Merge pull request #161 from bimberlabinternal/24.3_fb_merge

Merge discvr-23.11 to discvr-24.3

Author: bbimber

mcc/resources/queries/study/demographicsLittermates.query.xml

@@ -0,0 +1,23 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <description>Littermates of Any Animal</description>
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="demographicsLittermates" tableDbType="NOT_IN_DB">
+                <description>Littermates of Any Animal</description>
+                <columns>
+                    <column columnName="Id">
+                        <isKeyField>true</isKeyField>
+                        <isHidden>true</isHidden>
+                    </column>
+                    <column columnName="litterId">
+
+                    </column>
+                    <column columnName="litterMates">
+                        <columnTitle>Littermate(s)</columnTitle>
+                    </column>
+                </columns>
+                <titleColumn>Relationship</titleColumn>
+            </table>
+        </tables>
+    </metadata>
+</query>

mcc/resources/queries/study/demographicsLittermates.sql

@@ -0,0 +1,16 @@
+SELECT
+
+d1.Id,
+d1.litterId,
+
+GROUP_CONCAT(d2.Id, ',') as litterMates,
+
+FROM study.Demographics d1
+
+JOIN study.Demographics d2 ON (d1.litterId = d2.litterId AND d1.id != d2.id)
+
+WHERE
+    d1.qcstate.publicdata = true AND
+    d2.qcstate.publicdata = true
+
+GROUP BY d1.Id, d1.litterId

mcc/src/org/labkey/mcc/query/MccEhrCustomizer.java

@@ -96,6 +96,13 @@ private void customizeAnimalTable(AbstractTableInfo ti)
             ti.addColumn(col);
         }
 
+        if (ti.getColumn("littermates") == null)
+        {
+            var col = getWrappedIdCol(ti.getUserSchema(), ti, "littermates", "demographicsLittermates");
+            col.setLabel("Littermates");
+            col.setDescription("The IDs of ");
+            ti.addColumn(col);
+        }
     }
 
     private BaseColumnInfo getWrappedIdCol(UserSchema us, AbstractTableInfo ds, String name, String queryName)

primeseq/src/org/labkey/primeseq/PrimeseqModule.java

@@ -32,8 +32,6 @@
 import org.labkey.api.view.WebPartFactory;
 import org.labkey.primeseq.analysis.CombineMethylationRatesHandler;
 import org.labkey.primeseq.analysis.MethylationRateComparisonHandler;
-import org.labkey.primeseq.pipeline.BisSnpGenotyperAnalysis;
-import org.labkey.primeseq.pipeline.BisSnpIndelRealignerStep;
 import org.labkey.primeseq.pipeline.BismarkWrapper;
 import org.labkey.primeseq.pipeline.BlastPipelineJobResourceAllocator;
 import org.labkey.primeseq.pipeline.ClusterMaintenanceTask;
@@ -114,9 +112,6 @@ public PipelineStartup()
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.Provider());
                 SequencePipelineService.get().registerPipelineStep(new BismarkWrapper.MethylationExtractorProvider());
 
-                SequencePipelineService.get().registerPipelineStep(new BisSnpIndelRealignerStep.Provider());
-                SequencePipelineService.get().registerPipelineStep(new BisSnpGenotyperAnalysis.Provider());
-
                 SequenceAnalysisService.get().registerFileHandler(new MethylationRateComparisonHandler());
                 SequenceAnalysisService.get().registerFileHandler(new CombineMethylationRatesHandler());