# HG changeset patch
# User charles-bernard
# Date 1477996826 14400
# Node ID 424d6204a298dd2e264f6919ac6e4b372e8bacc6
# Parent  c7dbef0e9ed7c632e51dfab6b1afe0bed6b94690
Uploaded

diff -r c7dbef0e9ed7 -r 424d6204a298 data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py
--- a/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Tue Nov 01 06:32:34 2016 -0400
+++ b/data_manager_build_alfa_indexes/data_manager/data_manager_build_alfa_indexes.py	Tue Nov 01 06:40:26 2016 -0400
@@ -8,7 +8,6 @@
 import gzip
 import os
 import tempfile
-import logging
 from optparse import OptionParser
 from galaxy.util.json import from_json_string, to_json_string
 
@@ -80,7 +79,6 @@
     species_lines_matched, grep_error = grep_result.communicate()
     if grep_error != None or species_lines_matched == "":
         msg = 'The species \'%s\' is not referenced on Ensembl (%s)' % (species_name, kingdom)
-        logging.critical(msg)
         sys.exit(msg)
 
     species_lines = species_lines_matched.split('\n')
@@ -115,7 +113,6 @@
                 print("-> Referenced !\n")
                 return species_name, species_lines[i]
         msg = 'The string \'%s\' has been matched against the list of Ensembl Species but is not a complete species name.\nPlease retry with one of the following species names:\n%s' % (species_name, list_species[0:])
-        logging.critical(msg)
         sys.exit(msg)
 
 def get_ensembl_collection(kingdom, species_line):
@@ -162,7 +159,6 @@
     alfa_out, alfa_err = alfa_result.communicate()
     if alfa_err != None and not re.search('### End of program', alfa_err):
         msg = 'Generation Failed due an alfa error: %s' % (alfa_err)
-        logging.critical(msg)
         sys.exit(msg)
     print("Alfa prompt:\n%s" % alfa_out)
     print("-> Generated !\n")
@@ -187,7 +183,6 @@
 
     if options.output_filename == None:
         msg = 'No json output file specified'
-        logging.critical(msg)
         sys.exit(msg)
     output_filename = options.output_filename
     params = from_json_string(open(output_filename).read())