Bug/taxa in descriptions

ImperialCollegeLondon / safedata_validator

Python tools to validate and publish datasets using the safedata metadata format.

https://safedata-validator.readthedocs.io/

MIT License

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Bug/taxa in descriptions #40

Closed davidorme closed 1 year ago

davidorme commented 1 year ago

This PR:

Merges ncbi_index_to_text and taxon_index_to_text to take advantage of the synchronised taxon index tags to remove duplicated code.
The remaining taxon_index_to_text has an auth argument to switch between the different taxon name formatting rules for GBIF vs NCBI.
Fixes #39 resulting from the changed taxon index tags.

An example of the outputs of the function for GBIF and NCBI can be seen here: https://sandbox.zenodo.org/record/1143772

jacobcook1995 commented 1 year ago

Ahh another query as well, was slightly surprised to see that tests passed without any modifications to the test files, but realised that neither of the index_to_text functions had any tests defined. I can't tell if there's a good reason for this, suspect I might have forgotten to add them when I was making the ncbi_index_to_text function

davidorme commented 1 year ago

That is a good point. There are no tests on zenodo.py either - that would require mocking the external zenodo responses.

davidorme commented 1 year ago

Are you happy to approve this without tests? It would be good to move to a release, even if that release does have an "improve testing in these areas" issue hanging over it?