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TestWrite.test_missing_entries() #533

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@joeflack4 joeflack4 commented May 20, 2024

addresses #534

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  • Add: TestWrite.test_missing_entries()

@joeflack4 joeflack4 requested a review from matentzn May 20, 2024 01:19
@joeflack4 joeflack4 self-assigned this May 20, 2024
@joeflack4 joeflack4 added enhancement New feature or request bug Something isn't working and removed bug Something isn't working labels May 20, 2024
@joeflack4 joeflack4 force-pushed the missing-entries branch 2 times, most recently from ef955af to 97d9ab1 Compare May 20, 2024 01:41
# TODO: Determine assertions that should pass
# TODO: Fix failing assertions that should pass
# TODO: before merging, remove pass/fail comments at end of assertion lines
def test_missing_entries(self):
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Get assertions to pass

  • 1. Determine assertions that should pass @matentzn
  • 2. Fix failing assertions that should pass
  • 3. before merging, remove pass/fail comments at end of assertion lines

# TODO: Determine assertions that should pass
# TODO: Fix failing assertions that should pass
# TODO: before merging, remove pass/fail comments at end of assertion lines
def test_missing_entries(self):
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Which assertions are appropriate?

Can you look at the assertions I've made and determine which ones you think should be expected to pass, and which should not?

I've left temporary comments next to each assertion showing their current pass/fail status.

"mapping_provider": "https://www.orpha.net/",
}

# When passing Converter
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FYI: 2 different setups

I have a set of assertions for 2 cases of MappingSetDataFrame instantiation:

  • with inclusion of a Converter
  • with no inclusion of a Converter

@joeflack4 joeflack4 added the bug Something isn't working label May 20, 2024
@joeflack4 joeflack4 marked this pull request as draft May 20, 2024 01:47
@joeflack4 joeflack4 force-pushed the missing-entries branch 3 times, most recently from 001557e to 43fa8f5 Compare May 20, 2024 01:53
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This is a very good test! Thank you!

tests/test_writers.py Outdated Show resolved Hide resolved
with open(tmp_file, "w") as f:
write_table(msdf, f)
msdf2 = parse_sssom_table(tmp_file)
self.assertIn("curie_map", msdf2.metadata) # fail
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This behaviour is expected for now, because curie_map sort if lives outside the metadata. however, it will soon be solved: mapping-commons/sssom#349

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@joeflack4 joeflack4 May 22, 2024

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Wow, I'm surprised it wasn't part of the data model.

From an implementation standpoint, I was thinking that maybe msdf.prefix_map and msdf.metadata['curie_map'] could point to the same Python dictionary object. Right now they are different objects and, as these assertions show, can get out of sync.

@joeflack4 joeflack4 linked an issue May 31, 2024 that may be closed by this pull request
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TestWrite.test_missing_entries()
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