Merge pull request #5215 from nsoranzo/python3

Python3: finish first pass on whole codebase

.ci/py3_sources.txt

@@ -1,84 +0,0 @@
-client/galaxy/style/source_material/circle.py
-contrib/
-cron/
-doc/parse_gx_xsd.py
-doc/patch.py
-lib/galaxy/actions/
-lib/galaxy/auth/
-lib/galaxy/config.py
-lib/galaxy/containers/
-lib/galaxy/dataset_collections/
-lib/galaxy/datatypes/
-lib/galaxy/dependencies/
-lib/galaxy/eggs/
-lib/galaxy/exceptions/
-lib/galaxy/external_services/
-lib/galaxy/forms/
-lib/galaxy/jobs/
-lib/galaxy/managers/
-lib/galaxy/model/
-lib/galaxy/objectstore/
-lib/galaxy/openid/
-lib/galaxy/quota/
-lib/galaxy/sample_tracking/
-lib/galaxy/security/
-lib/galaxy/tags/
-lib/galaxy/tools/
-lib/galaxy/tours/
-lib/galaxy/util/
-lib/galaxy/visualization/
-lib/galaxy/web/
-lib/galaxy/webapps/galaxy/api/histories.py
-lib/galaxy/webapps/galaxy/api/library_datasets.py
-lib/galaxy/webapps/galaxy/api/tours.py
-lib/galaxy/webapps/galaxy/api/users.py
-lib/galaxy/webapps/galaxy/api/workflows.py
-lib/galaxy/webapps/galaxy/buildapp.py
-lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
-lib/galaxy/webapps/galaxy/controllers/external_services.py
-lib/galaxy/webapps/galaxy/controllers/forms.py
-lib/galaxy/webapps/galaxy/controllers/history.py
-lib/galaxy/webapps/galaxy/controllers/library_common.py
-lib/galaxy/webapps/galaxy/controllers/search.py
-lib/galaxy/webapps/galaxy/controllers/userskeys.py
-lib/galaxy/webapps/reports/config.py
-lib/galaxy/webapps/reports/controllers/tools.py
-lib/galaxy/webapps/reports/__init__.py
-lib/galaxy/webapps/tool_shed/config.py
-lib/galaxy/webapps/tool_shed/controllers/groups.py
-lib/galaxy/webapps/tool_shed/controllers/user.py
-lib/galaxy/webapps/tool_shed/framework/middleware/remoteuser.py
-lib/galaxy/webapps/tool_shed/__init__.py
-lib/galaxy/webapps/tool_shed/model/__init__.py
-lib/galaxy/webapps/tool_shed/search/repo_search.py
-lib/galaxy/webapps/tool_shed/util/ratings_util.py
-lib/galaxy/webhooks/
-lib/galaxy/work/
-lib/galaxy/workflow/
-lib/galaxy_ext/
-lib/log_tempfile.py
-lib/mimeparse.py
-lib/psyco_full.py
-lib/tool_shed/
-scripts/api/
-scripts/auth/
-scripts/bootstrap_history.py
-scripts/build_toolbox.py
-scripts/check_eggs.py
-scripts/check_galaxy.py
-scripts/check_python.py
-scripts/cleanup_datasets/
-scripts/communication/
-scripts/data_libraries/build_whoosh_index.py
-scripts/db_shell.py
-scripts/drmaa_external_runner.py
-scripts/metagenomics/
-scripts/microbes/BeautifulSoup.py
-scripts/microbes/harvest_bacteria.py
-scripts/secret_decoder_ring.py
-scripts/tool_shed/api/common.py
-scripts/tool_shed/build_ts_whoosh_index.py
-scripts/tool_shed/deprecate_repositories_without_metadata.py
-test/
-tool_list.py
-tools/

config/plugins/webhooks/demo/tour_generator/helper/__init__.py

@@ -174,7 +174,7 @@ class TourGenerator(object):
             elif input.type == 'select':
                 params = []
                 if name in test_inputs:
-                    for option in self._tool.inputs[name].static_options:
+                    for option in input.static_options:
                         for test_option in self._test.inputs[name]:
                             if test_option == option[1]:
                                 params.append(option[0])

lib/galaxy/containers/docker_swarm_manager.py

@@ -46,7 +46,7 @@ SWARM_MANAGER_CONF_DEFAULTS = {
     'service_wait_count_limit': 0,
     'service_wait_time_limit': 5,
     'slots_min_limit': 0,
-    'slots_max_limit': sys.maxint,
+    'slots_max_limit': sys.maxsize,
     'slots_min_spare': 0,
     'node_idle_limit': 120,
     'limits': [],
@@ -137,7 +137,7 @@ class SwarmManager(object):
             state = node_state['state']
             if not nodes:
                 nodes = self._docker_interface.nodes()
-            node = (filter(lambda x: x.name == name, nodes) + [None])[0]
+            node = ([x for x in nodes if x.name == name] + [None])[0]
             if not node:
                 if elapsed > self._conf.spawn_wait_time:
                     log.warning("spawning node '%s' not found in `docker node ls` and spawn_wait_time exceeded! %d seconds have elapsed", name, elapsed)

lib/galaxy/datatypes/proteomics.py

@@ -449,7 +449,7 @@ class ImzML(Binary):
     def generate_primary_file(self, dataset=None):
         rval = ['<html><head><title>imzML Composite Dataset </title></head><p/>']
         rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
             opt_text = ''
             if composite_file.get('description'):
@@ -493,7 +493,7 @@ class Analyze75(Binary):
     def generate_primary_file(self, dataset=None):
         rval = ['<html><head><title>Analyze75 Composite Dataset.</title></head><p/>']
         rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-        for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).items():
             fn = composite_name
             opt_text = ''
             if composite_file.optional:

lib/galaxy/dependencies/pinned-hashed-requirements.txt

@@ -35,7 +35,7 @@ SQLAlchemy==1.0.15 --hash:sha256=7cbac295f87d2af82aac08346b52f72d0b0c00712290495
                    --hash:sha256=f819742f33ae543ca2c48bc43e35bd75372f7c3e379e4881f9040549d3df94b6 \
                    --hash:sha256=fce29753f720f8a6920185bd5a4d1670fa6b6936819475197b2bce7644243766 \
                    --hash:sha256=aa8843df6869f6c999400ae32de5480fba1b7711fe535c168a14225ffd1d3de4
-mercurial==3.7.3 --hash:sha256=49f596820f005ac6f94266b89a0dbd815c0ee0aacd3aa86545dc39fb349ea4bf \
+mercurial==3.7.3; python_version < '3.0' --hash:sha256=49f596820f005ac6f94266b89a0dbd815c0ee0aacd3aa86545dc39fb349ea4bf \
                  --hash:sha256=75f5b6b708bec2d6e0e68ec8912725a5dcac42df00b122fa73a8c4bd21495039 \
                  --hash:sha256=8c07cb3404d26641d8829099bd1047582b76def49eca067ba6bea9a73d261775 \
                  --hash:sha256=6a05bf22101b79b5f56421f7a1c6d301000f759f0114827f37cc9f847c1ab352 \

lib/galaxy/dependencies/pinned-requirements.txt

@@ -7,7 +7,7 @@ MarkupSafe==1.0
 PyYAML==3.12
 SQLAlchemy==1.0.15
 sqlalchemy-utils==0.32.19
-mercurial==3.7.3
+mercurial==3.7.3; python_version < '3.0'
 pycrypto==2.6.1
 uWSGI==2.0.15
 # Flexible BAM index naming is new to core pysam

lib/galaxy/dependencies/requirements.txt

@@ -5,7 +5,7 @@ bx-python
 MarkupSafe
 PyYAML
 SQLAlchemy
-mercurial
+mercurial; python_version < '3.0'
 pycrypto
 # Flexible BAM index naming is new to main pysam
 pysam>=0.13

lib/galaxy/jobs/handler.py

@@ -5,11 +5,11 @@ import datetime
 import logging
 import os
 import time
-from Queue import (
+
+from six.moves.queue import (
     Empty,
     Queue
 )
-
 from sqlalchemy.sql.expression import (
     and_,
     func,
@@ -343,7 +343,7 @@ class JobHandlerQueue(Monitors, object):
         if not self.track_jobs_in_database:
             self.waiting_jobs = new_waiting_jobs
         # Remove cached wrappers for any jobs that are no longer being tracked
-        for id in self.job_wrappers.keys():
+        for id in list(self.job_wrappers.keys()):
             if id not in new_waiting_jobs:
                 del self.job_wrappers[id]
         # Flush, if we updated the state
@@ -896,7 +896,7 @@ class DefaultJobDispatcher(object):
             job_wrapper.fail(DEFAULT_JOB_PUT_FAILURE_MESSAGE)
 
     def shutdown(self):
-        for runner in self.job_runners.itervalues():
+        for runner in self.job_runners.values():
             try:
                 runner.shutdown()
             except Exception:

lib/galaxy/jobs/runners/chronos.py

@@ -232,7 +232,7 @@ class ChronosJobRunner(AsynchronousJobRunner):
 
     def parse_destination_params(self, params):
         parsed_params = {}
-        for k, spec in self.DESTINATION_PARAMS_SPEC.iteritems():
+        for k, spec in self.DESTINATION_PARAMS_SPEC.items():
             value = params.get(k, spec.get('default'))
             map_to = spec.get('map_name')
             mapper = spec.get('map')
@@ -264,7 +264,7 @@ class ChronosJobRunner(AsynchronousJobRunner):
 
     def _retrieve_job(self, job_id):
         jobs = self._chronos_client.list()
-        job = filter((lambda x: x['name'] == job_id), jobs)
+        job = [x for x in jobs if x['name'] == job_id]
         if len(job) > 1:
             msg = 'Multiple jobs found with name {name!r}'.format(name=job_id)
             LOGGER.error(msg)

lib/galaxy/managers/hdas.py

@@ -373,10 +373,10 @@ class HDASerializer(  # datasets._UnflattenedMetadataDatasetAssociationSerialize
         Return dictionary containing new-style display app urls.
         """
         display_apps = []
-        for display_app in hda.get_display_applications(trans).itervalues():
+        for display_app in hda.get_display_applications(trans).values():
 
             app_links = []
-            for link_app in display_app.links.itervalues():
+            for link_app in display_app.links.values():
                 app_links.append({
                     'target': link_app.url.get('target_frame', '_blank'),
                     'href': link_app.get_display_url(hda, trans),

lib/galaxy/managers/workflows.py

@@ -413,7 +413,7 @@ class WorkflowContentsManager(UsesAnnotations):
             else:
                 inputs = step.module.get_runtime_inputs(connections=step.output_connections)
                 step_model = {
-                    'inputs' : [input.to_dict(trans) for input in inputs.itervalues()]
+                    'inputs' : [input.to_dict(trans) for input in inputs.values()]
                 }
             step_model['step_type'] = step.type
             step_model['step_label'] = step.label
@@ -713,7 +713,7 @@ class WorkflowContentsManager(UsesAnnotations):
             # tools. This should be removed at some point. Mirrored
             # hack in _workflow_from_dict should never be removed so
             # existing workflow exports continue to function.
-            for input_name, input_conn in dict(input_conn_dict).iteritems():
+            for input_name, input_conn in dict(input_conn_dict).items():
                 if len(input_conn) == 1:
                     input_conn_dict[input_name] = input_conn[0]
             step_dict['input_connections'] = input_conn_dict
@@ -790,7 +790,7 @@ class WorkflowContentsManager(UsesAnnotations):
         supplied_steps = data['steps']
         # Try to iterate through imported workflow in such a way as to
         # preserve step order.
-        step_indices = supplied_steps.keys()
+        step_indices = list(supplied_steps.keys())
         try:
             step_indices = sorted(step_indices, key=int)
         except ValueError:
@@ -927,7 +927,7 @@ class WorkflowContentsManager(UsesAnnotations):
         """
         for step in steps:
             # Input connections
-            for input_name, conn_list in step.temp_input_connections.iteritems():
+            for input_name, conn_list in step.temp_input_connections.items():
                 if not conn_list:
                     continue
                 if not isinstance(conn_list, list):  # Older style singleton connection

lib/galaxy/openid/providers.py

@@ -4,6 +4,8 @@ Contains OpenID provider functionality
 import logging
 import os
 
+import six
+
 from galaxy.util import parse_xml, string_as_bool
 from galaxy.util.odict import odict
 
@@ -87,7 +89,7 @@ class OpenIDProvider(object):
 
     def post_authentication(self, trans, openid_manager, info):
         sreg_attributes = openid_manager.get_sreg(info)
-        for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems():
+        for store_pref_name, store_pref_value_name in self.store_user_preference.items():
             if store_pref_value_name in (self.sreg_optional + self.sreg_required):
                 trans.user.preferences[store_pref_name] = sreg_attributes.get(store_pref_value_name)
             else:
@@ -129,10 +131,10 @@ class OpenIDProviders(object):
             self.providers = providers
         else:
             self.providers = odict()
-        self._banned_identifiers = [provider.op_endpoint_url for provider in self.providers.itervalues() if provider.never_associate_with_user]
+        self._banned_identifiers = [provider.op_endpoint_url for provider in self.providers.values() if provider.never_associate_with_user]
 
     def __iter__(self):
-        for provider in self.providers.itervalues():
+        for provider in six.itervalues(self.providers):
             yield provider
 
     def get(self, name, default=None):

lib/galaxy/tools/__init__.py

@@ -339,7 +339,7 @@ class DefaultToolState(object):
         """
         self.inputs = {}
         context = ExpressionContext(self.inputs)
-        for input in tool.inputs.itervalues():
+        for input in tool.inputs.values():
             self.inputs[input.name] = input.get_initial_value(trans, context)
 
     def encode(self, tool, app, nested=False):

lib/galaxy/tools/cwl/representation.py

@@ -78,9 +78,9 @@ def to_cwl_job(tool, param_dict, local_working_directory):
         else:
             return str(param_dict_value)
 
-    for input_name, input in inputs.iteritems():
+    for input_name, input in inputs.items():
         if input.type == "repeat":
-            only_input = input.inputs.values()[0]
+            only_input = next(iter(input.inputs.values()))
             array_value = []
             for instance in param_dict[input_name]:
                 array_value.append(simple_value(only_input, instance[input_name[:-len("_repeat")]]))
@@ -112,7 +112,7 @@ def to_galaxy_parameters(tool, as_dict):
         else:
             return param_dict_value
 
-    for input_name, input in inputs.iteritems():
+    for input_name, input in inputs.items():
         as_dict_value = as_dict.get(input_name, NOT_PRESENT)
         galaxy_input_type = input.type
 
@@ -120,7 +120,7 @@ def to_galaxy_parameters(tool, as_dict):
             if input_name not in as_dict:
                 continue
 
-            only_input = input.inputs.values()[0]
+            only_input = next(iter(input.inputs.values()))
             for index, value in enumerate(as_dict_value):
                 key = "%s_repeat_0|%s" % (input_name, only_input.name)
                 galaxy_value = from_simple_value(only_input, value)

lib/galaxy/tools/imp_exp/__init__.py

@@ -240,7 +240,7 @@ class JobImportHistoryArchiveWrapper(object, UsesAnnotations):
 
                     # Set parameters. May be useful to look at metadata.py for creating parameters.
                     # TODO: there may be a better way to set parameters, e.g.:
-                    #   for name, value in tool.params_to_strings( incoming, trans.app ).iteritems():
+                    #   for name, value in tool.params_to_strings( incoming, trans.app ).items():
                     #       job.add_parameter( name, value )
                     # to make this work, we'd need to flesh out the HDA objects. The code below is
                     # relatively similar.

lib/galaxy/util/permutations.py

@@ -39,13 +39,12 @@ def expand_multi_inputs(inputs, classifier, key_filter=None):
 
 def __split_inputs(inputs, classifier, key_filter):
     key_filter = key_filter or (lambda x: True)
-    input_keys = filter(key_filter, inputs)
 
     single_inputs = {}
     matched_multi_inputs = {}
     multiplied_multi_inputs = {}
 
-    for input_key in input_keys:
+    for input_key in filter(key_filter, inputs):
         input_type, expanded_val = classifier(input_key)
         if input_type == input_classification.SINGLE:
             single_inputs[input_key] = expanded_val
@@ -73,14 +72,14 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
 
     matched_multi_inputs = []
 
-    first_multi_input_key = multi_inputs.keys()[0]
+    first_multi_input_key = next(iter(multi_inputs.keys()))
     first_multi_value = multi_inputs.get(first_multi_input_key)
 
     for value in first_multi_value:
         new_inputs = __copy_and_extend_inputs(single_inputs, first_multi_input_key, value)
         matched_multi_inputs.append(new_inputs)
 
-    for multi_input_key, multi_input_values in multi_inputs.iteritems():
+    for multi_input_key, multi_input_values in multi_inputs.items():
         if multi_input_key == first_multi_input_key:
             continue
         if len(multi_input_values) != len(first_multi_value):
@@ -95,7 +94,7 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
 def __extend_with_multiplied_combos(input_combos, multi_inputs):
     combos = input_combos
 
-    for multi_input_key, multi_input_value in multi_inputs.iteritems():
+    for multi_input_key, multi_input_value in multi_inputs.items():
         iter_combos = []
 
         for combo in combos:

lib/galaxy/util/script.py

@@ -42,7 +42,7 @@ def _app_properties(args):
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
     parser.add_argument('action', metavar='ACTION', type=str,
-                        choices=ACTIONS.keys(),
+                        choices=list(ACTIONS.keys()),
                         default=DEFAULT_ACTION,
                         nargs='?' if DEFAULT_ACTION is not None else None,
                         help='action to perform')

lib/galaxy/visualization/data_providers/basic.py

@@ -37,7 +37,7 @@ class BaseDataProvider(object):
         """
         raise Exception("Unimplemented Function")
 
-    def get_data(self, chrom, start, end, start_val=0, max_vals=sys.maxint, **kwargs):
+    def get_data(self, chrom, start, end, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Returns data as specified by kwargs. start_val is the first element to
         return and max_vals indicates the number of values to return.

lib/galaxy/visualization/data_providers/genome.py

@@ -44,8 +44,8 @@ def get_bounds(reads, start_pos_index, end_pos_index):
     '''
     Returns the minimum and maximum position for a set of reads.
     '''
-    max_low = sys.maxint
-    max_high = -sys.maxint
+    max_low = sys.maxsize
+    max_high = -sys.maxsize
     for read in reads:
         if read[start_pos_index] < max_low:
             max_low = read[start_pos_index]
@@ -182,7 +182,7 @@ class GenomeDataProvider(BaseDataProvider):
         """
         raise Exception("Unimplemented Function")
 
-    def get_data(self, chrom=None, low=None, high=None, start_val=0, max_vals=sys.maxint, **kwargs):
+    def get_data(self, chrom=None, low=None, high=None, start_val=0, max_vals=sys.maxsize, **kwargs):
         """
         Returns data in region defined by chrom, start, and end. start_val and
         max_vals are used to denote the data to return: start_val is the first element to
@@ -233,7 +233,7 @@ class GenomeDataProvider(BaseDataProvider):
             column_names = self.original_dataset.datatype.column_names
         except AttributeError:
             try:
-                column_names = range(self.original_dataset.metadata.columns)
+                column_names = list(range(self.original_dataset.metadata.columns))
             except Exception:  # Give up
                 return []
 
@@ -511,7 +511,7 @@ class BedDataProvider(GenomeDataProvider):
             if length >= 12:
                 block_sizes = [int(n) for n in feature[10].split(',') if n != '']
                 block_starts = [int(n) for n in feature[11].split(',') if n != '']
-                blocks = zip(block_sizes, block_starts)
+                blocks = list(zip(block_sizes, block_starts))
                 payload.append([(int(feature[1]) + block[1], int(feature[1]) + block[1] + block[0]) for block in blocks])
 
             # Score (filter data)
@@ -1022,7 +1022,7 @@ class BamDataProvider(GenomeDataProvider, FilterableMixin):
                 count += 1
 
         # Take care of reads whose mates are out of range.
-        for qname, read in paired_pending.iteritems():
+        for qname, read in paired_pending.items():
             if read['mate_start'] < read['start']:
                 # Mate is before read.
                 read_start = read['mate_start']
@@ -1286,7 +1286,7 @@ class IntervalIndexDataProvider(FilterableMixin, GenomeDataProvider):
                         out.write(line)
                     else:
                         reader = GFFReaderWrapper(source, fix_strand=True)
-                        feature = reader.next()
+                        feature = next(reader)
                         for interval in feature.intervals:
                             out.write('\t'.join(interval.fields) + '\n')
 
@@ -1328,7 +1328,7 @@ class IntervalIndexDataProvider(FilterableMixin, GenomeDataProvider):
 
                 # GFF dataset.
                 reader = GFFReaderWrapper(source, fix_strand=True)
-                feature = reader.next()
+                feature = next(reader)
                 payload = package_gff_feature(feature, no_detail, filter_cols)
                 payload.insert(0, offset)
 
@@ -1604,7 +1604,7 @@ class ChromatinInteractionsDataProvider(GenomeDataProvider):
 
 
 class ChromatinInteractionsTabixDataProvider(TabixDataProvider, ChromatinInteractionsDataProvider):
-    def get_iterator(self, data_file, chrom, start=0, end=sys.maxint, interchromosomal=False, **kwargs):
+    def get_iterator(self, data_file, chrom, start=0, end=sys.maxsize, interchromosomal=False, **kwargs):
         """
         """
         # Modify start as needed to get earlier interactions with start region.
@@ -1661,7 +1661,7 @@ def package_gff_feature(feature, no_detail=False, filter_cols=[]):
     # Add blocks.
     block_sizes = [(interval.end - interval.start) for interval in feature_intervals]
     block_starts = [(interval.start - feature.start) for interval in feature_intervals]
-    blocks = zip(block_sizes, block_starts)
+    blocks = list(zip(block_sizes, block_starts))
     payload.append([(feature.start + block[1], feature.start + block[1] + block[0]) for block in blocks])
 
     # Add filter data to payload.

lib/galaxy/webapps/config_manage.py

@@ -1,5 +1,4 @@
-from __future__ import absolute_import
-from __future__ import print_function
+from __future__ import absolute_import, print_function
 
 import argparse
 import copy
@@ -268,7 +267,7 @@ def main(argv=None):
 def _arg_parser():
     parser = argparse.ArgumentParser(description=DESCRIPTION)
     parser.add_argument('action', metavar='ACTION', type=str,
-                        choices=ACTIONS.keys(),
+                        choices=list(ACTIONS.keys()),
                         help='action to perform')
     parser.add_argument('app', metavar='APP', type=str, nargs="?",
                         help=APP_DESCRIPTION)
@@ -691,7 +690,7 @@ def _ordered_dump(data, stream=None, Dumper=yaml.Dumper, **kwds):
     def _dict_representer(dumper, data):
         return dumper.represent_mapping(
             yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
-            data.items())
+            list(data.items()))
     OrderedDumper.add_representer(OrderedDict, _dict_representer)
     return yaml.dump(data, stream, OrderedDumper, **kwds)
 

lib/galaxy/webapps/galaxy/api/authenticate.py

@@ -12,7 +12,8 @@ Returns:
 """
 import logging
 from base64 import b64decode
-from urllib import unquote
+
+from six.moves.urllib.parse import unquote
 
 from galaxy import exceptions
 from galaxy.managers import api_keys

lib/galaxy/webapps/galaxy/api/configuration.py

@@ -88,7 +88,7 @@ class ConfigurationController(BaseAPIController):
     @require_admin
     def dynamic_tool_confs(self, trans):
         confs = self.app.toolbox.dynamic_confs(include_migrated_tool_conf=True)
-        return map(_tool_conf_to_dict, confs)
+        return list(map(_tool_conf_to_dict, confs))
 
     @expose_api
     @require_admin

lib/galaxy/webapps/galaxy/api/datasets.py

@@ -383,5 +383,5 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
             return converted
 
         except model.NoConverterException:
-            exc_data = dict(source=original.ext, target=target_ext, available=original.get_converter_types().keys())
+            exc_data = dict(source=original.ext, target=target_ext, available=list(original.get_converter_types().keys()))
             raise galaxy_exceptions.RequestParameterInvalidException('Conversion not possible', **exc_data)

lib/galaxy/webapps/galaxy/api/datatypes.py

@@ -42,7 +42,7 @@ class DatatypesController(BaseAPIController):
                     if extension in datatypes_registry.datatypes_by_extension:
                         composite_files = datatypes_registry.datatypes_by_extension[extension].composite_files
                         if composite_files:
-                            dictionary['composite_files'] = [_.dict() for _ in composite_files.itervalues()]
+                            dictionary['composite_files'] = [_.dict() for _ in composite_files.values()]
                     rval.append(dictionary)
                 return rval
         except Exception as exception:
@@ -61,7 +61,7 @@ class DatatypesController(BaseAPIController):
         try:
             ext_to_class_name = dict()
             classes = []
-            for k, v in self._datatypes_registry.datatypes_by_extension.iteritems():
+            for k, v in self._datatypes_registry.datatypes_by_extension.items():
                 c = v.__class__
                 ext_to_class_name[k] = c.__module__ + "." + c.__name__
                 classes.append(c)
@@ -109,7 +109,7 @@ class DatatypesController(BaseAPIController):
     @expose_api_anonymous_and_sessionless
     def converters(self, trans, **kwd):
         converters = []
-        for (source_type, targets) in self._datatypes_registry.datatype_converters.iteritems():
+        for (source_type, targets) in self._datatypes_registry.datatype_converters.items():
             for target_type in targets:
                 converters.append({
                     'source': source_type,

lib/galaxy/webapps/galaxy/api/folder_contents.py

@@ -92,7 +92,7 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM
                 if content_item.description:
                     return_item.update(dict(description=content_item.description))
 
-            if content_item.api_type == 'file':
+            elif content_item.api_type == 'file':
                 #  Is the dataset public or private?
                 #  When both are False the dataset is 'restricted'
                 #  Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency

lib/galaxy/webapps/galaxy/api/history_contents.py

@@ -96,7 +96,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
 
         contents_kwds = {'types': types}
         if ids:
-            ids = map(lambda id: self.decode_id(id), ids.split(','))
+            ids = [self.decode_id(id) for id in ids.split(',')]
             contents_kwds['ids'] = ids
             # If explicit ids given, always used detailed result.
             details = 'all'
@@ -209,7 +209,7 @@ class HistoryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibrary
         else:
             ids = util.listify(ids)
             types = util.listify(types)
-        return map(lambda s: self.encode_all_ids(trans, s), fetch_job_states(self.app, trans.sa_session, ids, types))
+        return [self.encode_all_ids(trans, s) for s in fetch_job_states(self.app, trans.sa_session, ids, types)]
 
     @expose_api_anonymous
     def show_jobs_summary(self, trans, id, history_id, **kwd):

lib/galaxy/webapps/galaxy/api/jobs.py

@@ -231,7 +231,7 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
     def __dictify_associations(self, trans, *association_lists):
         rval = []
         for association_list in association_lists:
-            rval.extend(map(lambda a: self.__dictify_association(trans, a), association_list))
+            rval.extend(self.__dictify_association(trans, a) for a in association_list)
         return rval
 
     def __dictify_association(self, trans, job_dataset_association):
@@ -293,7 +293,7 @@ class JobController(BaseAPIController, UsesLibraryMixinItems):
             raise exceptions.ObjectAttributeMissingException("No inputs defined")
         inputs = payload.get('inputs', {})
         # Find files coming in as multipart file data and add to inputs.
-        for k, v in payload.iteritems():
+        for k, v in payload.items():
             if k.startswith('files_') or k.startswith('__files_'):
                 inputs[k] = v
         request_context = WorkRequestContext(app=trans.app, user=trans.user, history=trans.history)

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -253,8 +253,8 @@ class ToolShedRepositoriesController(BaseAPIController):
                 # this is ever not the case, this code will need to be updated.
                 tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_ids[0].split('/')[0])
             found_repository = json.loads(util.url_get(tool_shed_url, params=dict(tool_ids=','.join(tool_ids)), pathspec=['api', 'repositories']))
-            fr_keys = found_repository.keys()
-            tsr_id = found_repository[fr_keys[0]]['repository_id']
+            fr_first_key = next(iter(found_repository.keys()))
+            tsr_id = found_repository[fr_first_key]['repository_id']
             repository_data['current_changeset'] = found_repository['current_changeset']
             repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', tsr_id]))
             del found_repository['current_changeset']
@@ -537,7 +537,7 @@ class ToolShedRepositoriesController(BaseAPIController):
                                                            id=trans.security.encode_id(tool_shed_repository.id))
             return tool_shed_repository_dict
         if installed_tool_shed_repositories:
-            return map(to_dict, installed_tool_shed_repositories)
+            return list(map(to_dict, installed_tool_shed_repositories))
         message = "No repositories were installed, possibly because the selected repository has already been installed."
         return dict(status="ok", message=message)
 

lib/galaxy/webapps/galaxy/api/tools.py

@@ -1,7 +1,8 @@
 import logging
-import urllib
 from json import dumps
 
+from six.moves.urllib.parse import unquote_plus
+
 import galaxy.queue_worker
 from galaxy import exceptions, managers, util, web
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
@@ -201,7 +202,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             lineage_dict = None
         tool_shed_dependencies = tool.installed_tool_dependencies
         if tool_shed_dependencies:
-            tool_shed_dependencies_dict = map(to_dict, tool_shed_dependencies)
+            tool_shed_dependencies_dict = list(map(to_dict, tool_shed_dependencies))
         else:
             tool_shed_dependencies_dict = None
         return {
@@ -209,7 +210,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             "tool_version": tool.version,
             "dependency_shell_commands": tool.build_dependency_shell_commands(),
             "lineage": lineage_dict,
-            "requirements": map(to_dict, tool.requirements),
+            "requirements": list(map(to_dict, tool.requirements)),
             "installed_tool_shed_dependencies": tool_shed_dependencies_dict,
             "tool_dir": tool.tool_dir,
             "tool_shed": tool.tool_shed,
@@ -326,19 +327,19 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         # Set up inputs.
         inputs = payload.get('inputs', {})
         # Find files coming in as multipart file data and add to inputs.
-        for k, v in payload.iteritems():
+        for k, v in payload.items():
             if k.startswith('files_') or k.startswith('__files_'):
                 inputs[k] = v
 
         # for inputs that are coming from the Library, copy them into the history
         input_patch = {}
-        for k, v in inputs.iteritems():
+        for k, v in inputs.items():
             if isinstance(v, dict) and v.get('src', '') == 'ldda' and 'id' in v:
                 ldda = trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(self.decode_id(v['id']))
                 if trans.user_is_admin() or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset):
                     input_patch[k] = ldda.to_history_dataset_association(target_history, add_to_history=True)
 
-        for k, v in input_patch.iteritems():
+        for k, v in input_patch.items():
             inputs[k] = v
 
         # TODO: encode data ids and decode ids.
@@ -375,7 +376,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
             output_dict['output_name'] = output_name
             rval['output_collections'].append(output_dict)
 
-        for output_name, collection_instance in vars.get('implicit_collections', {}).iteritems():
+        for output_name, collection_instance in vars.get('implicit_collections', {}).items():
             history = target_history or trans.history
             output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history)
             output_dict['output_name'] = output_name
@@ -387,7 +388,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     # -- Helper methods --
     #
     def _get_tool(self, id, tool_version=None, user=None):
-        id = urllib.unquote_plus(id)
+        id = unquote_plus(id)
         tool = self.app.toolbox.get_tool(id, tool_version)
         if not tool:
             raise exceptions.ObjectNotFound("Could not find tool with id '%s'." % id)
@@ -466,7 +467,7 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
         # TODO: need to handle updates to conditional parameters; conditional
         # params are stored in dicts (and dicts within dicts).
         new_inputs = payload['inputs']
-        tool_params.update(dict([(key, dumps(value)) for key, value in new_inputs.items() if key in tool.inputs and new_inputs[key] is not None]))
+        tool_params.update(dict([(key, dumps(value)) for key, value in new_inputs.items() if key in tool.inputs and value is not None]))
         tool_params = tool.params_from_strings(tool_params, self.app)
 
         #

lib/galaxy/webapps/galaxy/api/toolshed.py

@@ -243,8 +243,8 @@ class ToolShedController(BaseAPIController):
                 # this is ever not the case, this code will need to be updated.
                 tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_ids[0].split('/')[0])
             found_repository = json.loads(util.url_get(tool_shed_url, params=dict(tool_ids=','.join(tool_ids)), pathspec=['api', 'repositories']))
-            fr_keys = found_repository.keys()
-            repository_id = found_repository[fr_keys[0]]['repository_id']
+            fr_first_key = next(iter(found_repository.keys()))
+            repository_id = found_repository[fr_first_key]['repository_id']
             repository_data['current_changeset'] = found_repository['current_changeset']
             repository_data['repository'] = json.loads(util.url_get(tool_shed_url, pathspec=['api', 'repositories', repository_id]))
             del found_repository['current_changeset']

lib/galaxy/webapps/galaxy/controllers/admin.py

@@ -1368,7 +1368,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
         if users:
             if trans.request.method == 'GET':
                 return {
-                    'message': 'Changes password(s) for: %s.' % ', '.join([user.email for user in users.itervalues()]),
+                    'message': 'Changes password(s) for: %s.' % ', '.join(user.email for user in users.values()),
                     'status' : 'info',
                     'inputs' : [{'name' : 'password', 'label' : 'New password', 'type' : 'password'},
                                 {'name' : 'confirm', 'label' : 'Confirm password', 'type' : 'password'}]
@@ -1380,7 +1380,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
                     return self.message_exception(trans, 'Use a password of at least 6 characters.')
                 elif password != confirm:
                     return self.message_exception(trans, 'Passwords do not match.')
-                for user in users.itervalues():
+                for user in users.values():
                     user.set_password_cleartext(password)
                     trans.sa_session.add(user)
                     trans.sa_session.flush()

lib/galaxy/webapps/galaxy/controllers/async.py

@@ -5,9 +5,9 @@ Upload class
 from __future__ import absolute_import
 
 import logging
-import urllib
 
 import requests
+from six.moves.urllib.parse import urlencode
 
 from galaxy import jobs, web
 from galaxy.util import Params
@@ -75,10 +75,10 @@ class ASync(BaseUIController):
 
                 # Assume there is exactly one output file possible
                 TOOL_OUTPUT_TYPE = None
-                for idx, obj in enumerate(tool.outputs.values()):
+                for key, obj in tool.outputs.items():
                     try:
                         TOOL_OUTPUT_TYPE = obj.format
-                        params[tool.outputs.keys()[idx]] = data.id
+                        params[key] = data.id
                         break
                     except Exception:
                         # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption
@@ -163,7 +163,7 @@ class ASync(BaseUIController):
                     url_join_char = '&'
                 else:
                     url_join_char = '?'
-                url = "%s%s%s" % (url, url_join_char, urllib.urlencode(params.flatten()))
+                url = "%s%s%s" % (url, url_join_char, urlencode(params.flatten()))
                 log.debug("connecting to -> %s" % url)
                 trans.log_event("Async connecting to -> %s" % url)
                 text = requests.get(url).text.strip()

lib/galaxy/webapps/galaxy/controllers/data_manager.py

@@ -65,7 +65,7 @@ class DataManager(BaseUIController):
                 data_manager_json = {}
                 error_messages.append(escape("Unable to obtain data_table info for hda (%s): %s" % (hda.id, e)))
             values = []
-            for key, value in data_manager_json.get('data_tables', {}).iteritems():
+            for key, value in data_manager_json.get('data_tables', {}).items():
                 values.append((key, value))
             data_manager_output.append(values)
         return trans.fill_template("data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status, error_messages=error_messages)

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -1,10 +1,13 @@
 import logging
 import os
-import urllib
 
 import paste.httpexceptions
 from markupsafe import escape
 from six import string_types, text_type
+from six.moves.urllib.parse import (
+    quote_plus,
+    unquote_plus
+)
 from sqlalchemy import false, true
 
 from galaxy import (
@@ -276,7 +279,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 return self.message_exception(trans, 'Please wait until this dataset finishes uploading before attempting to edit its metadata.')
             # let's not overwrite the imported datatypes module with the variable datatypes?
             # the built-in 'id' is overwritten in lots of places as well
-            ldatatypes = [(dtype_name, dtype_name) for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change]
+            ldatatypes = [(dtype_name, dtype_name) for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.items() if dtype_value.allow_datatype_change]
             ldatatypes.sort()
             all_roles = [(r.name, trans.security.encode_id(r.id)) for r in trans.app.security_agent.get_legitimate_roles(trans, data.dataset, 'root')]
             data_metadata = [(name, spec) for name, spec in data.metadata.spec.items()]
@@ -352,11 +355,10 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             permission_inputs = list()
             if trans.user:
                 if data.dataset.actions:
-                    permitted_actions = trans.app.model.Dataset.permitted_actions.items()
                     in_roles = {}
                     for action, roles in trans.app.security_agent.get_permissions(data.dataset).items():
                         in_roles[action.action] = [trans.security.encode_id(role.id) for role in roles]
-                    for index, action in permitted_actions:
+                    for index, action in trans.app.model.Dataset.permitted_actions.items():
                         if action == trans.app.security_agent.permitted_actions.DATASET_ACCESS:
                             help_text = action.description + '<br/>NOTE: Users must have every role associated with this dataset in order to access it.'
                         else:
@@ -415,6 +417,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                 if job_to_dataset_association.job.state not in [job_to_dataset_association.job.states.OK, job_to_dataset_association.job.states.ERROR, job_to_dataset_association.job.states.DELETED]:
                     return False
             return True
+
         message = None
         status = 'success'
         dataset_id = payload.get('dataset_id')
@@ -483,9 +486,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
             if not trans.user:
                 return self.message_exception(trans, 'You must be logged in if you want to change permissions.')
             if trans.app.security_agent.can_manage_dataset(trans.get_current_user_roles(), data.dataset):
-                permitted_actions = trans.app.model.Dataset.permitted_actions.items()
                 payload_permissions = {}
-                for action, key in permitted_actions:
+                for action in trans.app.model.Dataset.permitted_actions.keys():
                     payload_permissions[action] = [trans.security.decode_id(role_id) for role_id in util.listify(payload.get(action))]
                 # The user associated the DATASET_ACCESS permission on the dataset with 1 or more roles.  We
                 # need to ensure that they did not associate roles that would cause accessibility problems.
@@ -730,7 +732,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         if 'display_url' not in kwd or 'redirect_url' not in kwd:
             return trans.show_error_message('Invalid parameters specified for "display at" link, please contact a Galaxy administrator')
         try:
-            redirect_url = kwd['redirect_url'] % urllib.quote_plus(kwd['display_url'])
+            redirect_url = kwd['redirect_url'] % quote_plus(kwd['display_url'])
         except Exception:
             redirect_url = kwd['redirect_url']  # not all will need custom text
         if trans.app.security_agent.dataset_is_public(data.dataset):
@@ -746,7 +748,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         """Access to external display applications"""
         # Build list of parameters to pass in to display application logic (app_kwds)
         app_kwds = {}
-        for name, value in dict(kwds).iteritems():  # clone kwds because we remove stuff as we go.
+        for name, value in dict(kwds).items():  # clone kwds because we remove stuff as we go.
             if name.startswith("app_"):
                 app_kwds[name[len("app_"):]] = value
                 del kwds[name]
@@ -763,8 +765,8 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
         else:
             user_roles = []
         # Decode application name and link name
-        app_name = urllib.unquote_plus(app_name)
-        link_name = urllib.unquote_plus(link_name)
+        app_name = unquote_plus(app_name)
+        link_name = unquote_plus(link_name)
         if None in [app_name, link_name]:
             return trans.show_error_message("A display application name and link name must be provided.")
         if self._can_access_dataset(trans, data, additional_roles=user_roles):
@@ -1143,7 +1145,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
                     target_histories = [history]
                 if len(target_histories) != len(target_history_ids):
                     error_msg = error_msg + "You do not have permission to add datasets to %i requested histories.  " % (len(target_history_ids) - len(target_histories))
-                source_contents = map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids)
+                source_contents = list(map(trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get, decoded_dataset_ids))
                 source_contents.extend(map(trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get, decoded_dataset_collection_ids))
                 source_contents.sort(key=lambda content: content.hid)
                 for content in source_contents:

lib/galaxy/webapps/galaxy/controllers/root.py

@@ -152,7 +152,7 @@ class RootController(controller.JSAppLauncher, UsesAnnotations):
         if len(query) > 2:
             search_results = trans.app.toolbox_search.search(query)
             if 'tags[]' in kwd:
-                results = filter(lambda x: x in results, search_results)
+                results = [x for x in search_results if x in results]
             else:
                 results = search_results
         return results

lib/galaxy/webapps/galaxy/controllers/user.py

@@ -5,10 +5,10 @@ Contains the user interface in the Universe class
 import logging
 import random
 import socket
-import urllib
 from datetime import datetime, timedelta
 
 from markupsafe import escape
+from six.moves.urllib.parse import unquote
 from sqlalchemy import (
     and_,
     func,
@@ -868,7 +868,7 @@ class User(BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Create
         Check whether token fits the user and then activate the user's account.
         """
         params = util.Params(kwd, sanitize=False)
-        email = urllib.unquote(params.get('email', None))
+        email = unquote(params.get('email', None))
         activation_token = params.get('activation_token', None)
 
         if email is None or activation_token is None:

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -1,7 +1,6 @@
 from __future__ import absolute_import
 
 import base64
-import httplib
 import json
 import logging
 import os
@@ -9,6 +8,7 @@ import sgmllib
 
 import requests
 from markupsafe import escape
+from six.moves.http_client import HTTPConnection
 from sqlalchemy import and_
 from sqlalchemy.orm import joinedload
 from sqlalchemy.sql import expression
@@ -680,7 +680,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
         auth_header = base64.b64encode('%s:%s' % (myexp_username, myexp_password))
         headers = {"Content-type": "text/xml", "Accept": "text/xml", "Authorization": "Basic %s" % auth_header}
         myexp_url = trans.app.config.get("myexperiment_url", self.__myexp_url)
-        conn = httplib.HTTPConnection(myexp_url)
+        conn = HTTPConnection(myexp_url)
         # NOTE: blocks web thread.
         conn.request("POST", "/workflow.xml", request, headers)
         response = conn.getresponse()
@@ -989,7 +989,7 @@ class WorkflowController(BaseUIController, SharableMixin, UsesStoredWorkflowMixi
                     # Extract just the output flags for this step.
                     p = "%s|otag|" % step.id
                     l = len(p)
-                    outputs = [k[l:] for (k, v) in kwargs.iteritems() if k.startswith(p)]
+                    outputs = [k[l:] for (k, v) in kwargs.items() if k.startswith(p)]
                     if step.workflow_outputs:
                         for existing_output in step.workflow_outputs:
                             if existing_output.output_name not in outputs:
@@ -1060,10 +1060,10 @@ def _expand_multiple_inputs(kwargs):
     input_combos = _extend_with_multiplied_combos(input_combos, multiplied_multi_inputs)
 
     # Input name that are multiply specified
-    multi_input_keys = matched_multi_inputs.keys() + multiplied_multi_inputs.keys()
+    multi_input_keys = list(matched_multi_inputs.keys()) + list(multiplied_multi_inputs.keys())
 
     for input_combo in input_combos:
-        for key, value in input_combo.iteritems():
+        for key, value in input_combo.items():
             kwargs[key] = value
         yield (kwargs, multi_input_keys)
 
@@ -1074,14 +1074,14 @@ def _extend_with_matched_combos(single_inputs, multi_inputs):
 
     matched_multi_inputs = []
 
-    first_multi_input_key = multi_inputs.keys()[0]
+    first_multi_input_key = next(iter(multi_inputs.keys()))
     first_multi_value = multi_inputs.get(first_multi_input_key)
 
     for value in first_multi_value:
         new_inputs = _copy_and_extend_inputs(single_inputs, first_multi_input_key, value)
         matched_multi_inputs.append(new_inputs)
 
-    for multi_input_key, multi_input_values in multi_inputs.iteritems():
+    for multi_input_key, multi_input_values in multi_inputs.items():
         if multi_input_key == first_multi_input_key:
             continue
         if len(multi_input_values) != len(first_multi_value):
@@ -1094,7 +1094,7 @@ def _extend_with_matched_combos(single_inputs, multi_inputs):
 def _extend_with_multiplied_combos(input_combos, multi_inputs):
     combos = input_combos
 
-    for multi_input_key, multi_input_value in multi_inputs.iteritems():
+    for multi_input_key, multi_input_value in multi_inputs.items():
         iter_combos = []
 
         for combo in combos:
@@ -1114,7 +1114,7 @@ def _copy_and_extend_inputs(inputs, key, value):
 def _split_inputs(kwargs):
     """
     """
-    input_keys = filter(lambda a: a.endswith('|input'), kwargs)
+    input_keys = [a for a in kwargs if a.endswith('|input')]
     single_inputs = {}
     matched_multi_inputs = {}
     multiplied_multi_inputs = {}

lib/galaxy/webapps/tool_shed/api/repositories.py

@@ -1,12 +1,12 @@
 import json
 import logging
 import os
-import StringIO
 import tarfile
 from cgi import FieldStorage
 from collections import namedtuple
 from time import strftime
 
+from six import StringIO
 from sqlalchemy import and_, false
 
 from galaxy import (
@@ -1075,7 +1075,7 @@ class RepositoriesController(BaseAPIController):
         file_data = payload.get('file')
         # Code stolen from gx's upload_common.py
         if isinstance(file_data, FieldStorage):
-            assert not isinstance(file_data.file, StringIO.StringIO)
+            assert not isinstance(file_data.file, StringIO)
             assert file_data.file.name != '<fdopen>'
             local_filename = util.mkstemp_ln(file_data.file.name, 'upload_file_data_')
             file_data.file.close()

lib/galaxy/webapps/tool_shed/controllers/admin.py

@@ -46,7 +46,7 @@ class AdminController(BaseUIController, Admin):
                                                                 **kwd))
             elif operation == "repositories_by_user":
                 # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
+                for k, v in list(kwd.items()):
                     if k.startswith('f-'):
                         del kwd[k]
                 if 'user_id' in kwd:
@@ -61,7 +61,7 @@ class AdminController(BaseUIController, Admin):
                     kwd['f-email'] = repository.user.email
             elif operation == "repositories_by_category":
                 # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
+                for k, v in list(kwd.items()):
                     if k.startswith('f-'):
                         del kwd[k]
                 category_id = kwd.get('id', None)

lib/galaxy/webapps/tool_shed/controllers/repository.py

@@ -120,7 +120,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             operation = kwd['operation'].lower()
             if operation in ["repositories_by_category", "repositories_by_user"]:
                 # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
+                for k, v in list(kwd.items()):
                     if k.startswith('f-'):
                         del kwd[k]
                 return trans.response.send_redirect(web.url_for(controller='repository',
@@ -274,7 +274,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
     def browse_repositories_by_user(self, trans, **kwd):
         """Display the list of repositories owned by a specified user."""
         # Eliminate the current search filters if any exist.
-        for k, v in kwd.items():
+        for k, v in list(kwd.items()):
             if k.startswith('f-'):
                 del kwd[k]
         if 'operation' in kwd:
@@ -522,7 +522,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
             operation = kwd['operation'].lower()
             if operation in ["valid_repositories_by_category", "valid_repositories_by_user"]:
                 # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
+                for k, v in list(kwd.items()):
                     if k.startswith('f-'):
                         del kwd[k]
                 return trans.response.send_redirect(web.url_for(controller='repository',
@@ -560,7 +560,7 @@ class RepositoryController(BaseUIController, ratings_util.ItemRatings):
                                                                 changeset_revision=latest_installable_changeset_revision))
             elif operation == "valid_repositories_by_category":
                 # Eliminate the current filters if any exist.
-                for k, v in kwd.items():
+                for k, v in list(kwd.items()):
                     if k.startswith('f-'):
                         del kwd[k]
                 category_id = kwd.get('id', None)

lib/galaxy/webapps/tool_shed/security/__init__.py

@@ -32,7 +32,7 @@ class RBACAgent:
         When getting permitted actions from an untrusted source like a
         form, ensure that they match our actual permitted actions.
         """
-        return filter(lambda x: x is not None, [self.permitted_actions.get(action_string) for action_string in permitted_action_strings])
+        return [x for x in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings] if x is not None]
 
     def create_private_user_role(self, user):
         raise Exception("Unimplemented Method")
@@ -46,7 +46,7 @@ class RBACAgent:
 
     def get_actions(self):
         """Get all permitted actions as a list of Action objects"""
-        return self.permitted_actions.__dict__.values()
+        return list(self.permitted_actions.__dict__.values())
 
     def get_item_actions(self, action, item):
         raise Exception('No valid method of retrieving action (%s) for item %s.' % (action, item))

lib/galaxy/webapps/tool_shed/util/hgweb_config.py

@@ -1,10 +1,11 @@
-import ConfigParser
 import logging
 import os
 import shutil
 import threading
 from datetime import date
 
+from six.moves import configparser
+
 log = logging.getLogger(__name__)
 
 new_hgweb_config_template = """
@@ -60,12 +61,12 @@ class HgWebConfigManager(object):
         self.read_config()
         try:
             entry = self.in_memory_config.get('paths', lhs)
-        except ConfigParser.NoOptionError:
+        except configparser.NoOptionError:
             try:
                 # We have a multi-threaded front-end, so one of the threads may not have the latest version of the hgweb.config file.
                 self.read_config(force_read=True)
                 entry = self.in_memory_config.get('paths', lhs)
-            except ConfigParser.NoOptionError:
+            except configparser.NoOptionError:
                 raise Exception("Entry for repository %s missing in file %s." % (lhs, self.hgweb_config))
         return entry
 
@@ -92,7 +93,7 @@ class HgWebConfigManager(object):
 
     def read_config(self, force_read=False):
         if force_read or self.in_memory_config is None:
-            config = ConfigParser.ConfigParser()
+            config = configparser.ConfigParser()
             config.read(self.hgweb_config)
             self.in_memory_config = config
 

scripts/build_universe_config.py

@@ -1,9 +1,10 @@
-from ConfigParser import ConfigParser
 from os import listdir
 from os.path import join
 from re import match
 from sys import argv
 
+from six.moves.configparser import ConfigParser
+
 
 def merge():
     """

scripts/data_libraries/build_lucene_index.py

@@ -9,13 +9,13 @@ details.
 Run from the ~/scripts/data_libraries directory:
 %sh build_lucene_index.sh
 """
-import ConfigParser
 import csv
 import os
 import sys
-import urllib
 
 import requests
+from six.moves.configparser import ConfigParser
+from six.moves.urllib.parse import urlencode
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
@@ -39,7 +39,7 @@ def main(ini_file):
 
 
 def build_index(search_url, dataset_file):
-    url = "%s/index?%s" % (search_url, urllib.urlencode({"docfile": dataset_file}))
+    url = "%s/index?%s" % (search_url, urlencode({"docfile": dataset_file}))
     requests.put(url)
 
 
@@ -89,7 +89,7 @@ def _get_folder_info(folder):
 
 
 def get_sa_session(ini_file):
-    conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
+    conf_parser = ConfigParser({'here': os.getcwd()})
     conf_parser.read(ini_file)
     kwds = dict()
     for key, value in conf_parser.items("app:main"):

scripts/galaxy-main

@@ -31,10 +31,7 @@ import threading
 from argparse import ArgumentParser
 from logging.config import fileConfig
 
-try:
-    import ConfigParser as configparser
-except ImportError:
-    import configparser
+from six.moves.configparser import ConfigParser
 
 try:
     from daemonize import Daemonize
@@ -219,7 +216,7 @@ class GalaxyConfigBuilder(object):
         if not self.config_file:
             return
         if self.config_is_ini:
-            raw_config = configparser.ConfigParser()
+            raw_config = ConfigParser()
             raw_config.read([self.config_file])
             if raw_config.has_section('loggers'):
                 config_file = os.path.abspath(self.config_file)

scripts/helper.py

@@ -8,9 +8,10 @@ from __future__ import print_function
 
 import os
 import sys
-from ConfigParser import ConfigParser
 from optparse import OptionParser
 
+from six.moves.configparser import ConfigParser
+
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, 'lib'))
 
 from galaxy.model import mapping

scripts/loc_files/create_all_fasta_loc.py

@@ -149,18 +149,6 @@ VARIANT_MAP = {'canon': 'Canonical',
                'male': 'Male'}
 
 
-# alphabetize ignoring case
-def caseless_compare(a, b):
-    au = a.upper()
-    bu = b.upper()
-    if au > bu:
-        return 1
-    elif au == bu:
-        return 0
-    elif au < bu:
-        return -1
-
-
 def __main__():
     # command line variables
     parser = optparse.OptionParser()
@@ -257,14 +245,13 @@ def __main__():
                         else:
                             unmatching_fasta_paths.append(os.path.join(dirpath, fn))
         # remove redundant fasta files
-        if variant_exclusions.keys():
-            for k in variant_exclusions.keys():
-                leave_in = '%s%s' % (genome_subdir, k)
-                if leave_in in fasta_locs:
-                    to_remove = ['%s%s' % (genome_subdir, k) for k in variant_exclusions[k]]
-                    for tr in to_remove:
-                        if tr in fasta_locs:
-                            del fasta_locs[tr]
+        for k, v in variant_exclusions.items():
+            leave_in = '%s%s' % (genome_subdir, k)
+            if leave_in in fasta_locs:
+                to_remove = ['%s%s' % (genome_subdir, _) for _ in v]
+                for tr in to_remove:
+                    if tr in fasta_locs:
+                        del fasta_locs[tr]
 
     # output results
     print('\nThere were %s fasta files found that were not included because they did not have the expected file names.' % len(unmatching_fasta_paths))
@@ -286,8 +273,8 @@ def __main__():
         else:
             all_fasta_loc.write('%s\n' % open('%s.sample' % loc_path, 'rb').read().strip())
     # output list of fasta files in alphabetical order
-    fasta_bases = fasta_locs.keys()
-    fasta_bases.sort(caseless_compare)
+    fasta_bases = list(fasta_locs.keys())
+    fasta_bases.sort(key=str.upper)
     for fb in fasta_bases:
         out_line = []
         for col in col_values:

scripts/microbes/create_bacteria_loc_file.py

@@ -20,25 +20,25 @@ def __main__():
         this_base_dir, sub_dirs, files = result
         for file in files:
             if file[-5:] == ".info":
-                dict = {}
+                tmp_dict = {}
                 info_file = open(os.path.join(this_base_dir, file), 'r')
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
                     fields = line.replace("\n", "").split("=")
-                    dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in dict.keys():
-                    name = dict['genome project id']
-                    if 'build' in dict.keys():
-                        name = dict['build']
+                    tmp_dict[fields[0]] = "=".join(fields[1:])
+                if 'genome project id' in tmp_dict.keys():
+                    name = tmp_dict['genome project id']
+                    if 'build' in tmp_dict.keys():
+                        name = tmp_dict['build']
                     if name not in organisms.keys():
                         organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
-                    for key in dict.keys():
-                        organisms[name][key] = dict[key]
+                    for key in tmp_dict.keys():
+                        organisms[name][key] = tmp_dict[key]
                 else:
-                    if dict['organism'] not in organisms.keys():
-                        organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
+                    if tmp_dict['organism'] not in organisms.keys():
+                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
     for org in organisms:
         org = organisms[org]
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation

scripts/microbes/create_bacteria_table.py

@@ -20,32 +20,31 @@ def __main__():
         this_base_dir, sub_dirs, files = result
         for file in files:
             if file[-5:] == ".info":
-                dict = {}
+                tmp_dict = {}
                 info_file = open(os.path.join(this_base_dir, file), 'r')
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
                     fields = line.replace("\n", "").split("=")
-                    dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in dict.keys():
-                    name = dict['genome project id']
-                    if 'build' in dict.keys():
-                        name = dict['build']
+                    tmp_dict[fields[0]] = "=".join(fields[1:])
+                if 'genome project id' in tmp_dict.keys():
+                    name = tmp_dict['genome project id']
+                    if 'build' in tmp_dict.keys():
+                        name = tmp_dict['build']
                     if name not in organisms.keys():
                         organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
-                    for key in dict.keys():
-                        organisms[name][key] = dict[key]
+                    for key in tmp_dict.keys():
+                        organisms[name][key] = tmp_dict[key]
                 else:
-                    if dict['organism'] not in organisms.keys():
-                        organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
+                    if tmp_dict['organism'] not in organisms.keys():
+                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
 
-    orgs = organisms.keys()
-    for org in orgs:
-        if 'name' not in organisms[org]:
-            del organisms[org]
+    for org_name, org in list(organisms.items()):
+        if 'name' not in org:
+            del organisms[org_name]
 
-    orgs = organisms.keys()
+    orgs = list(organisms.keys())
     # need to sort by name
     swap_test = False
     for i in range(0, len(orgs) - 1):
@@ -58,8 +57,7 @@ def __main__():
 
     print("||'''Organism'''||'''Kingdom'''||'''Group'''||'''Links to UCSC Archaea Browser'''||")
 
-    for org in orgs:
-        org = organisms[org]
+    for org in organisms.values():
         at_ucsc = False
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation
         try:

scripts/microbes/create_nib_seq_loc_file.py

@@ -29,25 +29,25 @@ def __main__():
         this_base_dir, sub_dirs, files = result
         for file in files:
             if file[-5:] == ".info":
-                dict = {}
+                tmp_dict = {}
                 info_file = open(os.path.join(this_base_dir, file), 'r')
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
                     fields = line.replace("\n", "").split("=")
-                    dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in dict.keys():
-                    name = dict['genome project id']
-                    if 'build' in dict.keys():
-                        name = dict['build']
+                    tmp_dict[fields[0]] = "=".join(fields[1:])
+                if 'genome project id' in tmp_dict.keys():
+                    name = tmp_dict['genome project id']
+                    if 'build' in tmp_dict.keys():
+                        name = tmp_dict['build']
                     if name not in organisms.keys():
                         organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
-                    for key in dict.keys():
-                        organisms[name][key] = dict[key]
+                    for key in tmp_dict.keys():
+                        organisms[name][key] = tmp_dict[key]
                 else:
-                    if dict['organism'] not in organisms.keys():
-                        organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
+                    if tmp_dict['organism'] not in organisms.keys():
+                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
 
     for org in organisms:
         org = organisms[org]

scripts/microbes/get_builds_lengths.py

@@ -20,25 +20,25 @@ def __main__():
         this_base_dir, sub_dirs, files = result
         for file in files:
             if file[-5:] == ".info":
-                dict = {}
+                tmp_dict = {}
                 info_file = open(os.path.join(this_base_dir, file), 'r')
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
                     fields = line.replace("\n", "").split("=")
-                    dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in dict.keys():
-                    name = dict['genome project id']
-                    if 'build' in dict.keys():
-                        name = dict['build']
+                    tmp_dict[fields[0]] = "=".join(fields[1:])
+                if 'genome project id' in tmp_dict.keys():
+                    name = tmp_dict['genome project id']
+                    if 'build' in tmp_dict.keys():
+                        name = tmp_dict['build']
                     if name not in organisms.keys():
                         organisms[name] = {'chrs': {}, 'base_dir': this_base_dir}
-                    for key in dict.keys():
-                        organisms[name][key] = dict[key]
+                    for key in tmp_dict.keys():
+                        organisms[name][key] = tmp_dict[key]
                 else:
-                    if dict['organism'] not in organisms.keys():
-                        organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
+                    if tmp_dict['organism'] not in organisms.keys():
+                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
     for org in organisms:
         org = organisms[org]
         # if no gpi, then must be a ncbi chr which corresponds to a UCSC org, w/o matching UCSC designation

scripts/microbes/harvest_bacteria.py

@@ -12,10 +12,10 @@ import time
 from ftplib import FTP
 
 import requests
-from BeautifulSoup import BeautifulSoup
 from six.moves.urllib.request import urlretrieve
 
-from util import (  # noqa: I202
+from BeautifulSoup import BeautifulSoup  # noqa: I100, I202
+from util import (
     get_bed_from_genbank,
     get_bed_from_GeneMark,
     get_bed_from_GeneMarkHMM,

scripts/microbes/ncbi_to_ucsc.py

@@ -7,10 +7,11 @@ from __future__ import print_function
 
 import os
 import sys
-import urllib
 from shutil import move
 from xml.etree import ElementTree
 
+from six.moves.urllib.request import urlopen
+
 
 def __main__():
     base_dir = os.path.join(os.getcwd(), "bacteria")
@@ -24,29 +25,29 @@ def __main__():
         this_base_dir, sub_dirs, files = result
         for file in files:
             if file[-5:] == ".info":
-                dict = {}
+                tmp_dict = {}
                 info_file = open(os.path.join(this_base_dir, file), 'r')
                 info = info_file.readlines()
                 info_file.close()
                 for line in info:
                     fields = line.replace("\n", "").split("=")
-                    dict[fields[0]] = "=".join(fields[1:])
-                if 'genome project id' in dict.keys():
-                    if dict['genome project id'] not in organisms.keys():
-                        organisms[dict['genome project id']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    for key in dict.keys():
-                        organisms[dict['genome project id']][key] = dict[key]
+                    tmp_dict[fields[0]] = "=".join(fields[1:])
+                if 'genome project id' in tmp_dict.keys():
+                    if tmp_dict['genome project id'] not in organisms.keys():
+                        organisms[tmp_dict['genome project id']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    for key in tmp_dict.keys():
+                        organisms[tmp_dict['genome project id']][key] = tmp_dict[key]
                 else:
-                    if dict['organism'] not in organisms.keys():
-                        organisms[dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
-                    organisms[dict['organism']]['chrs'][dict['chromosome']] = dict
+                    if tmp_dict['organism'] not in organisms.keys():
+                        organisms[tmp_dict['organism']] = {'chrs': {}, 'base_dir': this_base_dir}
+                    organisms[tmp_dict['organism']]['chrs'][tmp_dict['chromosome']] = tmp_dict
 
     # get UCSC data
 
     URL = "http://archaea.ucsc.edu/cgi-bin/das/dsn"
 
     try:
-        page = urllib.urlopen(URL)
+        page = urlopen(URL)
     except Exception:
         print("#Unable to open " + URL)
         print("?\tunspecified (?)")
@@ -65,7 +66,7 @@ def __main__():
     for dsn in tree:
         build = dsn.find("SOURCE").attrib['id']
         try:
-            org_page = urllib.urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db=" + build).read().replace("\n", "").split("<table border=2 cellspacing=2 cellpadding=2>")[1].split("</table>")[0].split("</tr>")
+            org_page = urlopen("http://archaea.ucsc.edu/cgi-bin/hgGateway?db=" + build).read().replace("\n", "").split("<table border=2 cellspacing=2 cellpadding=2>")[1].split("</table>")[0].split("</tr>")
         except Exception:
             print("NO CHROMS FOR", build)
             continue

scripts/microbes/util.py

@@ -137,7 +137,7 @@ def get_bed_from_GeneMark(geneMark_filename, chr):
     for block in orfs.split("\n\n"):
         if block.startswith("List of Regions of interest"):
             break
-        best_block = {'start': 0, 'end': 0, 'strand': '+', 'avg_prob': -sys.maxint, 'start_prob': -sys.maxint, 'name': 'DNE'}
+        best_block = {'start': 0, 'end': 0, 'strand': '+', 'avg_prob': -sys.maxsize, 'start_prob': -sys.maxsize, 'name': 'DNE'}
         ctr += 1
         ctr2 = 0
         for line in block.split("\n"):
@@ -158,9 +158,8 @@ def get_bed_from_GeneMark(geneMark_filename, chr):
             except Exception:
                 start_prob = 0
             name = "orf_" + str(ctr) + "_" + str(ctr2)
-            if avg_prob >= best_block['avg_prob']:
-                if start_prob > best_block['start_prob']:
-                    best_block = {'start': start, 'end': end, 'strand': strand, 'avg_prob': avg_prob, 'start_prob': start_prob, 'name': name}
+            if avg_prob >= best_block['avg_prob'] and start_prob > best_block['start_prob']:
+                best_block = {'start': start, 'end': end, 'strand': strand, 'avg_prob': avg_prob, 'start_prob': start_prob, 'name': name}
         regions.append(chr + "\t" + str(best_block['start']) + "\t" + str(best_block['end']) + "\t" + best_block['name'] + "\t" + str(int(best_block['avg_prob'] * 1000)) + "\t" + best_block['strand'])
     return regions
 
@@ -198,8 +197,8 @@ def get_bed_from_GeneMarkHMM(geneMarkHMM_filename, chr):
 # converts glimmer3 to bed, doing some linear scaling (probably not correct?) on scores
 # returns an array of bed regions
 def get_bed_from_glimmer3(glimmer3_filename, chr):
-    max_score = -sys.maxint
-    min_score = sys.maxint
+    max_score = -sys.maxsize
+    min_score = sys.maxsize
     orfs = []
     for line in open(glimmer3_filename).readlines():
         if line.startswith(">"):

scripts/others/incorrect_gops_jobs.py

@@ -5,12 +5,12 @@ wherein the second dataset doesn't have chr, start and end in standard columns 1
 """
 from __future__ import print_function
 
-import ConfigParser
 import os
 import sys
 import tempfile
 
 import sqlalchemy as sa
+from six.moves.configparser import ConfigParser
 
 import galaxy.app
 import galaxy.model.mapping
@@ -34,7 +34,7 @@ class TestApplication(object):
 
 def main():
     ini_file = sys.argv[1]
-    conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
+    conf_parser = ConfigParser({'here': os.getcwd()})
     conf_parser.read(ini_file)
     configuration = {}
     for key, value in conf_parser.items("app:main"):

scripts/others/incorrect_gops_join_jobs.py

@@ -4,12 +4,12 @@ Fetch gops_join wherein the use specified minimum coverage is not 1.
 """
 from __future__ import print_function
 
-import ConfigParser
 import os
 import sys
 import tempfile
 
 import sqlalchemy as sa
+from six.moves.configparser import ConfigParser
 
 import galaxy.app
 import galaxy.model.mapping
@@ -33,7 +33,7 @@ class TestApplication(object):
 
 def main():
     ini_file = sys.argv[1]
-    conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
+    conf_parser = ConfigParser({'here': os.getcwd()})
     conf_parser.read(ini_file)
     configuration = {}
     for key, value in conf_parser.items("app:main"):

scripts/paster.py

@@ -4,14 +4,15 @@ Bootstrap the Galaxy framework.
 This should not be called directly!  Use the run.sh script in Galaxy's
 top level directly.
 """
+from __future__ import absolute_import
+
 import os
 import sys
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
 from galaxy.util.pastescript import serve
-
-from check_python import check_python  # noqa: I100
+from check_python import check_python  # noqa: I100, I201
 
 # ensure supported version
 try:

scripts/set_dataset_sizes.py

@@ -3,9 +3,9 @@ from __future__ import print_function
 
 import os
 import sys
-from ConfigParser import ConfigParser
 from optparse import OptionParser
 
+from six.moves.configparser import ConfigParser
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 

scripts/set_user_disk_usage.py

@@ -3,9 +3,10 @@ from __future__ import print_function
 
 import os
 import sys
-from ConfigParser import ConfigParser
 from optparse import OptionParser
 
+from six.moves.configparser import ConfigParser
+
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
 
 import galaxy.config

scripts/sync_reports_config.py

@@ -1,6 +1,7 @@
-from ConfigParser import ConfigParser
 from sys import argv
 
+from six.moves.configparser import ConfigParser
+
 REPLACE_PROPERTIES = ["file_path", "database_connection", "new_file_path"]
 MAIN_SECTION = "app:main"
 

scripts/tool_shed/api/get_filtered_repository_revisions.py

@@ -74,9 +74,9 @@ def main(options):
                     if latest_revision_only:
                         latest_revision = repository_dict.get('latest_revision', hg_util.INITIAL_CHANGELOG_HASH)
                         if changeset_revision == latest_revision:
-                            repository_dicts.append(dict(repository_dict.items() + baseline_repository_dict.items()))
+                            repository_dicts.append(dict(list(repository_dict.items()) + list(baseline_repository_dict.items())))
                     else:
-                        repository_dicts.append(dict(repository_dict.items() + baseline_repository_dict.items()))
+                        repository_dicts.append(dict(list(repository_dict.items()) + list(baseline_repository_dict.items())))
         print('\n\n', repository_dicts)
         print('\nThe url:\n\n', api_url, '\n\nreturned ', len(repository_dicts), ' repository dictionaries...')
 

scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py

@@ -1,15 +1,15 @@
 #!/usr/bin/python
 from __future__ import print_function
 
-import ConfigParser
 import optparse
 import os
 import sys
 
-sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
-
+from six.moves.configparser import ConfigParser
 from sqlalchemy.exc import OperationalError, ProgrammingError
 
+sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
+
 import galaxy.webapps.tool_shed.model.mapping as tool_shed_model
 from tool_shed.util import xml_util
 
@@ -50,7 +50,7 @@ def check_db(config_parser):
         pass
 
     if config_parser.has_option('app:main', 'hgweb_config_dir'):
-        hgweb_config_parser = ConfigParser.ConfigParser()
+        hgweb_config_parser = ConfigParser()
         hgweb_dir = config_parser.get('app:main', 'hgweb_config_dir')
         hgweb_config_file = os.path.join(hgweb_dir, 'hgweb.config')
         if not os.path.exists(hgweb_config_file):
@@ -104,7 +104,7 @@ def get_local_tool_shed_url(config_parser):
 
 
 def main(args):
-    config_parser = ConfigParser.ConfigParser()
+    config_parser = ConfigParser()
 
     if os.path.exists(args.config):
         config_parser.read(args.config)

scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py

@@ -1,21 +1,21 @@
 #!/usr/bin/env python
 from __future__ import print_function
 
-import ConfigParser
 import logging
 import optparse
 import os
 import re
 import sys
 
+from six.moves.configparser import ConfigParser
+
 sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
 sys.path.insert(1, os.path.join(os.path.dirname(__file__)))
 
 import galaxy.webapps.tool_shed.config as tool_shed_config
 from galaxy.web import security
 from galaxy.webapps.tool_shed.model import mapping
-
-from bootstrap_util import admin_user_info  # noqa: I100
+from bootstrap_util import admin_user_info  # noqa: I100,I201
 
 log = logging.getLogger(__name__)
 
@@ -124,7 +124,7 @@ if __name__ == "__main__":
     parser.add_option('-c', dest='config', action='store', help='.ini file to retried toolshed configuration from')
     (args, options) = parser.parse_args()
     ini_file = args.config
-    config_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
+    config_parser = ConfigParser({'here': os.getcwd()})
     print("Reading ini file: ", ini_file)
     config_parser.read(ini_file)
     config_dict = {}

scripts/tool_shed/check_download_urls.py

@@ -5,10 +5,14 @@
 from __future__ import print_function
 
 import os
-import urllib2
 import xml.etree.ElementTree as ET
 from optparse import OptionParser
 
+from six.moves.urllib.request import (
+    Request,
+    urlopen
+)
+
 FILENAMES = ['tool_dependencies.xml']
 ACTION_TYPES = ['download_by_url', 'download_file']
 
@@ -30,7 +34,7 @@ def main():
                         for element in root.findall(".//action[@type='%s']" % action_type):
                             url = element.text.strip()
                             try:
-                                urllib2.urlopen(urllib2.Request(url))
+                                urlopen(Request(url))
                             except Exception as e:
                                 print("Bad URL '%s' in file '%s': %s" % (url, path, e))
                 except Exception as e:

scripts/tool_shed/migrate_tools_to_repositories.py

@@ -20,7 +20,6 @@ To run this script, use "sh migrate_tools_to_repositories.sh" from this director
 '''
 from __future__ import print_function
 
-import ConfigParser
 import os
 import shutil
 import sys
@@ -29,6 +28,7 @@ import tempfile
 from time import strftime
 
 from mercurial import hg, ui
+from six.moves import configparser
 
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, 'lib')))
 
@@ -276,11 +276,11 @@ def main():
     print("%s - Migrating current tool archives to new tool repositories" % now)
     # tool_shed_wsgi.ini file
     ini_file = sys.argv[1]
-    conf_parser = ConfigParser.ConfigParser({'here': os.getcwd()})
+    conf_parser = configparser.ConfigParser({'here': os.getcwd()})
     conf_parser.read(ini_file)
     try:
         db_conn_str = conf_parser.get("app:main", "database_connection")
-    except ConfigParser.NoOptionError:
+    except configparser.NoOptionError:
         db_conn_str = conf_parser.get("app:main", "database_file")
     print('DB Connection: ', db_conn_str)
     # Instantiate app

scripts/transfer.py

@@ -4,18 +4,15 @@ Downloads files to temp locations.  This script is invoked by the Transfer
 Manager (galaxy.jobs.transfer_manager) and should not normally be invoked by
 hand.
 """
-import ConfigParser
 import json
 import logging
 import optparse
 import os
 import random
-import SocketServer
 import sys
 import tempfile
 import threading
 import time
-import urllib2
 
 try:
     import pexpect
@@ -23,6 +20,12 @@ except ImportError:
     pexpect = None
 
 from daemon import DaemonContext
+from six.moves import (
+    configparser,
+    socketserver
+)
+from six.moves.urllib.error import URLError
+from six.moves.urllib.request import urlopen
 from sqlalchemy import create_engine, MetaData, Table
 from sqlalchemy.orm import scoped_session, sessionmaker
 
@@ -82,7 +85,7 @@ class GalaxyApp(object):
     model/database.
     """
     def __init__(self, config_file):
-        self.config = ConfigParser.ConfigParser(dict(database_file='database/universe.sqlite',
+        self.config = configparser.ConfigParser(dict(database_file='database/universe.sqlite',
                                                      file_path='database/files',
                                                      transfer_worker_port_range='12275-12675',
                                                      transfer_worker_log=None))
@@ -95,7 +98,7 @@ class GalaxyApp(object):
         default_dburl = 'sqlite:///%s?isolation_level=IMMEDIATE' % self.config.get('app:main', 'database_file')
         try:
             dburl = self.config.get('app:main', 'database_connection')
-        except ConfigParser.NoOptionError:
+        except configparser.NoOptionError:
             dburl = default_dburl
         engine = create_engine(dburl)
         metadata = MetaData(engine)
@@ -107,7 +110,7 @@ class GalaxyApp(object):
         return self.sa_session.query(self.model.TransferJob).get(int(id))
 
 
-class ListenerServer(SocketServer.ThreadingTCPServer):
+class ListenerServer(socketserver.ThreadingTCPServer):
     """
     The listener will accept state requests and new transfers for as long as
     the manager is running.
@@ -118,7 +121,7 @@ class ListenerServer(SocketServer.ThreadingTCPServer):
         while True:
             random_port = random.choice(port_range)
             try:
-                SocketServer.ThreadingTCPServer.__init__(self, ('localhost', random_port), RequestHandlerClass)
+                super(ListenerServer, self).__init__(('localhost', random_port), RequestHandlerClass)
                 log.info('Listening on port %s' % random_port)
                 break
             except Exception as e:
@@ -128,7 +131,7 @@ class ListenerServer(SocketServer.ThreadingTCPServer):
         app.sa_session.flush()
 
 
-class ListenerRequestHandler(SocketServer.BaseRequestHandler):
+class ListenerRequestHandler(socketserver.BaseRequestHandler):
     """
     Handle state or transfer requests received on the socket.
     """
@@ -217,8 +220,8 @@ def http_transfer(transfer_job):
     url = transfer_job.params['url']
     assert url.startswith('http://') or url.startswith('https://')
     try:
-        f = urllib2.urlopen(url)
-    except urllib2.URLError as e:
+        f = urlopen(url)
+    except URLError as e:
         yield dict(state=transfer_job.states.ERROR, info='Unable to open URL: %s' % str(e))
         return
     size = f.info().getheader('Content-Length')

scripts/update_shed_config_path.py

@@ -1,10 +1,10 @@
 from __future__ import print_function
 
 import argparse
-import ConfigParser
 import os
 import sys
 
+from six.moves.configparser import SafeConfigParser
 from sqlalchemy import create_engine, MetaData
 from sqlalchemy.orm import scoped_session, sessionmaker
 
@@ -27,7 +27,7 @@ def main(opts, session, model):
 
 
 def create_database(config_file):
-    parser = ConfigParser.SafeConfigParser()
+    parser = SafeConfigParser()
     parser.read(config_file)
     # Determine which database connection to use.
     database_connection = parser.get('app:main', 'install_database_connection')

tools/genomespace/genomespace_importer.py

@@ -54,7 +54,7 @@ def _prepare_json_param_dict(param_dict):
     JSON serialization Support functions for exec_before_job hook
     """
     rval = {}
-    for key, value in param_dict.iteritems():
+    for key, value in param_dict.items():
         if isinstance(value, dict):
             rval[key] = _prepare_json_param_dict(value)
         elif isinstance(value, list):
@@ -83,7 +83,7 @@ def exec_before_job(app, inp_data, out_data, param_dict=None, tool=None):
                                      GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'),
                                      TOOL_PROVIDED_JOB_METADATA_FILE=galaxy.jobs.TOOL_PROVIDED_JOB_METADATA_FILE)
     json_filename = None
-    for i, (out_name, data) in enumerate(out_data.iteritems()):
+    for i, (out_name, data) in enumerate(out_data.items()):
         file_name = data.get_file_name()
         data_dict = dict(out_data_name=out_name,
                          ext=data.ext,