Issue 51432: special character cause aliquot rollup and assay transform script to work unexpectedly #6125
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XingY
changed the title
labkey-susanh
approved these changes
Dec 6, 2024
| .filter(s -> !StringUtils.isEmpty(s)) | ||
| .toList(); | ||
| if (!parents.isEmpty()) | ||
| return parents.get(0); |
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If we have more than one parent after all this work, should that throw or log an error or warning?
| .map(String::trim) | ||
| .map(s -> Pair.of(parentColName, s)) | ||
| .collect(Collectors.toSet()); | ||
| if (parentNames != null) |
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Looks like parentNames can't actually be null here.
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Rationale
The app quotes parent names that contains comma, including any data/material parents or aliquot parent names. The AliquotRollupDataIterator is fetching parent specified by aliquotedFrom as is, which might contain enclosing quotes, which resulted in parent sample not found and rollup skipped.
Separately, PlateSamplesTest.testAssayImportWithTransformScript fails to transform and import data when well sample name contains double quote. The PR fixed the intermediate tsv file that LKS writes so the transfom script can work on the correct file. The other part of the problem is transcript script itself (for example, R) might not know how to property quote values when writing files back to LKS, which this PR doesn't address.
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