add strict=True to converter.expand for debugging

monarch-initiative · Dec 7, 2023 · 95beb1b · 95beb1b
1 parent f567ae0
commit 95beb1b
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Showing 3 changed files with 6 additions and 7 deletions.
diff --git a/backend/src/monarch_py/api/config.py b/backend/src/monarch_py/api/config.py
@@ -1,10 +1,8 @@
 import os
 import requests as rq
-
 from functools import lru_cache
 
 from pydantic import BaseModel
-
 # from pydantic_settings import BaseSettings
 
 from monarch_py.implementations.solr.solr_implementation import SolrImplementation

diff --git a/backend/src/monarch_py/service/curie_service.py b/backend/src/monarch_py/service/curie_service.py
@@ -20,4 +20,4 @@ def initialize(self):
         self.converter = load_converter(["merged"])
 
     def expand(self, curie: str) -> str:
-        return self.converter.expand(curie)
+        return self.converter.expand(curie, strict=True)
diff --git a/backend/tests/unit/test_curie_service.py b/backend/tests/unit/test_curie_service.py
@@ -11,20 +11,21 @@
         ),  # this is a little odd, fb vs. flybase, but both resolve
         ("FlyBase:FBgn0000008", "http://identifiers.org/fb/FBgn0000008"),
         ("MONDO:0005737", "http://purl.obolibrary.org/obo/MONDO_0005737"),
-        ("OMIM:613647", "http://identifiers.org/mim/613647"),
         ("NCBIGene:1017", "https://identifiers.org/ncbigene/1017"),
         ("ZFIN:ZDB-GENE-980526-166", "https://identifiers.org/zfin/ZDB-GENE-980526-166"),
         ("MGI:1918910", "https://identifiers.org/MGI/1918910"),
-        ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"),
         ("HP:0000001", "http://purl.obolibrary.org/obo/HP_0000001"),
-        ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"),
         ("GO:0000001", "http://purl.obolibrary.org/obo/GO_0000001"),
         ("CL:0000001", "http://purl.obolibrary.org/obo/CL_0000001"),
-        ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"),
         ("WB:WBGene00000001", "https://identifiers.org/wb/WBGene00000001"),
         ("SGD:S000000001", "https://identifiers.org/sgd/S000000001"),
         ("RGD:1", "https://identifiers.org/rgd/1"),
         ("HGNC:5", "http://identifiers.org/hgnc/5"),
+        ### These prefixes are currently broken in the curie service
+        ("ENSEMBL:ENSG00000157764", "http://identifiers.org/ensembl/ENSG00000157764"),
+        ("OMIM:613647", "http://identifiers.org/mim/613647"),
+        ("UBERON:0000001", "http://purl.obolibrary.org/obo/UBERON_0000001"),
+        ("WormBase:WBGene00000001", "http://identifiers.org/wb/WBGene00000001"),
     ],
 )
 def test_curie_expansion(curie, expanded_curie_part):