error thrown when provided invalid uid

[Anwesh1]

This handles the scenario when only a uid is provided without the text and this uid is invalid. The response looks like this:

P.S. I made an accidental pull request before this, but I closed it. Hopefully that doesn't cause any issues.

closes #81

[JohnGiorgi]

Cool! I left one comment.

Also, think you could add a test here to make sure that an invalid PMID throws an error? Pytest supports out of the box: https://docs.pytest.org/en/reorganize-docs/new-docs/user/pytest_raises.html

[Anwesh1]

Hey @JohnGiorgi, I'm not exactly sure why this codecov/patch check is failing.

[JohnGiorgi]

Hey @JohnGiorgi, I'm not exactly sure why this codecov/patch check is failing.

Don't worry about that!

Can you add a test that checks that this error is thrown for an invalid pmid? I linked some relevant pytest documentation above

[Anwesh1]

Hey @JohnGiorgi, I was trying something like this:

import pytest

from fastapi.exceptions import HTTPException

from semantic_search import ncbi
from semantic_search.ncbi import uids_to_docs

def test_invalid_uid_test():
    with pytest.raises(HTTPException):
        uid = ['93846392868']
        uids_to_docs(uid)

However, the pytest test failed and said this:

    def test_invalid_uid_test():
        with pytest.raises(HTTPException):
            uid = ['93846392868']
>           uids_to_docs(uid)
E           Failed: DID NOT RAISE <class 'fastapi.exceptions.HTTPException'>

tests/test_ncbi.py:11: Failed

Do I need to actually start up the FastAPI app?

[JohnGiorgi]

Weird! No I don't think we need to start the app unless I am really misunderstanding.

What if you just remove the "with" statement and see what kind of error is raised for that PMID

[Anwesh1]

When I send that request on Insomnia with this uid, I get the invalid uid HTTPException. However, if I take out the with statement, the pytest test passes with no errors.

[JohnGiorgi]

It is _medline_to_docs you added the new code to, right? I think that is the function that the unit test should call then

[Anwesh1]

Oh I see, I was going to call the whole process but this works now, I have updated it.

[JohnGiorgi]

LGTM!