add multiple attempts at connecting to uniprot.org

rhapsody/features/Uniprot.py

@@ -6,6 +6,7 @@
 import re
 import pickle
 import datetime
+import time
 import numpy as np
 import prody as pd
 from prody import LOGGER, SETTINGS
@@ -25,11 +26,21 @@
            'seqScanning', 'printSAVlist']
 
 
-def queryUniprot(*args, **kwargs):
+def queryUniprot(*args, n_attempts=3, dt=1, **kwargs):
     """
     Redefine prody function to check for no internet connection
     """
-    _ = openURL('http://www.uniprot.org/')
+    attempt = 0
+    while attempt < n_attempts:
+        try:
+            print(f'attempt {attempt}')
+            _ = openURL('http://www.uniprot.org/')
+            break
+        except:
+            attempt += 1
+            time.sleep((attempt+1)*dt)
+    else:
+        _ = openURL('http://www.uniprot.org/')
     return pd.queryUniprot(*args, **kwargs)
 
 

rhapsody/predict/core.py

@@ -380,9 +380,11 @@ def getUniqueSAVcoords(self):
                     [SAV['SAV coords'], SAV['unique SAV coords']] +
                     SAV['unique SAV coords'].split()
                 )
-            except Exception as e:
-                LOGGER.warn(f'Invalid Uniprot coordinates at line {i}: {e}')
-                uSAVcoords[i] = tuple(['?', -999, '?', '?'])
+            except Exception:
+                LOGGER.warn(
+                    'Invalid Uniprot coordinates at line {}: {}'.format(
+                    i, SAV['unique SAV coords']))
+                uSAVcoords[i] = tuple(['?', '?', '?', -999, '?', '?'])
         return uSAVcoords
 
     def calcFeatures(self, filename='rhapsody-features.txt', refresh=False):