Merge discvr-23.7 to discvr-23.11

Author: bbimber

MccColony/resources/queries/study/demographics/.qview.xml

@@ -17,7 +17,9 @@
             </properties>
         </column>
         <column name="dam"/>
+        <column name="damMccAlias"/>
         <column name="sire"/>
+        <column name="sireMccAlias"/>
         <column name="birth"/>
         <column name="death"/>
         <column name="species"/>

PMR/resources/data/calculated_status_codes.tsv

@@ -0,0 +1,9 @@
+code    meaning
+Alive
+Dead
+ERROR
+No Record
+Shipped
+u   Unknown
+Unknown
+Fetus

PMR/resources/queries/study/pedigree.sql

@@ -26,4 +26,4 @@ d.id.demographics.species,
 'Demographics' as source
 
 FROM study.demographicsParents d
-WHERE d.numParents > 0
+WHERE d.numParents > 0 and d.id.demographics.species IS NOT NULL

PMR/resources/views/populateData.html

@@ -169,7 +169,7 @@
         },{
             label: 'Calculated Status Code',
             populateFn: 'populateFromFile',
-            moduleName: 'ehr',
+            moduleName: 'pmr',
             schemaName: 'ehr_lookups',
             queryName: 'calculated_status_codes',
             pk: 'rowid'

mGAP/resources/etls/prime-seq.xml

@@ -108,6 +108,8 @@
                     <column>sitesOnlyVcfId/name</column>
                     <column>novelSitesVcfId/dataid/DataFileUrl</column>
                     <column>novelSitesVcfId/name</column>
+                    <column>luceneIndex/dataid/DataFileUrl</column>
+                    <column>luceneIndex/name</column>
                     <column>humanJbrowseId</column>
                     <column>objectId</column>
                 </sourceColumns>
@@ -119,6 +121,7 @@
                     <column source="variantTable/dataid/DataFileUrl" target="variantTable" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
                     <column source="sitesOnlyVcfId/dataid/DataFileUrl" target="sitesOnlyVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
                     <column source="novelSitesVcfId/dataid/DataFileUrl" target="novelSitesVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
+                    <column source="luceneIndex/dataid/DataFileUrl" target="luceneIndex" transformClass="org.labkey.mgap.columnTransforms.LuceneIndexTransform" />
                     <column source="jbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseSessionTransform"/>
                     <column source="liftedVcfId/dataid/DataFileUrl" target="liftedVcfId" transformClass="org.labkey.mgap.columnTransforms.LiftedVcfTransform" />
                     <column source="humanJbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseHumanSessionTransform"/>

mGAP/resources/queries/mGAP/userRequests/.qview.xml

@@ -5,6 +5,8 @@
         <column name="lastName"/>
         <column name="title"/>
         <column name="institution"/>
+        <column name="category"/>
+        <column name="country"/>
         <column name="reason"/>
         <column name="userId"/>
         <column name="hasAccess"/>

mGAP/resources/schemas/dbscripts/postgresql/mgap-16.68-16.69.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.userRequests ADD country varchar(1000);

mGAP/resources/schemas/dbscripts/postgresql/mgap-16.69-16.70.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD luceneIndex int;

mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.68-16.69.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.userRequests ADD country varchar(1000);

mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.69-16.70.sql

@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD luceneIndex int;