Merge 25.7 to develop

Author: labkey-teamcity

lincs/resources/web/lincs/lincs.js

@@ -29,6 +29,7 @@
 import org.labkey.api.query.FilteredTable;
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.settings.AppProps;
+import org.labkey.api.util.DOM;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.util.HtmlString;
 import org.labkey.api.util.LinkBuilder;
@@ -45,7 +46,11 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import static org.labkey.api.util.DOM.Attribute.height;
+import static org.labkey.api.util.DOM.Attribute.src;
 import static org.labkey.api.util.DOM.Attribute.style;
+import static org.labkey.api.util.DOM.Attribute.width;
+import static org.labkey.api.util.DOM.IMG;
 import static org.labkey.api.util.DOM.SPAN;
 import static org.labkey.api.util.DOM.at;
 
@@ -278,7 +283,12 @@ public boolean isSortable()
             return false;
         }
 
-        private String getAnalyticsScript(String eventAction, String fileName, boolean addWaitTime)
+        private HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
+        {
+            return externalHeatmapViewerLink(fileName, assayType, getGctDavUrl(fileName));
+        }
+
+        private static String getAnalyticsScript(String eventAction, String fileName, boolean addWaitTime)
         {
             if (!StringUtils.isBlank(AnalyticsService.getTrackingScript()))
             {
@@ -288,31 +298,38 @@ private String getAnalyticsScript(String eventAction, String fileName, boolean a
                 // request if the download opens on the same page.
                 String timeout = addWaitTime ? "that=this; setTimeout(function(){location.href=that.href;},400);return false;" : "";
 
-                // Universal Analytics - remove after conversion to GA4 is complete
-                String onClickScript = "try {_gaq.push(['_trackEvent', 'Lincs', " + PageFlowUtil.qh(eventAction) + ", " + PageFlowUtil.qh(fileName) + "]); } catch (err) {}";
                 // GA4 variant
-                onClickScript += "try {gtag('event', 'Lincs', {eventAction: " + PageFlowUtil.qh(eventAction) + ", fileName: " + PageFlowUtil.qh(fileName) + "}); } catch(err) {}";
+                String onClickScript = "try {gtag('event', 'Lincs', {eventAction: " + PageFlowUtil.qh(eventAction) + ", fileName: " + PageFlowUtil.qh(fileName) + "}); } catch(err) {}";
                 onClickScript += timeout;
                 return onClickScript;
             }
             return null;
         }
 
-        private HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType)
+        public static HtmlString externalHeatmapViewerLink(String fileName, LincsModule.LincsAssay assayType, String gctFileDavUrl)
         {
-            String gctFileUrl = davUrl + "GCT/" + PageFlowUtil.encodePath(fileName);
-            String morpheusUrl = getMorpheusUrl(gctFileUrl, assayType);
+            String morpheusUrl = getMorpheusUrl(gctFileDavUrl, assayType);
 
             String analyticsScript = getAnalyticsScript("Morpheus", fileName, false);
-            String onclickEvt = StringUtils.isBlank(analyticsScript) ? "" : "onclick=\"" + analyticsScript + "\"";
 
             String imgUrl = AppProps.getInstance().getContextPath() + "/lincs/GENE-E_icon.png";
 
-            // TODO: Should use a LinkBuilder, etc.
-            return HtmlString.unsafe("[&nbsp;<a target=\"_blank\" " + onclickEvt +  " href=\"" + morpheusUrl + "\">View in Morpheus</a> <img src=" + imgUrl + " width=\"13\", height=\"13\"/>&nbsp;]");
+            LinkBuilder viewInMorpheusLink = LinkBuilder.simpleLink("View in Morpheus", morpheusUrl).target("_blank");
+            if (analyticsScript != null)
+            {
+                viewInMorpheusLink.onClick(analyticsScript);
+            }
+
+            return HtmlString.of(DOM.SPAN("[",
+                    HtmlString.NBSP,
+                    viewInMorpheusLink,
+                    HtmlString.NBSP,
+                    IMG(at(src, imgUrl).at(width, 13).at(height, 13)),
+                    HtmlString.NBSP,
+                    "]"));
         }
 
-        private String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayType)
+        private static String getMorpheusUrl(String gctFileUrl, LincsModule.LincsAssay assayType)
         {
             String morpheusJson = "{\"dataset\":\"" + gctFileUrl + "\",";
             if(assayType == LincsModule.LincsAssay.P100)

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

@@ -26,6 +26,12 @@
 <%@ page import="org.labkey.lincs.LincsController.SelectedAnnotation" %>
 <%@ page import="java.util.List" %>
 <%@ page import="java.util.stream.Collectors" %>
+<%@ page import="org.labkey.api.files.FileContentService" %>
+<%@ page import="java.net.URI" %>
+<%@ page import="org.labkey.lincs.LincsController" %>
+<%@ page import="org.labkey.lincs.LincsModule.LincsAssay" %>
+<%@ page import="org.labkey.api.util.HtmlString" %>
+<%@ page import="org.labkey.lincs.LincsDataTable.GctColumnPSP" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <labkey:errors/>
@@ -34,7 +40,7 @@
     @Override
     public void addClientDependencies(ClientDependencies dependencies)
     {
-        dependencies.add("Ext4");
+        dependencies.add("/lincs/lincs.css");
     }
 %>
 <%
@@ -46,31 +52,15 @@
     ActionURL downloadGctUrl = urlFor(DownloadCustomGCTReportAction.class);
     String fileName = FileUtil.getFileName(gctBean.getGctFile());
     downloadGctUrl.addParameter("fileName", fileName);
-%>
-
-<script type="text/javascript" nonce="<%=getScriptNonce()%>">
-
-    LABKEY.requiresCss("/lincs/lincs.css");
-    LABKEY.requiresScript("/lincs/lincs.js");
-
-    // Initialize
-    Ext4.onReady(init);
-    function init()
-    {
-        var container = LABKEY.ActionURL.getContainer();
-        var assayType = container.indexOf("P100") !== -1 ? "P100" : "GCP";
-        console.log("Initializing for <%=h(fileName)%>");
-        var morpheusUrl = externalHeatmapViewerLink(container, '<%=h(fileName)%>', "morpheusLink", assayType);
-        console.log("Morpheus URL: " + morpheusUrl);
-    }
-
-</script>
-
 
+    URI webDavUri = FileContentService.get().getWebDavUrl(gctBean.getGctFile(), getContainer(), FileContentService.PathType.full);
+    LincsAssay assayType = LincsController.getLincsAssayType(getContainer());
+    HtmlString morpheusViewerLink = GctColumnPSP.externalHeatmapViewerLink(fileName, assayType, webDavUri.toString());
+%>
 
 <div style="margin:20px 10px 20px 10px">
 <span style="font-weight:bold;"><a href="<%=h(downloadGctUrl)%>">[Download GCT]</a></span>
-<span style="font-weight:bold;" id="morpheusLink"></span>
+<span style="font-weight:bold;" id="morpheusLink"><%=morpheusViewerLink%></span>
 <div style="color:red; margin-bottom:20px;">NOTE: The file will be deleted from the server after it is downloaded.</div>
 
 <div style="margin:20px 10px 20px 10px">
@@ -92,4 +82,5 @@
     <div># Replicates: <%=gctBean.getReplicateCount()%></div>
     <div># Probe Annotations: <%=gctBean.getProbeAnnotationCount()%></div>
     <div># Replicate Annotations: <%=gctBean.getReplicateAnnotationCount()%></div>
+</div>
 </div>

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

@@ -78,16 +78,6 @@ function addSlides(json)
             appendText(entry, slideshowTexts);
         }
 
-        // Attach the 'onclick' event handlers
-        for(let i = 0; i < catalog.length; i++)
-        {
-            const index = i + existingSlideCount + 1;
-            const el = document.getElementById(DOT_NAV_ID_PREFIX + index);
-            if (el)
-            {
-                el.onclick = function() { currentSlide(index); };
-            }
-        }
         showSlides();
     }
     else
@@ -117,13 +107,11 @@ function appendCoverSlide(entry, coverslideContainer)
 
 function appendDot(dotsContainer, index)
 {
-    // Examples:
-    // <span class="dot active" onclick="currentSlide(1)"></span>
-    // <span class="dot" onclick="currentSlide(2)"></span>
     const dot = document.createElement('span');
     const cls = index === 1 ? "dot active" : "dot";
     dot.setAttribute('class', cls);
     dot.setAttribute('id', DOT_NAV_ID_PREFIX + index);
+    dot['onclick'] = function(){ currentSlide(index); }; // CSP-compliant
     dotsContainer.appendChild(dot);
     dotsContainer.appendChild(document.createTextNode(" ") );
 }
@@ -276,8 +264,8 @@ function appendSlidesContainer(parentDivId)
                      '</div>';
 
     parentDiv.innerHTML = slideshowHtml;
-    document.getElementById(nextSlideBtnId).onclick = function() { plusSlides(-1); };
-    document.getElementById(prevSlideBtnId).onclick = function() { plusSlides(1); };
+    document.getElementById(nextSlideBtnId)['onclick'] = function() { plusSlides(-1); };
+    document.getElementById(prevSlideBtnId)['onclick'] = function() { plusSlides(1); };
 
     return true;
 }