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Merge discvr-25.11 to develop #269

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Merged
bbimber merged 8 commits into from
Nov 25, 2025
Merged

Merge discvr-25.11 to develop #269

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16d4c5e
Add filter to PVL query
bbimber Nov 24, 2025
976fa54
Improve logic to simplify vector backbones
bbimber Nov 24, 2025
8bcc183
Improve logic to simplify vector backbones
bbimber Nov 24, 2025
9da91b9
Increase aligner index RAM
bbimber Nov 25, 2025
1bc4849
Merge discvr-25.7 to discvr-25.11
bbimber Nov 25, 2025
e928c69
npm dependency updates
bbimber Nov 25, 2025
b22aacb
Merge pull request #203 from bimberlabinternal/25.11_fb_merge
bbimber Nov 25, 2025
d1a23af
Merge discvr-25.11 to develop
bbimber Nov 25, 2025
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2 changes: 1 addition & 1 deletion IDR/resources/queries/bimber_data/idrPvlSource.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,4 @@ c_PVL as result,
'Hansen/IDR' as dataSource

FROM bimber_data.pvl
WHERE c_PVL != 'missing from box'
WHERE c_PVL != 'missing from box' AND c_PVL != 'pending'
19 changes: 16 additions & 3 deletions SivStudies/src/org/labkey/sivstudies/etl/PerformManualIdrStepsTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.regex.Pattern;

public class PerformManualIdrStepsTask implements TaskRefTask
{
Expand Down Expand Up @@ -88,6 +89,10 @@ private void pruneSivChallenges(PipelineJob pipelineJob) throws PipelineJobExcep
}
}

private static final Pattern mir126_RE = Pattern.compile("miR[- ]{0,1}126", Pattern.CASE_INSENSITIVE);
private static final Pattern mir142_RE = Pattern.compile("miR[- ]{0,1}142", Pattern.CASE_INSENSITIVE);
private static final Pattern mir126_142_RE = Pattern.compile("miR[- ]{0,1}142[ ,-]{1,2}126", Pattern.CASE_INSENSITIVE);

private void updateVaccineInformation(PipelineJob pipelineJob) throws PipelineJobException
{
TableInfo ti = QueryService.get().getUserSchema(_containerUser.getUser(), _containerUser.getContainer(), "study").getTable("immunizations");
Expand All @@ -105,18 +110,26 @@ private void updateVaccineInformation(PipelineJob pipelineJob) throws PipelineJo

if (backbone != null && backbone.contains("68-1"))
{
if (treatment.contains("miR-142-126"))
if (mir126_142_RE.matcher(treatment).find())
{
updatedRow.put("backbone", "68-1 MHC-1A-only");
}
else if (treatment.contains("miR-126"))
else if (mir126_RE.matcher(treatment).find() && !treatment.contains("142"))
{
updatedRow.put("backbone", "68-1 MHC-E-only");
}
else if (treatment.contains("miR-142"))
else if (mir142_RE.matcher(treatment).find() && !treatment.contains("126"))
{
updatedRow.put("backbone", "68-1 MHC-II-only");
}
else if (treatment.contains("RhCMV FL"))
{
updatedRow.put("backbone", "68-1 FL");
}
else if (treatment.contains("RhCMV") && treatment.contains("d186-189"))
{
updatedRow.put("backbone", "68-1 d186-189");
}
}

if (treatment.toUpperCase().contains("MOCK"))
Expand Down
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