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Convert SSSOM TSV => JSON => TSV and confirm the MappingSetDataFrame object remains consistent. #429

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Convert SSSOM TSV => JSON => TSV and confirm the MappingSetDataFrame object remains consistent. #429

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831a58e
Convert SSSOM TSV => JSON => TSV and confirm the MappingSetDataFrame …
hrshdhgd Sep 26, 2023
1854d29
Add more explicit tests
cthoyt Sep 26, 2023
e00f4d4
Merge branch 'master' into issue-321
hrshdhgd Oct 3, 2023
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8 changes: 7 additions & 1 deletion src/sssom/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,13 @@ def clean_prefix_map(self, strict: bool = True) -> None:
if self.metadata:
prefixes_in_table.update(get_prefixes_used_in_metadata(self.metadata))

missing_prefixes = prefixes_in_table - self.converter.get_prefixes()
# Convert prefixes_in_table to lowercase
prefixes_in_table_lower = {prefix.lower() for prefix in prefixes_in_table}
# Convert self.converter.get_prefixes() to lowercase
converter_prefixes_lower = {prefix.lower() for prefix in self.converter.get_prefixes()}
missing_prefixes = prefixes_in_table_lower - converter_prefixes_lower
# missing_prefixes = prefixes_in_table - self.converter.get_prefixes()

if missing_prefixes and strict:
raise ValueError(
f"{missing_prefixes} are used in the SSSOM mapping set but it does not exist in the prefix map"
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8 changes: 8 additions & 0 deletions tests/data/sample1.sssom.tsv
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@@ -0,0 +1,8 @@
#curie_map:
# FBbt: "http://purl.obolibrary.org/obo/FBbt_"
# ORCID: "https://orcid.org/"
# UBERON: "http://purl.obolibrary.org/obo/UBERON_"
#creator_id:
# - "ORCID:0000-0002-6095-8718"
subject_id subject_label predicate_id object_id mapping_justification
FBbt:00000001 organism semapv:crossSpeciesExactMatch UBERON:0000468 semapv:ManualMappingCuration
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