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Merge discvr-25.7 to develop
2 parents 4ef8bcf + 16681ba commit 6db0795

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‎.github/workflows/build.yml‎

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

‎IDR/resources/queries/bimber_data/idrOutcomeSource.sql‎

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@@ -6,6 +6,7 @@ cohortStart as date,
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CASE
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WHEN contprog = 'C' THEN 'Controller'
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WHEN contprog = 'P' THEN 'Progressor'
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ELSE contprog
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END as outcome,
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'Hansen/IDR' as dataSource

‎IDR/resources/queries/bimber_data/idrSampleSource.sql‎

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@@ -5,7 +5,10 @@ ID as sampleid,
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SampleDate as date,
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Tissue as sampleType,
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CellCnt as quantity,
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freezer,
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rack,
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box,
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"position",
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'Hansen/IDR' as dataSource
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FROM bimber_data.ln_loc
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Rh as Id,
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ID as sampleid,
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SampleDate as date,
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Tissue as sampleType,
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CASE
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WHEN (Tissue IS NOT NULL AND Tissue != '') AND (SampleType IS NOT NULL AND SampleType != '') THEN (SampleType || ' / ' || Tissue)
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WHEN (Tissue IS NOT NULL AND Tissue != '') THEN Tissue
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WHEN (SampleType IS NOT NULL AND SampleType != '') THEN SampleType
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ELSE NULL
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END AS sampleType,
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null as quantity,
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freezer,
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rack,
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box,
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"position",
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'Hansen/IDR' as dataSource
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FROM bimber_data.ult_loc

‎PMR/resources/etls/prime-blooddraws.xml‎

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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="blood"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-chemistryResults.xml‎

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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>testId</column>
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<column>result</column>
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<column>units</column>
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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="chemistryResults" targetOption="merge" bulkLoad="true" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="chemistryResults"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-clinpathRuns.xml‎

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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="clinpathRuns" bulkLoad="true" targetOption="merge" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="clinpathRuns"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-hematologyResults.xml‎

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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>testId</column>
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<column>result</column>
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<column>units</column>
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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="hematologyResults" targetOption="merge" bulkLoad="true" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="hematologyResults"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-histology.xml‎

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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="histology" targetOption="merge" bulkLoad="true" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="histology"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-microbiology.xml‎

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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="microbiology" targetOption="merge" bulkLoad="true" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="microbiology"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

‎PMR/resources/etls/prime-pathologyDiagnoses.xml‎

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<sourceColumns>
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<column>Id</column>
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<column>date</column>
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<column>ageAtTime</column>
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<column>sort_order</column>
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<column>codes</column>
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<column>objectid</column>
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<column>created</column>
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<column>modified</column>
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<column>QCState/Label</column>
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</sourceColumns>
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<sourceFilters>
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<sourceFilter column="qcstate/label" operator="eq" value="Completed"/>
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</sourceFilters>
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</source>
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<destination schemaName="study" queryName="pathologyDiagnoses" targetOption="merge" bulkLoad="true" batchSize="1000">
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<alternateKeys>
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<setting name="destSchema" value="study"/>
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<setting name="destQuery" value="pathologyDiagnoses"/>
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<setting name="destColumn" value="objectId"/>
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<setting name="reportOnly" value="false"/>
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</settings>
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</taskref>
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</transform>

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