Merge pull request #30 from bento-platform/fix/feature-query

fix: type hinting issues
bento-platform · Dec 12, 2024 · 6567c1c · 6567c1c
2 parents df7d9f4 + bf1733b
commit 6567c1c
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/bento_reference_service/db.py b/bento_reference_service/db.py
@@ -280,7 +280,7 @@ def deserialize_genome_feature(rec: asyncpg.Record) -> GenomeFeature:
             feature_name=rec["feature_name"],
             feature_type=rec["feature_type"],
             source=rec["source"],
-            entries=tuple(map(Database.deserialize_genome_feature_entry, json.loads(rec["entries"] or "[]"))),
+            entries=list(map(Database.deserialize_genome_feature_entry, json.loads(rec["entries"] or "[]"))),
             gene_id=rec["gene_nat_id"],
             attributes=json.loads(rec["attributes"] or "{}"),
             parents=tuple(rec["parents"] or ()),  # tuple of parent IDs
@@ -524,6 +524,7 @@ async def bulk_ingest_genome_features(self, features: tuple[GenomeFeature, ...])
 
                     feature_types.add((feature.feature_type,))
 
+                    e: GenomeFeatureEntry
                     entries.extend(
                         (
                             row_id,

diff --git a/bento_reference_service/routers/refget.py b/bento_reference_service/routers/refget.py
@@ -246,7 +246,7 @@ class RefGetSequenceMetadata(BaseModel):
     md5: str
     ga4gh: str
     length: int
-    aliases: list[Alias]
+    aliases: tuple[Alias, ...]
 
 
 class RefGetSequenceMetadataResponse(BaseModel):

diff --git a/tests/test_db.py b/tests/test_db.py
@@ -119,6 +119,7 @@ async def test_genome_features_summary(db: Database, db_cleanup):
         (SARS_COV_2_GENOME_ID, dict(q="ORF1ab"), 3),
         (SARS_COV_2_GENOME_ID, dict(q="ENSSASG00005000002"), 1),
         (SARS_COV_2_GENOME_ID, dict(q="protein_coding", q_fzy=True, limit=100), 24),
+        (SARS_COV_2_GENOME_ID, dict(q="tein_cod", q_fzy=True, limit=100), 24),
         # hg38 subset
         (HG38_CHR1_F100K_GENOME_ID, dict(position="chr1:11869-"), 3),
         (HG38_CHR1_F100K_GENOME_ID, dict(start=12000), 10),