Fixed bug in fetch_sequences

nf-core · May 13, 2024 · 78f2e1e · 78f2e1e
1 parent a1a65eb
commit 78f2e1e
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/bin/fetch_sequences.py b/bin/fetch_sequences.py
@@ -18,6 +18,8 @@ def fetch_seqs_oma(path: str, prefix: str) -> list[str]:
 
     payload = {"ids": ids}
 
+    print(payload, file=sys.stderr)
+
     res = safe_post("https://omabrowser.org/api/protein/bulk_retrieve/", json=payload)
 
     if not res.ok:

diff --git a/bin/utils.py b/bin/utils.py
@@ -20,12 +20,12 @@ def safe_get(url: str):
         raise RequestException(f"A network issue occurred. Retrying request. Details:\n{e}")
 
 
-def safe_post(url: str, data: dict):
+def safe_post(url: str, data: dict = dict(), json: dict = dict()):
     """
     Post data to a URL and return the response.
     """
     try:
-        return requests.post(url, data=data)
+        return requests.post(url, data=data, json=json)
     except requests.exceptions.RequestException as e:
         raise RequestException(f"A network issue occurred. Retrying request. Details:\n{e}")