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bierapp-element.html
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<script src="bower_components/jsorolla/src/lib/utils.js"></script>
<script src="bower_components/jsorolla/src/lib/opencga-manager.js"></script>
<script src="bower_components/jsorolla/src/lib/cellbase-manager.js"></script>
<link rel="import" href="bower_components/polymer/polymer.html">
<link rel="import" href="bower_components/iron-flex-layout/iron-flex-layout-classes.html">
<!-- <link rel="import" href="bower_components/paper-slider/paper-slider.html"> -->
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-application-behavior.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/jso-opencga-manager-behavior.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-panel.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-wizard.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-tooltip.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-opencga-input-text.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-select.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-opencga-button-tooltip.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-help-menu.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-genome-viewer-element.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/variant/jso-variant-frequencies-grid.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/table/jso-table.html">
<link rel="import" href="bower_components/jsorolla/src/lib/validator/jso-validator.html">
<script src="bower_components/jsorolla/src/lib/validator/bed-validator.js"></script>
<link rel="import" href="bower_components/iron-list/iron-list.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/jso-opencga-header.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/jso-opencga-footer.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/files/jso-opencga-job-browser.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/samples/jso-opencga-sample-browser.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/files/jso-opencga-upload-file.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/files/jso-opencga-create-study.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/files/jso-opencga-create-project.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/opencga/files/jso-opencga-browser.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/variant/jso-variant-browser.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/ontology/jso-ontology-tree.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/ontology/jso-ontology-tree-item.html">
<link rel="import" href="bower_components/jsorolla/src/lib/components/jso-genome-viewer-element.html">
<!--<link rel="import" href="/lib/jsorolla/src/lib/components/opencga/dashboard/jso-dashboard.html">-->
<link rel="import" href="src/bierapp-home.html">
<script src="src/FilterHistory.js"></script>
<dom-module id="bierapp-element">
<style is="custom-style" include="iron-flex iron-flex-reverse iron-flex-alignment iron-flex-factors iron-positioning">
:host {
display: block;
position: relative;
cursor: default;
font-size: 13px;
background-color: var(--default-primary-color);
height: 100%;
width: 100%;
}
/*.menu > div {
margin-left: 10px;
cursor: pointer;
text-align: center;
padding: 0 5px;
}*/
#menu div.option {
box-sizing: border-box;
margin-right: 1vw;
margin-top: 15px;
margin-bottom: 15px;
cursor: pointer;
text-align: center;
line-height: 30px;
padding: 0 5px;
}
#menu div.option:hover {
border-bottom: 1px solid var(--divider-color);
}
#menu div.option[active] {
font-weight: normal;
border-bottom: 2px solid var(--accent-color);
}
jso-opencga-header {
position: absolute;
top: 0;
}
jso-opencga-footer {
position: absolute;
bottom: 0;
height: 60px;
}
.content {
position: absolute;
width: 100%;
top: 60px;
/*height: calc(100vh - 60px);*/
/*background-color: transparent;*/
}
bierapp-home {
height: calc(100vh - 120px);
overflow-y: auto;
color: var(--text-primary-color)
}
jso-dashboard {
height: calc(100vh - 60px);
}
jso-variant-browser {
height: calc(100vh - 60px);
overflow-y: scroll;
}
#browserPanel {
position: absolute;
left: 0;
top: 0;
width: 600px;
}
div.icon {
margin-left: 15px;
}
div.menu-button {
padding: 0 10px;
}
div.menu-button:hover {
background-color: rgba(0, 0, 0, 0.20);
}
#sampleBrowserPanel {
position: absolute;
left: 0;
top: 0;
width: 600px;
}
</style>
<template>
<div class="content" menu-option="home">
<bierapp-home data-option="home"></bierapp-home>
</div>
<div id="content" class="content" menu-option="home,variantbrowser">
<jso-panel hidden collapsible closable movable id="browserPanel" on-hidden="handlePanelHidden">
<!-- <jso-panel id="browserPanel" modal movable closable hidden$="{{browserHidden}}"> -->
<div class="header">
<i class="fa fa-folder-open-o"></i> File Browser
</div>
<jso-opencga-browser enable-auto-index class="container" id="browser" projects="{{projects}}" bioformats="{{bioformats}}" mode="file" on-need-refresh="handleUserNeedRefresh"></jso-opencga-browser>
</jso-panel>
<jso-panel hidden collapsible closable movable id="sampleBrowserPanel" on-hidden="handlePanelHidden">
<div class="header">
<i class="fa fa-folder-open-o"></i> Study Browser
</div>
<jso-opencga-sample-browser enable-auto-index enable-variant-browser class="container" id="sampleBrowser" projects="{{projects}}" bioformats="{{bioformats}}" samples="{{samples}}" filtered-samples="{{filteredSamples}}" on-viewvariantbrowser="handleSampleSelect"
on-need-refresh="handleUserNeedRefresh"></jso-opencga-sample-browser>
</jso-panel>
</div>
<div class="content" menu-option="variantbrowser" style="height: 100%;">
<jso-variant-browser id="variantBrowser"></jso-variant-browser>
</div>
<jso-opencga-header id="jsoHeader" selected-option="{{selectedOption}}" user-data="{{userData}}" on-logout="handleLogout" hide-jobs hide-browse show-menu-on-login>
<span class="icon">
<img src="images/bier-text.svg" style="height: 50px;margin: 5px 0px 0 0;">
</span>
<span class="title">BiERapp</span>
<span class="description">1.5.0</span>
<div id="menu" class="menu horizontal layout flex">
<div style="margin-left:2vw;"></div>
<div title="Browse my data" class="option" on-click="handleLoggedOnlyMenuPanel" data-panel="browserPanel">
<i class="fa fa-cloud"></i>
<span class="option-text">My data</span>
</div>
<div title="Browse samples" class="option" on-click="handleLoggedOnlyMenuPanel" data-panel="sampleBrowserPanel">
<i class="fa fa-users"></i>
<span class="option-text">Study Browser</span>
</div>
</div>
<jso-help-menu class="helpmenu" selectedOption="{{selectedOption}}">
<a href="https://github.com/babelomics/bierapp/wiki" target="_blank">
<i class="fa fa-book"></i> Documentation
</a>
<a href="https://github.com/babelomics/bierapp/wiki/Tutorial" target="_blank">
<i class="fa fa-compass"></i> Tutorial
</a>
<a href="https://github.com/babelomics/bierapp/" target="_blank">
<i class="fa fa-github"></i> Source code
</a>
</jso-help-menu>
</jso-opencga-header>
<jso-opencga-footer menu-option="home,loging,singup,profile,remember">
BierApp 2016
<br> Created by <b>Computational Genomics Department</b> at <b>Centro de Investigación Principe Felipe</b>
</jso-opencga-footer>
</template>
</dom-module>
<script>
Polymer({
is: "bierapp-element",
behaviors: [JsoApplicationBehavior],
properties: {
userData: {
type: Object,
notify: true,
observer: 'userDataChanged'
},
projects: {
type: Array,
notify: true,
observer: 'projectsChanged'
},
allowedTools: {
type: Array,
value: function() {
return ["bierapp"];
}
},
browserHidden: {
type: Boolean,
value: true,
reflectToAttribute: true
},
uploadHidden: {
type: Boolean,
value: true,
reflectToAttribute: true
},
createStudyHidden: {
type: Boolean,
value: true,
reflectToAttribute: true
},
createProjectHidden: {
type: Boolean,
value: true,
reflectToAttribute: true
},
bioformats: {
type: Array,
notify: true,
value: [{
text: "VCF 4.0",
value: "VARIANT",
validator: VCFValidator
}]
},
samples: {
type: Array,
value: function() {
return [];
},
observer: "samplesChanged"
},
filteredSamples: {
type: Array,
value: function() {
return [];
},
observer: "filteredSamplesChanged"
},
},
ready: function() {},
setMenu: function(option) {
if (option) {
this.selectedOption = option;
}
},
projectsChanged: function(neo, old) {},
handleLogout: function() {
this.$.browserPanel.hide();
},
handleUserNeedRefresh: function() {
this.$.jsoHeader.getUserInfo(true);
},
userDataChanged: function(neo, old) {
var me = this;
if (this.userData) {
var projectIds = [];
for (var i = 0; i < this.userData.projects.length; i++) {
var p = this.userData.projects[i];
projectIds.push(p.id);
}
var projects = [];
OpencgaManager.projects.studies({
id: projectIds.join(','),
query: {
sid: Cookies("bioinfo_sid")
},
request: {
success: function(response) {
if (response.response[0].errorMsg === '' || response.response[0].errorMsg == null) {
for (var i = 0; i < response.response.length; i++) {
var r = response.response[i];
me.userData.projects[i].studies = r.result;
projects.push(me.userData.projects[i]);
}
/* update projects property*/
me.projects = projects;
} else {
console.log(response.error);
console.log(response.response[0].errorMsg);
}
me.loading = false;
},
error: function() {
console.log('Server error, try again later.');
me.loading = false;
}
}
});
} else {
console.log("no user data")
}
},
annonymousLogin: function() {
this.$.jsoHeader.anonymousSign();
},
handleSampleSelect: function(e) {
var samplesArray = [];
var samplesIds = [];
var samples = e.currentTarget.querySelectorAll('jso-opencga-sample-list-item[selected]');
if (samples.length == 0) {
if (this.filteredSamples.length == 0) {
alert('You must select at least one sample');
return;
} else {
for (var i = 0; i < this.filteredSamples.length; i++) {
var s = this.filteredSamples[i];
if (s.status != 'READY') {
alert('All selected samples must be READY');
return;
}
}
this.$.variantBrowser.samples = this.filteredSamples;
this.$.variantBrowser.study = this.$.sampleBrowser.selectedStudy.study;
}
} else {
for (var i = 0; i < samples.length; i++) {
samplesIds.push(samples[i].sample.id);
samplesArray.push(samples[i].sample);
}
for (var i = 0; i < samplesArray.length; i++) {
var s = samplesArray[i];
if (s.status != 'READY') {
alert('All selected samples must be READY');
return;
}
}
var selectedStudy = this.$.sampleBrowser.selectedStudy.study;
this.$.variantBrowser.samples = samplesArray;
this.$.variantBrowser.study = selectedStudy;
}
this.setMenu('variantbrowser');
this.$.sampleBrowserPanel.hidden = true;
this.$.browserPanel.hidden = true;
},
samplesChanged: function(neo, old) {},
filteredSamplesChanged: function(neo, old) {}
});
</script>
</polymer-element>