Merge discvr-23.11 to develop

Author: bbimber

mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.annotations ADD inDefaultColumns boolean;

mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.annotations ADD inDefaultColumns bit;

mGAP/resources/schemas/mgap.xml

@@ -1224,6 +1224,9 @@
             <column columnName="allowableValues">
                 <columnTitle>Allowable Values</columnTitle>
             </column>
+            <column columnName="inDefaultColumns">
+                <columnTitle>In Default Columns?</columnTitle>
+            </column>
             <column columnName="container">
                 <isHidden>true</isHidden>
             </column>

mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java

@@ -17,6 +17,7 @@ public class AnnotationModel
     private String _formatString;
     private Boolean _hidden = false;
     private Boolean _isIndexed = false;
+    private Boolean _inDefaultColumns = false;
     private String _allowableValues;
 
     public AnnotationModel()
@@ -166,7 +167,8 @@ public void setHidden(Boolean hidden)
 
     public boolean isIndexed()
     {
-        return _isIndexed == null || _isIndexed;
+        // Defaults to false when null
+        return _isIndexed != null && _isIndexed;
     }
 
     public void setIndexed(Boolean indexed)
@@ -183,4 +185,15 @@ public void setAllowableValues(String allowableValues)
     {
         _allowableValues = allowableValues;
     }
+
+    public Boolean isInDefaultColumns()
+    {
+        // Defaults to false when null
+        return _inDefaultColumns != null && _inDefaultColumns;
+    }
+
+    public void setInDefaultColumns(Boolean inDefaultColumns)
+    {
+        _inDefaultColumns = inDefaultColumns;
+    }
 }

mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java

@@ -50,6 +50,11 @@ else if (ams.size() > 1)
             field.setIndexed(true);
         }
 
+        if (am.isInDefaultColumns())
+        {
+            field.setInDefaultColumns(true);
+        }
+
         if (StringUtils.trimToNull(am.getDescription()) != null)
         {
             field.setDescription(am.getDescription());

mGAP/src/org/labkey/mgap/mGAPController.java

@@ -1209,6 +1209,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
                         getOptionalField(line, header, "FormatString", row, "formatString");
                         getOptionalField(line, header, "AllowableValues", row, "allowableValues");
                         getOptionalField(line, header, "IsIndexed", row, "isIndexed");
+                        getOptionalField(line, header, "InDefaultColumns", row, "inDefaultColumns");
 
                         toAdd.add(row);
                     }

mGAP/src/org/labkey/mgap/mGAPManager.java

@@ -99,7 +99,7 @@ public Set<User> getNotificationUsers()
 
             if (u == null)
             {
-                _log.error("Unknown user registered for mGAP notifcations: " + username);
+                _log.error("Unknown user registered for mGAP notifications: " + username);
             }
 
             if (u != null)

mGAP/src/org/labkey/mgap/mGAPModule.java

@@ -74,7 +74,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 16.70;
+        return 16.71;
     }
 
     @Override

mcc/resources/queries/mcc/duplicatedAggregatedDemographics.sql

@@ -1,7 +1,8 @@
 SELECT
 
     m.Id,
-    GROUP_CONCAT(distinct m.originalId, ',') as originalIds
+    GROUP_CONCAT(distinct m.originalId, ',') as originalIds,
+    GROUP_CONCAT(distinct m.container.name, ',') as folders
 
 FROM mcc.aggregatedDemographics m
 

mcc/src/client/RequestReview/components/RabReviewForm.tsx

@@ -117,6 +117,7 @@ export default function RabReviewForm(props: {requestId: string}) {
                         <MenuItem value={"I recommend this proposal"}>I recommend this proposal</MenuItem>
                         <MenuItem value={"I recommend this proposal with conditions"}>I recommend this proposal with conditions</MenuItem>
                         <MenuItem value={"I do not recommend this proposal"}>I do not recommend this proposal</MenuItem>
+                        <MenuItem value={"I abstain from voting"}>I abstain from voting</MenuItem>
                     </Select>
                 </TableCell>
             </TableRow>