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GitHub Issue 875: Luminex Multi-File Transform Import Skips First Data Row #7456

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GitHub Issue 875: Luminex Multi-File Transform Import Skips First Data Row #7456

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26a8aba
GitHub Issue #875: TsvDataSerializer.exportData() to write first row …
cnathe Feb 25, 2026
27c9858
GitHub Issue #875: TsvDataSerializer.exportData() to write first row …
cnathe Feb 25, 2026
8d49ed4
Experiment module metric (assayRunsWithMultipleInputFiles) for count …
cnathe Feb 26, 2026
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2 changes: 1 addition & 1 deletion api/src/org/labkey/api/qc/TsvDataSerializer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -91,8 +91,8 @@ private List<String> exportData(DataIteratorBuilder data, List<String> columns,
sep = "\t";
}
pw.println();
writeRow(row, columns, pw, tsvWriter);
}
writeRow(row, columns, pw, tsvWriter); // GitHub Issue #875: write the first row regardless of whether we had a header or not

// write the remaining rows
while (iter.next())
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11 changes: 11 additions & 0 deletions experiment/src/org/labkey/experiment/ExperimentModule.java
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Expand Up @@ -652,6 +652,17 @@ SELECT COUNT(DISTINCT DD.DomainURI) FROM
JOIN exp.DomainDescriptor DD on PD.domainID = DD.domainId
WHERE DD.domainUri LIKE ? AND D.rangeURI = ?""", "urn:lsid:%:" + ExpProtocol.AssayDomainTypes.Result.getPrefix() + ".%", PropertyType.FILE_LINK.getTypeUri()).getObject(Long.class));

// metric to count the number of Luminex and Standard assay runs that were imported with > 1 data file
assayMetrics.put("assayRunsWithMultipleInputFiles", new SqlSelector(schema, """
SELECT COUNT(*) FROM (
SELECT sourceapplicationid, COUNT(*) AS count FROM exp.data
WHERE name NOT LIKE '%.log' AND name NOT LIKE '%.Rout' AND name NOT LIKE '%.pdf' AND sourceapplicationid IN (
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@labkey-klum labkey-klum Feb 27, 2026

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Wouldn't the .Rout extension only apply to transform scripts written in R? Maybe I'm wrong but I thought that whatever files are left after the transform script has completed get added as a data output.

It looks like there is data type information encoded into the exp.data lsid. I haven't looked into it but wondering whether filtering on that might work.

SELECT rowid FROM exp.protocolapplication
WHERE lsid LIKE '%:SimpleProtocol.CoreStep' AND (protocollsid LIKE '%:LuminexAssayProtocol.%' OR protocollsid LIKE '%:GeneralAssayProtocol.%')
)
GROUP BY sourceapplicationid
) x WHERE count > 1""").getObject(Long.class));

Map<String, Object> sampleLookupCountMetrics = new HashMap<>();
SQLFragment baseAssaySampleLookupSQL = new SQLFragment("SELECT COUNT(*) FROM exp.propertydescriptor WHERE (lookupschema = 'samples' OR (lookupschema = 'exp' AND lookupquery = 'Materials')) AND propertyuri LIKE ?");

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