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Commit 16434d54 authored by Piotr Gawron's avatar Piotr Gawron
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simple overlay panel functionality (general overlays)

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1 merge request!5Frontend refactor
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with 1090 additions and 14 deletions
frontend-js/src/main/js/gui/AbstractPanel.js → frontend-js/src/main/js/gui/AbstractDbPanel.js
+ 268
− 0
View file @ 16434d54
......@@ -4,20 +4,28 @@
var Promise = require("bluebird");
var GuiConnector= require('../GuiConnector');
var ObjectWithListeners = require('../ObjectWithListeners');
var Panel = require('./Panel');
var logger = require('../logger');
function AbstractPanel(params) {
ObjectWithListeners.call(this, params);
Panel.call(this, params);
var self = this;
this.setPanelName(params.panelName);
this.setElement(params.element);
this.setMap(params.customMap);
if (this.getNavElement() === undefined) {
throw new Error("No nav-tabs div found in the search panel element");
}
if (this.getContentElement() === undefined) {
throw new Error("No tab-content div found in the search panel element");
}
if (this.getSearchButton() === undefined) {
throw new Error("No searchButton found in the search panel element");
}
if (this.getSearchInput() === undefined) {
throw new Error("No searchInput found in the search panel element");
}
this.setOverlayDb (self.getMap().getOverlayByName(params.panelName));
......@@ -53,24 +61,9 @@ function AbstractPanel(params) {
this._tabIdCount = 0;
}
AbstractPanel.prototype = Object.create(ObjectWithListeners.prototype);
AbstractPanel.prototype = Object.create(Panel.prototype);
AbstractPanel.prototype.constructor = AbstractPanel;
AbstractPanel.prototype.disablePanel = function(message){
this.getSearchQueryElement().style.visibility ="hidden";
this.getSearchResultsElement().style.visibility ="hidden";
var hideReasonDiv = document.createElement("div");
hideReasonDiv.className="searchPanel";
var center = document.createElement("center");
var messageDiv = document.createElement("h4");
messageDiv .innerHTML=message;
center.appendChild(messageDiv);
hideReasonDiv.appendChild(center);
this.getElement().insertBefore(hideReasonDiv, this.getSearchQueryElement());
};
AbstractPanel.prototype.setOverlayDb = function(overlayDb){
if (overlayDb === undefined) {
throw new Error("Undefined overlayDb");
......@@ -82,173 +75,6 @@ AbstractPanel.prototype.getOverlayDb = function(){
return this._overlayDb;
};
AbstractPanel.prototype. createLabel=function(value) {
var result = document.createElement("span");
result.innerHTML = value;
result.className = "searchDescriptionLabel";
return result;
};
AbstractPanel.prototype.createPostTranslationalModifications = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
AbstractPanel.prototype.createCandidates=function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
AbstractPanel.prototype.createChebiTree=function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
AbstractPanel.prototype.createSeparator=function() {
var result = document.createElement("hr");
return result;
};
AbstractPanel.prototype.createNewLine=function(count) {
var result = document.createElement("p");
if (count > 0) {
result.style.height = ((count-1) * 10) + "px";
}
return result;
};
AbstractPanel.prototype.createLink=function(url, name) {
var link = document.createElement("a");
link.href = url;
link.innerHTML = name;
link.style.textDecoration = "underline";
return link;
};
AbstractPanel.prototype.createAnnotationLink=function(element, showType) {
var name, type, hint;
if (element.title!==undefined) {
hint = element.title+" "+element.authors.join(", ")+", "+element.year+", "+ element.journal;
type = "PUBMED";
name = element.id;
} else {
name = element.name;
type = element.type;
}
var link;
if (showType) {
link = this.createLink(element.link, type + " (" + name + ")");
} else {
link = this.createLink(element.link, name);
}
if (hint!==undefined) {
var div = document.createElement("div");
div.title = hint;
div.appendChild(link);
return div;
} else {
return link;
}
};
AbstractPanel.prototype.createAnnotations=function(label, value, options) {
var showType = true;
var inline = false;
if (options!== undefined) {
if (options.showType!==undefined) {
showType = options.showType;
}
if (options.inline!==undefined) {
inline = options.inline;
}
}
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
var self = this;
result.appendChild(self.createLabel(label));
if (!inline) {
result.appendChild(self.createNewLine());
}
for (var i = 0; i < value.length; i++) {
var element = value[i];
var link = this.createAnnotationLink(element, showType);
if (inline) {
if (i>0){
var coma = document.createElement("span");
coma.innerHTML = ", ";
result.appendChild(coma);
}
result.appendChild(link);
} else {
var row = document.createElement("div");
row.style.height = "26px";
if (i % 2 === 0) {
row.className = "annotationRowOdd";
} else {
row.className = "annotationRowEven";
}
var header = document.createElement("div");
header.style.width = "24px";
header.style.float = "left";
header.innerHTML = "[" + (i + 1) + "]";
row.appendChild(header);
var body = document.createElement("div");
body.style.float = "left";
body.appendChild(link);
row.appendChild(body);
result.appendChild(row);
}
}
}
return result;
};
AbstractPanel.prototype.setMap = function(map) {
this._map = map;
};
AbstractPanel.prototype.getMap = function() {
return this._map;
};
AbstractPanel.prototype.setPanelName = function(panelName) {
this._panelName = panelName;
};
AbstractPanel.prototype.getPanelName = function() {
return this._panelName;
};
AbstractPanel.prototype.setElement = function(element) {
if (element === undefined || element === null) {
throw new Error("DOM Element must be defined");
}
this._element = element;
if (this.getNavElement() === undefined) {
throw new Error("No nav-tabs div found in the search panel element");
}
if (this.getContentElement() === undefined) {
throw new Error("No tab-content div found in the search panel element");
}
if (this.getSearchButton() === undefined) {
throw new Error("No searchButton found in the search panel element");
}
if (this.getSearchInput() === undefined) {
throw new Error("No searchInput found in the search panel element");
}
};
AbstractPanel.prototype.getSearchQueryElement = function() {
var children = this.getElement().children;
for (var i = 0; i < children.length; i++) {
......@@ -283,23 +109,6 @@ AbstractPanel.prototype.getNavElement = function() {
}
};
AbstractPanel.prototype.getElementByName = function(element, name) {
if (element!==undefined) {
if (element.getAttribute("name") === name) {
return element;
}
var children = element.children;
for (var i=0;i<children.length;i++) {
var child = children[i];
var res = this.getElementByName(child, name);
if (res!==undefined) {
return res;
}
}
}
return undefined;
};
AbstractPanel.prototype.getSearchButton = function() {
return this.getElementByName(this.getSearchQueryElement(),"searchButton");
};
......@@ -322,10 +131,6 @@ AbstractPanel.prototype.getContentElement = function() {
}
};
AbstractPanel.prototype.getElement = function() {
return this._element;
};
AbstractPanel.prototype.clearResults = function() {
var navElement = this.getNavElement();
while (navElement.firstChild) {
......@@ -360,64 +165,6 @@ AbstractPanel.prototype.refreshSearchResults = function() {
};
AbstractPanel.prototype.createLabelText = function(value) {
var result = document.createElement("span");
if (value !== undefined) {
result.innerHTML = value;
}
return result;
};
AbstractPanel.prototype.createParamLine = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
var self = this;
result.appendChild(self.createLabel(label));
result.appendChild(self.createLabelText(value));
result.appendChild(self.createNewLine());
}
return result;
};
AbstractPanel.prototype.createIcon = function(icon) {
var result = document.createElement("div");
if (icon !== undefined && icon !== null) {
var img = document.createElement("img");
img.src=GuiConnector.getImgPrefix()+icon;
img.style.float="left";
img.hspace="5";
result.appendChild(img);
}
return result;
};
AbstractPanel.prototype.createArrayParamLine = function(label, value) {
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
var self = this;
result.appendChild(self.createLabel(label));
result.appendChild(self.createLabelText(value.join(",")));
result.appendChild(self.createNewLine());
}
return result;
};
AbstractPanel.prototype.createSubMapLink = function(label, element) {
var self = this;
var result = document.createElement("div");
if (element !== undefined) {
var button = document.createElement("button");
button.text = element.getModelId();
button.onclick = function() {
return self.getMap().openSubmodel(element.getModelId());
};
result.appendChild(this.createLabel("Submodel: "));
result.appendChild(button);
}
return result;
};
AbstractPanel.prototype.getAutocomplete = function() {
logger.warn("Get autocomplete not implemented");
};
......@@ -518,5 +265,4 @@ AbstractPanel.prototype.createTargetRow = function(target, icon) {
return result;
};
module.exports = AbstractPanel;
frontend-js/src/main/js/gui/ChemicalPanel.js
+ 3
− 3
View file @ 16434d54
......@@ -3,17 +3,17 @@
/* exported logger */
var logger = require('../logger');
var AbstractPanel = require('./AbstractPanel');
var AbstractDbPanel = require('./AbstractDbPanel');
function ChemicalPanel(params) {
params.panelName = "chemical";
AbstractPanel.call(this, params);
AbstractDbPanel.call(this, params);
if (params.disease===undefined) {
this.disablePanel("DISEASE NOT DEFINED FOR PROJECT. PLEASE, DEFINE IT IN THE ADMIN SECTION.");
}
}
ChemicalPanel.prototype = Object.create(AbstractPanel.prototype);
ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
ChemicalPanel.prototype.constructor = ChemicalPanel;
ChemicalPanel.prototype.createPreamble = function(chemical) {
......
frontend-js/src/main/js/gui/DrugPanel.js
+ 3
− 3
View file @ 16434d54
......@@ -3,13 +3,13 @@
/* exported logger */
var logger = require('../logger');
var AbstractPanel = require('./AbstractPanel');
var AbstractDbPanel = require('./AbstractDbPanel');
function DrugPanel(params) {
params.panelName = "drug";
AbstractPanel.call(this, params);
AbstractDbPanel.call(this, params);
}
DrugPanel.prototype = Object.create(AbstractPanel.prototype);
DrugPanel.prototype = Object.create(AbstractDbPanel.prototype);
DrugPanel.prototype.constructor = DrugPanel;
DrugPanel.prototype.createPreamble = function(drug) {
......
frontend-js/src/main/js/gui/MiRnaPanel.js
+ 3
− 3
View file @ 16434d54
......@@ -3,13 +3,13 @@
/* exported logger */
var logger = require('../logger');
var AbstractPanel = require('./AbstractPanel');
var AbstractDbPanel = require('./AbstractDbPanel');
function MiRnaPanel(params) {
params.panelName = "mirna";
AbstractPanel.call(this, params);
AbstractDbPanel.call(this, params);
}
MiRnaPanel.prototype = Object.create(AbstractPanel.prototype);
MiRnaPanel.prototype = Object.create(AbstractDbPanel.prototype);
MiRnaPanel.prototype.constructor = MiRnaPanel;
MiRnaPanel.prototype.createPreamble = function(miRna) {
......
frontend-js/src/main/js/gui/OverlayPanel.js 0 → 100644
+ 189
− 0
View file @ 16434d54
"use strict";
/* exported logger */
var Panel = require('./Panel');
var logger = require('../logger');
function OverlayPanel(params) {
params.panelName = "overlays";
Panel.call(this, params);
var self = this;
self.setPanelName(params.panelName);
self.setElement(params.element);
self.setMap(params.customMap);
self.refresh();
}
OverlayPanel.prototype = Object.create(Panel.prototype);
OverlayPanel.prototype.constructor = OverlayPanel;
OverlayPanel.prototype.clear = function() {
var table = this.getGeneralOverlaysTabElement();
while (table.firstChild) {
table.removeChild(table.firstChild);
}
table = this.getCustomOverlaysTabElement();
while (table.firstChild) {
table.removeChild(table.firstChild);
}
};
OverlayPanel.prototype.createTableHeader = function(edit) {
var result = document.createElement("thead");
var row = document.createElement("tr");
var nameTd = document.createElement("th");
nameTd.innerHTML = "Name";
row.appendChild(nameTd);
var viewTd = document.createElement("th");
viewTd.innerHTML = "View";
row.appendChild(viewTd);
var dataTd = document.createElement("th");
dataTd.innerHTML = "Data";
row.appendChild(dataTd);
if (edit) {
var editTd = document.createElement("th");
editTd.innerHTML = "Edit";
row.appendChild(editTd);
}
result.appendChild(row);
return result;
};
OverlayPanel.prototype.createOverlayRow = function(overlay, checked) {
var self = this;
var result = document.createElement("tr");
if (checked) {
result.className = "active";
}
var nameTd = document.createElement("td");
nameTd.innerHTML = overlay.getName();
result.appendChild(nameTd);
var viewTd = document.createElement("td");
if (overlay.getInputDataAvailable()) {
var checkbox = document.createElement("input");
checkbox.type = "checkbox";
checkbox.checked = checked;
checkbox.onclick = function() {
if (this.checked) {
self.getMap().addSelectedLayout(overlay.getId());
} else {
self.getMap().removeSelectedLayout(overlay.getId());
}
};
viewTd.appendChild(checkbox);
} else {
var img = this.createIcon("icons/search.png");
var link = document.createElement("a");
link.href = "#";
link.onclick = function() {
self.getMap().openLayoutById(overlay.getId());
$(result).addClass('active').siblings().removeClass('active');
};
link.appendChild(img);
viewTd.appendChild(link);
}
result.appendChild(viewTd);
var dataTd = document.createElement("td");
if (overlay.getInputDataAvailable()) {
var button = document.createElement("button");
button.onclick = function() {
throw new Error("Not implemented");
};
dataTd.appendChild(button);
}
result.appendChild(dataTd);
if (overlay.getCreator() !== "" && overlay.getCreator() !== undefined) {
var editTd = document.createElement("td");
var editButton = document.createElement("button");
editButton.onclick = function() {
throw new Error("Not implemented");
};
editTd.appendChild(editButton);
result.appendChild(editTd);
}
return result;
};
OverlayPanel.prototype.refresh = function() {
var self = this;
return ServerConnector.getOverlays().then(function(customOverlays) {
var selectedOverlayIds = self.getMap().getSelectedLayouts();
var selectedOverlay = [];
for (var j = 0; j < selectedOverlayIds.length; j++) {
selectedOverlay[selectedOverlayIds[j]] = true;
}
var id = self.getMap().getGoogleMap().getMapTypeId().substring(2);
selectedOverlay[id] = true;
self.clear();
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 table = self.getGeneralOverlaysTabElement();
table.appendChild(self.createTableHeader());
var body = document.createElement("tbody");
table.appendChild(body);
for (i = 0; i < generalOverlays.length; i++) {
overlay = generalOverlays[i];
body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
}
table = self.getCustomOverlaysTabElement();
table.appendChild(self.createTableHeader(true));
body = document.createElement("tbody");
table.appendChild(body);
for (i = 0; i < customOverlays.length; i++) {
overlay = customOverlays[i];
body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()]));
}
return null;
});
};
OverlayPanel.prototype.getGeneralOverlaysElement = function() {
return this.getElementByName(this.getElement(), "generalOverlays");
};
OverlayPanel.prototype.getGeneralOverlaysTabElement = function() {
return this.getElementByName(this.getElement(), "generalOverlaysTab");
};
OverlayPanel.prototype.getCustomOverlaysElement = function() {
return this.getElementByName(this.getElement(), "customOverlays");
};
OverlayPanel.prototype.getCustomOverlaysTabElement = function() {
return this.getElementByName(this.getElement(), "customOverlaysTab");
};
module.exports = OverlayPanel;
frontend-js/src/main/js/gui/Panel.js 0 → 100644
+ 270
− 0
View file @ 16434d54
"use strict";
/* exported logger */
var GuiConnector = require('../GuiConnector');
var ObjectWithListeners = require('../ObjectWithListeners');
var logger = require('../logger');
function Panel(params) {
ObjectWithListeners.call(this, params);
var self = this;
self.setPanelName(params.panelName);
self.setElement(params.element);
self.setMap(params.customMap);
}
Panel.prototype = Object.create(ObjectWithListeners.prototype);
Panel.prototype.constructor = Panel;
Panel.prototype.disablePanel = function(message) {
this.getSearchQueryElement().style.visibility = "hidden";
this.getSearchResultsElement().style.visibility = "hidden";
var hideReasonDiv = document.createElement("div");
hideReasonDiv.className = "searchPanel";
var center = document.createElement("center");
var messageDiv = document.createElement("h4");
messageDiv.innerHTML = message;
center.appendChild(messageDiv);
hideReasonDiv.appendChild(center);
this.getElement().insertBefore(hideReasonDiv, this.getSearchQueryElement());
};
Panel.prototype.createLabel = function(value) {
var result = document.createElement("span");
result.innerHTML = value;
result.className = "searchDescriptionLabel";
return result;
};
Panel.prototype.createPostTranslationalModifications = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
Panel.prototype.createCandidates = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
Panel.prototype.createChebiTree = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
throw new Error("Not implemented");
}
return result;
};
Panel.prototype.createSeparator = function() {
var result = document.createElement("hr");
return result;
};
Panel.prototype.createNewLine = function(count) {
var result = document.createElement("p");
if (count > 0) {
result.style.height = ((count - 1) * 10) + "px";
}
return result;
};
Panel.prototype.createLink = function(url, name) {
var link = document.createElement("a");
link.href = url;
link.innerHTML = name;
link.style.textDecoration = "underline";
return link;
};
Panel.prototype.createAnnotationLink = function(element, showType) {
var name, type, hint;
if (element.title !== undefined) {
hint = element.title + " " + element.authors.join(", ") + ", " + element.year + ", " + element.journal;
type = "PUBMED";
name = element.id;
} else {
name = element.name;
type = element.type;
}
var link;
if (showType) {
link = this.createLink(element.link, type + " (" + name + ")");
} else {
link = this.createLink(element.link, name);
}
if (hint !== undefined) {
var div = document.createElement("div");
div.title = hint;
div.appendChild(link);
return div;
} else {
return link;
}
};
Panel.prototype.createAnnotations = function(label, value, options) {
var showType = true;
var inline = false;
if (options !== undefined) {
if (options.showType !== undefined) {
showType = options.showType;
}
if (options.inline !== undefined) {
inline = options.inline;
}
}
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
var self = this;
result.appendChild(self.createLabel(label));
if (!inline) {
result.appendChild(self.createNewLine());
}
for (var i = 0; i < value.length; i++) {
var element = value[i];
var link = this.createAnnotationLink(element, showType);
if (inline) {
if (i > 0) {
var coma = document.createElement("span");
coma.innerHTML = ", ";
result.appendChild(coma);
}
result.appendChild(link);
} else {
var row = document.createElement("div");
row.style.height = "26px";
if (i % 2 === 0) {
row.className = "annotationRowOdd";
} else {
row.className = "annotationRowEven";
}
var header = document.createElement("div");
header.style.width = "24px";
header.style.float = "left";
header.innerHTML = "[" + (i + 1) + "]";
row.appendChild(header);
var body = document.createElement("div");
body.style.float = "left";
body.appendChild(link);
row.appendChild(body);
result.appendChild(row);
}
}
}
return result;
};
Panel.prototype.setMap = function(map) {
this._map = map;
};
Panel.prototype.getMap = function() {
return this._map;
};
Panel.prototype.setPanelName = function(panelName) {
this._panelName = panelName;
};
Panel.prototype.getPanelName = function() {
return this._panelName;
};
Panel.prototype.setElement = function(element) {
if (element === undefined || element === null) {
throw new Error("DOM Element must be defined");
}
this._element = element;
};
Panel.prototype.getElement = function() {
return this._element;
};
Panel.prototype.createLabelText = function(value) {
var result = document.createElement("span");
if (value !== undefined) {
result.innerHTML = value;
}
return result;
};
Panel.prototype.createParamLine = function(label, value) {
var result = document.createElement("div");
if (value !== undefined) {
var self = this;
result.appendChild(self.createLabel(label));
result.appendChild(self.createLabelText(value));
result.appendChild(self.createNewLine());
}
return result;
};
Panel.prototype.createIcon = function(icon) {
var result = document.createElement("div");
if (icon !== undefined && icon !== null) {
var img = document.createElement("img");
img.src = GuiConnector.getImgPrefix() + icon;
img.style.float = "left";
img.hspace = "5";
result.appendChild(img);
}
return result;
};
Panel.prototype.createArrayParamLine = function(label, value) {
var result = document.createElement("div");
if (value !== undefined && value.length > 0) {
var self = this;
result.appendChild(self.createLabel(label));
result.appendChild(self.createLabelText(value.join(",")));
result.appendChild(self.createNewLine());
}
return result;
};
Panel.prototype.createSubMapLink = function(label, element) {
var self = this;
var result = document.createElement("div");
if (element !== undefined) {
var button = document.createElement("button");
button.text = element.getModelId();
button.onclick = function() {
return self.getMap().openSubmodel(element.getModelId());
};
result.appendChild(this.createLabel("Submodel: "));
result.appendChild(button);
}
return result;
};
Panel.prototype.getElementByName = function(element, name) {
if (element!==undefined) {
if (element.getAttribute("name") === name) {
return element;
}
var children = element.children;
for (var i=0;i<children.length;i++) {
var child = children[i];
var res = this.getElementByName(child, name);
if (res!==undefined) {
return res;
}
}
}
return undefined;
};
module.exports = Panel;
frontend-js/src/main/js/gui/SearchPanel.js
+ 3
− 3
View file @ 16434d54
......@@ -2,21 +2,21 @@
/* exported logger */
var AbstractPanel = require('./AbstractPanel');
var AbstractDbPanel = require('./AbstractDbPanel');
var Alias = require('../map/data/Alias');
var Reaction = require('../map/data/Reaction');
var logger = require('../logger');
function SearchPanel(params) {
params.panelName = "search";
AbstractPanel.call(this, params);
AbstractDbPanel.call(this, params);
if (this.getSearchPerfectMatch() === undefined) {
throw new Error("No searchPerfectMatch found in the search panel element");
}
}
SearchPanel.prototype = Object.create(AbstractPanel.prototype);
SearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
SearchPanel.prototype.constructor = SearchPanel;
SearchPanel.prototype.getSearchPerfectMatch = function() {
......
frontend-js/src/main/js/map/data/LayoutData.js
+ 9
− 0
View file @ 16434d54
......@@ -20,6 +20,7 @@ function LayoutData(layoutId, name) {
this.setId(object.idObject);
this.setName(object.name);
this.setDirectory(object.directory);
this.setCreator(object.creator);
this.setInputDataAvailable(object.inputDataAvailable);
} else {
// default two param call
......@@ -60,6 +61,14 @@ LayoutData.prototype.setId = function(id) {
this.id = parseInt(id);
};
LayoutData.prototype.getCreator = function() {
return this._creator;
};
LayoutData.prototype.setCreator = function(creator) {
this._creator = creator;
};
LayoutData.prototype.getInputDataAvailable = function() {
return this._inputDataAvailable;
};
......
frontend-js/src/main/js/minerva.js
+ 6
− 0
View file @ 16434d54
......@@ -12,6 +12,7 @@ var DrugDbOverlay = require('./map/overlay/DrugDbOverlay');
var DrugPanel = require('./gui/DrugPanel');
var MiRnaDbOverlay = require('./map/overlay/MiRnaDbOverlay');
var MiRnaPanel = require('./gui/MiRnaPanel');
var OverlayPanel = require('./gui/OverlayPanel');
var SearchDbOverlay = require('./map/overlay/SearchDbOverlay');
var SearchPanel = require('./gui/SearchPanel');
......@@ -169,6 +170,11 @@ function create(params) {
logger.warn("No overlay collection defined");
}
new OverlayPanel({
element : document.getElementById("overlayTab"),
customMap : result
});
return new Promise(function(resolve, reject) {
restoreSearchQuery(result).then(function(){
......
frontend-js/src/test/js/gui/OverlayPanel-test.js 0 → 100644
+ 48
− 0
View file @ 16434d54
"use strict";
var Helper = require('../helper');
require("../mocha-config.js");
var OverlayPanel = require('../../../main/js/gui/OverlayPanel');
var chai = require('chai');
var assert = chai.assert;
var logger = require('../logger');
describe('OverlayPanel', function() {
var helper;
before(function() {
helper = new Helper();
});
it('contructor', function() {
var div = helper.createOverlayTab();
var map = helper.createCustomMap();
new OverlayPanel({
element : div,
customMap : map
});
assert.equal(logger.getWarnings().length, 0);
});
it('refresh', function() {
var div = helper.createOverlayTab();
var map = helper.createCustomMap();
var panel = new OverlayPanel({
element : div,
customMap : map
});
return panel.refresh().then(function(){
assert.ok(panel.getElement().innerHTML.indexOf("testLayout")>=0);
});
});
});
frontend-js/src/test/js/helper.js
+ 22
− 0
View file @ 16434d54
......@@ -79,6 +79,28 @@ Helper.prototype.createPanelTab = function(id) {
return result;
};
Helper.prototype.createOverlayTab = function() {
var result = document.createElement("div");
result.id = "overlayTab";
var generalOverlaysDiv = document.createElement("div");
generalOverlaysDiv.setAttribute("name", "generalOverlays");
result.appendChild(generalOverlaysDiv);
var generalOverlaysTabDiv = document.createElement("table");
generalOverlaysTabDiv.setAttribute("name", "generalOverlaysTab");
generalOverlaysDiv.appendChild(generalOverlaysTabDiv);
var customOverlaysDiv = document.createElement("div");
customOverlaysDiv.setAttribute("name", "customOverlays");
result.appendChild(customOverlaysDiv);
var customOverlaysTabDiv = document.createElement("table");
customOverlaysTabDiv.setAttribute("name", "customOverlaysTab");
customOverlaysDiv.appendChild(customOverlaysTabDiv);
return result;
};
Helper.prototype.createCommentDbOverlay = function(map) {
var result = new CommentDbOverlay({
map : map,
......
frontend-js/src/test/js/minerva-test.js
+ 4
− 0
View file @ 16434d54
......@@ -29,6 +29,9 @@ describe('minerva global', function() {
global.mirnaTab = helper.createMiRnaTab();
document.body.appendChild(global.mirnaTab);
global.overlayTab = helper.createOverlayTab();
document.body.appendChild(global.overlayTab);
});
afterEach(function() {
......@@ -36,6 +39,7 @@ describe('minerva global', function() {
document.body.removeChild(global.drugTab);
document.body.removeChild(global.chemicalTab);
document.body.removeChild(global.mirnaTab);
document.body.removeChild(global.overlayTab);
});
it('create', function() {
......
rest-api/src/main/java/lcsb/mapviewer/api/controller/UserController.java
+ 27
− 0
View file @ 16434d54
......@@ -25,6 +25,9 @@ public class UserController extends BaseController {
@Autowired
private IUserService userService;
@Autowired
private UserRestImpl userRest;
@RequestMapping(value = "/login", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
public AuthenticationToken login(@RequestParam(value = "login", defaultValue = Configuration.ANONYMOUS_LOGIN) String login,
@RequestParam(value = "password", required = false) String password) {
......@@ -37,6 +40,13 @@ public class UserController extends BaseController {
return userService.getToken(token);
}
@RequestMapping(value = "/getUser", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
public Map<String, Object> getUser(@RequestParam(value = "token", required = false) String token,
@RequestParam(value = "userId", defaultValue = "") String userId,
@RequestParam(value = "columns", defaultValue = "") String columns) throws SecurityException {
return userRest.getUser(token, userId, columns);
}
@RequestMapping(value = "/logout", method = { RequestMethod.GET, RequestMethod.POST }, produces = { MediaType.APPLICATION_JSON_VALUE })
public Map<String, String> logout(@RequestParam(value = "token", required = false) String token) throws SecurityException {
userService.logout(token);
......@@ -61,4 +71,21 @@ public class UserController extends BaseController {
public void setUserService(IUserService userService) {
this.userService = userService;
}
/**
* @return the userRest
* @see #userRest
*/
public UserRestImpl getUserRest() {
return userRest;
}
/**
* @param userRest
* the userRest to set
* @see #userRest
*/
public void setUserRest(UserRestImpl userRest) {
this.userRest = userRest;
}
}
\ No newline at end of file
rest-api/src/main/java/lcsb/mapviewer/api/controller/UserRestImpl.java 0 → 100644
+ 177
− 0
View file @ 16434d54
package lcsb.mapviewer.api.controller;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.user.BasicPrivilege;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.interfaces.IUserService;
@Transactional(value = "txManager")
public class UserRestImpl {
@Autowired
private IUserService userService;
@Autowired
private ILayoutService layoutService;
/**
* @return the userService
* @see #userService
*/
public IUserService getUserService() {
return userService;
}
/**
* @param userService
* the userService to set
* @see #userService
*/
public void setUserService(IUserService userService) {
this.userService = userService;
}
public Map<String, Object> getUser(String token, String userId, String columns) throws SecurityException {
User ownUserData = userService.getUserByToken(token);
Integer id = null;
if (userId != null && !userId.isEmpty()) {
id = Integer.valueOf(userId);
} else {
id = ownUserData.getId();
}
Set<String> columnSet = createUserColumnSet(columns);
boolean isAdmin = userService.userHasPrivilege(ownUserData, PrivilegeType.USER_MANAGEMENT);
if (ownUserData.getId().equals(id)) {
return prepareUse(ownUserData, columnSet, true);
} else if (isAdmin) {
User user = userService.getUserById(id);
if (user == null) {
throw new SecurityException("You cannot access data of the user with given id");
}
return prepareUse(user, columnSet, isAdmin);
} else {
throw new SecurityException("You cannot access data of the user with given id");
}
}
private Set<String> createUserColumnSet(String columns) {
Set<String> columnsSet = new HashSet<>();
if (columns.equals("")) {
columnsSet.add("id");
columnsSet.add("login");
columnsSet.add("name");
columnsSet.add("surname");
columnsSet.add("email");
columnsSet.add("minColor");
columnsSet.add("maxColor");
columnsSet.add("removed");
columnsSet.add("privileges");
} else {
for (String str : columns.split(",")) {
columnsSet.add(str);
}
}
return columnsSet;
}
private Map<String, Object> prepareUse(User user, Set<String> columnsSet, boolean admin) {
Map<String, Object> result = new HashMap<>();
for (String string : columnsSet) {
String column = string.toLowerCase();
Object value = null;
if (column.equals("id") || column.equals("idobject")) {
value = user.getId();
} else if (column.equals("name")) {
value = user.getName();
} else if (column.equals("surname")) {
value = user.getSurname();
} else if (column.equals("login")) {
value = user.getLogin();
} else if (column.equals("email")) {
value = user.getEmail();
} else if (column.equals("mincolor")) {
value = user.getMinColor();
} else if (column.equals("maxcolor")) {
value = user.getMaxColor();
} else if (column.equals("removed")) {
value = user.isRemoved();
} else if (column.equals("privileges") && admin) {
value = preparePrivileges(user);
} else {
value = "Unknown column";
}
result.put(string, value);
}
return result;
}
private List<Map<String, Object>> preparePrivileges(User user) {
List<Map<String, Object>> result = new ArrayList<>();
for (BasicPrivilege privilege : user.getPrivileges()) {
if (privilege instanceof ObjectPrivilege) {
result.add(prepareObjectPrivilege((ObjectPrivilege) privilege));
} else {
result.add(prepareBasicPrivilege(privilege));
}
}
Map<String, Object> customLayouts = new HashMap<>();
customLayouts.put("type", "CUSTOM_LAYOUTS_AVAILABLE");
customLayouts.put("value", layoutService.getAvailableCustomLayoutsNumber(user));
result.add(customLayouts);
return result;
}
private Map<String, Object> prepareObjectPrivilege(ObjectPrivilege privilege) {
Map<String, Object> result = new HashMap<>();
result.put("type", privilege.getType());
result.put("value", privilege.getLevel());
result.put("objectId", privilege.getIdObject());
return result;
}
private Map<String, Object> prepareBasicPrivilege(BasicPrivilege privilege) {
Map<String, Object> result = new HashMap<>();
if (privilege.getClass().equals(BasicPrivilege.class)) {
result.put("type", privilege.getType());
result.put("value", privilege.getLevel());
return result;
} else {
throw new InvalidArgumentException("Don't know how to handle class: " + privilege.getClass());
}
}
/**
* @return the layoutService
* @see #layoutService
*/
public ILayoutService getLayoutService() {
return layoutService;
}
/**
* @param layoutService
* the layoutService to set
* @see #layoutService
*/
public void setLayoutService(ILayoutService layoutService) {
this.layoutService = layoutService;
}
}
rest-api/src/main/resources/applicationContext-rest.xml
+ 1
− 0
View file @ 16434d54
......@@ -18,5 +18,6 @@
<bean id="MiRnaRestImpl" class="lcsb.mapviewer.api.mirna.MiRnaRestImpl"/>
<bean id="OverlayRestImpl" class="lcsb.mapviewer.api.overlay.OverlayRestImpl"/>
<bean id="ProjectRestImpl" class="lcsb.mapviewer.api.project.ProjectRestImpl"/>
<bean id="UserRestImpl" class="lcsb.mapviewer.api.controller.UserRestImpl"/>
</beans>
\ No newline at end of file
rest-api/src/test/java/lcsb/mapviewer/api/AllRestTests.java
+ 3
− 1
View file @ 16434d54
......@@ -5,11 +5,13 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
import lcsb.mapviewer.api.comment.AllCommentTests;
import lcsb.mapviewer.api.controller.AllUserTests;
import lcsb.mapviewer.api.project.AllProjectTests;
@RunWith(Suite.class)
@SuiteClasses({ AllCommentTests.class, //
AllProjectTests.class,//
AllProjectTests.class, //
AllUserTests.class,//
})
public class AllRestTests {
......
rest-api/src/test/java/lcsb/mapviewer/api/controller/AllUserTests.java 0 → 100644
+ 11
− 0
View file @ 16434d54
package lcsb.mapviewer.api.controller;
import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ UserRestImplTest.class })
public class AllUserTests {
}
rest-api/src/test/java/lcsb/mapviewer/api/controller/UserRestImplTest.java 0 → 100644
+ 43
− 0
View file @ 16434d54
package lcsb.mapviewer.api.controller;
import static org.junit.Assert.assertNotNull;
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.api.RestTestFunctions;
public class UserRestImplTest extends RestTestFunctions {
Logger logger = Logger.getLogger(UserRestImplTest.class);
@Autowired
UserRestImpl userRestImpl;
@AfterClass
public static void tearDownAfterClass() throws Exception {
}
@Before
public void setUp() throws Exception {
}
@After
public void tearDown() throws Exception {
}
@Test
public void test() throws Exception {
try {
Object response = userRestImpl.getUser(token.getId(), "", "");
assertNotNull(response);
} catch (Exception e) {
e.printStackTrace();
throw e;
}
}
}
web/src/main/webapp/index.xhtml
+ 0
− 1
View file @ 16434d54
......@@ -50,7 +50,6 @@ function initMap(){
dataCollections: [
{name: "search"},
{name: "missingConnection"},
{name: "drug", allowSearchById:true, allowGeneralSearch: true},
{name: "chemical", allowSearchById:#{chemicalMB.linkedToDisease()}, allowGeneralSearch: #{chemicalMB.linkedToDisease() == true}},
{name: "mirna", allowSearchById:true, allowGeneralSearch: true},
......
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