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vagishavagisha
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- Deleted lincs.js. downloadCustomGCT.jsp uses morpheus viewer link generating code from LincsDataTable instead.
1 parent 70ac24d commit 37f8e49

3 files changed

Lines changed: 75 additions & 172 deletions

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‎lincs/resources/web/lincs/lincs.js‎

Lines changed: 0 additions & 88 deletions
This file was deleted.

‎lincs/src/org/labkey/lincs/LincsDataTable.java‎

Lines changed: 67 additions & 62 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,6 @@
3030
import org.labkey.api.query.UserSchema;
3131
import org.labkey.api.settings.AppProps;
3232
import org.labkey.api.util.DOM;
33-
import org.labkey.api.util.DOM.Renderable;
3433
import org.labkey.api.util.FileUtil;
3534
import org.labkey.api.util.HtmlString;
3635
import org.labkey.api.util.LinkBuilder;
@@ -284,65 +283,10 @@ public boolean isSortable()
284283
return false;
285284
}
286285

287-
private String getAnalyticsScript(String eventAction, String fileName, boolean addWaitTime)
286+
private HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
288287
{
289-
if (!StringUtils.isBlank(AnalyticsService.getTrackingScript()))
290-
{
291-
// http://www.blastam.com/blog/how-to-track-downloads-in-google-analytics
292-
// Tell the browser to wait 400ms before going to the download. This is to ensure
293-
// that the GA tracking request goes through. Some browsers will interrupt the tracking
294-
// request if the download opens on the same page.
295-
String timeout = addWaitTime ? "that=this; setTimeout(function(){location.href=that.href;},400);return false;" : "";
296-
297-
// GA4 variant
298-
String onClickScript = "try {gtag('event', 'Lincs', {eventAction: " + PageFlowUtil.qh(eventAction) + ", fileName: " + PageFlowUtil.qh(fileName) + "}); } catch(err) {}";
299-
onClickScript += timeout;
300-
return onClickScript;
301-
}
302-
return null;
303-
}
304-
305-
private Renderable externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
306-
{
307-
String gctFileUrl = davUrl + "GCT/" + PageFlowUtil.encodePath(fileName);
308-
String morpheusUrl = getMorpheusUrl(gctFileUrl, assayType);
309-
310-
String analyticsScript = getAnalyticsScript("Morpheus", fileName, false);
311-
312-
String imgUrl = AppProps.getInstance().getContextPath() + "/lincs/GENE-E_icon.png";
313-
314-
LinkBuilder viewInMorpheusLink = LinkBuilder.simpleLink("View in Morpheus", morpheusUrl).target("_blank");
315-
if (analyticsScript != null)
316-
{
317-
viewInMorpheusLink.onClick(analyticsScript);
318-
}
319-
320-
return DOM.SPAN("[",
321-
HtmlString.NBSP,
322-
viewInMorpheusLink,
323-
IMG(at(src, imgUrl).at(width, 13).at(height, 13)),
324-
HtmlString.NBSP,
325-
"]");
326-
}
327-
328-
private String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayType)
329-
{
330-
String morpheusJson = "{\"dataset\":\"" + gctFileUrl + "\",";
331-
if(assayType == LincsModule.LincsAssay.P100)
332-
{
333-
morpheusJson += "\"rows\":[{\"field\":\"pr_p100_modified_peptide_code\",\"display\":\"Text\"},{\"field\":\"pr_gene_symbol\",\"display\":\"Text\"},{\"field\":\"pr_p100_phosphosite\",\"display\":\"Text\"},{\"field\":\"pr_uniprot_id\",\"display\":\"Text\"}],";
334-
}
335-
if(assayType == LincsModule.LincsAssay.GCP)
336-
{
337-
morpheusJson += "\"rows\":[{\"field\":\"pr_gcp_histone_mark\",\"display\":\"Text\"},{\"field\":\"pr_gcp_modified_peptide_code\",\"display\":\"Text\"}],";
338-
}
339-
morpheusJson += "\"columns\":[{\"field\":\"pert_iname\",\"display\":\"Text\"},{\"field\":\"det_well\",\"display\":\"Text\"}],";
340-
morpheusJson += "\"colorScheme\":{\"type\":\"fixed\",\"map\":[{\"value\":-3,\"color\":\"blue\"},{\"value\":0,\"color\":\"white\"},{\"value\":3,\"color\":\"red\"}]}";
341-
morpheusJson += "}";
342-
343-
String morpheusUrl= "http://www.broadinstitute.org/cancer/software/morpheus/?json=";
344-
morpheusUrl += PageFlowUtil.encodeURIComponent(morpheusJson);
345-
return morpheusUrl;
288+
String gctFileUrl = getDavUrl() + "GCT/" + PageFlowUtil.encodePath(fileName);
289+
return LincsDataTable.externalHeatmapViewerLink(fileName, assayType, gctFileUrl);
346290
}
347291

348292
@Override
@@ -378,12 +322,12 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
378322

379323
String actionName = (getLevel() == LincsModule.LincsLevel.Config) ? "DownloadConfig" : "DownloadGCT";
380324
String analyticsScript = getAnalyticsScript(actionName, downloadFileName, true);
381-
Renderable morpheusUrl = externalHeatmapViewerLink(downloadFileName, getAssayType(), getLevel());
325+
HtmlString morpheusUrl = externalHeatmapViewerLink(downloadFileName, getAssayType(), getLevel());
382326
String downloadText = (getLevel() == LincsModule.LincsLevel.Config) ? "CFG" : "GCT";
383327
renderGridCell(out, analyticsScript, getGctDavUrlUnencoded(downloadFileName), downloadText, morpheusUrl);
384328
}
385329

386-
private void renderGridCell(HtmlWriter out, String analyticsScript, String downloadUrl, String downloadText, Renderable morpheusUrl)
330+
private void renderGridCell(HtmlWriter out, String analyticsScript, String downloadUrl, String downloadText, HtmlString morpheusUrl)
387331
{
388332
// <span style="white-space: nowrap;"> is recommended instead of deprecated <nobr></nobr>
389333
SPAN(
@@ -421,7 +365,7 @@ private boolean fileAvailable(Integer runId, String downloadFileName)
421365
}
422366
}
423367

424-
@Nullable Renderable externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, LincsModule.LincsLevel level)
368+
@Nullable HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, LincsModule.LincsLevel level)
425369
{
426370
if(level == LincsModule.LincsLevel.Config)
427371
{
@@ -497,4 +441,65 @@ public Object getDisplayValue(RenderContext ctx)
497441
return getValue(ctx);
498442
}
499443
}
444+
445+
private static String getAnalyticsScript(String eventAction, String fileName, boolean addWaitTime)
446+
{
447+
if (!StringUtils.isBlank(AnalyticsService.getTrackingScript()))
448+
{
449+
// http://www.blastam.com/blog/how-to-track-downloads-in-google-analytics
450+
// Tell the browser to wait 400ms before going to the download. This is to ensure
451+
// that the GA tracking request goes through. Some browsers will interrupt the tracking
452+
// request if the download opens on the same page.
453+
String timeout = addWaitTime ? "that=this; setTimeout(function(){location.href=that.href;},400);return false;" : "";
454+
455+
// GA4 variant
456+
String onClickScript = "try {gtag('event', 'Lincs', {eventAction: " + PageFlowUtil.qh(eventAction) + ", fileName: " + PageFlowUtil.qh(fileName) + "}); } catch(err) {}";
457+
onClickScript += timeout;
458+
return onClickScript;
459+
}
460+
return null;
461+
}
462+
463+
public static HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, String gctFileDavUrl)
464+
{
465+
String morpheusUrl = getMorpheusUrl(gctFileDavUrl, assayType);
466+
467+
String analyticsScript = getAnalyticsScript("Morpheus", fileName, false);
468+
469+
String imgUrl = AppProps.getInstance().getContextPath() + "/lincs/GENE-E_icon.png";
470+
471+
LinkBuilder viewInMorpheusLink = LinkBuilder.simpleLink("View in Morpheus", morpheusUrl).target("_blank");
472+
if (analyticsScript != null)
473+
{
474+
viewInMorpheusLink.onClick(analyticsScript);
475+
}
476+
477+
return HtmlString.of(DOM.SPAN("[",
478+
HtmlString.NBSP,
479+
viewInMorpheusLink,
480+
HtmlString.NBSP,
481+
IMG(at(src, imgUrl).at(width, 13).at(height, 13)),
482+
HtmlString.NBSP,
483+
"]"));
484+
}
485+
486+
private static String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayType)
487+
{
488+
String morpheusJson = "{\"dataset\":\"" + gctFileUrl + "\",";
489+
if(assayType == LincsModule.LincsAssay.P100)
490+
{
491+
morpheusJson += "\"rows\":[{\"field\":\"pr_p100_modified_peptide_code\",\"display\":\"Text\"},{\"field\":\"pr_gene_symbol\",\"display\":\"Text\"},{\"field\":\"pr_p100_phosphosite\",\"display\":\"Text\"},{\"field\":\"pr_uniprot_id\",\"display\":\"Text\"}],";
492+
}
493+
if(assayType == LincsModule.LincsAssay.GCP)
494+
{
495+
morpheusJson += "\"rows\":[{\"field\":\"pr_gcp_histone_mark\",\"display\":\"Text\"},{\"field\":\"pr_gcp_modified_peptide_code\",\"display\":\"Text\"}],";
496+
}
497+
morpheusJson += "\"columns\":[{\"field\":\"pert_iname\",\"display\":\"Text\"},{\"field\":\"det_well\",\"display\":\"Text\"}],";
498+
morpheusJson += "\"colorScheme\":{\"type\":\"fixed\",\"map\":[{\"value\":-3,\"color\":\"blue\"},{\"value\":0,\"color\":\"white\"},{\"value\":3,\"color\":\"red\"}]}";
499+
morpheusJson += "}";
500+
501+
String morpheusUrl= "http://www.broadinstitute.org/cancer/software/morpheus/?json=";
502+
morpheusUrl += PageFlowUtil.encodeURIComponent(morpheusJson);
503+
return morpheusUrl;
504+
}
500505
}

‎lincs/src/org/labkey/lincs/view/downloadCustomGCT.jsp‎

Lines changed: 8 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -28,8 +28,10 @@
2828
<%@ page import="java.util.stream.Collectors" %>
2929
<%@ page import="org.labkey.api.files.FileContentService" %>
3030
<%@ page import="java.net.URI" %>
31-
<%@ page import="org.apache.commons.lang3.StringUtils" %>
32-
<%@ page import="org.labkey.api.analytics.AnalyticsService" %>
31+
<%@ page import="org.labkey.lincs.LincsDataTable" %>
32+
<%@ page import="org.labkey.lincs.LincsController" %>
33+
<%@ page import="org.labkey.lincs.LincsModule.LincsAssay" %>
34+
<%@ page import="org.labkey.api.util.HtmlString" %>
3335
<%@ page extends="org.labkey.api.jsp.JspBase" %>
3436
<%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
3537
<labkey:errors/>
@@ -40,7 +42,6 @@
4042
{
4143
dependencies.add("Ext4");
4244
dependencies.add("/lincs/lincs.css");
43-
dependencies.add("/lincs/lincs.js");
4445
}
4546
%>
4647
<%
@@ -54,29 +55,13 @@
5455
downloadGctUrl.addParameter("fileName", fileName);
5556
5657
URI webDavUri = FileContentService.get().getWebDavUrl(gctBean.getGctFile(), getContainer(), FileContentService.PathType.full);
57-
boolean hasAnalyticsTrackingScript = !StringUtils.isBlank(AnalyticsService.getTrackingScript());
58+
LincsAssay assayType = LincsController.getLincsAssayType(getContainer());
59+
HtmlString morpheusViewerLink = LincsDataTable.externalHeatmapViewerLink(fileName, assayType, webDavUri.toString());
5860
%>
5961

60-
<script type="text/javascript" nonce="<%=getScriptNonce()%>">
61-
62-
// Initialize
63-
Ext4.onReady(init);
64-
function init()
65-
{
66-
const container = LABKEY.ActionURL.getContainer();
67-
const assayType = container.indexOf("P100") !== -1 ? "P100" : "GCP";
68-
console.log("Initializing for <%=h(fileName)%>");
69-
const morpheusUrl = externalHeatmapViewerLink(<%=qh(webDavUri.toString())%>, <%=qh(fileName)%>, "morpheusLink", assayType, <%=hasAnalyticsTrackingScript%>);
70-
console.log("Morpheus URL: " + morpheusUrl);
71-
}
72-
73-
</script>
74-
75-
76-
7762
<div style="margin:20px 10px 20px 10px">
7863
<span style="font-weight:bold;"><a href="<%=h(downloadGctUrl)%>">[Download GCT]</a></span>
79-
<span style="font-weight:bold;" id="morpheusLink"></span>
64+
<span style="font-weight:bold;" id="morpheusLink"><%=morpheusViewerLink%></span>
8065
<div style="color:red; margin-bottom:20px;">NOTE: The file will be deleted from the server after it is downloaded.</div>
8166

8267
<div style="margin:20px 10px 20px 10px">
@@ -98,4 +83,5 @@
9883
<div># Replicates: <%=gctBean.getReplicateCount()%></div>
9984
<div># Probe Annotations: <%=gctBean.getProbeAnnotationCount()%></div>
10085
<div># Replicate Annotations: <%=gctBean.getReplicateAnnotationCount()%></div>
86+
</div>
10187
</div>

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