Signal Data Update (#22)

LabKey · Sep 14, 2024 · 6101486 · 6101486
1 parent 580deb5
commit 6101486
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Showing 10 changed files with 71 additions and 41 deletions.
diff --git a/resources/assay/signalData/views/begin.html b/resources/assay/signalData/views/begin.html
@@ -3,7 +3,7 @@
     <span id="manage-signaldata-link"></span>
     <div id="runsResult"></div>
 </div>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
     (function() {
 
         function init() {

diff --git a/resources/assay/signalData/views/upload.html b/resources/assay/signalData/views/upload.html
@@ -1,5 +1,5 @@
 <div id="signaldata-upload-content"></div>
-<script type="application/javascript">
+<script type="application/javascript" nonce="<%=scriptNonce%>">
     var wp = new LABKEY.WebPart({
         renderTo: 'signaldata-upload-content',
         partName: 'Signal Data Upload',

diff --git a/resources/views/mockSignalDataWatch.html b/resources/views/mockSignalDataWatch.html
@@ -1,7 +1,7 @@
 <input type="button" class="signaldata-run-btn" value="Load Assay Samples">
 <div class="signaldata-error-log" style="color: red;"></div>
 <div><ul class="signaldata-status-log"></ul></div>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
 
     (function() {
 

diff --git a/resources/views/qc.html b/resources/views/qc.html
@@ -1,5 +1,5 @@
 <div id="qctool"></div>
-<script type="text/javascript">
+<script type="text/javascript" nonce="<%=scriptNonce%>">
 
     Ext4.onReady(function() {
         Ext4.create('LABKEY.SignalData.QualityControl', {

diff --git a/resources/views/signalDataUpload.html b/resources/views/signalDataUpload.html
@@ -13,8 +13,8 @@
             <tr>
                 <td class="labkey-form-label" style="width: 100px;">Upload Type:</td>
                 <td>
-                    <input type="radio" name="uploadType" value="paste"  onchange="LABKEY.SignalData.disableFileUpload()">Cut/Paste<br/>
-                    <input type="radio" name="uploadType" value="file" checked="checked" onchange="LABKEY.SignalData.enableFileUpload()">File
+                    <input type="radio" name="uploadType" value="paste" id="upload-type-paste">Cut/Paste<br/>
+                    <input type="radio" name="uploadType" value="file" id="upload-type-file" checked="checked">File
                 </td>
             </tr>
             <tr>
@@ -30,24 +30,30 @@
     <div class="signaldata-upload-result-files"></div>
 
 
-<script type="application/javascript">
+<script type="application/javascript" nonce="<%=scriptNonce%>">
     (function($) {
-        var context = <%=webpartContext%>;
-        var metadataFormElId = LABKEY.Utils.id();
-        var metadataFileId = LABKEY.Utils.id();
-        var metadataTSVId = LABKEY.Utils.id();
-        var buttonId = LABKEY.Utils.id();
-        var fileUploadElementId = LABKEY.Utils.id();
-        var templateDivId = LABKEY.Utils.id();
+        LABKEY.Utils.onReady(function(){
+            var context = <%=webpartContext%>;
+            var metadataFormElId = LABKEY.Utils.id();
+            var metadataFileId = LABKEY.Utils.id();
+            var metadataTSVId = LABKEY.Utils.id();
+            var buttonId = LABKEY.Utils.id();
+            var fileUploadElementId = LABKEY.Utils.id();
+            var templateDivId = LABKEY.Utils.id();
 
-        $('#' + context.wrapperDivId + ' .signaldata-upload-target').attr('id', metadataFormElId);
-        $('#' + context.wrapperDivId + ' .signaldata-upload-file').attr('id', metadataFileId);
-        $('#' + context.wrapperDivId + ' .signaldata-upload-tsv').attr('id', metadataTSVId);
-        $('#' + context.wrapperDivId + ' .signaldata-upload-button').attr('id', buttonId);
-        $('#' + context.wrapperDivId + ' .signaldata-upload-result-files').attr('id', fileUploadElementId);
-        $('#' + context.wrapperDivId + ' .signaldata-upload-templatelink').attr('id', templateDivId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-target').attr('id', metadataFormElId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-file').attr('id', metadataFileId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-tsv').attr('id', metadataTSVId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-button').attr('id', buttonId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-result-files').attr('id', fileUploadElementId);
+            $('#' + context.wrapperDivId + ' .signaldata-upload-templatelink').attr('id', templateDivId);
 
-        LABKEY.SignalData.initializeUploadForm(metadataFormElId, metadataFileId, metadataTSVId, buttonId, fileUploadElementId, templateDivId);
+            // register click handlers
+            $('#upload-type-paste').on('click', function(){LABKEY.SignalData.disableFileUpload();});
+            $('#upload-type-file').on('click', function(){LABKEY.SignalData.enableFileUpload();});
+
+            LABKEY.SignalData.initializeUploadForm(metadataFormElId, metadataFileId, metadataTSVId, buttonId, fileUploadElementId, templateDivId);
+        });
 
     })(jQuery);
 </script>
diff --git a/resources/web/signaldata/QCView/DataService.js b/resources/web/signaldata/QCView/DataService.js
@@ -25,7 +25,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
             if (content)
             {
                 if (Ext4.isFunction(callback))
-                    callback.call(scope || this, content);
+                    callback.call(scope || this, content, expData);
             }
             else
             {
@@ -35,7 +35,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
                     {
                         this._ContentCache[path] = c;
                         if (Ext4.isFunction(callback))
-                            callback.call(scope || this, c);
+                            callback.call(scope || this, c, expData);
                     },
                     failure: function (error)
                     {
@@ -61,7 +61,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
     getData : function(datacontent, xleft, xright, mod) {
         var data = [];
         if (datacontent) {
-            var _data = datacontent.sheets[0].data;
+            var _data = [...datacontent.sheets[0].data];
             _data.shift(); // get rid of column headers
             var newData = [], d, xy;
 
@@ -75,7 +75,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
                 //
                 if (xleft == 0 && xright == 0) {
                     for (d=0; d < _data.length; d++) {
-                        xy = _data[d][0].split(' ');
+                        xy = this.getXYRow(_data[d]);
                         xy[0] = parseFloat(xy[0]);
                         xy[1] = parseFloat(xy[1]);
                         newData.push(xy);
@@ -86,7 +86,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
                     // using bounds
                     //
                     for (d=0; d < _data.length; d++) {
-                        xy = _data[d][0].split(' ');
+                        xy = this.getXYRow(_data[d]);
                         xy[0] = parseFloat(xy[0]);
                         xy[1] = parseFloat(xy[1]);
                         if (xy[0] > xleft && xy[0] < xright)
@@ -101,7 +101,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
                 if (xleft == 0 && xright == 0) {
                     for (d=0; d < _data.length; d++) {
                         if (d%mod == 0) {
-                            xy = _data[d][0].split(' ');
+                            xy = this.getXYRow(_data[d]);
                             xy[0] = parseFloat(xy[0]);
                             xy[1] = parseFloat(xy[1]);
                             newData.push(xy);
@@ -114,7 +114,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
                     //
                     for (d=0; d < _data.length; d++) {
                         if (d%mod == 0) {
-                            xy = _data[d][0].split(' ');
+                            xy = this.getXYRow(_data[d]);
                             xy[0] = parseFloat(xy[0]);
                             xy[1] = parseFloat(xy[1]);
                             if (xy[0] > xleft && xy[0] < xright)
@@ -129,6 +129,19 @@ Ext4.define('LABKEY.SignalData.DataService', {
         return data;
     },
 
+    /**
+     * Helper to return an XY array from the raw input data file. This helps normalize
+     * different data file delimiter types.
+     */
+    getXYRow : function(row) {
+        // space delimited
+        if (row.length === 1)
+            return row[0].split(' ');
+
+        // all others
+        return row;
+    },
+
     /**
      * Get the max y value * 110%
      * @param datacontents
@@ -147,7 +160,7 @@ Ext4.define('LABKEY.SignalData.DataService', {
 
                 for (d = 0; d < _data.length; d++)
                 {
-                    xy = _data[d][0].split(' ');
+                    xy = this.getXYRow(_data[d]);
                     y = parseFloat(xy[1]);
                     if (y > maxY)
                     {

diff --git a/resources/web/signaldata/QCView/SampleCreator.js b/resources/web/signaldata/QCView/SampleCreator.js
@@ -285,26 +285,29 @@ Ext4.define('LABKEY.SignalData.SampleCreator', {
                     allContent = [],
                     contentMap = {};
 
-                var done = function(content) {
+                var done = function(content, pr) {
                     received++;
+                    content.runName = pr.runName;
                     allContent.push(content);
-                    contentMap[content.fileName] = content;
+                    contentMap[pr.runName] = content;
                     if (received == expected) {
                         this.allContent = allContent;
                         this.contentMap = contentMap;
                         this.renderPlot(allContent, true);
                     }
                 };
 
-                for (var d=0; d < provisionalRuns.length; d++) {
-                    var pr = provisionalRuns[d].get('expDataRun');
+                Ext4.each(provisionalRuns, function(run){
+                    var pr = run.get('expDataRun');
                     if (pr) {
+                        // use the run name as the key for all data
+                        pr.runName = run.get('name');
                         SignalDataService.FileContentCache(pr, done, this);
                     }
                     else {
                         console.error('Failed to load expDataRun from provisional run.');
                     }
-                }
+                }, this);
 
             }, this);
         }
@@ -449,7 +452,7 @@ Ext4.define('LABKEY.SignalData.SampleCreator', {
         var modelname = sample.get('name');
 
         if (modelname) {
-            this.highlighted = sample.get('name') + '.'  + sample.get('fileExt');
+            this.highlighted = sample.get('name');
             this.renderPlot(this.allContent);
         }
     },
@@ -481,7 +484,7 @@ Ext4.define('LABKEY.SignalData.SampleCreator', {
                 include = this._getNode(view, model, 'input[name="include"]');
                 response = this._getNode(view, model, 'span[name="response"]');
 
-                var fileContent = this.contentMap[model.get('name') + '.' + model.get('fileExt')];
+                var fileContent = this.contentMap[model.get('name')];
                 var data = SignalDataService.getData(fileContent, xleft, xright, false);
                 var aucPeak = LABKEY.SignalData.Stats.getAUC(data, base);
                 response.update(+aucPeak.auc.toFixed(3));

diff --git a/resources/web/signaldata/QCView/SpectrumPlot.js b/resources/web/signaldata/QCView/SpectrumPlot.js
@@ -64,7 +64,7 @@ Ext4.define('LABKEY.SignalData.SpectrumPlot', {
             color = colors[c%colors.length];
 
             if (useHighlight) {
-                isHighlight = (this.highlight === contents[i].fileName);
+                isHighlight = (this.highlight === contents[i].runName);
 
                 if (!isHighlight) {
                     color = '#A09C9C';

diff --git a/resources/web/signaldata/UploadView/UploadLog.js b/resources/web/signaldata/UploadView/UploadLog.js
@@ -276,7 +276,7 @@ Ext4.define('LABKEY.SignalData.UploadLog', {
             function done(file, results) {
 
                 var store = me.getStore();
-                var idx = store.findExact(me.DATA_FILE, file.text);
+                var idx = store.find(me.DATA_FILE, file.text);
                 var process = store.getAt(idx);
 
                 //Set upload time
@@ -411,7 +411,7 @@ Ext4.define('LABKEY.SignalData.UploadLog', {
     workingDirectory: '',
     containsFile: function(file) {
         var store = this.getStore();
-        var idx = store.findExact(this.DATA_FILE, file.name);
+        var idx = store.find(this.DATA_FILE, file.name);
         return store.getAt(idx);
     }
 });
diff --git a/resources/web/signaldata/UploadView/uploadResultFiles.js b/resources/web/signaldata/UploadView/uploadResultFiles.js
@@ -192,7 +192,7 @@ LABKEY.SignalData.initializeDataFileUploadForm = function (metadataFormId, eleme
 
                         //get modelInstance from store that matches file.name
                         var store = uploadLog.getStore();
-                        var idx = store.findExact('DataFile', file.name);
+                        var idx = store.find('DataFile', file.name);
                         var process = store.getAt(idx);
 
                         //Set upload time
@@ -354,8 +354,16 @@ LABKEY.SignalData.initializeDataFileUploadForm = function (metadataFormId, eleme
             },
             success: function() {
                 clearCachedReports(false, function() {
+                    let returnUrl = LABKEY.ActionURL.getReturnUrl();
+                    if (returnUrl) {
+                        if (window.location.hash)
+                            returnUrl = returnUrl.concat(window.location.hash);
+                    }
+                    else {
+                        returnUrl = LABKEY.ActionURL.buildURL('assay', 'assayBegin', null, {rowId: assay.id});
+                    }
                     uploadLog.workingDirectory = setWorkingDirectory();
-                    window.location = LABKEY.ActionURL.buildURL('assay', 'assayBegin', null, {rowId: assay.id});
+                    window.location = returnUrl;
                 },this);
             },
             failure: function(response){