check lca database error text

[ctb]

In src/sourmash/lca/lca_db.py, the LCA_Database.load(...) class method checks to make sure that the filename is a directory, and if it is not, it raises a ValueError with the following string: "'{db_name}' is not a file and cannot be loaded as an LCA database". Currently this string is not checked for in the relevant tests.

Add a check for this string value in tests/test_lca.py functions test_databases_load_fail_on_dir and test_databases_load_fail_on_not_exist by looking at str(exc.value) after the pytest.raises block.

[keyabarve]

@ctb Can I try working on this issue? I'm a little unclear on what exactly needs to be done.

[ctb]

go for it!

this is the key instruction:

Add a check for this string value in tests/test_lca.py functions test_databases_load_fail_on_dir and test_databases_load_fail_on_not_exist by looking at str(exc.value) after the pytest.raises block.

For an example of us doing something similar to this, see test_gather_error_no_sigs_traverse() in tests/test_sourmash.py - the assert statements at the bottom are basically what you want to do here, suitably modified.

[ctb]

note that you can run just the two tests you are working on by doing py.test tests -k test_databases_load_fail_on_dir.

[keyabarve]

Will try, thanks!

[keyabarve]

@ctb I can't seem to find the functions test_databases_load_fail_on_dir and test_databases_load_fail_on_not_exist in tests/test_lca.py. Do I need to create these functions?

[ctb]

argh, I think they're buried in some pull request, actually. I'll go find them and report back :)

[ctb]

ahh! they are here, #1406.

if you want to work on this, you can! You will need to start from branch refactor/db_load_multiindex instead of latest, and then set up the pull request into that branch (instead of latest).

Alternatively, you could wait until #1406 is merged :).

apologies for the confusion!

[ctb]

whups, well, #1406 is merged - so you should be able to update to latest and see the functions!

[keyabarve]

Alright, thanks!

[keyabarve]

@ctb Could you provide some clarification on what exactly needs to be done?

[ctb]

please see this comment and give it a try; once you have an open PR with some changes, I'd be happy to help further.

[keyabarve]

Alright, I'll do that. Thanks!