Initial port to python3

[htsworkflow.git] / htsworkflow / pipelines / retrieve_config.py

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index a189f097e3017b8c8aac8b26b3d96ccbb0ec4460..43c0af6a625cb87d78931ea2916a4acb38f2c0a8 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -1,18 +1,19 @@
 #!/usr/bin/env python
 
 import csv
-from ConfigParser import RawConfigParser
+from configparser import RawConfigParser
 import logging
 from optparse import OptionParser, IndentedHelpFormatter
 import os
 import sys
 import types
-import urllib
-import urllib2
+import urllib.request, urllib.parse, urllib.error
+import urllib.request, urllib.error, urllib.parse
+import collections
 
 try:
     import json
-except ImportError, e:
+except ImportError as e:
     import simplejson as json
 
 from htsworkflow.frontend.auth import apidata
@@ -47,9 +48,9 @@ def retrieve_flowcell_info(base_host_url, flowcell):
     url = api.flowcell_url(base_host_url, flowcell)
 
     try:
-        apipayload = urllib.urlencode(apidata)
-        web = urllib2.urlopen(url, apipayload)
-    except urllib2.URLError, e:
+        apipayload = urllib.parse.urlencode(apidata)
+        web = urllib.request.urlopen(url, apipayload)
+    except urllib.error.URLError as e:
         errmsg = 'URLError: %d %s' % (e.code, e.msg)
         LOGGER.error(errmsg)
         LOGGER.error('opened %s' % (url,))
@@ -90,7 +91,7 @@ def group_lane_parameters(flowcell_info):
     (The same species, read length, and eland vs sequencing)
     """
     lane_groups = {}
-    for lane_number, lane_contents in flowcell_info['lane_set'].items():
+    for lane_number, lane_contents in list(flowcell_info['lane_set'].items()):
         for lane_info in lane_contents:
             index = (lane_info['read_length'],
                      lane_info['library_species'],
@@ -139,11 +140,11 @@ def format_gerald_config(options, flowcell_info, genome_map):
     analysis_suffix = eland_analysis_suffix[flowcell_info['paired_end']]
     sequence_suffix = sequence_analysis_suffix[flowcell_info['paired_end']]
     lane_groups = group_lane_parameters(flowcell_info)
-    for lane_index, lane_numbers in lane_groups.items():
+    for lane_index, lane_numbers in list(lane_groups.items()):
         # lane_index is return value of group_lane_parameters
         read_length, species, is_sequencing = lane_index
         lane_numbers.sort()
-        lane_prefix = u"".join(lane_numbers)
+        lane_prefix = "".join(lane_numbers)
 
         species_path = genome_map.get(species, None)
         LOGGER.debug("Looked for genome '%s' got location '%s'" % (species, species_path))
@@ -310,18 +311,18 @@ def saveConfigFile(options):
   (i.e. http://sub.domain.edu:port)
   """
   LOGGER.info('USING OPTIONS:')
-  LOGGER.info(u'     URL: %s' % (options.url,))
-  LOGGER.info(u'     OUT: %s' % (options.output_filepath,))
-  LOGGER.info(u'      FC: %s' % (options.flowcell,))
+  LOGGER.info('     URL: %s' % (options.url,))
+  LOGGER.info('     OUT: %s' % (options.output_filepath,))
+  LOGGER.info('      FC: %s' % (options.flowcell,))
   #LOGGER.info(': %s' % (options.genome_dir,))
-  LOGGER.info(u'post_run: %s' % ( unicode(options.post_run),))
+  LOGGER.info('post_run: %s' % ( str(options.post_run),))
 
   flowcell_info = retrieve_flowcell_info(options.url, options.flowcell)
 
   LOGGER.debug('genome_dir: %s' % ( options.genome_dir, ))
   available_genomes = getAvailableGenomes(options.genome_dir)
   genome_map = constructMapperDict(available_genomes)
-  LOGGER.debug('available genomes: %s' % ( unicode( genome_map.keys() ),))
+  LOGGER.debug('available genomes: %s' % ( str( list(genome_map.keys()) ),))
 
   config = format_gerald_config(options, flowcell_info, genome_map)
 
@@ -367,7 +368,7 @@ def save_sample_sheet(outstream, options, flowcell_info):
                 htsw_field = illumina_to_htsw_map.get(illumina_name, None)
                 if htsw_field is None:
                     continue
-                if callable(htsw_field):
+                if isinstance(htsw_field, collections.Callable):
                     renamed[illumina_name] = htsw_field(options,
                                                         flowcell_info,
                                                         library)
@@ -403,14 +404,14 @@ def format_pooled_libraries(shared, library):
     sequences = library.get('index_sequence', None)
     if sequences is None:
         return []
-    elif (type(sequences) in types.StringTypes and
+    elif (type(sequences) in str and
           sequences.lower().startswith('err')):
         shared['Index'] = ''
         shared['SampleProject'] = library['library_id']
         return [shared]
-    elif (type(sequences) == types.DictType):
+    elif (type(sequences) == dict):
         pooled = []
-        multiplex_ids = sequences.keys()
+        multiplex_ids = list(sequences.keys())
         multiplex_ids.sort(cmp=alphanum.alphanum)
         for multiplex_id in multiplex_ids:
             sample = {}