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TestWrite.test_missing_entries() #533

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TestWrite.test_missing_entries() #533

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66 changes: 66 additions & 0 deletions tests/test_writers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
import unittest
from typing import Any, Dict

import curies
import pandas as pd
from curies import Converter

Expand Down Expand Up @@ -191,3 +192,68 @@ def test_write_sssom_ontoportal_json(self):
self.mapping_count,
f"{path} has the wrong number of mappings.",
)

# 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

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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.

"""Test to make sure that missing entires do not appear."""
tmp_file = os.path.join(test_out_dir, "test_missing_entries.sssom.tsv")
df = pd.DataFrame(
[
{
"subject_id": "Orphanet:58",
"subject_label": "Alexander disease",
"predicate_id": "skos:exactMatch",
"object_id": "icd11.foundation:2023359698",
"object_label": "Alexander disease",
"mapping_justification": "semapv:UnspecifiedMatching",
}
]
)
metadata = {
"creator_id": "orcid:0000-0002-2906-7319",
"curie_map": {
"MONDO": "http://purl.obolibrary.org/obo/MONDO_",
"Orphanet": "http://www.orpha.net/ORDO/Orphanet_",
"icd11.foundation": "http://id.who.int/icd/entity/",
"oboInOwl": "http://www.geneontology.org/formats/oboInOwl#",
"orcid": "https://orcid.org/",
"owl": "http://www.w3.org/2002/07/owl#",
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
"rdfs": "http://www.w3.org/2000/01/rdf-schema#",
"semapv": "https://w3id.org/semapv/",
"skos": "http://www.w3.org/2004/02/skos/core#",
"sssom": "https://w3id.org/sssom/",
},
"license": "http://w3id.org/sssom/license/unspecified",
"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

msdf: MappingSetDataFrame = MappingSetDataFrame(
converter=curies.Converter.from_prefix_map(metadata["curie_map"]),
df=df,
metadata=metadata,
)
self.assertIn("curie_map", msdf.metadata) # pass
self.assertIn("icd11.foundation", msdf.metadata["curie_map"]) # pass
self.assertIn("icd11.foundation", msdf.prefix_map) # pass
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.

self.assertIn("icd11.foundation", msdf2.metadata["curie_map"]) # KeyError
self.assertIn("icd11.foundation", msdf2.prefix_map) # pass

# When no passed Converter
msdf: MappingSetDataFrame = MappingSetDataFrame(df=df, metadata=metadata)
self.assertIn("curie_map", msdf.metadata) # pass
self.assertIn("icd11.foundation", msdf.metadata["curie_map"]) # pass
self.assertIn("icd11.foundation", msdf.prefix_map) # fail
with open(tmp_file, "w") as f:
write_table(msdf, f)
msdf2 = parse_sssom_table(tmp_file)
self.assertIn("curie_map", msdf2.metadata) # fail
self.assertIn("icd11.foundation", msdf2.metadata["curie_map"]) # KeyError
self.assertIn("icd11.foundation", msdf2.prefix_map) # fail
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