Merge pull request #184 from LabKey/fb_merge_23.11_to_develop

Merge discvr-23.11 to develop

Author: bbimber

GenotypeAssays/src/org/labkey/genotypeassays/GeneticsTableCustomizer.java

@@ -143,8 +143,7 @@ private void customizeSummaryByLineage(AbstractTableInfo ti)
             newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=assay." + ap.getName().replaceAll(" ", "") + "." + protocols.get(0).getName() + "&query.queryName=data&query.analysisId~eq=${analysis_id}", (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer())));
             ti.addColumn(newCol);
 
-            String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult.").append(d.getStorageTableName()).append(" a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = ").append(ti.getSqlDialect().getBooleanTRUE()).append(") WHERE a.analysisId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".analysis_id AND a.result IS NULL AND hs.name = ").append(ExprColumn.STR_TABLE_ALIAS).append(".lineages)");
+            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, getNewlineSql(ti))).append(" as expr FROM assayresult.").append(d.getStorageTableName()).append(" a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = ").append(ti.getSqlDialect().getBooleanTRUE()).append(") WHERE a.analysisId = ").append(ExprColumn.STR_TABLE_ALIAS).append(".analysis_id AND a.result IS NULL AND hs.name = ").append(ExprColumn.STR_TABLE_ALIAS).append(".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");
             ti.addColumn(newCol3);
@@ -169,7 +168,7 @@ private void customizeSummaryGrouped(AbstractTableInfo ti)
 
             Domain d = ap.getResultsDomain(protocols.get(0));
             String chr = ti.getSqlDialect().isPostgreSQL() ? "chr" : "char";
-            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, chr + "(10)")).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
+            SQLFragment sql3 = new SQLFragment("(select ").append(ti.getSqlDialect().getGroupConcat(new SQLFragment("hs.haplotype"), true, true, getNewlineSql(ti))).append(" as expr FROM assayresult." + d.getStorageTableName() + " a JOIN sequenceanalysis.haplotype_sequences hs ON (a.marker = hs.haplotype AND hs.type = 'Lineage' AND hs.present = " + ti.getSqlDialect().getBooleanTRUE() + ") WHERE a.analysisId = " + ExprColumn.STR_TABLE_ALIAS + ".analysis_id AND a.result IS NULL AND hs.name = " + ExprColumn.STR_TABLE_ALIAS + ".lineages)");
             ExprColumn newCol3 = new ExprColumn(ti, "cachedHaplotypes", sql3, JdbcType.VARCHAR, ti.getColumn("analysis_id"), ti.getColumn("lineages"));
             newCol3.setLabel("Matching Cached Haplotypes");
             ti.addColumn(newCol3);

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);