genes_load_wb.py: "--taxonomy_id" argument not being used

greenelab / django-genes

A Django package to represent genes

BSD 3-Clause "New" or "Revised" License

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genes_load_wb.py: "--taxonomy_id" argument not being used #17

Open dongbohu opened 5 years ago

dongbohu commented 5 years ago

According to the docstring in: https://github.com/greenelab/django-genes/blob/master/genes/management/commands/genes_load_wb.py this management command accepts three arguments:

--wb_url (required)
--taxonomy_id (required)
--db_name (optional)

but the code doesn't use the value of taxonomy_id argument at all. Should we remove this option completely?

dongbohu commented 5 years ago

@cgreene Any idea why --taxonomy_id was originally added? I want to confirm that this option should be deleted.

dongbohu commented 5 years ago

By the way, this management command is not being used by either Tribe or Adage deployment.

cgreene commented 5 years ago

tricky question! turns out that this assumes that the genes have already been created, so no organism needs to be specified. this is just loading synonyms. The command may actually be required for Tribe if tribe uses c elegans, but the taxonomy_id flag shouldn't be required.

dongbohu commented 5 years ago

Thanks. I will remove taxonomy_id flag from the code.

cgreene commented 5 years ago

sounds good 👍