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Merged
bbimber merged 31 commits into from
Aug 21, 2025
Merged

Merge discvr-25.7 to develop #260

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578024e
Update mGAP Query
bbimber Jul 24, 2025
f58e9f3
Expand study/cohort fields
bbimber Jul 27, 2025
551ad88
Expand challenge query
bbimber Jul 27, 2025
14915d8
Fix challenge query
bbimber Jul 29, 2025
ab29c30
Improve returnUrl logic for mGAP's login page
bbimber Jul 30, 2025
47abfbd
Merge discvr-25.3 to discvr-25.7
bbimber Jul 30, 2025
d2cde06
Merge pull request #192 from bimberlabinternal/25.7_fb_merge
bbimber Jul 31, 2025
2c1ec22
Test fix and support VCF 4.4
bbimber Aug 4, 2025
feff0ec
Ensure lifted VCF is sorted and indexed
bbimber Aug 4, 2025
1f2da5b
Ignore half-called GTs in KING
bbimber Aug 4, 2025
5b4d5fe
Add pvl_outcomes table
bbimber Aug 4, 2025
4cf34f1
Merge discvr-25.3 to discvr-25.7
bbimber Aug 5, 2025
db6458f
Use lsid instead of objectId for ETL
bbimber Aug 5, 2025
dbe3cdc
Merge pull request #193 from bimberlabinternal/25.7_fb_merge
bbimber Aug 5, 2025
9f86bac
Use Audit table for PMR ETL deletes
bbimber Aug 6, 2025
d79c6a7
Add celltype column to tcr stats table
bbimber Aug 6, 2025
22a4369
Add tcrdb column
bbimber Aug 7, 2025
c04c297
Add study validation notification
bbimber Aug 8, 2025
22c2039
Correct column name in ETL
bbimber Aug 8, 2025
0e99631
Add ETL task to verify source/dest row counts
bbimber Aug 8, 2025
a93767f
Use maxRows in SelectRowsCommand
bbimber Aug 10, 2025
5c19329
Update ETL batchSize
bbimber Aug 11, 2025
61ee678
Simplify mGAP ETL
bbimber Aug 12, 2025
48bd615
Many improvements to EHR-related ETLs
bbimber Aug 12, 2025
ad75704
Improve mGAP QC
bbimber Aug 13, 2025
ccef459
Add MCC column showing numAnimalsRequested
bbimber Aug 19, 2025
bfaffc2
Sql fix
bbimber Aug 19, 2025
550b30f
Add url to column
bbimber Aug 20, 2025
d17c281
Merge discvr-25.3 to discvr-25.7
bbimber Aug 20, 2025
c838d02
Merge pull request #195 from bimberlabinternal/25.7_fb_merge
bbimber Aug 20, 2025
05cf4ff
Merge discvr-25.7 to develop
bbimber Aug 21, 2025
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1 change: 1 addition & 0 deletions GenotypeAssays/test/src/org/labkey/test/tests/external/labModules/GenotypeAssaysTest.java
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Expand Up @@ -182,6 +182,7 @@ private void beadStudioImportTest()

Ext4FieldRef.getForLabel(this, "Run Description").setValue("Description");

waitForElement(Ext4Helper.Locators.ext4Button("Download Example Data"));
File exampleData = clickAndWaitForDownload(Ext4Helper.Locators.ext4Button("Download Example Data"));

waitAndClick(Ext4Helper.Locators.radiobutton(this, "File Upload"));
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1 change: 1 addition & 0 deletions PMR/build.gradle
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Expand Up @@ -9,6 +9,7 @@ dependencies {
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:DiscvrLabKeyModules:discvrcore", depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:onprcEHRModules:GeneticsCore", depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: ":server:modules:BimberLabKeyModules:primeseq", depProjectConfig: "published", depExtension: "module")

BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:DiscvrLabKeyModules:Studies", depProjectConfig: "apiJarFile")
BuildUtils.addLabKeyDependency(project: project, config: "implementation", depProjectPath: ":server:modules:premiumModules:dataintegration", depProjectConfig: "apiJarFile")
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198 changes: 0 additions & 198 deletions PMR/resources/etls/pmr-datasets.xml
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43 changes: 0 additions & 43 deletions PMR/resources/etls/pmr-demographics.xml
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79 changes: 76 additions & 3 deletions PMR/resources/etls/pmrClinicalData.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,91 @@
<transform id="demographics" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/pmr-demographics"/>
<setting name="transformId" value="{PMR}/prime-demographics"/>
</settings>
</taskref>
</transform>

<transform id="datasets" type="TaskrefTransformStep">
<transform id="birth" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/pmr-datasets"/>
<setting name="transformId" value="{PMR}/prime-birth"/>
</settings>
</taskref>
</transform>

<transform id="blooddraws" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-blooddraws"/>
</settings>
</taskref>
</transform>

<transform id="chemistryResults" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-chemistryResults"/>
</settings>
</taskref>
</transform>

<transform id="clinpathRuns" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-clinpathRuns"/>
</settings>
</taskref>
</transform>

<transform id="hematologyResults" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-hematologyResults"/>
</settings>
</taskref>
</transform>

<transform id="histology" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-histology"/>
</settings>
</taskref>
</transform>

<transform id="microbiology" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-microbiology"/>
</settings>
</taskref>
</transform>

<transform id="parentage" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-parentage"/>
</settings>
</taskref>
</transform>

<transform id="pathologyDiagnoses" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-pathologyDiagnoses"/>
</settings>
</taskref>
</transform>

<transform id="weight" type="TaskrefTransformStep">
<taskref ref="org.labkey.di.steps.QueueJobTask">
<settings>
<setting name="transformId" value="{PMR}/prime-weight"/>
</settings>
</taskref>
</transform>

</transforms>
<schedule>
<cron expression="0 30 1 * * ?"/>
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