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Remove SqlserverOnlyTest marker interface from tests - #297

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labkey-tchad merged 1 commit into
release26.3-SNAPSHOTfrom
26.3_fb_removeSqlServerOnlyInterface
Jul 21, 2026
Merged

Remove SqlserverOnlyTest marker interface from tests#297
labkey-tchad merged 1 commit into
release26.3-SNAPSHOTfrom
26.3_fb_removeSqlServerOnlyInterface

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@labkey-tchad

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Rationale

The PMR module seems to have always supported Postgres. The test was flagged as SQL Server only, presumably because it wasn't actually deployed to any postgres servers.
The SqlserverOnlyTest marker interface will soon be unnecessary and should be removed from tests.

Changes

  • Remove SqlserverOnlyTest marker interface from tests

@labkey-tchad

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The kinship ETL is failing for some reason:

ERROR PipelineJob              2026-07-20T14:38:42,972            JobThread-7.6 : (from pipeline job log file /mnt/teamcity/work/8063137bf091310a/build/deploy/embedded/files/PMRTest Project/@files/kinship/EHR Kinship Calculation/kinship.txt_2026-07-20_14-38-41.log: Failed running /usr/lib/R/bin/Rscript, exit code 1)
org.labkey.api.pipeline.ToolExecutionException: Failed running /usr/lib/R/bin/Rscript, exit code 1
	at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1405)
	at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1275)
	at org.labkey.api.pipeline.PipelineJob.runSubProcess(PipelineJob.java:1265)
	at org.labkey.ehr.pipeline.GeneticCalculationsRTask.runScript(GeneticCalculationsRTask.java:140)
	at org.labkey.ehr.pipeline.GeneticCalculationsRTask.run(GeneticCalculationsRTask.java:107)

@bbimber

bbimber commented Jul 20, 2026

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It seems like the R packages arent installed: https://teamcity-artifacts.labkey.org/presignedTokenAuth/3f1b83bd-8860-4912-87f6-8a534a51e7de/repository/download/LabKey_263Release_Community_ExternalModulesTestPostgres/4100566:id/PMRTest.tar.gz!/PMRTest%20Project/%40files/kinship/EHR%20Kinship%20Calculation/kinship.txt_2026-07-20_14-38-41.log?__nodeId=secondary

20 Jul 2026 14:38:42,708 INFO : running: /usr/lib/R/bin/Rscript --no-save --no-environ --no-init-file --no-restore /mnt/teamcity/work/8063137bf091310a/build/deploy/embedded/modules/ehr/pipeline/kinship/populateInbreeding.r -f /mnt/teamcity/work/8063137bf091310a/build/deploy/embedded/files/PMRTest Project/@files/kinship/EHR Kinship Calculation/pedigree.txt
20 Jul 2026 14:38:42,962 INFO : Error in library(pedigree) : there is no package called ‘pedigree’
20 Jul 2026 14:38:42,962 INFO : Execution halted

@labkey-tchad
labkey-tchad merged commit 4c0798e into release26.3-SNAPSHOT Jul 21, 2026
10 of 11 checks passed
@labkey-tchad
labkey-tchad deleted the 26.3_fb_removeSqlServerOnlyInterface branch July 21, 2026 00:18
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3 participants