Merge branch 'main' into bugfix/18-link-to-help-documentation-is-broken

Dockerfile

@@ -36,4 +36,4 @@ RUN poetry install --only-root
 
 WORKDIR /app/src
 
-CMD ["poetry", "run", "gunicorn", "--limit-request-line", "8190", "--bind", "0.0.0.0:8000", "application:app"]
+CMD ["poetry", "run", "gunicorn", "--timeout", "300", "--limit-request-line", "8190", "--bind", "0.0.0.0:8000", "application:app"]

src/annotator.py

@@ -13,6 +13,7 @@
 # END Upload Fix
 
 import geneweaverdb
+from time import sleep
 
 
 NCBO_URL = 'http://data.bioontology.org'
@@ -132,15 +133,15 @@ def fetch_ncbo_annotations(text, ncboids):
     ## for-else construct: if the loop doesn't break (in our case this
     ## indicates success) then this statement is executed
     else:
-        print('Failed to retrieve annotation data after three attempts')
+        print('Failed to retrieve NCBO annotation data after three attempts')
         return []
 
     return json.loads(res)
 
 
 def get_ncbo_link(link):
     """
-    Since NCBO enjoys testing the sanity of it's users, (almost) every member
+    Since NCBO enjoys testing the sanity of its users, (almost) every member
     of an object returned by the NCBO API is in the form of a link which then
     requires further API calls to retrieve the data.
     This function calls any API returned link and (hopefully) returns the
@@ -149,29 +150,31 @@ def get_ncbo_link(link):
     :arg str: JSON-LD link
     :ret dict: json object representing whatever data we retrieved
     """
+    headers = {
+        'Authorization': f'apikey token={API_KEY}'
+    }
 
-    opener = urllib.request.build_opener()
-    opener.addheaders = [('Authorization', 'apikey token=' + API_KEY)]
-
-    for _ in range(3):
+    response = None
+    for attempt in range(3):
         try:
-            res = opener.open(link)
-            res = res.read()
-
-        except urllib.error.HTTPError as e:
-            print('Failed to retrieve annotation data from an NCBO link:')
-            print(e)
+            response = requests.get(link, headers=headers)
+            response.raise_for_status()
+            return response.json()
+        except requests.HTTPError as e:
+            print(f'HTTPError on attempt {attempt + 1}: {e}')
+            if response is not None:
+                print(f'Response content: {response.content}')  # Log the response content
+            sleep(1)
+            continue
+        except Exception as e:
+            print(f'Unknown error on attempt {attempt + 1}: {e}')
+            print(traceback.format_exc())  # Print the full traceback for debugging
+            sleep(1)
             continue
-
-        ## Success
-        break
-
     else:
         print('Failed to retrieve data from an NCBO URL')
         return None
 
-    return json.loads(res)
-
 
 def parse_ncbo_annotations(annots):
     """
@@ -261,7 +264,7 @@ def fetch_monarch_annotations(text):
     ## for-else construct: if the loop doesn't break (in our case this
     ## indicates success) then this statement is executed
     else:
-        print('Failed to retrieve annotation data after three attempts')
+        print('Failed to retrieve Monarch annotation data after three attempts')
         return []
 
     return json.loads(res)