add an optional test to make sure full validate produce is run when l…

[sierra-moxon]

The first iteration of this PR had methods to download, store, use, and then clean up metadata from the go-site repo during the test execution, but it involved a lot of file wrangling that ended up being overly complicated and hard to maintain. I decided to just copy over the basic metadata into the resources/metadata directories in this PR and use it statically. This lets me run the full 'validate.produce' command as an automated test.

It also adds the download and maintenance of go-basic.obo as a pytest fixture. Since this is just one file, and since it gets it from snapshot that can sometimes be unavailable, it felt like a worthwhile resource to grab and maintain dynamically.

Finally, it adds some logic to implementations that use poetry so that this test gets executed locally
(e.g. I will run it always by default locally) but doesn't run as part of CI (because it takes quite a bit of time to run). There are other tests that execute parts and pieces of the validate.produce command, but there are several cases I want to test that require the full step here to run (e.g. does the final GAF produced have isoforms as subjects or not).

This all just saves me from forgetting to run this full test of the validate.produce command manually as underlying routines change.

[kltm]

@sierra-moxon This looks like a good set of ease-of-use and separation changes. I'm fine with this being merged as-is.

One thing that I might be interested in, from past experience, would be a README somewhere that explains how to update the metadata (and the rationale for making things static), in case things change enough to warrant updates.

[dustine32]

@sierra-moxon I'm getting these errors when attempting make travis_test_full, though I'm still using the antiquated venv environment so maybe this doesn't happen with poetry:

$ .env/bin/activate
(env)$ python3 --version
Python 3.10.3
(env)$ make travis_test_full
...
=============================================== ERRORS ================================================
______________________ ERROR at setup of test_validate_resulting_gaf[gaf_setup0] ______________________
ScopeMismatch: You tried to access the function scoped fixture runner with a session scoped request object, involved factories:
tests/test_validate_cli.py:47:  def gaf_setup(request, runner, go_json)
tests/test_validate_cli.py:15:  def runner()
______________________ ERROR at setup of test_validate_resulting_gaf[gaf_setup1] ______________________
ScopeMismatch: You tried to access the function scoped fixture runner with a session scoped request object, involved factories:
tests/test_validate_cli.py:47:  def gaf_setup(request, runner, go_json)
tests/test_validate_cli.py:15:  def runner()
______________________ ERROR at setup of test_validate_resulting_gaf[gaf_setup2] ______________________
ScopeMismatch: You tried to access the function scoped fixture runner with a session scoped request object, involved factories:
tests/test_validate_cli.py:47:  def gaf_setup(request, runner, go_json)
tests/test_validate_cli.py:15:  def runner()
______________________ ERROR at setup of test_validate_resulting_gaf[gaf_setup3] ______________________
ScopeMismatch: You tried to access the function scoped fixture runner with a session scoped request object, involved factories:
tests/test_validate_cli.py:47:  def gaf_setup(request, runner, go_json)
tests/test_validate_cli.py:15:  def runner()

[dustine32]

@sierra-moxon Actually, these tests are running in poetry since I see this at the top of the output:

Running tests in Poetry environment...

Guessing it's because I have both a venv folder and pyproject.toml file to meet this criteria:

ontobio/Makefile

Line 52 in 97f3bab

@if [ -d ".venv" ] && [ -f "pyproject.toml" ]; then \

I'll keep debugging these errors...

[sierra-moxon]

Hi @dustine32 - thank you so much for testing the travis_test_full target. Would you mind try pulling and running the test again (I fixed the fixture failure you found, but I'd like to make sure there aren't any venv issues)?

You can configure the slow test datasets in ontobio/tests/test_validate_cli.py by modifying datasets_to_test list if you just want to see that it runs for you (the fastest are goa-cow and tair; noting that the available metadata is for: mgi, cdg, tair, goa-cow|chicken, zfin at the moment, so any of those should work as test datasets).

I have not been able to recreate the snapshot pipeline error that we found in this ticket with this branch: #689 (I believe it was taken care of in a previous PR -- the solution was/is to GPI files before and after the isoform check).

[dustine32]

Thanks @sierra-moxon! The make travis_test_full now passes (btw took about 5min for me).