Loading...
";}');
+ if (this.store.case) {
+ trackArray.push('case=' + this.store.case)
}
- if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') {
+ if (this.store.size) {
+ trackArray.push('size=' + this.store.size)
+ }
+
+ if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/CNVs') {
trackArray.push("autoscale=local");
trackArray.push("bicolor_pivot=0");
}
diff --git a/gdc-viewer/js/View/Export/TrackConfigJson.js b/gdc-viewer/js/View/Export/TrackConfigJson.js
index cf2e573..fc47086 100644
--- a/gdc-viewer/js/View/Export/TrackConfigJson.js
+++ b/gdc-viewer/js/View/Export/TrackConfigJson.js
@@ -16,24 +16,22 @@ return declare( ExportBase,
},
_printHeader: function() {
- var storeArray = (this.store.config.storeClass).split('/')
+ var storeArray = (this.store.config.type).split('/')
var trackObject = {
- 'label': this.store.config.label,
- 'storeClass': this.store.config.storeClass,
+ 'label': this.track.labelHTML,
+ 'storeClass': this.store.config.type,
'type': this.track.config.type,
- 'key': this.store.config.key,
+ 'key': this.track.key,
'metadata': {
'datatype': storeArray[storeArray.length - 1]
},
- 'unsafePopup': true
+ 'unsafePopup': true,
+ 'case': this.store.case,
+ 'size': this.store.size
}
- if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/SimpleSomaticMutations' || this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/Genes') {
- trackObject['fmtDetailValue_projects'] = 'function(value) { return "Loading...
";}';
- }
-
- if (this.store.config.storeClass === 'gdc-viewer/Store/SeqFeature/CNVs') {
+ if (this.store.config.type === 'gdc-viewer/Store/SeqFeature/CNVs') {
trackObject['autoscale'] = 'local';
trackObject['bicolor_pivot'] = 0;
}
diff --git a/gdc-viewer/js/View/GDCDialog.js b/gdc-viewer/js/View/GDCDialog.js
index 96677c3..d98fcbd 100644
--- a/gdc-viewer/js/View/GDCDialog.js
+++ b/gdc-viewer/js/View/GDCDialog.js
@@ -234,7 +234,7 @@ function (
var geneLoading = thisB.createLoadingIcon(thisB.geneFacetTab.containerNode);
// Update the accordions with results from the GDC
- fetch(thisB.baseGraphQLUrl, {
+ fetch(thisB.baseGraphQLUrl + '/facets', {
method: 'post',
headers: { 'X-Requested-With': null },
body: JSON.stringify(bodyVal)
@@ -1055,7 +1055,7 @@ function (
},
/**
- * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the ICGC response
+ * Creates pagination buttons for search results in the given 'holder' using the 'pagination' object from the GDC response
* @param {object} holder DOM location to place pagination buttons
* @param {number} totalPages the total number of pages for the given query results
* @param {string} type the type of results to create pagination button for
@@ -1367,7 +1367,6 @@ function (
trackConf.autoscale = 'local';
trackConf.bicolor_pivot = 0;
} else if (storeClass === 'Genes') {
- trackConf.fmtDetailValue_projects = function(value) { return "Loading...Loading...Loading...Loading...Loading...Loading...Open in New Tab';
+ var linkElement = domConstruct.toDom(linkString);
+ domConstruct.place(linkElement, details);
+
+ return details;
+ }
});
}
);
\ No newline at end of file
diff --git a/gdc-viewer/js/View/Track/SSMTrack.js b/gdc-viewer/js/View/Track/SSMTrack.js
index c3c5041..451726c 100644
--- a/gdc-viewer/js/View/Track/SSMTrack.js
+++ b/gdc-viewer/js/View/Track/SSMTrack.js
@@ -1,24 +1,24 @@
define(
[
"dojo/_base/declare",
- "JBrowse/View/Track/CanvasFeatures",
+ "JBrowse/View/Track/HTMLFeatures",
'JBrowse/View/Track/_ExportMixin',
'dojo/dom-construct'
],
function(
declare,
- CanvasFeatures,
+ HTMLFeatures,
ExportMixin,
domConstruct) {
- return declare([ CanvasFeatures, ExportMixin ], {
+ return declare([ HTMLFeatures, ExportMixin ], {
_exportFormats: function() {
return [
{name: 'gdc-viewer/View/Export/GFF3', label: 'GFF3', fileExt: 'gff3'},
{name: 'gdc-viewer/View/Export/BED', label: 'BED', fileExt: 'bed'},
{name: 'gdc-viewer/View/Export/CSV', label: 'CSV', fileExt: 'csv'},
- {name: 'icgc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
- {name: 'gdc-viewer/View/Export/TrackConfig', label: 'Track Config INI', fileExt: 'conf'},
+ {name: 'gdc-viewer/View/Export/SequinTable', label: 'Sequin Table', fileExt: 'sqn'},
+ {name: 'gdc-viewer/View/Export/TrackConfig', label: 'Track Config', fileExt: 'conf'},
{name: 'gdc-viewer/View/Export/TrackConfigJson', label: 'Track Config JSON', fileExt: 'json'}];
},
@@ -47,6 +47,64 @@ define(
var projectSection = dojo.create('div', { style: 'flex-grow:1; flex-basis: 0' }, thirdRow)
this.renderDetailField( projectSection, 'projects', f.get('projects'), f, undefined, track.store.getTagMetadata('projects'))
},
+
+ _trackMenuOptions: function () {
+ var track = this;
+ var options = this.inherited(arguments);
+ options.push({
+ label: 'Share Track as URL',
+ action: "contentDialog",
+ title: 'Share Track as URL',
+ content: dojo.hitch(this,'_shareableLinkContent')
+ });
+ return options;
+ },
+
+ _shareableLinkContent: function() {
+ var track = this;
+ var details = domConstruct.create('div', { className: 'detail', style: 'display: flex; flex-direction: column; align-items: center; justify-content: center;' });
+
+ // Create addTracks value
+ var addTracksArray = [];
+ var addTrackConf = {};
+ addTrackConf.label = track.config.label;
+ addTrackConf.storeClass = track.store.config.type;
+ addTrackConf.type = track.config.type;
+ addTrackConf.key = track.config.key;
+ addTrackConf.metadata = track.config.metadata;
+ addTrackConf.unsafePopup = true;
+ addTrackConf.filters = track.store.config.filters;
+ addTrackConf.case = track.store.config.case;
+ addTrackConf.size = track.config.size;
+ addTracksArray.push(addTrackConf);
+ addTracksArray = JSON.stringify(addTracksArray);
+
+ // Create a shareable URL
+ var params = new URLSearchParams(window.location.search);
+ params.set("addTracks", addTracksArray);
+ var shareableLink = window.location.protocol + "//" + window.location.host + window.location.pathname + '?' + params.toString();
+
+ // Create help text
+ var helpString = '
Use the following link to share the selected track at the current location.
';
+ var helpElement = domConstruct.toDom(helpString);
+ domConstruct.place(helpElement, details);
+
+ // Create text area with shareable link
+ var textArea = domConstruct.create(
+ 'textarea',{
+ rows: 10,
+ value: shareableLink,
+ style: "width: 80%",
+ readOnly: true
+ }, details );
+
+ // Create a DOM element for the link
+ var linkString = '
Open in New Tab';
+ var linkElement = domConstruct.toDom(linkString);
+ domConstruct.place(linkElement, details);
+
+ return details;
+ }
});
}
);
\ No newline at end of file