diff --git a/mutalyzer_retriever/request.py b/mutalyzer_retriever/request.py index e8d9cf4..30120fd 100644 --- a/mutalyzer_retriever/request.py +++ b/mutalyzer_retriever/request.py @@ -14,7 +14,7 @@ def __init__(self, error): self.response = error.response -def request(url, params=None, headers=None, timeout=1, max_retries=1, sleep=1): +def request(url, params=None, headers=None, timeout=20, max_retries=1, sleep=1): retries = 0 errors = [] while retries < max_retries: diff --git a/mutalyzer_retriever/sources/ensembl.py b/mutalyzer_retriever/sources/ensembl.py index 437c5ac..b1339a6 100644 --- a/mutalyzer_retriever/sources/ensembl.py +++ b/mutalyzer_retriever/sources/ensembl.py @@ -99,9 +99,7 @@ def fetch_json(reference_id, reference_version, api_base, assembly="GRCh38", tim "stable_id_version": reference_version, "expand": "translations, genes, exons", } - req = requests.request( - method="get", url=f"{api_base}/{endpoint}", params=params, timeout=timeout - ) + req = requests.request(method="get", url=f"{api_base}/{endpoint}", params=params, timeout=timeout) return req.json() @@ -111,7 +109,7 @@ def get_rest_api_base(r_id, r_version): return settings.get("ENSEMBL_API"), "GRCh38" elif r_version == _get_most_recent_version(r_id, settings.get("ENSEMBL_API_GRCH37")): return settings.get("ENSEMBL_API_GRCH37"), "GRCh37" - raise ValueError(f"Cannot fetch {r_id}.{r_version} from Ensembl REST") + raise NameError(f"Cannot fetch {r_id}.{r_version} from Ensembl REST") def get_transcript_api_base(r_id, r_version, r_source): @@ -123,7 +121,7 @@ def get_transcript_api_base(r_id, r_version, r_source): return settings.get("ENSEMBL_TARK_API"), "GRCh38" elif r_version in tark_versions_37: return settings.get("ENSEMBL_TARK_API"), "GRCh37" - raise ValueError(f"Cannot fetch {r_id} from Ensembl Tark") + raise NameError(f"Cannot fetch {r_id} from Ensembl Tark") def fetch(reference_id, reference_type=None, reference_source=None, timeout=1): @@ -146,7 +144,7 @@ def fetch(reference_id, reference_type=None, reference_source=None, timeout=1): elif reference_type == "fasta": return fetch_fasta(r_id, api_base, timeout), "fasta" elif reference_type == "json": - if reference_source in [None, "ensembl_tark"]: + if reference_source in [None, "ensembl", "ensembl_tark"]: return fetch_json(r_id, r_version, api_base, assembly, timeout), "json" elif reference_type == "genbank":