MzTabExporter/ExpDesign silently merges duplicate filenames #5357
Description
I am pretty sure it was compatible to old files at some point.
E.g. running it on https://github.com/OpenMS/OpenMS/blob/develop/src/tests/topp/FeatureLinkerUnlabeled_4_output.consensusXML
fails with:
Map descriptions (file name + label) in ConsensusMap are not unique:
file: UNKNOWN label: file: UNKNOWN label: file: UNKNOWN label:
No MS file associated (primary MS run path).
No fractions annotated in consensusXML. Assuming unfractionated.
Error: Unexpected internal error (PSM does not map to an MS file registered in the quantitative metadata. Check your merging and filtering steps and/or report the issue, please.)
<No fractions annotated in consensusXML. Assuming unfractionated.> occurred 3 times
<No MS file associated (primary MS run path).> occurred 3 times
This actually breaks some pipelines since not all tools correctly annotate everything, yet. I thought we had fallbacks for that
@timosachsenberg