From dc581fa06e74ed4ac6b6f7b0305ac2a9f9b6caee Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 30 Nov 2016 17:56:14 +0100
Subject: [PATCH] additional rest methods
getElements
getReactions
getOverlays
---
.../api/overlay/OverlayController.java | 14 ++
.../api/overlay/OverlayRestImpl.java | 45 +++-
.../api/project/ProjectController.java | 17 ++
.../api/project/ProjectRestImpl.java | 164 ++++++++++++++
.../services/impl/CommentService.java | 201 +-----------------
.../services/impl/LayoutService.java | 65 ++++--
.../mapviewer/services/impl/ModelService.java | 52 ++++-
.../services/interfaces/ICommentService.java | 23 --
.../services/interfaces/ILayoutService.java | 20 +-
.../services/interfaces/IModelService.java | 3 +-
.../services/impl/CommentServiceTest.java | 70 ------
.../services/impl/LayoutServiceTest.java | 32 +--
.../services/impl/ProjectServiceTest.java | 18 +-
.../java/lcsb/mapviewer/bean/ExportBean.java | 2 +-
.../java/lcsb/mapviewer/bean/GalaxyBean.java | 5 +-
.../java/lcsb/mapviewer/bean/LayoutBean.java | 15 +-
.../java/lcsb/mapviewer/bean/MapBean.java | 6 +-
.../lcsb/mapviewer/bean/GalaxyBeanTest.java | 7 +-
18 files changed, 405 insertions(+), 354 deletions(-)
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayController.java b/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayController.java
index 951a544c14..2f0648325b 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayController.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.api.overlay;
import java.util.List;
+import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
@@ -27,6 +28,19 @@ public class OverlayController extends BaseController {
return overlayController.getOverlayList(token, projectId);
}
+ @RequestMapping(value = "/getOverlayById", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public LayoutView getOverlayById(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId, @RequestParam(value = "overlayId") String overlayId)
+ throws SecurityException, QueryException {
+ return overlayController.getOverlayById(token, projectId, overlayId);
+ }
+
+ @RequestMapping(value = "/getOverlayElements", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getOverlayElements(@RequestParam(value = "token") String token, @RequestParam(value = "projectId") String projectId,
+ @RequestParam(value = "overlayId") String overlayId, @RequestParam(value = "columns", defaultValue = "") String columns)
+ throws SecurityException, QueryException {
+ return overlayController.getOverlayElements(token, projectId, Integer.valueOf(overlayId), columns);
+ }
+
/**
* @return the overlayController
* @see #overlayController
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayRestImpl.java
index ad5c2cbdf3..d2638f89fe 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/overlay/OverlayRestImpl.java
@@ -1,16 +1,23 @@
package lcsb.mapviewer.api.overlay;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.layout.LightLayoutAliasView;
+import lcsb.mapviewer.services.search.layout.LightLayoutReactionView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
@Transactional(value = "txManager")
@@ -26,7 +33,8 @@ public class OverlayRestImpl {
private ILayoutService layoutService;
public List<LayoutView> getOverlayList(String token, String projectId) throws SecurityException, QueryException {
- Model model = modelService.getLastModelByProjectId(projectId);
+ AuthenticationToken authenticationToken = userService.getToken(token);
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
if (model == null) {
throw new QueryException("Project with given id doesn't exist");
}
@@ -84,4 +92,39 @@ public class OverlayRestImpl {
this.modelService = modelService;
}
+ 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 = userService.getToken(token);
+
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ List<LightLayoutAliasView> speciesList = layoutService.getAliasesForLayout(model, overlayId, authenticationToken);
+ for (LightLayoutAliasView lightLayoutAliasView : speciesList) {
+ Map<String, Object> element = new HashMap<>();
+ element.put("type", "ALIAS");
+ element.put("overlayContent", lightLayoutAliasView);
+ result.add(element);
+ }
+
+ List<LightLayoutReactionView> reactions = layoutService.getReactionsForLayout(model, overlayId, authenticationToken);
+ for (LightLayoutReactionView lightLayoutAliasView : reactions) {
+ Map<String, Object> element = new HashMap<>();
+ element.put("type", "REACTION");
+ element.put("overlayContent", lightLayoutAliasView);
+ result.add(element);
+ }
+ return result;
+ }
+
+ public LayoutView getOverlayById(String token, String projectId, String overlayId) throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = userService.getToken(token);
+ Model model = modelService.getLastModelByProjectId(projectId, authenticationToken);
+ if (model == null) {
+ throw new QueryException("Project with given id doesn't exist");
+ }
+ return layoutService.getLayoutById(model, Integer.valueOf(overlayId), authenticationToken);
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java
index b9bd9dcc00..d68310bbe4 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectController.java
@@ -1,5 +1,8 @@
package lcsb.mapviewer.api.project;
+import java.util.List;
+import java.util.Map;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.MediaType;
import org.springframework.web.bind.annotation.RequestMapping;
@@ -9,6 +12,8 @@ import org.springframework.web.bind.annotation.RestController;
import lcsb.mapviewer.api.BaseController;
import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.search.ElementView;
+import lcsb.mapviewer.services.search.data.LightAliasView;
@RestController
@RequestMapping("/project")
@@ -22,4 +27,16 @@ public class ProjectController extends BaseController {
return projectController.getMetaData(projectId, token);
}
+ @RequestMapping(value = "/getElements", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getElements(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "id", defaultValue = "") String id,
+ @RequestParam(value = "columns", defaultValue = "") String columns, @RequestParam(value = "token") String token) throws SecurityException {
+ return projectController.getElements(projectId, id, columns, token);
+ }
+
+ @RequestMapping(value = "/getReactions", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
+ public List<Map<String, Object>> getReactions(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "id", defaultValue = "") String id,
+ @RequestParam(value = "columns", defaultValue = "") String columns, @RequestParam(value = "token") String token) throws SecurityException {
+ return projectController.getReactions(projectId, id, columns, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
index 8691ef1ed4..f216787ea3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/project/ProjectRestImpl.java
@@ -1,13 +1,27 @@
package lcsb.mapviewer.api.project;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.RequestParam;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.services.SecurityException;
+import lcsb.mapviewer.services.UserAccessException;
+import lcsb.mapviewer.services.interfaces.IModelService;
import lcsb.mapviewer.services.interfaces.IProjectService;
import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.data.LightReactionView;
@Transactional(value = "txManager")
public class ProjectRestImpl {
@@ -18,6 +32,9 @@ public class ProjectRestImpl {
@Autowired
private IProjectService projectService;
+ @Autowired
+ private IModelService modelService;
+
public ProjectMetaData getMetaData(@RequestParam(value = "projectId") String projectId, @RequestParam(value = "token") String token)
throws SecurityException {
@@ -43,4 +60,151 @@ public class ProjectRestImpl {
this.userService = userService;
}
+ public List<Map<String, Object>> getElements(String projectId, String id, String columns, String token) throws UserAccessException, SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ Set<String> columnsSet = createElementColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ List<Model> models = new ArrayList<>();
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ for (Model model2 : models) {
+ for (Element element : model2.getElements()) {
+ if (ids.size() == 0 || ids.contains(element.getId())) {
+ result.add(preparedElement(element, columnsSet));
+ }
+ }
+ }
+
+ return result;
+ }
+
+ public List<Map<String, Object>> getReactions(String projectId, String id, String columns, String token) throws UserAccessException, SecurityException {
+ Model model = modelService.getLastModelByProjectId(projectId, userService.getToken(token));
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ Set<String> columnsSet = createReactionColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ List<Model> models = new ArrayList<>();
+ models.addAll(model.getSubmodels());
+ models.add(model);
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (ids.size() == 0 || ids.contains(reaction.getId())) {
+ result.add(preparedReaction(reaction, columnsSet));
+ }
+ }
+ }
+
+ return result;
+ }
+
+ private Map<String, Object> preparedReaction(Reaction reaction, Set<String> columnsSet) {
+ Map<String, Object> result = new HashMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idObject")) {
+ value = reaction.getId();
+ } else if (column.equals("modelid")) {
+ value = reaction.getModelData().getId();
+ } else if (column.equals("name")) {
+ value = reaction.getName();
+ } else if (column.equals("centerPoint")) {
+ value = reaction.getCenterPoint();
+ } else if (column.equals("type")) {
+ value = reaction.getStringType();
+ } else if (column.equals("lines")) {
+ value = new LightReactionView(reaction).getLines();
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Map<String, Object> preparedElement(Element element, Set<String> columnsSet) {
+ Map<String, Object> result = new HashMap<>();
+ for (String string : columnsSet) {
+ String column = string.toLowerCase();
+ Object value = null;
+ if (column.equals("id") || column.equals("idObject")) {
+ value = element.getId();
+ } else if (column.equals("modelid")) {
+ value = element.getModelData().getId();
+ } else if (column.equals("name")) {
+ value = element.getName();
+ } else if (column.equals("type")) {
+ value = element.getStringType();
+ } else if (column.equals("bounds")) {
+ value = new Rectangle2D.Double(element.getX(), element.getY(), element.getWidth(), element.getHeight());
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createElementColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("modelId");
+ columnsSet.add("name");
+ columnsSet.add("type");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ private Set<String> createReactionColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("modelId");
+ columnsSet.add("type");
+ columnsSet.add("lines");
+ } else {
+ for (String str : columns.split(",")) {
+ columnsSet.add(str);
+ }
+ }
+ return columnsSet;
+ }
+
+ /**
+ * @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;
+ }
+
}
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 19400e3cc9..4e26e586b3 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/CommentService.java
@@ -1,9 +1,6 @@
package lcsb.mapviewer.services.impl;
import java.awt.geom.Point2D;
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
-import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
@@ -19,13 +16,11 @@ import lcsb.mapviewer.common.ObjectUtils;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.model.map.Comment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.dao.map.CommentDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
@@ -57,79 +52,12 @@ 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.
*/
- private static final double COMMENT_POINT_DISTANCE_EPSILON = 0.02;
+ private static final double COMMENT_POINT_DISTANCE_EPSILON = 0.02;
/**
* Default class logger.
*/
- private static Logger logger = Logger.getLogger(CommentService.class);
-
- /**
- * Number of line with content in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_CONTENT_LINE = 0;
-
- /**
- * Number of line with coordinates of the comment t in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_COORDINATES_LINE = 1;
-
- /**
- * Number of line with email in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_EMAIL_LINE = 2;
-
- /**
- * Number of line with project title in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_PROJECT_TITLE_LINE = 3;
-
- /**
- * Number of line with user name in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_USER_NAME_LINE = 4;
-
- /**
- * Number of line with reason of removing in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_REMOVE_REASON_LINE = 5;
-
- /**
- * Number of line with identifier of the commented object in serialized
- * comment.
- */
- private static final int COMMENT_SERIALIZATION_IDENTIFIER_LINE = 6;
-
- /**
- * Number of line with class type of the commented object in serialized
- * comment.
- */
- private static final int COMMENT_SERIALIZATION_CLASS_TYPE_LINE = 7;
-
- /**
- * Number of line with user login in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_USER_LOGIN_LINE = 8;
-
- /**
- * Number of line with pinned value in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_PINNED_LINE = 9;
-
- /**
- * Number of line with deleted value in serialized comment.
- */
- private static final int COMMENT_SERIALIZATION_DELETED_LINE = 10;
-
- /**
- * Encoding used for serialization/deserialization.
- */
- private static final String SERIALIZATION_ENCODING = "UTF-8";
-
- /**
- * Field separator used in serialization.
- */
- private String fieldSeparatorInSerialization = "\t";
+ private static Logger logger = Logger.getLogger(CommentService.class);
/**
* Data access object fir comments.
@@ -270,131 +198,6 @@ public class CommentService implements ICommentService {
return commentDao.getCount();
}
- @Override
- public String createCustomSerializationOfComment(Comment comment) {
- Model model = comment.getModelData().getModel();
- String result = "";
- try {
- result += URLEncoder.encode(comment.getContent(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- result += URLEncoder.encode(comment.getCoordinates().getX() + "," + comment.getCoordinates().getY(), SERIALIZATION_ENCODING)
- + fieldSeparatorInSerialization;
- result += URLEncoder.encode(comment.getEmail(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- result += URLEncoder.encode(comment.getModelData().getProject().getProjectId() + "," + comment.getModelData().getMapVersion(), SERIALIZATION_ENCODING)
- + fieldSeparatorInSerialization;
- result += URLEncoder.encode(comment.getName(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- result += URLEncoder.encode(comment.getRemoveReason(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
-
- String identifier = "";
- if (comment.getTableName() != null) {
- if (comment.getTableName().getName().contains("Reaction")) {
- Reaction reaction = model.getReactionByDbId(comment.getTableId());
- if (reaction != null) {
- identifier = reaction.getIdReaction();
- } else {
- logger.warn("Invalid reaction dbID: " + comment.getTableId() + ". Table: " + comment.getTableName().getName());
- }
- } else {
- Element alias = model.getElementByDbId(comment.getTableId());
- if (alias != null) {
- identifier = ((Species) alias).getElementId();
- } else {
- logger.warn("Invalid alias dbID: " + comment.getTableId());
- }
- }
- }
- result += URLEncoder.encode(identifier, SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- if (comment.getTableName() == null) {
- result += URLEncoder.encode("", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- } else {
- result += URLEncoder.encode(comment.getTableName().getCanonicalName(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- }
- if (comment.getUser() == null) {
- result += URLEncoder.encode("", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- } else {
- result += URLEncoder.encode(comment.getUser().getLogin(), SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- }
- if (comment.isPinned()) {
- result += URLEncoder.encode("true", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- } else {
- result += URLEncoder.encode("false", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- }
-
- if (comment.isDeleted()) {
- result += URLEncoder.encode("true", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- } else {
- result += URLEncoder.encode("false", SERIALIZATION_ENCODING) + fieldSeparatorInSerialization;
- }
-
- result += "eof" + fieldSeparatorInSerialization;
- } catch (UnsupportedEncodingException e) {
- logger.error("UnsupportedEncodingException: " + SERIALIZATION_ENCODING);
- }
- return result;
- }
-
- @Override
- public Comment deserializeCustomSerializationOfComment(String serializedComment) {
- Comment result = new Comment();
- String[] lines = serializedComment.split(fieldSeparatorInSerialization);
- try {
- result.setContent(URLDecoder.decode(lines[COMMENT_SERIALIZATION_CONTENT_LINE], SERIALIZATION_ENCODING));
- String[] params = URLDecoder.decode(lines[COMMENT_SERIALIZATION_COORDINATES_LINE], SERIALIZATION_ENCODING).split(",");
- String xStr = params[0];
- String yStr = params[1];
- double x = Double.parseDouble(xStr);
- double y = Double.parseDouble(yStr);
- result.setCoordinates(new Point2D.Double(x, y));
- result.setEmail(URLDecoder.decode(lines[COMMENT_SERIALIZATION_EMAIL_LINE], SERIALIZATION_ENCODING));
- String projectName = URLDecoder.decode(lines[COMMENT_SERIALIZATION_PROJECT_TITLE_LINE], SERIALIZATION_ENCODING).split(",")[0];
- String mapVersion = URLDecoder.decode(lines[COMMENT_SERIALIZATION_PROJECT_TITLE_LINE], SERIALIZATION_ENCODING).split(",")[1];
- Model model = (Model) modelService.getLastModelByProjectId(projectName);
- if (model != null) {
- if (model.getMapVersion().equals(mapVersion)) {
- result.setModel(model);
- } else {
- throw new NotImplementedException();
- }
- } else {
- throw new InvalidArgumentException("Unknown project: " + projectName);
- }
- result.setName(URLDecoder.decode(lines[COMMENT_SERIALIZATION_USER_NAME_LINE], SERIALIZATION_ENCODING));
- result.setRemoveReason(URLDecoder.decode(lines[COMMENT_SERIALIZATION_REMOVE_REASON_LINE], SERIALIZATION_ENCODING));
- String id = URLDecoder.decode(lines[COMMENT_SERIALIZATION_IDENTIFIER_LINE], SERIALIZATION_ENCODING);
- if (id.startsWith("re")) {
- Reaction reaction = model.getReactionByReactionId(id);
- if (reaction == null) {
- logger.error("Unknown reaction: " + id);
- } else {
- Integer dbId = model.getReactionByReactionId(id).getId();
- result.setTableId(dbId);
- }
- } else if (id.startsWith("sa")) {
- Integer dbId = model.getElementByElementId(id).getId();
- result.setTableId(dbId);
- }
- String className = URLDecoder.decode(lines[COMMENT_SERIALIZATION_CLASS_TYPE_LINE], SERIALIZATION_ENCODING);
- if (className != null && !className.equals("")) {
- try {
- Class<?> clazz = Class.forName(className);
- result.setTableName(clazz);
- } catch (ClassNotFoundException e) {
- logger.error("Class not found: " + className);
- }
- }
- String login = URLDecoder.decode(lines[COMMENT_SERIALIZATION_USER_LOGIN_LINE], SERIALIZATION_ENCODING);
- if (login == null || login.equals("null")) {
- User user = userService.getUserByLogin(login);
- result.setUser(user);
- }
- result.setPinned(URLDecoder.decode(lines[COMMENT_SERIALIZATION_PINNED_LINE], SERIALIZATION_ENCODING).equalsIgnoreCase("true"));
- result.setDeleted(URLDecoder.decode(lines[COMMENT_SERIALIZATION_DELETED_LINE], SERIALIZATION_ENCODING).equalsIgnoreCase("true"));
-
- } catch (UnsupportedEncodingException e) {
- logger.error("UnsupportedEncodingException: " + SERIALIZATION_ENCODING);
- }
- return result;
- }
-
@Override
public void removeCommentsForModel(Model model) {
List<Comment> comments = commentDao.getCommentByModel(model, null, null);
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 a9133ea39f..8bd55947eb 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/LayoutService.java
@@ -67,7 +67,7 @@ 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.ConfigurationView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
import lcsb.mapviewer.services.view.LayoutViewFactory;
@@ -176,9 +176,7 @@ public class LayoutService implements ILayoutService {
List<Layout> layouts = layoutDao.getLayoutsByModel(model);
for (Layout layout : layouts) {
if (!layout.isPublicLayout() && layout.getCreator() != null) {
- if (layout.getCreator().getLogin().equals(user.getLogin())) {
- result.add(layoutViewFactory.create(layout));
- } else if (userService.userHasPrivilege(user, PrivilegeType.LAYOUT_VIEW, layout)) {
+ if (userCanViewOverlay(layout, user)) {
result.add(layoutViewFactory.create(layout));
}
}
@@ -187,6 +185,23 @@ public class LayoutService implements ILayoutService {
return result;
}
+ private boolean userCanViewOverlay(Layout overlay, User user) {
+ if (overlay.isPublicLayout()) {
+ return true;
+ }
+ if (overlay.getCreator() == null) {
+ return true;
+ }
+ if (overlay.getCreator().getLogin().equals(user.getLogin())) {
+ return true;
+ }
+
+ if (userService.userHasPrivilege(user, PrivilegeType.LAYOUT_VIEW, overlay)) {
+ return true;
+ }
+ return false;
+ }
+
@Override
public List<LayoutView> getGeneralLayouts(Model model) {
List<LayoutView> result = new ArrayList<LayoutView>();
@@ -872,8 +887,8 @@ public class LayoutService implements ILayoutService {
}
@Override
- public byte[] getInputDataForLayout(LayoutView layoutView) {
- return getInputDataForLayout(layoutView.getIdObject());
+ public byte[] getInputDataForLayout(LayoutView layoutView, AuthenticationToken token) throws SecurityException {
+ return getInputDataForLayout(layoutView.getIdObject(), token);
}
/**
@@ -885,9 +900,14 @@ public class LayoutService implements ILayoutService {
* data
* @return original data file for given layout, if such file is not stored in
* database (compatibility reasons) then null is returned
+ * @throws SecurityException
*/
- private byte[] getInputDataForLayout(int layoutId) {
+ private byte[] getInputDataForLayout(int layoutId, AuthenticationToken token) throws SecurityException {
Layout layout = layoutDao.getById(layoutId);
+ User user = userService.getUserByToken(token);
+ if (!userCanViewOverlay(layout, user)) {
+ throw new SecurityException("User doesn't have access to overlay");
+ }
if (layout == null) {
return null;
} else {
@@ -900,10 +920,10 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId) {
+ public List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
@@ -922,10 +942,10 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId) {
+ public List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
- Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ Collection<ColorSchema> schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
@@ -944,11 +964,11 @@ public class LayoutService implements ILayoutService {
}
@Override
- public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId) {
+ public Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, AuthenticationToken token) throws SecurityException {
try {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
return command.getModifiedElements();
@@ -960,7 +980,8 @@ public class LayoutService implements ILayoutService {
}
@Override
- public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId) {
+ public List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId, AuthenticationToken token)
+ throws SecurityException {
try {
Set<Integer> ids = new HashSet<>();
for (Pair<Integer, Integer> pair : identifiers) {
@@ -969,7 +990,7 @@ public class LayoutService implements ILayoutService {
ColorSchemaReader reader = new ColorSchemaReader();
Collection<ColorSchema> schemas;
- schemas = reader.readColorSchema(getInputDataForLayout(layoutId));
+ schemas = reader.readColorSchema(getInputDataForLayout(layoutId, token));
// colors here are not important
ColorModelCommand command = new ColorModelCommand(model, schemas, new ColorExtractor(Color.BLACK, Color.BLACK));
FullLayoutAliasViewFactory factory = new FullLayoutAliasViewFactory();
@@ -1006,4 +1027,18 @@ public class LayoutService implements ILayoutService {
public List<LayoutView> getCustomLayouts(Model model, String token) throws SecurityException {
return this.getCustomLayouts(model, userService.getUserByToken(token));
}
+
+ @Override
+ public LayoutView getLayoutById(Model model, int overlayId, AuthenticationToken token) throws SecurityException {
+ User user = userService.getUserByToken(token);
+ Layout layout = layoutDao.getById(overlayId);
+ if (!layout.isPublicLayout() && layout.getCreator() != null) {
+ if (userCanViewOverlay(layout, user)) {
+ return layoutViewFactory.create(layout);
+ } else {
+ throw new SecurityException("User doesn't have access to the overlay");
+ }
+ }
+ return layoutViewFactory.create(layout);
+ }
}
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 65b0ce3877..190a4fdd5a 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -31,15 +31,19 @@ import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.map.ModelDao;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
import lcsb.mapviewer.services.search.data.FullAliasView;
import lcsb.mapviewer.services.search.data.FullAliasViewFactory;
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;
@@ -69,12 +73,21 @@ public class ModelService implements IModelService {
*/
private static Set<String> modelsInLoadStage = new HashSet<>();
+ /**
+ * Service that manages and gives access to user information.
+ */
+ @Autowired
+ private IUserService userService;
+
/**
* Data access object for models.
*/
@Autowired
private ModelDao modelDao;
+ @Autowired
+ private ProjectDao projectDao;
+
/**
* Object allowing access to the mesh database.
*/
@@ -118,7 +131,7 @@ public class ModelService implements IModelService {
private TaxonomyBackend taxonomyBackend;
@Override
- public Model getLastModelByProjectId(String projectName) {
+ public Model getLastModelByProjectId(String projectName, AuthenticationToken token) {
if (projectName == null) {
return null;
}
@@ -171,6 +184,9 @@ public class ModelService implements IModelService {
}
}
}
+ if (!userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject())) {
+ throw new SecurityException("User doesn't have access to project");
+ }
return model;
}
@@ -513,4 +529,38 @@ public class ModelService implements IModelService {
return result;
}
+ /**
+ * @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 projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao
+ * the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
+
}
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 7e916fc60e..5a693b923e 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ICommentService.java
@@ -73,29 +73,6 @@ public interface ICommentService {
*/
long getCommentCount();
- /**
- *
- * Sometimes we have to dump all coments from the model without information
- * about primary keys in the database. This method is responsible for this
- * task (it changes all PK into identifiers used by external source).
- *
- * @param comment
- * comment to serialize
- * @return serialized string of the comment
- */
- String createCustomSerializationOfComment(Comment comment);
-
- /**
- * Method used for deserialization of comment. Serialized object doesn't have
- * information about primary/foreign keys (only identifiers from external
- * sources) - this information must be restored from DB.
- *
- * @param serializedComment
- * serialized comment
- * @return Comment after deserialization
- */
- Comment deserializeCustomSerializationOfComment(String serializedComment);
-
/**
* Removes comments from the model.
*
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 4ba5e2c952..f93121cc18 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/ILayoutService.java
@@ -19,7 +19,7 @@ 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.ConfigurationView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
/**
@@ -430,8 +430,9 @@ public interface ILayoutService {
* 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);
+ byte[] getInputDataForLayout(LayoutView layout, AuthenticationToken token) throws SecurityException;
/**
* Returns a list of {@link LightLayoutAliasView aliases} that are visualized
@@ -443,8 +444,9 @@ public interface ILayoutService {
* 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);
+ List<LightLayoutAliasView> getAliasesForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException;
/**
* Returns a list of {@link LightLayoutReactionView reactions} that are
@@ -456,8 +458,9 @@ public interface ILayoutService {
* 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);
+ List<LightLayoutReactionView> getReactionsForLayout(Model model, int layoutId, AuthenticationToken token) throws SecurityException;
/**
* Returns mapping between {@link lcsb.mapviewer.model.map.species.Element
@@ -471,8 +474,9 @@ public interface ILayoutService {
* 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);
+ Map<Object, ColorSchema> getElementsForLayout(Model model, Integer layoutId, AuthenticationToken token) throws SecurityException;
/**
* Returns a list of {@link FullLayoutAliasView aliases} that are visualized
@@ -491,8 +495,10 @@ public interface ILayoutService {
* 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);
+ List<FullLayoutAliasView> getFullAliasesForLayoutByIds(Model model, List<Pair<Integer, Integer>> identifiers, int layoutId, AuthenticationToken token)
+ throws SecurityException;
/**
* Returns {@link EmailSender} used by the service.
@@ -511,4 +517,6 @@ public interface ILayoutService {
List<LayoutView> getCustomLayouts(Model model, String token) throws SecurityException;
+ LayoutView getLayoutById(Model model, int overlayId, AuthenticationToken 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 6dd73441b5..8c80125bac 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.search.data.FullAliasView;
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;
@@ -29,7 +30,7 @@ public interface IModelService {
* {@link lcsb.mapviewer.model.Project#projectId project identifier}
* @return the newest model for the project
*/
- Model getLastModelByProjectId(String projectId);
+ Model getLastModelByProjectId(String projectId, AuthenticationToken token);
/**
* Caches information about all pubmed articles for the given model.
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 df6d60a4f6..f8dbf01337 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/CommentServiceTest.java
@@ -185,76 +185,6 @@ public class CommentServiceTest extends ServiceTestFunctions {
}
}
- @Test
- public void testSerialization() 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, true, model);
-
- List<Comment> comments = commentDao.getCommentByModel(model, null, null);
-
- for (Comment comment : comments) {
- String serializedObject = commentService.createCustomSerializationOfComment(comment);
- Comment comment2 = commentService.deserializeCustomSerializationOfComment(serializedObject);
-
- assertTrue("Comparison of comments doesn't work.", areCommentsEqual(comment, comment));
- assertTrue("Serialized comments are different.", areCommentsEqual(comment, comment2));
-
- String serializedObject2 = commentService.createCustomSerializationOfComment(comment2);
- assertEquals(serializedObject, serializedObject2);
- }
-
- for (Comment comment : comments) {
- commentDao.delete(comment);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private boolean areCommentsEqual(Comment comment1, Comment comment2) {
- boolean result = true;
-
- if (comment1 == null)
- return comment2 == null;
- if (comment2 == null)
- return false;
- if (comment1.getContent() != null) {
- result &= comment1.getContent().equals(comment2.getContent());
- } else {
- result &= (comment2.getContent() == null);
- }
- result &= comment1.getCoordinates().equals(comment2.getCoordinates());
- result &= comment1.getEmail().equals(comment2.getEmail());
- result &= comment1.getModelData().getMapVersion().equals(comment2.getModelData().getMapVersion());
- result &= comment1.getName().equals(comment2.getName());
- result &= comment1.getRemoveReason().equals(comment2.getRemoveReason());
- if (comment1.getTableId() != null)
- result &= comment1.getTableId().equals(comment2.getTableId());
- else
- result &= (comment2.getTableId() == null);
- if (comment1.getTableName() == null)
- result &= (comment2.getTableName() == null);
- else
- result &= comment1.getTableName().equals(comment2.getTableName());
-
- if (comment1.getUser() == null) {
- result &= (comment2.getUser() == null);
- } else {
- result &= comment1.getUser().getLogin().equals(comment2.getUser().getLogin());
- }
-
- result &= comment1.isPinned() == comment2.isPinned();
- result &= comment1.isDeleted() == comment2.isDeleted();
-
- return result;
- }
-
@Test
public void testReactionComment() throws Exception {
try {
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 2fdd6be5f2..d7f39c505b 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/LayoutServiceTest.java
@@ -44,29 +44,29 @@ import lcsb.mapviewer.services.view.AuthenticationToken;
import lcsb.mapviewer.services.view.LayoutView;
public class LayoutServiceTest extends ServiceTestFunctions {
- Logger logger = Logger.getLogger(LayoutServiceTest.class);
+ Logger logger = Logger.getLogger(LayoutServiceTest.class);
- Project project = null;
- Model model = null;
+ Project project = null;
+ Model model = null;
- String projectId = "Some_id";
- String clearProjectId = "Some_id2";
+ String projectId = "Some_id";
+ String clearProjectId = "Some_id2";
@Autowired
- LayoutDao layoutDao;
+ LayoutDao layoutDao;
- EmailSender originalSender;
+ EmailSender originalSender;
@Autowired
- ILayoutService layoutService;
+ ILayoutService layoutService;
// assume that we have admin account with all the privileges
- AuthenticationToken adminToken;
+ AuthenticationToken adminToken;
@Before
public void setUp() throws Exception {
adminToken = userService.login("admin", "admin");
-
+
logService.setLoggedUser(userService.getUserByLogin(Configuration.ANONYMOUS_LOGIN));
// we use custom threads because in layoutservice there is commit method
@@ -227,7 +227,7 @@ public class LayoutServiceTest extends ServiceTestFunctions {
assertEquals(0, layouts.size());
// null user shouldn't have acces to custom layouts
- layouts = layoutService.getCustomLayouts(model, (User)null);
+ layouts = layoutService.getCustomLayouts(model, (User) null);
assertEquals(0, layouts.size());
layoutService.removeLayout(row, null);
@@ -433,10 +433,12 @@ public class LayoutServiceTest extends ServiceTestFunctions {
LayoutView row = layoutService.createLayout(params);
+ AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+
assertNotNull(row);
assertNotNull(row.getIdObject());
assertTrue("true".equalsIgnoreCase(row.getInputDataAvailable()));
- byte[] inputData = layoutService.getInputDataForLayout(row);
+ byte[] inputData = layoutService.getInputDataForLayout(row, token);
assertNotNull(inputData);
byte[] originalData = IOUtils.toByteArray(new FileInputStream("testFiles/enricoData/ge001.txt"));
assertEquals(new String(originalData, StandardCharsets.UTF_8), new String(inputData, StandardCharsets.UTF_8));
@@ -468,11 +470,13 @@ public class LayoutServiceTest extends ServiceTestFunctions {
LayoutView row = layoutService.createLayout(params);
- List<LightLayoutAliasView> result = layoutService.getAliasesForLayout(model, row.getIdObject());
+ AuthenticationToken token = userService.login(user.getLogin(), "passwd");
+
+ List<LightLayoutAliasView> result = layoutService.getAliasesForLayout(model, row.getIdObject(), token);
assertTrue(result.size() > 0);
- List<LightLayoutReactionView> result2 = layoutService.getReactionsForLayout(model, row.getIdObject());
+ List<LightLayoutReactionView> result2 = layoutService.getReactionsForLayout(model, row.getIdObject(), token);
assertEquals(1, result2.size());
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 fe60864e19..3014801953 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceTest.java
@@ -260,7 +260,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AuthenticationToken token = userService.login("gawi", "gawi");
Project project = projectService.getProjectByProjectId(projectId, token);
- Model model = modelService.getLastModelByProjectId(projectId);
+ Model model = modelService.getLastModelByProjectId(projectId, token);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -654,7 +654,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/complex_model_with_data_mining.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -709,7 +709,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/complex_model_with_images.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -754,7 +754,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
AuthenticationToken token = userService.login("gawi", "gawi");
Project project = projectService.getProjectByProjectId(projectId, token);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -776,7 +776,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/complex_model_with_layouts.zip";
Project project = createComplexProject(projectId, filename);
- Model model = modelService.getLastModelByProjectId(projectId);
+ Model model = modelService.getLastModelByProjectId(projectId, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -806,7 +806,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/complex_model_with_submaps.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(ProjectStatus.DONE, project.getStatus());
@@ -825,7 +825,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/empty_complex_model.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals(ProjectStatus.DONE, project.getStatus());
projectService.removeProject(project, null, false, adminToken);
@@ -842,7 +842,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/empty_complex_model2.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals(ProjectStatus.DONE, project.getStatus());
projectService.removeProject(project, null, false, adminToken);
@@ -859,7 +859,7 @@ public class ProjectServiceTest extends ServiceTestFunctions {
String filename = "testFiles/complexModel/empty_complex_model3.zip";
Project project = createComplexProject(name, filename);
- Model model = modelService.getLastModelByProjectId(name);
+ Model model = modelService.getLastModelByProjectId(name, adminToken);
assertNotNull(model);
assertEquals(ProjectStatus.DONE, project.getStatus());
projectService.removeProject(project, null, false, adminToken);
diff --git a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
index 98492a664e..a516eed1bd 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/ExportBean.java
@@ -1217,7 +1217,7 @@ public class ExportBean extends AbstractManagedBean {
model(colorModel);
List<Integer> visibleLayoutIds = deserializeIdList(visibleLayouts);
for (Integer integer : visibleLayoutIds) {
- Map<Object, ColorSchema> map = getLayoutService().getElementsForLayout(colorModel, integer);
+ Map<Object, ColorSchema> map = getLayoutService().getElementsForLayout(colorModel, integer, userBean.getAuthenticationToken());
params.addVisibleLayout(map);
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java b/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
index 76f48ed82a..38aa8ac6b8 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java
@@ -83,9 +83,10 @@ public class GalaxyBean extends AbstractManagedBean implements Serializable {
String login = requestParams.get("login");
String password = requestParams.get("password");
String modelName = requestParams.get("model");
- Model model = (Model) modelService.getLastModelByProjectId(modelName);
- User user = null;
+
AuthenticationToken token = userService.login(login, password);
+ Model model = (Model) modelService.getLastModelByProjectId(modelName, token);
+ User user = null;
if (token != null) {
user = userService.getUserByToken(token);
}
diff --git a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java b/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
index 4335317709..6ade0bf8dc 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/LayoutBean.java
@@ -31,6 +31,7 @@ import lcsb.mapviewer.events.ObjectRemovedEvent;
import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.ILayoutService.CreateLayoutParams;
import lcsb.mapviewer.services.interfaces.IModelService;
@@ -289,7 +290,7 @@ public class LayoutBean extends AbstractManagedBean implements Serializable {
*/
public void addAnonymousLayout(ProjectView project) {
errorOccurred = false;
- Model model = modelService.getLastModelByProjectId(project.getProjectId());
+ Model model = modelService.getLastModelByProjectId(project.getProjectId(), userBean.getAuthenticationToken());
addLayout(model, null);
}
@@ -663,10 +664,11 @@ public class LayoutBean extends AbstractManagedBean implements Serializable {
*
* @throws IOException
* thrown when there are some problems with sending file
+ * @throws SecurityException
*/
- public void downloadInputData(LayoutView layout) throws IOException {
+ public void downloadInputData(LayoutView layout) throws IOException, SecurityException {
// get input data from database
- byte[] data = layoutService.getInputDataForLayout(layout);
+ byte[] data = layoutService.getInputDataForLayout(layout, userBean.getAuthenticationToken());
String string = new String(data, StandardCharsets.UTF_8);
sendFileAsResponse(string, "layout_" + layout.getIdObject() + ".txt", MimeType.TEXT);
@@ -718,7 +720,7 @@ public class LayoutBean extends AbstractManagedBean implements Serializable {
int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
String string = "[]";
try {
- List<LightLayoutAliasView> list = layoutService.getAliasesForLayout(getCurrentTopModel(), layoutId);
+ List<LightLayoutAliasView> list = layoutService.getAliasesForLayout(getCurrentTopModel(), layoutId, userBean.getAuthenticationToken());
LightLayoutAliasViewFactory factory = new LightLayoutAliasViewFactory();
string = factory.createGson(list);
} catch (Exception e) {
@@ -741,7 +743,8 @@ public class LayoutBean extends AbstractManagedBean implements Serializable {
String string = "[]";
try {
List<Pair<Integer, Integer>> identifiers = deserializeJsonIds(getRequestParameter("ids"));
- List<FullLayoutAliasView> list = layoutService.getFullAliasesForLayoutByIds(getCurrentTopModel(), identifiers, layoutId);
+ List<FullLayoutAliasView> list = layoutService
+ .getFullAliasesForLayoutByIds(getCurrentTopModel(), identifiers, layoutId, userBean.getAuthenticationToken());
string = new FullLayoutAliasViewFactory().createGson(list);
} catch (Exception e) {
sendError("Internal server error", e);
@@ -761,7 +764,7 @@ public class LayoutBean extends AbstractManagedBean implements Serializable {
int layoutId = Integer.valueOf(getRequestParameter("layoutId").replace("cv", ""));
String string = "[]";
try {
- List<LightLayoutReactionView> list = layoutService.getReactionsForLayout(getCurrentTopModel(), layoutId);
+ List<LightLayoutReactionView> list = layoutService.getReactionsForLayout(getCurrentTopModel(), layoutId, userBean.getAuthenticationToken());
LightLayoutReactionViewFactory factory = new LightLayoutReactionViewFactory();
string = factory.createGson(list);
} catch (Exception e) {
diff --git a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
index 96969e65a2..8274f958c8 100644
--- a/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
+++ b/web/src/main/java/lcsb/mapviewer/bean/MapBean.java
@@ -425,10 +425,10 @@ public class MapBean extends AbstractManagedBean implements Serializable {
public void propertyChange(final PropertyChangeEvent arg0) {
if (CURRENT_MODEL_ID_PROPERTY.equals(arg0.getPropertyName())) {
try {
- setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getNewValue()));
+ 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()));
+ setCurrentTopModel(getModelService().getLastModelByProjectId((String) arg0.getOldValue(), userBean.getAuthenticationToken()));
logger.error(e, e);
}
}
@@ -959,7 +959,7 @@ public class MapBean extends AbstractManagedBean implements Serializable {
*/
protected final Model getCurrentTopModel() {
if (currentMap == null) {
- setCurrentTopModel(this.getModelService().getLastModelByProjectId(getCurrentMapId()));
+ setCurrentTopModel(this.getModelService().getLastModelByProjectId(getCurrentMapId(), userBean.getAuthenticationToken()));
}
return currentMap;
}
diff --git a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java b/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
index e262ca8c8d..12824a1765 100644
--- a/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
+++ b/web/src/test/java/lcsb/mapviewer/bean/GalaxyBeanTest.java
@@ -12,8 +12,7 @@ import org.junit.Test;
public class GalaxyBeanTest extends WebTestFunctions {
- GalaxyBean galaxyBean;
-
+ GalaxyBean galaxyBean;
@Before
public void setUp() throws Exception {
@@ -28,7 +27,9 @@ public class GalaxyBeanTest extends WebTestFunctions {
@Test
@Ignore
public void test() {
- galaxyBean.createLayout("CC75308E16F6AA9C", "NAME\tVALUE\nSNCA\t1\nPINK1\t-1\n", (Model) modelService.getLastModelByProjectId("pdmap"), userService.getUserByLogin("galaxy"));
+ galaxyBean.createLayout(
+ "CC75308E16F6AA9C", "NAME\tVALUE\nSNCA\t1\nPINK1\t-1\n", (Model) modelService.getLastModelByProjectId("pdmap", adminToken),
+ userService.getUserByLogin("galaxy"));
}
/**
--
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