diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index c6df9c7c99481ffb3a9bb6c6d65fe61878a2c4d8..3c2213a19f51780e9ee49f1a2ec5cfe540dc3338 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -11,6 +11,7 @@ var request = require('request');
var HttpStatus = require('http-status-codes');
var Alias = require('./map/data/Alias');
+var Annotation = require('./map/data/Annotation');
var Chemical = require('./map/data/Chemical');
var Comment = require('./map/data/Comment');
var Configuration = require('./Configuration');
@@ -40,23 +41,51 @@ var ObjectWithListeners = require('./ObjectWithListeners');
* This object contains methods that will communicate with server.
*/
var ServerConnector = new ObjectWithListeners();
-ServerConnector.registerListenerType("onDataLoadStart");
-ServerConnector.registerListenerType("onDataLoadStop");
+ServerConnector.init = function () {
+ var self = this;
-ServerConnector._configurationParam = [];
-ServerConnector._serverBaseUrl= undefined;
+ self._configurationParam = [];
+ self._projects = [];
+ self._projectsById = [];
+ self._users = [];
+ self._usersByLogin = [];
+
+ self._customMap = null;
+ self._sessionData = undefined;
+ self._configuration = undefined;
+ self._loggedUser = undefined;
+ self._serverBaseUrl = undefined;
+
+ var i;
+ var listeners = self.getListeners("onDataLoadStart");
+ for (i = 0; i < listeners.length; i++) {
+ self.removeListener("onDataLoadStart", listeners[i]);
+ }
+
+ listeners = self.getListeners("onDataLoadStop");
+ for (i = 0; i < listeners.length; i++) {
+ self.removeListener("onDataLoadStop", listeners[i]);
+ }
+
+};
+ServerConnector.registerListenerType("onDataLoadStart");
+ServerConnector.registerListenerType("onDataLoadStop");
+ServerConnector.init();
ServerConnector.getMinOverlayColorInt = function () {
var self = this;
- var userColor;
return self.getLoggedUser().then(function (user) {
- userColor = user.getMinColor();
- return self.getConfigurationParam(ConfigurationType.MIN_COLOR_VAL);
- }).then(function (systemMinColor) {
+ var userColor = user.getMinColor();
+ return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.MIN_COLOR_VAL));
+ });
+};
+
+ServerConnector.returnUserOrSystemColor = function (userColor, systemPromisedColor) {
+ return systemPromisedColor.then(function (systemColor) {
var color = userColor;
if (userColor === null || userColor === undefined || userColor === "") {
- color = systemMinColor;
+ color = systemColor;
}
color = parseInt(color, 16);
/* jslint bitwise: true */
@@ -67,54 +96,48 @@ ServerConnector.getMinOverlayColorInt = function () {
ServerConnector.getSimpleOverlayColorInt = function () {
var self = this;
- var userColor;
return self.getLoggedUser().then(function (user) {
- userColor = user.getSimpleColor();
- return self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL);
- }).then(function (systemSimpleColor) {
- var color = userColor;
- if (userColor === null || userColor === undefined || userColor === "") {
- color = systemSimpleColor;
- }
- color = parseInt(color, 16);
- /* jslint bitwise: true */
- color = (color & 0xFFFFFF);
- return color;
+ var userColor = user.getSimpleColor();
+ return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.SIMPLE_COLOR_VAL));
});
};
ServerConnector.getMaxOverlayColorInt = function () {
var self = this;
- var userColor;
return self.getLoggedUser().then(function (user) {
- userColor = user.getMaxColor();
- return self.getConfigurationParam(ConfigurationType.MAX_COLOR_VAL);
- }).then(function (systemMaxColor) {
- var color = userColor;
- if (userColor === null || userColor === undefined || userColor === "") {
- color = systemMaxColor;
- }
- color = parseInt(color, 16);
- /* jslint bitwise: true */
- color = (color & 0xFFFFFF);
- return color;
+ var userColor = user.getMaxColor();
+ return self.returnUserOrSystemColor(userColor, self.getConfigurationParam(ConfigurationType.MAX_COLOR_VAL));
+ });
+};
+
+ServerConnector.sendGetRequest = function (url, description) {
+ return this.sendRequest({
+ url: url,
+ description: description,
+ method: "GET"
});
};
-ServerConnector.readFile = function (url, description) {
+ServerConnector.sendRequest = function (params) {
var self = this;
+ if (arguments.length > 1) {
+ return Promise.reject(new Error("Only two arguments are supported"));
+ }
if (self.getSessionData().getToken() === undefined) {
self.getSessionData().setLogin(undefined);
window.location.reload(false);
}
- if (description === undefined) {
- description = url;
+ var description = params.url;
+ if (params.description !== undefined) {
+ description = params.description;
+ params.description = undefined;
}
+
var content;
return self.callListeners("onDataLoadStart", description).then(function () {
- return self._readFile(url);
+ return self._sendRequest(params);
}).then(function (result) {
content = result;
return self.callListeners("onDataLoadStop", description);
@@ -125,132 +148,64 @@ ServerConnector.readFile = function (url, description) {
}).then(function () {
return content;
});
-};
-ServerConnector._readFile = function (url) {
- return new Promise(function (resolve, reject) {
- request.get(url, function (error, response, body) {
- if (error) {
- reject(error);
- } else if (response.statusCode !== 200) {
- reject(new NetworkError(url + " rejected with status code: " + response.statusCode, {
- content: body,
- url: url,
- statusCode: response.statusCode
- }));
- } else {
- resolve(body);
- }
- });
- });
};
-ServerConnector.sendPostRequest = function (url, params) {
- var self = this;
- if (self.getSessionData().getToken() === undefined) {
- self.getSessionData().setLogin(undefined);
- window.location.reload(false);
- }
+ServerConnector._sendRequest = function (params) {
return new Promise(function (resolve, reject) {
- request.post({
- url: url,
- form: params
- }, function (error, response, body) {
+ request(params, function (error, response, body) {
if (error) {
reject(new NetworkError(error.message, {
content: body,
url: url
}));
-
} else if (response.statusCode !== 200) {
- reject(new NetworkError(url + " rejected with status code: " + response.statusCode, {
+ reject(new NetworkError(params.url + " rejected with status code: " + response.statusCode, {
content: body,
- url: url,
+ url: params.url,
statusCode: response.statusCode
}));
} else {
- resolve(body);
+ // for some reason sometimes result is an object not a string
+ if (typeof body === 'string' || body instanceof String) {
+ resolve(body);
+ } else {
+ resolve(JSON.stringify(body));
+ }
}
});
});
};
-ServerConnector.sendPutRequest = function (url, params) {
- var self = this;
- if (self.getSessionData().getToken() === undefined) {
- self.getSessionData().setLogin(undefined);
- window.location.reload(false);
- }
- return new Promise(function (resolve, reject) {
- request.put({
- url: url,
- form: params
- }, function (error, response, body) {
- if (error) {
- reject(error);
- } else if (response.statusCode !== 200) {
- reject(new Error(url + " rejected with status code: " + response.statusCode));
- } else {
- resolve(body);
- }
- });
+ServerConnector.sendPostRequest = function (url, params) {
+ return this.sendRequest({
+ method: "POST",
+ url: url,
+ form: params
});
};
-ServerConnector.sendDeleteRequest = function (url, params) {
- var self = this;
- if (self.getSessionData().getToken() === undefined) {
- self.getSessionData().setLogin(undefined);
- window.location.reload(false);
- }
- return new Promise(function (resolve, reject) {
- request({
- method: "DELETE",
- url: url,
- json: params,
- }, function (error, response, body) {
- if (error) {
- reject(error);
- } else if (response.statusCode !== 200) {
- reject(new Error(url + " rejected with status code: " + response.statusCode));
- } else {
- resolve(body);
- }
- });
+ServerConnector.sendDeleteRequest = function (url, json) {
+ return this.sendRequest({
+ method: "DELETE",
+ url: url,
+ json: json
});
};
-ServerConnector.sendPatchRequest = function (url, params) {
- var self = this;
- if (self.getSessionData().getToken() === undefined) {
- self.getSessionData().setLogin(undefined);
- window.location.reload(false);
- }
- return new Promise(function (resolve, reject) {
- request({
- method: "PATCH",
- url: url,
- json: params,
- }, function (error, response, body) {
- if (error) {
- reject(error);
- } else if (response.statusCode !== 200) {
- reject(new Error(url + " rejected with status code: " + response.statusCode));
- } else {
- resolve(body);
- }
- });
+ServerConnector.sendPatchRequest = function (url, json) {
+ return this.sendRequest({
+ method: "PATCH",
+ url: url,
+ json: json
});
};
-ServerConnector.getToken = function (token) {
- if (token !== undefined) {
- return Promise.resolve(token);
- }
-
+ServerConnector.getToken = function () {
var self = this;
- token = self.getSessionData(null).getToken();
- var login = self.getSessionData(null).getLogin()
+
+ var login = self.getSessionData(null).getLogin();
+ var token = self.getSessionData(null).getToken();
if (token === undefined || login === undefined) {
return self.login();
} else {
@@ -259,6 +214,8 @@ ServerConnector.getToken = function (token) {
if (self.getSessionData().getProject() === null) {
return self.getConfiguration().then(function () {
return token;
+ // if there was an error accessing configuration it means our token is
+ // invalid
}, function () {
return self.login();
});
@@ -275,8 +232,8 @@ ServerConnector.getApiBaseUrl = function () {
ServerConnector.getServerBaseUrl = function () {
if (this._serverBaseUrl === undefined) {
var url = "" + window.location.href;
- if (url.indexOf("?")>=0) {
- url = url.substr(0,url.indexOf("?"));
+ if (url.indexOf("?") >= 0) {
+ url = url.substr(0, url.indexOf("?"));
}
if (!url.endsWith("/")) {
url = url.substr(0, url.lastIndexOf("/") + 1);
@@ -324,16 +281,12 @@ ServerConnector.createGetParams = function (params, prefix) {
ServerConnector.getApiUrl = function (paramObj) {
var type = paramObj.type;
- var method = paramObj.method;
var params = this.createGetParams(paramObj.params);
var result = paramObj.url;
if (result === undefined) {
result = this.getApiBaseUrl() + "/" + type;
}
- if (method !== undefined) {
- result += "/" + method;
- }
if (params !== "") {
result += "?" + params;
}
@@ -342,32 +295,23 @@ ServerConnector.getApiUrl = function (paramObj) {
ServerConnector.getProjectsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- type: "projects/" + queryParams.projectId + "/",
+ type: "projects/",
params: filterParams,
-=======
- type : "projects/",
- params : filterParams,
});
};
-ServerConnector.getProjectUrl = function(queryParams, filterParams) {
+ServerConnector.getProjectUrl = function (queryParams, filterParams) {
+ var id = this.getIdOrAsterisk(queryParams.projectId);
return this.getApiUrl({
- url : this.getProjectsUrl(queryParams) + queryParams.projectId + "/",
- params : filterParams,
->>>>>>> list of available projects
+ url: this.getProjectsUrl(queryParams) + id + "/",
+ params: filterParams,
});
};
ServerConnector.getProjectStatisticsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "statistics/",
+ url: this.getProjectUrl(queryParams) + "statistics/",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "statistics/",
- params : filterParams,
->>>>>>> list of available projects
});
};
@@ -406,7 +350,7 @@ ServerConnector.logoutUrl = function () {
ServerConnector.getSuggestedQueryListUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getBioEntitiesUrl(queryParams) + "suggestedQueryList/",
- params: filterParams,
+ params: filterParams
});
};
@@ -430,19 +374,20 @@ ServerConnector.updateOverlayUrl = function (queryParams) {
ServerConnector.deleteOverlayUrl = function (queryParams) {
return this.getApiUrl({
- url: this.getOverlayByIdUrl(queryParams),
+ url: this.getOverlayByIdUrl(queryParams)
+ });
+};
+
+ServerConnector.deleteCommentUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getProjectUrl(queryParams) + "comments/" + queryParams.commentId + "/",
});
};
ServerConnector.getOverlaysUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "overlays/",
+ url: this.getProjectUrl(queryParams) + "overlays/",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "overlays/",
- params : filterParams,
->>>>>>> list of available projects
});
};
@@ -496,7 +441,11 @@ ServerConnector.idsToString = function (ids) {
var result = "";
if (ids !== undefined) {
ids.sort(function (a, b) {
- return a - b;
+ if (typeof a === "string") {
+ return a.localeCompare(b);
+ } else {
+ return a - b;
+ }
});
for (var i = 0; i < ids.length; i++) {
if (result !== "") {
@@ -515,13 +464,6 @@ ServerConnector.pointToString = function (point) {
return point.x.toFixed(2) + "," + point.y.toFixed(2);
};
-ServerConnector.columnsToString = function (columns) {
- if (columns === undefined) {
- return "";
- }
- return columns;
-};
-
ServerConnector.getModelsUrl = function (queryParams) {
var modelId = this.getIdOrAsterisk(queryParams.modelId);
var overlayId = queryParams.overlayId;
@@ -552,65 +494,58 @@ ServerConnector.getIdOrAsterisk = function (id) {
ServerConnector.getReactionsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getBioEntitiesUrl(queryParams) + "reactions/",
- params: filterParams,
+ params: filterParams
});
};
ServerConnector.getAliasesUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getBioEntitiesUrl(queryParams) + "elements/",
- params: filterParams,
+ params: filterParams
});
};
ServerConnector.getConfigurationUrl = function (queryParams, filterParams) {
- var result = this.getApiUrl({
+ return this.getApiUrl({
type: "configuration/",
params: filterParams
});
- return result;
};
+ServerConnector.getConfigurationOptionUrl = function (queryParams, filterParams) {
+ var self = this;
+ return self.getApiUrl({
+ url: self.getConfigurationUrl() + "options/" + queryParams.type,
+ params: filterParams
+ });
+};
+
+
ServerConnector.getSearchUrl = function (queryParams, filterParams) {
return this.getApiUrl({
url: this.getModelsUrl(queryParams) + "bioEntities:search",
- params: filterParams,
+ params: filterParams
});
};
ServerConnector.getSearchDrugsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "drugs:search",
+ url: this.getProjectUrl(queryParams) + "drugs:search",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "drugs:search",
- params : filterParams,
->>>>>>> list of available projects
});
};
ServerConnector.getSearchMiRnasUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "miRnas:search",
+ url: this.getProjectUrl(queryParams) + "miRnas:search",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "miRnas:search",
- params : filterParams,
->>>>>>> list of available projects
});
};
ServerConnector.getSearchChemicalsUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "chemicals:search",
+ url: this.getProjectUrl(queryParams) + "chemicals:search",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "chemicals:search",
- params : filterParams,
->>>>>>> list of available projects
});
};
@@ -623,25 +558,15 @@ ServerConnector.getOverlaySourceUrl = function (queryParams, filterParams) {
ServerConnector.getImageUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "models/" + queryParams.modelId + ":downloadImage",
+ url: this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadImage",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadImage",
- params : filterParams,
->>>>>>> list of available projects
});
};
ServerConnector.getModelPartUrl = function (queryParams, filterParams) {
return this.getApiUrl({
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- url: this.getProjectsUrl(queryParams) + "models/" + queryParams.modelId + ":downloadModel",
+ url: this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadModel",
params: filterParams,
-=======
- url : this.getProjectUrl(queryParams) + "models/" + queryParams.modelId + ":downloadModel",
- params : filterParams,
->>>>>>> list of available projects
});
};
@@ -652,18 +577,61 @@ ServerConnector.getProjectSourceUrl = function (queryParams, filterParams) {
});
};
-ServerConnector.getUserUrl = function (queryParams, filterParams) {
+
+ServerConnector.getFilesUrl = function () {
+ return this.getApiUrl({
+ type: "files/"
+ });
+};
+
+ServerConnector.getCreateFileUrl = function () {
+ return this.getApiUrl({
+ url: this.getFilesUrl()
+ });
+};
+ServerConnector.getFileUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getFilesUrl() + "/" + queryParams.id
+ });
+};
+ServerConnector.getUploadFileUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getFileUrl(queryParams) + ":uploadContent"
+ });
+};
+
+
+ServerConnector.getUsersUrl = function (queryParams, filterParams) {
return this.getApiUrl({
type: "users/",
- method: queryParams.login,
+ params: filterParams
+ });
+};
+
+ServerConnector.getUserUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ url: this.getUsersUrl() + queryParams.login,
params: filterParams,
});
};
+ServerConnector.getUpdateUserPrivilegesUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ url: this.getUserUrl(queryParams) + ":updatePrivileges",
+ params: filterParams,
+ });
+};
+ServerConnector.getUpdateUserPreferencesUrl = function (queryParams, filterParams) {
+ return this.getApiUrl({
+ url: this.getUserUrl(queryParams) + ":updatePreferences",
+ params: filterParams
+ });
+};
+
ServerConnector.getConfiguration = function () {
var self = this;
if (this._configuration === undefined) {
- return self.readFile(self.getConfigurationUrl()).then(function (content) {
+ return self.sendGetRequest(self.getConfigurationUrl()).then(function (content) {
self._configuration = new Configuration(JSON.parse(content));
return Promise.resolve(self._configuration);
});
@@ -678,18 +646,35 @@ ServerConnector.getConfigurationParam = function (paramId) {
}
var self = this;
return self.getConfiguration().then(function (configuration) {
- return configuration.getOption(paramId);
+ var option = configuration.getOption(paramId);
+ if (option.getValue !== undefined) {
+ return option.getValue();
+ } else {
+ return option;
+ }
});
};
+ServerConnector.updateConfigurationOption = function (option) {
+ var self = this;
+ var queryParams = {
+ type: option.getType()
+ };
+ var filterParams = {
+ option: {
+ type: option.getType(),
+ value: option.getValue()
+ }
+ };
+ return self.sendPatchRequest(self.getConfigurationOptionUrl(queryParams), filterParams);
+};
ServerConnector.getModels = function (projectId) {
var queryParams = {};
var filterParams = {};
- var project;
var self = this;
return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getModelsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getModelsUrl(queryParams, filterParams));
}).then(function (content) {
var models = [];
var parsedJson = JSON.parse(content);
@@ -699,30 +684,34 @@ ServerConnector.getModels = function (projectId) {
return models;
});
};
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
-ServerConnector.getProject = function (projectId) {
-=======
-ServerConnector.getProject = function(projectId) {
->>>>>>> list of available projects
+ServerConnector.getProject = function (projectId) {
var queryParams = {};
var filterParams = {};
var project;
var self = this;
return self.getProjectId(projectId).then(function (result) {
+ projectId = result;
queryParams.projectId = result;
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
- return self.readFile(self.getProjectsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getProjectUrl(queryParams, filterParams));
}).then(function (content) {
-=======
- return self.readFile(self.getProjectUrl(queryParams, filterParams));
- }).then(function(content) {
->>>>>>> list of available projects
- project = new Project(content);
+ var downloadedProject = new Project(content);
+ if (self._projectsById[projectId] !== undefined) {
+ self._projectsById[projectId].update(downloadedProject);
+ } else {
+ self._projectsById[projectId] = downloadedProject;
+ }
+ project = self._projectsById[projectId];
return self.getModels(projectId);
}).then(function (models) {
project.setModel(models[0]);
- return self.getOverlays(projectId);
+ return self.getLoggedUser();
+ }).then(function (user) {
+ return self.getOverlays({
+ projectId: projectId,
+ creator: user.getLogin(),
+ publicOverlay: false,
+ });
}).then(function (overlays) {
project.getModel().addLayouts(overlays);
return project;
@@ -742,34 +731,133 @@ ServerConnector.getProject = function(projectId) {
});
};
-<<<<<<< 9ae57951d8f3069d115122223234b4aac60c546f
-ServerConnector.getProjectStatistics = function (projectId) {
-=======
-ServerConnector.getProjects = function() {
+ServerConnector.updateProject = function (project) {
+ var self = this;
+ var queryParams = {
+ projectId: project.getProjectId()
+ };
+ var filterParams = {
+ project: {
+ name: project.getName(),
+ version: project.getVersion(),
+ notifyEmail: project.getNotifyEmail(),
+ organism: self.serialize(project.getOrganism()),
+ disease: self.serialize(project.getDisease()),
+ },
+ };
+ return self.sendPatchRequest(self.getProjectUrl(queryParams), filterParams).then(function (content) {
+ var downloadedProject = new Project(content);
+ project.update(downloadedProject);
+ return project;
+ }).then(null, function (error) {
+ if ((error instanceof NetworkError)) {
+ switch (error.statusCode) {
+ case HttpStatus.FORBIDDEN:
+ return Promise.reject(new SecurityError("Access denied."));
+ default:
+ return Promise.reject(error);
+ }
+ } else {
+ return Promise.reject(error);
+ }
+ });
+};
+
+ServerConnector.removeProject = function (projectId) {
+ var self = this;
+ var queryParams = {
+ projectId: projectId
+ };
+ return self.sendDeleteRequest(self.getProjectUrl(queryParams)).then(function (content) {
+ var project = new Project(content);
+ if (self._projectsById[project.getProjectId()] !== undefined) {
+ self._projectsById[project.getProjectId()].update(project);
+ } else {
+ self._projectsById[project.getProjectId()] = project;
+ }
+ return self._projectsById[project.getProjectId()];
+ }).then(null, function (error) {
+ if ((error instanceof NetworkError)) {
+ switch (error.statusCode) {
+ case HttpStatus.FORBIDDEN:
+ return Promise.reject(new SecurityError("Access denied."));
+ default:
+ return Promise.reject(error);
+ }
+ } else {
+ return Promise.reject(error);
+ }
+ });
+};
+
+ServerConnector.addProject = function (options) {
var self = this;
- if (self._projects !== undefined) {
+ var queryParams = {
+ projectId: options.projectId
+ };
+ return self.sendPostRequest(self.getProjectUrl(queryParams), options).then(function (content) {
+ var project = new Project(content);
+ if (self._projectsById[project.getProjectId()] !== undefined) {
+ self._projectsById[project.getProjectId()].update(project);
+ } else {
+ self._projectsById[project.getProjectId()] = project;
+ }
+ return project;
+ }).then(null, function (error) {
+ if ((error instanceof NetworkError)) {
+ switch (error.statusCode) {
+ case HttpStatus.FORBIDDEN:
+ return Promise.reject(new SecurityError("Access denied."));
+ default:
+ return Promise.reject(error);
+ }
+ } else {
+ return Promise.reject(error);
+ }
+ });
+};
+
+ServerConnector.serialize = function (object) {
+ var result = {};
+ if (object instanceof Annotation) {
+ result.type = object.getType();
+ result.resource = object.getResource();
+ } else {
+ throw new Error("Unhandled object type: " + (typeof object));
+ }
+ return result;
+};
+
+ServerConnector.getProjects = function (reload) {
+ var self = this;
+ if (self._projects.length > 0 && !reload) {
return Promise.resolve(self._projects);
} else {
- return self.readFile(self.getProjectsUrl()).then(function(content) {
+ return self.sendGetRequest(self.getProjectsUrl()).then(function (content) {
var parsedData = JSON.parse(content);
- self._projects = [];
+ self._projects.length = 0;
for (var i = 0; i < parsedData.length; i++) {
- self._projects.push(new Project(JSON.stringify(parsedData[i])));
+ var project = new Project(JSON.stringify(parsedData[i]));
+ if (self._projectsById[project.getProjectId()] !== undefined) {
+ self._projectsById[project.getProjectId()].update(project);
+ } else {
+ self._projectsById[project.getProjectId()] = project;
+ }
+ self._projects.push(self._projectsById[project.getProjectId()]);
}
return self._projects;
});
}
};
-ServerConnector.getProjectStatistics = function(projectId) {
->>>>>>> list of available projects
+ServerConnector.getProjectStatistics = function (projectId) {
var queryParams = {};
var filterParams = {};
var self = this;
var content;
return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getProjectStatisticsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getProjectStatisticsUrl(queryParams, filterParams));
}).then(function (result) {
content = JSON.parse(result);
return self.getConfiguration();
@@ -793,24 +881,169 @@ ServerConnector.getLoggedUser = function () {
ServerConnector.getUser = function (login) {
var self = this;
var queryParams = {
- login: login,
+ login: login
};
var filterParams = {};
- return self.readFile(self.getUserUrl(queryParams, filterParams)).then(function (content) {
+ return self.sendGetRequest(self.getUserUrl(queryParams, filterParams)).then(function (content) {
+ var obj = JSON.parse(content);
+ var user = new User(obj);
+ if (self._usersByLogin[user.getLogin()] !== undefined) {
+ self._usersByLogin[user.getLogin()].update(user);
+ } else {
+ self._usersByLogin[user.getLogin()] = user;
+ }
+ return self._usersByLogin[user.getLogin()];
+ }).then(null, function (error) {
+ return self.processNetworkError(error);
+ });
+};
+
+ServerConnector.updateUser = function (user) {
+ var self = this;
+ var queryParams = {
+ login: user.getLogin()
+ };
+ var filterParams = {
+ user: {
+ name: user.getName(),
+ surname: user.getSurname(),
+ password: user.getPassword(),
+ email: user.getEmail()
+ }
+ };
+ return self.sendPatchRequest(self.getUserUrl(queryParams), filterParams).then(function () {
+ return self.getConfiguration();
+ }).then(function (configuration) {
+ return self.updateUserPrivileges({user: user, privileges: user.privilegesToExport(configuration)});
+ });
+
+};
+ServerConnector.addUser = function (user) {
+ var self = this;
+ var queryParams = {
+ login: user.getLogin()
+ };
+ var filterParams = {
+ login: user.getLogin(),
+ name: user.getName(),
+ surname: user.getSurname(),
+ password: user.getPassword(),
+ email: user.getEmail()
+ };
+ return self.sendPostRequest(self.getUserUrl(queryParams), filterParams).then(function () {
+ return self.getConfiguration();
+ }).then(function (configuration) {
+ return self.updateUserPrivileges({user: user, privileges: user.privilegesToExport(configuration)});
+ });
+
+};
+
+ServerConnector.removeUser = function (login) {
+ var self = this;
+ var queryParams = {
+ login: login
+ };
+ return self.sendDeleteRequest(self.getUserUrl(queryParams));
+
+};
+
+ServerConnector.updateUserPrivileges = function (params) {
+ var self = this;
+ var queryParams = {
+ login: params.user.getLogin()
+ };
+
+ return self.sendPatchRequest(self.getUpdateUserPrivilegesUrl(queryParams), {
+ privileges: params.privileges
+ }).then(function (content) {
+ var obj = JSON.parse(content);
+ var user = new User(obj);
+ if (self._usersByLogin[user.getLogin()] !== undefined) {
+ self._usersByLogin[user.getLogin()].update(user);
+ } else {
+ self._usersByLogin[user.getLogin()] = user;
+ }
+ return self._usersByLogin[user.getLogin()];
+ }).then(null, function (error) {
+ return self.processNetworkError(error);
+ });
+};
+
+ServerConnector.processNetworkError = function (error) {
+ if ((error instanceof NetworkError)) {
+ switch (error.statusCode) {
+ case HttpStatus.NOT_FOUND:
+ return null;
+ case HttpStatus.FORBIDDEN:
+ return Promise.reject(new SecurityError("Access denied."));
+ default:
+ return Promise.reject(error);
+ }
+ } else {
+ return Promise.reject(error);
+ }
+};
+
+
+ServerConnector.updateUserPreferences = function (params) {
+ var self = this;
+ var queryParams = {
+ login: params.user.getLogin()
+ };
+
+ return self.sendPatchRequest(self.getUpdateUserPreferencesUrl(queryParams), {
+ preferences: params.preferences.toExport()
+ }).then(function (content) {
var obj = JSON.parse(content);
- return new User(obj);
+ var user = new User(obj);
+ if (self._usersByLogin[user.getLogin()] !== undefined) {
+ self._usersByLogin[user.getLogin()].update(user);
+ } else {
+ self._usersByLogin[user.getLogin()] = user;
+ }
+ return self._usersByLogin[user.getLogin()];
});
};
-ServerConnector.getOverlays = function (projectId) {
+ServerConnector.getUsers = function (forceRefresh) {
var self = this;
+
+ if (self._users.length > 0 && !forceRefresh) {
+ return Promise.resolve(self._users);
+ } else {
+ return self.sendGetRequest(self.getUsersUrl()).then(function (content) {
+ var parsedData = JSON.parse(content);
+ self._users.length = 0;
+ for (var i = 0; i < parsedData.length; i++) {
+ var user = new User(parsedData[i]);
+ if (self._usersByLogin[user.getLogin()] !== undefined) {
+ self._usersByLogin[user.getLogin()].update(user);
+ } else {
+ self._usersByLogin[user.getLogin()] = user;
+ }
+ self._users.push(self._usersByLogin[user.getLogin()]);
+ }
+ return self._users;
+ });
+ }
+
+};
+
+ServerConnector.getOverlays = function (params) {
+ var self = this;
+ if (params === undefined) {
+ params = {};
+ }
var queryParams = {};
- var filterParams = {};
+ var filterParams = {
+ creator: params.creator,
+ publicOverlay: params.publicOverlay,
+ };
return new Promise(function (resolve, reject) {
- self.getProjectId(projectId).then(function (result) {
+ self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getOverlaysUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getOverlaysUrl(queryParams, filterParams));
}).then(function (content) {
var arr = JSON.parse(content);
var result = [];
@@ -835,7 +1068,7 @@ ServerConnector.getOverlayElements = function (overlayId, projectId) {
var filterParams = {};
return self.getProjectId(projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getOverlayElementsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getOverlayElementsUrl(queryParams, filterParams));
}).then(function (content) {
var arr = JSON.parse(content);
var result = [];
@@ -865,7 +1098,7 @@ ServerConnector.getFullOverlayElement = function (params) {
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getFullOverlayElementUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getFullOverlayElementUrl(queryParams, filterParams));
}).then(function (content) {
var element = JSON.parse(content);
var result = null;
@@ -911,13 +1144,13 @@ ServerConnector.getOverlayById = function (overlayId, projectId) {
var filterParams = {};
return self.getProjectId(projectId).then(function (data) {
queryParams.projectId = data;
- return self.readFile(self.getOverlayByIdUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getOverlayByIdUrl(queryParams, filterParams));
}).then(function (content) {
return new LayoutData(JSON.parse(content));
});
};
-ServerConnector.getReactions = function(params) {
+ServerConnector.getReactions = function (params) {
var self = this;
var queryParams = {};
if (params.ids === undefined) {
@@ -936,10 +1169,10 @@ ServerConnector.getReactions = function(params) {
if (filterParams.id.length > 100 || filterParams.participantId.length > 100) {
return self.sendPostRequest(self.getReactionsUrl(queryParams), filterParams);
} else {
- return self.readFile(self.getReactionsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getReactionsUrl(queryParams, filterParams));
}
- }).then(function(content) {
+ }).then(function (content) {
var array = JSON.parse(content);
var result = [];
for (var i = 0; i < array.length; i++) {
@@ -952,7 +1185,7 @@ ServerConnector.getReactions = function(params) {
ServerConnector.getAliases = function (params) {
var self = this;
var queryParams = {
- modelId: params.modelId,
+ modelId: params.modelId
};
if (params.ids === undefined) {
params.ids = [];
@@ -964,11 +1197,11 @@ ServerConnector.getAliases = function (params) {
params.excludedCompartmentIds = [];
}
var filterParams = {
- id : params.ids,
- columns : params.columns,
- type : params.type,
- excludedCompartmentIds : params.excludedCompartmentIds,
- includedCompartmentIds : params.includedCompartmentIds,
+ id: params.ids,
+ columns: params.columns,
+ type: params.type,
+ excludedCompartmentIds: params.excludedCompartmentIds,
+ includedCompartmentIds: params.includedCompartmentIds
};
return self.getProjectId(params.projectId).then(function (result) {
@@ -976,7 +1209,7 @@ ServerConnector.getAliases = function (params) {
if (filterParams.id.length > 100) {
return self.sendPostRequest(self.getAliasesUrl(queryParams), filterParams);
} else {
- return self.readFile(self.getAliasesUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getAliasesUrl(queryParams, filterParams));
}
}).then(function (content) {
var array = JSON.parse(content);
@@ -1005,7 +1238,7 @@ ServerConnector.getComments = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getCommentsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getCommentsUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1037,7 +1270,7 @@ ServerConnector.getClosestElementsByCoordinates = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1074,7 +1307,7 @@ ServerConnector.logout = function () {
var self = this;
self.getSessionData().setToken(undefined);
self.getSessionData().setLogin(undefined);
- return self.readFile(self.logoutUrl());
+ return self.sendGetRequest(self.logoutUrl());
};
ServerConnector.getElementsByQuery = function (params) {
@@ -1089,7 +1322,7 @@ ServerConnector.getElementsByQuery = function (params) {
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1108,7 +1341,7 @@ ServerConnector.getDrugsByQuery = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchDrugsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchDrugsUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1127,7 +1360,7 @@ ServerConnector.getMiRnasByQuery = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchMiRnasUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchMiRnasUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1146,7 +1379,7 @@ ServerConnector.getChemicalsByQuery = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchChemicalsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchChemicalsUrl(queryParams, filterParams));
}).then(function (content) {
var array = JSON.parse(content);
var result = [];
@@ -1245,7 +1478,7 @@ ServerConnector.getDrugNamesByTarget = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchDrugsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchDrugsUrl(queryParams, filterParams));
}).then(function (content) {
var result = [];
var object = JSON.parse(content);
@@ -1265,7 +1498,7 @@ ServerConnector.getMiRnaNamesByTarget = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchMiRnasUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchMiRnasUrl(queryParams, filterParams));
}).then(function (content) {
var result = [];
var object = JSON.parse(content);
@@ -1285,7 +1518,7 @@ ServerConnector.getChemicalNamesByTarget = function (params) {
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getSearchChemicalsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getSearchChemicalsUrl(queryParams, filterParams));
}).then(function (content) {
var result = [];
var object = JSON.parse(content);
@@ -1302,7 +1535,7 @@ ServerConnector.addComment = function (params) {
elementId: params.elementId,
elementType: params.elementType,
coordinates: self.pointToString(params.coordinates),
- modelId: params.modelId,
+ modelId: params.modelId
};
var filterParams = params;
delete filterParams.elementId;
@@ -1323,34 +1556,40 @@ ServerConnector.addComment = function (params) {
};
ServerConnector.addOverlay = function (params) {
+ var overlay = params.overlay;
+ if (!(overlay instanceof LayoutData)) {
+ throw new Error("Invalid overlay: " + overlay);
+ }
var self = this;
var queryParams = {};
+ var data = {
+ name: overlay.getName(),
+ description: overlay.getDescription(),
+ content: overlay.getContent(),
+ filename: overlay.getFilename()
+ };
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.sendPostRequest(self.addOverlayUrl(queryParams), params);
+ return self.sendPostRequest(self.addOverlayUrl(queryParams), data);
}).then(function (content) {
return new LayoutData(JSON.parse(content));
});
};
-ServerConnector.updateOverlay = function (params) {
+ServerConnector.updateOverlay = function (overlay) {
var self = this;
var queryParams = {
- overlayId: params.overlayId
+ overlayId: overlay.getId()
};
var filterParams = {
- overlay: {}
+ overlay: {
+ name: overlay.getName(),
+ description: overlay.getDescription(),
+ creator: overlay.getCreator(),
+ publicOverlay: overlay.getPublicOverlay()
+ }
};
- if (params.name !== undefined) {
- filterParams.overlay.name = params.name;
- }
- if (params.description !== undefined) {
- filterParams.overlay.description = params.description;
- }
- return self.getProjectId(params.projectId).then(function (result) {
- queryParams.projectId = result;
- return self.sendPatchRequest(self.updateOverlayUrl(queryParams), filterParams);
- });
+ return self.sendPatchRequest(self.updateOverlayUrl(queryParams), filterParams);
};
ServerConnector.removeOverlay = function (params) {
@@ -1365,11 +1604,23 @@ ServerConnector.removeOverlay = function (params) {
});
};
+ServerConnector.removeComment = function (params) {
+ var self = this;
+ var queryParams = {
+ commentId: params.commentId
+ };
+ var filterParams = {};
+ return self.getProjectId(params.projectId).then(function (result) {
+ queryParams.projectId = result;
+ return self.sendDeleteRequest(self.deleteCommentUrl(queryParams), filterParams);
+ });
+};
+
ServerConnector.getSuggestedQueryList = function (projectId) {
var self = this;
return self.getProjectId(projectId).then(function (result) {
projectId = result;
- return self.readFile(self.getSuggestedQueryListUrl({
+ return self.sendGetRequest(self.getSuggestedQueryListUrl({
projectId: projectId
}));
}).then(function (content) {
@@ -1396,11 +1647,11 @@ ServerConnector.getPublications = function (params) {
length: params.length,
sortColumn: params.sortColumn,
sortOrder: params.sortOrder,
- search: params.search,
+ search: params.search
};
return self.getProjectId(params.projectId).then(function (result) {
queryParams.projectId = result;
- return self.readFile(self.getPublicationsUrl(queryParams, filterParams));
+ return self.sendGetRequest(self.getPublicationsUrl(queryParams, filterParams));
}).then(function (content) {
return JSON.parse(content);
});
@@ -1409,9 +1660,39 @@ ServerConnector.getPublications = function (params) {
ServerConnector.getReferenceGenome = function (params) {
var self = this;
var filterParams = {};
- return self.readFile(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
+ return self.sendGetRequest(self.getReferenceGenomeUrl(params, filterParams)).then(function (content) {
return new ReferenceGenome(JSON.parse(content));
});
};
+ServerConnector.uploadFile = function (params) {
+ var CHUNK_SIZE = 65535;
+ var self = this;
+ var data = new Uint8Array(params.content);
+ var filterParams = {
+ filename: params.filename,
+ length: data.length
+ };
+
+ return self.sendPostRequest(self.getCreateFileUrl(), filterParams).then(function (response) {
+ var uploadedLength = 0;
+ var createPromise = function (resultFileJson) {
+ var resultFile = JSON.parse(resultFileJson);
+ if (uploadedLength >= data.length) {
+ return Promise.resolve(resultFile);
+ } else {
+ var chunk = data.slice(uploadedLength, uploadedLength + CHUNK_SIZE);
+ logger.debug("SEND " + chunk.length + " bytes");
+ var url = self.getUploadFileUrl({id: resultFile.id});
+ return self.sendRequest({method: "POST", url: url, body: chunk}).then(function (resultFileJson) {
+ uploadedLength += chunk.length;
+ logger.debug("RESPONSE ", resultFileJson);
+ return createPromise(resultFileJson);
+ })
+ }
+ };
+ return createPromise(response);
+ });
+};
+
module.exports = ServerConnector;