Merge branch 'discvr-21.7' of https://github.com/BimberLab/DiscvrLabKeyModules into discvr-21.7

Author: bbimber

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantDisplay/model.js

@@ -83,6 +83,11 @@ export default jbrowse => {
                            self.renderProps().config.color1.set(color)
 
                            const { centerLineInfo } = getContainingView(self)
+                           if (!centerLineInfo) {
+                                console.error('error! centerLineInfo is null')
+                                return;
+                           }
+
                            const { refName, assemblyName, offset } = centerLineInfo
                            const centerBp = Math.round(offset) + 1
 
@@ -136,14 +141,14 @@ export default jbrowse => {
             const trackId = getConf(track, 'trackId')
             const session = getSession(self)
             var widgetId = 'Variant-' + trackId;
-
             const featureWidget = session.addWidget(
                'ExtendedVariantWidget',
                widgetId,
-               { featureData: feature.toJSON(),
-                 extendedVariantDisplayConfig: extendedVariantDisplayConfig,
-                 message: message }
-            )
+               { featureData: feature,
+                   trackId: trackId,
+                   extendedVariantDisplayConfig: extendedVariantDisplayConfig,
+                   message: message
+           })
             session.showWidget(featureWidget)
             session.setSelection(feature)
          },

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/ExtendedVariantWidget.js

@@ -121,9 +121,9 @@ export default jbrowse => {
         return displayJSX
     }
 
-    function makeChart(samples, feat, classes){
+    function makeChart(samples, feat, classes, trackId){
         // Abort if there are no samples
-        if (Object.keys(samples).length === 0) {
+        if (!samples || Object.keys(samples).length === 0) {
             return null;
         }
 
@@ -234,9 +234,6 @@ export default jbrowse => {
                 )
             }
             const gtTitle = "Genotype Frequency (" + gtTotal.toString() + ")"
-
-            // TODO - get variables, prepare genotypeTable link
-            const trackId = 0
             const contig = feat["CHROM"];
             const start = feat["POS"];
             const end = feat["end"];
@@ -290,9 +287,14 @@ export default jbrowse => {
         const classes = styles()
         const { model } = props
         const feat = JSON.parse(JSON.stringify(model.featureData))
-        const samples = model.featureData.samples
+        const { samples } = feat
         feat["samples"] = null
 
+        const trackId = model.trackId
+        if (!trackId) {
+            console.error('Error! No trackId')
+        }
+
         const configDisplays = model.extendedVariantDisplayConfig
         const displays = makeDisplays(feat, configDisplays, classes)
         for (let i in configDisplays){
@@ -333,7 +335,7 @@ export default jbrowse => {
                     {infoDisplays}
                     {displays}
                     {annTable}
-                    {makeChart(samples, feat, classes)}
+                    {makeChart(samples, feat, classes, trackId)}
                 </Paper>
         )
     }

jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantWidget/index.js

@@ -10,9 +10,9 @@ export default jbrowse => {
       id: ElementId,
       type: types.literal('ExtendedVariantWidget'),
       featureData: types.frozen({}),
+      trackId: types.string,
       extendedVariantDisplayConfig: types.frozen([]),
       message: types.string
-
     })
     .actions(self => ({
       setFeatureData(data) {

jbrowse/src/org/labkey/jbrowse/JBrowseController.java

@@ -477,29 +477,11 @@ public class GetGenotypesAction extends ReadOnlyApiAction<GetGenotypesForm>
     {
         private List<JsonFile> getJsonFiles(GetGenotypesForm form)
         {
-            String field;
-            Integer rowId;
-            if (form.getTrackId().startsWith("data"))
-            {
-                field = "outputfile";
-                rowId = ConvertHelper.convert(form.getTrackId().replaceAll("^data(-)?", ""), Integer.class);
-
-            }
-            else if (form.getTrackId().startsWith("track"))
-            {
-                field = "trackid";
-                rowId = ConvertHelper.convert(form.getTrackId().replaceAll("^track(-)?", ""), Integer.class);
-            }
-            else
-            {
-                return null;
-            }
-
             Container targetContainer = getContainer().isWorkbook() ? getContainer().getParent() : getContainer();
             UserSchema us = QueryService.get().getUserSchema(getUser(), targetContainer, JBrowseSchema.NAME);
 
             TableInfo ti = us.getTable(JBrowseSchema.TABLE_JSONFILES);
-            TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString(field), rowId, CompareType.EQUAL), null);
+            TableSelector ts = new TableSelector(ti, new SimpleFilter(FieldKey.fromString("objectId"), form.getTrackId(), CompareType.EQUAL), null);
 
             return ts.getArrayList(JsonFile.class);
         }
@@ -515,17 +497,11 @@ public void validateForm(GetGenotypesForm form, Errors errors)
 
 
             List<JsonFile> jsonFiles = getJsonFiles(form);
-            if (jsonFiles == null)
+            if (jsonFiles == null || jsonFiles.isEmpty())
             {
                 errors.reject(ERROR_MSG, "Unknown trackId: " + form.getTrackId());
                 return;
             }
-
-            if (jsonFiles.isEmpty())
-            {
-                errors.reject(ERROR_MSG, "Unable to find trackId: " + form.getTrackId());
-                return;
-            }
             else if (jsonFiles.size() > 1)
             {
                 logger.error("More than one jsonfile returned for: " + form.getTrackId());