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ENA request: fix new URL + better check #323

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merged 1 commit into from
Mar 18, 2024
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ENA request: fix new URL + better check #323

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7 changes: 6 additions & 1 deletion src/python/ensembl/io/genomio/seq_region/prepare.py
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Original file line number Diff line number Diff line change
Expand Up @@ -160,9 +160,14 @@ def add_mitochondrial_codon_table(seq_regions: List[SeqRegion], taxon_id: int) -
taxon_id: The species taxon ID.

"""
url = f"https://www.ebi.ac.uk/ena/data/taxonomy/v1/taxon/tax-id/{str(taxon_id)}"
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{str(taxon_id)}"
response = requests.get(url, headers={"Content-Type": "application/json"}, timeout=60)
response.raise_for_status()
# In case we've been redirected, check for html opening tag
if response.text.startswith("<"):
raise ValueError(f"Response from {url} is not JSON")
decoded = response.json()

if "mitochondrialGeneticCode" not in decoded:
logging.warning("No mitochondria genetic code found for taxon {taxon_id}")
else:
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