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Assay transform script run properties to include reRunId when applicable #8061

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Assay transform script run properties to include reRunId when applicable #8061

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6e40202
TsvDataExchangeHandler to include reRunId in transform script propert…
cnathe Sep 18, 2026
8c4e1a2
TsvDataExchangeHandler to guard against SampleRunUploadContext
cnathe Sep 18, 2026
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9 changes: 9 additions & 0 deletions api/src/org/labkey/api/qc/TsvDataExchangeHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,7 @@ public enum Props {
protocolId, // protocol row id
protocolLsid,
protocolDescription,
reRunId, // row id of the run being replaced, only present for a re-import

runDataFile,
runDataUploadedFile,
Expand Down Expand Up @@ -491,6 +492,14 @@ private Map<String, String> getContextProperties(DataTransformService.TransformO
FileLike originalFileLocation = context.getOriginalFileLocation();
if (originalFileLocation != null)
map.put(Props.originalFileLocation.name(), originalFileLocation.toNioPathForRead().toFile().getPath());

// Note: the replaced run isn't marked as replaced until after the transform, this is the RowId of the run that is being re-imported
if (!(context instanceof SampleRunUploadContext))
{
Long reRunId = context.getReRunId();
if (reRunId != null)
map.put(Props.reRunId.name(), String.valueOf(reRunId));
}
}

map.put(Props.baseUrl.name(), AppProps.getInstance().getBaseServerUrl() + AppProps.getInstance().getContextPath());
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