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Merged
bbimber merged 21 commits into from
Feb 11, 2022
Merged

Merge discvr-21.11 to develop #98

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8ce0885
Bugfix to update cluster resources when using more than one job
bbimber Jan 23, 2022
5a6b7b9
Add sample type to import and fully implement insertRows
bbimber Jan 24, 2022
da3a9ee
Improvements to COVID sample import
bbimber Jan 26, 2022
025c575
Fix typo in MCC permissions
bbimber Jan 26, 2022
cfb6761
Update path to match new LK build
bbimber Jan 26, 2022
2c92db5
More QC for COVID sample import
bbimber Jan 27, 2022
f38d96b
Force unique IDs in patient rows for COVID samples
bbimber Jan 29, 2022
7cc2ab8
Minor improvements to COVID sample import form
bbimber Jan 31, 2022
37349b1
Update npm dependencies
bbimber Feb 1, 2022
7893539
Add error messages and fix validation-flow bugs (#49)
bbimber Feb 4, 2022
e97ded0
Better email message for MCC
bbimber Feb 4, 2022
0355ce4
Support GPUs for exacloud
bbimber Feb 7, 2022
0447805
Always add GPUs when using cellbender
bbimber Feb 7, 2022
09c90ce
Allow filtering of aggregate CITEseq barcodes
bbimber Feb 8, 2022
b365c0a
Fix slurm param name
bbimber Feb 8, 2022
fbbdb08
Update logic to detect CellBender jobs
bbimber Feb 8, 2022
3c624d3
Add MCC admin page and action to import default study
bbimber Feb 9, 2022
ca5d4f3
Use MCC study import action (#51)
bbimber Feb 11, 2022
348c90b
Merge discvr-21.11 to develop
bbimber Feb 11, 2022
38b3d10
Refactor MCC reference study and test
bbimber Feb 11, 2022
43b43af
Update MCC study.xml
bbimber Feb 11, 2022
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10 changes: 7 additions & 3 deletions covidseq/resources/schemas/covidseq.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
<tableTitle>Samples</tableTitle>
<!-- <javaCustomizer class="org.labkey.laboratory.query.SamplesCustomizer" />-->
<insertUrl></insertUrl>
<importUrl>/covidseq/sampleImport.view</importUrl>
<importUrl>covidseq/sampleImport.view</importUrl>
<auditLogging>DETAILED</auditLogging>
<pkColumnName>rowid</pkColumnName>
<titleColumn>samplename</titleColumn>
Expand Down Expand Up @@ -134,7 +134,7 @@
<javaCustomizer class="org.labkey.ldk.query.DefaultTableCustomizer" />
<auditLogging>DETAILED</auditLogging>
<pkColumnName>patientId</pkColumnName>
<titleColumn>rowid</titleColumn>
<titleColumn>identifier</titleColumn>
<columns>
<column columnName="rowid">
<isAutoInc>true</isAutoInc>
Expand All @@ -148,7 +148,7 @@
<columnTitle>Patient Identifier</columnTitle>
</column>
<column columnName="patientid">
<nullable>true</nullable>
<nullable>false</nullable>
<columnTitle>Patient Id</columnTitle>
<phi>PHI</phi>
</column>
Expand All @@ -169,6 +169,10 @@
<nullable>true</nullable>
<columnTitle>Age (years)</columnTitle>
</column>
<column columnName="ageQualifier">
<nullable>true</nullable>
<columnTitle>Age Qualifier</columnTitle>
</column>
<column columnName="gender">
<columnTitle>Gender</columnTitle>
</column>
Expand Down
1 change: 1 addition & 0 deletions covidseq/resources/schemas/dbscripts/sqlserver/covidseq-21.002-21.003.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
ALTER TABLE covidseq.patients ADD ageQualifier varchar(200);
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