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Commit c337bf43 authored by Piotr Gawron's avatar Piotr Gawron
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copying annotators settings from other elemnts in tree and applying settings to subtree added

parent fef90d5e
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frontend-js/package-lock.json
View file @ c337bf43
......@@ -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": "15.6.15",
"@types/react-dom": "15.5.7"
}
},
"lodash": {
"version": "4.17.4",
"resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.4.tgz",
......
frontend-js/src/main/js/ServerConnector.js
View file @ c337bf43
......@@ -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;
}
......
frontend-js/src/main/js/gui/admin/AddProjectDialog.js
View file @ c337bf43
......@@ -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 {
......
frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
View file @ c337bf43
......@@ -62,15 +62,53 @@ function onChangeParameterValue(element, user) {
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);
......@@ -81,6 +119,52 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (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);
......@@ -90,7 +174,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var entries = [];
for (var i = 0; i < annotators.length; i++) {
for (i = 0; i < annotators.length; i++) {
var annotator = annotators[i];
var entry = {name: annotator.getName(), value: annotator.getClassName(), selected: false};
for (var j = 0; j < selectedAnnotators.length; j++) {
......@@ -115,9 +199,6 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
annotator = annotators[i];
}
}
var data = new UserPreferences();
var elementAnnotators = {};
if (selected) {
selectedAnnotators.push(annotator.getName());
} else {
......@@ -127,13 +208,12 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
}
}
createAnnotatorsParams();
elementAnnotators[elementType.className] = selectedAnnotators;
data.setElementAnnotators(elementAnnotators);
return ServerConnector.updateUserPreferences({
user: user,
preferences: data
}).then(null, GuiConnector.alert);
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);
};
checkboxList.addListener("select", function (element) {
......@@ -295,7 +375,7 @@ ChooseAnnotatorsDialog.prototype.open = function () {
});
}
$(div).dialog("open");
$(div).css("overflow","hidden");
$(div).css("overflow", "hidden");
};
module.exports = ChooseAnnotatorsDialog;
frontend-js/src/main/js/map/data/UserPreferences.js
View file @ c337bf43
......@@ -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;
};
......
frontend-js/src/test/js/gui/admin/ChooseAnnotatorsDialog-test.js
View file @ c337bf43
......@@ -10,23 +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('setElementType', function () {
var dialog = new ChooseAnnotatorsDialog({
element: testDiv,
customMap: null
});
var dialog = createDialog();
return ServerConnector.getConfiguration().then(function (configuration) {
return dialog.setElementType(configuration.getReactionTypes()[0]);
})
});
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, []);
});
});
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);
});
});
frontend-js/testFiles/apiCalls/users/anonymous.updatePreferences/PATCH_token=MOCK_TOKEN_ID& 0 → 100644
View file @ c337bf43
{"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 Ontology"],"lcsb.mapviewer.model.map.species.Protein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.ReceptorProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Rna":["HGNC"],"lcsb.mapviewer.model.map.species.SimpleMolecule":["Chebi"],"lcsb.mapviewer.model.map.species.Species":[],"lcsb.mapviewer.model.map.species.TruncatedProtein":["Biocompendium","HGNC"],"lcsb.mapviewer.model.map.species.Unknown":[]},"element-required-annotations":{"lcsb.mapviewer.model.map.BioEntity":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.BottomSquareCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.Compartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.LeftSquareCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.OvalCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.PathwayCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.RightSquareCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.SquareCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.compartment.TopSquareCompartment":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.Reaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.DissociationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.ReducedTriggerReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.TranslationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.TransportReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.TruncationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownReducedPhysicalStimulationReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownReducedTriggerReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction":{"annotation-list":["PUBMED"],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.AntisenseRna":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Chemical":{"annotation-list":["CHEBI","PUBCHEM","PUBCHEM_SUBSTANCE"],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Complex":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Degraded":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Drug":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Element":{"annotation-list":[],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Gene":{"annotation-list":["HGNC","HGNC_SYMBOL"],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.GenericProtein":{"annotation-list":["HGNC","HGNC_SYMBOL"],"require-at-least-one":true},"lcsb.mapviewer.model.map.species.Ion":{"annotation-list":["CHEBI","PUBCHEM","PUBCHEM_S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\ No newline at end of file
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