForLayout(getCurrentTopModel(), layoutId, userBean.getAuthenticationToken());
- LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
- string = factory.createGson(list);
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- executeJavascript("ServerConnector.addReactionsForLayout('" + layoutId + "','" + string + "');");
- }
-
- /**
- * @return the layoutType
- * @see #layoutType
- */
- public ColorSchemaType getLayoutType() {
- return layoutType;
- }
-
- /**
- * @param layoutType
- * the layoutType to set
- * @see #layoutType
- */
- public void setLayoutType(ColorSchemaType layoutType) {
- this.layoutType = layoutType;
- }
-
- /**
- * Returns list of available layout types.
- *
- * @return list of available layout types
- */
- public ColorSchemaType[] getColorSchemaTypes() {
- return ColorSchemaType.values();
- }
-
- /**
- * Returns currently browsed map.
- *
- * @return currently browsed map
- */
- private Model getCurrentTopModel() {
- return mapBean.getCurrentTopModel();
- }
+ /**
+ * String representing {@link #layoutFile} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LAYOUT_FILE_PROPERTY = "LAYOUT_FILE";
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(LayoutBean.class);
+
+ /**
+ * List of custom layouts available for current user.
+ */
+ private List<LayoutView> customLayouts = null;
+
+ /**
+ * List of general layouts.
+ */
+ private List<LayoutView> generalLayouts = null;
+
+ /**
+ * Layout selected by user for editing.
+ */
+ private LayoutView selectedLayout = null;
+
+ /**
+ * Name of currently edited/created layout.
+ */
+ private String layoutName = "";
+
+ /**
+ * Description of currently edited/created layout.
+ */
+ private String layoutDescription = "";
+
+ /**
+ * Type of uploaded layout.
+ */
+ private ColorSchemaType layoutType = ColorSchemaType.GENERIC;
+
+ /**
+ * Bool information if any error during parsing layout occurred.
+ */
+ private boolean errorOccurred = false;
+
+ /**
+ * This param should identifie layout currently visualized. However this is not
+ * handled properly yet.
+ */
+ private LayoutView visualizedLayout = new LayoutView();
+
+ /**
+ * File uploaded by user.
+ */
+ private transient File layoutFile = null;
+
+ /**
+ * Service used for managing layouts.
+ */
+ @ManagedProperty(value = "#{LayoutService}")
+ private transient ILayoutService layoutService;
+
+ /**
+ * Service used for accessing information about maps.
+ */
+ @ManagedProperty(value = "#{ModelService}")
+ private transient IModelService modelService;
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * users (including information about currently logged user).
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
+ /**
+ * Bean used for communication with the client side about the map currently
+ * visualized.
+ *
+ * @see MapBean
+ */
+ @ManagedProperty(value = "#{mapMB}")
+ private transient MapBean mapBean;
+
+ @Override
+ public void init() {
+ refreshCustomLayouts(null);
+
+ PropertyChangeListener uploadedFilePropertyChangeListener = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (LAYOUT_FILE_PROPERTY.equals(arg0.getPropertyName())) {
+ try {
+ File file = (File) arg0.getNewValue();
+ ZipEntryFileFactory zife = new ZipEntryFileFactory();
+ LayoutZipEntryFile zif = zife.createLayoutZipEntryFile(layoutName, new FileInputStream(file));
+ layoutName = zif.getName();
+ layoutDescription = zif.getDescription();
+ String typeStr = zif.getHeaderParameter(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE);
+ if (typeStr != null) {
+ try {
+ layoutType = ColorSchemaType.valueOf(typeStr);
+ } catch (IllegalArgumentException e) {
+ layoutType = ColorSchemaType.GENERIC;
+ sendError("Invalid type of overview: " + typeStr);
+ }
+ }
+ } catch (Exception e) {
+ sendError("Internal server error.", e);
+ }
+ }
+ }
+ };
+ addPropertyChangeListener(uploadedFilePropertyChangeListener);
+
+ // after object was added, refresh custom layouts list
+ this.registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(ObjectAddedEvent event) {
+ logger.debug("Refreshing layouts after add: ");
+ Model model = getCurrentTopModel();
+ LayoutView layout = (LayoutView) event.getObject();
+ if (model != null && model.getId().equals(layout.getModelId())) {
+ logger.debug("OK");
+ refreshCustomLayouts(null);
+ mapBean.updateModelView();
+ } else {
+ logger.debug("NOT OK");
+ }
+ }
+ });
+
+ // after object was removed, refresh custom layouts list
+ this.registerListener(new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(ObjectRemovedEvent event) {
+ Model model = getCurrentTopModel();
+ LayoutView layout = (LayoutView) event.getObject();
+ if (model != null && model.getId().equals(layout.getModelId())) {
+ refreshCustomLayouts(null);
+ mapBean.updateModelView();
+ }
+ }
+ });
+ }
+
+ /**
+ * Check if logged user has privilege to add new layout for current map.
+ *
+ * @return true if logged user has privilege to add new layout for current map
+ */
+ public boolean getUserHasAddLayoutPrivilege() {
+ User user = userBean.getLoggedUser();
+ Model model = getCurrentTopModel();
+ if (model == null) {
+ return false;
+ }
+ return layoutService.userCanAddLayout(model, user);
+ }
+
+ /**
+ * Check if user can remove actually selected layout.
+ *
+ * @return <i>true</i> if user can remove actually selected layout,<br/>
+ * <i>false</i> otherwise
+ */
+ public boolean getUserHasRemoveLayoutPrivilege() {
+ User user = userBean.getLoggedUser();
+ return layoutService.userCanRemoveLayout(selectedLayout, user);
+ }
+
+ /**
+ * Refresh list of custom layouts.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void refreshCustomLayouts(final ActionEvent actionEvent) {
+ User user = userBean.getLoggedUser();
+ Model model = getCurrentTopModel();
+ customLayouts = layoutService.getCustomLayouts(model, user, true, user);
+ generalLayouts = layoutService.getGeneralLayouts(model);
+ }
+
+ /**
+ * This method handle upload of a file.
+ *
+ * @param event
+ * event send by the client with a file reference
+ */
+ public void handleFileUpload(final FileUploadEvent event) {
+ try {
+ logger.debug(event.getFile().getFileName() + " is uploaded.");
+ UploadedFile uploadedFile = event.getFile();
+ String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
+ String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
+ File file = File.createTempFile(filename + "-layout-", "." + extension);
+ file.delete();
+ InputStream input = uploadedFile.getInputstream();
+ Files.copy(input, file.toPath());
+ input.close();
+ this.setLayoutFile(file);
+ } catch (Exception e) {
+ sendError("Problem with uploading...", e);
+ }
+ }
+
+ /**
+ * Adds public layout to the project selected in the parameter.
+ *
+ * @param project
+ * where the new layout should be added
+ * @throws SecurityException
+ */
+ public void addAnonymousLayout(ProjectView project) throws SecurityException {
+ errorOccurred = false;
+ Model model = modelService.getLastModelByProjectId(project.getProjectId(), userBean.getAuthenticationToken());
+ addLayout(model, null);
+ }
+
+ /**
+ * This method adds new layout to the model given in parameter.
+ *
+ *
+ * @param model
+ * where the new layout should be added
+ * @param user
+ * who should be the owenr of new layout (if <code>null</code> the
+ * layout will be available to everybody)
+ */
+ private void addLayout(Model model, User user) {
+ if (model == null) {
+ errorOccurred = true;
+ sendError("Unknown model.");
+ return;
+ }
+ try {
+ String directory = getProjectDeployPath() + "../map_images/" + model.getProject().getDirectory() + "/"
+ + model.getProject().getProjectId() + Math.random();
+
+ // the following call will execute asynchronically
+ CreateLayoutParams params = new CreateLayoutParams().name(layoutName).//
+ directory(directory).//
+ model(model).//
+ description(layoutDescription).//
+ colorInputStream(new FileInputStream(layoutFile)).//
+ layoutFileName(layoutFile.getName()).//
+ user(user).//
+ colorSchemaType(layoutType).//
+ async(true);
+ LayoutView view = layoutService.createLayout(params);
+ layoutName = "";
+ layoutFile = null;
+
+ ObjectAddedEvent event = new ObjectAddedEvent(view);
+ super.callListeners(event);
+
+ sendInfo("File processed successfully. Generating layout.");
+ } catch (IOException e) {
+ errorOccurred = true;
+ logger.error("Problem with uploading layout", e);
+ sendError(e.getMessage());
+ } catch (InvalidColorSchemaException e) {
+ errorOccurred = true;
+ logger.error("Problem with uploading layout", e);
+ sendError(e.getMessage());
+ } catch (Exception e) {
+ logger.error("Problem with uploading layout", e);
+ sendError("Unknown problem with uploaded file...");
+ }
+ }
+
+ /**
+ * This method adds a new custom layout to currently selected map.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void addLayout(final ActionEvent actionEvent) {
+ errorOccurred = false;
+ User user = userBean.getLoggedUser();
+ Model model = getCurrentTopModel();
+
+ if (!getUserHasAddLayoutPrivilege()) {
+ errorOccurred = true;
+ sendError("You cannot add new layout");
+ return;
+ }
+ addLayout(model, user);
+ }
+
+ /**
+ * Removes layout selected by the client.
+ *
+ * @param actionEvent
+ * action event from client side
+ */
+ public void removeLayout(final ActionEvent actionEvent) {
+ removeLayout(selectedLayout);
+ }
+
+ /**
+ * Removes layout given in the parameter.
+ *
+ * @param layout
+ * layout that should be removed
+ */
+ public void removeLayout(LayoutView layout) {
+ errorOccurred = false;
+ try {
+ User user = userBean.getLoggedUser();
+ if (!layoutService.userCanRemoveLayout(layout, user)) {
+ errorOccurred = true;
+ sendError("You cannot remove this layout");
+ return;
+ }
+ layoutService.removeLayout(layout, getProjectDeployPath());
+
+ ObjectRemovedEvent event = new ObjectRemovedEvent(layout);
+ super.callListeners(event);
+ } catch (Exception e) {
+ errorOccurred = true;
+ sendError("Problem with removing layout", e);
+ }
+ }
+
+ /**
+ * Updates selectedLayout in the service layer.
+ *
+ * @param actionEvent
+ * action event from client side
+ */
+ public void updateLayout(final ActionEvent actionEvent) {
+ errorOccurred = false;
+ if (!getUserHasRemoveLayoutPrivilege()) {
+ errorOccurred = true;
+ sendError("You cannot update this layout");
+ return;
+ }
+ try {
+ layoutService.updateLayout(selectedLayout);
+ refreshCustomLayouts(actionEvent);
+ } catch (Exception e) {
+ errorOccurred = true;
+ sendError("Problem with updating layout", e);
+ }
+ }
+
+ /**
+ * Updates layout in the service layer.
+ *
+ * @param layout
+ * layout for update
+ */
+ public void updateLayout(final LayoutView layout) {
+ errorOccurred = false;
+ User user = userBean.getLoggedUser();
+ if (!layoutService.userCanRemoveLayout(layout, user)) {
+ errorOccurred = true;
+ sendError("You cannot update this layout");
+ return;
+ }
+ try {
+ layoutService.updateLayout(layout);
+ refreshCustomLayouts(null);
+ } catch (Exception e) {
+ errorOccurred = true;
+ sendError("Problem with updating layout", e);
+ }
+ }
+
+ /**
+ * Returns the number of layouts that can be uploaded by the user.
+ *
+ * @return number of layouts that can still be uploaded by the user
+ */
+ public int getAvailableCustomLayoutNumber() {
+ User user = userBean.getLoggedUser();
+ return (int) layoutService.getAvailableCustomLayoutsNumber(user);
+ }
+
+ @Override
+ public void clear() {
+ setCustomLayouts(null);
+ setSelectedLayout(null);
+ setLayoutFile(null);
+ setLayoutName(null);
+ setErrorOccurred(false);
+ setLayoutType(ColorSchemaType.GENERIC);
+ }
+
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ /**
+ * @return the layoutService
+ * @see #layoutService
+ */
+ public ILayoutService getLayoutService() {
+ return layoutService;
+ }
+
+ /**
+ * @param layoutService
+ * the layoutService to set
+ * @see #layoutService
+ */
+ public void setLayoutService(ILayoutService layoutService) {
+ this.layoutService = layoutService;
+ }
+
+ /**
+ * @return the mapBean
+ * @see #mapBean
+ */
+ public MapBean getMapBean() {
+ return mapBean;
+ }
+
+ /**
+ * @param mapBean
+ * the mapBean to set
+ * @see #mapBean
+ */
+ public void setMapBean(MapBean mapBean) {
+ this.mapBean = mapBean;
+ }
+
+ /**
+ * @return the selectedLayout
+ * @see #selectedLayout
+ */
+ public LayoutView getSelectedLayout() {
+ return selectedLayout;
+ }
+
+ /**
+ * @param selectedLayout
+ * the selectedLayout to set
+ * @see #selectedLayout
+ */
+ public void setSelectedLayout(LayoutView selectedLayout) {
+ this.selectedLayout = selectedLayout;
+ }
+
+ /**
+ * @return the customLayouts
+ * @see #customLayouts
+ */
+ public List<LayoutView> getCustomLayouts() {
+ return customLayouts;
+ }
+
+ /**
+ * @param customLayouts
+ * the customLayouts to set
+ * @see #customLayouts
+ */
+ public void setCustomLayouts(List<LayoutView> customLayouts) {
+ this.customLayouts = customLayouts;
+ }
+
+ /**
+ * @return the layoutFile
+ * @see #layoutFile
+ */
+ public File getLayoutFile() {
+ return layoutFile;
+ }
+
+ /**
+ * @param layoutFile
+ * the layoutFile to set
+ * @see #layoutFile
+ */
+ public void setLayoutFile(File layoutFile) {
+ File oldFile = this.layoutFile;
+ this.layoutFile = layoutFile;
+ firePropertyChange(LAYOUT_FILE_PROPERTY, oldFile, layoutFile);
+ }
+
+ /**
+ * @return the layoutName
+ * @see #layoutName
+ */
+ public String getLayoutName() {
+ return layoutName;
+ }
+
+ /**
+ * @param layoutName
+ * the layoutName to set
+ * @see #layoutName
+ */
+ public void setLayoutName(String layoutName) {
+ this.layoutName = layoutName;
+ }
+
+ /**
+ * @return the errorOccurred
+ * @see #errorOccurred
+ */
+ public boolean isErrorOccurred() {
+ return errorOccurred;
+ }
+
+ /**
+ * @param errorOccurred
+ * the errorOccurred to set
+ * @see #errorOccurred
+ */
+ public void setErrorOccurred(boolean errorOccurred) {
+ this.errorOccurred = errorOccurred;
+ }
+
+ /**
+ * @return the visualizedLayout
+ * @see #visualizedLayout
+ */
+ public LayoutView getVisualizedLayout() {
+ return visualizedLayout;
+ }
+
+ /**
+ * @param visualizedLayout
+ * the visualizedLayout to set
+ * @see #visualizedLayout
+ */
+ public void setVisualizedLayout(LayoutView visualizedLayout) {
+ this.visualizedLayout = visualizedLayout;
+ }
+
+ /**
+ * Updates information in {@link #visualizedLayout} object.
+ *
+ * @param actionEvent
+ * action event from client side
+ */
+ public void getVisualizedLayoutDetails(final ActionEvent actionEvent) {
+ if (visualizedLayout.getName() != null && !visualizedLayout.getName().trim().equals("")) {
+ visualizedLayout = layoutService.getLayoutByName(getCurrentTopModel(), visualizedLayout.getName());
+ if (visualizedLayout == null) {
+ visualizedLayout = new LayoutView();
+ } else {
+ // we have new element to vizualize
+ ObjectAddedEvent event = new ObjectAddedEvent(visualizedLayout);
+ super.callListeners(event);
+ }
+ }
+ }
+
+ /**
+ * @return the generalLayouts
+ * @see #generalLayouts
+ */
+ public List<LayoutView> getGeneralLayouts() {
+ return generalLayouts;
+ }
+
+ /**
+ * @param generalLayouts
+ * the generalLayouts to set
+ * @see #generalLayouts
+ */
+ public void setGeneralLayouts(List<LayoutView> generalLayouts) {
+ this.generalLayouts = generalLayouts;
+ }
+
+ /**
+ * Method that allows to donlwoad input data for given layout.
+ *
+ * @param layout
+ * layout for which input data will be downloaded
+ *
+ * @throws IOException
+ * thrown when there are some problems with sending file
+ * @throws SecurityException
+ */
+ public void downloadInputData(LayoutView layout) throws IOException, SecurityException {
+ // get input data from database
+ byte[] data = layoutService.getInputDataForLayout(layout, userBean.getAuthenticationToken());
+ String string = new String(data, StandardCharsets.UTF_8);
+
+ sendFileAsResponse(string, "layout_" + layout.getIdObject() + ".txt", MimeType.TEXT);
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the layoutDescription
+ * @see #layoutDescription
+ */
+ public String getLayoutDescription() {
+ return layoutDescription;
+ }
+
+ /**
+ * @param layoutDescription
+ * the layoutDescription to set
+ * @see #layoutDescription
+ */
+ public void setLayoutDescription(String layoutDescription) {
+ this.layoutDescription = layoutDescription;
+ }
+
+ /**
+ * This method sends list of aliases that should be visualized in a
+ * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
+ *
+ * @throws IOException
+ * thrown when there is a problem with accessing information about
+ * layout
+ */
+ public void retreiveActiveAliasesForLayout() throws IOException {
+ int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
+ String string = "[]";
+ try {
+ List<LightLayoutAliasView> list = layoutService.getAliasesForLayout(getCurrentTopModel(), layoutId,
+ userBean.getAuthenticationToken());
+ LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
+ string = factory.createGson(list);
+ } catch (Exception e) {
+ sendError("Internal server error", e);
+ }
+ executeJavascript("ServerConnector.addAliasesForLayout('" + layoutId + "','" + string + "');");
+ }
+
+ /**
+ * This method sends full information about aliases that are visualized in a
+ * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser and identified
+ * by list of identifiers.
+ *
+ * @throws IOException
+ * thrown when there is a problem with accessing information about
+ * layout
+ */
+ public void retreiveFullAliasesForLayout() {
+ int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
+ String string = "[]";
+ try {
+ List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
+ List<FullLayoutAliasView> list = layoutService.getFullAliasesForLayoutByIds(getCurrentTopModel(), identifiers,
+ layoutId, userBean.getAuthenticationToken());
+ string = new FullLayoutAliasViewFactory().createGson(list);
+ } catch (Exception e) {
+ sendError("Internal server error", e);
+ }
+ executeJavascript("ServerConnector.updateAliasesForLayout('" + layoutId + "','" + string + "');");
+ }
+
+ /**
+ * This method sends list of reactions that should be visualized in a
+ * {@link lcsb.mapviewer.model.map.layout.Layout} to the browser.
+ *
+ * @throws IOException
+ * thrown when there is a problem with accessing information about
+ * layout
+ */
+ public void retreiveActiveReactionsForLayout() throws IOException {
+ int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
+ String string = "[]";
+ try {
+ List<LightLayoutReactionView> list = layoutService.getReactionsForLayout(getCurrentTopModel(), layoutId,
+ userBean.getAuthenticationToken());
+ LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
+ string = factory.createGson(list);
+ } catch (Exception e) {
+ sendError("Internal server error", e);
+ }
+ executeJavascript("ServerConnector.addReactionsForLayout('" + layoutId + "','" + string + "');");
+ }
+
+ /**
+ * @return the layoutType
+ * @see #layoutType
+ */
+ public ColorSchemaType getLayoutType() {
+ return layoutType;
+ }
+
+ /**
+ * @param layoutType
+ * the layoutType to set
+ * @see #layoutType
+ */
+ public void setLayoutType(ColorSchemaType layoutType) {
+ this.layoutType = layoutType;
+ }
+
+ /**
+ * Returns list of available layout types.
+ *
+ * @return list of available layout types
+ */
+ public ColorSchemaType[] getColorSchemaTypes() {
+ return ColorSchemaType.values();
+ }
+
+ /**
+ * Returns currently browsed map.
+ *
+ * @return currently browsed map
+ */
+ private Model getCurrentTopModel() {
+ return mapBean.getCurrentTopModel();
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
index d8c6f2d8d8ebf90c7f09148860a4c804f208f192..bf2709f766b291eef1fb78ad4c7170f014474a41 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
@@ -33,6 +33,7 @@ import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.user.ConfigurationElementType;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectService;
@@ -58,966 +59,979 @@ import lcsb.mapviewer.services.view.ProjectView;
@ViewScoped
public class MapBean extends AbstractManagedBean implements Serializable {
- /**
- * String representing {@link #currentMapId} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String CURRENT_MODEL_ID_PROPERTY = "CURRENT_MODEL_ID";
-
- /**
- * String representing {@link #currentMap} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String CURRENT_MODEL_PROPERTY = "CURRENT_MODEL";
-
- /**
- * Name of the session field that store {@link ClientMapData#centerCoordinateY
- * y coordinate} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String Y_COORD_SESSION_PARAM = "Y_COORD";
-
- /**
- * Name of the session field that store {@link ClientMapData#centerCoordinateX
- * x coordinate} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String X_COORD_SESSION_PARAM = "X_COORD";
-
- /**
- * Name of the session field that store {@link ClientMapData#zoomLevel zoom
- * level} of the browsable model (this will is used when page is refreshed).
- */
- public static final String ZOOM_LEVEL_SESSION_PARAM = "LEVEL";
-
- /**
- * Name of the session field that store {@link ClientMapData#selectedLayout
- * selected layout} of the browsable model (this will is used when page is
- * refreshed).
- */
- public static final String SELECTED_LAYOUT_SESSION_PARAM = "SELECTED_LAYOUT";
-
- /**
- * Default organism by which results should be filtered (homo sapiens by
- * default).
- */
-
- private static final MiriamData DEFAULT_ORGANISM = TaxonomyBackend.HUMAN_TAXONOMY;
-
- /**
- * Object representing currently visualized project.
- */
- private ProjectView currentProjectView = null;
-
- /**
- * Name of the current project.
- */
- private String currentMapId = null;
-
- /**
- * Map currently browsed.
- */
- private transient Model currentMap = null;
-
- /**
- * This class store information about browsing single map/submap.
- *
- * @author Piotr Gawron
- *
- */
- public class ClientMapData implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Configuration of the map used by the javascript frontend.
- */
- private ModelView mapConfig = null;
-
- /**
- * Converter of coordinates dedicated to the map (every map must have a
- * different converter, because the size and number of layers in the maps
- * are different).
- */
- private CoordinationConverter cConverter;
-
- /**
- * Type of the model (used only in case of submodels).
- */
- private String type = "";
-
- /**
- * X coordinate of map center.
- */
- private String centerCoordinateX = "";
-
- /**
- * Y coordinate of map center.
- */
- private String centerCoordinateY = "";
-
- /**
- * Level at which map is browsed.
- */
- private String zoomLevel = "" + Configuration.MIN_ZOOM_LEVEL;
-
- /**
- * Layout currently visualized.
- */
- private String selectedLayout = "";
-
- /**
- * @return the mapConfig
- * @see #mapConfig
- */
- public ModelView getMapConfig() {
- return mapConfig;
- }
-
- /**
- * @param mapConfig
- * the mapConfig to set
- * @see #mapConfig
- */
- public void setMapConfig(ModelView mapConfig) {
- this.mapConfig = mapConfig;
- // set information about location and zooming (if it's set in the session)
- if (getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setZoomLevel((String) getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()));
- // when we refresh map and have defined coordinates then tell the client
- // side that it shouldn't fit it into the bounds
- mapConfig.setFitMapBounds(false);
- } else {
- setZoomLevel("");
- }
- if (getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setCenterCoordinateX((String) getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()));
- // when we refresh map and have defined coordinates then tell the client
- // side that it shouldn't fit it into the bounds
- mapConfig.setFitMapBounds(false);
- } else {
- setCenterCoordinateX("");
- }
- if (getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setCenterCoordinateY((String) getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()));
- } else {
- setCenterCoordinateY("");
- }
- setSelectedLayout("");
- if (getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()) != null) {
- setSelectedLayout((String) getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()));
- } else {
- if (mapConfig.getLayouts().size() > 0) {
- setSelectedLayout("cv" + mapConfig.getLayouts().get(0).getIdObject());
- } else {
- logger.warn("No layouts for model: " + mapConfig.getIdObject());
-
- }
- }
- }
-
- /**
- * @return the cConverter
- * @see #cConverter
- */
- public CoordinationConverter getcConverter() {
- return cConverter;
- }
-
- /**
- * @param cConverter
- * the cConverter to set
- * @see #cConverter
- */
- public void setcConverter(CoordinationConverter cConverter) {
- this.cConverter = cConverter;
- }
-
- /**
- * @return the centerCoordinateX
- * @see #centerCoordinateX
- */
- public String getCenterCoordinateX() {
- return centerCoordinateX;
- }
-
- /**
- * @param centerCoordinateX
- * the centerCoordinateX to set
- * @see #centerCoordinateX
- */
- public void setCenterCoordinateX(String centerCoordinateX) {
- if (centerCoordinateX != null && !centerCoordinateX.isEmpty()) {
- addSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateX);
- }
- this.centerCoordinateX = centerCoordinateX;
- }
-
- /**
- * @return the centerCoordinateY
- * @see #centerCoordinateY
- */
- public String getCenterCoordinateY() {
- return centerCoordinateY;
- }
-
- /**
- * @param centerCoordinateY
- * the centerCoordinateY to set
- * @see #centerCoordinateY
- */
- public void setCenterCoordinateY(String centerCoordinateY) {
- if (centerCoordinateY != null && !centerCoordinateY.isEmpty()) {
- addSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateY);
- }
- this.centerCoordinateY = centerCoordinateY;
- }
-
- /**
- * @return the zoomLevel
- * @see #zoomLevel
- */
- public String getZoomLevel() {
- return zoomLevel;
- }
-
- /**
- * @param zoomLevel
- * the zoomLevel to set
- * @see #zoomLevel
- */
- public void setZoomLevel(String zoomLevel) {
- if (zoomLevel != null && !zoomLevel.isEmpty()) {
- addSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject(), zoomLevel);
- }
- this.zoomLevel = zoomLevel;
- }
-
- /**
- * @return the selectedLayout
- * @see #selectedLayout
- */
- public String getSelectedLayout() {
- return selectedLayout;
- }
-
- /**
- * @param selectedLayout
- * the selectedLayout to set
- * @see #selectedLayout
- */
- public void setSelectedLayout(String selectedLayout) {
- if (selectedLayout != null && !selectedLayout.isEmpty()) {
- addSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject(), selectedLayout);
- }
- this.selectedLayout = selectedLayout;
- }
-
- /**
- * @return the type
- * @see #type
- */
- public String getType() {
- return type;
- }
-
- /**
- * @param type
- * the type to set
- * @see #type
- */
- public void setType(String type) {
- this.type = type;
- }
-
- }
-
- /**
- * Top map of currently browsed model.
- */
- private ClientMapData topModelMapData = null;
-
- /**
- * List of all model/submodels that are browsed in the current window.
- */
- private List<ClientMapData> mapDataList = new ArrayList<>();
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService confService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Factory used to create {@link FullAliasView} elements.
- */
- @ManagedProperty(value = "#{FullAliasViewFactory}")
- private transient FullAliasViewFactory fullAliasViewFactory;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(MapBean.class);
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- @Override
- public void init() {
- // when model is changed we have to change few parameters as well
- PropertyChangeListener modelChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (CURRENT_MODEL_PROPERTY.equals(arg0.getPropertyName())) {
- updateModelView();
- }
- }
-
- };
- addPropertyChangeListener(modelChanged);
-
- // when we change id we should propagate the change to model
- PropertyChangeListener mapIdChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (CURRENT_MODEL_ID_PROPERTY.equals(arg0.getPropertyName())) {
- try {
- setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getNewValue(), userBean.getAuthenticationToken()));
- setCurrentProjectView(getProjectService().getProjectViewByProjectId(currentMap.getProject().getProjectId(), userBean.getAuthenticationToken()));
- } catch (Exception e) {
- setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getOldValue(), userBean.getAuthenticationToken()));
- logger.error(e, e);
- }
- }
- }
-
- };
- addPropertyChangeListener(mapIdChangeListener);
-
- // when we change id we should propagate the change to model
- VetoableChangeListener vetoMapIdChangeListener = new VetoableChangeListener() {
- @Override
- public void vetoableChange(PropertyChangeEvent arg0) throws PropertyVetoException {
- if (!getProjectService().projectExists((String) arg0.getNewValue())) {
- throw new PropertyVetoException("Project with id \"" + arg0.getNewValue() + "\" doesn't exist.", arg0);
- }
- }
-
- };
- addVetoablePropertyChangeListener(vetoMapIdChangeListener);
-
- // set id from request parameters (id is the url GET parameter)
- setCurrentMapId(getRequestParameter("id"));
-
- }
-
- /**
- * Refresh information about models.
- */
- protected void updateModelView() {
-
- Model model = getCurrentTopModel();
- // configuration
- ModelView topView = modelService.getModelView(model, userBean.getLoggedUser());
-
- mapDataList = new ArrayList<>();
-
- ClientMapData cmd = new ClientMapData();
- cmd.setMapConfig(topView);
- cmd.setType("N/A");
- // coordinates converter
- cmd.setcConverter(new CoordinationConverter(model));
-
- mapDataList.add(cmd);
- topModelMapData = cmd;
-
- for (ModelView view : topView.getSubmodels()) {
- cmd = new ClientMapData();
- cmd.setMapConfig(view);
- // coordinates converter
- cmd.setcConverter(new CoordinationConverter(model.getSubmodelById(view.getIdObject())));
- cmd.setType(model.getSubmodelConnectionById(view.getIdObject()).getType().getCommonName());
- mapDataList.add(cmd);
- }
- }
-
- /**
- * This method center map in the client using coordinates from client.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void centerMap(final ActionEvent actionEvent) {
- createSubmodelDialog(actionEvent);
-
- // we have plain coordinates (not lat lng)
- String xCoord = getRequestParameter("xCoord");
- String yCoord = getRequestParameter("yCoord");
- String modelIdentifier = getRequestParameter("submodelId");
- if (modelIdentifier == null) {
- sendError("submodelId param wasn't set");
- return;
- }
- Integer modelId = Integer.valueOf(modelIdentifier);
-
- ClientMapData selectedMapData = null;
- for (ClientMapData mapData : getMapDataList()) {
- if (mapData.getMapConfig().getIdObject().equals(modelId)) {
- selectedMapData = mapData;
- }
- }
- if (selectedMapData == null) {
- sendError("Cannot find map with the identifier: " + modelId);
- return;
- }
-
- LatLng latLng;
- if (xCoord != null && yCoord != null) {
- double x = Double.parseDouble(xCoord);
- double y = Double.parseDouble(yCoord);
- latLng = selectedMapData.getcConverter().toLatLng(new Point2D.Double(x, y));
- } else {
- String latCoord = getRequestParameter("latCoord");
- String lngCoord = getRequestParameter("lngCoord");
- double lat = Double.parseDouble(latCoord);
- double lng = Double.parseDouble(lngCoord);
- latLng = new LatLng(lat, lng);
- }
- centerMapInJavascript(latLng, selectedMapData);
- }
-
- /**
- * Method responsible for centering map in client using coordinates given as a
- * parameter.
- *
- * @param mapData
- * defines which map we want to center. If the value is not set then
- * default one is selected
- *
- * @param latLng
- * - coordinates
- */
- private void centerMapInJavascript(final LatLng latLng, ClientMapData mapData) {
- double lat = latLng.getLat();
- double lng = latLng.getLng();
- logger.debug("Center map in js (" + lat + "," + lng + ")");
- executeJavascript("customMap.setCenter(" + mapData.getMapConfig().getIdObject() + ", new google.maps.LatLng(" + lat + "," + lng + "));");
- }
-
- /**
- * Check if user can see the map.
- *
- * @return <i>true</i> if user can see the map,<br/>
- * <i> false otherwise</i>
- */
- public boolean getUserHasViewPrivilege() {
- Project project = getCurrentProject();
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project);
- if (!result) {
- logger.debug("User doesn't have privilege");
- }
- return result;
- }
-
- /**
- * This is artifitial method called by the client side to pass some parameters
- * to the bean:
- * <ul>
- * <li>{@link #centerCoordinateX},</li>
- * <li>{@link #centerCoordinateY},</li>
- * <li>{@link #selectedLayout},</li>
- * <li>{@link #zoomLevel}.</li>
- * </ul>
- */
- public void actualizeParams() {
-
- }
-
- /**
- * Returns the index of layout that is currently visualized.
- *
- * @return index of layout that is currently visualized.
- */
- public Integer getSelectedLayoutIdentifier() {
- if (topModelMapData.getSelectedLayout() == null) {
- return null;
- } else {
- String str = topModelMapData.getSelectedLayout().replaceAll("[^0-9]", "");
- Integer id = null;
- try {
- id = Integer.parseInt(str);
- } catch (NumberFormatException e) {
- logger.warn("Problem with layout identifier: " + topModelMapData.getSelectedLayout());
- }
- return id;
- }
- }
-
- /**
- * Returns level on which the map is currently browsed. It's not equal to the
- * zoom level, becuse zoom level is shifted by
- * {@link lcsb.mapviewer.common.Configuration.MIN_ZOOM_LEVEL} value.
- *
- * @param mapData
- * defines on which map we are looking for zoom level. If the value
- * is not set then default one is selected
- * @return level on which the map is currently browsed
- */
- public Integer getLevel(ClientMapData mapData) {
- String zoomLevel = mapData.getZoomLevel();
- if (zoomLevel == null) {
- return null;
- }
- Integer res = null;
- try {
- res = Integer.valueOf(zoomLevel) - Configuration.MIN_ZOOM_LEVEL;
- } catch (NumberFormatException e) {
- logger.warn("Problem with zoomLevel: " + zoomLevel);
- }
- return res;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the mapDataList
- * @see #mapDataList
- */
- public List<ClientMapData> getMapDataList() {
- return mapDataList;
- }
-
- /**
- * Creates dialog on client side for submodel.
- *
- * @param actionEvent
- * event from the client
- */
- public void createSubmodelDialog(final ActionEvent actionEvent) {
- try {
- String dialogGroup = "_gmapForm:submodelDialogGroup";
- String idParamName = "submodelId";
- String dialogIdPrefix = "submodelDialog";
-
- UIComponent panelGroup = findComponent(dialogGroup);
- if (panelGroup == null) {
- sendError("Cannot find " + dialogGroup + " component.");
- return;
- }
- String id = getRequestParameter(idParamName);
- if (id == null) {
- sendError(idParamName + " request param cannot be null.");
- return;
- }
- if (id.equals(getCurrentTopModel().getId() + "")) {
- logger.debug("TopModel doesn't require window");
- return;
- }
- id = dialogIdPrefix + id;
- for (UIComponent child : panelGroup.getChildren()) {
- if (child instanceof Dialog) {
- if (child.getId().equals(id)) {
- logger.debug("Dialog " + id + " found");
- return;
- }
- }
- }
- for (ModelSubmodelConnection model : getCurrentTopModel().getSubmodelConnections()) {
- Integer modelId = model.getSubmodel().getId();
- id = dialogIdPrefix + modelId;
- Dialog dialog = new Dialog();
- dialog.setId(id);
- dialog.setWidgetVar(id);
- dialog.setHeader("Submodel: " + model.getSubmodel().getName());
- dialog.setMinimizable(true);
- panelGroup.getChildren().add(dialog);
- }
-
- RequestContext requestContext = RequestContext.getCurrentInstance();
- requestContext.update(dialogGroup);
-
- } catch (Exception e) {
- logger.error(e, e);
- sendError(e.getMessage());
- }
- }
-
- /**
- * Returns map configuration in Gson format.
- *
- * @return map configuration in Gson format
- */
- public String getGsonConfiguration() {
- return new Gson().toJson(getMapDataList().get(0).getMapConfig());
- }
-
- /**
- * @return the topModelMapData
- * @see #topModelMapData
- */
- public ClientMapData getTopModelMapData() {
- if (topModelMapData == null) {
- updateModelView();
- }
- return topModelMapData;
- }
-
- /**
- * @param topModelMapData
- * the topModelMapData to set
- * @see #topModelMapData
- */
- public void setTopModelMapData(ClientMapData topModelMapData) {
- this.topModelMapData = topModelMapData;
- }
-
- /**
- * Returns {@link ClientMapData} for (sub)model identified by identifier.
- *
- * @param identifier
- * identifier of the model
- * @return {@link ClientMapData}
- */
- public ClientMapData getMapDataByMapIdentifier(String identifier) {
- Integer id = Integer.parseInt(identifier);
- return getMapDataByMapIdentifier(id);
- }
-
- /**
- * Returns {@link ClientMapData} for (sub)model identified by identifier.
- *
- * @param identifier
- * identifier of the model
- * @return {@link ClientMapData}
- */
- public ClientMapData getMapDataByMapIdentifier(Integer identifier) {
- // in case we haven't initialized mapdata we need to do it here (it's a
- // workaround...)
- if (getMapDataList().size() == 0) {
- updateModelView();
- }
- for (ClientMapData md : getMapDataList()) {
- if (md.getMapConfig().getIdObject().equals(identifier)) {
- return md;
- }
- }
- return null;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * Sets zoom level for submodel. Parameters are passed using http request
- * mechainsm/
- */
- public void setModelZoomLevel() {
- String mapId = getRequestParameter("mapId");
- String zoomLevel = getRequestParameter("zoomLevel");
-
- Integer id = Integer.valueOf(mapId);
-
- for (ClientMapData cmd : getMapDataList()) {
- if (cmd.getMapConfig().getIdObject().equals(id)) {
- cmd.setZoomLevel(zoomLevel);
- return;
- }
- }
- sendError("Cannot find model with id: " + id);
-
- }
-
- /**
- * Sends list of aliases (with given identifiers) to the browser. Identifiers
- * are passed as a json string in request parameter <i>ids</i>. Each
- * identifier is a pair containing information about {@link Model#getId()
- * model id} and {@link lcsb.mapviewer.model.map.species.Element#id alias id}.
- * Data is very light - contains only information about the location on the
- * model.
- *
- */
- public void retreiveLightAliases() {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<LightAliasView> list = modelService.getLightAliasesByIds(getCurrentTopModel(), identifiers);
- LightAliasViewFactory factory = new LightAliasViewFactory();
- String string = factory.createGson(list);
- executeJavascript("ServerConnector.addAliases(" + string + ");");
- }
-
- /**
- * Sends list of reactions (with given identifiers) to the browser.
- * Identifiers are passed as a json string in request parameter <i>ids</i>.
- * Each identifier is a pair containing information about {@link Model#getId()
- * model id} and {@link lcsb.mapviewer.model.map.reaction.Reaction#id reaction
- * id}.
- *
- */
- public void retreiveLightReactions() {
- List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<LightReactionView> list = modelService.getLightReactionsByIds(getCurrentTopModel(), identifiers);
- LightReactionViewFactory factory = new LightReactionViewFactory();
- String string = factory.createGson(list);
- executeJavascript("ServerConnector.addReactions('" + string + "');");
- }
-
- /**
- * @return the fullAliasViewFactory
- * @see #fullAliasViewFactory
- */
- public FullAliasViewFactory getFullAliasViewFactory() {
- if (fullAliasViewFactory == null) {
- fullAliasViewFactory = findBean(FullAliasViewFactory.class);
- }
- return fullAliasViewFactory;
- }
-
- /**
- * @param fullAliasViewFactory
- * the fullAliasViewFactory to set
- * @see #fullAliasViewFactory
- */
- public void setFullAliasViewFactory(FullAliasViewFactory fullAliasViewFactory) {
- this.fullAliasViewFactory = fullAliasViewFactory;
- }
-
- /**
- * @return the currentMapId
- * @see #currentMapId
- */
- public final String getCurrentMapId() {
- // if user didn't provide id then use default one
- if (currentMapId == null) {
- String tmp = confService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
- if (tmp == null) {
- logger.warn("Cannot find default map in the system.");
- }
- setCurrentMapId(tmp);
- }
- return currentMapId;
- }
-
- /**
- * @param currentMapId
- * the currentMapId to set
- * @see #currentMapId
- */
- public final void setCurrentMapId(String currentMapId) {
- try {
- fireVetoableChange(CURRENT_MODEL_ID_PROPERTY, this.currentMapId, currentMapId);
- String oldValue = this.currentMapId;
- this.currentMapId = currentMapId;
- firePropertyChange(CURRENT_MODEL_ID_PROPERTY, oldValue, currentMapId);
- } catch (PropertyVetoException e) {
- logger.warn("Cannot change property: " + CURRENT_MODEL_ID_PROPERTY + ". Form: \"" + this.currentMapId + "\" into: \"" + currentMapId + "\"");
- }
- }
-
- /**
- * Return {@link #currentMap currently browsed map}.
- *
- * @return currently browsed map
- */
- protected final Model getCurrentTopModel() {
- if (currentMap == null) {
- setCurrentTopModel(this.getModelService().getLastModelByProjectId(getCurrentMapId(), userBean.getAuthenticationToken()));
- }
- return currentMap;
- }
-
- /**
- * @return the currentProject
- * @see #currentProject
- */
- public Project getCurrentProject() {
- return getCurrentTopModel().getProject();
- }
-
- /**
- * @param topModel
- * the topModel to set
- * @see #currentMap
- */
- private void setCurrentTopModel(Model topModel) {
- Model oldValue = this.currentMap;
- this.currentMap = topModel;
- firePropertyChange(CURRENT_MODEL_PROPERTY, oldValue, topModel);
- }
-
- /**
- * @return the currentProjectView
- * @see #currentProjectView
- */
- public ProjectView getCurrentProjectView() {
- return currentProjectView;
- }
-
- /**
- * @param currentProjectView
- * the currentProjectView to set
- * @see #currentProjectView
- */
- public void setCurrentProjectView(ProjectView currentProjectView) {
- this.currentProjectView = currentProjectView;
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the confService
- * @see #confService
- */
- public IConfigurationService getConfService() {
- return confService;
- }
-
- /**
- * @param confService
- * the confService to set
- * @see #confService
- */
- public void setConfService(IConfigurationService confService) {
- this.confService = confService;
- }
-
- /**
- * Returns organism associated with currently viewed project. If organism is
- * not set then {@link #DEFAULT_ORGANISM} is returned.
- *
- * @return organism associated with currently viewed project
- */
- public MiriamData getOrganism() {
- MiriamData organism = getCurrentProject().getOrganism();
- if (organism == null || organism.getResource().isEmpty()) {
- organism = DEFAULT_ORGANISM;
- }
- return organism;
- }
+ /**
+ * String representing {@link #currentMapId} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String CURRENT_MODEL_ID_PROPERTY = "CURRENT_MODEL_ID";
+
+ /**
+ * String representing {@link #currentMap} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String CURRENT_MODEL_PROPERTY = "CURRENT_MODEL";
+
+ /**
+ * Name of the session field that store {@link ClientMapData#centerCoordinateY y
+ * coordinate} of the browsable model (this will is used when page is
+ * refreshed).
+ */
+ public static final String Y_COORD_SESSION_PARAM = "Y_COORD";
+
+ /**
+ * Name of the session field that store {@link ClientMapData#centerCoordinateX x
+ * coordinate} of the browsable model (this will is used when page is
+ * refreshed).
+ */
+ public static final String X_COORD_SESSION_PARAM = "X_COORD";
+
+ /**
+ * Name of the session field that store {@link ClientMapData#zoomLevel zoom
+ * level} of the browsable model (this will is used when page is refreshed).
+ */
+ public static final String ZOOM_LEVEL_SESSION_PARAM = "LEVEL";
+
+ /**
+ * Name of the session field that store {@link ClientMapData#selectedLayout
+ * selected layout} of the browsable model (this will is used when page is
+ * refreshed).
+ */
+ public static final String SELECTED_LAYOUT_SESSION_PARAM = "SELECTED_LAYOUT";
+
+ /**
+ * Default organism by which results should be filtered (homo sapiens by
+ * default).
+ */
+
+ private static final MiriamData DEFAULT_ORGANISM = TaxonomyBackend.HUMAN_TAXONOMY;
+
+ /**
+ * Object representing currently visualized project.
+ */
+ private ProjectView currentProjectView = null;
+
+ /**
+ * Name of the current project.
+ */
+ private String currentMapId = null;
+
+ /**
+ * Map currently browsed.
+ */
+ private transient Model currentMap = null;
+
+ /**
+ * This class store information about browsing single map/submap.
+ *
+ * @author Piotr Gawron
+ *
+ */
+ public class ClientMapData implements Serializable {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Configuration of the map used by the javascript frontend.
+ */
+ private ModelView mapConfig = null;
+
+ /**
+ * Converter of coordinates dedicated to the map (every map must have a
+ * different converter, because the size and number of layers in the maps are
+ * different).
+ */
+ private CoordinationConverter cConverter;
+
+ /**
+ * Type of the model (used only in case of submodels).
+ */
+ private String type = "";
+
+ /**
+ * X coordinate of map center.
+ */
+ private String centerCoordinateX = "";
+
+ /**
+ * Y coordinate of map center.
+ */
+ private String centerCoordinateY = "";
+
+ /**
+ * Level at which map is browsed.
+ */
+ private String zoomLevel = "" + Configuration.MIN_ZOOM_LEVEL;
+
+ /**
+ * Layout currently visualized.
+ */
+ private String selectedLayout = "";
+
+ /**
+ * @return the mapConfig
+ * @see #mapConfig
+ */
+ public ModelView getMapConfig() {
+ return mapConfig;
+ }
+
+ /**
+ * @param mapConfig
+ * the mapConfig to set
+ * @see #mapConfig
+ */
+ public void setMapConfig(ModelView mapConfig) {
+ this.mapConfig = mapConfig;
+ // set information about location and zooming (if it's set in the session)
+ if (getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()) != null) {
+ setZoomLevel((String) getSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject()));
+ // when we refresh map and have defined coordinates then tell the client
+ // side that it shouldn't fit it into the bounds
+ mapConfig.setFitMapBounds(false);
+ } else {
+ setZoomLevel("");
+ }
+ if (getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
+ setCenterCoordinateX((String) getSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject()));
+ // when we refresh map and have defined coordinates then tell the client
+ // side that it shouldn't fit it into the bounds
+ mapConfig.setFitMapBounds(false);
+ } else {
+ setCenterCoordinateX("");
+ }
+ if (getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()) != null) {
+ setCenterCoordinateY((String) getSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject()));
+ } else {
+ setCenterCoordinateY("");
+ }
+ setSelectedLayout("");
+ if (getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()) != null) {
+ setSelectedLayout((String) getSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject()));
+ } else {
+ if (mapConfig.getLayouts().size() > 0) {
+ setSelectedLayout("cv" + mapConfig.getLayouts().get(0).getIdObject());
+ } else {
+ logger.warn("No layouts for model: " + mapConfig.getIdObject());
+
+ }
+ }
+ }
+
+ /**
+ * @return the cConverter
+ * @see #cConverter
+ */
+ public CoordinationConverter getcConverter() {
+ return cConverter;
+ }
+
+ /**
+ * @param cConverter
+ * the cConverter to set
+ * @see #cConverter
+ */
+ public void setcConverter(CoordinationConverter cConverter) {
+ this.cConverter = cConverter;
+ }
+
+ /**
+ * @return the centerCoordinateX
+ * @see #centerCoordinateX
+ */
+ public String getCenterCoordinateX() {
+ return centerCoordinateX;
+ }
+
+ /**
+ * @param centerCoordinateX
+ * the centerCoordinateX to set
+ * @see #centerCoordinateX
+ */
+ public void setCenterCoordinateX(String centerCoordinateX) {
+ if (centerCoordinateX != null && !centerCoordinateX.isEmpty()) {
+ addSessionParam(X_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateX);
+ }
+ this.centerCoordinateX = centerCoordinateX;
+ }
+
+ /**
+ * @return the centerCoordinateY
+ * @see #centerCoordinateY
+ */
+ public String getCenterCoordinateY() {
+ return centerCoordinateY;
+ }
+
+ /**
+ * @param centerCoordinateY
+ * the centerCoordinateY to set
+ * @see #centerCoordinateY
+ */
+ public void setCenterCoordinateY(String centerCoordinateY) {
+ if (centerCoordinateY != null && !centerCoordinateY.isEmpty()) {
+ addSessionParam(Y_COORD_SESSION_PARAM + mapConfig.getIdObject(), centerCoordinateY);
+ }
+ this.centerCoordinateY = centerCoordinateY;
+ }
+
+ /**
+ * @return the zoomLevel
+ * @see #zoomLevel
+ */
+ public String getZoomLevel() {
+ return zoomLevel;
+ }
+
+ /**
+ * @param zoomLevel
+ * the zoomLevel to set
+ * @see #zoomLevel
+ */
+ public void setZoomLevel(String zoomLevel) {
+ if (zoomLevel != null && !zoomLevel.isEmpty()) {
+ addSessionParam(ZOOM_LEVEL_SESSION_PARAM + mapConfig.getIdObject(), zoomLevel);
+ }
+ this.zoomLevel = zoomLevel;
+ }
+
+ /**
+ * @return the selectedLayout
+ * @see #selectedLayout
+ */
+ public String getSelectedLayout() {
+ return selectedLayout;
+ }
+
+ /**
+ * @param selectedLayout
+ * the selectedLayout to set
+ * @see #selectedLayout
+ */
+ public void setSelectedLayout(String selectedLayout) {
+ if (selectedLayout != null && !selectedLayout.isEmpty()) {
+ addSessionParam(SELECTED_LAYOUT_SESSION_PARAM + mapConfig.getIdObject(), selectedLayout);
+ }
+ this.selectedLayout = selectedLayout;
+ }
+
+ /**
+ * @return the type
+ * @see #type
+ */
+ public String getType() {
+ return type;
+ }
+
+ /**
+ * @param type
+ * the type to set
+ * @see #type
+ */
+ public void setType(String type) {
+ this.type = type;
+ }
+
+ }
+
+ /**
+ * Top map of currently browsed model.
+ */
+ private ClientMapData topModelMapData = null;
+
+ /**
+ * List of all model/submodels that are browsed in the current window.
+ */
+ private List<ClientMapData> mapDataList = new ArrayList<>();
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Service used to access information about users.
+ *
+ * @see IUserService
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @ManagedProperty(value = "#{ModelService}")
+ private transient IModelService modelService;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @ManagedProperty(value = "#{ProjectService}")
+ private transient IProjectService projectService;
+
+ /**
+ * Service used to access configuration parameters.
+ *
+ * @see IConfigurationService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService confService;
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * users (including information about currently logged user).
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
+ /**
+ * Factory used to create {@link FullAliasView} elements.
+ */
+ @ManagedProperty(value = "#{FullAliasViewFactory}")
+ private transient FullAliasViewFactory fullAliasViewFactory;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(MapBean.class);
+
+ /**
+ * Service used to access configuration parameters.
+ *
+ * @see IConfigurationService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ @Override
+ public void init() {
+ // when model is changed we have to change few parameters as well
+ PropertyChangeListener modelChanged = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (CURRENT_MODEL_PROPERTY.equals(arg0.getPropertyName())) {
+ updateModelView();
+ }
+ }
+
+ };
+ addPropertyChangeListener(modelChanged);
+
+ // when we change id we should propagate the change to model
+ PropertyChangeListener mapIdChangeListener = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (CURRENT_MODEL_ID_PROPERTY.equals(arg0.getPropertyName())) {
+ try {
+ setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getNewValue(),
+ userBean.getAuthenticationToken()));
+ setCurrentProjectView(getProjectService().getProjectViewByProjectId(currentMap.getProject().getProjectId(),
+ userBean.getAuthenticationToken()));
+ } catch (Exception e) {
+ try {
+ setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getOldValue(),
+ userBean.getAuthenticationToken()));
+ } catch (SecurityException e1) {
+ logger.error(e1, e1);
+ }
+ logger.error(e, e);
+ }
+ }
+ }
+
+ };
+ addPropertyChangeListener(mapIdChangeListener);
+
+ // when we change id we should propagate the change to model
+ VetoableChangeListener vetoMapIdChangeListener = new VetoableChangeListener() {
+ @Override
+ public void vetoableChange(PropertyChangeEvent arg0) throws PropertyVetoException {
+ if (!getProjectService().projectExists((String) arg0.getNewValue())) {
+ throw new PropertyVetoException("Project with id \"" + arg0.getNewValue() + "\" doesn't exist.", arg0);
+ }
+ }
+
+ };
+ addVetoablePropertyChangeListener(vetoMapIdChangeListener);
+
+ // set id from request parameters (id is the url GET parameter)
+ setCurrentMapId(getRequestParameter("id"));
+
+ }
+
+ /**
+ * Refresh information about models.
+ */
+ protected void updateModelView() {
+
+ Model model = getCurrentTopModel();
+ // configuration
+ ModelView topView = modelService.getModelView(model, userBean.getLoggedUser());
+
+ mapDataList = new ArrayList<>();
+
+ ClientMapData cmd = new ClientMapData();
+ cmd.setMapConfig(topView);
+ cmd.setType("N/A");
+ // coordinates converter
+ cmd.setcConverter(new CoordinationConverter(model));
+
+ mapDataList.add(cmd);
+ topModelMapData = cmd;
+
+ for (ModelView view : topView.getSubmodels()) {
+ cmd = new ClientMapData();
+ cmd.setMapConfig(view);
+ // coordinates converter
+ cmd.setcConverter(new CoordinationConverter(model.getSubmodelById(view.getIdObject())));
+ cmd.setType(model.getSubmodelConnectionById(view.getIdObject()).getType().getCommonName());
+ mapDataList.add(cmd);
+ }
+ }
+
+ /**
+ * This method center map in the client using coordinates from client.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void centerMap(final ActionEvent actionEvent) {
+ createSubmodelDialog(actionEvent);
+
+ // we have plain coordinates (not lat lng)
+ String xCoord = getRequestParameter("xCoord");
+ String yCoord = getRequestParameter("yCoord");
+ String modelIdentifier = getRequestParameter("submodelId");
+ if (modelIdentifier == null) {
+ sendError("submodelId param wasn't set");
+ return;
+ }
+ Integer modelId = Integer.valueOf(modelIdentifier);
+
+ ClientMapData selectedMapData = null;
+ for (ClientMapData mapData : getMapDataList()) {
+ if (mapData.getMapConfig().getIdObject().equals(modelId)) {
+ selectedMapData = mapData;
+ }
+ }
+ if (selectedMapData == null) {
+ sendError("Cannot find map with the identifier: " + modelId);
+ return;
+ }
+
+ LatLng latLng;
+ if (xCoord != null && yCoord != null) {
+ double x = Double.parseDouble(xCoord);
+ double y = Double.parseDouble(yCoord);
+ latLng = selectedMapData.getcConverter().toLatLng(new Point2D.Double(x, y));
+ } else {
+ String latCoord = getRequestParameter("latCoord");
+ String lngCoord = getRequestParameter("lngCoord");
+ double lat = Double.parseDouble(latCoord);
+ double lng = Double.parseDouble(lngCoord);
+ latLng = new LatLng(lat, lng);
+ }
+ centerMapInJavascript(latLng, selectedMapData);
+ }
+
+ /**
+ * Method responsible for centering map in client using coordinates given as a
+ * parameter.
+ *
+ * @param mapData
+ * defines which map we want to center. If the value is not set then
+ * default one is selected
+ *
+ * @param latLng
+ * - coordinates
+ */
+ private void centerMapInJavascript(final LatLng latLng, ClientMapData mapData) {
+ double lat = latLng.getLat();
+ double lng = latLng.getLng();
+ logger.debug("Center map in js (" + lat + "," + lng + ")");
+ executeJavascript("customMap.setCenter(" + mapData.getMapConfig().getIdObject() + ", new google.maps.LatLng(" + lat
+ + "," + lng + "));");
+ }
+
+ /**
+ * Check if user can see the map.
+ *
+ * @return <i>true</i> if user can see the map,<br/>
+ * <i> false otherwise</i>
+ */
+ public boolean getUserHasViewPrivilege() {
+ Project project = getCurrentProject();
+ User user = userBean.getLoggedUser();
+ boolean result = userService.userHasPrivilege(user, PrivilegeType.VIEW_PROJECT, project);
+ if (!result) {
+ logger.debug("User doesn't have privilege");
+ }
+ return result;
+ }
+
+ /**
+ * This is artifitial method called by the client side to pass some parameters
+ * to the bean:
+ * <ul>
+ * <li>{@link #centerCoordinateX},</li>
+ * <li>{@link #centerCoordinateY},</li>
+ * <li>{@link #selectedLayout},</li>
+ * <li>{@link #zoomLevel}.</li>
+ * </ul>
+ */
+ public void actualizeParams() {
+
+ }
+
+ /**
+ * Returns the index of layout that is currently visualized.
+ *
+ * @return index of layout that is currently visualized.
+ */
+ public Integer getSelectedLayoutIdentifier() {
+ if (topModelMapData.getSelectedLayout() == null) {
+ return null;
+ } else {
+ String str = topModelMapData.getSelectedLayout().replaceAll("[^0-9]", "");
+ Integer id = null;
+ try {
+ id = Integer.parseInt(str);
+ } catch (NumberFormatException e) {
+ logger.warn("Problem with layout identifier: " + topModelMapData.getSelectedLayout());
+ }
+ return id;
+ }
+ }
+
+ /**
+ * Returns level on which the map is currently browsed. It's not equal to the
+ * zoom level, becuse zoom level is shifted by
+ * {@link lcsb.mapviewer.common.Configuration.MIN_ZOOM_LEVEL} value.
+ *
+ * @param mapData
+ * defines on which map we are looking for zoom level. If the value is
+ * not set then default one is selected
+ * @return level on which the map is currently browsed
+ */
+ public Integer getLevel(ClientMapData mapData) {
+ String zoomLevel = mapData.getZoomLevel();
+ if (zoomLevel == null) {
+ return null;
+ }
+ Integer res = null;
+ try {
+ res = Integer.valueOf(zoomLevel) - Configuration.MIN_ZOOM_LEVEL;
+ } catch (NumberFormatException e) {
+ logger.warn("Problem with zoomLevel: " + zoomLevel);
+ }
+ return res;
+ }
+
+ @Override
+ public void clear() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the mapDataList
+ * @see #mapDataList
+ */
+ public List<ClientMapData> getMapDataList() {
+ return mapDataList;
+ }
+
+ /**
+ * Creates dialog on client side for submodel.
+ *
+ * @param actionEvent
+ * event from the client
+ */
+ public void createSubmodelDialog(final ActionEvent actionEvent) {
+ try {
+ String dialogGroup = "_gmapForm:submodelDialogGroup";
+ String idParamName = "submodelId";
+ String dialogIdPrefix = "submodelDialog";
+
+ UIComponent panelGroup = findComponent(dialogGroup);
+ if (panelGroup == null) {
+ sendError("Cannot find " + dialogGroup + " component.");
+ return;
+ }
+ String id = getRequestParameter(idParamName);
+ if (id == null) {
+ sendError(idParamName + " request param cannot be null.");
+ return;
+ }
+ if (id.equals(getCurrentTopModel().getId() + "")) {
+ logger.debug("TopModel doesn't require window");
+ return;
+ }
+ id = dialogIdPrefix + id;
+ for (UIComponent child : panelGroup.getChildren()) {
+ if (child instanceof Dialog) {
+ if (child.getId().equals(id)) {
+ logger.debug("Dialog " + id + " found");
+ return;
+ }
+ }
+ }
+ for (ModelSubmodelConnection model : getCurrentTopModel().getSubmodelConnections()) {
+ Integer modelId = model.getSubmodel().getId();
+ id = dialogIdPrefix + modelId;
+ Dialog dialog = new Dialog();
+ dialog.setId(id);
+ dialog.setWidgetVar(id);
+ dialog.setHeader("Submodel: " + model.getSubmodel().getName());
+ dialog.setMinimizable(true);
+ panelGroup.getChildren().add(dialog);
+ }
+
+ RequestContext requestContext = RequestContext.getCurrentInstance();
+ requestContext.update(dialogGroup);
+
+ } catch (Exception e) {
+ logger.error(e, e);
+ sendError(e.getMessage());
+ }
+ }
+
+ /**
+ * Returns map configuration in Gson format.
+ *
+ * @return map configuration in Gson format
+ */
+ public String getGsonConfiguration() {
+ return new Gson().toJson(getMapDataList().get(0).getMapConfig());
+ }
+
+ /**
+ * @return the topModelMapData
+ * @see #topModelMapData
+ */
+ public ClientMapData getTopModelMapData() {
+ if (topModelMapData == null) {
+ updateModelView();
+ }
+ return topModelMapData;
+ }
+
+ /**
+ * @param topModelMapData
+ * the topModelMapData to set
+ * @see #topModelMapData
+ */
+ public void setTopModelMapData(ClientMapData topModelMapData) {
+ this.topModelMapData = topModelMapData;
+ }
+
+ /**
+ * Returns {@link ClientMapData} for (sub)model identified by identifier.
+ *
+ * @param identifier
+ * identifier of the model
+ * @return {@link ClientMapData}
+ */
+ public ClientMapData getMapDataByMapIdentifier(String identifier) {
+ Integer id = Integer.parseInt(identifier);
+ return getMapDataByMapIdentifier(id);
+ }
+
+ /**
+ * Returns {@link ClientMapData} for (sub)model identified by identifier.
+ *
+ * @param identifier
+ * identifier of the model
+ * @return {@link ClientMapData}
+ */
+ public ClientMapData getMapDataByMapIdentifier(Integer identifier) {
+ // in case we haven't initialized mapdata we need to do it here (it's a
+ // workaround...)
+ if (getMapDataList().size() == 0) {
+ updateModelView();
+ }
+ for (ClientMapData md : getMapDataList()) {
+ if (md.getMapConfig().getIdObject().equals(identifier)) {
+ return md;
+ }
+ }
+ return null;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * Sets zoom level for submodel. Parameters are passed using http request
+ * mechainsm/
+ */
+ public void setModelZoomLevel() {
+ String mapId = getRequestParameter("mapId");
+ String zoomLevel = getRequestParameter("zoomLevel");
+
+ Integer id = Integer.valueOf(mapId);
+
+ for (ClientMapData cmd : getMapDataList()) {
+ if (cmd.getMapConfig().getIdObject().equals(id)) {
+ cmd.setZoomLevel(zoomLevel);
+ return;
+ }
+ }
+ sendError("Cannot find model with id: " + id);
+
+ }
+
+ /**
+ * Sends list of aliases (with given identifiers) to the browser. Identifiers
+ * are passed as a json string in request parameter <i>ids</i>. Each identifier
+ * is a pair containing information about {@link Model#getId() model id} and
+ * {@link lcsb.mapviewer.model.map.species.Element#id alias id}. Data is very
+ * light - contains only information about the location on the model.
+ *
+ */
+ public void retreiveLightAliases() {
+ List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
+ List<LightAliasView> list = modelService.getLightAliasesByIds(getCurrentTopModel(), identifiers);
+ LightAliasViewFactory factory = new LightAliasViewFactory();
+ String string = factory.createGson(list);
+ executeJavascript("ServerConnector.addAliases(" + string + ");");
+ }
+
+ /**
+ * Sends list of reactions (with given identifiers) to the browser. Identifiers
+ * are passed as a json string in request parameter <i>ids</i>. Each identifier
+ * is a pair containing information about {@link Model#getId() model id} and
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction#id reaction id}.
+ *
+ */
+ public void retreiveLightReactions() {
+ List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
+ List<LightReactionView> list = modelService.getLightReactionsByIds(getCurrentTopModel(), identifiers);
+ LightReactionViewFactory factory = new LightReactionViewFactory();
+ String string = factory.createGson(list);
+ executeJavascript("ServerConnector.addReactions('" + string + "');");
+ }
+
+ /**
+ * @return the fullAliasViewFactory
+ * @see #fullAliasViewFactory
+ */
+ public FullAliasViewFactory getFullAliasViewFactory() {
+ if (fullAliasViewFactory == null) {
+ fullAliasViewFactory = findBean(FullAliasViewFactory.class);
+ }
+ return fullAliasViewFactory;
+ }
+
+ /**
+ * @param fullAliasViewFactory
+ * the fullAliasViewFactory to set
+ * @see #fullAliasViewFactory
+ */
+ public void setFullAliasViewFactory(FullAliasViewFactory fullAliasViewFactory) {
+ this.fullAliasViewFactory = fullAliasViewFactory;
+ }
+
+ /**
+ * @return the currentMapId
+ * @see #currentMapId
+ */
+ public final String getCurrentMapId() {
+ // if user didn't provide id then use default one
+ if (currentMapId == null) {
+ String tmp = confService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
+ if (tmp == null) {
+ logger.warn("Cannot find default map in the system.");
+ }
+ setCurrentMapId(tmp);
+ }
+ return currentMapId;
+ }
+
+ /**
+ * @param currentMapId
+ * the currentMapId to set
+ * @see #currentMapId
+ */
+ public final void setCurrentMapId(String currentMapId) {
+ try {
+ fireVetoableChange(CURRENT_MODEL_ID_PROPERTY, this.currentMapId, currentMapId);
+ String oldValue = this.currentMapId;
+ this.currentMapId = currentMapId;
+ firePropertyChange(CURRENT_MODEL_ID_PROPERTY, oldValue, currentMapId);
+ } catch (PropertyVetoException e) {
+ logger.warn("Cannot change property: " + CURRENT_MODEL_ID_PROPERTY + ". Form: \"" + this.currentMapId
+ + "\" into: \"" + currentMapId + "\"");
+ }
+ }
+
+ /**
+ * Return {@link #currentMap currently browsed map}.
+ *
+ * @return currently browsed map
+ */
+ protected final Model getCurrentTopModel() {
+ if (currentMap == null) {
+ try {
+ setCurrentTopModel(
+ this.getModelService().getLastModelByProjectId(getCurrentMapId(), userBean.getAuthenticationToken()));
+ } catch (SecurityException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ return currentMap;
+ }
+
+ /**
+ * @return the currentProject
+ * @see #currentProject
+ */
+ public Project getCurrentProject() {
+ return getCurrentTopModel().getProject();
+ }
+
+ /**
+ * @param topModel
+ * the topModel to set
+ * @see #currentMap
+ */
+ private void setCurrentTopModel(Model topModel) {
+ Model oldValue = this.currentMap;
+ this.currentMap = topModel;
+ firePropertyChange(CURRENT_MODEL_PROPERTY, oldValue, topModel);
+ }
+
+ /**
+ * @return the currentProjectView
+ * @see #currentProjectView
+ */
+ public ProjectView getCurrentProjectView() {
+ return currentProjectView;
+ }
+
+ /**
+ * @param currentProjectView
+ * the currentProjectView to set
+ * @see #currentProjectView
+ */
+ public void setCurrentProjectView(ProjectView currentProjectView) {
+ this.currentProjectView = currentProjectView;
+ }
+
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService
+ * the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ /**
+ * @return the confService
+ * @see #confService
+ */
+ public IConfigurationService getConfService() {
+ return confService;
+ }
+
+ /**
+ * @param confService
+ * the confService to set
+ * @see #confService
+ */
+ public void setConfService(IConfigurationService confService) {
+ this.confService = confService;
+ }
+
+ /**
+ * Returns organism associated with currently viewed project. If organism is not
+ * set then {@link #DEFAULT_ORGANISM} is returned.
+ *
+ * @return organism associated with currently viewed project
+ */
+ public MiriamData getOrganism() {
+ MiriamData organism = getCurrentProject().getOrganism();
+ if (organism == null || organism.getResource().isEmpty()) {
+ organism = DEFAULT_ORGANISM;
+ }
+ return organism;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
index 2dc3e22ad04d8d13be320d3621936042a2e1fa8f..6a6c30a73b45ce4dc5f82c14421deb226c664252 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ProjectBean.java
@@ -76,1434 +76,1448 @@ import lcsb.mapviewer.services.view.ProjectView;
@ViewScoped
public class ProjectBean extends AbstractManagedBean implements Serializable {
- /**
- * String representing {@link #selectedProject} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String SELECTED_PROJECT_PROPERTY = "SELECTED_PROJECT";
-
- /**
- * String representing {@link #mapFile} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String MAP_FILE_PROPERTY = "MAP_FILE";
-
- /**
- * String representing {@link #newMapAutoResize} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String AUTO_RESIZE_MAP_PROPERTY = "AUTO_RESIZE_MAP";
-
- /**
- * String representing {@link #newProjectId} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String PROJECT_ID_PROPERTY = "PROJECT_ID";
-
- /**
- * String representing {@link #newMapVersion} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String MAP_VERSION_PROPERTY = "MAP_VERSION";
-
- /**
- * String representing {@link #selectedAnnotatorTreeNodeData} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY = "SELECTED_ANNOTATOR_TREE_NODE_DATA";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ProjectBean.class);
-
- /**
- * List of projects visible on client side. It's lazy loaded.
- */
- private List<ProjectView> projects = null;
-
- /**
- * Project selected for editing (or new project to create).
- */
- private ProjectView selectedProject;
-
- /**
- * Identifier of the project.
- */
- private String newProjectId = "auto_name";
-
- /**
- * Name of the project.
- */
- private String newProjectName = "UNKNOWN DISEASE MAP";
-
- /**
- * Disease of the project.
- */
- private String newProjectDisease;
-
- /**
- * Organism of the project.
- */
- private String newProjectOrganism;
-
- /**
- * Version of the project.
- */
- private String newMapVersion = "0";
-
- /**
- * Should we annotate model automatically.
- */
- private String annotateModel = "false";
-
- /**
- * Should we cache data from external resources connected to this map.
- */
- private String cacheModel = "false";
-
- /**
- * Should the maunal annotations of the model be verified.
- */
- private String verifyAnnotationsModel = "false";
-
- /**
- * Should we resize the model (to normalize margins).
- */
- private String newMapAutoResize = "true";
-
- /**
- * Is the uploaded model a complex multi-files project or not.
- */
- private String complexModel = "false";
-
- /**
- * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
- * default layout when generating new project.
- */
- private String networkLayoutAsDefault = "false";
-
- /**
- * List of zip entries corresponding to model (and submodels) in the complex
- * project thas is to be uploaded.
- */
- private List<ModelZipEntryFile> modelZipEntries = new ArrayList<ModelZipEntryFile>();
-
- /**
- * List of zip entries corresponding to data mining files in the complex
- * project.
- */
- private List<DataMiningZipEntryFile> dataMiningZipEntries = new ArrayList<DataMiningZipEntryFile>();
-
- /**
- * List of zip entries corresponding to layout files in the complex project.
- */
- private List<LayoutZipEntryFile> layoutZipEntries = new ArrayList<LayoutZipEntryFile>();
-
- /**
- * Should the map be displayed in SBGN format.
- */
- private String sbgnFormat = "false";
-
- private String semanticOverlay = "false";
-
- /**
- * List of zip entries corresponding to
- * {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} files in the
- * complex project.
- */
- private List<ImageZipEntryFile> imageZipEntries = new ArrayList<ImageZipEntryFile>();
-
- /**
- * Uploaded file with the data in CellDesigner format.
- */
- private File mapFile = null;
-
- /**
- * Service used to access information about projects.
- *
- * @see IProjectService
- */
- @ManagedProperty(value = "#{ProjectService}")
- private transient IProjectService projectService;
-
- /**
- * Bean used for communication with the client side about the data related to
- * users (including information about currently logged user).
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{userMB}")
- private transient UserBean userBean;
-
- /**
- * Bean used for communication with the client side about the data related to
- * layouts.
- *
- * @see UserBean
- */
- @ManagedProperty(value = "#{layoutMB}")
- private transient LayoutBean layoutBean;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service that allows to access and manage models.
- */
- @ManagedProperty(value = "#{ModelService}")
- private transient IModelService modelService;
-
- /**
- * Tree with information about classes that can be annotated and which
- * annotators should be used for these classes.
- */
- private TreeNode annotatorsTree;
-
- /**
- * Element of {@link #annotatorsTree} that is currently edited.
- */
- private AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData;
-
- /**
- * List of annotators for {@link #selectedAnnotatorTreeNodeData} that is
- * currently edited.
- */
- private DualListModel<String> annotators = new DualListModel<String>();
-
- /**
- * List of valid {@link MiriamType} for {@link #selectedAnnotatorTreeNodeData}
- * that is currently edited.
- */
- private DualListModel<MiriamType> validMiriam = new DualListModel<MiriamType>();
-
- /**
- * List of required {@link MiriamType} for
- * {@link #selectedAnnotatorTreeNodeData} that is currently edited.
- */
- private DualListModel<MiriamType> requiredMiriam = new DualListModel<MiriamType>();
-
- /**
- * List of all {@link DataMiningType}.
- */
- private List<DataMiningType> dataMiningTypes = new ArrayList<DataMiningType>();
-
- /**
- * Listener used to verify the modification of the project.
- */
- private transient VetoableChangeListener selectedProjectVetoChanged;
-
- {
- selectedProjectVetoChanged = new VetoableChangeListener() {
- @Override
- public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
- try {
- if (SELECTED_PROJECT_PROPERTY.equals(arg0.getPropertyName())) {
-
- ProjectView oldVal = (ProjectView) arg0.getOldValue();
- ProjectView newVal = (ProjectView) arg0.getNewValue();
-
- // if we change to null then it's ok
- if (newVal == null) {
- return;
- }
-
- ProjectView fromDb = projectService.getProjectViewByProjectId(newVal.getProjectId(), userBean.getAuthenticationToken());
- String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
-
- // check if we change the name properly
- if (oldVal != null && oldVal.getIdObject() != null && oldVal.getIdObject().equals(newVal.getIdObject())) {
- if (oldVal.getProjectId().equals(newVal.getProjectId())) {
- // name hasn't changed
- return;
- } else if (oldVal.getProjectId().equals(defaultMap)) {
- // we try to change the name of default map
- throw new PropertyVetoException("Cannot change the name of default project.", arg0);
- } else if (fromDb == null || fromDb.getIdObject() == null) {
- // there is no project with the new name
- return;
- } else if (fromDb.getIdObject().equals(newVal.getIdObject())) {
- // project with the same id is the same project
- return;
- } else {
- throw new PropertyVetoException("Cannot change the name of project. Project with this name already exists.", arg0);
- }
-
- }
-
- if (fromDb != null && fromDb.getIdObject() != null) {
- if (fromDb.getIdObject().equals(newVal.getIdObject())) {
- return;
- } else {
- throw new PropertyVetoException("Project with this name already exists.", arg0);
- }
- }
-
- }
- } catch (Exception e) {
- throw new PropertyVetoException("Unexpected problem: " + e.getMessage(), arg0);
- }
- }
- };
- }
-
- @Override
- public void init() {
-
- addVetoablePropertyChangeListener(selectedProjectVetoChanged);
-
- // uploaded file chagnge listener
- PropertyChangeListener mapFileChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (MAP_FILE_PROPERTY.equals(arg0.getPropertyName())) {
- File file = (File) arg0.getNewValue();
- clearZipEntriesData();
- complexModel = "false";
- if (file != null) {
- if (file.getName().toLowerCase().endsWith("zip")) {
- // when zip file is uploaded preprocess it to retrieve entries in
- // zip file
- ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
- complexModel = "true";
- try {
- ZipFile zipFile = new ZipFile(file);
- Enumeration<? extends ZipEntry> entries = zipFile.entries();
- while (entries.hasMoreElements()) {
- ZipEntry entry = entries.nextElement();
- ZipEntryFile zef = zefFactory.createZipEntryFile(entry, zipFile);
- if (zef != null) {
- // assign zip entries to proper lists
- if (zef instanceof ModelZipEntryFile) {
- modelZipEntries.add((ModelZipEntryFile) zef);
- } else if (zef instanceof ImageZipEntryFile) {
- imageZipEntries.add((ImageZipEntryFile) zef);
- } else if (zef instanceof LayoutZipEntryFile) {
- layoutZipEntries.add((LayoutZipEntryFile) zef);
- } else if (zef instanceof DataMiningZipEntryFile) {
- dataMiningZipEntries.add((DataMiningZipEntryFile) zef);
- } else {
- logger.warn("Unknown class type: " + zef.getClass());
- sendError("Internal server error");
- }
- }
- }
- zipFile.close();
- } catch (IOException e) {
- logger.error(e, e);
- }
- }
- }
- String name = FilenameUtils.getName(file.getName()).replaceAll(" ", "_");
- if (name.indexOf("-cd-") > 0) {
- name = name.substring(0, name.indexOf("-cd-"));
- }
- setNewProjectId(name);
- }
- }
-
- };
- addPropertyChangeListener(mapFileChangeListener);
-
- annotatorsTree = projectService.createClassAnnotatorTree(userBean.getLoggedUser());
-
- // this listener will be called when user start to edit list of
- // ElementAnnotator for a given class type
- PropertyChangeListener selectedAnnotatorTreeNodeChangeListener = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY.equals(arg0.getPropertyName())) {
- AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) arg0.getNewValue();
- annotators = new DualListModel<String>(data.getValidAnnotators(), data.getUsedAnnotators());
- validMiriam = new DualListModel<MiriamType>(data.getMissingValidAnnotations(), data.getValidAnnotations());
- requiredMiriam = new DualListModel<MiriamType>(data.getMissingRequiredAnnotations(), data.getRequiredAnnotations());
- }
- }
-
- };
-
- addPropertyChangeListener(selectedAnnotatorTreeNodeChangeListener);
-
- Listener<ObjectAddedEvent> layoutAddedListener = new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- boolean projectFound = false;
- LayoutView layout = (LayoutView) event.getObject();
-
- for (ProjectView project : getProjects()) {
- if (project.getModelId() != null && project.getModelId().equals(layout.getModelId())) {
- projectFound = true;
- project.addLayout(layout);
- }
- }
-
- if (!projectFound) {
- logger.warn("After adding layout cannot find project for the layout. LayoutId: " + layout.getIdObject() + "; ModelId: " + layout.getModelId());
- }
- }
- };
- layoutBean.registerListener(layoutAddedListener);
-
- layoutBean.registerListener(createLayoutRemovedListener());
-
- setSelectedAnnotatorTreeNodeData((AnnotatedObjectTreeRow) annotatorsTree.getData());
-
- for (DataMiningType dm : DataMiningType.values()) {
- dataMiningTypes.add(dm);
- }
-
- // when new project is added refresh list of projects
- registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectAddedEvent event) {
- refreshProjectList(null);
- }
- });
-
- customizeUserParameters();
-
- }
-
- /**
- * Sets default values for some checkboxes specific for a user. (The values
- * are stored in databsae)
- */
- public void customizeUserParameters() {
- if (userBean.getLoggedUser() != null) {
- User user = userBean.getLoggedUser();
- if (user.getAnnotationSchema() != null) {
- setSbgnFormat(user.getAnnotationSchema().getSbgnFormat());
- setNetworkLayoutAsDefault(user.getAnnotationSchema().getNetworkLayoutAsDefault());
- }
- }
- }
-
- /**
- * Sets {@link #networkLayoutAsDefault}.
- *
- * @param value
- * new value
- */
- private void setNetworkLayoutAsDefault(Boolean value) {
- if (value) {
- setNetworkLayoutAsDefault("true");
- } else {
- setNetworkLayoutAsDefault("false");
- }
- }
-
- /**
- * Sets {@link #sbgnFormat}.
- *
- * @param value
- * new value
- */
- private void setSbgnFormat(boolean value) {
- if (value) {
- setSbgnFormat("true");
- } else {
- setSbgnFormat("false");
- }
- }
-
- /**
- * Creates listener that should be called when layout is removed.
- *
- * @return listener that should be called when layout is removed
- */
- public Listener<ObjectRemovedEvent> createLayoutRemovedListener() {
- return new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- @Override
- protected void handle(ObjectRemovedEvent event) {
- boolean projectFound = false;
- LayoutView layout = (LayoutView) event.getObject();
- for (ProjectView project : getProjects()) {
- if (project.getModelId().equals(layout.getModelId())) {
- projectFound = true;
- LayoutView layoutToRemove = null;
- for (LayoutView oldLayout : project.getLayouts()) {
- if (oldLayout.getIdObject().equals(layout.getIdObject())) {
- layoutToRemove = oldLayout;
- }
- }
- if (layoutToRemove == null) {
- logger.warn(
- "After removing layout from db cannot find layout in the project to remove. LayoutId: " + layout.getIdObject() + "; ModelId: "
- + layout.getModelId());
- } else {
- project.getLayouts().remove(layoutToRemove);
- }
- }
- }
-
- if (!projectFound) {
- logger.warn("After removing layout cannot find project for the layout. LayoutId: " + layout.getIdObject() + "; ModelId: " + layout.getModelId());
- }
- }
- };
- }
-
- /**
- * Refresh list of projects.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void refreshProjectList(final ActionEvent actionEvent) {
- if (projects == null) {
- logger.warn("Strange behaviour: refreshing project list withouth accessing...");
- projects = new ArrayList<>();
- }
- projects.clear();
- List<ProjectView> localProjectList = projectService.getAllProjectViews(userBean.getAuthenticationToken());
- for (ProjectView projectRow : localProjectList) {
- projects.add(projectRow);
- }
- Collections.sort(projects);
- }
-
- /**
- * This method handle upload of a file.
- *
- * @param event
- * event send by the client with a file reference
- */
- public void handleFileUpload(final FileUploadEvent event) {
- try {
- logger.debug(event.getFile().getFileName() + " is uploaded.");
- UploadedFile uploadedFile = event.getFile();
- String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
- String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
- File file = File.createTempFile(filename + "-cd-", "." + extension);
- file.delete();
- InputStream input = uploadedFile.getInputstream();
- Files.copy(input, file.toPath());
- input.close();
-
- this.setMapFile(file);
- } catch (Exception e) {
- sendError("Problem with uploading...", e);
- }
- }
-
- /**
- * Generates project based on the information provided by the client.
- *
- * @param file
- * file with the model in CellDesigner format
- * @throws SecurityException
- */
- protected void generateProject(final File file) throws SecurityException {
- // if project with this name already exists then add random suffix
- String projectId = getNewProjectId();
- if (projectService.projectExists(getNewProjectId())) {
- sendError("Project with identifier: \"" + getNewProjectId() + "\" already exists.");
- return;
- }
-
- // get proper paths:
- // to directory with images
- String imagePath = getProjectDeployPath() + "/../map_images/" + md5(projectId) + "/";
- String version = getNewMapVersion();
-
- boolean autoResize = newMapAutoResize.equalsIgnoreCase("true");
-
- CreateProjectParams params = new CreateProjectParams();
-
- params.complex("true".equalsIgnoreCase(complexModel));
- params.projectId(projectId);
- params.projectName(newProjectName);
- params.projectDisease(newProjectDisease);
- params.projectOrganism(newProjectOrganism);
- params.version(version);
- params.projectFile(file);
- params.autoResize(autoResize);
- params.images(true);
- params.async(true);
- params.notifyEmail(userBean.getLoggedUser().getEmail());
- params.projectDir(imagePath);
- params.annotatorsMap(annotatorsTree);
- params.addUser(userBean.getLogin(), null);
- params.annotations("true".equalsIgnoreCase(annotateModel));
- params.analyzeAnnotations("true".equalsIgnoreCase(verifyAnnotationsModel));
- params.cacheModel("true".equalsIgnoreCase(cacheModel));
- params.validAnnotations(annotatorsTree);
- params.requiredAnnotations(annotatorsTree);
- params.authenticationToken(userBean.getAuthenticationToken());
- for (ZipEntryFile submodel : getZipEntries()) {
- params.addZipEntry(submodel);
- }
- params.sbgnFormat("true".equalsIgnoreCase(sbgnFormat));
- params.semanticZoom("true".equalsIgnoreCase(semanticOverlay));
- params.networkLayoutAsDefault("true".equalsIgnoreCase(networkLayoutAsDefault));
- projectService.createProject(params);
- projectService.updateClassAnnotatorTreeForUser(
- userBean.getLoggedUser(), annotatorsTree, sbgnFormat.equalsIgnoreCase("true"), networkLayoutAsDefault.equalsIgnoreCase("true"));
-
- ObjectAddedEvent event = new ObjectAddedEvent(projectService.getProjectByProjectId(projectId, userBean.getAuthenticationToken()));
- callListeners(event);
- }
-
- /**
- * Returns list of all zip entries in the currently processed file.
- *
- * @return list of all zip entries in the currently processed file
- */
- private Collection<ZipEntryFile> getZipEntries() {
- List<ZipEntryFile> result = new ArrayList<ZipEntryFile>();
- result.addAll(modelZipEntries);
- result.addAll(imageZipEntries);
- result.addAll(layoutZipEntries);
- result.addAll(dataMiningZipEntries);
- return result;
- }
-
- /**
- * 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;
- }
-
- /**
- * Returns project currently selected and edited by the client side.
- *
- * @return project view currently selected and edited by the client side
- */
- public ProjectView getSelectedProject() {
- if (selectedProject == null) {
- selectedProject = projectService.createEmpty();
- }
- return selectedProject;
- }
-
- /**
- * Set new currently selected and edited project.
- *
- * @param selectedProject
- * view of the new currently selected and edited project
- */
- public void setSelectedProject(final ProjectView selectedProject) {
- ProjectView oldValue = this.selectedProject;
- this.selectedProject = selectedProject;
- try {
- fireVetoableChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
- firePropertyChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
- logger.debug("Selected project was set to: " + this.selectedProject.getProjectId());
- } catch (PropertyVetoException e) {
- this.selectedProject = oldValue;
- sendError(e.getMessage(), e);
- }
- }
-
- /**
- * Method which update a project.
- *
- * @param actionEvent
- * event from thefrom the client
- * @throws UserAccessException
- */
- public void updateSelectedProject(final ActionEvent actionEvent) throws UserAccessException {
-
- // first we need small trick (maybe this should be improved)
-
- ProjectView newProject = selectedProject;
- // get old version of the project from db
- ProjectView oldProject = projectService.getProjectViewById(newProject.getIdObject(), userBean.getAuthenticationToken());
-
- // set old version
- setSelectedProject(oldProject);
- // now, change to the new one (property change listener will ensure that
- // everything is fine)
- setSelectedProject(newProject);
-
- // if everything is ok then update in db
- if (selectedProject != null) {
- projectService.updateProject(selectedProject);
- } else {
- logger.warn("Problem during updating project...");
- }
- refreshProjectList(actionEvent);
-
- callListeners(new ObjectModifiedEvent(newProject));
- }
-
- /**
- * Removes project selected by client.
- *
- * @param actionEvent
- * client side action
- */
- public void removeSelectedProject(final ActionEvent actionEvent) {
- try {
- logger.debug("Removing project: " + selectedProject);
- String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
- String projectId = selectedProject.getProjectId();
-
- // find out what is the name of the project in db
- ProjectView project = projectService.getProjectViewById(selectedProject.getIdObject(), userBean.getAuthenticationToken());
- if (project != null) {
- projectId = project.getProjectId();
- }
-
- logger.debug("Removing project: " + projectId);
-
- // if the project name is a default one then don't remove it
- if (defaultMap.equals(projectId)) {
- sendError("Cannot remove default map. To remove this map change the default map in configuration tab first.");
- } else {
- projectService.removeProject(selectedProject, getProjectDeployPath(), true, userBean.getAuthenticationToken());
- callListeners(new ObjectRemovedEvent(selectedProject));
- refreshProjectList(actionEvent);
- }
- } catch (Exception e) {
- sendError("Internal server error", e);
- }
- }
-
- /**
- * Checks if user can manage projects.
- *
- * @return <code>true</code> if user can amange projects, <code>false</code>
- * otherwise
- */
- public boolean getUserHasManagePrivileges() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.PROJECT_MANAGEMENT);
- return result;
- }
-
- /**
- * Checks if user can add project.
- *
- * @return <code>true</code> if user can add projects, <code>false</code>
- * otherwise
- */
- public boolean getUserHasAddMapPrivileges() {
- User user = userBean.getLoggedUser();
- boolean result = userService.userHasPrivilege(user, PrivilegeType.ADD_MAP);
- return result;
- }
-
- /**
- * Gets project identifier for newly created project.
- *
- * @return name of the new project
- */
- public String getNewProjectId() {
- return newProjectId;
- }
-
- /**
- * Sets project identifier for the newly created project.
- *
- * @param newProjectId
- * new name for the new project
- */
- public void setNewProjectId(final String newProjectId) {
- String oldValue = this.newProjectId;
- this.newProjectId = newProjectId;
- firePropertyChange(PROJECT_ID_PROPERTY, oldValue, newProjectId);
- }
-
- /**
- * @return {@link #newMapVersion}
- */
- public String getNewMapVersion() {
- return newMapVersion;
- }
-
- /**
- * Sets new value for {@link #newMapVersion}. Property change listeners will
- * be thrown for "newMapVersion" property.
- *
- * @param newMapVersion
- * {@link #newMapVersion}
- */
- public void setNewMapVersion(final String newMapVersion) {
- String oldValue = this.newMapVersion;
- this.newMapVersion = newMapVersion;
- firePropertyChange(MAP_VERSION_PROPERTY, oldValue, newMapVersion);
- }
-
- /**
- *
- * @return {@link #mapFile}
- */
- public File getMapFile() {
- return mapFile;
- }
-
- /**
- * Sets new value for {@link #mapFile}. Property change listeners will be
- * thrown for "mapFile" property.
- *
- * @param mapFile
- * {@link #mapFile}
- */
- public void setMapFile(final File mapFile) {
- File oldValue = this.mapFile;
- this.mapFile = mapFile;
- firePropertyChange(MAP_FILE_PROPERTY, oldValue, mapFile);
- }
-
- /**
- * Method that creates a project.
- */
- public void createProject() {
- try {
- if (getMapFile() == null) {
- sendError("File cannot be null");
- } else {
- generateProject(getMapFile());
- }
- } catch (Exception e) {
- sendError("Internal server error.", e);
- }
- }
-
- /**
- *
- * @return {@link #newMapAutoResize}
- */
- public String getNewMapAutoResize() {
- return newMapAutoResize;
- }
-
- /**
- * Sets new value for {@link #newMapAutoResize}. Property change listeners
- * will be thrown for "newMapAutoResize" property.
- *
- * @param newMapAutoResize
- * {@link #newMapAutoResize}
- */
- public void setNewMapAutoResize(final String newMapAutoResize) {
- String oldValue = this.newMapAutoResize;
- this.newMapAutoResize = newMapAutoResize;
- firePropertyChange(AUTO_RESIZE_MAP_PROPERTY, oldValue, newMapAutoResize);
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the projectService
- * @see #projectService
- */
- public IProjectService getProjectService() {
- return projectService;
- }
-
- /**
- * @param projectService
- * the projectService to set
- * @see #projectService
- */
- public void setProjectService(IProjectService projectService) {
- this.projectService = projectService;
- }
-
- /**
- * @return the projects
- * @see #projects
- */
- public List<ProjectView> getProjects() {
- if (projects == null) {
- projects = new ArrayList<>();
- refreshProjectList(null);
- }
- return projects;
- }
-
- /**
- * @param projects
- * the projects to set
- * @see #projects
- */
- public void setProjects(List<ProjectView> projects) {
- this.projects = projects;
- }
-
- /**
- * @return the userBean
- * @see #userBean
- */
- public UserBean getUserBean() {
- return userBean;
- }
-
- /**
- * @param userBean
- * the userBean to set
- * @see #userBean
- */
- public void setUserBean(UserBean userBean) {
- this.userBean = userBean;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the modelService
- * @see #modelService
- */
- public IModelService getModelService() {
- return modelService;
- }
-
- /**
- * @param modelService
- * the modelService to set
- * @see #modelService
- */
- public void setModelService(IModelService modelService) {
- this.modelService = modelService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the annotateModel
- * @see #annotateModel
- */
- public String getAnnotateModel() {
- return annotateModel;
- }
-
- /**
- * @param annotateModel
- * the annotateModel to set
- * @see #annotateModel
- */
- public void setAnnotateModel(String annotateModel) {
- this.annotateModel = annotateModel;
- }
-
- /**
- * @return the cacheModel
- * @see #cacheModel
- */
- public String getCacheModel() {
- return cacheModel;
- }
-
- /**
- * @param cacheModel
- * the cacheModel to set
- * @see #cacheModel
- */
- public void setCacheModel(String cacheModel) {
- this.cacheModel = cacheModel;
- }
-
- /**
- * @return the verifyAnnotationsModel
- * @see #verifyAnnotationsModel
- */
- public String getVerifyAnnotationsModel() {
- return verifyAnnotationsModel;
- }
-
- /**
- * @param verifyAnnotationsModel
- * the verifyAnnotationsModel to set
- * @see #verifyAnnotationsModel
- */
- public void setVerifyAnnotationsModel(String verifyAnnotationsModel) {
- this.verifyAnnotationsModel = verifyAnnotationsModel;
- }
-
- /**
- * Method that exports selected project warnings.
- *
- * @throws IOException
- * thrown when there are some problems with sending file
- */
- public void downloadWarnings() throws IOException {
- // and send it as response
- sendFileAsResponse(StringUtils.join(selectedProject.getWarnings(), "\n"), "warnings.txt", MimeType.TEXT);
- }
-
- /**
- * @return the complexModel
- * @see #complexModel
- */
- public String getComplexModel() {
- return complexModel;
- }
-
- /**
- * @param complexModel
- * the complexModel to set
- * @see #complexModel
- */
- public void setComplexModel(String complexModel) {
- this.complexModel = complexModel;
- }
-
- /**
- * Returns list of all available submodel types.
- *
- * @return list of all available submodel types
- */
- public SubmodelType[] getSubmodelTypes() {
- return SubmodelType.values();
- }
-
- /**
- * Returns list of all possible {@link InputFileType}.
- *
- * @return array with all possible values of {@link InputFileType} enum
- */
- public InputFileType[] getFileTypes() {
- return InputFileType.values();
- }
-
- /**
- * @return the annotatorsTree
- * @see #annotatorsTree
- */
- public TreeNode getAnnotatorsTree() {
- return annotatorsTree;
- }
-
- /**
- * @param annotatorsTree
- * the annotatorsTree to set
- * @see #annotatorsTree
- */
- public void setAnnotatorsTree(TreeNode annotatorsTree) {
- this.annotatorsTree = annotatorsTree;
- }
-
- /**
- * @return the annotators
- * @see #annotators
- */
- public DualListModel<String> getAnnotators() {
- return annotators;
- }
-
- /**
- * @param annotators
- * the annotators to set
- * @see #annotators
- */
- public void setAnnotators(DualListModel<String> annotators) {
- this.annotators = annotators;
- }
-
- /**
- * @return the selectedAnnotatorTreeNodeData
- * @see #selectedAnnotatorTreeNodeData
- */
- public AnnotatedObjectTreeRow getSelectedAnnotatorTreeNodeData() {
- return selectedAnnotatorTreeNodeData;
- }
-
- /**
- * @param selectedAnnotatorTreeNodeData
- * the selectedAnnotatorTreeNodeData to set
- * @see #selectedAnnotatorTreeNodeData
- */
- public void setSelectedAnnotatorTreeNodeData(AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData) {
- AnnotatedObjectTreeRow oldValue = this.selectedAnnotatorTreeNodeData;
- this.selectedAnnotatorTreeNodeData = selectedAnnotatorTreeNodeData;
-
- firePropertyChange(SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY, oldValue, selectedAnnotatorTreeNodeData);
- }
-
- /**
- * Method called when list of annotators in {@link #annotators} changed.
- *
- * @param event
- * primefaces event
- */
- public void onTransfer(TransferEvent event) {
- updateAnnotatorTreeNodeData();
- }
-
- /**
- * This method updates data in {@link #selectedAnnotatorTreeNodeData}.
- */
- private void updateAnnotatorTreeNodeData() {
- this.selectedAnnotatorTreeNodeData.setValidAnnotators(annotators.getSource());
- this.selectedAnnotatorTreeNodeData.setUsedAnnotators(annotators.getTarget());
- this.selectedAnnotatorTreeNodeData.setMissingValidAnnotations(validMiriam.getSource());
- this.selectedAnnotatorTreeNodeData.setValidAnnotations(validMiriam.getTarget());
- this.selectedAnnotatorTreeNodeData.setMissingRequiredAnnotations(requiredMiriam.getSource());
- this.selectedAnnotatorTreeNodeData.setRequiredAnnotations(requiredMiriam.getTarget());
- }
-
- /**
- * Method called when list of annotators in {@link #annotators} changed order.
- */
- public void onReorder() {
- updateAnnotatorTreeNodeData();
- }
-
- /**
- * @return the validMiriam
- * @see #validMiriam
- */
- public DualListModel<MiriamType> getValidMiriam() {
- return validMiriam;
- }
-
- /**
- * @param validMiriam
- * the validMiriam to set
- * @see #validMiriam
- */
- public void setValidMiriam(DualListModel<MiriamType> validMiriam) {
- this.validMiriam = validMiriam;
- }
-
- /**
- * @return the requiredMiriam
- * @see #requiredMiriam
- */
- public DualListModel<MiriamType> getRequiredMiriam() {
- return requiredMiriam;
- }
-
- /**
- * @param requiredMiriam
- * the requiredMiriam to set
- * @see #requiredMiriam
- */
- public void setRequiredMiriam(DualListModel<MiriamType> requiredMiriam) {
- this.requiredMiriam = requiredMiriam;
- }
-
- /**
- * @return the dataMiningTypes
- * @see #dataMiningTypes
- */
- public List<DataMiningType> getDataMiningTypes() {
- return dataMiningTypes;
- }
-
- /**
- * @param dataMiningTypes
- * the dataMiningTypes to set
- * @see #dataMiningTypes
- */
- public void setDataMiningTypes(List<DataMiningType> dataMiningTypes) {
- this.dataMiningTypes = dataMiningTypes;
- }
-
- /**
- * @return the layoutBean
- * @see #layoutBean
- */
- public LayoutBean getLayoutBean() {
- return layoutBean;
- }
-
- /**
- * @param layoutBean
- * the layoutBean to set
- * @see #layoutBean
- */
- public void setLayoutBean(LayoutBean layoutBean) {
- this.layoutBean = layoutBean;
- }
-
- /**
- * Clears list with information about zip entries in currently processed zip
- * file.
- */
- private void clearZipEntriesData() {
- dataMiningZipEntries.clear();
- imageZipEntries.clear();
- layoutZipEntries.clear();
- modelZipEntries.clear();
-
- }
-
- /**
- * @return the dataMiningZipEntries
- * @see #dataMiningZipEntries
- */
- public List<DataMiningZipEntryFile> getDataMiningZipEntries() {
- return dataMiningZipEntries;
- }
-
- /**
- * @param dataMiningZipEntries
- * the dataMiningZipEntries to set
- * @see #dataMiningZipEntries
- */
- public void setDataMiningZipEntries(List<DataMiningZipEntryFile> dataMiningZipEntries) {
- this.dataMiningZipEntries = dataMiningZipEntries;
- }
-
- /**
- * @return the modelZipEntries
- * @see #modelZipEntries
- */
- public List<ModelZipEntryFile> getModelZipEntries() {
- return modelZipEntries;
- }
-
- /**
- * @param modelZipEntries
- * the modelZipEntries to set
- * @see #modelZipEntries
- */
- public void setModelZipEntries(List<ModelZipEntryFile> modelZipEntries) {
- this.modelZipEntries = modelZipEntries;
- }
-
- /**
- * @return the layoutZipEntries
- * @see #layoutZipEntries
- */
- public List<LayoutZipEntryFile> getLayoutZipEntries() {
- return layoutZipEntries;
- }
-
- /**
- * @param layoutZipEntries
- * the layoutZipEntries to set
- * @see #layoutZipEntries
- */
- public void setLayoutZipEntries(List<LayoutZipEntryFile> layoutZipEntries) {
- this.layoutZipEntries = layoutZipEntries;
- }
-
- /**
- * @return the imageZipEntries
- * @see #imageZipEntries
- */
- public List<ImageZipEntryFile> getImageZipEntries() {
- return imageZipEntries;
- }
-
- /**
- * @param imageZipEntries
- * the imageZipEntries to set
- * @see #imageZipEntries
- */
- public void setImageZipEntries(List<ImageZipEntryFile> imageZipEntries) {
- this.imageZipEntries = imageZipEntries;
- }
-
- /**
- * @return the newProjectName
- * @see #newProjectName
- */
- public String getNewProjectName() {
- return newProjectName;
- }
-
- /**
- * @param newProjectName
- * the newProjectName to set
- * @see #newProjectName
- */
- public void setNewProjectName(String newProjectName) {
- this.newProjectName = newProjectName;
- }
-
- /**
- * @return the sbgnFormat
- * @see #sbgnFormat
- */
- public String getSbgnFormat() {
- return sbgnFormat;
- }
-
- /**
- * @param sbgnFormat
- * the sbgnFormat to set
- * @see #sbgnFormat
- */
- public void setSbgnFormat(String sbgnFormat) {
- this.sbgnFormat = sbgnFormat;
- }
-
- /**
- * @return the networkLayoutAsDefault
- * @see #networkLayoutAsDefault
- */
- public String getNetworkLayoutAsDefault() {
- return networkLayoutAsDefault;
- }
-
- /**
- * @param networkLayoutAsDefault
- * the networkLayoutAsDefault to set
- * @see #networkLayoutAsDefault
- */
- public void setNetworkLayoutAsDefault(String networkLayoutAsDefault) {
- this.networkLayoutAsDefault = networkLayoutAsDefault;
- }
-
- /**
- * @return new project disease.
- */
- public String getNewProjectDisease() {
- return newProjectDisease;
- }
-
- /**
- * @param newProjectDisease
- * sets the disease
- */
- public void setNewProjectDisease(String newProjectDisease) {
- this.newProjectDisease = newProjectDisease;
- }
-
- /**
- * Method that trigger download of a file in jsf. The file is the source file
- * used to create project given in the parameter.
- *
- * @param projectView
- * view of the {@link Project} for which we are looking for an
- * original source file
- * @throws IOException
- * thrown when there is a problem with sending file
- * @throws UserAccessException
- */
- public void downloadInputData(ProjectView projectView) throws IOException, UserAccessException {
- // get input data from database
- byte[] data = projectService.getInputDataForProject(projectView);
- Project project = projectService.getProjectByProjectId(projectView.getProjectId(), userBean.getAuthenticationToken());
- String string = new String(data, StandardCharsets.UTF_8);
-
- String fileName = project.getInputData().getOriginalFileName();
- MimeType respMimeType = null;
- if (fileName.endsWith("xml")) {
- respMimeType = MimeType.XML;
- } else if (fileName.endsWith("zip")) {
- respMimeType = MimeType.ZIP;
- } else if (fileName.endsWith("sbgn")) {
- respMimeType = MimeType.XML;
- } else {
- logger.warn("Cannot determine mime type of file: " + fileName);
- respMimeType = MimeType.TEXT;
- }
- sendFileAsResponse(string, fileName, respMimeType);
- }
-
- /**
- * @return the newProjectOrganism
- * @see #newProjectOrganism
- */
- public String getNewProjectOrganism() {
- return newProjectOrganism;
- }
-
- /**
- * @param newProjectOrganism
- * the newProjectOrganism to set
- * @see #newProjectOrganism
- */
- public void setNewProjectOrganism(String newProjectOrganism) {
- this.newProjectOrganism = newProjectOrganism;
- }
-
- /**
- * @return the semanticOverlay
- * @see #semanticOverlay
- */
- public String getSemanticOverlay() {
- return semanticOverlay;
- }
-
- /**
- * @param semanticOverlay
- * the semanticOverlay to set
- * @see #semanticOverlay
- */
- public void setSemanticOverlay(String semanticOverlay) {
- this.semanticOverlay = semanticOverlay;
- }
+ /**
+ * String representing {@link #selectedProject} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String SELECTED_PROJECT_PROPERTY = "SELECTED_PROJECT";
+
+ /**
+ * String representing {@link #mapFile} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String MAP_FILE_PROPERTY = "MAP_FILE";
+
+ /**
+ * String representing {@link #newMapAutoResize} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String AUTO_RESIZE_MAP_PROPERTY = "AUTO_RESIZE_MAP";
+
+ /**
+ * String representing {@link #newProjectId} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String PROJECT_ID_PROPERTY = "PROJECT_ID";
+
+ /**
+ * String representing {@link #newMapVersion} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String MAP_VERSION_PROPERTY = "MAP_VERSION";
+
+ /**
+ * String representing {@link #selectedAnnotatorTreeNodeData} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY = "SELECTED_ANNOTATOR_TREE_NODE_DATA";
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ProjectBean.class);
+
+ /**
+ * List of projects visible on client side. It's lazy loaded.
+ */
+ private List<ProjectView> projects = null;
+
+ /**
+ * Project selected for editing (or new project to create).
+ */
+ private ProjectView selectedProject;
+
+ /**
+ * Identifier of the project.
+ */
+ private String newProjectId = "auto_name";
+
+ /**
+ * Name of the project.
+ */
+ private String newProjectName = "UNKNOWN DISEASE MAP";
+
+ /**
+ * Disease of the project.
+ */
+ private String newProjectDisease;
+
+ /**
+ * Organism of the project.
+ */
+ private String newProjectOrganism;
+
+ /**
+ * Version of the project.
+ */
+ private String newMapVersion = "0";
+
+ /**
+ * Should we annotate model automatically.
+ */
+ private String annotateModel = "false";
+
+ /**
+ * Should we cache data from external resources connected to this map.
+ */
+ private String cacheModel = "false";
+
+ /**
+ * Should the maunal annotations of the model be verified.
+ */
+ private String verifyAnnotationsModel = "false";
+
+ /**
+ * Should we resize the model (to normalize margins).
+ */
+ private String newMapAutoResize = "true";
+
+ /**
+ * Is the uploaded model a complex multi-files project or not.
+ */
+ private String complexModel = "false";
+
+ /**
+ * Is the {@link lcsb.mapviewer.services.utils.data.BuildInLayout#NORMAL}
+ * default layout when generating new project.
+ */
+ private String networkLayoutAsDefault = "false";
+
+ /**
+ * List of zip entries corresponding to model (and submodels) in the complex
+ * project thas is to be uploaded.
+ */
+ private List<ModelZipEntryFile> modelZipEntries = new ArrayList<ModelZipEntryFile>();
+
+ /**
+ * List of zip entries corresponding to data mining files in the complex
+ * project.
+ */
+ private List<DataMiningZipEntryFile> dataMiningZipEntries = new ArrayList<DataMiningZipEntryFile>();
+
+ /**
+ * List of zip entries corresponding to layout files in the complex project.
+ */
+ private List<LayoutZipEntryFile> layoutZipEntries = new ArrayList<LayoutZipEntryFile>();
+
+ /**
+ * Should the map be displayed in SBGN format.
+ */
+ private String sbgnFormat = "false";
+
+ private String semanticOverlay = "false";
+
+ /**
+ * List of zip entries corresponding to
+ * {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} files in the
+ * complex project.
+ */
+ private List<ImageZipEntryFile> imageZipEntries = new ArrayList<ImageZipEntryFile>();
+
+ /**
+ * Uploaded file with the data in CellDesigner format.
+ */
+ private File mapFile = null;
+
+ /**
+ * Service used to access information about projects.
+ *
+ * @see IProjectService
+ */
+ @ManagedProperty(value = "#{ProjectService}")
+ private transient IProjectService projectService;
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * users (including information about currently logged user).
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{userMB}")
+ private transient UserBean userBean;
+
+ /**
+ * Bean used for communication with the client side about the data related to
+ * layouts.
+ *
+ * @see UserBean
+ */
+ @ManagedProperty(value = "#{layoutMB}")
+ private transient LayoutBean layoutBean;
+
+ /**
+ * Service used to access configuration parameters.
+ *
+ * @see IConfigurationService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ /**
+ * Service used to access information about users.
+ *
+ * @see IUserService
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Service that allows to access and manage models.
+ */
+ @ManagedProperty(value = "#{ModelService}")
+ private transient IModelService modelService;
+
+ /**
+ * Tree with information about classes that can be annotated and which
+ * annotators should be used for these classes.
+ */
+ private TreeNode annotatorsTree;
+
+ /**
+ * Element of {@link #annotatorsTree} that is currently edited.
+ */
+ private AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData;
+
+ /**
+ * List of annotators for {@link #selectedAnnotatorTreeNodeData} that is
+ * currently edited.
+ */
+ private DualListModel<String> annotators = new DualListModel<String>();
+
+ /**
+ * List of valid {@link MiriamType} for {@link #selectedAnnotatorTreeNodeData}
+ * that is currently edited.
+ */
+ private DualListModel<MiriamType> validMiriam = new DualListModel<MiriamType>();
+
+ /**
+ * List of required {@link MiriamType} for
+ * {@link #selectedAnnotatorTreeNodeData} that is currently edited.
+ */
+ private DualListModel<MiriamType> requiredMiriam = new DualListModel<MiriamType>();
+
+ /**
+ * List of all {@link DataMiningType}.
+ */
+ private List<DataMiningType> dataMiningTypes = new ArrayList<DataMiningType>();
+
+ /**
+ * Listener used to verify the modification of the project.
+ */
+ private transient VetoableChangeListener selectedProjectVetoChanged;
+
+ {
+ selectedProjectVetoChanged = new VetoableChangeListener() {
+ @Override
+ public void vetoableChange(final PropertyChangeEvent arg0) throws PropertyVetoException {
+ try {
+ if (SELECTED_PROJECT_PROPERTY.equals(arg0.getPropertyName())) {
+
+ ProjectView oldVal = (ProjectView) arg0.getOldValue();
+ ProjectView newVal = (ProjectView) arg0.getNewValue();
+
+ // if we change to null then it's ok
+ if (newVal == null) {
+ return;
+ }
+
+ ProjectView fromDb = projectService.getProjectViewByProjectId(newVal.getProjectId(),
+ userBean.getAuthenticationToken());
+ String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
+
+ // check if we change the name properly
+ if (oldVal != null && oldVal.getIdObject() != null && oldVal.getIdObject().equals(newVal.getIdObject())) {
+ if (oldVal.getProjectId().equals(newVal.getProjectId())) {
+ // name hasn't changed
+ return;
+ } else if (oldVal.getProjectId().equals(defaultMap)) {
+ // we try to change the name of default map
+ throw new PropertyVetoException("Cannot change the name of default project.", arg0);
+ } else if (fromDb == null || fromDb.getIdObject() == null) {
+ // there is no project with the new name
+ return;
+ } else if (fromDb.getIdObject().equals(newVal.getIdObject())) {
+ // project with the same id is the same project
+ return;
+ } else {
+ throw new PropertyVetoException(
+ "Cannot change the name of project. Project with this name already exists.", arg0);
+ }
+
+ }
+
+ if (fromDb != null && fromDb.getIdObject() != null) {
+ if (fromDb.getIdObject().equals(newVal.getIdObject())) {
+ return;
+ } else {
+ throw new PropertyVetoException("Project with this name already exists.", arg0);
+ }
+ }
+
+ }
+ } catch (Exception e) {
+ throw new PropertyVetoException("Unexpected problem: " + e.getMessage(), arg0);
+ }
+ }
+ };
+ }
+
+ @Override
+ public void init() {
+
+ addVetoablePropertyChangeListener(selectedProjectVetoChanged);
+
+ // uploaded file chagnge listener
+ PropertyChangeListener mapFileChangeListener = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (MAP_FILE_PROPERTY.equals(arg0.getPropertyName())) {
+ File file = (File) arg0.getNewValue();
+ clearZipEntriesData();
+ complexModel = "false";
+ if (file != null) {
+ if (file.getName().toLowerCase().endsWith("zip")) {
+ // when zip file is uploaded preprocess it to retrieve entries in
+ // zip file
+ ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
+ complexModel = "true";
+ try {
+ ZipFile zipFile = new ZipFile(file);
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ ZipEntryFile zef = zefFactory.createZipEntryFile(entry, zipFile);
+ if (zef != null) {
+ // assign zip entries to proper lists
+ if (zef instanceof ModelZipEntryFile) {
+ modelZipEntries.add((ModelZipEntryFile) zef);
+ } else if (zef instanceof ImageZipEntryFile) {
+ imageZipEntries.add((ImageZipEntryFile) zef);
+ } else if (zef instanceof LayoutZipEntryFile) {
+ layoutZipEntries.add((LayoutZipEntryFile) zef);
+ } else if (zef instanceof DataMiningZipEntryFile) {
+ dataMiningZipEntries.add((DataMiningZipEntryFile) zef);
+ } else {
+ logger.warn("Unknown class type: " + zef.getClass());
+ sendError("Internal server error");
+ }
+ }
+ }
+ zipFile.close();
+ } catch (IOException e) {
+ logger.error(e, e);
+ }
+ }
+ }
+ String name = FilenameUtils.getName(file.getName()).replaceAll(" ", "_");
+ if (name.indexOf("-cd-") > 0) {
+ name = name.substring(0, name.indexOf("-cd-"));
+ }
+ setNewProjectId(name);
+ }
+ }
+
+ };
+ addPropertyChangeListener(mapFileChangeListener);
+
+ annotatorsTree = projectService.createClassAnnotatorTree(userBean.getLoggedUser());
+
+ // this listener will be called when user start to edit list of
+ // ElementAnnotator for a given class type
+ PropertyChangeListener selectedAnnotatorTreeNodeChangeListener = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY.equals(arg0.getPropertyName())) {
+ AnnotatedObjectTreeRow data = (AnnotatedObjectTreeRow) arg0.getNewValue();
+ annotators = new DualListModel<String>(data.getValidAnnotators(), data.getUsedAnnotators());
+ validMiriam = new DualListModel<MiriamType>(data.getMissingValidAnnotations(), data.getValidAnnotations());
+ requiredMiriam = new DualListModel<MiriamType>(data.getMissingRequiredAnnotations(),
+ data.getRequiredAnnotations());
+ }
+ }
+
+ };
+
+ addPropertyChangeListener(selectedAnnotatorTreeNodeChangeListener);
+
+ Listener<ObjectAddedEvent> layoutAddedListener = new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(ObjectAddedEvent event) {
+ boolean projectFound = false;
+ LayoutView layout = (LayoutView) event.getObject();
+
+ for (ProjectView project : getProjects()) {
+ if (project.getModelId() != null && project.getModelId().equals(layout.getModelId())) {
+ projectFound = true;
+ project.addLayout(layout);
+ }
+ }
+
+ if (!projectFound) {
+ logger.warn("After adding layout cannot find project for the layout. LayoutId: " + layout.getIdObject()
+ + "; ModelId: " + layout.getModelId());
+ }
+ }
+ };
+ layoutBean.registerListener(layoutAddedListener);
+
+ layoutBean.registerListener(createLayoutRemovedListener());
+
+ setSelectedAnnotatorTreeNodeData((AnnotatedObjectTreeRow) annotatorsTree.getData());
+
+ for (DataMiningType dm : DataMiningType.values()) {
+ dataMiningTypes.add(dm);
+ }
+
+ // when new project is added refresh list of projects
+ registerListener(new Listener<ObjectAddedEvent>(ObjectAddedEvent.class) {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(ObjectAddedEvent event) {
+ refreshProjectList(null);
+ }
+ });
+
+ customizeUserParameters();
+
+ }
+
+ /**
+ * Sets default values for some checkboxes specific for a user. (The values are
+ * stored in databsae)
+ */
+ public void customizeUserParameters() {
+ if (userBean.getLoggedUser() != null) {
+ User user = userBean.getLoggedUser();
+ if (user.getAnnotationSchema() != null) {
+ setSbgnFormat(user.getAnnotationSchema().getSbgnFormat());
+ setNetworkLayoutAsDefault(user.getAnnotationSchema().getNetworkLayoutAsDefault());
+ }
+ }
+ }
+
+ /**
+ * Sets {@link #networkLayoutAsDefault}.
+ *
+ * @param value
+ * new value
+ */
+ private void setNetworkLayoutAsDefault(Boolean value) {
+ if (value) {
+ setNetworkLayoutAsDefault("true");
+ } else {
+ setNetworkLayoutAsDefault("false");
+ }
+ }
+
+ /**
+ * Sets {@link #sbgnFormat}.
+ *
+ * @param value
+ * new value
+ */
+ private void setSbgnFormat(boolean value) {
+ if (value) {
+ setSbgnFormat("true");
+ } else {
+ setSbgnFormat("false");
+ }
+ }
+
+ /**
+ * Creates listener that should be called when layout is removed.
+ *
+ * @return listener that should be called when layout is removed
+ */
+ public Listener<ObjectRemovedEvent> createLayoutRemovedListener() {
+ return new Listener<ObjectRemovedEvent>(ObjectRemovedEvent.class) {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected void handle(ObjectRemovedEvent event) {
+ boolean projectFound = false;
+ LayoutView layout = (LayoutView) event.getObject();
+ for (ProjectView project : getProjects()) {
+ if (project.getModelId().equals(layout.getModelId())) {
+ projectFound = true;
+ LayoutView layoutToRemove = null;
+ for (LayoutView oldLayout : project.getLayouts()) {
+ if (oldLayout.getIdObject().equals(layout.getIdObject())) {
+ layoutToRemove = oldLayout;
+ }
+ }
+ if (layoutToRemove == null) {
+ logger.warn("After removing layout from db cannot find layout in the project to remove. LayoutId: "
+ + layout.getIdObject() + "; ModelId: " + layout.getModelId());
+ } else {
+ project.getLayouts().remove(layoutToRemove);
+ }
+ }
+ }
+
+ if (!projectFound) {
+ logger.warn("After removing layout cannot find project for the layout. LayoutId: " + layout.getIdObject()
+ + "; ModelId: " + layout.getModelId());
+ }
+ }
+ };
+ }
+
+ /**
+ * Refresh list of projects.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void refreshProjectList(final ActionEvent actionEvent) {
+ if (projects == null) {
+ logger.warn("Strange behaviour: refreshing project list withouth accessing...");
+ projects = new ArrayList<>();
+ }
+ projects.clear();
+ List<ProjectView> localProjectList;
+ try {
+ localProjectList = projectService.getAllProjectViews(userBean.getAuthenticationToken());
+ for (ProjectView projectRow : localProjectList) {
+ projects.add(projectRow);
+ }
+ Collections.sort(projects);
+ } catch (SecurityException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * This method handle upload of a file.
+ *
+ * @param event
+ * event send by the client with a file reference
+ */
+ public void handleFileUpload(final FileUploadEvent event) {
+ try {
+ logger.debug(event.getFile().getFileName() + " is uploaded.");
+ UploadedFile uploadedFile = event.getFile();
+ String filename = FilenameUtils.getBaseName(uploadedFile.getFileName());
+ String extension = FilenameUtils.getExtension(uploadedFile.getFileName());
+ File file = File.createTempFile(filename + "-cd-", "." + extension);
+ file.delete();
+ InputStream input = uploadedFile.getInputstream();
+ Files.copy(input, file.toPath());
+ input.close();
+
+ this.setMapFile(file);
+ } catch (Exception e) {
+ sendError("Problem with uploading...", e);
+ }
+ }
+
+ /**
+ * Generates project based on the information provided by the client.
+ *
+ * @param file
+ * file with the model in CellDesigner format
+ * @throws SecurityException
+ */
+ protected void generateProject(final File file) throws SecurityException {
+ // if project with this name already exists then add random suffix
+ String projectId = getNewProjectId();
+ if (projectService.projectExists(getNewProjectId())) {
+ sendError("Project with identifier: \"" + getNewProjectId() + "\" already exists.");
+ return;
+ }
+
+ // get proper paths:
+ // to directory with images
+ String imagePath = getProjectDeployPath() + "/../map_images/" + md5(projectId) + "/";
+ String version = getNewMapVersion();
+
+ boolean autoResize = newMapAutoResize.equalsIgnoreCase("true");
+
+ CreateProjectParams params = new CreateProjectParams();
+
+ params.complex("true".equalsIgnoreCase(complexModel));
+ params.projectId(projectId);
+ params.projectName(newProjectName);
+ params.projectDisease(newProjectDisease);
+ params.projectOrganism(newProjectOrganism);
+ params.version(version);
+ params.projectFile(file);
+ params.autoResize(autoResize);
+ params.images(true);
+ params.async(true);
+ params.notifyEmail(userBean.getLoggedUser().getEmail());
+ params.projectDir(imagePath);
+ params.annotatorsMap(annotatorsTree);
+ params.addUser(userBean.getLogin(), null);
+ params.annotations("true".equalsIgnoreCase(annotateModel));
+ params.analyzeAnnotations("true".equalsIgnoreCase(verifyAnnotationsModel));
+ params.cacheModel("true".equalsIgnoreCase(cacheModel));
+ params.validAnnotations(annotatorsTree);
+ params.requiredAnnotations(annotatorsTree);
+ params.authenticationToken(userBean.getAuthenticationToken());
+ for (ZipEntryFile submodel : getZipEntries()) {
+ params.addZipEntry(submodel);
+ }
+ params.sbgnFormat("true".equalsIgnoreCase(sbgnFormat));
+ params.semanticZoom("true".equalsIgnoreCase(semanticOverlay));
+ params.networkLayoutAsDefault("true".equalsIgnoreCase(networkLayoutAsDefault));
+ projectService.createProject(params);
+ projectService.updateClassAnnotatorTreeForUser(userBean.getLoggedUser(), annotatorsTree,
+ sbgnFormat.equalsIgnoreCase("true"), networkLayoutAsDefault.equalsIgnoreCase("true"));
+
+ ObjectAddedEvent event = new ObjectAddedEvent(
+ projectService.getProjectByProjectId(projectId, userBean.getAuthenticationToken()));
+ callListeners(event);
+ }
+
+ /**
+ * Returns list of all zip entries in the currently processed file.
+ *
+ * @return list of all zip entries in the currently processed file
+ */
+ private Collection<ZipEntryFile> getZipEntries() {
+ List<ZipEntryFile> result = new ArrayList<ZipEntryFile>();
+ result.addAll(modelZipEntries);
+ result.addAll(imageZipEntries);
+ result.addAll(layoutZipEntries);
+ result.addAll(dataMiningZipEntries);
+ return result;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * Returns project currently selected and edited by the client side.
+ *
+ * @return project view currently selected and edited by the client side
+ */
+ public ProjectView getSelectedProject() {
+ if (selectedProject == null) {
+ selectedProject = projectService.createEmpty();
+ }
+ return selectedProject;
+ }
+
+ /**
+ * Set new currently selected and edited project.
+ *
+ * @param selectedProject
+ * view of the new currently selected and edited project
+ */
+ public void setSelectedProject(final ProjectView selectedProject) {
+ ProjectView oldValue = this.selectedProject;
+ this.selectedProject = selectedProject;
+ try {
+ fireVetoableChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
+ firePropertyChange(SELECTED_PROJECT_PROPERTY, oldValue, selectedProject);
+ logger.debug("Selected project was set to: " + this.selectedProject.getProjectId());
+ } catch (PropertyVetoException e) {
+ this.selectedProject = oldValue;
+ sendError(e.getMessage(), e);
+ }
+ }
+
+ /**
+ * Method which update a project.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ * @throws SecurityException
+ */
+ public void updateSelectedProject(final ActionEvent actionEvent) throws SecurityException {
+
+ // first we need small trick (maybe this should be improved)
+
+ ProjectView newProject = selectedProject;
+ // get old version of the project from db
+ ProjectView oldProject = projectService.getProjectViewById(newProject.getIdObject(),
+ userBean.getAuthenticationToken());
+
+ // set old version
+ setSelectedProject(oldProject);
+ // now, change to the new one (property change listener will ensure that
+ // everything is fine)
+ setSelectedProject(newProject);
+
+ // if everything is ok then update in db
+ if (selectedProject != null) {
+ projectService.updateProject(selectedProject);
+ } else {
+ logger.warn("Problem during updating project...");
+ }
+ refreshProjectList(actionEvent);
+
+ callListeners(new ObjectModifiedEvent(newProject));
+ }
+
+ /**
+ * Removes project selected by client.
+ *
+ * @param actionEvent
+ * client side action
+ */
+ public void removeSelectedProject(final ActionEvent actionEvent) {
+ try {
+ logger.debug("Removing project: " + selectedProject);
+ String defaultMap = configurationService.getConfigurationValue(ConfigurationElementType.DEFAULT_MAP);
+ String projectId = selectedProject.getProjectId();
+
+ // find out what is the name of the project in db
+ ProjectView project = projectService.getProjectViewById(selectedProject.getIdObject(),
+ userBean.getAuthenticationToken());
+ if (project != null) {
+ projectId = project.getProjectId();
+ }
+
+ logger.debug("Removing project: " + projectId);
+
+ // if the project name is a default one then don't remove it
+ if (defaultMap.equals(projectId)) {
+ sendError("Cannot remove default map. To remove this map change the default map in configuration tab first.");
+ } else {
+ projectService.removeProject(selectedProject, getProjectDeployPath(), true, userBean.getAuthenticationToken());
+ callListeners(new ObjectRemovedEvent(selectedProject));
+ refreshProjectList(actionEvent);
+ }
+ } catch (Exception e) {
+ sendError("Internal server error", e);
+ }
+ }
+
+ /**
+ * Checks if user can manage projects.
+ *
+ * @return <code>true</code> if user can amange projects, <code>false</code>
+ * otherwise
+ */
+ public boolean getUserHasManagePrivileges() {
+ User user = userBean.getLoggedUser();
+ boolean result = userService.userHasPrivilege(user, PrivilegeType.PROJECT_MANAGEMENT);
+ return result;
+ }
+
+ /**
+ * Checks if user can add project.
+ *
+ * @return <code>true</code> if user can add projects, <code>false</code>
+ * otherwise
+ */
+ public boolean getUserHasAddMapPrivileges() {
+ User user = userBean.getLoggedUser();
+ boolean result = userService.userHasPrivilege(user, PrivilegeType.ADD_MAP);
+ return result;
+ }
+
+ /**
+ * Gets project identifier for newly created project.
+ *
+ * @return name of the new project
+ */
+ public String getNewProjectId() {
+ return newProjectId;
+ }
+
+ /**
+ * Sets project identifier for the newly created project.
+ *
+ * @param newProjectId
+ * new name for the new project
+ */
+ public void setNewProjectId(final String newProjectId) {
+ String oldValue = this.newProjectId;
+ this.newProjectId = newProjectId;
+ firePropertyChange(PROJECT_ID_PROPERTY, oldValue, newProjectId);
+ }
+
+ /**
+ * @return {@link #newMapVersion}
+ */
+ public String getNewMapVersion() {
+ return newMapVersion;
+ }
+
+ /**
+ * Sets new value for {@link #newMapVersion}. Property change listeners will be
+ * thrown for "newMapVersion" property.
+ *
+ * @param newMapVersion
+ * {@link #newMapVersion}
+ */
+ public void setNewMapVersion(final String newMapVersion) {
+ String oldValue = this.newMapVersion;
+ this.newMapVersion = newMapVersion;
+ firePropertyChange(MAP_VERSION_PROPERTY, oldValue, newMapVersion);
+ }
+
+ /**
+ *
+ * @return {@link #mapFile}
+ */
+ public File getMapFile() {
+ return mapFile;
+ }
+
+ /**
+ * Sets new value for {@link #mapFile}. Property change listeners will be thrown
+ * for "mapFile" property.
+ *
+ * @param mapFile
+ * {@link #mapFile}
+ */
+ public void setMapFile(final File mapFile) {
+ File oldValue = this.mapFile;
+ this.mapFile = mapFile;
+ firePropertyChange(MAP_FILE_PROPERTY, oldValue, mapFile);
+ }
+
+ /**
+ * Method that creates a project.
+ */
+ public void createProject() {
+ try {
+ if (getMapFile() == null) {
+ sendError("File cannot be null");
+ } else {
+ generateProject(getMapFile());
+ }
+ } catch (Exception e) {
+ sendError("Internal server error.", e);
+ }
+ }
+
+ /**
+ *
+ * @return {@link #newMapAutoResize}
+ */
+ public String getNewMapAutoResize() {
+ return newMapAutoResize;
+ }
+
+ /**
+ * Sets new value for {@link #newMapAutoResize}. Property change listeners will
+ * be thrown for "newMapAutoResize" property.
+ *
+ * @param newMapAutoResize
+ * {@link #newMapAutoResize}
+ */
+ public void setNewMapAutoResize(final String newMapAutoResize) {
+ String oldValue = this.newMapAutoResize;
+ this.newMapAutoResize = newMapAutoResize;
+ firePropertyChange(AUTO_RESIZE_MAP_PROPERTY, oldValue, newMapAutoResize);
+ }
+
+ @Override
+ public void clear() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * @return the projectService
+ * @see #projectService
+ */
+ public IProjectService getProjectService() {
+ return projectService;
+ }
+
+ /**
+ * @param projectService
+ * the projectService to set
+ * @see #projectService
+ */
+ public void setProjectService(IProjectService projectService) {
+ this.projectService = projectService;
+ }
+
+ /**
+ * @return the projects
+ * @see #projects
+ */
+ public List<ProjectView> getProjects() {
+ if (projects == null) {
+ projects = new ArrayList<>();
+ refreshProjectList(null);
+ }
+ return projects;
+ }
+
+ /**
+ * @param projects
+ * the projects to set
+ * @see #projects
+ */
+ public void setProjects(List<ProjectView> projects) {
+ this.projects = projects;
+ }
+
+ /**
+ * @return the userBean
+ * @see #userBean
+ */
+ public UserBean getUserBean() {
+ return userBean;
+ }
+
+ /**
+ * @param userBean
+ * the userBean to set
+ * @see #userBean
+ */
+ public void setUserBean(UserBean userBean) {
+ this.userBean = userBean;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the modelService
+ * @see #modelService
+ */
+ public IModelService getModelService() {
+ return modelService;
+ }
+
+ /**
+ * @param modelService
+ * the modelService to set
+ * @see #modelService
+ */
+ public void setModelService(IModelService modelService) {
+ this.modelService = modelService;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the annotateModel
+ * @see #annotateModel
+ */
+ public String getAnnotateModel() {
+ return annotateModel;
+ }
+
+ /**
+ * @param annotateModel
+ * the annotateModel to set
+ * @see #annotateModel
+ */
+ public void setAnnotateModel(String annotateModel) {
+ this.annotateModel = annotateModel;
+ }
+
+ /**
+ * @return the cacheModel
+ * @see #cacheModel
+ */
+ public String getCacheModel() {
+ return cacheModel;
+ }
+
+ /**
+ * @param cacheModel
+ * the cacheModel to set
+ * @see #cacheModel
+ */
+ public void setCacheModel(String cacheModel) {
+ this.cacheModel = cacheModel;
+ }
+
+ /**
+ * @return the verifyAnnotationsModel
+ * @see #verifyAnnotationsModel
+ */
+ public String getVerifyAnnotationsModel() {
+ return verifyAnnotationsModel;
+ }
+
+ /**
+ * @param verifyAnnotationsModel
+ * the verifyAnnotationsModel to set
+ * @see #verifyAnnotationsModel
+ */
+ public void setVerifyAnnotationsModel(String verifyAnnotationsModel) {
+ this.verifyAnnotationsModel = verifyAnnotationsModel;
+ }
+
+ /**
+ * Method that exports selected project warnings.
+ *
+ * @throws IOException
+ * thrown when there are some problems with sending file
+ */
+ public void downloadWarnings() throws IOException {
+ // and send it as response
+ sendFileAsResponse(StringUtils.join(selectedProject.getWarnings(), "\n"), "warnings.txt", MimeType.TEXT);
+ }
+
+ /**
+ * @return the complexModel
+ * @see #complexModel
+ */
+ public String getComplexModel() {
+ return complexModel;
+ }
+
+ /**
+ * @param complexModel
+ * the complexModel to set
+ * @see #complexModel
+ */
+ public void setComplexModel(String complexModel) {
+ this.complexModel = complexModel;
+ }
+
+ /**
+ * Returns list of all available submodel types.
+ *
+ * @return list of all available submodel types
+ */
+ public SubmodelType[] getSubmodelTypes() {
+ return SubmodelType.values();
+ }
+
+ /**
+ * Returns list of all possible {@link InputFileType}.
+ *
+ * @return array with all possible values of {@link InputFileType} enum
+ */
+ public InputFileType[] getFileTypes() {
+ return InputFileType.values();
+ }
+
+ /**
+ * @return the annotatorsTree
+ * @see #annotatorsTree
+ */
+ public TreeNode getAnnotatorsTree() {
+ return annotatorsTree;
+ }
+
+ /**
+ * @param annotatorsTree
+ * the annotatorsTree to set
+ * @see #annotatorsTree
+ */
+ public void setAnnotatorsTree(TreeNode annotatorsTree) {
+ this.annotatorsTree = annotatorsTree;
+ }
+
+ /**
+ * @return the annotators
+ * @see #annotators
+ */
+ public DualListModel<String> getAnnotators() {
+ return annotators;
+ }
+
+ /**
+ * @param annotators
+ * the annotators to set
+ * @see #annotators
+ */
+ public void setAnnotators(DualListModel<String> annotators) {
+ this.annotators = annotators;
+ }
+
+ /**
+ * @return the selectedAnnotatorTreeNodeData
+ * @see #selectedAnnotatorTreeNodeData
+ */
+ public AnnotatedObjectTreeRow getSelectedAnnotatorTreeNodeData() {
+ return selectedAnnotatorTreeNodeData;
+ }
+
+ /**
+ * @param selectedAnnotatorTreeNodeData
+ * the selectedAnnotatorTreeNodeData to set
+ * @see #selectedAnnotatorTreeNodeData
+ */
+ public void setSelectedAnnotatorTreeNodeData(AnnotatedObjectTreeRow selectedAnnotatorTreeNodeData) {
+ AnnotatedObjectTreeRow oldValue = this.selectedAnnotatorTreeNodeData;
+ this.selectedAnnotatorTreeNodeData = selectedAnnotatorTreeNodeData;
+
+ firePropertyChange(SELECTED_ANNOTATOR_TREE_NODE_DATA_PROPERTY, oldValue, selectedAnnotatorTreeNodeData);
+ }
+
+ /**
+ * Method called when list of annotators in {@link #annotators} changed.
+ *
+ * @param event
+ * primefaces event
+ */
+ public void onTransfer(TransferEvent event) {
+ updateAnnotatorTreeNodeData();
+ }
+
+ /**
+ * This method updates data in {@link #selectedAnnotatorTreeNodeData}.
+ */
+ private void updateAnnotatorTreeNodeData() {
+ this.selectedAnnotatorTreeNodeData.setValidAnnotators(annotators.getSource());
+ this.selectedAnnotatorTreeNodeData.setUsedAnnotators(annotators.getTarget());
+ this.selectedAnnotatorTreeNodeData.setMissingValidAnnotations(validMiriam.getSource());
+ this.selectedAnnotatorTreeNodeData.setValidAnnotations(validMiriam.getTarget());
+ this.selectedAnnotatorTreeNodeData.setMissingRequiredAnnotations(requiredMiriam.getSource());
+ this.selectedAnnotatorTreeNodeData.setRequiredAnnotations(requiredMiriam.getTarget());
+ }
+
+ /**
+ * Method called when list of annotators in {@link #annotators} changed order.
+ */
+ public void onReorder() {
+ updateAnnotatorTreeNodeData();
+ }
+
+ /**
+ * @return the validMiriam
+ * @see #validMiriam
+ */
+ public DualListModel<MiriamType> getValidMiriam() {
+ return validMiriam;
+ }
+
+ /**
+ * @param validMiriam
+ * the validMiriam to set
+ * @see #validMiriam
+ */
+ public void setValidMiriam(DualListModel<MiriamType> validMiriam) {
+ this.validMiriam = validMiriam;
+ }
+
+ /**
+ * @return the requiredMiriam
+ * @see #requiredMiriam
+ */
+ public DualListModel<MiriamType> getRequiredMiriam() {
+ return requiredMiriam;
+ }
+
+ /**
+ * @param requiredMiriam
+ * the requiredMiriam to set
+ * @see #requiredMiriam
+ */
+ public void setRequiredMiriam(DualListModel<MiriamType> requiredMiriam) {
+ this.requiredMiriam = requiredMiriam;
+ }
+
+ /**
+ * @return the dataMiningTypes
+ * @see #dataMiningTypes
+ */
+ public List<DataMiningType> getDataMiningTypes() {
+ return dataMiningTypes;
+ }
+
+ /**
+ * @param dataMiningTypes
+ * the dataMiningTypes to set
+ * @see #dataMiningTypes
+ */
+ public void setDataMiningTypes(List<DataMiningType> dataMiningTypes) {
+ this.dataMiningTypes = dataMiningTypes;
+ }
+
+ /**
+ * @return the layoutBean
+ * @see #layoutBean
+ */
+ public LayoutBean getLayoutBean() {
+ return layoutBean;
+ }
+
+ /**
+ * @param layoutBean
+ * the layoutBean to set
+ * @see #layoutBean
+ */
+ public void setLayoutBean(LayoutBean layoutBean) {
+ this.layoutBean = layoutBean;
+ }
+
+ /**
+ * Clears list with information about zip entries in currently processed zip
+ * file.
+ */
+ private void clearZipEntriesData() {
+ dataMiningZipEntries.clear();
+ imageZipEntries.clear();
+ layoutZipEntries.clear();
+ modelZipEntries.clear();
+
+ }
+
+ /**
+ * @return the dataMiningZipEntries
+ * @see #dataMiningZipEntries
+ */
+ public List<DataMiningZipEntryFile> getDataMiningZipEntries() {
+ return dataMiningZipEntries;
+ }
+
+ /**
+ * @param dataMiningZipEntries
+ * the dataMiningZipEntries to set
+ * @see #dataMiningZipEntries
+ */
+ public void setDataMiningZipEntries(List<DataMiningZipEntryFile> dataMiningZipEntries) {
+ this.dataMiningZipEntries = dataMiningZipEntries;
+ }
+
+ /**
+ * @return the modelZipEntries
+ * @see #modelZipEntries
+ */
+ public List<ModelZipEntryFile> getModelZipEntries() {
+ return modelZipEntries;
+ }
+
+ /**
+ * @param modelZipEntries
+ * the modelZipEntries to set
+ * @see #modelZipEntries
+ */
+ public void setModelZipEntries(List<ModelZipEntryFile> modelZipEntries) {
+ this.modelZipEntries = modelZipEntries;
+ }
+
+ /**
+ * @return the layoutZipEntries
+ * @see #layoutZipEntries
+ */
+ public List<LayoutZipEntryFile> getLayoutZipEntries() {
+ return layoutZipEntries;
+ }
+
+ /**
+ * @param layoutZipEntries
+ * the layoutZipEntries to set
+ * @see #layoutZipEntries
+ */
+ public void setLayoutZipEntries(List<LayoutZipEntryFile> layoutZipEntries) {
+ this.layoutZipEntries = layoutZipEntries;
+ }
+
+ /**
+ * @return the imageZipEntries
+ * @see #imageZipEntries
+ */
+ public List<ImageZipEntryFile> getImageZipEntries() {
+ return imageZipEntries;
+ }
+
+ /**
+ * @param imageZipEntries
+ * the imageZipEntries to set
+ * @see #imageZipEntries
+ */
+ public void setImageZipEntries(List<ImageZipEntryFile> imageZipEntries) {
+ this.imageZipEntries = imageZipEntries;
+ }
+
+ /**
+ * @return the newProjectName
+ * @see #newProjectName
+ */
+ public String getNewProjectName() {
+ return newProjectName;
+ }
+
+ /**
+ * @param newProjectName
+ * the newProjectName to set
+ * @see #newProjectName
+ */
+ public void setNewProjectName(String newProjectName) {
+ this.newProjectName = newProjectName;
+ }
+
+ /**
+ * @return the sbgnFormat
+ * @see #sbgnFormat
+ */
+ public String getSbgnFormat() {
+ return sbgnFormat;
+ }
+
+ /**
+ * @param sbgnFormat
+ * the sbgnFormat to set
+ * @see #sbgnFormat
+ */
+ public void setSbgnFormat(String sbgnFormat) {
+ this.sbgnFormat = sbgnFormat;
+ }
+
+ /**
+ * @return the networkLayoutAsDefault
+ * @see #networkLayoutAsDefault
+ */
+ public String getNetworkLayoutAsDefault() {
+ return networkLayoutAsDefault;
+ }
+
+ /**
+ * @param networkLayoutAsDefault
+ * the networkLayoutAsDefault to set
+ * @see #networkLayoutAsDefault
+ */
+ public void setNetworkLayoutAsDefault(String networkLayoutAsDefault) {
+ this.networkLayoutAsDefault = networkLayoutAsDefault;
+ }
+
+ /**
+ * @return new project disease.
+ */
+ public String getNewProjectDisease() {
+ return newProjectDisease;
+ }
+
+ /**
+ * @param newProjectDisease
+ * sets the disease
+ */
+ public void setNewProjectDisease(String newProjectDisease) {
+ this.newProjectDisease = newProjectDisease;
+ }
+
+ /**
+ * Method that trigger download of a file in jsf. The file is the source file
+ * used to create project given in the parameter.
+ *
+ * @param projectView
+ * view of the {@link Project} for which we are looking for an original
+ * source file
+ * @throws IOException
+ * thrown when there is a problem with sending file
+ * @throws SecurityException
+ */
+ public void downloadInputData(ProjectView projectView) throws IOException, SecurityException {
+ // get input data from database
+ byte[] data = projectService.getInputDataForProject(projectView);
+ Project project = projectService.getProjectByProjectId(projectView.getProjectId(),
+ userBean.getAuthenticationToken());
+ String string = new String(data, StandardCharsets.UTF_8);
+
+ String fileName = project.getInputData().getOriginalFileName();
+ MimeType respMimeType = null;
+ if (fileName.endsWith("xml")) {
+ respMimeType = MimeType.XML;
+ } else if (fileName.endsWith("zip")) {
+ respMimeType = MimeType.ZIP;
+ } else if (fileName.endsWith("sbgn")) {
+ respMimeType = MimeType.XML;
+ } else {
+ logger.warn("Cannot determine mime type of file: " + fileName);
+ respMimeType = MimeType.TEXT;
+ }
+ sendFileAsResponse(string, fileName, respMimeType);
+ }
+
+ /**
+ * @return the newProjectOrganism
+ * @see #newProjectOrganism
+ */
+ public String getNewProjectOrganism() {
+ return newProjectOrganism;
+ }
+
+ /**
+ * @param newProjectOrganism
+ * the newProjectOrganism to set
+ * @see #newProjectOrganism
+ */
+ public void setNewProjectOrganism(String newProjectOrganism) {
+ this.newProjectOrganism = newProjectOrganism;
+ }
+
+ /**
+ * @return the semanticOverlay
+ * @see #semanticOverlay
+ */
+ public String getSemanticOverlay() {
+ return semanticOverlay;
+ }
+
+ /**
+ * @param semanticOverlay
+ * the semanticOverlay to set
+ * @see #semanticOverlay
+ */
+ public void setSemanticOverlay(String semanticOverlay) {
+ this.semanticOverlay = semanticOverlay;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/UserBean.java b/web/src/main/java/lcsb/mapviewer/bean/UserBean.java
index 39c957b9171225f1b259f2d27f4de6e149056393..ad57da482f7c29d33617020b9ad8c47d93131ad0 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/UserBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/UserBean.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.bean;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.IOException;
-import java.util.Calendar;
import java.util.Map;
import javax.faces.application.FacesMessage;
@@ -35,7 +34,6 @@ import lcsb.mapviewer.services.interfaces.IConfigurationService;
import lcsb.mapviewer.services.interfaces.ILogService;
import lcsb.mapviewer.services.interfaces.ILogService.LogParams;
import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.UserView;
/**
@@ -48,551 +46,560 @@ import lcsb.mapviewer.services.view.UserView;
@SessionScoped
public class UserBean extends AbstractManagedBean {
- /**
- * String representing {@link #login} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGIN_PROPERTY = "LOGIN";
-
- /**
- * String representing {@link #password} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String PASSWORD_PROPERTY = "PASSWORD";
-
- /**
- * String representing {@link #loggedUser} property used by
- * {@link #firePropertyChange(String, Object, Object)}.
- */
- public static final String LOGGED_USER_PROPERTY = "USER";
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UserBean.class);
-
- /**
- * Login of currently logged user.
- */
- private String login = "";
-
- private AuthenticationToken authenticationToken;
-
- /**
- * Password of currently logged user.
- */
- private String password = "";
-
- /**
- * Email address that should be used when requesting an account.
- */
- private String requestAccountEmail = "";
-
- /**
- * Currently logged user. The user is transient because it contains
- * information from db and to serialize it properly we should provide
- * apropriate converter.
- */
- private User loggedUser = null;
-
- /**
- * Object to use to edit user's profile.
- */
- private UserView editUser = null;
-
- /**
- * Service used to access information about users.
- *
- * @see IUserService
- */
- @ManagedProperty(value = "#{UserService}")
- private transient IUserService userService;
-
- /**
- * Service used to access logs.
- *
- * @see ILogService
- */
- @ManagedProperty(value = "#{LogService}")
- private transient ILogService logService;
-
- /**
- * Service used to access configuration parameters.
- *
- * @see IConfigurationService
- */
- @ManagedProperty(value = "#{ConfigurationService}")
- private transient IConfigurationService configurationService;
-
- /**
- * Default constructor.
- */
- public UserBean() {
- super();
- // we have to clear default list of property change listeners (we don't
- // want
- // to put passwords in the log file ;-))
- for (PropertyChangeListener listener : getPropertyChangeListeners()) {
- removePropertyChangeListener(listener);
- }
-
- // and now add custom logger property listener
- PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: *** New: ***");
- } else {
- logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: " + arg0.getNewValue());
- }
- }
-
- };
- addPropertyChangeListener(propertyChangeLogger);
- }
-
- @Override
- public void init() {
- PropertyChangeListener loginPasswordChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGIN_PROPERTY.equals(arg0.getPropertyName()) || PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
- authenticationToken = getUserService().login(login, password);
- if (authenticationToken != null) {
- setLoggedUser(getUserService().getUserByLogin(login));
- } else {
- authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
- setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- }
- }
- }
- };
- addPropertyChangeListener(loginPasswordChanged);
-
- PropertyChangeListener loggedUserChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
- getLogService().setLoggedUser(getLoggedUser());
- }
- }
- };
- addPropertyChangeListener(loggedUserChanged);
-
- PropertyChangeListener logServiceLoggedUserChanged = new PropertyChangeListener() {
- @Override
- public void propertyChange(final PropertyChangeEvent arg0) {
- if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
- if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getOldValue())) {
- LogParams params = new LogParams().type(LogType.USER_LOGOUT).object(arg0.getOldValue());
- getLogService().log(params);
- }
-
- if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getNewValue())) {
- LogParams params = new LogParams().type(LogType.USER_LOGIN).object(arg0.getNewValue());
- getLogService().log(params);
- }
- }
- }
- };
- addPropertyChangeListener(logServiceLoggedUserChanged);
-
- setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
- setRequestAccountEmail(getConfigurationService().getConfigurationValue(ConfigurationElementType.REQUEST_ACCOUNT_EMAIL));
-
- }
-
- /**
- *
- * @return {@link #login}
- */
- public String getLogin() {
- return login;
- }
-
- /**
- * Sets new login value. Property change listeners for "login" property will
- * be thrown after setting this value.
- *
- * @param login
- * new {@link #login} value
- */
- public void setLogin(final String login) {
- String oldLogin = this.login;
- this.login = login;
- firePropertyChange(LOGIN_PROPERTY, oldLogin, login);
- }
-
- /**
- * Perform spring login operation.
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void doLogin() throws IOException, ServletException {
- doLogin(null);
- }
-
- /**
- * Perform spring login operation.
- *
- * @param id
- * name of the map which should be used after authentication
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void doLogin(String id) throws IOException, ServletException {
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
-
- ServletRequest request = (ServletRequest) externalContext.getRequest();
- Map<?, ?> map = request.getParameterMap();
- for (Object obj : map.keySet()) {
- try {
- String[] arr = (String[]) map.get(obj);
- if (obj.equals("username")) {
- setLogin(arr[0]);
- }
- if (obj.equals("password")) {
- setPassword(arr[0]);
- }
- } catch (ClassCastException e) {
- logger.error("WTF", e);
- }
- }
-
- // now perform spring authentication
- String requestDispatcher = Configuration.SPRING_SECURITY_ACTION;
- logger.debug(id);
- if (id != null) {
- requestDispatcher += "?id=" + id;
- }
- logger.debug(requestDispatcher);
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest()).getRequestDispatcher(requestDispatcher);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- }
-
- /**
- * Performs spring login as anonymous.
- *
- * @throws IOException
- * thrown when underlaying layer throws this exception
- * @throws ServletException
- * thrown when underlaying layer will throw this exception
- */
- public void anonymousLogin() throws IOException, ServletException {
- setLogin(Configuration.ANONYMOUS_LOGIN);
- setPassword("");
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
- ServletRequest request = (ServletRequest) externalContext.getRequest();
- Map<?, ?> map = request.getParameterMap();
- for (Object obj : map.keySet()) {
- try {
- String[] arr = (String[]) map.get(obj);
- if (obj.equals("username")) {
- arr[0] = Configuration.ANONYMOUS_LOGIN;
- }
- if (obj.equals("password")) {
- arr[0] = "";
- }
- } catch (ClassCastException e) {
- logger.error("WTF", e);
- }
- }
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest()).getRequestDispatcher(Configuration.SPRING_SECURITY_ACTION);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- }
-
- /**
- * Perform spring logout operation.
- *
- * @param actionEvent
- * event from thefrom the client
- */
- public void doLogout(final ActionEvent actionEvent) {
- try {
- FacesContext context = FacesContext.getCurrentInstance();
- ExternalContext externalContext = context.getExternalContext();
-
- RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest()).getRequestDispatcher(Configuration.SPRING_SECURITY_LOGOUT);
-
- dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
-
- context.responseComplete();
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
-
- }
- }
-
- /**
- *
- * @return {@link #password}
- */
- public String getPassword() {
- return password;
- }
-
- /**
- * Sets new password value. Property change listeners for "password" property
- * will be thrown after setting this value.
- *
- * @param password
- * new {@link #password} value
- */
- public void setPassword(final String password) {
- String oldPassword = this.password;
- this.password = password;
- firePropertyChange(PASSWORD_PROPERTY, oldPassword, password);
- }
-
- /**
- *
- * @return {@link #loggedUser}
- */
- public User getLoggedUser() {
- if (loggedUser == null) {
- loggedUser = getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN);
- }
- return loggedUser;
- // return userService.getUserById(loggedUser.getIdObject());
- }
-
- /**
- * Sets new loggedUser value. Property change listeners for "loggedUser"
- * property will be thrown after setting this value.
- *
- * @param user
- * new {@link #loggedUser} value
- */
- public void setLoggedUser(final User user) {
- User oldUser = this.loggedUser;
- // loggedUser = getUserService().getUserView(user);
- loggedUser = user;
- firePropertyChange(LOGGED_USER_PROPERTY, oldUser, loggedUser);
- }
-
- /**
- * Check if user has privileges to manage the users.
- *
- * @return <i>true</i> if user has privileges to manage the users,<br/>
- * <i>false</i> otherwise
- */
- public boolean getUserHasManagePrivileges() {
- User user = getLoggedUser();
- if (user == null) {
- return false;
- }
- boolean result = getUserService().userHasPrivilege(user, PrivilegeType.USER_MANAGEMENT);
- return result;
- }
-
- @Override
- public void clear() {
- throw new NotImplementedException();
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- if (userService == null) {
- userService = findBean(IUserService.class);
- }
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the configurationService
- * @see #configurationService
- */
- public IConfigurationService getConfigurationService() {
- if (configurationService == null) {
- configurationService = findBean(IConfigurationService.class);
- }
- return configurationService;
- }
-
- /**
- * @param configurationService
- * the configurationService to set
- * @see #configurationService
- */
- public void setConfigurationService(IConfigurationService configurationService) {
- this.configurationService = configurationService;
- }
-
- /**
- * @return the requestAccountEmail
- * @see #requestAccountEmail
- */
- public String getRequestAccountEmail() {
- return requestAccountEmail;
- }
-
- /**
- * @param requestAccountEmail
- * the requestAccountEmail to set
- * @see #requestAccountEmail
- */
- public void setRequestAccountEmail(String requestAccountEmail) {
- this.requestAccountEmail = requestAccountEmail;
- }
-
- /**
- * @return the logService
- * @see #logService
- */
- public ILogService getLogService() {
- if (logService == null) {
- logService = findBean(ILogService.class);
- }
- return logService;
- }
-
- /**
- * @param logService
- * the logService to set
- * @see #logService
- */
- public void setLogService(ILogService logService) {
- this.logService = logService;
- }
-
- /**
- * Refresh edit user.
- */
- public void refreshEditUser() {
- if (!loggedUser.getLogin().equals(Configuration.ANONYMOUS_LOGIN)) {
- this.setEditUser(getUserService().getUserRow(loggedUser));
- RequestContext.getCurrentInstance().reset(":tabView:userForm2:panel");
- }
- }
-
- /**
- * @param ctx
- * context
- * @param component
- * ui component
- * @param value
- * the new value
- * @throws ValidatorException
- * if validation fails
- */
- public void checkOldPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
- UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
- if (passwordComp != null) {
- String password = null;
- password = (String) passwordComp.getValue();
- if (password != null && !password.isEmpty()) {
- String oldPassword = (String) value;
- if (oldPassword == null || oldPassword.isEmpty() || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
- ((UIInput) component).setValid(false);
- FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Typed old password does not match stored one.", null);
- throw new ValidatorException(message);
- }
- }
- }
- }
-
- /**
- * @param ctx
- * context
- * @param component
- * ui component
- * @param value
- * the new value
- * @throws ValidatorException
- * if validation fails
- */
- public void checkNewPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
- UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
- if (passwordComp != null) {
- String password = null;
- password = (String) passwordComp.getValue();
- if (password != null && !password.isEmpty()) {
- String oldPassword = (String) value;
- if (oldPassword == null || oldPassword.isEmpty() || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
- ((UIInput) component).setValid(false);
- FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR, "Typed old password does not match stored one.", null);
- throw new ValidatorException(message);
- }
- }
- }
- }
-
- /**
- * Update selected user.
- */
- public void updateUser() {
- getUserService().updateUser(editUser);
- setLoggedUser(getUserService().getUserByLogin(login));
- ObjectModifiedEvent event = new ObjectModifiedEvent(editUser);
- callListeners(event);
- }
-
- /**
- * @return editable instance of the object.
- */
- public UserView getEditUser() {
- return editUser;
- }
-
- /**
- * @param editUser
- * instance to be edited.
- */
- public void setEditUser(UserView editUser) {
- this.editUser = editUser;
- }
-
- /**
- * @return the authenticationToken
- * @see #authenticationToken
- */
- public AuthenticationToken getAuthenticationToken() {
- if (authenticationToken == null) {
- authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
- }
- return authenticationToken;
- }
-
- /**
- * @param authenticationToken
- * the authenticationToken to set
- * @see #authenticationToken
- */
- public void setAuthenticationToken(AuthenticationToken authenticationToken) {
- this.authenticationToken = authenticationToken;
- }
+ /**
+ * String representing {@link #login} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LOGIN_PROPERTY = "LOGIN";
+
+ /**
+ * String representing {@link #password} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String PASSWORD_PROPERTY = "PASSWORD";
+
+ /**
+ * String representing {@link #loggedUser} property used by
+ * {@link #firePropertyChange(String, Object, Object)}.
+ */
+ public static final String LOGGED_USER_PROPERTY = "USER";
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UserBean.class);
+
+ /**
+ * Login of currently logged user.
+ */
+ private String login = "";
+
+ private String authenticationToken;
+
+ /**
+ * Password of currently logged user.
+ */
+ private String password = "";
+
+ /**
+ * Email address that should be used when requesting an account.
+ */
+ private String requestAccountEmail = "";
+
+ /**
+ * Currently logged user. The user is transient because it contains information
+ * from db and to serialize it properly we should provide apropriate converter.
+ */
+ private User loggedUser = null;
+
+ /**
+ * Object to use to edit user's profile.
+ */
+ private UserView editUser = null;
+
+ /**
+ * Service used to access information about users.
+ *
+ * @see IUserService
+ */
+ @ManagedProperty(value = "#{UserService}")
+ private transient IUserService userService;
+
+ /**
+ * Service used to access logs.
+ *
+ * @see ILogService
+ */
+ @ManagedProperty(value = "#{LogService}")
+ private transient ILogService logService;
+
+ /**
+ * Service used to access configuration parameters.
+ *
+ * @see IConfigurationService
+ */
+ @ManagedProperty(value = "#{ConfigurationService}")
+ private transient IConfigurationService configurationService;
+
+ /**
+ * Default constructor.
+ */
+ public UserBean() {
+ super();
+ // we have to clear default list of property change listeners (we don't
+ // want
+ // to put passwords in the log file ;-))
+ for (PropertyChangeListener listener : getPropertyChangeListeners()) {
+ removePropertyChangeListener(listener);
+ }
+
+ // and now add custom logger property listener
+ PropertyChangeListener propertyChangeLogger = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
+ logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: *** New: ***");
+ } else {
+ logger.debug("Property changed: " + arg0.getPropertyName() + ". Old: " + arg0.getOldValue() + " New: "
+ + arg0.getNewValue());
+ }
+ }
+
+ };
+ addPropertyChangeListener(propertyChangeLogger);
+ }
+
+ @Override
+ public void init() {
+ PropertyChangeListener loginPasswordChanged = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (LOGIN_PROPERTY.equals(arg0.getPropertyName()) || PASSWORD_PROPERTY.equals(arg0.getPropertyName())) {
+ authenticationToken = getUserService().login(login, password);
+ if (authenticationToken != null) {
+ setLoggedUser(getUserService().getUserByLogin(login));
+ } else {
+ authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
+ setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
+ }
+ }
+ }
+ };
+ addPropertyChangeListener(loginPasswordChanged);
+
+ PropertyChangeListener loggedUserChanged = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
+ getLogService().setLoggedUser(getLoggedUser());
+ }
+ }
+ };
+ addPropertyChangeListener(loggedUserChanged);
+
+ PropertyChangeListener logServiceLoggedUserChanged = new PropertyChangeListener() {
+ @Override
+ public void propertyChange(final PropertyChangeEvent arg0) {
+ if (LOGGED_USER_PROPERTY.equals(arg0.getPropertyName())) {
+ if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getOldValue())) {
+ LogParams params = new LogParams().type(LogType.USER_LOGOUT).object(arg0.getOldValue());
+ getLogService().log(params);
+ }
+
+ if (!getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN).equals(arg0.getNewValue())) {
+ LogParams params = new LogParams().type(LogType.USER_LOGIN).object(arg0.getNewValue());
+ getLogService().log(params);
+ }
+ }
+ }
+ };
+ addPropertyChangeListener(logServiceLoggedUserChanged);
+
+ setLoggedUser(getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN));
+ setRequestAccountEmail(
+ getConfigurationService().getConfigurationValue(ConfigurationElementType.REQUEST_ACCOUNT_EMAIL));
+
+ }
+
+ /**
+ *
+ * @return {@link #login}
+ */
+ public String getLogin() {
+ return login;
+ }
+
+ /**
+ * Sets new login value. Property change listeners for "login" property will be
+ * thrown after setting this value.
+ *
+ * @param login
+ * new {@link #login} value
+ */
+ public void setLogin(final String login) {
+ String oldLogin = this.login;
+ this.login = login;
+ firePropertyChange(LOGIN_PROPERTY, oldLogin, login);
+ }
+
+ /**
+ * Perform spring login operation.
+ *
+ * @throws IOException
+ * thrown when underlaying layer throws this exception
+ * @throws ServletException
+ * thrown when underlaying layer will throw this exception
+ */
+ public void doLogin() throws IOException, ServletException {
+ doLogin(null);
+ }
+
+ /**
+ * Perform spring login operation.
+ *
+ * @param id
+ * name of the map which should be used after authentication
+ *
+ * @throws IOException
+ * thrown when underlaying layer throws this exception
+ * @throws ServletException
+ * thrown when underlaying layer will throw this exception
+ */
+ public void doLogin(String id) throws IOException, ServletException {
+ FacesContext context = FacesContext.getCurrentInstance();
+ ExternalContext externalContext = context.getExternalContext();
+
+ ServletRequest request = (ServletRequest) externalContext.getRequest();
+ Map<?, ?> map = request.getParameterMap();
+ for (Object obj : map.keySet()) {
+ try {
+ String[] arr = (String[]) map.get(obj);
+ if (obj.equals("username")) {
+ setLogin(arr[0]);
+ }
+ if (obj.equals("password")) {
+ setPassword(arr[0]);
+ }
+ } catch (ClassCastException e) {
+ logger.error("WTF", e);
+ }
+ }
+
+ // now perform spring authentication
+ String requestDispatcher = Configuration.SPRING_SECURITY_ACTION;
+ logger.debug(id);
+ if (id != null) {
+ requestDispatcher += "?id=" + id;
+ }
+ logger.debug(requestDispatcher);
+
+ RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
+ .getRequestDispatcher(requestDispatcher);
+
+ dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
+
+ context.responseComplete();
+ }
+
+ /**
+ * Performs spring login as anonymous.
+ *
+ * @throws IOException
+ * thrown when underlaying layer throws this exception
+ * @throws ServletException
+ * thrown when underlaying layer will throw this exception
+ */
+ public void anonymousLogin() throws IOException, ServletException {
+ setLogin(Configuration.ANONYMOUS_LOGIN);
+ setPassword("");
+ FacesContext context = FacesContext.getCurrentInstance();
+ ExternalContext externalContext = context.getExternalContext();
+ ServletRequest request = (ServletRequest) externalContext.getRequest();
+ Map<?, ?> map = request.getParameterMap();
+ for (Object obj : map.keySet()) {
+ try {
+ String[] arr = (String[]) map.get(obj);
+ if (obj.equals("username")) {
+ arr[0] = Configuration.ANONYMOUS_LOGIN;
+ }
+ if (obj.equals("password")) {
+ arr[0] = "";
+ }
+ } catch (ClassCastException e) {
+ logger.error("WTF", e);
+ }
+ }
+
+ RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
+ .getRequestDispatcher(Configuration.SPRING_SECURITY_ACTION);
+
+ dispatcher.forward((ServletRequest) externalContext.getRequest(), (ServletResponse) externalContext.getResponse());
+
+ context.responseComplete();
+ }
+
+ /**
+ * Perform spring logout operation.
+ *
+ * @param actionEvent
+ * event from thefrom the client
+ */
+ public void doLogout(final ActionEvent actionEvent) {
+ try {
+ FacesContext context = FacesContext.getCurrentInstance();
+ ExternalContext externalContext = context.getExternalContext();
+
+ RequestDispatcher dispatcher = ((ServletRequest) externalContext.getRequest())
+ .getRequestDispatcher(Configuration.SPRING_SECURITY_LOGOUT);
+
+ dispatcher.forward((ServletRequest) externalContext.getRequest(),
+ (ServletResponse) externalContext.getResponse());
+
+ context.responseComplete();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+
+ }
+ }
+
+ /**
+ *
+ * @return {@link #password}
+ */
+ public String getPassword() {
+ return password;
+ }
+
+ /**
+ * Sets new password value. Property change listeners for "password" property
+ * will be thrown after setting this value.
+ *
+ * @param password
+ * new {@link #password} value
+ */
+ public void setPassword(final String password) {
+ String oldPassword = this.password;
+ this.password = password;
+ firePropertyChange(PASSWORD_PROPERTY, oldPassword, password);
+ }
+
+ /**
+ *
+ * @return {@link #loggedUser}
+ */
+ public User getLoggedUser() {
+ if (loggedUser == null) {
+ loggedUser = getUserService().getUserByLogin(Configuration.ANONYMOUS_LOGIN);
+ }
+ return loggedUser;
+ // return userService.getUserById(loggedUser.getIdObject());
+ }
+
+ /**
+ * Sets new loggedUser value. Property change listeners for "loggedUser"
+ * property will be thrown after setting this value.
+ *
+ * @param user
+ * new {@link #loggedUser} value
+ */
+ public void setLoggedUser(final User user) {
+ User oldUser = this.loggedUser;
+ // loggedUser = getUserService().getUserView(user);
+ loggedUser = user;
+ firePropertyChange(LOGGED_USER_PROPERTY, oldUser, loggedUser);
+ }
+
+ /**
+ * Check if user has privileges to manage the users.
+ *
+ * @return <i>true</i> if user has privileges to manage the users,<br/>
+ * <i>false</i> otherwise
+ */
+ public boolean getUserHasManagePrivileges() {
+ User user = getLoggedUser();
+ if (user == null) {
+ return false;
+ }
+ boolean result = getUserService().userHasPrivilege(user, PrivilegeType.USER_MANAGEMENT);
+ return result;
+ }
+
+ @Override
+ public void clear() {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ if (userService == null) {
+ userService = findBean(IUserService.class);
+ }
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the configurationService
+ * @see #configurationService
+ */
+ public IConfigurationService getConfigurationService() {
+ if (configurationService == null) {
+ configurationService = findBean(IConfigurationService.class);
+ }
+ return configurationService;
+ }
+
+ /**
+ * @param configurationService
+ * the configurationService to set
+ * @see #configurationService
+ */
+ public void setConfigurationService(IConfigurationService configurationService) {
+ this.configurationService = configurationService;
+ }
+
+ /**
+ * @return the requestAccountEmail
+ * @see #requestAccountEmail
+ */
+ public String getRequestAccountEmail() {
+ return requestAccountEmail;
+ }
+
+ /**
+ * @param requestAccountEmail
+ * the requestAccountEmail to set
+ * @see #requestAccountEmail
+ */
+ public void setRequestAccountEmail(String requestAccountEmail) {
+ this.requestAccountEmail = requestAccountEmail;
+ }
+
+ /**
+ * @return the logService
+ * @see #logService
+ */
+ public ILogService getLogService() {
+ if (logService == null) {
+ logService = findBean(ILogService.class);
+ }
+ return logService;
+ }
+
+ /**
+ * @param logService
+ * the logService to set
+ * @see #logService
+ */
+ public void setLogService(ILogService logService) {
+ this.logService = logService;
+ }
+
+ /**
+ * Refresh edit user.
+ */
+ public void refreshEditUser() {
+ if (!loggedUser.getLogin().equals(Configuration.ANONYMOUS_LOGIN)) {
+ this.setEditUser(getUserService().getUserRow(loggedUser));
+ RequestContext.getCurrentInstance().reset(":tabView:userForm2:panel");
+ }
+ }
+
+ /**
+ * @param ctx
+ * context
+ * @param component
+ * ui component
+ * @param value
+ * the new value
+ * @throws ValidatorException
+ * if validation fails
+ */
+ public void checkOldPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
+ UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
+ if (passwordComp != null) {
+ String password = null;
+ password = (String) passwordComp.getValue();
+ if (password != null && !password.isEmpty()) {
+ String oldPassword = (String) value;
+ if (oldPassword == null || oldPassword.isEmpty()
+ || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
+ ((UIInput) component).setValid(false);
+ FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR,
+ "Typed old password does not match stored one.", null);
+ throw new ValidatorException(message);
+ }
+ }
+ }
+ }
+
+ /**
+ * @param ctx
+ * context
+ * @param component
+ * ui component
+ * @param value
+ * the new value
+ * @throws ValidatorException
+ * if validation fails
+ */
+ public void checkNewPassword(FacesContext ctx, UIComponent component, Object value) throws ValidatorException {
+ UIInput passwordComp = (UIInput) component.getAttributes().get("passwordComp");
+ if (passwordComp != null) {
+ String password = null;
+ password = (String) passwordComp.getValue();
+ if (password != null && !password.isEmpty()) {
+ String oldPassword = (String) value;
+ if (oldPassword == null || oldPassword.isEmpty()
+ || !this.getUserService().encodePassword(oldPassword).equals(editUser.getCryptedPassword())) {
+ ((UIInput) component).setValid(false);
+ FacesMessage message = new FacesMessage(FacesMessage.SEVERITY_ERROR,
+ "Typed old password does not match stored one.", null);
+ throw new ValidatorException(message);
+ }
+ }
+ }
+ }
+
+ /**
+ * Update selected user.
+ */
+ public void updateUser() {
+ getUserService().updateUser(editUser);
+ setLoggedUser(getUserService().getUserByLogin(login));
+ ObjectModifiedEvent event = new ObjectModifiedEvent(editUser);
+ callListeners(event);
+ }
+
+ /**
+ * @return editable instance of the object.
+ */
+ public UserView getEditUser() {
+ return editUser;
+ }
+
+ /**
+ * @param editUser
+ * instance to be edited.
+ */
+ public void setEditUser(UserView editUser) {
+ this.editUser = editUser;
+ }
+
+ /**
+ * @return the authenticationToken
+ * @see #authenticationToken
+ */
+ public String getAuthenticationToken() {
+ if (authenticationToken == null) {
+ authenticationToken = getUserService().login(Configuration.ANONYMOUS_LOGIN, "");
+ }
+ return authenticationToken;
+ }
+
+ /**
+ * @param authenticationToken
+ * the authenticationToken to set
+ * @see #authenticationToken
+ */
+ public void setAuthenticationToken(String authenticationToken) {
+ this.authenticationToken = authenticationToken;
+ }
}
diff --git a/web/src/main/java/lcsb/mapviewer/security/MvInvalidSessionStrategy.java b/web/src/main/java/lcsb/mapviewer/security/MvInvalidSessionStrategy.java
index e3c433620d78980b1e66eeae73f7a604ec160eae..b457ecbfe317618e8179068358c1ff5ee2b541e8 100644
--- a/web/src/main/java/lcsb/mapviewer/security/MvInvalidSessionStrategy.java
+++ b/web/src/main/java/lcsb/mapviewer/security/MvInvalidSessionStrategy.java
@@ -43,38 +43,38 @@ public class MvInvalidSessionStrategy implements InvalidSessionStrategy {
@Override
public void onInvalidSessionDetected(HttpServletRequest request, HttpServletResponse response) throws IOException, ServletException {
- boolean ajaxRedirect = "partial/ajax".equals(request.getHeader(FACES_REQUEST_HEADER));
-
- if (!response.isCommitted()) {
- if (ajaxRedirect) {
- // with expired ajax queries we have a problem.. We must refresh webpage
- // and create a new session,
- // we cannot redirect directly to the original page, because browser
- // won't reload it,
- // so the trick is to send javascript code that will reload browser
- String reloadString = createAjaxReloadPageXml();
- logger.info("Session expired with Ajax request, reloadXml:" + reloadString);
-
- response.setContentType("text/xml");
- response.getWriter().write(reloadString);
-
- } else {
- String requestURI;
- if (!Configuration.LOGIN_PAGE.endsWith(request.getServletPath())) {
- // we don't want to redirect, let's keep the last url
- requestURI = getRequestUrl(request);
- logger.info("Session expired without Ajax request:" + requestURI);
- } else {
- requestURI = getRequestUrl(request);
- logger.info("User forced logout" + requestURI);
- }
-
- logger.info("Staring new session");
- request.getSession(true);
- response.sendRedirect(requestURI);
- }
- }
- return;
+// boolean ajaxRedirect = "partial/ajax".equals(request.getHeader(FACES_REQUEST_HEADER));
+//
+// if (!response.isCommitted()) {
+// if (ajaxRedirect) {
+// // with expired ajax queries we have a problem.. We must refresh webpage
+// // and create a new session,
+// // we cannot redirect directly to the original page, because browser
+// // won't reload it,
+// // so the trick is to send javascript code that will reload browser
+// String reloadString = createAjaxReloadPageXml();
+// logger.info("Session expired with Ajax request, reloadXml:" + reloadString);
+//
+// response.setContentType("text/xml");
+// response.getWriter().write(reloadString);
+//
+// } else {
+// String requestURI;
+// if (!Configuration.LOGIN_PAGE.endsWith(request.getServletPath())) {
+// // we don't want to redirect, let's keep the last url
+// requestURI = getRequestUrl(request);
+// logger.info("Session expired without Ajax request:" + requestURI);
+// } else {
+// requestURI = getRequestUrl(request);
+// logger.info("User forced logout" + requestURI);
+// }
+//
+// logger.info("Staring new session");
+// request.getSession(true);
+// response.sendRedirect(requestURI);
+// }
+// }
+// return;
}
/**
diff --git a/web/src/main/webapp/WEB-INF/security-context.xml b/web/src/main/webapp/WEB-INF/security-context.xml
index f294a895dd74770d90d5065fdb99f0879e920906..41c1b8c8345460bcd9bdaa0ae1320bfb3f61de05 100644
--- a/web/src/main/webapp/WEB-INF/security-context.xml
+++ b/web/src/main/webapp/WEB-INF/security-context.xml
@@ -48,7 +48,7 @@
<bean id="sessionManagementFilter" class="org.springframework.security.web.session.SessionManagementFilter">
<constructor-arg name="securityContextRepository" ref="httpSessionSecurityContextRepository" />
- <property name="invalidSessionStrategy" ref="mapViewerInvalidSessionStrategy"/>
+<!-- <property name="invalidSessionStrategy" ref="mapViewerInvalidSessionStrategy"/> -->
<property name="authenticationFailureHandler" ref="authenticationFailureHandler"/>
</bean>
@@ -95,13 +95,6 @@
<bean id="sessionRegistry" class="org.springframework.security.core.session.SessionRegistryImpl" />
- <bean id="jsfRedirectStrategy" class="lcsb.mapviewer.security.MvJsfRedirectStrategy" />
-
- <bean id="mapViewerInvalidSessionStrategy" class="lcsb.mapviewer.security.MvInvalidSessionStrategy" >
-<!-- <constructor-arg name="invalidSessionUrl" value="viewExpired.xhtml"/> -->
- <constructor-arg value="index.xhtml"/>
-<!-- <constructor-arg name="invalidSessionUrl" value="index.xhtml"/> -->
- </bean>
<bean id="httpSessionSecurityContextRepository" class="org.springframework.security.web.context.HttpSessionSecurityContextRepository"/>
diff --git a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
index 12824a17655664fa85b0a0bd6c9ac6576d99f6c2..21b132558e623e4bf1a8e8468fa9fdb3ad4aeee9 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
@@ -2,47 +2,47 @@ package lcsb.mapviewer.bean;
import java.io.Serializable;
-import lcsb.mapviewer.model.map.model.Model;
-
import org.apache.commons.lang3.SerializationUtils;
import org.junit.After;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.services.SecurityException;
+
public class GalaxyBeanTest extends WebTestFunctions {
- GalaxyBean galaxyBean;
-
- @Before
- public void setUp() throws Exception {
- galaxyBean = new GalaxyBean();
- galaxyBean.setLayoutService(layoutService);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- @Ignore
- public void test() {
- galaxyBean.createLayout(
- "CC75308E16F6AA9C", "NAME\tVALUE\nSNCA\t1\nPINK1\t-1\n", (Model) modelService.getLastModelByProjectId("pdmap", adminToken),
- userService.getUserByLogin("galaxy"));
- }
-
- /**
- * Checks if bean implements {@link Serializable} properly.
- */
- @Test
- public void testSearialization() {
- try {
- SerializationUtils.serialize(galaxyBean);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ GalaxyBean galaxyBean;
+
+ @Before
+ public void setUp() throws Exception {
+ galaxyBean = new GalaxyBean();
+ galaxyBean.setLayoutService(layoutService);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ @Ignore
+ public void test() throws SecurityException {
+ galaxyBean.createLayout("CC75308E16F6AA9C", "NAME\tVALUE\nSNCA\t1\nPINK1\t-1\n",
+ (Model) modelService.getLastModelByProjectId("pdmap", adminToken), userService.getUserByLogin("galaxy"));
+ }
+
+ /**
+ * Checks if bean implements {@link Serializable} properly.
+ */
+ @Test
+ public void testSearialization() {
+ try {
+ SerializationUtils.serialize(galaxyBean);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
index fccf8ea97ff33d35499ff9af035184565b46f1f5..af6b07728d1bdf9579c96fd73c5bb37ed04109a4 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/WebTestFunctions.java
@@ -81,639 +81,638 @@ import lcsb.mapviewer.services.interfaces.ISearchService;
import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.db.chemical.IChemicalService;
import lcsb.mapviewer.services.search.db.drug.IDrugService;
-import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.ModelViewFactory;
@Transactional(value = "txManager")
@Rollback(true)
@ContextConfiguration(locations = { "/applicationContext-persist.xml", //
- "/applicationContext-annotation.xml", //
- "/applicationContext-service.xml", //
- "/dataSource.xml", //
+ "/applicationContext-annotation.xml", //
+ "/applicationContext-service.xml", //
+ "/dataSource.xml", //
})
@RunWith(SpringJUnit4ClassRunner.class)
public abstract class WebTestFunctions {
- private Logger logger = Logger.getLogger(WebTestFunctions.class);
+ private Logger logger = Logger.getLogger(WebTestFunctions.class);
- @Autowired
- protected ChEMBLParser chemblParser;
+ @Autowired
+ protected ChEMBLParser chemblParser;
- @Autowired
- protected DrugbankHTMLParser drugBankHTMLParser;
+ @Autowired
+ protected DrugbankHTMLParser drugBankHTMLParser;
- @Autowired
- protected ModelAnnotator modelAnnotator;
+ @Autowired
+ protected ModelAnnotator modelAnnotator;
- @Autowired
- protected BiocompendiumAnnotator restService;
+ @Autowired
+ protected BiocompendiumAnnotator restService;
- public double EPSILON = 1e-6;
+ public double EPSILON = 1e-6;
- @Autowired
- protected IConfigurationService configurationService;
+ @Autowired
+ protected IConfigurationService configurationService;
- @Autowired
- protected IModelService modelService;
+ @Autowired
+ protected IModelService modelService;
- @Autowired
- protected IExternalServicesService externalServicesService;
+ @Autowired
+ protected IExternalServicesService externalServicesService;
- @Autowired
- protected ILayoutService layoutService;
+ @Autowired
+ protected ILayoutService layoutService;
- @Autowired
- protected ILogService logService;
+ @Autowired
+ protected ILogService logService;
- @Autowired
- protected IExporterService exportService;
+ @Autowired
+ protected IExporterService exportService;
- @Autowired
- protected LogDao logDao;
+ @Autowired
+ protected LogDao logDao;
- @Autowired
- protected SearchHistoryDao searchHistoryDao;
+ @Autowired
+ protected SearchHistoryDao searchHistoryDao;
- @Autowired
- protected PasswordEncoder passwordEncoder;
+ @Autowired
+ protected PasswordEncoder passwordEncoder;
- @Autowired
- protected IUserService userService;
+ @Autowired
+ protected IUserService userService;
- @Autowired
- protected ConfigurationDao configurationDao;
+ @Autowired
+ protected ConfigurationDao configurationDao;
- @Autowired
- protected IDataMiningService dataMiningService;
+ @Autowired
+ protected IDataMiningService dataMiningService;
- @Autowired
- protected ISearchService searchService;
+ @Autowired
+ protected ISearchService searchService;
- @Autowired
- protected IDrugService drugService;
+ @Autowired
+ protected IDrugService drugService;
- @Autowired
- protected IChemicalService chemicalService;
+ @Autowired
+ protected IChemicalService chemicalService;
- @Autowired
- protected IProjectService projectService;
+ @Autowired
+ protected IProjectService projectService;
- @Autowired
- protected ProjectDao projectDao;
+ @Autowired
+ protected ProjectDao projectDao;
- @Autowired
- protected CacheQueryDao cacheQueryDao;
+ @Autowired
+ protected CacheQueryDao cacheQueryDao;
- @Autowired
- protected PolylineDao polylineDao;
+ @Autowired
+ protected PolylineDao polylineDao;
- @Autowired
- protected ModelDao modelDao;
+ @Autowired
+ protected ModelDao modelDao;
- @Autowired
- protected ICommentService commentService;
+ @Autowired
+ protected ICommentService commentService;
- @Autowired
- protected UserDao userDao;
+ @Autowired
+ protected UserDao userDao;
- @Autowired
- protected PrivilegeDao privilegeDao;
+ @Autowired
+ protected PrivilegeDao privilegeDao;
- @Autowired
- protected CommentDao commentDao;
+ @Autowired
+ protected CommentDao commentDao;
- @Autowired
- protected DbUtils dbUtils;
+ @Autowired
+ protected DbUtils dbUtils;
- @Autowired
- protected ReactionDao reactionDao;
+ @Autowired
+ protected ReactionDao reactionDao;
- @Autowired
- protected ElementDao aliasDao;
+ @Autowired
+ protected ElementDao aliasDao;
- @Autowired
- protected ModelViewFactory modelViewFactory;
+ @Autowired
+ protected ModelViewFactory modelViewFactory;
- @Autowired
- protected IReferenceGenomeService referenceGenomeService;
+ @Autowired
+ protected IReferenceGenomeService referenceGenomeService;
- protected User user;
+ protected User user;
- private ConfigurationBean configurationBean;
- private LayoutBean layoutBean;
- private MapBean mapBean;
- private ProjectBean projectBean;
- private UserBean userBean;
+ private ConfigurationBean configurationBean;
+ private LayoutBean layoutBean;
+ private MapBean mapBean;
+ private ProjectBean projectBean;
+ private UserBean userBean;
- private ExportBean exportBean;
+ private ExportBean exportBean;
- private FeedbackBean feedbackBean;
- private MiriamBean miriamBean;
- private MissingConnectionBean missingConnectionBean;
- private SearchBean searchBean;
- private UsersBean usersBean;
+ private FeedbackBean feedbackBean;
+ private MiriamBean miriamBean;
+ private MissingConnectionBean missingConnectionBean;
+ private SearchBean searchBean;
+ private UsersBean usersBean;
- private ReferenceGenomeBean referenceGenomeBean;
+ private ReferenceGenomeBean referenceGenomeBean;
- protected CustomPrimefacesUtils primefacesUtils = new CustomPrimefacesUtils();
+ protected CustomPrimefacesUtils primefacesUtils = new CustomPrimefacesUtils();
- AuthenticationToken token;
+ String token;
- AuthenticationToken adminToken;
+ String adminToken;
- @Before
- public void generalSetUp() {
- dbUtils.setAutoFlush(false);
- createConfigurationBean();
- createLayoutBean();
- createMapBean();
- createProjectBean();
- createUserBean();
- createExportBean();
- createFeedbackBean();
- createMiriamBean();
- createMissingConnectionBean();
- createSearchBean();
- createUsersBean();
- createReferenceGenomeBean();
-
- configurationBean.internalInit();
- layoutBean.internalInit();
- mapBean.internalInit();
- projectBean.internalInit();
- userBean.internalInit();
-
- exportBean.internalInit();
-
- feedbackBean.internalInit();
- miriamBean.internalInit();
- missingConnectionBean.internalInit();
- searchBean.internalInit();
- usersBean.internalInit();
-
- referenceGenomeBean.internalInit();
-
- token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
-
- // assume that we have admin account with all the privileges
- adminToken = userService.login("admin", "admin");
-
- }
-
- @After
- public void generatTearDown() throws IOException {
- File f = new File("map_images");
- if (f.exists()) {
- logger.info("Removing output test directory: " + f.getAbsolutePath());
- FileUtils.deleteDirectory(f);
- }
-
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- /**
- * This method remove model with all connections from db (used only when the
- * db must be handled manually)
- *
- * @param id
- */
- protected void removeModelById(int id) {
- modelDao.delete(modelDao.getById(id));
- }
-
- protected void createUser() {
- user = userDao.getUserByLogin("john.doe");
- if (user == null) {
- user = new User();
- user.setName("John");
- user.setSurname("Doe");
- user.setEmail("john.doe@uni.lu");
- user.setLogin("john.doe");
- user.setCryptedPassword(passwordEncoder.encode("passwd"));
- userDao.add(user);
- }
- }
-
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- }
- Model result = WebTestFunctions.models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- WebTestFunctions.models.put(fileName, result);
- }
- return result;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, boolean includeHeadNode) {
- if (node == null)
- return null;
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
-
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public PrivilegeDao getPrivilegeDao() {
- return privilegeDao;
- }
-
- public void setPrivilegeDao(PrivilegeDao privilegeDao) {
- this.privilegeDao = privilegeDao;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
- protected UserBean getUserBean() {
- if (userBean == null) {
- createUserBean();
- }
- return userBean;
- }
-
- protected LayoutBean getLayoutBean() {
- if (layoutBean == null) {
- createLayoutBean();
- }
- return layoutBean;
- }
-
- private void createUserBean() {
- if (userBean != null) {
- return;
- }
- userBean = new UserBean();
- userBean.setPrimefacesUtils(primefacesUtils);
-
- userBean.setUserService(userService);
- userBean.setConfigurationService(configurationService);
- userBean.setLogService(logService);
-
- }
-
- private void createLayoutBean() {
- if (layoutBean != null) {
- return;
- }
- layoutBean = new LayoutBean();
- layoutBean.setPrimefacesUtils(primefacesUtils);
-
- layoutBean.setLayoutService(layoutService);
- layoutBean.setModelService(modelService);
- layoutBean.setUserBean(getUserBean());
- layoutBean.setMapBean(getMapBean());
-
- }
-
- protected MapBean getMapBean() {
- if (mapBean == null) {
- createMapBean();
- }
- return mapBean;
- }
-
- private void createMapBean() {
- if (mapBean != null) {
- return;
- }
- mapBean = new MapBean();
- mapBean.setPrimefacesUtils(primefacesUtils);
-
- mapBean.setConfService(configurationService);
- mapBean.setModelService(modelService);
- mapBean.setProjectService(projectService);
- mapBean.setConfigurationService(configurationService);
- mapBean.setModelService(modelService);
- mapBean.setUserService(userService);
- mapBean.setUserBean(getUserBean());
- }
-
- protected ProjectBean getProjectBean() {
- if (projectBean == null) {
- createProjectBean();
- }
- return projectBean;
- }
-
- private void createProjectBean() {
- if (projectBean != null) {
- return;
- }
- projectBean = new ProjectBean();
- projectBean.setPrimefacesUtils(primefacesUtils);
-
- projectBean.setConfigurationService(configurationService);
- projectBean.setModelService(modelService);
- projectBean.setProjectService(projectService);
- projectBean.setUserService(userService);
-
- projectBean.setLayoutBean(getLayoutBean());
- projectBean.setUserBean(getUserBean());
- }
-
- protected ExportBean getExportBean() {
- if (exportBean == null) {
- createExportBean();
- }
- return exportBean;
- }
-
- private void createExportBean() {
- if (exportBean != null) {
- return;
- }
- exportBean = new ExportBean();
- exportBean.setPrimefacesUtils(primefacesUtils);
-
- exportBean.setExporterService(exportService);
- exportBean.setMapBean(getMapBean());
- }
-
- protected ConfigurationBean getConfigurationBean() {
- if (configurationBean == null) {
- createConfigurationBean();
- }
- return configurationBean;
- }
-
- private void createConfigurationBean() {
- if (configurationBean != null) {
- return;
- }
- configurationBean = new ConfigurationBean();
- configurationBean.setPrimefacesUtils(primefacesUtils);
-
- configurationBean.setConfigurationService(configurationService);
- configurationBean.setUserService(userService);
- configurationBean.setProjectService(projectService);
-
- configurationBean.setUserBean(getUserBean());
- }
-
- protected FeedbackBean getFeedbackBean() {
- if (feedbackBean == null) {
- createFeedbackBean();
- }
- return feedbackBean;
- }
-
- protected MiriamBean getMiriamBean() {
- if (miriamBean == null) {
- createMiriamBean();
- }
- return miriamBean;
- }
-
- protected MissingConnectionBean getMissingConnectionBean() {
- if (missingConnectionBean == null) {
- createMissingConnectionBean();
- }
- return missingConnectionBean;
- }
-
- protected SearchBean getSearchBean() {
- if (searchBean == null) {
- createSearchBean();
- }
- return searchBean;
- }
-
- protected UsersBean getUsersBean() {
- if (usersBean == null) {
- createUsersBean();
- }
- return usersBean;
- }
-
- private void createFeedbackBean() {
- if (feedbackBean != null) {
- return;
- }
- feedbackBean = new FeedbackBean();
- feedbackBean.setPrimefacesUtils(primefacesUtils);
-
- feedbackBean.setCommentService(commentService);
- feedbackBean.setUserService(userService);
- feedbackBean.setUserBean(userBean);
-
- feedbackBean.setUserBean(getUserBean());
- feedbackBean.setMapBean(getMapBean());
-
- }
-
- private void createMiriamBean() {
- if (miriamBean != null) {
- return;
- }
- miriamBean = new MiriamBean();
- miriamBean.setPrimefacesUtils(primefacesUtils);
-
- }
-
- private void createMissingConnectionBean() {
- if (missingConnectionBean != null) {
- return;
- }
- missingConnectionBean = new MissingConnectionBean();
- missingConnectionBean.setPrimefacesUtils(primefacesUtils);
- }
-
- private void createSearchBean() {
- if (searchBean != null) {
- return;
- }
- searchBean = new SearchBean();
- searchBean.setPrimefacesUtils(primefacesUtils);
-
- searchBean.setConfigurationService(configurationService);
- searchBean.setUserService(userService);
-
- searchBean.setUserBean(getUserBean());
- searchBean.setMapBean(getMapBean());
- }
-
- private void createUsersBean() {
- if (usersBean != null) {
- return;
- }
- usersBean = new UsersBean();
- usersBean.setPrimefacesUtils(primefacesUtils);
-
- usersBean.setUserService(userService);
-
- usersBean.setUserBean(getUserBean());
- usersBean.setProjectBean(getProjectBean());
- }
-
- public ReferenceGenomeBean getReferenceGenomeBean() {
- if (referenceGenomeBean == null) {
- createReferenceGenomeBean();
- }
- return referenceGenomeBean;
- }
-
- private void createReferenceGenomeBean() {
- if (referenceGenomeBean != null) {
- return;
- }
- referenceGenomeBean = new ReferenceGenomeBean();
- referenceGenomeBean.setPrimefacesUtils(primefacesUtils);
-
- referenceGenomeBean.setReferenceGenomeService(referenceGenomeService);
- referenceGenomeBean.setUserBean(getUserBean());
- referenceGenomeBean.setUserService(userService);
- referenceGenomeBean.setMapBean(getMapBean());
-
- }
+ @Before
+ public void generalSetUp() {
+ dbUtils.setAutoFlush(false);
+ createConfigurationBean();
+ createLayoutBean();
+ createMapBean();
+ createProjectBean();
+ createUserBean();
+ createExportBean();
+ createFeedbackBean();
+ createMiriamBean();
+ createMissingConnectionBean();
+ createSearchBean();
+ createUsersBean();
+ createReferenceGenomeBean();
+
+ configurationBean.internalInit();
+ layoutBean.internalInit();
+ mapBean.internalInit();
+ projectBean.internalInit();
+ userBean.internalInit();
+
+ exportBean.internalInit();
+
+ feedbackBean.internalInit();
+ miriamBean.internalInit();
+ missingConnectionBean.internalInit();
+ searchBean.internalInit();
+ usersBean.internalInit();
+
+ referenceGenomeBean.internalInit();
+
+ token = userService.login(Configuration.ANONYMOUS_LOGIN, null);
+
+ // assume that we have admin account with all the privileges
+ adminToken = userService.login("admin", "admin");
+
+ }
+
+ @After
+ public void generatTearDown() throws IOException {
+ File f = new File("map_images");
+ if (f.exists()) {
+ logger.info("Removing output test directory: " + f.getAbsolutePath());
+ FileUtils.deleteDirectory(f);
+ }
+
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ /**
+ * This method remove model with all connections from db (used only when the db
+ * must be handled manually)
+ *
+ * @param id
+ */
+ protected void removeModelById(int id) {
+ modelDao.delete(modelDao.getById(id));
+ }
+
+ protected void createUser() {
+ user = userDao.getUserByLogin("john.doe");
+ if (user == null) {
+ user = new User();
+ user.setName("John");
+ user.setSurname("Doe");
+ user.setEmail("john.doe@uni.lu");
+ user.setLogin("john.doe");
+ user.setCryptedPassword(passwordEncoder.encode("passwd"));
+ userDao.add(user);
+ }
+ }
+
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ protected Model getModelForFile(String fileName, boolean fromCache) throws Exception {
+ if (!fromCache) {
+ logger.debug("File without cache: " + fileName);
+ return new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
+ }
+ Model result = WebTestFunctions.models.get(fileName);
+ if (result == null) {
+ logger.debug("File to cache: " + fileName);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
+ WebTestFunctions.models.put(fileName, result);
+ }
+ return result;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, boolean includeHeadNode) {
+ if (node == null)
+ return null;
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
+
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public PrivilegeDao getPrivilegeDao() {
+ return privilegeDao;
+ }
+
+ public void setPrivilegeDao(PrivilegeDao privilegeDao) {
+ this.privilegeDao = privilegeDao;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+
+ protected UserBean getUserBean() {
+ if (userBean == null) {
+ createUserBean();
+ }
+ return userBean;
+ }
+
+ protected LayoutBean getLayoutBean() {
+ if (layoutBean == null) {
+ createLayoutBean();
+ }
+ return layoutBean;
+ }
+
+ private void createUserBean() {
+ if (userBean != null) {
+ return;
+ }
+ userBean = new UserBean();
+ userBean.setPrimefacesUtils(primefacesUtils);
+
+ userBean.setUserService(userService);
+ userBean.setConfigurationService(configurationService);
+ userBean.setLogService(logService);
+
+ }
+
+ private void createLayoutBean() {
+ if (layoutBean != null) {
+ return;
+ }
+ layoutBean = new LayoutBean();
+ layoutBean.setPrimefacesUtils(primefacesUtils);
+
+ layoutBean.setLayoutService(layoutService);
+ layoutBean.setModelService(modelService);
+ layoutBean.setUserBean(getUserBean());
+ layoutBean.setMapBean(getMapBean());
+
+ }
+
+ protected MapBean getMapBean() {
+ if (mapBean == null) {
+ createMapBean();
+ }
+ return mapBean;
+ }
+
+ private void createMapBean() {
+ if (mapBean != null) {
+ return;
+ }
+ mapBean = new MapBean();
+ mapBean.setPrimefacesUtils(primefacesUtils);
+
+ mapBean.setConfService(configurationService);
+ mapBean.setModelService(modelService);
+ mapBean.setProjectService(projectService);
+ mapBean.setConfigurationService(configurationService);
+ mapBean.setModelService(modelService);
+ mapBean.setUserService(userService);
+ mapBean.setUserBean(getUserBean());
+ }
+
+ protected ProjectBean getProjectBean() {
+ if (projectBean == null) {
+ createProjectBean();
+ }
+ return projectBean;
+ }
+
+ private void createProjectBean() {
+ if (projectBean != null) {
+ return;
+ }
+ projectBean = new ProjectBean();
+ projectBean.setPrimefacesUtils(primefacesUtils);
+
+ projectBean.setConfigurationService(configurationService);
+ projectBean.setModelService(modelService);
+ projectBean.setProjectService(projectService);
+ projectBean.setUserService(userService);
+
+ projectBean.setLayoutBean(getLayoutBean());
+ projectBean.setUserBean(getUserBean());
+ }
+
+ protected ExportBean getExportBean() {
+ if (exportBean == null) {
+ createExportBean();
+ }
+ return exportBean;
+ }
+
+ private void createExportBean() {
+ if (exportBean != null) {
+ return;
+ }
+ exportBean = new ExportBean();
+ exportBean.setPrimefacesUtils(primefacesUtils);
+
+ exportBean.setExporterService(exportService);
+ exportBean.setMapBean(getMapBean());
+ }
+
+ protected ConfigurationBean getConfigurationBean() {
+ if (configurationBean == null) {
+ createConfigurationBean();
+ }
+ return configurationBean;
+ }
+
+ private void createConfigurationBean() {
+ if (configurationBean != null) {
+ return;
+ }
+ configurationBean = new ConfigurationBean();
+ configurationBean.setPrimefacesUtils(primefacesUtils);
+
+ configurationBean.setConfigurationService(configurationService);
+ configurationBean.setUserService(userService);
+ configurationBean.setProjectService(projectService);
+
+ configurationBean.setUserBean(getUserBean());
+ }
+
+ protected FeedbackBean getFeedbackBean() {
+ if (feedbackBean == null) {
+ createFeedbackBean();
+ }
+ return feedbackBean;
+ }
+
+ protected MiriamBean getMiriamBean() {
+ if (miriamBean == null) {
+ createMiriamBean();
+ }
+ return miriamBean;
+ }
+
+ protected MissingConnectionBean getMissingConnectionBean() {
+ if (missingConnectionBean == null) {
+ createMissingConnectionBean();
+ }
+ return missingConnectionBean;
+ }
+
+ protected SearchBean getSearchBean() {
+ if (searchBean == null) {
+ createSearchBean();
+ }
+ return searchBean;
+ }
+
+ protected UsersBean getUsersBean() {
+ if (usersBean == null) {
+ createUsersBean();
+ }
+ return usersBean;
+ }
+
+ private void createFeedbackBean() {
+ if (feedbackBean != null) {
+ return;
+ }
+ feedbackBean = new FeedbackBean();
+ feedbackBean.setPrimefacesUtils(primefacesUtils);
+
+ feedbackBean.setCommentService(commentService);
+ feedbackBean.setUserService(userService);
+ feedbackBean.setUserBean(userBean);
+
+ feedbackBean.setUserBean(getUserBean());
+ feedbackBean.setMapBean(getMapBean());
+
+ }
+
+ private void createMiriamBean() {
+ if (miriamBean != null) {
+ return;
+ }
+ miriamBean = new MiriamBean();
+ miriamBean.setPrimefacesUtils(primefacesUtils);
+
+ }
+
+ private void createMissingConnectionBean() {
+ if (missingConnectionBean != null) {
+ return;
+ }
+ missingConnectionBean = new MissingConnectionBean();
+ missingConnectionBean.setPrimefacesUtils(primefacesUtils);
+ }
+
+ private void createSearchBean() {
+ if (searchBean != null) {
+ return;
+ }
+ searchBean = new SearchBean();
+ searchBean.setPrimefacesUtils(primefacesUtils);
+
+ searchBean.setConfigurationService(configurationService);
+ searchBean.setUserService(userService);
+
+ searchBean.setUserBean(getUserBean());
+ searchBean.setMapBean(getMapBean());
+ }
+
+ private void createUsersBean() {
+ if (usersBean != null) {
+ return;
+ }
+ usersBean = new UsersBean();
+ usersBean.setPrimefacesUtils(primefacesUtils);
+
+ usersBean.setUserService(userService);
+
+ usersBean.setUserBean(getUserBean());
+ usersBean.setProjectBean(getProjectBean());
+ }
+
+ public ReferenceGenomeBean getReferenceGenomeBean() {
+ if (referenceGenomeBean == null) {
+ createReferenceGenomeBean();
+ }
+ return referenceGenomeBean;
+ }
+
+ private void createReferenceGenomeBean() {
+ if (referenceGenomeBean != null) {
+ return;
+ }
+ referenceGenomeBean = new ReferenceGenomeBean();
+ referenceGenomeBean.setPrimefacesUtils(primefacesUtils);
+
+ referenceGenomeBean.setReferenceGenomeService(referenceGenomeService);
+ referenceGenomeBean.setUserBean(getUserBean());
+ referenceGenomeBean.setUserService(userService);
+ referenceGenomeBean.setMapBean(getMapBean());
+
+ }
}