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galaxy-genome-annotation / python-apollo

Python library for talking to Apollo API
MIT License
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Expose the returnAllOrganisms paramater for AddOrganism #40

Closed MoffMade closed 4 years ago

MoffMade commented 4 years ago

For apollo instances with many organisms, the addOrganism call can often timeout as it builds the FindAllOrganisms call at the end of the method on the Apollo side. They have the option returnAllOrganisms: boolean (optional) Return all organisms (true / false) (default true) listed in the Webservices API, which disables this behavior and causes it to return an empty JSON instead of one containing all the organisms in the database.

I'd like to extend the current add_organisms call to make use of this parameter so that it can be made available down the line in some of the Galaxy tools that we use experiencing this issue.

MoffMade commented 4 years ago

Submitted PR #41 but I think it's missing some of the auto-generation steps for arrow/docs.

MoffMade commented 4 years ago

Tested and merged in #41 thank you @nathandunn!

MoffMade commented 4 years ago

Included this logic in delete_organism and update_organism as well in #44