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| author | Frederick Muriuki Muriithi | 2025-02-28 12:44:55 -0600 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2025-02-28 12:44:55 -0600 |
| commit | ef1436bca390ee916b7119036ab2d3de8d1344fb (patch) | |
| tree | 8ed0197669d51d2f825080bfbda10e35fa2403aa /scripts | |
| parent | 4edc4450e6fe578212600ad9733f0fa6eb3ffc9f (diff) | |
| download | genenetwork3-ef1436bca390ee916b7119036ab2d3de8d1344fb.tar.gz | |
Fix linting errors.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/pub_med.py | 6 | ||||
| -rwxr-xr-x | scripts/update_rif_table.py | 2 |
2 files changed, 4 insertions, 4 deletions
diff --git a/scripts/pub_med.py b/scripts/pub_med.py index 82b1730..0a94355 100644 --- a/scripts/pub_med.py +++ b/scripts/pub_med.py @@ -155,8 +155,8 @@ def fetch_id_lossy_search(query, db_name, max_results): try: response = requests.get(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db={db_name}&retmode=json&retmax={max_results}&term={query}", - headers={"content-type": "application/json"} - ) + headers={"content-type": "application/json"}, + timeout=300) return response["esearchresult"]["idlist"] except requests.exceptions.RequestException as error: @@ -174,7 +174,7 @@ def search_pubmed_lossy(pubmed_id, db_name): - dict: Records fetched based on PubMed ID. """ url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db={db_name}&id={",".join(pubmed_id)}&retmode=json' - response = requests.get(url) + response = requests.get(url, timeout=300) response.raise_for_status() data = response.json() if db_name.lower() == "pmc": diff --git a/scripts/update_rif_table.py b/scripts/update_rif_table.py index 24edf3d..f936f5b 100755 --- a/scripts/update_rif_table.py +++ b/scripts/update_rif_table.py @@ -35,7 +35,7 @@ VALUES (%s, %s, %s, %s, %s, %s, %s, %s) def download_file(url: str, dest: pathlib.Path): """Saves the contents of url in dest""" - with requests.get(url, stream=True) as resp: + with requests.get(url, stream=True, timeout=300) as resp: resp.raise_for_status() with open(dest, "wb") as downloaded_file: for chunk in resp.iter_content(chunk_size=8192): |