Merge pull request #159 from bimberlabinternal/24.3_fb_merge

Merge discvr-23.11 to discvr-24.3
bimberlabinternal · Jun 5, 2024 · b2fb1d5 · b2fb1d5
2 parents 17523ed + e4f15bf
commit b2fb1d5
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Showing 7 changed files with 22 additions and 4 deletions.
diff --git a/MccColony/resources/queries/study/demographics/.qview.xml b/MccColony/resources/queries/study/demographics/.qview.xml
@@ -26,6 +26,7 @@
         <column name="Id/MostRecentWeight/MostRecentWeightGrams"/>
         <column name="Id/MostRecentWeight/MostRecentWeightDate"/>
         <column name="alternateIds"/>
+        <column name="litterId"/>
         <column name="excludeFromCensus"/>
         <column name="Id/mostRecentObservations/availability::observation">
             <properties>

diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java b/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java
@@ -174,7 +174,7 @@ private static class FieldData
     public static void filterCodingPotential(Set<String> codingPotential)
     {
         //due to overlapping transcripts, this is often added.  remove these less-specific terms in order
-        for (String type : Arrays.asList("intragenic_variant", "non_coding_transcript_variant", "intron_variant"))
+        for (String type : Arrays.asList("custom", "intergenic_variant", "intragenic_variant"))
         {
             if (codingPotential.size() > 1)
             {
@@ -184,9 +184,8 @@ public static void filterCodingPotential(Set<String> codingPotential)
 
         if (codingPotential.contains("synonymous_variant") || codingPotential.contains("missense_variant"))
         {
+            codingPotential.remove("intergenic_variant");
             codingPotential.remove("intragenic_variant");
-            codingPotential.remove("non_coding_transcript_variant");
-            codingPotential.remove("intron_variant");
         }
     }
 

diff --git a/mcc/resources/queries/mcc/aggregatedDemographics.sql b/mcc/resources/queries/mcc/aggregatedDemographics.sql
@@ -19,6 +19,7 @@ SELECT
     WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/SNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
     ELSE false
   END as u24_status,
+  d.litterId,
   d.Id.mostRecentDeparture.mostRecentDeparture,
   o.availability,
   o.current_housing_status,
@@ -67,6 +68,7 @@ SELECT
     WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/WNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
     ELSE false
   END as u24_status,
+  d.litterId,
   d.Id.mostRecentDeparture.mostRecentDeparture,
   o.availability,
   o.current_housing_status,
@@ -112,6 +114,7 @@ SELECT
     d.objectid,
     d.calculated_status,
     d.u24_status,
+    d.litterId,
     d.Id.mostRecentDeparture.mostRecentDeparture,
     o.availability,
     o.current_housing_status,
@@ -160,6 +163,7 @@ SELECT
     d.objectid,
     d.calculated_status,
     d.u24_status,
+    d.litterId,
     d.Id.mostRecentDeparture.mostRecentDeparture,
     o.availability,
     o.current_housing_status,

diff --git a/mcc/resources/queries/study/demographics.query.xml b/mcc/resources/queries/study/demographics.query.xml
@@ -9,7 +9,7 @@
                 <deleteUrl />
                 <columns>
                     <column columnName="Id">
-                        <url></url>
+                        <url />
                     </column>
                     <column columnName="date">
                         <isHidden>true</isHidden>
@@ -121,6 +121,13 @@
                     <column columnName="alternateIds">
                         <columnTitle>Alternate IDs</columnTitle>
                     </column>
+                    <column columnName="litterId">
+                        <columnTitle>Litter ID</columnTitle>
+                        <url>/query/executeQuery.view?schemaName=study&amp;
+                            query.queryName=Demographics&amp;
+                            query.litterId~eq=${litterId}
+                        </url>
+                    </column>
                     <column columnName="remark">
 
                     </column>

diff --git a/mcc/resources/queries/study/demographics/.qview.xml b/mcc/resources/queries/study/demographics/.qview.xml
@@ -36,6 +36,7 @@
         <column name="usage_current"/>
         <column name="usage_future"/>
         <column name="date_of_observations"/>
+        <column name="litterId"/>
     </columns>
     <sorts>
         <sort column="Id" descending="false"/>

diff --git a/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml b/mcc/resources/referenceStudy/study/datasets/datasets_metadata.xml
@@ -685,6 +685,9 @@
             <column columnName="excludeFromCensus">
                 <datatype>boolean</datatype>
             </column>
+            <column columnName="litterId">
+                <datatype>varchar</datatype>
+            </column>
         </columns>
         <tableTitle>Demographics</tableTitle>
     </table>

diff --git a/primeseq/resources/etls/mcc.xml b/primeseq/resources/etls/mcc.xml
@@ -12,6 +12,9 @@
                     <column>sire</column>
                     <column>gender</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="Id" value="" operator="isnonblank"/>
+                </sourceFilters>
             </source>
             <destination schemaName="laboratory" queryName="subjects" targetOption="truncate" bulkLoad="true">
                 <constants>