Refactored metadata collection and fixes an issue with newly loaded datasets #7
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Refaactoring. I refactored metadata collection script in hopes to make it more readable. I splitted separate steps in functions and added a lot of fail checks.
Issue fix. There is an issue with newly loaded datasets where they are (it seems so at least) separately loaded to SRA and GEO. So ENA and SRA metadata files do not contain any information about GSM identifiers. We don't like this so I added parsing of GEO's
soft_familyfile to get GSM to SRS to BioSample relationsTests. I've added a draft lists of datasets that represent common problems with metadata collection. The list below will be extended:
https://claptar.notion.site/Trouble-shooting-datasets-160b0afc4069801ea8bcc412a971b22f?pvs=4