# HG changeset patch
# User mvdbeek
# Date 1472119818 14400
# Node ID 86a9ce3761d8b4d6624cfe88b2f3ab6d1f121ceb
# Parent  0007b48a5bb98a78e4159fffe72908ec8d7fd5b4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_dbkeys_all_fasta commit c6314fce6475715c091db463f26703440d71349c-dirty

diff -r 0007b48a5bb9 -r 86a9ce3761d8 data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py
--- a/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Thu Aug 25 05:51:13 2016 -0400
+++ b/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.py	Thu Aug 25 06:10:18 2016 -0400
@@ -14,7 +14,7 @@
 try:
     # For Python 3.0 and later
     from urllib.request import urlopen
-    from io import BytesIO as StringIO
+    from io import StringIO
     from io import UnsupportedOperation
 except ImportError:
     # Fall back to Python 2's urllib2
@@ -37,6 +37,13 @@
     sys.exit(1)
 
 
+def read_urllib(response):
+    charset = response.headers.get_content_charset()
+    if not charset:
+        charset = 'utf-8'
+    response.read().decode(charset))
+
+
 def get_dbkey_dbname_id_name( params, dbkey_description=None ):
     dbkey = params['param_dict']['dbkey_source']['dbkey']
     #TODO: ensure sequence_id is unique and does not already appear in location file
@@ -204,7 +211,7 @@
 def _download_file(start, fh):
     tmp = tempfile.NamedTemporaryFile()
     tmp.write(start)
-    tmp.write(fh.read())
+    tmp.write(read_urllib(fh))
     tmp.flush()
     tmp.seek(0)
     return tmp
@@ -430,7 +437,7 @@
     
     filename = args[0]
     
-    params = loads( open( filename ).read() )
+    params = loads( open( filename ).read().decode('utf-8'))
     target_directory = params[ 'output_data' ][0]['extra_files_path']
     os.mkdir( target_directory )
     data_manager_dict = {}