LabKey · bbimber · Nov 6, 2025 · Sep 8, 2025 · Sep 9, 2025 · Sep 9, 2025
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -10,6 +10,11 @@ jobs:
     if: github.repository == 'BimberLabInternal/BimberLabKeyModules'
     runs-on: ubuntu-latest
     steps:
+      # Note: use slight delay in case there are associated commits across repos
+      - name: "Sleep for 30 seconds"
+        run: sleep 30s
+        shell: bash
+
       - name: "Build DISCVR"
         uses: bimberlabinternal/DevOps/githubActions/discvr-build@master
         with:

diff --git a/IDR/resources/queries/bimber_data/idrOutcomeSource.sql b/IDR/resources/queries/bimber_data/idrOutcomeSource.sql
@@ -6,6 +6,7 @@ cohortStart as date,
 CASE
     WHEN contprog = 'C' THEN 'Controller'
     WHEN contprog = 'P' THEN 'Progressor'
+    ELSE contprog
 END as outcome,
 
 'Hansen/IDR' as dataSource

diff --git a/IDR/resources/queries/bimber_data/idrSampleSource.sql b/IDR/resources/queries/bimber_data/idrSampleSource.sql
@@ -5,7 +5,10 @@ ID as sampleid,
 SampleDate as date,
 Tissue as sampleType,
 CellCnt as quantity,
-
+freezer,
+rack,
+box,
+"position",
 'Hansen/IDR' as dataSource
 
 FROM bimber_data.ln_loc
@@ -18,9 +21,17 @@ SELECT
 Rh as Id,
 ID as sampleid,
 SampleDate as date,
-Tissue as sampleType,
+CASE
+    WHEN (Tissue IS NOT NULL AND Tissue != '') AND (SampleType IS NOT NULL AND SampleType != '') THEN (SampleType || ' / ' || Tissue)
+    WHEN (Tissue IS NOT NULL AND Tissue != '') THEN Tissue
+    WHEN (SampleType IS NOT NULL AND SampleType != '') THEN SampleType
+    ELSE NULL
+END AS sampleType,
 null as quantity,
-
+freezer,
+rack,
+box,
+"position",
 'Hansen/IDR' as dataSource
 
 FROM bimber_data.ult_loc

diff --git a/PMR/resources/etls/prime-blooddraws.xml b/PMR/resources/etls/prime-blooddraws.xml
@@ -34,6 +34,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="blood"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-chemistryResults.xml b/PMR/resources/etls/prime-chemistryResults.xml
@@ -8,7 +8,6 @@
                 <sourceColumns>
                     <column>Id</column>
                     <column>date</column>
-                    <column>ageAtTime</column>
                     <column>testId</column>
                     <column>result</column>
                     <column>units</column>
@@ -18,6 +17,9 @@
                     <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="chemistryResults" targetOption="merge" bulkLoad="true" batchSize="1000">
                 <alternateKeys>
@@ -37,6 +39,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="chemistryResults"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-clinpathRuns.xml b/PMR/resources/etls/prime-clinpathRuns.xml
@@ -19,6 +19,9 @@
                     <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="clinpathRuns" bulkLoad="true" targetOption="merge" batchSize="1000">
                 <alternateKeys>
@@ -38,6 +41,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="clinpathRuns"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-hematologyResults.xml b/PMR/resources/etls/prime-hematologyResults.xml
@@ -8,7 +8,6 @@
                 <sourceColumns>
                     <column>Id</column>
                     <column>date</column>
-                    <column>ageAtTime</column>
                     <column>testId</column>
                     <column>result</column>
                     <column>units</column>
@@ -18,6 +17,9 @@
                     <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="hematologyResults" targetOption="merge" bulkLoad="true" batchSize="1000">
                 <alternateKeys>
@@ -37,6 +39,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="hematologyResults"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-histology.xml b/PMR/resources/etls/prime-histology.xml
@@ -17,6 +17,9 @@
                     <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="histology" targetOption="merge" bulkLoad="true" batchSize="1000">
                 <alternateKeys>
@@ -36,6 +39,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="histology"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-microbiology.xml b/PMR/resources/etls/prime-microbiology.xml
@@ -18,6 +18,9 @@
                     <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="microbiology" targetOption="merge" bulkLoad="true" batchSize="1000">
                 <alternateKeys>
@@ -37,6 +40,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="microbiology"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-pathologyDiagnoses.xml b/PMR/resources/etls/prime-pathologyDiagnoses.xml
@@ -8,14 +8,14 @@
                 <sourceColumns>
                     <column>Id</column>
                     <column>date</column>
-                    <column>ageAtTime</column>
                     <column>sort_order</column>
                     <column>codes</column>
                     <column>objectid</column>
-                    <column>created</column>
-                    <column>modified</column>
                     <column>QCState/Label</column>
                 </sourceColumns>
+                <sourceFilters>
+                    <sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
+                </sourceFilters>
             </source>
             <destination schemaName="study" queryName="pathologyDiagnoses" targetOption="merge" bulkLoad="true" batchSize="1000">
                 <alternateKeys>
@@ -35,6 +35,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="pathologyDiagnoses"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/PMR/resources/etls/prime-weight.xml b/PMR/resources/etls/prime-weight.xml
@@ -37,6 +37,8 @@
                     <setting name="destSchema" value="study"/>
                     <setting name="destQuery" value="weight"/>
                     <setting name="destColumn" value="objectId"/>
+
+                    <setting name="reportOnly" value="false"/>
                 </settings>
             </taskref>
         </transform>

diff --git a/SivStudies/resources/etls/idr-data.xml b/SivStudies/resources/etls/idr-data.xml
@@ -15,7 +15,7 @@
                     <setting name="dataSourceQuery" value="subjects"/>
                     <setting name="dataSourceSubjectColumn" value="Rh"/>
                     <setting name="dataSourceColumns" value="Rh,cohortStart,cohortEnd,cohort,RhCode"/>
-                    <setting name="dataSourceColumnMapping" value="Rh=Id,cohortStart=date,cohortEnd=enddate,RhCode=cohortId,cohort=study"/>
+                    <setting name="dataSourceColumnMapping" value="Rh=Id,cohortStart=date,cohortEnd=enddate,RhCode=cohortAlias,cohort=study"/>
                     <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
                     <setting name="dataSourceAdditionalFilters" value="cohortStart~neq=0000-00-00"/>
 
@@ -37,7 +37,7 @@
                     <setting name="dataSourceSchema" value="bimber_data"/>
                     <setting name="dataSourceQuery" value="idrSampleSource"/>
                     <setting name="dataSourceSubjectColumn" value="Id"/>
-                    <setting name="dataSourceColumns" value="Id,date,sampleId,sampleType,quantity"/>
+                    <setting name="dataSourceColumns" value="Id,date,sampleId,sampleType,quantity,freezer,rack,box,position"/>
                     <setting name="dataSourceColumnDefaults" value="dataSource=Hansen/IDR"/>
 
                     <setting name="targetSchema" value="study"/>

diff --git a/SivStudies/resources/etls/idr-subjects.xml b/SivStudies/resources/etls/idr-subjects.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<etl xmlns="http://labkey.org/etl/xml">
+    <name>Hansen/IDR Subjects</name>
+    <description>Hansen/IDR Subjects</description>
+    <transforms>
+        <transform id="subjects" type="TaskRefTransformStep">
+            <taskref ref="org.labkey.sivstudies.etl.AddMissingIdrSubjects">
+
+            </taskref>
+        </transform>
+    </transforms>
+    <schedule>
+        <cron expression="0 15 20 * * ?"/>
+    </schedule>
+</etl>
diff --git a/SivStudies/resources/queries/study/additionalDatatypes.query.xml b/SivStudies/resources/queries/study/additionalDatatypes.query.xml
@@ -18,6 +18,9 @@
                     <column columnName="description">
                         <columnTitle>Description</columnTitle>
                     </column>
+                    <column columnName="comments">
+                        <columnTitle>Comments</columnTitle>
+                    </column>
                 </columns>
             </table>
         </tables>

diff --git a/SivStudies/resources/queries/study/additionalDatatypes/.qview.xml b/SivStudies/resources/queries/study/additionalDatatypes/.qview.xml
@@ -5,6 +5,7 @@
         <column name="timePostSivChallenge/daysPostInfection"/>
         <column name="category"/>
         <column name="description"/>
+        <column name="comments"/>
         <column name="dataSource"/>
     </columns>
     <sorts>

diff --git a/SivStudies/resources/queries/study/assignment.query.xml b/SivStudies/resources/queries/study/assignment.query.xml
@@ -18,15 +18,24 @@
                     <column columnName="subgroup">
                         <columnTitle>Sub-Group</columnTitle>
                     </column>
-                    <column columnName="cohortId">
-                        <columnTitle>Cohort ID</columnTitle>
+                    <column columnName="cohortAlias">
+                        <columnTitle>Cohort Alias</columnTitle>
                     </column>
                     <column columnName="dataSource">
                         <columnTitle>Data Source</columnTitle>
                     </column>
                     <column columnName="category">
                         <columnTitle>Category</columnTitle>
                     </column>
+                    <column columnName="cohortId">
+                        <columnTitle>Cohort ID</columnTitle>
+                        <fk>
+                            <fkDbSchema>studies</fkDbSchema>
+                            <fkTable>studyCohorts</fkTable>
+                            <fkColumnName>rowId</fkColumnName>
+                            <fkDisplayColumnName>labelOrName</fkDisplayColumnName>
+                        </fk>
+                    </column>
                     <column columnName="description">
                         <columnTitle>Description</columnTitle>
                         <isHidden>true</isHidden>

diff --git a/SivStudies/resources/queries/study/assignment/.qview.xml b/SivStudies/resources/queries/study/assignment/.qview.xml
@@ -5,8 +5,9 @@
         <column name="enddate"/>
         <column name="study"/>
         <column name="subgroup"/>
-        <column name="cohortId"/>
+        <column name="cohortAlias"/>
         <column name="category"/>
+        <column name="cohortId"/>
         <column name="dataSource"/>
     </columns>
     <sorts>

diff --git a/SivStudies/resources/queries/study/flow.query.xml b/SivStudies/resources/queries/study/flow.query.xml
@@ -24,7 +24,7 @@
                     <column columnName="units">
                         <columnTitle>Units</columnTitle>
                     </column>
-                    <column columnName="comment">
+                    <column columnName="comments">
                         <columnTitle>Comments</columnTitle>
                     </column>
                     <column columnName="dataSource">

diff --git a/SivStudies/resources/queries/study/flow/.qview.xml b/SivStudies/resources/queries/study/flow/.qview.xml
@@ -7,6 +7,7 @@
         <column name="population"/>
         <column name="result"/>
         <column name="units"/>
+        <column name="comments"/>
         <column name="dataSource"/>
         <column name="viralLoad"/>
     </columns>

diff --git a/SivStudies/resources/queries/study/genetics.query.xml b/SivStudies/resources/queries/study/genetics.query.xml
@@ -23,6 +23,10 @@
                     <column columnName="score">
                         <columnTitle>Score</columnTitle>
                     </column>
+                    <column columnName="comments">
+                        <columnTitle>Comments</columnTitle>
+                        <inputType>textarea</inputType>
+                    </column>
                     <column columnName="dataSource">
                         <columnTitle>Data Source</columnTitle>
                     </column>

diff --git a/SivStudies/resources/queries/study/genetics/.qview.xml b/SivStudies/resources/queries/study/genetics/.qview.xml
@@ -7,6 +7,7 @@
         <column name="marker"/>
         <column name="result"/>
         <column name="score"/>
+        <column name="comments"/>
         <column name="dataSource"/>
     </columns>
     <sorts>

diff --git a/SivStudies/resources/queries/study/immunizations.query.xml b/SivStudies/resources/queries/study/immunizations.query.xml
@@ -27,6 +27,10 @@
                     <column columnName="reason">
                         <columnTitle>Reason</columnTitle>
                     </column>
+                    <column columnName="comments">
+                        <columnTitle>Comments</columnTitle>
+                        <inputType>textarea</inputType>
+                    </column>
                     <column columnName="dataSource">
                         <columnTitle>Data Source</columnTitle>
                     </column>

diff --git a/SivStudies/resources/queries/study/immunizations/.qview.xml b/SivStudies/resources/queries/study/immunizations/.qview.xml
@@ -7,6 +7,7 @@
         <column name="route"/>
         <column name="quantity"/>
         <column name="quantity_units"/>
+        <column name="comments"/>
         <column name="dataSource"/>
     </columns>
     <sorts>

diff --git a/SivStudies/resources/queries/study/labwork.query.xml b/SivStudies/resources/queries/study/labwork.query.xml
@@ -34,6 +34,10 @@
                     <column columnName="method">
                         <columnTitle>Method</columnTitle>
                     </column>
+                    <column columnName="comments">
+                        <columnTitle>Comments</columnTitle>
+                        <inputType>textarea</inputType>
+                    </column>
                     <column columnName="dataSource">
                         <columnTitle>Data Source</columnTitle>
                     </column>

diff --git a/SivStudies/resources/queries/study/labwork/.qview.xml b/SivStudies/resources/queries/study/labwork/.qview.xml
@@ -7,6 +7,7 @@
         <column name="result"/>
         <column name="units"/>
         <column name="method"/>
+        <column name="comments"/>
         <column name="dataSource"/>
         <column name="viralLoad"/>
         <column name="ageAtTime/AgeAtTime"/>

diff --git a/SivStudies/resources/queries/study/procedures.query.xml b/SivStudies/resources/queries/study/procedures.query.xml
@@ -15,6 +15,10 @@
                     <column columnName="procedure">
                         <columnTitle>Procedure</columnTitle>
                     </column>
+                    <column columnName="comments">
+                        <columnTitle>Comments</columnTitle>
+                        <inputType>textarea</inputType>
+                    </column>
                     <column columnName="dataSource">
                         <columnTitle>Data Source</columnTitle>
                     </column>

diff --git a/SivStudies/resources/queries/study/procedures/.qview.xml b/SivStudies/resources/queries/study/procedures/.qview.xml
@@ -4,6 +4,7 @@
         <column name="date"/>
         <column name="category"/>
         <column name="procedure"/>
+        <column name="comments"/>
         <column name="dataSource"/>
         <column name="viralLoad"/>
     </columns>