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 \
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
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
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
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):
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)
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
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,))