Initial port to python3

[htsworkflow.git] / htsworkflow / submission / daf.py

diff --git a/htsworkflow/submission/daf.py b/htsworkflow/submission/daf.py
index f04ac8fe5328e738a012738a5d256b9307e11504..51595931ff2fa7699109d6644214ebdd89d531d3 100644 (file)
--- a/htsworkflow/submission/daf.py
+++ b/htsworkflow/submission/daf.py
@@ -5,9 +5,9 @@ import os
 from pprint import pformat
 import re
 import string
-from StringIO import StringIO
+from io import StringIO
 import types
-import urlparse
+import urllib.parse
 
 import RDF
 from htsworkflow.util.rdfhelp import \
@@ -139,7 +139,7 @@ def _consume_whitespace(line, start=0):
 
     returns length of string if it can't find anything
     """
-    for i in xrange(start, len(line)):
+    for i in range(start, len(line)):
         if line[i] not in string.whitespace:
             return i
 
@@ -151,7 +151,7 @@ def _extract_name_index(line, start=0):
 
     returns length of string if nothing matches
     """
-    for i in xrange(start, len(line)):
+    for i in range(start, len(line)):
         if line[i] in string.whitespace:
             return i
 
@@ -232,7 +232,7 @@ def submission_uri_to_string(submission_uri):
 
 def get_view_namespace(submission_uri):
     submission_uri = submission_uri_to_string(submission_uri)
-    view_uri = urlparse.urljoin(submission_uri, 'view/')
+    view_uri = urllib.parse.urljoin(submission_uri, 'view/')
     viewNS = RDF.NS(view_uri)
     return viewNS
 
@@ -296,11 +296,11 @@ class UCSCSubmission(object):
     def scan_submission_dirs(self, result_map):
         """Examine files in our result directory
         """
-        for lib_id, result_dir in result_map.items():
+        for lib_id, result_dir in list(result_map.items()):
             LOGGER.info("Importing %s from %s" % (lib_id, result_dir))
             try:
                 self.import_submission_dir(result_dir, lib_id)
-            except MetadataLookupException, e:
+            except MetadataLookupException as e:
                 LOGGER.error("Skipping %s: %s" % (lib_id, str(e)))
 
     def import_submission_dir(self, submission_dir, library_id):
@@ -491,7 +491,7 @@ class UCSCSubmission(object):
             self.__view_map = self._get_filename_view_map()
 
         results = []
-        for pattern, view in self.__view_map.items():
+        for pattern, view in list(self.__view_map.items()):
             if re.match(pattern, filename):
                 results.append(view)
 
@@ -531,7 +531,7 @@ class UCSCSubmission(object):
             LOGGER.debug("Found: %s" % (literal_re,))
             try:
                 filename_re = re.compile(literal_re)
-            except re.error, e:
+            except re.error as e:
                 LOGGER.error("Unable to compile: %s" % (literal_re,))
             patterns[literal_re] = view_name
         return patterns
@@ -588,7 +588,7 @@ class UCSCSubmission(object):
 
         base_daf = self.daf_name
 
-        for result_dir in result_map.values():
+        for result_dir in list(result_map.values()):
             if not os.path.exists(result_dir):
                 raise RuntimeError(
                     "Couldn't find target directory %s" %(result_dir,))