Issue 511 #514
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Issue 511 #514
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…serialized in isatab2json conversion
The response[0] in core was setting what was supposed to be a list to a single string from the list instead. The check for whether a ontology source was in the list was nested beneath another check instead of being its own check.
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
terazus
reviewed
Feb 12, 2024
There were 2 tests that needed to be changed to match the new naming.
Fairly significant changes to check_protocol_fields
Changed messaging on study assays errors
Extended 511
The problem with trying to do this is that some of the protocol types in the yaml file have "Sample Name" and "Extract Name" as the headers and this causes those headers to be added multiple times. It might be better to leave those empty. Also might be good to change headers to a list to get rid of the special case for "nucleic acid hybridization".
For some reason the bottom part of the function only logged errors and did not add them to the validator dictionary. They also did not indicate which filename the error was from, so tracking down where the problem is was difficult. This might just be an oversight since the warnings at the top of the function were just fine.
Added better messaging
Refactor isatab loader
Protocol types refactor
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fixes issue 511 and issue 512.