[bot] Fast-forward for 26.9.0

GeneticsCore/resources/etls/MHC_Typing.xml

@@ -11,6 +11,7 @@
                     <column>marker</column>
                     <column>result</column>
                     <column>assaytype</column>
+                    <column>librarytype</column>
                     <column>score</column>
                     <column>totalTests</column>
                     <column>objectid</column>

GeneticsCore/resources/queries/geneticscore/mhc_data_source.sql

@@ -13,6 +13,7 @@ SELECT
     s.totalRecords as totalTests,
     s.status as result,
     cast('SSP' as varchar) as assaytype,
+    'N/A' as librarytype,
     NULL as score
 
 FROM assay.SSP_assay.SSP.SSP_Summary s
@@ -27,6 +28,7 @@ SELECT
     count(*) as totalTests,
     cast('POS' as varchar) as result,
     cast('SBT' as varchar) as assaytype,
+    group_concat(DISTINCT a.analysisId.readset.libraryType, ',') as librarytype,
     sum(a.result) / (SELECT count(DISTINCT a2.analysisId) as total FROM assay.GenotypeAssay.Genotype.Data a2 WHERE a2.subjectId = a.subjectId AND a2.run.assayType = 'SBT' ) AS score,
 
 FROM assay.GenotypeAssay.Genotype.Data a
@@ -42,6 +44,7 @@ DISTINCT s.subjectId,
          1 as totalTests,
          cast('NEG' as varchar) as result,
          cast('SBT' as varchar) as assaytype,
+         null as librarytype,
          NULL as score,
 
 --we want any IDs with SBT data, but lacking data for these special-cased markers

GeneticsCore/resources/schemas/dbscripts/postgresql/geneticscore-17.14-17.15.sql

@@ -0,0 +1 @@
+ALTER TABLE geneticscore.mhc_data ADD librarytype varchar(1000);

GeneticsCore/resources/schemas/dbscripts/sqlserver/geneticscore-17.14-17.15.sql

@@ -0,0 +1 @@
+ALTER TABLE geneticscore.mhc_data ADD libraryType varchar(1000);

GeneticsCore/resources/schemas/geneticscore.xml

@@ -44,6 +44,9 @@
             <ns:column columnName="assaytype">
                 <ns:columnTitle>Assay Type</ns:columnTitle>
             </ns:column>
+            <ns:column columnName="librarytype">
+                <ns:columnTitle>Library Type</ns:columnTitle>
+            </ns:column>
             <ns:column columnName="objectid">
                 <ns:columnTitle>Key</ns:columnTitle>
                 <ns:isHidden>true</ns:isHidden>

GeneticsCore/resources/views/mhcDataDashboard.html

@@ -86,6 +86,12 @@
                             schemaName: 'geneticscore',
                             queryName: 'mhc_data'
                         })
+                    },{
+                        name: 'Manage Library Types',
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {
+                            schemaName: 'sequenceanalysis',
+                            queryName: 'library_types'
+                        })
                     }]
                 },{
                     header: 'Data Archival',

GeneticsCore/src/org/labkey/GeneticsCore/GeneticsCoreModule.java

@@ -40,7 +40,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 17.14;
+        return 17.15;
     }
 
     @Override

GeneticsCore/src/org/labkey/GeneticsCore/mhc/MhcTaskRef.java

@@ -159,7 +159,7 @@ private void processSubject(PipelineJob job, String subject) throws PipelineJobE
         }
 
         List<Map<String, Object>> toInsert = new ArrayList<>();
-        Set<String> fields = PageFlowUtil.set("subjectid", "marker", "result", "assaytype", "totalTests", "score");
+        Set<String> fields = PageFlowUtil.set("subjectid", "marker", "result", "assaytype", "totalTests", "score", "librarytype");
         new TableSelector(us.getTable("mhc_data_source"), fields, new SimpleFilter(FieldKey.fromString("subjectId"), subject), null).forEachResults(rs -> {
             CaseInsensitiveHashMap<Object> map = new CaseInsensitiveHashMap<>();
             for (String f : fields)

ONPRC_EHR_ComplianceDB/module.properties

@@ -1,4 +1,4 @@
 Name: ONPRC_EHR_ComplianceDB
 ModuleClass: org.labkey.ONPRCEHR_ComplianceDB.ONPRC_EHR_ComplianceDBModule
-SupportedDatabases: mssql
-ManageVersion: false
+SupportedDatabases: mssql, pgsql
+ManageVersion: true