diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index 29898ad842e00b3eb7c8dd24e29d521cd5cf3cef..5db0016f8df18b58e138862b0a2d99c344a5f5fd 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -11,9 +11,9 @@
"dev": true
},
"@types/react": {
- "version": "15.6.14",
- "resolved": "https://registry.npmjs.org/@types/react/-/react-15.6.14.tgz",
- "integrity": "sha512-k6YJBmHfzkCtk3iT6aN2hclkPYL2fxlSc3dW//G2kENlmMJ/V+pKhqsHdJJeVluIi1bA296cCLLGATLm7WXToQ==",
+ "version": "15.6.15",
+ "resolved": "https://registry.npmjs.org/@types/react/-/react-15.6.15.tgz",
+ "integrity": "sha512-LOHbyeKRNYLEotniN3DlRGrpXorXupvFSbKrNzc9dZ87uL+IJDbGYVerxKaG1jbnhuc7RhEWxlNmUVtYm3mtNg==",
"dev": true
},
"@types/react-dom": {
@@ -22,7 +22,7 @@
"integrity": "sha512-XGLjgNtPnBuO1cITYWZAk4KbH0UEDqMg2kuG3xx0UgnrcSd6ijO57Fp9rimmrDKcBnx3b2vFQuEYRXu2GihRYQ==",
"dev": true,
"requires": {
- "@types/react": "15.6.14"
+ "@types/react": "15.6.15"
}
},
"JSONStream": {
@@ -45,30 +45,38 @@
"litemol": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b"
},
"dependencies": {
+ "ProtVista": {
+ "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
+ "dev": true,
+ "requires": {
+ "d3": "3.5.17",
+ "file-saver": "1.3.3",
+ "jquery": "2.2.4",
+ "jszip": "3.1.4",
+ "underscore": "1.8.3"
+ },
+ "dependencies": {
+ "jquery": {
+ "version": "2.2.4",
+ "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
+ "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
+ "dev": true
+ }
+ }
+ },
"jquery": {
"version": "3.3.1",
"resolved": "https://registry.npmjs.org/jquery/-/jquery-3.3.1.tgz",
"integrity": "sha512-Ubldcmxp5np52/ENotGxlLe6aGMvmF4R8S6tZjsP6Knsaxd/xp3Zrh50cG93lR6nPXyUFwzN3ZSOQI0wRJNdGg==",
"dev": true
- }
- }
- },
- "ProtVista": {
- "version": "git://github.com/davidhoksza/protvista.git#4e4bb737ba1e183291505bd25f8bae2e651ce21e",
- "dev": true,
- "requires": {
- "d3": "3.5.17",
- "file-saver": "1.3.3",
- "jquery": "2.2.4",
- "jszip": "3.1.4",
- "underscore": "1.8.3"
- },
- "dependencies": {
- "jquery": {
- "version": "2.2.4",
- "resolved": "https://registry.npmjs.org/jquery/-/jquery-2.2.4.tgz",
- "integrity": "sha1-LInWiJterFIqfuoywUUhVZxsvwI=",
- "dev": true
+ },
+ "litemol": {
+ "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
+ "dev": true,
+ "requires": {
+ "@types/react": "15.6.15",
+ "@types/react-dom": "15.5.7"
+ }
}
}
},
@@ -2050,14 +2058,6 @@
"immediate": "3.0.6"
}
},
- "litemol": {
- "version": "github:dsehnal/LiteMol#a5419c696faa84530dd93acd55b747cf8136902b",
- "dev": true,
- "requires": {
- "@types/react": "15.6.14",
- "@types/react-dom": "15.5.7"
- }
- },
"lodash": {
"version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",
@@ -2389,6 +2389,11 @@
"integrity": "sha1-VgiurfwAvmwpAd9fmGF4jeDVl8g=",
"dev": true
},
+ "multi-checkbox-list": {
+ "version": "0.2.0",
+ "resolved": "https://registry.npmjs.org/multi-checkbox-list/-/multi-checkbox-list-0.2.0.tgz",
+ "integrity": "sha512-b1HVb8XqCNtC2OAu2AVgs/eaNnMS9Zudv61Nsi3OR9527P5c5IfwGbCzgLyBHiT0pHeL7Kpk6V+6bQYM8sYaTg=="
+ },
"nave": {
"version": "0.5.3",
"resolved": "https://registry.npmjs.org/nave/-/nave-0.5.3.tgz",
diff --git a/frontend-js/package.json b/frontend-js/package.json
index feff0ba36e760ab9d2c38435db2947ea5a37d133..a6345728a80f84bacd029cabca6a84b59c234f9a 100644
--- a/frontend-js/package.json
+++ b/frontend-js/package.json
@@ -4,7 +4,7 @@
"description": "frontentd for minerva google maps interface",
"main": "minerva.js",
"scripts": {
- "build:css": "cleancss --skip-rebase -o dist/minerva.css node_modules/dual-listbox/dist/*.css src/main/css/*.css",
+ "build:css": "cleancss --skip-rebase -o dist/minerva.css node_modules/dual-listbox/dist/*.css node_modules/multi-checkbox-list/dist/*.css src/main/css/*.css",
"build:js": "browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js ",
"//": "rm -rf dist & rmdir /q /s dist & mkdir dist & browserify --debug --standalone minerva src/main/js/minerva.js | exorcist dist/minerva.js.map > dist/minerva.js & uglifyjs --compress --mangle --in-source-map dist/minerva.js.map --source-map-include-sources --source-map dist/minerva.min.js.map -o dist/minerva.min.js dist/minerva.js",
"build-deploy": "npm run build && npm run deploy",
@@ -17,6 +17,7 @@
},
"author": "Piotr Gawron",
"devDependencies": {
+ "MolStar": "git://github.com/davidhoksza/MolStar.git",
"assert": "1.4.1",
"bluebird": "^3.4.6",
"bootstrap": "^3.3.7",
@@ -36,7 +37,6 @@
"log4js-memory-appender": "1.0.5",
"mkdirp": "^0.5.1",
"mocha": "^3.5.3",
- "MolStar": "git://github.com/davidhoksza/MolStar.git",
"uglifyjs": "^2.4.10"
},
"dependencies": {
@@ -49,6 +49,7 @@
"jstree": "^3.3.4",
"jszip": "^3.1.4",
"log4js": "0.6.38",
+ "multi-checkbox-list": "^0.2.0",
"pileup": "^0.6.8",
"request": "^2.82.0",
"spectrum-colorpicker": "^1.8.0",
diff --git a/frontend-js/src/main/js/Configuration.js b/frontend-js/src/main/js/Configuration.js
index 2e543b48870c327e8c24acd8b4ae5d9a6165a77d..4755bee12f43b880d69f54d33f45bfd23d8ccff9 100644
--- a/frontend-js/src/main/js/Configuration.js
+++ b/frontend-js/src/main/js/Configuration.js
@@ -370,4 +370,54 @@ Configuration.prototype.update = function (original) {
}
};
+Configuration.prototype.getElementTypeTree = function () {
+ var elementTypes = this.getElementTypes();
+ var reactionTypes = this.getReactionTypes();
+
+ var treeNodes = {
+ "lcsb.mapviewer.model.map.BioEntity": {
+ text: "BioEntity",
+ children: []
+ }
+ };
+
+ var i, type;
+ for (i = 0; i < elementTypes.length; i++) {
+ type = elementTypes[i];
+ var name = type.className;
+ if (name.indexOf(".") > 0) {
+ name = name.substr(name.lastIndexOf(".") + 1);
+ }
+ treeNodes[type.className] = {
+ text: name,
+ data: type,
+ children: []
+ };
+ }
+
+ for (i = 0; i < reactionTypes.length; i++) {
+ type = reactionTypes[i];
+ treeNodes[type.className] = {
+ text: type.name,
+ data: type,
+ children: []
+ };
+ }
+
+ for (var treeNodeName in treeNodes) {
+ if (treeNodes.hasOwnProperty(treeNodeName)) {
+ var treeNode = treeNodes[treeNodeName];
+ if (treeNode.data !== undefined) {
+ var parentNode = treeNodes[treeNode.data.parentClass];
+ if (parentNode.data===undefined || parentNode.data.name !== "Compartment") {
+ parentNode.children.push(treeNode);
+ }
+ }
+ }
+ }
+
+ return treeNodes["lcsb.mapviewer.model.map.BioEntity"];
+};
+
+
module.exports = Configuration;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 48c374d88e905eb1a63193a0336715b074115ba2..c08e3bddbecf4019f15b05e46b0213cbc69824bc 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1105,7 +1105,7 @@ ServerConnector.updateUserPreferences = function (params) {
var obj = JSON.parse(content);
var user = new User(obj);
if (self._usersByLogin[user.getLogin()] !== undefined) {
- self._usersByLogin[user.getLogin()].update(user);
+ self._usersByLogin[user.getLogin()].getPreferences().update(user.getPreferences());
} else {
self._usersByLogin[user.getLogin()] = user;
}
diff --git a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
index 22d5dc4f982a105bb6dbf9aea5a5efc14de836a7..d6bc264d41e533742610f5ee739ad409383c17a5 100644
--- a/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AddProjectDialog.js
@@ -129,7 +129,8 @@ AddProjectDialog.prototype.showAnnotatorsDialog = function () {
if (self._annotatorsDialog === undefined) {
self._annotatorsDialog = new ChooseAnnotatorsDialog({
element: Functions.createElement({type: "div"}),
- customMap: null
+ customMap: null,
+ configuration: self.getConfiguration()
});
promise = self._annotatorsDialog.init();
} else {
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 1eeddfc1711839108c2f4611c62fbd98d883c1d7..2282b96c74a7b84883b7b53e89072cb71d27bc33 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -3,11 +3,11 @@
/* exported logger */
var AbstractGuiElement = require('../AbstractGuiElement');
-var DualListbox = require('dual-listbox').DualListbox;
var GuiConnector = require("../../GuiConnector");
+var MultiCheckboxList = require("multi-checkbox-list");
var UserPreferences = require("../../map/data/UserPreferences");
-var InvalidArgumentError = require ('../../InvalidArgumentError');
+var InvalidArgumentError = require('../../InvalidArgumentError');
var Functions = require('../../Functions');
var logger = require('../../logger');
@@ -27,40 +27,30 @@ ChooseAnnotatorsDialog.prototype.createGui = function () {
var self = this;
var content = Functions.createElement({
type: "div",
- style: "display:table"
+ style: "display:table;height:100%;width:100%"
});
content.appendChild(Functions.createElement({
type: "div",
- style: "display:table-cell",
- content: "<div name='elementTree'/>",
+ style: "display:table-cell;height:100%;",
+ content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
xss: false
}));
var annotatorsDiv = Functions.createElement({
type: "div",
- style: "display:table-cell",
+ style: "display:table-cell;width:100%",
+ content: "<div style='height:100%;width:100%;overflow-y:auto;'><div name='annotatorListBox'></div><div class='minerva-annotators-params'></div></div>",
xss: false
});
-
- annotatorsDiv.appendChild(Functions.createElement({
- type: "div",
- name: "annotatorListBox"
- }));
-
- annotatorsDiv.appendChild(Functions.createElement({
- type: "div",
- className: "minerva-annotators-params"
- }));
-
- content.appendChild(annotatorsDiv);
+ content.appendChild(annotatorsDiv);
self.getElement().appendChild(content);
};
-function onChangeParameterValue(element, user){
+function onChangeParameterValue(element, user) {
var name = $(element).siblings(".minerva-annotator-param-name")[0].childNodes[0].nodeValue;
var annotatorClassName = $(element).parent().parent().attr('name');
-
+
var data = new UserPreferences();
var annotatorsParams = {};
@@ -69,47 +59,173 @@ function onChangeParameterValue(element, user){
else annotatorsParams[annotatorClassName][name] = element.value;
data.setAnnotatorsParameters(annotatorsParams);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+ return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
}
+ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, selectedAnnotators) {
+ selectedAnnotators = selectedAnnotators.slice();
+ return ServerConnector.getLoggedUser().then(function (user) {
+
+ var data = new UserPreferences();
+
+ var elementAnnotators = {};
+ for (var i = 0; i < elementTypes.length; i++) {
+ elementAnnotators[elementTypes[i].className] = selectedAnnotators;
+
+ var userAnnotators = user.getPreferences().getElementAnnotators(elementTypes[i].className);
+ userAnnotators.length = 0;
+ userAnnotators.push.apply(userAnnotators, selectedAnnotators);
+ }
+ data.setElementAnnotators(elementAnnotators);
+ return ServerConnector.updateUserPreferences({
+ user: user,
+ preferences: data
+ });
+ }).catch(GuiConnector.alert);
+};
+
+ChooseAnnotatorsDialog.prototype.getAllChildrenTypesIfNeeded = function (elementType, includeChildren) {
+ var result = [elementType];
+ if (includeChildren) {
+ var queue = [elementType];
+ var elementTypes = this.getConfiguration().getElementTypes();
+ while (queue.length > 0) {
+ var type = queue.shift();
+ for (var i = 0; i < elementTypes.length; i++) {
+ if (type.className === elementTypes[i].parentClass) {
+ queue.push(elementTypes[i]);
+ result.push(elementTypes[i]);
+ }
+ }
+ }
+ }
+ return result;
+};
+
+
ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var self = this;
- var configuration;
+ var configuration = self.getConfiguration();
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- return ServerConnector.getLoggedUser();
- }).then(function (user) {
+ return ServerConnector.getLoggedUser().then(function (user) {
var element = $("[name='annotatorListBox']", self.getElement())[0];
var annotatorsParams = $(".minerva-annotators-params", self.getElement())[0];
Functions.removeChildren(element);
-
+
var selectElement = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
+ type: "div",
+ style: "width:50%; height:200px;float:left; OVERFLOW-Y:scroll"
});
- var annotators = configuration.getElementAnnotators(elementType);
+ element.appendChild(selectElement);
+ var includeChildrenCheckbox = Functions.createElement({type: "input", inputType: "checkbox"});
+ element.appendChild(includeChildrenCheckbox);
+ element.appendChild(Functions.createElement({type: "span", content: "Apply to all in subtree"}));
+ element.appendChild(Functions.createElement({type: "br"}));
+ var copyFromButton = Functions.createElement({
+ type: "button", content: "Copy from", onclick: function () {
+ var typeClassName = copyFromSelect.value;
+ var annotators;
+ for (var i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ if (typeClassName === type.className) {
+ annotators = user.getPreferences().getElementAnnotators(typeClassName);
+ }
+ }
+ if (annotators === undefined) {
+ return GuiConnector.alert("Invalid element type: " + copyFromSelect.value);
+ } else {
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), annotators).then(function () {
+ return self.setElementType(elementType);
+ });
+ }
+ }
+ });
+ element.appendChild(copyFromButton);
+ var copyFromSelect = Functions.createElement({type: "select", style: "margin:5px"});
+ element.appendChild(copyFromSelect);
+ var options = [], i;
+ for (i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ var name = type.className;
+ if (name.indexOf(".") > 0) {
+ name = name.substr(name.lastIndexOf(".") + 1);
+ }
+ options.push(Functions.createElement({
+ type: "option",
+ value: type.className,
+ content: name
+ }));
+ }
+ options.sort(function (a, b) {
+ return a.text === b.text ? 0 : a.text < b.text ? -1 : 1
+ });
+ for (i = 0; i < options.length; i++) {
+ copyFromSelect.appendChild(options[i]);
+ }
+
+ var annotators = configuration.getElementAnnotators(elementType);
var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
- for (var i = 0; i < annotators.length; i++) {
+ var selectedValues = [];
+
+ var entries = [];
+
+ for (i = 0; i < annotators.length; i++) {
var annotator = annotators[i];
- var selected = false;
+ var entry = {name: annotator.getName(), value: annotator.getClassName(), selected: false};
for (var j = 0; j < selectedAnnotators.length; j++) {
if (annotator.getName() === selectedAnnotators[j]) {
- selected = true;
- }
+ entry.selected = true;
+ }
}
- var option = new Option();
- option.value = annotator.getClassName();
- option.attributes.selected = selected;
- option.innerHTML = "<div>" + annotator.getName() + "</div>";
- selectElement.appendChild(option);
+ entries.push(entry);
+ }
+ var checkboxList = new MultiCheckboxList(selectElement, {
+ entries: entries,
+ listTitle: "Available annotators",
+ selectedTitle: "Selected annotators",
+ selectedList: true
+ });
+ var changeSelection = function (elementId, selected) {
+
+ var annotators = configuration.getElementAnnotators();
+ var annotator;
+ for (var i = 0; i < annotators.length; i++) {
+ if (elementId === annotators[i].getClassName()) {
+ annotator = annotators[i];
+ }
+ }
+ if (selected) {
+ selectedAnnotators.push(annotator.getName());
+ } else {
+ var index = selectedAnnotators.indexOf(annotator.getName());
+ if (index > -1) {
+ selectedAnnotators.splice(index, 1);
+ }
+ }
+ createAnnotatorsParams();
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
+ };
+ includeChildrenCheckbox.onchange = function () {
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
};
- function createAnnotatorsParams(){
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
+ });
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
+ });
+
+
+ function createAnnotatorsParams() {
+
var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
Functions.removeChildren(annotatorsParams);
@@ -117,35 +233,34 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var annotator = annotators[i];
for (var j = 0; j < selectedAnnotators.length; j++) {
if (annotator.getName() === selectedAnnotators[j]) {
-
var paramsDefs = annotator.getParametersDefinitions();
if (paramsDefs.length > 0) {
-
+
annotatorsParams.appendChild(Functions.createElement({
- type: "div",
+ type: "div",
className: "minerva-annotators-params-header",
content: '<div>Available parameters</div>'
- }))
-
+ }));
+
var annotatorParams = Functions.createElement({
- type: "div",
+ type: "div",
className: "minerva-annotator-params",
name: annotator.getClassName()
});
-
+
annotatorParams.appendChild(Functions.createElement({
- type: "div",
+ type: "div",
className: "minerva-annotator-params-header",
content: annotator.getName()
}));
-
+
for (var k = 0; k < paramsDefs.length; k++) {
- var param = paramsDefs[k];
+ var param = paramsDefs[k];
var paramElement = Functions.createElement({
- type: "div",
+ type: "div",
className: "minerva-annotator-param"
});
-
+
var paramName = Functions.createElement({
type: "div",
className: "minerva-annotator-param-name",
@@ -153,10 +268,10 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
});
var tooltipContainer = Functions.createElement({
- type: "span"
+ type: "span"
});
tooltipContainer.appendChild(Functions.createElement({
- type: "span",
+ type: "span",
className: "glyphicon glyphicon-question-sign tooltip-icon"
}));
tooltipContainer.appendChild(Functions.createElement({
@@ -164,104 +279,60 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
className: "annotator-tooltip",
content: param.description
}));
-
- paramName.appendChild(tooltipContainer)
- paramElement.appendChild(paramName);
-
+
+ paramName.appendChild(tooltipContainer);
+ paramElement.appendChild(paramName);
+
var paramValue;
-
+
var existingParamValue;
if (existingAnnotatorsParameters[annotator.getClassName()]) {
existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
}
-
+
if (param.type.indexOf("String") >= 0) {
paramValue = Functions.createElement({
type: "textarea",
- onchange: function(){return onChangeParameterValue(this, user);}
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
});
if (existingParamValue) paramValue.value = existingParamValue;
} else if (param.type.indexOf("Integer") >= 0) {
paramValue = Functions.createElement({
type: "input",
inputType: "number",
- onchange: function(){return onChangeParameterValue(this, user);}
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
});
if (existingParamValue) paramValue.value = existingParamValue;
} else if (param.type.indexOf("Boolean") >= 0) {
paramValue = Functions.createElement({
type: "input",
inputType: "checkbox",
- onchange: function(){return onChangeParameterValue(this, user);}
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
});
paramValue.checked = (existingParamValue && existingParamValue === 'true');
} else {
throw new InvalidAlgorithmError("Unknown annotator parameter type");
- }
-
+ }
+
paramElement.appendChild(paramValue);
- annotatorParams.appendChild(paramElement);
+ annotatorParams.appendChild(paramElement);
}
-
+
annotatorsParams.appendChild(annotatorParams);
}
- }
- }
- };
-
- }
- createAnnotatorsParams();
-
- element.appendChild(selectElement);
- new DualListbox(selectElement, {
- addEvent: function (value) {
- var annotators = configuration.getElementAnnotators();
- var annotator;
- for (var i = 0; i < annotators.length; i++) {
- if (value === annotators[i].getClassName()) {
- annotator = annotators[i];
}
}
- selectedAnnotators.push(annotator.getName());
+ }
+ }
- createAnnotatorsParams();
-
- var data = new UserPreferences();
-
- var elementAnnotators = {};
- elementAnnotators[elementType.className] = selectedAnnotators;
- data.setElementAnnotators(elementAnnotators);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- removeEvent: function (value) {
- var annotators = configuration.getElementAnnotators();
- var annotator;
- for (var i = 0; i < annotators.length; i++) {
- if (value === annotators[i].getClassName()) {
- annotator = annotators[i];
- }
- }
- var index = selectedAnnotators.indexOf(annotator.getName());
- if (index > -1) {
- selectedAnnotators.splice(index, 1);
- }
+ createAnnotatorsParams();
- createAnnotatorsParams();
-
- var data = new UserPreferences();
-
- var elementAnnotators = {};
- elementAnnotators[elementType.className] = selectedAnnotators;
- data.setElementAnnotators(elementAnnotators);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- availableTitle: 'Available',
- selectedTitle: 'Used',
- addButtonText: '>',
- removeButtonText: '<',
- addAllButtonText: '>>',
- removeAllButtonText: '<<'
- });
});
};
@@ -270,7 +341,7 @@ ChooseAnnotatorsDialog.prototype.init = function () {
var self = this;
return ServerConnector.getConfiguration().then(function (configuration) {
- var treeData = self.createElementTree(configuration);
+ var treeData = configuration.getElementTypeTree();
var element = $('[name="elementTree"]', self.getElement());
element.jstree({
@@ -287,54 +358,6 @@ ChooseAnnotatorsDialog.prototype.init = function () {
});
};
-ChooseAnnotatorsDialog.prototype.createElementTree = function (configuration) {
-
- var elementTypes = configuration.getElementTypes();
- var reactionTypes = configuration.getReactionTypes();
-
- var treeNodes = {
- "lcsb.mapviewer.model.map.BioEntity": {
- text: "BioEntity",
- children: []
- }
- };
-
- var i;
- for (i = 0; i < elementTypes.length; i++) {
- var type = elementTypes[i];
- var name = type.className;
- if (name.indexOf(".") > 0) {
- name = name.substr(name.lastIndexOf(".") + 1);
- }
- treeNodes[type.className] = {
- text: name,
- data: type,
- children: []
- };
- }
-
- for (i = 0; i < reactionTypes.length; i++) {
- var type = reactionTypes[i];
- treeNodes[type.className] = {
- text: type.name,
- data: type,
- children: []
- };
- }
-
- for (var treeNodeName in treeNodes) {
- if (treeNodes.hasOwnProperty(treeNodeName)) {
- var treeNode = treeNodes[treeNodeName];
- if (treeNode.data !== undefined) {
- var parentNode = treeNodes[treeNode.data.parentClass];
- parentNode.children.push(treeNode);
- }
- }
- }
-
- return treeNodes["lcsb.mapviewer.model.map.BioEntity"];
-};
-
ChooseAnnotatorsDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
@@ -351,8 +374,8 @@ ChooseAnnotatorsDialog.prototype.open = function () {
});
}
-
$(div).dialog("open");
+ $(div).css("overflow", "hidden");
};
module.exports = ChooseAnnotatorsDialog;
diff --git a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
index 5dba50c8917f3a5bcab685c50653529ae7a1a32b..1241d1c4e0eab5527b165a179657f645e62f8106 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
@@ -6,6 +6,7 @@ var AbstractGuiElement = require('../AbstractGuiElement');
var DualListbox = require('dual-listbox').DualListbox;
var GuiConnector = require("../../GuiConnector");
var UserPreferences = require("../../map/data/UserPreferences");
+var MultiCheckboxList = require("multi-checkbox-list");
var Functions = require('../../Functions');
var logger = require('../../logger');
@@ -25,19 +26,19 @@ ChooseValidatorsDialog.prototype.createGui = function () {
var self = this;
var content = Functions.createElement({
type: "div",
- style: "display:table"
+ style: "display:table;height:100%;width:100%"
});
content.appendChild(Functions.createElement({
type: "div",
- style: "display:table-cell",
- content: "<div name='elementTree'/>",
+ style: "display:table-cell;height:100%;",
+ content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
xss: false
}));
content.appendChild(Functions.createElement({
type: "div",
- style: "display:table-cell",
- content: "<div name='annotatorListBox'/>",
+ style: "display:table-cell;height:100%;width:100%;",
+ content: "<div name='annotatorListBox' style='height:100%;width:100%;overflow-y:auto;'><span> </span></div>",
xss: false
}));
@@ -79,66 +80,61 @@ ChooseValidatorsDialog.prototype.createValidAnnotationsDualListBox = function (u
var validAnnotations = user.getPreferences().getElementValidAnnotations(elementType.className);
+ var entries = [];
+
+
for (var i = 0; i < miriamTypes.length; i++) {
var miriamType = miriamTypes[i];
+ var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
+
var selected = false;
for (var j = 0; j < validAnnotations.length; j++) {
if (miriamType.getName() === validAnnotations[j]) {
- selected = true;
+ entry.selected = true;
}
}
- var option = new Option();
- option.value = miriamType.getName();
- option.attributes.selected = selected;
- option.innerHTML = "<div>" + miriamType.getCommonName() + "</div>";
- validAnnotationSelect.appendChild(option);
+ entries.push(entry);
}
- new DualListbox(validAnnotationSelect, {
- addEvent: function (value) {
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (value === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
- }
- validAnnotations.push(miriamType.getName());
-
- var data = new UserPreferences();
+ var checkboxList = new MultiCheckboxList(validAnnotationSelect, {
+ entries: entries,
+ listTitle: "Available",
+ selectedTitle: "Selected",
+ selectedList: true
+ });
- var elementAnnotators = {};
- elementAnnotators[elementType.className] = validAnnotations;
- data.setElementValidAnnotations(elementAnnotators);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- removeEvent: function (value) {
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (value === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
+ var changeSelection = function (elementId, selected) {
+ var miriamTypes = configuration.getMiriamTypes();
+ var miriamType;
+ for (var i = 0; i < miriamTypes.length; i++) {
+ if (elementId === miriamTypes[i].getName()) {
+ miriamType = miriamTypes[i];
}
+ }
+ if (selected) {
+ validAnnotations.push(miriamType.getName());
+ } else {
var index = validAnnotations.indexOf(miriamType.getName());
if (index > -1) {
validAnnotations.splice(index, 1);
}
+ }
- var data = new UserPreferences();
+ var data = new UserPreferences();
- var elementAnnotators = {};
- elementAnnotators[elementType.className] = validAnnotations;
- data.setElementValidAnnotations(elementAnnotators);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- availableTitle: 'Available',
- selectedTitle: 'Used',
- addButtonText: '>',
- removeButtonText: '<',
- addAllButtonText: '>>',
- removeAllButtonText: '<<'
+ var elementAnnotators = {};
+ elementAnnotators[elementType.className] = validAnnotations;
+ data.setElementValidAnnotations(elementAnnotators);
+ return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+ };
+
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
});
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
+ });
+
};
ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (user, configuration, elementType, verifyAnnotationSelect) {
@@ -162,6 +158,8 @@ ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (
}
});
checkbox.checked = requiredAnnotationsData.requiredAtLeastOnce;
+ verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
+ verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
verifyCheckboxDiv.appendChild(checkbox);
verifyCheckboxDiv.appendChild(Functions.createElement({
type: "span",
@@ -171,80 +169,69 @@ ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (
var miriamTypes = configuration.getMiriamTypes();
+ var entries = [];
for (var i = 0; i < miriamTypes.length; i++) {
var miriamType = miriamTypes[i];
- var selected = false;
+ var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
for (var j = 0; j < requiredAnnotationsData.list.length; j++) {
if (miriamType.getName() === requiredAnnotationsData.list[j]) {
- selected = true;
+ entry.selected = true;
}
}
- var option = new Option();
- option.value = miriamType.getName();
- option.attributes.selected = selected;
- option.innerHTML = "<div>" + miriamType.getCommonName() + "</div>";
- verifyAnnotationSelect.appendChild(option);
+ entries.push(entry);
}
- new DualListbox(verifyAnnotationSelect, {
- addEvent: function (value) {
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (value === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
- }
- requiredAnnotationsData.list.push(miriamType.getName());
+ var checkboxList = new MultiCheckboxList(verifyAnnotationSelect, {
+ entries: entries,
+ listTitle: "Available",
+ selectedTitle: "Selected",
+ selectedList: true
+ });
- var data = new UserPreferences();
+ var changeSelection = function (elementId, selected) {
- var elementRequiredAnnotations = {};
- elementRequiredAnnotations[elementType.className] = {
- "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
- "annotation-list": requiredAnnotationsData.list
- };
- data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- removeEvent: function (value) {
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (value === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
+ var miriamTypes = configuration.getMiriamTypes();
+ var miriamType;
+ for (var i = 0; i < miriamTypes.length; i++) {
+ if (elementId === miriamTypes[i].getName()) {
+ miriamType = miriamTypes[i];
}
+ }
+ if (selected) {
+ requiredAnnotationsData.list.push(miriamType.getName());
+ } else {
var index = requiredAnnotationsData.list.indexOf(miriamType.getName());
if (index > -1) {
requiredAnnotationsData.list.splice(index, 1);
}
+ }
- var data = new UserPreferences();
+ var data = new UserPreferences();
- var elementRequiredAnnotations = {};
- elementRequiredAnnotations[elementType.className] = {
- "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
- "annotation-list": requiredAnnotationsData.list
- };
- data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
- },
- availableTitle: 'Available',
- selectedTitle: 'Used',
- addButtonText: '>',
- removeButtonText: '<',
- addAllButtonText: '>>',
- removeAllButtonText: '<<'
+ var elementRequiredAnnotations = {};
+ elementRequiredAnnotations[elementType.className] = {
+ "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
+ "annotation-list": requiredAnnotationsData.list
+ };
+ data.setElementRequiredAnnotations(elementRequiredAnnotations);
+ return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+ };
+
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
+ });
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
});
+
};
ChooseValidatorsDialog.prototype.init = function () {
var self = this;
return ServerConnector.getConfiguration().then(function (configuration) {
- var treeData = self.createElementTree(configuration);
+ var treeData = configuration.getElementTypeTree();
var element = $('[name="elementTree"]', self.getElement());
element.jstree({
@@ -261,54 +248,6 @@ ChooseValidatorsDialog.prototype.init = function () {
});
};
-ChooseValidatorsDialog.prototype.createElementTree = function (configuration) {
-
- var elementTypes = configuration.getElementTypes();
- var reactionTypes = configuration.getReactionTypes();
-
- var treeNodes = {
- "lcsb.mapviewer.model.map.BioEntity": {
- text: "BioEntity",
- children: []
- }
- };
-
- var i, type;
- for (i = 0; i < elementTypes.length; i++) {
- type = elementTypes[i];
- var name = type.className;
- if (name.indexOf(".") > 0) {
- name = name.substr(name.lastIndexOf(".") + 1);
- }
- treeNodes[type.className] = {
- text: name,
- data: type,
- children: []
- };
- }
-
- for (i = 0; i < reactionTypes.length; i++) {
- type = reactionTypes[i];
- treeNodes[type.className] = {
- text: type.name,
- data: type,
- children: []
- };
- }
-
- for (var treeNodeName in treeNodes) {
- if (treeNodes.hasOwnProperty(treeNodeName)) {
- var treeNode = treeNodes[treeNodeName];
- if (treeNode.data !== undefined) {
- var parentNode = treeNodes[treeNode.data.parentClass];
- parentNode.children.push(treeNode);
- }
- }
- }
-
- return treeNodes["lcsb.mapviewer.model.map.BioEntity"];
-};
-
ChooseValidatorsDialog.prototype.destroy = function () {
$(this.getElement()).dialog("destroy");
};
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index 750c29555351c6e3217462e1f2f4ed5feb93902b..36ff821d76c9f6f184047d51a2875af2ce813b6a 100644
--- a/frontend-js/src/main/js/map/data/UserPreferences.js
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -81,7 +81,8 @@ UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
UserPreferences.prototype.getElementAnnotators = function (className) {
var result = this._elementAnnotators[className];
if (result === undefined) {
- result = [];
+ this._elementAnnotators[className] = [];
+ result = this._elementAnnotators[className];
}
return result;
};
diff --git a/frontend-js/src/test/js/Configuration-test.js b/frontend-js/src/test/js/Configuration-test.js
index 6a8adcbc5611e90a3b5253e970e9884ef38b3bb4..e8aadbf1284d8bee39e41b3fcac7bf81b1fa4185 100644
--- a/frontend-js/src/test/js/Configuration-test.js
+++ b/frontend-js/src/test/js/Configuration-test.js
@@ -107,4 +107,18 @@ describe('Configuration', function () {
});
});
});
+
+ it('getElementTypeTree', function () {
+
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var treeData = configuration.getElementTypeTree();
+
+ assert.ok(treeData);
+ assert.ok(treeData.text);
+ assert.ok(treeData.children);
+ assert.equal(2, treeData.children.length);
+ })
+ });
+
+
});
diff --git a/frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js b/frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js
index e7e321353be67a636b60147947759b85ba43662b..ee6700ba892626c817a31ae7d9f0aa772b8fd67e 100644
--- a/frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js
@@ -10,38 +10,50 @@ var chai = require('chai');
var assert = chai.assert;
describe('ChooseAnnotatorsDialog', function () {
- it('init', function () {
- var dialog = new ChooseAnnotatorsDialog({
+ function createDialog() {
+ return new ChooseAnnotatorsDialog({
element: testDiv,
- customMap: null
+ customMap: null,
+ configuration: helper.getConfiguration()
});
+ }
+
+ it('init', function () {
+ var dialog = createDialog();
assert.equal(0, logger.getWarnings().length);
return dialog.init();
});
- it('createElementTree', function () {
- var dialog = new ChooseAnnotatorsDialog({
- element: testDiv,
- customMap: null
- });
+ it('setElementType', function () {
+ var dialog = createDialog();
return ServerConnector.getConfiguration().then(function (configuration) {
- var treeData = dialog.createElementTree(configuration);
-
- assert.ok(treeData);
- assert.ok(treeData.text);
- assert.ok(treeData.children);
- assert.equal(2, treeData.children.length);
+ return dialog.setElementType(configuration.getReactionTypes()[0]);
})
});
- it('setElementType', function () {
- var dialog = new ChooseAnnotatorsDialog({
- element: testDiv,
- customMap: null
+ it('saveAnnotatorsInfo', function () {
+ var dialog = createDialog();
+ var user;
+ return ServerConnector.getLoggedUser().then(function (result) {
+ user = result;
+ return ServerConnector.getConfiguration();
+ }).then(function (configuration) {
+ var elementTypes = configuration.getElementTypes();
+ return dialog.saveAnnotatorsInfo(elementTypes, []);
});
- return ServerConnector.getConfiguration().then(function (configuration) {
- return dialog.setElementType(configuration.getReactionTypes()[0]);
- })
});
+ it('getAllChildrenTypesIfNeeded', function () {
+ var dialog = createDialog();
+ var configuration = helper.getConfiguration();
+ var elementTypes = configuration.getElementTypes();
+ var elementType;
+ for (var i = 0; i < elementTypes.length; i++) {
+ if (elementTypes[i].className === "lcsb.mapviewer.model.map.species.Protein") {
+ elementType = elementTypes[i];
+ }
+ }
+ assert.equal(1, dialog.getAllChildrenTypesIfNeeded(elementType, false).length);
+ assert.ok(dialog.getAllChildrenTypesIfNeeded(elementType, true).length >= 5);
+ });
});
diff --git a/frontend-js/src/test/js/gui/admin/ChooseValidatorsDialog-test.js b/frontend-js/src/test/js/gui/admin/ChooseValidatorsDialog-test.js
index ef96a952b42b83c668ae49e1f15afef37967b8d9..b92f7df9a55b821cb149554cf615923f9c926e58 100644
--- a/frontend-js/src/test/js/gui/admin/ChooseValidatorsDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/ChooseValidatorsDialog-test.js
@@ -19,21 +19,6 @@ describe('ChooseValidatorsDialog', function () {
return dialog.init();
});
- it('createElementTree', function () {
- var dialog = new ChooseValidatorsDialog({
- element: testDiv,
- customMap: null
- });
- return ServerConnector.getConfiguration().then(function (configuration) {
- var treeData = dialog.createElementTree(configuration);
-
- assert.ok(treeData);
- assert.ok(treeData.text);
- assert.ok(treeData.children);
- assert.equal(2, treeData.children.length);
- })
- });
-
it('setElementType', function () {
var dialog = new ChooseValidatorsDialog({
element: testDiv,
diff --git a/frontend-js/testFiles/apiCalls/users/anonymous.updatePreferences/PATCH_token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/users/anonymous.updatePreferences/PATCH_token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000000000000000000000000000000000..c194425b27770302c4302d9cb07dcb579ff46a44
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/users/anonymous.updatePreferences/PATCH_token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"preferences":{"annotators-parameters":{},"element-annotators":{"lcsb.mapviewer.model.map.BioEntity":[],"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.Compartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.OvalCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.PathwayCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.RightSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.SquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.compartment.TopSquareCompartment":["Gene Ontology"],"lcsb.mapviewer.model.map.reaction.Reaction":[],"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction":[],"lcsb.mapviewer.model.map.reaction.type.DissociationReaction":[],"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction":[],"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction":[],"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction":[],"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction":[],"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction":[],"lcsb.mapviewer.model.map.reaction.type.TranslationReaction":[],"lcsb.mapviewer.model.map.reaction.type.TransportReaction":[],"lcsb.mapviewer.model.map.reaction.type.TruncationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction":[],"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction":[],"lcsb.mapviewer.model.map.species.AntisenseRna":[],"lcsb.mapviewer.model.map.species.Chemical":["Chebi"],"lcsb.mapviewer.model.map.species.Complex":["Gene Ontology"],"lcsb.mapviewer.model.map.species.Degraded":[],"lcsb.mapviewer.model.map.species.Drug":[],"lcsb.mapviewer.model.map.species.Element":[],"lcsb.mapviewer.model.map.species.Gene":["HGNC"],"lcsb.mapviewer.model.map.species.GenericProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Ion":["Chebi"],"lcsb.mapviewer.model.map.species.IonChannelProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Phenotype":["Gene 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