From 996f1e2de258cc34f35c7848c039ac253411d899 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 20 Nov 2017 13:55:19 +0100
Subject: [PATCH] fix on retrieving reaction in submaps
---
frontend-js/src/main/js/ServerConnector.js | 4 +-
frontend-js/src/main/js/map/data/MapModel.js | 5 +-
...,329183,329184,329185&token=MOCK_TOKEN_ID& | 0
.../participantId=329167&token=MOCK_TOKEN_ID& | 0
.../reactions/ReactionsRestImpl.java | 325 +++++++++---------
5 files changed, 169 insertions(+), 165 deletions(-)
rename frontend-js/testFiles/apiCalls/projects/sample/models/{all => 15781}/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID& (100%)
rename frontend-js/testFiles/apiCalls/projects/sample/models/{all => 15781}/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID& (100%)
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 5dd2d408f4..a09ffb94f0 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1194,7 +1194,9 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
ServerConnector.getReactions = function (params) {
var self = this;
- var queryParams = {};
+ var queryParams = {
+ modelId: params.modelId
+ };
if (params.ids === undefined) {
params.ids = [];
}
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 1e4e53b9f6..000602857d 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -746,7 +746,8 @@ MapModel.prototype.getReactionsForElements = function(elements, complete) {
var result = [];
return ServerConnector.getReactions({
- participantId : ids,
+ modelId: self.getId(),
+ participantId : ids
}).then(function(reactions) {
result = reactions;
@@ -781,7 +782,7 @@ MapModel.prototype.getCompartments = function() {
promise = ServerConnector.getAliases({
columns : "id,bounds,modelId",
type : "Compartment",
- modelId : self.getId(),
+ modelId : self.getId()
}).then(function(compartments) {
self._compartments = [];
for (var i = 0; i < compartments.length; i++) {
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329156,329157,329158,329159,329160,329161,329162,329163,329164,329165,329166,329167,329168,329169,329170,329171,329172,329173,329174,329175,329176,329177,329178,329179,329180,329181,329182,329183,329184,329185&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
similarity index 100%
rename from frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
rename to frontend-js/testFiles/apiCalls/projects/sample/models/15781/bioEntities/reactions/participantId=329167&token=MOCK_TOKEN_ID&
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
index 276e9256cc..d8a8ed17ac 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/bioEntities/reactions/ReactionsRestImpl.java
@@ -28,167 +28,168 @@ import lcsb.mapviewer.services.search.data.LightReactionView;
@Transactional(value = "txManager")
public class ReactionsRestImpl extends BaseRestImpl {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
-
- @Autowired
- private IUserService userService;
-
- @Autowired
- private IModelService modelService;
-
- /**
- * @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>> getReactions(String projectId, String id, String columns, String modelId, String token, String participantElementId)
- 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<Element> elementSet = new HashSet<>();
- if (!participantElementId.equals("")) {
- for (String str : participantElementId.split(",")) {
- elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
- }
- }
- Set<String> columnsSet = createReactionColumnSet(columns);
-
- List<Map<String, Object>> result = new ArrayList<>();
-
- List<Model> models = getModels(projectId, modelId, token);
-
- for (Model model2 : models) {
- for (Reaction reaction : model2.getReactions()) {
- if (ids.size() == 0 || ids.contains(reaction.getId())) {
- if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
- result.add(preparedReaction(reaction, columnsSet));
- }
- }
- }
- }
-
- return result;
- }
-
- private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
- for (Element element : elementSet) {
- if (reaction.containsElement(element)) {
- return true;
- }
- }
- return false;
- }
-
- 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("reactionid")) {
- value = reaction.getIdReaction();
- } else if (column.equals("name")) {
- value = reaction.getName();
- } else if (column.equals("centerpoint")) {
- value = reaction.getCenterPoint();
- } else if (column.equals("products")) {
- List<Integer> ids = new ArrayList<>();
- for (Product product : reaction.getProducts()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("reactants")) {
- List<Integer> ids = new ArrayList<>();
- for (Reactant reactant : reaction.getReactants()) {
- ids.add(reactant.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("modifiers")) {
- List<Integer> ids = new ArrayList<>();
- for (Modifier product : reaction.getModifiers()) {
- ids.add(product.getElement().getId());
- }
- value = StringUtils.join(ids, ",");
- } else if (column.equals("type")) {
- value = reaction.getStringType();
- } else if (column.equals("hierarchyvisibilitylevel")) {
- value = reaction.getVisibilityLevel();
- } else if (column.equals("lines")) {
- value = new LightReactionView(reaction).getLines();
- } else if (column.equals("notes")) {
- value = reaction.getNotes();
- } else if (column.equals("references")) {
- value = createAnnotations(reaction.getMiriamData());
- } else {
- value = "Unknown column";
- }
- result.put(string, value);
- }
- return result;
- }
-
- private Set<String> createReactionColumnSet(String columns) {
- Set<String> columnsSet = new HashSet<>();
- if (columns.equals("")) {
- columnsSet.add("id");
- columnsSet.add("reactionId");
- columnsSet.add("modelId");
- columnsSet.add("type");
- columnsSet.add("lines");
- columnsSet.add("centerPoint");
- columnsSet.add("products");
- columnsSet.add("reactants");
- columnsSet.add("modifiers");
- columnsSet.add("hierarchyVisibilityLevel");
- columnsSet.add("references");
- columnsSet.add("notes");
- } 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;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionsRestImpl.class);
+
+ @Autowired
+ private IUserService userService;
+
+ @Autowired
+ private IModelService modelService;
+
+ /**
+ * @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>> getReactions(String projectId, String id, String columns, String modelId,
+ String token, String participantElementId) throws UserAccessException, SecurityException {
+ Set<Integer> ids = new HashSet<>();
+ if (!id.equals("")) {
+ for (String str : id.split(",")) {
+ ids.add(Integer.valueOf(str));
+ }
+ }
+ List<Model> models = getModels(projectId, modelId, token);
+
+ Set<Element> elementSet = new HashSet<>();
+ if (!participantElementId.equals("")) {
+ for (String str : participantElementId.split(",")) {
+ for (Model model : models) {
+ elementSet.add(model.getElementByDbId(Integer.valueOf(str)));
+ }
+ }
+ }
+ Set<String> columnsSet = createReactionColumnSet(columns);
+
+ List<Map<String, Object>> result = new ArrayList<>();
+
+ for (Model model2 : models) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (ids.size() == 0 || ids.contains(reaction.getId())) {
+ if (elementSet.size() == 0 || reactionContainsElement(reaction, elementSet)) {
+ result.add(preparedReaction(reaction, columnsSet));
+ }
+ }
+ }
+ }
+
+ return result;
+ }
+
+ private boolean reactionContainsElement(Reaction reaction, Set<Element> elementSet) {
+ for (Element element : elementSet) {
+ if (reaction.containsElement(element)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ 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("reactionid")) {
+ value = reaction.getIdReaction();
+ } else if (column.equals("name")) {
+ value = reaction.getName();
+ } else if (column.equals("centerpoint")) {
+ value = reaction.getCenterPoint();
+ } else if (column.equals("products")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Product product : reaction.getProducts()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("reactants")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Reactant reactant : reaction.getReactants()) {
+ ids.add(reactant.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("modifiers")) {
+ List<Integer> ids = new ArrayList<>();
+ for (Modifier product : reaction.getModifiers()) {
+ ids.add(product.getElement().getId());
+ }
+ value = StringUtils.join(ids, ",");
+ } else if (column.equals("type")) {
+ value = reaction.getStringType();
+ } else if (column.equals("hierarchyvisibilitylevel")) {
+ value = reaction.getVisibilityLevel();
+ } else if (column.equals("lines")) {
+ value = new LightReactionView(reaction).getLines();
+ } else if (column.equals("notes")) {
+ value = reaction.getNotes();
+ } else if (column.equals("references")) {
+ value = createAnnotations(reaction.getMiriamData());
+ } else {
+ value = "Unknown column";
+ }
+ result.put(string, value);
+ }
+ return result;
+ }
+
+ private Set<String> createReactionColumnSet(String columns) {
+ Set<String> columnsSet = new HashSet<>();
+ if (columns.equals("")) {
+ columnsSet.add("id");
+ columnsSet.add("reactionId");
+ columnsSet.add("modelId");
+ columnsSet.add("type");
+ columnsSet.add("lines");
+ columnsSet.add("centerPoint");
+ columnsSet.add("products");
+ columnsSet.add("reactants");
+ columnsSet.add("modifiers");
+ columnsSet.add("hierarchyVisibilityLevel");
+ columnsSet.add("references");
+ columnsSet.add("notes");
+ } 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;
+ }
}
--
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