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Update DB path for BLAST by adding the genome uuid prefix #58

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Update DB path for BLAST by adding the genome uuid prefix #58

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c626688
:pencil: update DB path for BLAST by adding the genome uuid prefix
bilalebi Jun 12, 2026
581b7cd
:pencil: fix path (typo)
bilalebi Jun 12, 2026
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3 changes: 2 additions & 1 deletion app/blast/blast.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,8 @@ class JobIDs(BaseModel):


def get_db_path(genome_id: str, db_type: str) -> str:
return f"ensembl/{genome_id}/{suffix_map.get(db_type, db_type)}"
genome_id_prefix = genome_id[:3]
return f"ensembl/{genome_id_prefix}/{genome_id}/{suffix_map.get(db_type, db_type)}"

@azangru azangru Jun 13, 2026

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Is this something that the tools api has to work out on its own, or something that it should ask metadata about?



# Submit a BLAST job to JD. Returns a resolvable for fetching the response.
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5 changes: 3 additions & 2 deletions app/tests/test_blast.py
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Expand Up @@ -26,10 +26,11 @@ def blast_payload():
# Test BLAST database path inference
def test_get_db_path(blast_payload):
genome_id = blast_payload["genome_ids"][0]
genome_id_prefix = genome_id[:3]
filename = get_db_path(genome_id, "dna_sm")
assert filename == f"ensembl/{genome_id}/softmasked"
assert filename == f"ensembl/{genome_id_prefix}/{genome_id}/softmasked"
filename = get_db_path(genome_id, "pep")
assert filename.endswith("pep")
assert filename == f"ensembl/{genome_id_prefix}/{genome_id}/pep"


# Test single BLAST job submission with a valid payload
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