Fix import order and Python3 compatibility for lib/galaxy/web/base/

.ci/flake8_lint_include_list.txt

@@ -79,9 +79,7 @@ lib/galaxy/visualization/__init__.py
 lib/galaxy/visualization/plugins/__init__.py
 lib/galaxy/visualization/plugins/utils.py
 lib/galaxy/visualization/tracks/
-lib/galaxy/web/base/controllers/__init__.py
-lib/galaxy/web/base/__init__.py
-lib/galaxy/web/base/interactive_environments.py
+lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/formatting.py
 lib/galaxy/web/framework/base.py

.ci/py3_sources.txt

@@ -27,6 +27,7 @@ lib/galaxy/tools/
 lib/galaxy/tours/
 lib/galaxy/util/
 lib/galaxy/visualization/
+lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/framework/base.py
 lib/galaxy/web/framework/decorators.py

lib/galaxy/web/base/controller.py

@@ -2,40 +2,63 @@
 Contains functionality needed in every web interface
 """
 import logging
-import operator
 import re
 
-from six import string_types, text_type
+from paste.httpexceptions import (
+    HTTPBadRequest,
+    HTTPInternalServerError,
+    HTTPNotImplemented,
+    HTTPRequestRangeNotSatisfiable
+)
+from six import (
+    string_types,
+    text_type
+)
 from sqlalchemy import true
 
-from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError
-from paste.httpexceptions import HTTPNotImplemented, HTTPRequestRangeNotSatisfiable
-from galaxy import exceptions
-from galaxy import web
-from galaxy import model
-from galaxy import security
-from galaxy import util
-
-from galaxy.web import error, url_for
-from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField
-from galaxy.web.form_builder import build_select_field, HistoryField, PasswordField, WorkflowField, WorkflowMappingField
-from galaxy.workflow.modules import WorkflowModuleInjector
-from galaxy.security.validate_user_input import validate_publicname
-from galaxy.util.sanitize_html import sanitize_html
-from galaxy.model.item_attrs import UsesAnnotations
-from galaxy.util.dictifiable import Dictifiable
-
+from galaxy import (
+    exceptions,
+    model,
+    security,
+    util,
+    web
+)
 from galaxy.datatypes.interval import ChromatinInteractions
-
-from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex, LibraryDatasetDatasetAssociation, HistoryDatasetAssociation
-
-from galaxy.managers import api_keys
-from galaxy.managers import tags
-from galaxy.managers import workflows
-from galaxy.managers import base as managers_base
-from galaxy.managers import users
-from galaxy.managers import configuration
-
+from galaxy.managers import (
+    api_keys,
+    base as managers_base,
+    configuration,
+    tags,
+    users,
+    workflows
+)
+from galaxy.model import (
+    ExtendedMetadata,
+    ExtendedMetadataIndex,
+    HistoryDatasetAssociation,
+    LibraryDatasetDatasetAssociation
+)
+from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.security.validate_user_input import validate_publicname
+from galaxy.util.dictifiable import Dictifiable
+from galaxy.util.sanitize_html import sanitize_html
+from galaxy.web import (
+    error,
+    url_for
+)
+from galaxy.web.form_builder import (
+    AddressField,
+    build_select_field,
+    CheckboxField,
+    HistoryField,
+    PasswordField,
+    SelectField,
+    TextArea,
+    TextField,
+    WorkflowField,
+    WorkflowMappingField
+)
+from galaxy.workflow.modules import WorkflowModuleInjector
 
 log = logging.getLogger( __name__ )
 
@@ -132,7 +155,7 @@ class BaseController( object ):
             values = [ values ]
         # TODO: it may be more helpful to the consumer if we error on incomplete 3-tuples
         #   (instead of relying on zip to shorten)
-        return zip( attrs, ops, values )
+        return list(zip( attrs, ops, values ))
 
     def parse_limit_offset( self, qdict ):
         """
@@ -211,8 +234,8 @@ class BaseAPIController( BaseController ):
             msg = "The following value(s) for associated users and/or groups could not be parsed: %s." % ', '.join( invalid )
             msg += "  Valid values are email addresses of users, names of groups, or IDs of both."
             raise Exception( msg )
-        payload['in_users'] = map( str, new_in_users )
-        payload['in_groups'] = map( str, new_in_groups )
+        payload['in_users'] = list(map( str, new_in_users ))
+        payload['in_groups'] = list(map( str, new_in_groups ))
 
     def not_implemented( self, trans, **kwd ):
         raise HTTPNotImplemented()
@@ -2311,6 +2334,6 @@ def sort_by_attr( seq, attr ):
     # (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not
     # only to provide stable sorting, but mainly to eliminate comparison of objects
     # (which can be expensive or prohibited) in case of equal attribute values.
-    intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ), xrange( len( seq ) ), seq )
+    intermed = [(getattr(v, attr), i, v) for i, v in enumerate(seq)]
     intermed.sort()
-    return map( operator.getitem, intermed, ( -1, ) * len( intermed ) )
+    return [_[-1] for _ in intermed]

lib/galaxy/web/base/interactive_environments.py

@@ -1,4 +1,3 @@
-import ConfigParser
 import json
 import logging
 import os
@@ -6,11 +5,11 @@ import random
 import stat
 import tempfile
 import uuid
-
 from subprocess import PIPE, Popen
 from sys import platform as _platform
 
 import yaml
+from six.moves import configparser
 
 from galaxy import model, web
 from galaxy.containers import build_container_interfaces
@@ -121,7 +120,7 @@ class InteractiveEnvironmentRequest(object):
 
     def load_deploy_config(self, default_dict={}):
         # For backwards compat, any new variables added to the base .ini file
-        # will need to be recorded here. The ConfigParser doesn't provide a
+        # will need to be recorded here. The configparser doesn't provide a
         # .get() that will ignore missing sections, so we must make use of
         # their defaults dictionary instead.
         default_dict = {
@@ -133,7 +132,7 @@ class InteractiveEnvironmentRequest(object):
             'docker_galaxy_temp_dir': None,
             'docker_connect_port': None,
         }
-        viz_config = ConfigParser.SafeConfigParser(default_dict)
+        viz_config = configparser.SafeConfigParser(default_dict)
         conf_path = os.path.join( self.attr.our_config_dir, self.attr.viz_id + ".ini" )
         if not os.path.exists( conf_path ):
             conf_path = "%s.sample" % conf_path
@@ -253,7 +252,7 @@ class InteractiveEnvironmentRequest(object):
             env_override = {}
         conf = self.get_conf_dict()
         conf.update(env_override)
-        return dict([(key.upper(), item) for key, item in conf.items()])
+        return dict((key.upper(), item) for key, item in conf.items())
 
     def _get_import_volume_for_run(self):
         if self.use_volumes and self.attr.import_volume:
@@ -271,8 +270,8 @@ class InteractiveEnvironmentRequest(object):
             volumes = []
         env = self._get_env_for_run(env_override)
         import_volume_def = self._get_import_volume_for_run()
-        env_str = ' '.join(['-e "%s=%s"' % (key, item) for key, item in env.items()])
-        volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) if self.use_volumes else ''
+        env_str = ' '.join('-e "%s=%s"' % (key, item) for key, item in env.items())
+        volume_str = ' '.join('-v "%s"' % volume for volume in volumes) if self.use_volumes else ''
         import_volume_str = '-v "{import_volume}"'.format(import_volume=import_volume_def) if import_volume_def else ''
         name = None
         # This is the basic docker command such as "sudo -u docker docker {docker_args}"

lib/galaxy/web/base/pluginframework.py

@@ -7,17 +7,19 @@ and base class for plugins that:
  * serve templated html
  * have some configuration at startup
 """
-
+import imp
+import logging
 import os.path
 import sys
-import imp
-
-from galaxy import util
-from galaxy.util import odict
-from galaxy.util import bunch
 
 import mako.lookup
-import logging
+
+from galaxy import util
+from galaxy.util import (
+    bunch,
+    odict
+)
+
 log = logging.getLogger( __name__ )