b508259e8ce75a2aa1f919b8152befea99a2e1df
chmalee
Fri Jan 27 10:31:59 2023 -0800
Prototype download track data button. An hg.conf controlled button that
allows users to download all of the track data in the current window
without leaving hgTracks, refs #30024
diff --git src/hg/js/hgTracks.js src/hg/js/hgTracks.js
index cd11a07..5eb2718 100644
--- src/hg/js/hgTracks.js
+++ src/hg/js/hgTracks.js
@@ -5101,30 +5101,233 @@
});
$('#tabs').show();
$("#tabs").tabs('option', 'selected', '#' + val);
if (val === 'simpleTab' && $('div#found').length < 1) {
$('input#simpleSearch').focus();
}
$("#tabs").css('font-family', jQuery('body').css('font-family'));
$("#tabs").css('font-size', jQuery('body').css('font-size'));
$('.submitOnEnter').keydown(trackSearch.searchKeydown);
findTracks.normalize();
findTracks.updateMdbHelp(0);
}
}
};
+////////
+// Download Current Tracks in window Dialog
+////////
+var downloadCurrentTrackData = {
+ downloadData: {}, // container for holding data while it comes in from the api
+ currentRequests: {}, // pending requests
+ intervalId: null, // the id of the timer that waits on the api
+
+ failedTrackDataRequest: function(msg) {
+ msgJson = JSON.parse(msg);
+ alert("Download failed. Error message: '" + msgJson.error);
+ },
+
+ receiveTrackData: function(track, data) {
+ downloadCurrentTrackData.downloadData[track] = data;
+ },
+
+ convertJson: function(data, outType) {
+ if (outType !== "tsv" && outType !== "csv") {
+ alert("ERROR: incorrect output format option");
+ return null;
+ }
+ outSep = outType === "tsv" ? '\t' : ',';
+ // TODO: someday we will probably want to include some of these fields
+ // for each track downloaded, perhaps as an option
+ ignoredKeys = new Set(["chrom", "dataTime", "dataTimeStamp", "downloadTime", "downloadTimeStamp",
+ "start", "end", "track", "trackType", "genome", "itemsReturned", "columnTypes",
+ "bigDataUrl", "chromSize"]);
+ // first get rid of top level non track object keys
+ _.each(data, function(val, key) {
+ if (ignoredKeys.has(key)) {delete data[key];}
+ });
+ // now go through each track and format it correctly
+ str = "";
+ _.each(data, function(val, track) {
+ str += "track name=\"" + track + "\"\n";
+ for (var row in val) {
+ for (var i = 0; i < val[row].length; i++) {
+ str += JSON.stringify(val[row][i]);
+ if (i < val[row].length) { str += outSep; }
+ }
+ str += "\n";
+ }
+ str += "\n"; // extra new line after each track oh well
+ });
+ return new Blob([str], {type: "text/plain"});
+ },
+
+ makeDownloadFile: function(key) {
+ if (_.keys(downloadCurrentTrackData.currentRequests).length === 0) {
+ // first stop the timer so we don't execute again
+ clearInterval(downloadCurrentTrackData.intervalId);
+ outType = $("#outputFormat")[0].selectedOptions[0].value;
+ var blob = null;
+ if (outType === 'json') {
+ blob = new Blob([JSON.stringify(downloadCurrentTrackData.downloadData[key])], {type: "text/plain"});
+ } else {
+ blob = downloadCurrentTrackData.convertJson(downloadCurrentTrackData.downloadData[key], outType);
+ }
+ if (blob) {
+ anchor = document.createElement("a");
+ anchor.href = URL.createObjectURL(blob);
+ fname = $("#downloadFileName")[0].value;
+ if (fname.length === 0) {
+ fname = "trackDownload.txt";
+ }
+ switch (outType) {
+ case "tsv":
+ if (!fname.endsWith(".tsv")) {fname += ".tsv";}
+ break;
+ case "csv":
+ if (!fname.endsWith(".csv")) {fname += ".csv";}
+ break;
+ default:
+ if (!fname.endsWith(".txt")) {fname += ".txt";}
+ break;
+ }
+ anchor.download = fname;
+ anchor.click();
+ window.URL.revokeObjectURL(anchor.href);
+ downloadCurrentTrackData.downloadData = {};
+ }
+ }
+ },
+
+ startDownload: function() {
+ trackList = [];
+ $(".downloadTrackName:checked").each(function(i, elem) {
+ trackList.push(elem.id);
+ });
+ chrom = hgTracks.chromName;
+ start = hgTracks.winStart;
+ end = hgTracks.winEnd;
+ db = getDb();
+ apiUrl = "../cgi-bin/hubApi/getData/track?";
+ apiUrl += "chrom=" + chrom;
+ apiUrl += ";start=" + start;
+ apiUrl += ";end=" + end;
+ apiUrl += ";genome=" + db;
+ apiUrl += ";jsonOutputArrays=1";
+ apiUrl += ";track=" + trackList.join(',');
+ // strip off final comma:
+ var xmlhttp = new XMLHttpRequest();
+ downloadCurrentTrackData.currentRequests[apiUrl] = true;
+ xmlhttp.onreadystatechange = function() {
+ if (4 === this.readyState && 200 === this.status) {
+ var mapData = JSON.parse(this.responseText);
+ downloadCurrentTrackData.receiveTrackData(apiUrl, mapData);
+ delete downloadCurrentTrackData.currentRequests[apiUrl];
+ } else {
+ if (4 === this.readyState && this.status >= 400) {
+ clearInterval(downloadCurrentTrackData.intervalId);
+ downloadCurrentTrackData.failedTrackDataRequest(this.responseText);
+ delete downloadCurrentTrackData.currentRequests[apiUrl];
+ }
+ }
+ };
+ xmlhttp.open("GET", apiUrl, true);
+ xmlhttp.send(); // sends request and exits this function
+ // the onreadystatechange callback above will trigger
+ // when the data has safely arrived
+ // wait for the request to complete before making the download file
+ downloadCurrentTrackData.intervalId = setInterval(downloadCurrentTrackData.makeDownloadFile, 200, apiUrl);
+ },
+
+
+ showDownloadUi: function() {
+ // Populate the dialog with the current list of tracks
+ // and allow the user to select which ones to download
+ // Grey out tracks that are currently unsupported by the api
+ // or are protected data
+ var downloadDialog = $("#downloadDialog")[0];
+ if (!downloadDialog) {
+ downloadDialog = document.createElement("div");
+ downloadDialog.id = "downloadDialog";
+ downloadDialog.style = "display: none";
+ htmlStr = "
Use this selection window to download track data" +
+ " for the current region (" + genomePos.get() + "). Please note that large regions" +
+ " may be slow to download.