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Corrections for accession-based mapping without multi-target mapping
1 parent f8586ce commit d38f364

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2 files changed

+7
-7
lines changed

2 files changed

+7
-7
lines changed

src/api/routers/map.py

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ async def map_scoreset(urn: str, store_path: Path | None = None) -> ScoresetMapp
4141
"""
4242
try:
4343
metadata = get_scoreset_metadata(urn, store_path)
44-
records = get_scoreset_records(urn, True, store_path)
44+
records = get_scoreset_records(metadata, True, store_path)
4545
except ScoresetNotSupportedError as e:
4646
return ScoresetMapping(
4747
metadata=None,
@@ -134,7 +134,7 @@ async def map_scoreset(urn: str, store_path: Path | None = None) -> ScoresetMapp
134134
).model_dump(exclude_none=True)
135135
)
136136
# TODO this should instead check if all values in dict are none. or might not need this at all.
137-
if vrs_results is None or len(vrs_results) == 0:
137+
if annotated_vrs_results is None or len(annotated_vrs_results) == 0:
138138
return ScoresetMapping(
139139
metadata=metadata,
140140
error_message="No annotated variant mappings available for this score set",
@@ -144,11 +144,11 @@ async def map_scoreset(urn: str, store_path: Path | None = None) -> ScoresetMapp
144144
# This version works for accession based score sets.
145145
# Not implementing multi-target changes because this will require corresponding changes on mavedb-api and we want to get this on staging quickly right now.
146146
# For now, only accept single-target score sets so that we don't need to change structure of JSON output.
147-
target_gene = list(metadata["target_genes"].keys())[0] # noqa: RUF015
147+
target_gene = list(metadata.target_genes.keys())[0] # noqa: RUF015
148148
try:
149149
raw_metadata = get_raw_scoreset_metadata(urn, store_path)
150150
preferred_layers = {
151-
_set_scoreset_layer(urn, vrs_results[target_gene]),
151+
_set_scoreset_layer(urn, annotated_vrs_results[target_gene]),
152152
}
153153

154154
reference_sequences = {
@@ -172,7 +172,7 @@ async def map_scoreset(urn: str, store_path: Path | None = None) -> ScoresetMapp
172172
)
173173

174174
mapped_scores: list[ScoreAnnotation] = []
175-
for m in vrs_results:
175+
for m in annotated_vrs_results[target_gene]:
176176
if m.annotation_layer in preferred_layers:
177177
# drop annotation layer from mapping object
178178
mapped_scores.append(ScoreAnnotation(**m.model_dump()))

src/dcd_mapping/schemas.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -213,9 +213,9 @@ class ScoresetMapping(BaseModel):
213213
# dict[str, ComputedReferenceSequence | MappedReferenceSequence | None],
214214
# ],
215215
# ] | None = None
216-
computed_protein_reference_sequence: ComputedReferenceSequence | None = None
216+
computed_protein_reference_sequence: ComputedReferenceSequence | MappedReferenceSequence | None = None
217217
mapped_protein_reference_sequence: MappedReferenceSequence | None = None
218-
computed_genomic_reference_sequence: ComputedReferenceSequence | None = None
218+
computed_genomic_reference_sequence: ComputedReferenceSequence | MappedReferenceSequence | None = None
219219
mapped_genomic_reference_sequence: MappedReferenceSequence | None = None
220220
mapped_scores: list[ScoreAnnotation] | None = None
221221
error_message: str | None = None

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