Initial port to python3

[htsworkflow.git] / encode_submission / ucsc_gather.py

diff --git a/encode_submission/ucsc_gather.py b/encode_submission/ucsc_gather.py
index c45e3820bbc8b9f146684bef9ed8f5443fb03f8e..695541aeb713252cd37345e5475739516a0f4dac 100644 (file)
--- a/encode_submission/ucsc_gather.py
+++ b/encode_submission/ucsc_gather.py
@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-from ConfigParser import SafeConfigParser
+from configparser import SafeConfigParser
 import fnmatch
 from glob import glob
 import json
@@ -9,18 +9,21 @@ from optparse import OptionParser, OptionGroup
 import os
 from pprint import pprint, pformat
 import shlex
-from StringIO import StringIO
+from io import StringIO
 import stat
 import sys
 import time
 import types
-import urllib
-import urllib2
-import urlparse
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import urllib.parse
 from zipfile import ZipFile
 
 import RDF
 
+if not 'DJANGO_SETTINGS_MODULE' in os.environ:
+    os.environ['DJANGO_SETTINGS_MODULE'] = 'htsworkflow.settings'
+
 from htsworkflow.util import api
 from htsworkflow.util.rdfhelp import \
      dafTermOntology, \
@@ -93,7 +96,8 @@ def main(cmdline=None):
         mapper.link_daf(results)
 
     if opts.fastq:
-        extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
                                        force=opts.force)
         extractor.create_scripts(results)
 
@@ -115,7 +119,7 @@ def main(cmdline=None):
 
     if opts.print_rdf:
         writer = get_serializer()
-        print writer.serialize_model_to_string(model)
+        print(writer.serialize_model_to_string(model))
 
 
 def make_parser():
@@ -173,7 +177,7 @@ def make_parser():
 
 def make_all_ddfs(view_map, library_result_map, daf_name, make_condor=True, force=False):
     dag_fragment = []
-    for lib_id, result_dir in library_result_map.items():
+    for lib_id, result_dir in list(library_result_map.items()):
         submissionNode = view_map.get_submission_node(result_dir)
         dag_fragment.extend(
             make_ddf(view_map, submissionNode, daf_name, make_condor, result_dir)
@@ -264,7 +268,7 @@ ORDER BY  ?submitView"""
             else:
                 current[variable_name] = value
 
-    for view in all_views.keys():
+    for view in list(all_views.keys()):
         line = []
         for variable_name in variables:
             if variable_name in ('files', 'md5sum'):