Implement API endpoint that returns TSV report about submissions that are pending review

[cristina-stonepedraza]

Add a script to api.py and a query to crud.py to pull information from the submission portal database, and then generate a report of NMDC submissions that have been submitted as a TSV.

This PR references issue 2047 in nmdc-schema: https://github.com/microbiomedata/nmdc-schema/issues/2047

[eecavanna]

Hi @cristina-stonepedraza, here's an example of an automated test that targets an endpoint like this one:

https://github.com/microbiomedata/nmdc-server/blob/36dbba5c9f4f82e438f3a940e9eb63b03c240982/tests/test_submission.py#L41-L125

There are actually two tests there because the endpoint in question is only accessible to admins. One of the tests focuses on that aspect (i.e. security).

By the way, I do wonder whether we will restrict access to this reporting endpoint also. You/we can discuss that with @mslarae13.

[mslarae13]

By the way, I do wonder whether we will restrict access to this reporting endpoint also. You/we can discuss that with @mslarae13.

@eecavanna I assume the submission status end point that I use for quarterly metrics is limited, yes? I think this should be the same.

[eecavanna]

That's correct, @mslarae13; the endpoint I implemented, which you use to get a submission report (TSV file) for our quarterly reports, is accessible only to users that are admins.

[eecavanna]

Great commit messages, by the way, @cristina-stonepedraza!

Next week, I can walk you through the process of logging into the Data Portal such that you can access protected endpoints via the Swagger UI page; and how you can "promote" yourself into an admin locally.

[eecavanna]

Just passing through as I've been seeing the notifications from GitHub. The code is looking excellent (in my opinion)! 👏

[cristina-stonepedraza]

@eecavanna I've got this to a place where all the tests pass, I think it's ready for another look when you have a chance!

[eecavanna]

If you add this parameter to the endpoint request handler function, the endpoint will become accessible to logged-in users only (but does not ensure they are admins—that will come next):

https://github.com/microbiomedata/nmdc-server/blob/c408d3430e2cdc50af54e273e43d0039e0aaff29/nmdc_server/api.py#L666

If you then add this snippet to the beginning of the function's body, the endpoint will become accessible to logged-in users who are admins only:

https://github.com/microbiomedata/nmdc-server/blob/c408d3430e2cdc50af54e273e43d0039e0aaff29/nmdc_server/api.py#L672-L673

In terms of testing, you can add a test like this to demonstrate that a logged-in user that is not an admin is unable to access the endpoint:

https://github.com/microbiomedata/nmdc-server/blob/c408d3430e2cdc50af54e273e43d0039e0aaff29/tests/test_submission.py#L41-L45

Finally, in the existing test you've already written, you can replace the existing logged-in user with a logged-in admin user by following the example in this snippet. Here, we make the test require a logged-in admin user, then we use a variable called logged_in_user to refer to that logged-in admin user so that the code below it can remain the same (since it already uses the latter variable name).

https://github.com/microbiomedata/nmdc-server/blob/c408d3430e2cdc50af54e273e43d0039e0aaff29/tests/test_submission.py#L48-L54

[eecavanna]

I'm also going to tag @naglepuff and @pkalita-lbl here as they, too, maintain the Data Portal API and I want them to be aware that this branch may be merged into the main branch soon.

FYI, @naglepuff and @pkalita-lbl: I've reviewed this branch and approve of it being merged into main once @mslarae13 has approved of its user-facing behavior.