Add support for mGAP annotations to supply InDefaultFields

bimberlabinternal · Dec 14, 2023 · b639934 · b639934
1 parent 62cf397
commit b639934
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Showing 8 changed files with 24 additions and 2 deletions.
diff --git a/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.70-16.71.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD inDefaultColumns boolean;
diff --git a/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.70-16.71.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD inDefaultColumns bit;
diff --git a/mGAP/resources/schemas/mgap.xml b/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>

diff --git a/mGAP/src/org/labkey/mgap/jbrowse/AnnotationModel.java b/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()
@@ -183,4 +184,14 @@ public void setAllowableValues(String allowableValues)
     {
         _allowableValues = allowableValues;
     }
+
+    public Boolean isInDefaultColumns()
+    {
+        return _inDefaultColumns;
+    }
+
+    public void setInDefaultColumns(Boolean inDefaultColumns)
+    {
+        _inDefaultColumns = inDefaultColumns;
+    }
 }
diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPFieldCustomizer.java b/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());

diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/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);
                     }

diff --git a/mGAP/src/org/labkey/mgap/mGAPManager.java b/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)

diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/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
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		ALTER TABLE mGAP.variantCatalogReleases ADD inDefaultColumns boolean;