Fix outdated prefix map

[matentzn]

@hrshdhgd can you fix this for me? It was still using the old prefix map..

[hrshdhgd]

I have the fix in place

self = <tests.test_parsers.TestParse testMethod=test_parse_obographs>
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:43)

(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:44)
    def test_parse_obographs(self):
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:45)
        """Test parsing OBO Graph JSON."""
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:46)
        msdf = from_obographs(
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:47)
            jsondoc=self.obographs,
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:48)
            prefix_map=self.metadata.prefix_map,
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:49)
            meta=self.metadata.metadata,
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:50)
        )
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:51)
        path = os.path.join(test_out_dir, "test_parse_obographs.tsv")
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:52)
        with open(path, "w") as file:
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:53)
            write_table(msdf, file)
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:54)
        self.assertEqual(
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:55)
            len(msdf.df),
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:56)
            9878,
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:57)
>           f"{self.obographs_file} has the wrong number of mappings.",
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:58)
        )
(https://github.com/mapping-commons/sssom-py/runs/7661877722?check_suite_focus=true#step:8:59)
E       AssertionError: 9876 != 9878 : /home/runner/work/sssom-py/sssom-py/tests/data/pato.json has the wrong number of mappings.

I do not know why this would change though? Thoughts?

[matentzn]

This is super cool, make sure this works when installing from pip (remember these problems with loading from a package-local path in the past?).

The changing numbers are sort of expected, if the prefix map does not know a prefix, its not added to the table when parsing with obo graphs..

[matentzn]

Does this work when installing with pip? Do we have a precedence in the code for this (loading the resource this way I mean). I feel schema_path should be in constants.py somehow, but up to you.

[hrshdhgd]

I forgot that schema_path was already implemented in constants.py. Updating code accordingly. The variable name is SCHEMA_YAML and is used in many parts of the project. So it definitely works since previous releases did not have any issues when we implemented sssom-schema.

[hrshdhgd]

@matentzn , ready for another review.

[matentzn]

I cant approve it with Github since I opened the PR but this is amazing, like - finally all your hard work engineering this stuff properly is paying off and changes are getting so much smaller and better. 3 months ago the same PR would have taken 1 week to implement with 100 lines of code.. Great!

[matentzn]

(approved)