Improve mGAP QC

Author: bbimber

mGAP/resources/queries/mGAP/sequenceDatasetsSource.query.xml

@@ -0,0 +1,10 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="" tableDbType="TABLE">
+                <tableTitle>mGAP Sequence Datasets</tableTitle>
+
+            </table>
+        </tables>
+    </metadata>
+</query>

mGAP/resources/queries/mGAP/sequenceDatasetsSource.sql

@@ -4,7 +4,8 @@ SELECT
   r.totalForwardReads as totalReads,
   r.sraRuns as sraAccession,
   r.subjectId as originalId,
-  (SELECT s.center FROM mgap.subjectssource s WHERE s.subjectName = am.externalAlias) as center
+  (SELECT s.center FROM mgap.subjectssource s WHERE s.subjectName = am.externalAlias) as center,
+  CASE WHEN (SELECT s.subjectName FROM mgap.subjectssource s WHERE s.subjectName = am.externalAlias) IS NULL THEN true ELSE false END as missingDemographics
 
 FROM sequenceanalysis.sequence_readsets r
 JOIN mgap.animalMapping am ON (r.subjectId = am.subjectname)

mGAP/resources/schemas/mgap.xml

@@ -291,6 +291,7 @@
                     <fkDbSchema>laboratory</fkDbSchema>
                     <fkTable>subjects</fkTable>
                     <fkColumnName>subjectname</fkColumnName>
+                    <fkDisplayColumnName useRawValue="true"/>
                 </fk>
             </column>
             <column columnName="sequenceType">

mGAP/resources/views/mgapDataDashboard.html

@@ -81,6 +81,13 @@
                             queryName: 'subjectCaseMismatch',
                             'query.externalAlias~isnonblank': ''
                         })
+                    }, {
+                        name: 'Sequence Datasets Missing Demographics',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'mgap',
+                            queryName: 'sequenceDatasetsSource',
+                            'query.missingDemographics~eq': 'true'
+                        })
                     }]
                 },{
                     header: 'Prior Releases',
@@ -102,6 +109,12 @@
                             schemaName: 'mgap',
                             queryName: 'subjectsSource'
                         })
+                    }, {
+                        name: 'Sequence Datasets Synced to mGAP',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'mgap',
+                            queryName: 'sequenceDatasetsSource'
+                        })
                     }]
                 },{
                     header: 'Data and Processing',