Python3: finish first pass on whole codebase

galaxyproject · Dec 14, 2017 · 14259b1 · 14259b1
1 parent 9adfa31
commit 14259b1
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Showing 65 changed files with 259 additions and 344 deletions.
diff --git a/.ci/py3_sources.txt b/.ci/py3_sources.txt
diff --git a/config/plugins/webhooks/demo/tour_generator/helper/__init__.py b/config/plugins/webhooks/demo/tour_generator/helper/__init__.py
@@ -174,7 +174,7 @@ def _generate_tour(self):
             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])

diff --git a/lib/galaxy/containers/docker_swarm_manager.py b/lib/galaxy/containers/docker_swarm_manager.py
@@ -46,7 +46,7 @@
     '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 @@ def _check_for_new_nodes(self):
             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)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
@@ -449,7 +449,7 @@ def __init__(self, **kwd):
     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 @@ def __init__(self, **kwd):
     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:

diff --git a/lib/galaxy/jobs/handler.py b/lib/galaxy/jobs/handler.py
@@ -5,11 +5,11 @@
 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 @@ def __monitor_step(self):
         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 @@ def recover(self, job, job_wrapper):
             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:

diff --git a/lib/galaxy/jobs/runners/chronos.py b/lib/galaxy/jobs/runners/chronos.py
@@ -232,7 +232,7 @@ def finish_job(self, job_state):
 
     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 @@ def _get_job_spec(self, job_wrapper):
 
     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)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
@@ -373,10 +373,10 @@ def serialize_display_apps(self, hda, key, trans=None, **context):
         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),

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -413,7 +413,7 @@ def _workflow_to_dict_run(self, trans, stored):
             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 @@ def callback(input, prefixed_name, **kwargs):
             # 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 @@ def __walk_step_dicts(self, data):
         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 @@ def __connect_workflow_steps(self, steps, steps_by_external_id):
         """
         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

diff --git a/lib/galaxy/openid/providers.py b/lib/galaxy/openid/providers.py
@@ -4,6 +4,8 @@
 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 @@ def __init__(self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=
 
     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 @@ def __init__(self, providers=None):
             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):

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -339,7 +339,7 @@ def initialize(self, trans, tool):
         """
         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):

diff --git a/lib/galaxy/tools/cwl/representation.py b/lib/galaxy/tools/cwl/representation.py
@@ -78,9 +78,9 @@ def simple_value(input, param_dict_value, cwl_type=None):
         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")]]))
@@ -112,15 +112,15 @@ def from_simple_value(input, param_dict_value, cwl_type=None):
         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
 
         if galaxy_input_type == "repeat":
             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)

diff --git a/lib/galaxy/tools/imp_exp/__init__.py b/lib/galaxy/tools/imp_exp/__init__.py
@@ -240,7 +240,7 @@ def default(self, obj):
 
                     # 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.

diff --git a/lib/galaxy/util/permutations.py b/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:

diff --git a/lib/galaxy/util/script.py b/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')

diff --git a/lib/galaxy/visualization/data_providers/basic.py b/lib/galaxy/visualization/data_providers/basic.py
@@ -37,7 +37,7 @@ def process_data(self, iterator, start_val=0, max_vals=None, **kwargs):
         """
         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.