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Update for latest changes of the SSSOM schema #552

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Merged
matentzn merged 2 commits into from
Aug 9, 2024
Merged

Update for latest changes of the SSSOM schema #552

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764cc7e
Update test for renaming of "semantic_similarity_score".
gouttegd Aug 7, 2024
9d91a44
Implement custom validation on top of LinkML.
gouttegd Aug 7, 2024
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10 changes: 10 additions & 0 deletions src/sssom/parsers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -914,6 +914,16 @@ def _ensure_valid_mapping_from_dict(mdict: Dict[str, Any]):

try:
m = Mapping(**mdict)
if m.subject_type == "rdfs literal":
if m.subject_label is None:
raise ValueError("Missing subject_label")
elif m.subject_id is None:
raise ValueError("Missing subject_id")
if m.object_type == "rdfs literal":
if m.object_label is None:
raise ValueError("Missing object_label")
elif m.object_id is None:
raise ValueError("Missing object_id")
except ValueError as e:
logging.warning(
f"One mapping in the mapping set is not well-formed, "
Expand Down
10 changes: 8 additions & 2 deletions tests/test_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import yaml
from curies import Converter, Record, chain
from sssom_schema import Mapping as SSSOM_Mapping
from sssom_schema import slots as SSSOM_Slots

from sssom.constants import (
CREATOR_ID,
Expand Down Expand Up @@ -409,14 +410,19 @@ def test_get_dict_from_mapping(self):
"match_string": "",
"subject_preprocessing": "",
"object_preprocessing": "",
"semantic_similarity_score": np.nan,
"semantic_similarity_measure": "",
"see_also": "",
"issue_tracker_item": "",
"other": "",
"comment": "",
}

if hasattr(SSSOM_Slots, "similarity_score"):
expected_result["similarity_score"] = np.nan
expected_result["similarity_measure"] = ""
else:
expected_result["semantic_similarity_score"] = np.nan
expected_result["semantic_similarity_measure"] = ""

result_with_mapping_object = get_dict_from_mapping(mapping_obj)
result_with_dict = get_dict_from_mapping(mapping_dict)
self.assertEqual(result_with_mapping_object, result_with_dict)
Expand Down