FIX issue #1: fixing psicquic registry and retry if connection fails

data/PSICQUIC_registry_imex.txt

@@ -1,10 +1,10 @@
 IntAct=https://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/psicquic
 DIP=https://imex.mbi.ucla.edu/psicquic-ws/webservices/psicquic
-MatrixDB=https://matrixdb.ibcp.fr:8080/webservices/psicquic
-MINT=https://mint.bio.uniroma2.it/mint/psicquic/webservices/psicquic
+MatrixDB=https://matrixdb.ibcp.fr:8080/psicquic/webservices
+MINT=https://www.ebi.ac.uk/Tools/webservices/psicquic/mint/webservices/psicquic
 I2D-IMEx=https://www.ebi.ac.uk/Tools/webservices/psicquic/i2d/webservices/psicquic
 InnateDB-IMEx=https://www.ebi.ac.uk/Tools/webservices/psicquic/innatedb/webservices/psicquic
 MolCon=https://www.ebi.ac.uk/Tools/webservices/psicquic/molcon/webservices/psicquic
 UniProt=https://www.ebi.ac.uk/Tools/webservices/psicquic/uniprot/webservices/psicquic
 MBInfo=https://www.ebi.ac.uk/Tools/webservices/psicquic/mbinfo/webservices/psicquic
-MPIDB=https://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/psicquic
+MPIDB=https://www.ebi.ac.uk/Tools/webservices/psicquic/mpidb/webservices/psicquic

data/download_psicquic.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 import urllib.request
+import time
 import os.path
 import re
 
@@ -23,6 +24,22 @@ def get_psicquic_services(filename):
  return services
 
 
+def urlopen_retry(url, retry = 3, delay = 1):
+ print("opening " + url)
+ i = 0
+ while (i < retry):
+ try:
+ cf = urllib.request.urlopen(url)
+ return cf
+ except urllib.error.HTTPError as e:
+ # try again
+ print("Failed to connect, retrying...")
+ time.sleep(delay)
+ i = i+1
+ if (i == retry):
+ return e
+
+
 def download_all_ppis(folder, basename):
  """
  Downloads all PPIs provided by the PSICQUIC registry
@@ -49,8 +66,17 @@ def download_all_ppis(folder, basename):
  # first get row count
  count_url = service_url + '/' + psicquic_query_url + '?format=count'
  tab25_url = service_url + '/' + psicquic_query_url + '?format=tab25'
- with urllib.request.urlopen(count_url) as cf:
+
+ # try opening URL
+ #with urllib.request.urlopen(count_url) as cf:
+ # count = int(cf.read())
+ try:
+ cf = urlopen_retry(count_url)
  count = int(cf.read())
+ cf.close()
+ except:
+ print("[ERROR] Failed to download PPI " + service_name + ", skipping...")
+ continue
 
  print("Downloading from '" + service_name + "': " + str(count)
  + " rows ...")