js.dataexplorer.js Maven / Gradle / Ivy
$.when( $,
window.top.molgenis = window.top.molgenis || {},
molgenis.getPluginSettings()
).then(
function($, molgenis, settingsXhr) {
"use strict";
var self = molgenis.dataexplorer = molgenis.dataexplorer || {};
// module api
self.getSelectedEntityMeta = getSelectedEntityMeta;
self.getSelectedAttributes = getSelectedAttributes;
self.getSelectedAttributesTree = getSelectedAttributesTree;
self.getEntityQuery = getEntityQuery;
self.createHeader = createHeader;
self.setGenomeAttributes = setGenomeAttributes;
self.getPosAttribute = getPosAttribute;
self.getChromosomeAttribute = getChromosomeAttribute;
self.getIdentifierAttribute = getIdentifierAttribute;
self.getPatientAttribute = getPatientAttribute;
self.getSelectedModule = getSelectedModule;
var restApi = new molgenis.RestClient();
var selectedEntityMetaData = null;
var attributeFilters = {};
var selectedAttributes = [];
var selectedAttributesTree = {};
var searchQuery = null;
var modules = [];
var posAttribute;
var chromosomeAttribute;
var identifierAttribute;
var patientAttribute;
if(settingsXhr[1] !== 'success') {
molgenis.createAlert([{message: 'An error occurred initializing the data explorer.'}], 'error');
}
var settings = settingsXhr[0];
self.settings = settings;
var stateDefault = {
entity: null,
query: null,
attrs: null,
mod: null,
hideselect: 'false'
};
var state;
/**
* @memberOf molgenis.dataexplorer
*/
function getSelectedModule() {
return state.mod;
}
/**
* @memberOf molgenis.dataexplorer
*/
function getSelectedEntityMeta() {
return selectedEntityMetaData;
}
/**
* @memberOf molgenis.dataexplorer
*/
function getSelectedAttributes() {
return selectedAttributes;
}
/**
* @memberOf molgenis.dataexplorer
*/
function getSelectedAttributesTree() {
return selectedAttributesTree;
}
/**
* @memberOf molgenis.dataexplorer
*/
function getEntityQuery() {
// N.B. There's a translation step between the query in the state, which is also shown on screen
// ("SEARCH 1:10050001") and the actual entity query which is used when retrieving data
// (CHROM = 1 AND POS = 1005001)
// So here we should return the *translated* query.
return createEntityQuery();
}
/**
* @memberOf molgenis.dataexplorer
*/
function createModuleNav(modules, entity, container) {
var items = [];
items.push('');
$.each(modules, function() {
var href = molgenis.getContextUrl() + '/module/' + this.id+'?entity=' + entity;
items.push('
' + this.label + '- ');
items.push('
');
items.push('
');
items.push('');
$.each(modules, function() {
items.push('Loading...');
});
items.push('');
// add menu to container
container.html(items.join(''));
}
/**
* @memberOf molgenis.dataexplorer
*/
function createEntityMetaTree(entityMetaData, attributes) {
var container = $('#feature-selection');
container.tree({
'entityMetaData' : entityMetaData,
'selectedAttributes' : attributes,
'onAttributesSelect' : function(selects) {
selectedAttributes = container.tree('getSelectedAttributes');
selectedAttributesTree = container.tree('getSelectedAttributesTree')
$(document).trigger('changeAttributeSelection', {
'attributes' : selectedAttributes,
'attributesTree' : selectedAttributesTree,
'totalNrAttributes' : Object.keys(entityMetaData.attributes).length
});
},
'onAttributeClick' : function(attribute) {
$(document).trigger('clickAttribute', {'attribute': attribute});
}
});
}
/**
* @memberOf molgenis.dataexplorer
*/
function createHeader(entityMetaData) {
$('#entity-class-name').html(entityMetaData.label);
if (entityMetaData.description) {
var description = $('');
description.html(abbreviate(entityMetaData.description, settings['header_abbreviate']));
description.attr('data-title', entityMetaData.description);
$('#entity-class-description').html(description.tooltip());
} else {
$('#entity-class-description').html('');
}
}
function getAttributeFromList(attributesString){
var result;
var attrs = getSelectedEntityMeta().attributes;
var list = attributesString.split(",");
for(var item in list){
result = attrs[list[item]];
if(result !== undefined){
break;
}
}
return result;
}
/**
* @memberOf molgenis.dataexplorer
*/
function setGenomeAttributes(start, chromosome, id, patient){
posAttribute = getAttributeFromList(start);
chromosomeAttribute = getAttributeFromList(chromosome);
identifierAttribute = getAttributeFromList(id);
patientAttribute = getAttributeFromList(patient);
}
function getPosAttribute(){return posAttribute};
function getChromosomeAttribute(){return chromosomeAttribute};
function getIdentifierAttribute(){return identifierAttribute};
function getPatientAttribute(){return patientAttribute};
/**
* @memberOf molgenis.dataexplorer
*/
function createEntityQuery() {
var entityCollectionRequest = {
q : []
};
// add rules for the search term to the query
if (searchQuery) {
if (/\S/.test(searchQuery)) {
var searchQueryRegex = /^\s*(?:chr)?([\d]{1,2}|X|Y|MT|XY):([\d]+)(?:-([\d]+)+)?\s*$/g;
if(searchQueryRegex && searchQuery.match(searchQueryRegex) && chromosomeAttribute !== undefined && posAttribute !== undefined) {
var match = searchQueryRegex.exec(searchQuery);
// only chromosome and position
if(match[3] === undefined){
var chromosome = match[1];
var position = match[2];
entityCollectionRequest.q =
[{
operator: "NESTED",
nestedRules: [{
field: chromosomeAttribute.name,
operator: "EQUALS",
value: chromosome
}]
}, {
operator: "AND"
}, {
operator: "NESTED",
nestedRules: [{
field: posAttribute.name,
operator: "EQUALS",
value: position
}]
}];
// chromosome:startPos - endPos
}else if(match[3]) {
var chromosome = match[1];
var startPosition = match[2];
var stopPosition = match[3];
if(parseInt(startPosition, 10) > parseInt(stopPosition, 10)) {
molgenis.createAlert([{message: 'The start position of the queried range is larger than the stop position. Please check the search query.'}], 'warning');
}else{
$('.alerts').empty();
}
entityCollectionRequest.q =
[{
operator: "NESTED",
nestedRules: [{
operator: "NESTED",
nestedRules: [{
field: chromosomeAttribute.name,
operator: "EQUALS",
value: chromosome
}]
}]
}, {
operator: "AND"
}, {
operator: "NESTED",
nestedRules: [{
field: posAttribute.name,
operator: "GREATER_EQUAL",
value: startPosition
}, {
operator: "AND"
}, {
field: posAttribute.name,
operator: "LESS_EQUAL",
value: stopPosition
}]
}];
}
} else {
entityCollectionRequest.q.push({
operator : 'SEARCH',
value : searchQuery
});
}
}
}
// add rules for attribute filters to the query
$.each(attributeFilters, function(attributeUri, filter) {
var rule = filter.createQueryRule();
if(rule){
if (entityCollectionRequest.q.length > 0) {
entityCollectionRequest.q.push({
operator : 'AND'
});
}
entityCollectionRequest.q.push(rule);
}
});
/**
* Debug info:
* Activate this code to see the query
*
* $("#debugFilterQuery").remove();
* $("#tab-data").append($('QUERY :
' + JSON.stringify(entityCollectionRequest) + '
'));
*/
return entityCollectionRequest;
}
/**
* @memberOf molgenis.dataexplorer
*/
function render() {
// Check if the copy button should be shown or not
$.get(molgenis.getContextUrl() + '/copy?entity=' + state.entity).done(function(data) {
if(data === true){
$("#copy-data-btn").removeClass('hidden');
}else{
$("#copy-data-btn").addClass('hidden');
}
});
// get entity meta data and update header and tree
var entityMetaDataRequest = restApi.getAsync('/api/v1/' + state.entity + '/meta', {expand: ['attributes']}, function(entityMetaData) {
selectedEntityMetaData = entityMetaData;
self.createHeader(entityMetaData);
// Loop through all the attributes in the meta data
$.each(entityMetaData.attributes, function(index, attribute) {
// Default expansion is false
// Expanded has to do with xref / mref attributes
attribute.expanded = false;
// If the state is empty or undefined, or is set to
// 'none', return null. All attributes will be shown
if (state.attrs === undefined || state.attrs === null) {
if(attribute.fieldType !== 'COMPOUND') selectedAttributes.push(attribute);
} else if (state.attrs === 'none') {
selectedAttributes = [];
} else {
// Loop through all the attributes mentioned in the state (url)
$.each(state.attrs, function(index, selectedAttrName) {
// If the attribute is in the state, add that attribute to the selectedAttributes
// For compound attributes, check the atomic attributes
if (attribute.name === selectedAttrName) {
selectedAttributes.push(attribute);
}
});
}
});
// Empties existing tree of selected attributes
selectedAttributesTree = {};
// For each selected attribute, check if it is expanded and fill the selectedAttributesTree map
$.each(selectedAttributes, function(index, attribute) {
var key = attribute.name;
var value = attribute.expanded === true ? {'*': null} : null;
selectedAttributesTree[key] = value;
});
createEntityMetaTree(entityMetaData, selectedAttributes);
if (settings['launch_wizard'] === true) {
self.filter.wizard.openFilterWizardModal(entityMetaData, attributeFilters);
}
});
// get entity modules and load visible module
$.get(molgenis.getContextUrl() + '/modules?entity=' + state.entity).done(function(data) {
var container = $('#module-nav');
modules = data.modules;
createModuleNav(data.modules, state.entity, container);
// select first tab
var moduleTab;
if(state.mod) {
moduleTab = $('a[data-toggle="tab"][data-target="#tab-' + state.mod + '"]', container);
} else {
moduleTab = $('a[data-toggle="tab"]', container).first();
}
state.mod = moduleTab.data('id');
// show tab once entity meta data is available
$.when(entityMetaDataRequest).done(function(){
moduleTab.tab('show');
});
function hideSelectors() {
$('#selectors').removeClass("col-md-3").addClass("hidden");
$('#modules').removeClass("col-md-9").addClass("col-md-12");
$('#toggleSelectorsIcon').removeClass("glyphicon glyphicon-resize-horizontal").addClass("glyphicon glyphicon-resize-small");
}
function showSelectors() {
$('#selectors').addClass("col-md-3").removeClass("hidden");
$('#modules').removeClass("col-md-12").addClass("col-md-9");
$('#toggleSelectorsIcon').removeClass("glyphicon glyphicon-resize-small").addClass("glyphicon glyphicon-resize-horizontal");
}
$('#toggleSelectors').on('click', function(){
if($('#selectors').hasClass("hidden")){
showSelectors();
}
else{
hideSelectors();
}
});
});
$('#observationset-search').focus();
}
function pushState() {
// shorten URL by removing attributes with null or undefined values
var cleanState = {};
for (var key in state) {
if (state.hasOwnProperty(key)) {
var val = state[key];
if(val) {
cleanState[key] = val;
}
}
}
// FIXME remove if clause as part of http://www.molgenis.org/ticket/3110
if(state.query) {
delete cleanState.query;
for (var i = 0; i < state.query.q.length; ++i) {
var rule = state.query.q[i];
if(rule.field === undefined && rule.operator === 'SEARCH') {
cleanState.query = { q: [rule] };
break;
}
}
}
// update browser state
history.pushState(state, '', molgenis.getContextUrl() + '?' + $.param(cleanState));
}
/**
* @memberOf molgenis.dataexplorer
*/
$(function() {
// lazy load tab contents
$(document).on('show.bs.tab', 'a[data-toggle="tab"]', function(e) {
var target = $($(e.target).attr('data-target')), entityHref = encodeURI($(e.target).attr('href'));
if(target.data('status') !== 'loaded') {
target.load(entityHref, function() {
target.data('status', 'loaded');
});
}
});
$(document).on('changeQuery', function(e, query) {
state.query = query;
pushState();
});
$(document).on('changeEntity', function(e, entity) {
// reset state
state = {
entity: entity,
attributes: [],
mod : null
};
pushState();
// reset
selectedEntityMetaData = null;
attributeFilters = {};
selectedAttributes = [];
searchQuery = null;
if($('#data-table-container').length > 0) {
React.unmountComponentAtNode($('#data-table-container')[0]); // must occur before mod-data is loaded
}
$('#feature-filters p').remove();
$("#observationset-search").val("");
$('#data-table-pager').empty();
// reset: unbind existing event handlers
$.each(modules, function() {
$(document).off('.' + this.id);
});
render();
});
$(document).on('changeModule', function(e, mod) {
state.mod = mod;
pushState();
});
$(document).on('changeAttributeSelection', function(e, data) {
if(data.attributes.length === 0) {
state.attrs = 'none';
}
else if(data.attributes.length === data.totalNrAttributes) {
state.attrs = null;
}
else {
state.attrs = $.map(data.attributes, function(attribute) {
return attribute.name;
});
}
pushState();
});
$(document).on('updateAttributeFilters', function(e, data) {
$.each(data.filters, function() {
if(this.isEmpty()){
delete attributeFilters[this.attribute.href];
}else{
attributeFilters[this.attribute.href] = this;
}
});
self.filter.createFilterQueryUserReadableList(attributeFilters);
$(document).trigger('changeQuery', createEntityQuery());
});
$(document).on('removeAttributeFilter', function(e, data) {
delete attributeFilters[data.attributeUri];
self.filter.createFilterQueryUserReadableList(attributeFilters);
$(document).trigger('changeQuery', createEntityQuery());
});
$(document).on('clickAttribute', function(e, data) {
var attr = data.attribute;
if(attr.fieldType !== 'COMPOUND' && (!attr.refEntity || !attr.parent))
self.filter.dialog.openFilterModal(data.attribute, attributeFilters[data.attribute.href]);
});
var container = $("#plugin-container");
if ($('#dataset-select').length > 0) {
$('#dataset-select').select2({ width: 'resolve' });
$('#dataset-select').change(function() {
$(document).trigger('changeEntity', $(this).val());
});
}
$("#observationset-search").change(function(e) {
searchQuery = $(this).val().trim();
$(document).trigger('changeQuery', createEntityQuery());
});
$('#search-clear-button').click(function(){
$("#observationset-search").val('');
$("#observationset-search").change();
});
$('#filter-wizard-btn').click(function() {
self.filter.wizard.openFilterWizardModal(selectedEntityMetaData, attributeFilters);
});
$('#module-nav').on('click', 'ul.nav > li > a', function(e) {
$(document).trigger('changeModule', $(this).data('id'));
});
$(container).on('click', '.feature-filter-edit', function(e) {
e.preventDefault();
var filter = attributeFilters[$(this).data('href')];
self.filter.dialog.openFilterModal(filter.attribute, filter);
});
$(container).on('click', '.feature-filter-remove', function(e) {
e.preventDefault();
$(document).trigger('removeAttributeFilter', {'attributeUri': $(this).data('href')});
});
$('#delete-data-btn').on('click', function(){
bootbox.confirm("Are you sure you want to delete all data for this entity?", function(confirmed){
if(confirmed){
$.ajax('/api/v1/' + selectedEntityMetaData.name, {'type': 'DELETE'}).done(function(){
document.location.href = '/menu/main/dataexplorer?entity=' + selectedEntityMetaData.name;
});
}
});
});
$('#copy-data-btn').on('click', function(){
bootbox.prompt({
title: "Copy entity [" + selectedEntityMetaData.label + "]" +
"Please enter a new entity name." +
"" +
"- Use max 30 characters." +
"
- Only letters (a-z, A-Z), digits (0-9), underscores (_) and hashes (#) are allowed.
" +
"
" +
"
By pushing the ok button you will create an new entity with copied data.",
value: selectedEntityMetaData.label + '_',
callback: function(result){
if(result !== null){
$.ajax({
headers: {
'Accept': 'application/json',
'Content-Type': 'application/json'
},
'type': 'POST',
'url': '/api/v2/copy/' + selectedEntityMetaData.name,
'data': JSON.stringify({'newEntityName': result}),
'dataType': 'json',
'success': function(newEntityName){
document.location.href = '/menu/main/dataexplorer?entity=' + newEntityName;
}
});
}
}
});
});
$('#delete-data-metadata-btn').on('click', function(){
bootbox.confirm("Are you sure you want to delete all data and metadata for this entity?", function(confirmed){
if(confirmed){
$.ajax('/api/v1/'+selectedEntityMetaData.name+'/meta', {'type': 'DELETE'}).done(function(){
document.location.href = "/menu/main/dataexplorer";
});
}
});
});
function init() {
// set entity in dropdown
if(!state.entity) {
state.entity = $('#dataset-select option:not(:empty)').first().val();
}
$('#dataset-select').select2('val', state.entity);
// hide entity dropdown
if(state.hideselect === 'true') {
$('#dataset-select-container').addClass('hidden');
} else {
$('#dataset-select-container').removeClass('hidden');
}
if (state.query) {
// set query in searchbox
for (var i = 0; i < state.query.q.length; ++i) {
var rule = state.query.q[i];
if(rule.field === undefined && rule.operator === 'SEARCH') {
$('#observationset-search').val(rule.value).change();
break;
}
}
// set filters in filter list
// FIXME implement as part of http://www.molgenis.org/ticket/3110
}
if (state.entity) {
render();
}
}
// set state from url
if(window.location.search && window.location.search.length > 0) {
var querystring = window.location.search.substring(1); // remove '?'
if(querystring.length > 0) {
state = $.deparam(querystring);
}
} else {
state = stateDefault;
}
// handle browser back event
window.onpopstate = function(event) {
if (event.state !== null) {
state = event.state;
init();
}
};
init();
});
});
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