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bigbio / sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files
Apache License 2.0
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Validation fails with some repeated columns #172

Open ypriverol opened 3 months ago

ypriverol commented 3 months ago 
Command output:
  /usr/local/lib/python3.12/site-packages/sdrf_pipelines/sdrf/sdrf_schema.py:355: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.
    validation_results = panda_sdrf.applymap(validate_string)
  /usr/local/lib/python3.12/site-packages/sdrf_pipelines/sdrf/sdrf_schema.py:355: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead.
    validation_results = panda_sdrf.applymap(validate_string)
  Multiple columns found for factor 'spiked compound': ['characteristics[spiked compound]', 'characteristics[spiked compound 2]', 'characteristics[spiked compound 3]', 'characteristics[spiked compound 4]'] -- ERROR
  Make sure your SDRF have a sample characteristics or data comment 'spiked compound.1' for your factor value column 'factor value[spiked compound].1' -- ERROR
  Make sure your SDRF have a sample characteristics or data comment 'spiked compound.2' for your factor value column 'factor value[spiked compound].2' -- ERROR
  Make sure your SDRF have a sample characteristics or data comment 'spiked compound.3' for your factor value column 'factor value[spiked compound].3' -- ERROR
ypriverol commented 3 months ago

Example file for the following error: https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv