diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..4c8e77f73dc9ab17d7d6cec19defa40c7f5d9f30
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,12 @@
+image: node
+
+before_script:
+ - cd frontend-js
+ - npm install
+ - cd ..
+
+test_frontend:
+ script:
+ - cd frontend-js
+ - npm test
+
\ No newline at end of file
diff --git a/CHANGELOG b/CHANGELOG
index 5ddd8c6f4e09fcd6ca9040e2e1f8b6b705d83b68..1eb8ddc1b403c90693a938fee296419777858e4b 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,8 @@
+minerva (11.0.1) stable; urgency=medium
+ * Bug fix: logout caused issues with session data
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Fri, 08 Sep 2017 12:00:00 +0200
+
minerva (11.0.0) stable; urgency=medium
* Bug fix: security issue - access to specific map can be restricted
diff --git a/README.md b/README.md
index c8bb6d65f4fc5cbd20d1234135c1e1d56efa5339..1c4a3a4035e872ea0c8f7505b3bbc12d039678ff 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,5 @@
+[](https://git-r3lab.uni.lu/piotr.gawron/minerva/commits/207-continous-integration-tests)
+
# Rest API (version 11)
## Introduction
diff --git a/frontend-js/.idea/preferred-vcs.xml b/frontend-js/.idea/preferred-vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..848cfc44550cbfba31b047a54bb77ecd25feb0c7
--- /dev/null
+++ b/frontend-js/.idea/preferred-vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+ <component name="PreferredVcsStorage">
+ <preferredVcsName>ApexVCS</preferredVcsName>
+ </component>
+</project>
\ No newline at end of file
diff --git a/frontend-js/package.json b/frontend-js/package.json
index 00e5bf58452424cfffd5ad900c0d90ba0c644a85..85fe7d0c95ad112e1c40c4e065ff83c9d56f190f 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -38,12 +38,14 @@
"uglifyjs": "^2.4.10"
},
"dependencies": {
+ "del": "^3.0.0",
"dual-listbox": "^1.0.7",
"file-saver": "^1.3.3",
"http-status-codes": "^1.1.6",
"js-cookie": "^2.1.3",
"jstree": "^3.3.4",
"log4js": "0.6.38",
+ "mkdirp": "^0.5.1",
"pileup": "^0.6.8",
"request": "^2.79.0"
}
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index 43406b51aa027a542c0a5c7bb22ae22653be023b..0b80b2c90bfff5dd1e496652569ddce87497c0da 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -8,7 +8,6 @@ var ValidationError = require('./ValidationError');
var GuiMessageError = require('./gui/GuiMessageError');
var NetworkError = require('./NetworkError');
-
/**
* This static global object contains set of functions that returns/set data in
* the Gui (html).
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 54a5ffc45dd568da95e2ac9052a2f9b2da0da47c..a7750836d8cb43ba18f5b8cf108712e132d24021 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -73,7 +73,7 @@ ServerConnector.registerListenerType("onDataLoadStart");
ServerConnector.registerListenerType("onDataLoadStop");
ServerConnector.init();
-ServerConnector.getMinOverlayColorInt = function () {
+ServerConnector.getMinOverlayColorInt = function() {
var self = this;
return self.getLoggedUser().then(function (user) {
var userColor = user.getMinColor();
@@ -96,7 +96,7 @@ ServerConnector.returnUserOrSystemColor = function (userColor, systemPromisedCol
ServerConnector.getSimpleOverlayColorInt = function () {
var self = this;
- return self.getLoggedUser().then(function (user) {
+ return self.getLoggedUser().then(function(user) {
var userColor = user.getSimpleColor();
return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL));
});
@@ -152,7 +152,10 @@ ServerConnector._sendRequest = function (params) {
return new Promise(function (resolve, reject) {
request(params, function (error, response, body) {
if (error) {
- reject(error);
+ reject(new NetworkError(error.message, {
+ content: body,
+ url: url
+ }));
} else if (response.statusCode !== 200) {
reject(new NetworkError(params.url + " rejected with status code: " + response.statusCode, {
content: body,
@@ -198,8 +201,9 @@ ServerConnector.sendPatchRequest = function (url, json) {
ServerConnector.getToken = function () {
var self = this;
+ var login = self.getSessionData(null).getLogin()
var token = self.getSessionData(null).getToken();
- if (token === undefined) {
+ if (token === undefined || login === undefined) {
return self.login();
} else {
// if the project is not initialized then check if we can download data
@@ -331,6 +335,12 @@ ServerConnector.loginUrl = function () {
});
};
+ServerConnector.logoutUrl = function () {
+ return this.getApiUrl({
+ type: "/doLogout",
+ });
+};
+
ServerConnector.getSuggestedQueryListUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getBioEntitiesUrl(queryParams) + "suggestedQueryList/",
@@ -580,10 +590,7 @@ ServerConnector.getUpdateUserPreferencesUrl = function (queryParams, filterParam
});
};
-ServerConnector.getConfiguration = function (params) {
- if (params === undefined) {
- params = {};
- }
+ServerConnector.getConfiguration = function () {
var self = this;
if (this._configuration === undefined) {
return self.sendGetRequest(self.getConfigurationUrl()).then(function (content) {
@@ -609,7 +616,7 @@ ServerConnector.getModels = function (projectId) {
var queryParams = {};
var filterParams = {};
var self = this;
- return self.getProjectId(projectId).then(function (result) {
+ return self.getProjectId(projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getModelsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -640,7 +647,7 @@ ServerConnector.getProject = function (projectId) {
}
project = self._projectsById[projectId];
return self.getModels(projectId);
- }).then(function (models) {
+ }).then(function(models) {
project.setModel(models[0]);
return self.getLoggedUser();
}).then(function (user) {
@@ -792,13 +799,13 @@ ServerConnector.getProjectStatistics = function (projectId) {
var filterParams = {};
var self = this;
var content;
- return self.getProjectId(projectId).then(function (result) {
+ return self.getProjectId(projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getProjectStatisticsUrl(queryParams, filterParams));
}).then(function (result) {
content = JSON.parse(result);
return self.getConfiguration();
- }).then(function (configuration) {
+ }).then(function(configuration) {
return new ProjectStatistics(content, configuration);
});
};
@@ -923,17 +930,17 @@ ServerConnector.getOverlays = function (params) {
});
};
-ServerConnector.getOverlayElements = function (overlayId, projectId) {
+ServerConnector.getOverlayElements = function(overlayId, projectId) {
var self = this;
if (overlayId === undefined) {
throw new Error("Layout id must be defined");
}
var queryParams = {
- overlayId: overlayId,
- modelId: "*",
+ overlayId : overlayId,
+ modelId : "*",
};
var filterParams = {};
- return self.getProjectId(projectId).then(function (result) {
+ return self.getProjectId(projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getOverlayElementsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1031,7 +1038,7 @@ ServerConnector.getReactions = function (params) {
columns: params.columns,
participantId: params.participantId,
};
- return self.getProjectId(params.projectId).then(function (result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
if (filterParams.id.length > 100 || filterParams.participantId.length > 100) {
return self.sendPostRequest(self.getReactionsUrl(queryParams), filterParams);
@@ -1049,10 +1056,10 @@ ServerConnector.getReactions = function (params) {
});
};
-ServerConnector.getAliases = function (params) {
+ServerConnector.getAliases = function(params) {
var self = this;
var queryParams = {
- modelId: params.modelId,
+ modelId : params.modelId,
};
if (params.ids === undefined) {
params.ids = [];
@@ -1071,14 +1078,14 @@ ServerConnector.getAliases = function (params) {
includedCompartmentIds: params.includedCompartmentIds,
};
- return self.getProjectId(params.projectId).then(function (result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
if (filterParams.id.length > 100) {
return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
} else {
return self.sendGetRequest(self.getAliasesUrl(queryParams, filterParams));
}
- }).then(function (content) {
+ }).then(function(content) {
var array = JSON.parse(content);
var result = [];
for (var i = 0; i < array.length; i++) {
@@ -1088,22 +1095,22 @@ ServerConnector.getAliases = function (params) {
});
};
-ServerConnector.getLightComments = function (params) {
- params.columns = ["id", "elementId", "modelId", "type", "icon", "removed", "pinned"];
+ServerConnector.getLightComments = function(params) {
+ params.columns = [ "id", "elementId", "modelId", "type", "icon", "removed", "pinned" ];
return this.getComments(params);
};
-ServerConnector.getComments = function (params) {
+ServerConnector.getComments = function(params) {
var self = this;
var queryParams = {
- elementId: params.elementId,
- elementType: params.elementType,
- coordinates: params.coordinates,
+ elementId : params.elementId,
+ elementType : params.elementType,
+ coordinates : params.coordinates,
};
var filterParams = {
- columns: params.columns
+ columns : params.columns
};
- return self.getProjectId(params.projectId).then(function (result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getCommentsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1151,7 +1158,7 @@ ServerConnector.getClosestElementsByCoordinates = function (params) {
ServerConnector.login = function (login, password) {
var self = this;
var params = {};
- if (login !== undefined) {
+ if (login !== undefined && login !== "") {
params.login = login;
params.password = password;
} else {
@@ -1174,7 +1181,7 @@ ServerConnector.logout = function () {
var self = this;
self.getSessionData().setToken(undefined);
self.getSessionData().setLogin(undefined);
- return Promise.resolve();
+ return self.sendGetRequest(self.logoutUrl());
};
ServerConnector.getElementsByQuery = function (params) {
@@ -1219,13 +1226,13 @@ ServerConnector.getDrugsByQuery = function (params) {
});
};
-ServerConnector.getMiRnasByQuery = function (params) {
+ServerConnector.getMiRnasByQuery = function(params) {
var self = this;
var queryParams = {};
var filterParams = {
- query: params.query
+ query : params.query
};
- return self.getProjectId(params.projectId).then(function (result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getSearchMiRnasUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1516,7 +1523,7 @@ ServerConnector.getPublications = function (params) {
sortOrder: params.sortOrder,
search: params.search,
};
- return self.getProjectId(params.projectId).then(function (result) {
+ return self.getProjectId(params.projectId).then(function(result) {
queryParams.projectId = result;
return self.sendGetRequest(self.getPublicationsUrl(queryParams, filterParams));
}).then(function (content) {
@@ -1524,7 +1531,7 @@ ServerConnector.getPublications = function (params) {
});
};
-ServerConnector.getReferenceGenome = function (params) {
+ServerConnector.getReferenceGenome = function(params) {
var self = this;
var filterParams = {};
return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index 937538e0ea799d3f991e4443b13b437429c77351..b78dc728ab4ed3fc4cb752f5e0a19e7e646f5394 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -8,7 +8,7 @@ var GuiUtils = require('./leftPanel/GuiUtils');
var LayoutData = require('../map/data/LayoutData');
var NetworkError = require('../NetworkError');
-var Functions = require('../functions');
+var Functions = require('../Functions');
var logger = require('../logger');
var HttpStatus = require('http-status-codes');
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 5f03de03494b0d8db8a87b41e892a8aeee8b0c11..5811bd86c8e30480f3682a6b2c5893a37006d79b 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -9,7 +9,7 @@ var ChooseValidatorsDialog = require('./ChooseValidatorsDialog');
var GuiConnector = require('../../GuiConnector');
var UserPreferences = require("../../map/data/UserPreferences");
-var Functions = require('../../functions');
+var Functions = require('../../Functions');
var logger = require('../../logger');
var guiUtils = new (require('../leftPanel/GuiUtils'))();
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index 1f0f64165f22aec5a0b2fca3acdb6f6cdf3a14c1..b7293b8c72e741e49cd07f51b0e18e0a8d0f7885 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -8,7 +8,7 @@ var AddOverlayDialog = require('../AddOverlayDialog');
var Annotation = require('../../map/data/Annotation');
var GuiConnector = require('../../GuiConnector');
-var Functions = require('../../functions');
+var Functions = require('../../Functions');
var logger = require('../../logger');
var guiUtils = new (require('../leftPanel/GuiUtils'))();
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 59a9c11b038ce6328d372d3801fa8aaa8fd67762..0fd22a3ee66b605e0b4bd1a3a207b7e63a962543 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -299,13 +299,13 @@ OverlayPanel.prototype.refresh = function () {
var generalOverlays = [];
var overlay;
- var overlays = self.getMap().getLayouts();
- for (var i = 0; i < overlays.length; i++) {
- overlay = overlays[i];
- if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
- generalOverlays.push(overlay);
+ var overlays = self.getMap().getLayouts();
+ for (var i = 0; i < overlays.length; i++) {
+ overlay = overlays[i];
+ if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
+ generalOverlays.push(overlay);
+ }
}
- }
var table = self.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
table.appendChild(self.createTableHeader());
diff --git a/frontend-js/testFiles/apiCalls/doLogout b/frontend-js/testFiles/apiCalls/doLogout
new file mode 100644
index 0000000000000000000000000000000000000000..1a36cf5fc27a0920a9f3668225f9d7aec239566e
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/doLogout
@@ -0,0 +1 @@
+{"status":"ok"}
\ No newline at end of file
diff --git a/persist/src/db/11.0.1/fix_db_20170908.sql b/persist/src/db/11.0.1/fix_db_20170908.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/11.0.1/fix_db_20170908.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
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 5b8e4672b56384b49e27ea69a1f509b94cd90894..041ac88052890ba222fc58db0307c450f3fb8e20 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
@@ -114,11 +114,27 @@ public class UserController extends BaseController {
}
@RequestMapping(value = "/doLogout", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token) throws SecurityException {
+ public Map<String, String> logout(@CookieValue(value = Configuration.AUTH_TOKEN) String token,
+ HttpServletResponse response //
+ ) throws SecurityException, IOException {
userService.logout(token);
- Map<String, String> response = new HashMap<>();
- response.put("status", "OK");
- return response;
+ Map<String, String> result = new HashMap<>();
+ result.put("status", "OK");
+
+ final Boolean useSecureCookie = false;
+ final String cookiePath = "/";
+
+ Cookie cookie = new Cookie("MINERVA_AUTH_TOKEN", token);
+
+ cookie.setSecure(useSecureCookie);
+ cookie.setMaxAge(0);
+ cookie.setPath(cookiePath);
+
+ response.addCookie(cookie);
+ response.getWriter().write("{\"status\":\"OK\"}");
+ response.getWriter().flush();
+ response.getWriter().close();
+ return result;
}
/**