[WIP] New ebi submit [WIP] #704
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| - All column headers will be transformed to lowercase | ||
| - Skips lines containing only whitespace | ||
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| headers = [x.strip().lower() for x in input_file.readline().split('\t')] |
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Yeah it could, but the prep/sample templates I get from Gail never have comment lines starting with #
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Thanks for the review @wasade, I'll implement these changes soon! |
| from make_per_sample_fastq import split_helper | ||
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| class InvalidMetadataError(Exception): |
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It would be nice to have descriptions for this and the subsequent Exceptions.
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I like how the code is looking! I would like to hear what your plans are for testing the main EBI object, as it stands right now, I can see that it's acting a lot as a data formatter, hence I would be inclined to leave the submission of files to a separate object, would be curious to hear what others think. |
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Agree, submit should be external
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| from xml.dom import minidom | ||
| from xml.sax.saxutils import escape | ||
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| from make_per_sample_fastq import split_helper |
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split_helper should be moved into here otherwise we have a circular dependency once the cmd line click'd interface imports EBISubmission
Almost there, but I thought I'd get this in now so that people can begin reviewing, it's kind of big.
Needs: