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ebi-ait / hca-to-scea-tools

Helpers and tools to assist in the conversion of HCA datasets into SCEA
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Check hca2scea works with multiple samples from same donor #102

Closed ami-day closed 2 years ago

ami-day commented 2 years ago

A spreadsheet with multiple samples derived from the same donor is failing to run ok. The spreadsheet is SRP218543.xlsx. Need to investigate this and create a new branch to fix this issue.

Running at the command-line: python3 hca2scea.py -s test/golden/SRP218543.xlsx -id c1a9a93d-d9de-4e65-9619-a9cec1052eaa -study SRP218543 -ac 50 -c AD -et differential -f disease -pd 2021-11-11 -hd 2019-09-05

Google sheet version: https://docs.google.com/spreadsheets/d/1qyme5BDj5w8RvvInv0YDDu-Wr7PwgSy3RTVElKZ1pYI/edit#gid=1472957495

ami-day commented 2 years ago

Closing this ticket. After some investigation, the script does handle these types of use cases. The problem was with the input spreadsheet, which had an orphan biomaterial (missing linking). There is a pull request waiting to be merged which looks for missing linking like this and returns as assertion error statement. I will add this input spreadsheet to the list of negative test examples inside that branch.