Merge pull request #4236 from nsoranzo/python3

Fix import order and Python3 compatibility for 51 files
2026-10-24 02:04:04 +08:00 · 2017-07-05 09:27:33 -04:00
parent 79f3dc00a6 6f98634dd5
commit 20ef3eebcf
54 changed files with 350 additions and 400 deletions
@@ -9,72 +9,15 @@ lib/galaxy/actions/
 lib/galaxy/auth/
 lib/galaxy/config.py
 lib/galaxy/containers/
-lib/galaxy/dataset_collections/builder.py
-lib/galaxy/dataset_collections/__init__.py
-lib/galaxy/dataset_collections/structure.py
-lib/galaxy/dataset_collections/subcollections.py
-lib/galaxy/dataset_collections/type_description.py
-lib/galaxy/dataset_collections/types/__init__.py
-lib/galaxy/datatypes/assembly.py
-lib/galaxy/datatypes/binary.py
-lib/galaxy/datatypes/checkers.py
-lib/galaxy/datatypes/constructive_solid_geometry.py
-lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
-lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
-lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.py
-lib/galaxy/datatypes/converters/bed_to_gff_converter.py
-lib/galaxy/datatypes/converters/bgzip.py
-lib/galaxy/datatypes/converters/fasta_to_len.py
-lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.py
-lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
-lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
-lib/galaxy/datatypes/converters/gff_to_bed_converter.py
-lib/galaxy/datatypes/converters/gff_to_interval_index_converter.py
-lib/galaxy/datatypes/converters/__init__.py
-lib/galaxy/datatypes/converters/interval_to_bed_converter.py
-lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
-lib/galaxy/datatypes/converters/interval_to_coverage.py
-lib/galaxy/datatypes/converters/interval_to_fli.py
-lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py
-lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
-lib/galaxy/datatypes/converters/lped_to_fped_converter.py
-lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
-lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
-lib/galaxy/datatypes/converters/maf_to_interval_converter.py
-lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
-lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
-lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py
-lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
-lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
-lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py
-lib/galaxy/datatypes/coverage.py
-lib/galaxy/datatypes/dataproviders/base.py
-lib/galaxy/datatypes/dataproviders/exceptions.py
-lib/galaxy/datatypes/dataproviders/__init__.py
-lib/galaxy/datatypes/data.py
-lib/galaxy/datatypes/display_applications/__init__.py
-lib/galaxy/datatypes/display_applications/util.py
-lib/galaxy/datatypes/genetics.py
-lib/galaxy/datatypes/images.py
-lib/galaxy/datatypes/__init__.py
-lib/galaxy/datatypes/interval.py
-lib/galaxy/datatypes/metadata.py
-lib/galaxy/datatypes/msa.py
-lib/galaxy/datatypes/ngsindex.py
-lib/galaxy/datatypes/proteomics.py
-lib/galaxy/datatypes/registry.py
-lib/galaxy/datatypes/sequence.py
-lib/galaxy/datatypes/tabular.py
-lib/galaxy/datatypes/text.py
-lib/galaxy/datatypes/tracks.py
-lib/galaxy/datatypes/util/
+lib/galaxy/dataset_collections/
+lib/galaxy/datatypes/
+lib/galaxy/dependencies/
 lib/galaxy/eggs/
-lib/galaxy/exceptions/__init__.py
+lib/galaxy/exceptions/
 lib/galaxy/external_services/__init__.py
 lib/galaxy/external_services/parameters.py
 lib/galaxy/external_services/result_handlers/basic.py
 lib/galaxy/external_services/result_handlers/__init__.py
-lib/galaxy_ext/
 lib/galaxy/forms/__init__.py
 lib/galaxy/jobs/actions/
 lib/galaxy/jobs/command_factory.py
@@ -113,15 +56,7 @@ lib/galaxy/managers/lddas.py
 lib/galaxy/managers/libraries.py
 lib/galaxy/managers/secured.py
 lib/galaxy/managers/taggable.py
-lib/galaxy/model/__init__.py
-lib/galaxy/model/item_attrs.py
-lib/galaxy/model/mapping.py
-lib/galaxy/model/metadata.py
-lib/galaxy/model/migrate/
-lib/galaxy/model/orm/
-lib/galaxy/model/tool_shed_install/migrate/__init__.py
-lib/galaxy/model/tool_shed_install/migrate/versions/
-lib/galaxy/model/util.py
+lib/galaxy/model/
 lib/galaxy/objectstore/pulsar.py
 lib/galaxy/objectstore/s3_multipart_upload.py
 lib/galaxy/openid/__init__.py
@@ -129,7 +64,7 @@ lib/galaxy/quota/
 lib/galaxy/sample_tracking/data_transfer.py
 lib/galaxy/sample_tracking/__init__.py
 lib/galaxy/sample_tracking/sample.py
-lib/galaxy/security/validate_user_input.py
+lib/galaxy/security/
 lib/galaxy/tags/
 lib/galaxy/tools/
 lib/galaxy/util/
@@ -174,6 +109,7 @@ lib/galaxy/webapps/galaxy/api/samples.py
 lib/galaxy/webapps/galaxy/api/tools.py
 lib/galaxy/webapps/galaxy/api/tours.py
 lib/galaxy/webapps/galaxy/api/workflows.py
+lib/galaxy/webapps/galaxy/config_watchers.py
 lib/galaxy/webapps/galaxy/controllers/async.py
 lib/galaxy/webapps/galaxy/controllers/data_manager.py
 lib/galaxy/webapps/galaxy/controllers/error.py
@@ -186,7 +122,6 @@ lib/galaxy/webapps/galaxy/controllers/requests.py
 lib/galaxy/webapps/galaxy/controllers/search.py
 lib/galaxy/webapps/galaxy/controllers/tool_runner.py
 lib/galaxy/webapps/galaxy/controllers/userskeys.py
-lib/galaxy/webapps/galaxy/config_watchers.py
 lib/galaxy/webapps/galaxy/__init__.py
 lib/galaxy/webapps/__init__.py
 lib/galaxy/webapps/reports/config.py
@@ -209,13 +144,11 @@ lib/galaxy/webapps/tool_shed/util/__init__.py
 lib/galaxy/webapps/tool_shed/util/ratings_util.py
 lib/galaxy/webapps/tool_shed/util/shed_statistics.py
 lib/galaxy/webapps/util.py
-lib/galaxy/workflow/extract.py
-lib/galaxy/workflow/__init__.py
-lib/galaxy/workflow/render.py
-lib/galaxy/workflow/run.py
-lib/galaxy/workflow/schedulers/
-lib/galaxy/workflow/steps.py
-lib/galaxy/work/__init__.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/
@@ -366,6 +299,7 @@ test/unit/shed_unit/test_fabric_util.py
 test/unit/shed_unit/test_td_common_util.py
 test/unit/test_galaxy_transactions.py
 test/unit/test_lazy_process.py
+test/unit/test_objectstore.py
 test/unit/test_routes.py
 test/unit/test_security_helper.py
 test/unit/test_sockets.py
@@ -393,6 +327,5 @@ test/unit/web/base/__init__.py
 test/unit/web/framework/__init__.py
 test/unit/web/__init__.py
 test/unit/workflows/
-test/unit/test_objectstore.py
 tool_list.py
 tools/
@@ -8,23 +8,7 @@ lib/galaxy/auth/
 lib/galaxy/config.py
 lib/galaxy/containers/
 lib/galaxy/dataset_collections/
-lib/galaxy/datatypes/assembly.py
-lib/galaxy/datatypes/binary.py
-lib/galaxy/datatypes/constructive_solid_geometry.py
-lib/galaxy/datatypes/converters/
-lib/galaxy/datatypes/dataproviders/
-lib/galaxy/datatypes/data.py
-lib/galaxy/datatypes/genetics.py
-lib/galaxy/datatypes/images.py
-lib/galaxy/datatypes/interval.py
-lib/galaxy/datatypes/msa.py
-lib/galaxy/datatypes/ngsindex.py
-lib/galaxy/datatypes/proteomics.py
-lib/galaxy/datatypes/registry.py
-lib/galaxy/datatypes/sequence.py
-lib/galaxy/datatypes/sniff.py
-lib/galaxy/datatypes/tabular.py
-lib/galaxy/datatypes/tracks.py
+lib/galaxy/datatypes/
 lib/galaxy/dependencies/
 lib/galaxy/eggs/
 lib/galaxy/exceptions/
@@ -32,12 +16,7 @@ lib/galaxy/external_services/
 lib/galaxy/forms/
 lib/galaxy/jobs/
 lib/galaxy/managers/
-lib/galaxy/model/__init__.py
-lib/galaxy/model/item_attrs.py
-lib/galaxy/model/mapping.py
-lib/galaxy/model/metadata.py
-lib/galaxy/model/migrate/
-lib/galaxy/model/orm/now.py
+lib/galaxy/model/
 lib/galaxy/objectstore/
 lib/galaxy/openid/
 lib/galaxy/quota/
@@ -69,11 +48,9 @@ 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/util/ratings_util.py
+lib/galaxy/webhooks/
 lib/galaxy/work/
-lib/galaxy/workflow/extract.py
-lib/galaxy/workflow/run.py
-lib/galaxy/workflow/schedulers/
-lib/galaxy/workflow/steps.py
+lib/galaxy/workflow/
 lib/galaxy_ext/
 lib/log_tempfile.py
 lib/psyco_full.py
@@ -1,6 +1,10 @@
-from galaxy.util import bunch
 from galaxy import exceptions
-from .structure import get_structure, leaf
+from galaxy.util import bunch
+
+from .structure import (
+    get_structure,
+    leaf
+)

 CANNOT_MATCH_ERROR_MESSAGE = "Cannot match collection types."

@@ -23,8 +27,8 @@ class CollectionsToMatch( object ):
    def has_collections( self ):
        return len( self.collections ) > 0

-    def iteritems( self ):
-        return self.collections.iteritems()
+    def items( self ):
+        return self.collections.items()


 class MatchingCollections( object ):
@@ -71,7 +75,7 @@ class MatchingCollections( object ):
            return None

        matching_collections = MatchingCollections()
-        for input_key, to_match in collections_to_match.iteritems():
+        for input_key, to_match in collections_to_match.items():
            hdca = to_match.hdca
            collection_type_description = collection_type_descriptions.for_collection_type( hdca.collection.collection_type )
            subcollection_type = to_match.subcollection_type
@@ -1,7 +1,10 @@
-from .types import list
-from .types import paired
 from galaxy import model

+from .types import (
+    list,
+    paired
+)
+
 PLUGIN_CLASSES = [list.ListDatasetCollectionType, paired.PairedDatasetCollectionType]


@@ -124,7 +124,7 @@ class Tree( object ):


 def dict_map( func, input_dict ):
-    return dict( [ ( k, func(v) ) for k, v in input_dict.items() ] )
+    return dict( ( k, func(v) ) for k, v in input_dict.items() )


 def get_structure( dataset_collection_instance, collection_type_description, leaf_subcollection_type=None ):
@@ -1,7 +1,7 @@
-from ..types import BaseDatasetCollectionType
-
 from galaxy.model import DatasetCollectionElement

+from ..types import BaseDatasetCollectionType
+

 class ListDatasetCollectionType( BaseDatasetCollectionType ):
    """ A flat list of named elements.
@@ -12,7 +12,7 @@ class ListDatasetCollectionType( BaseDatasetCollectionType ):
        pass

    def generate_elements( self, elements ):
-        for identifier, element in elements.iteritems():
+        for identifier, element in elements.items():
            association = DatasetCollectionElement(
                element=element,
                element_identifier=identifier,
@@ -1,7 +1,7 @@
-from ..types import BaseDatasetCollectionType
-
 from galaxy.model import DatasetCollectionElement, HistoryDatasetAssociation

+from ..types import BaseDatasetCollectionType
+
 FORWARD_IDENTIFIER = "forward"
 REVERSE_IDENTIFIER = "reverse"

@@ -30,14 +30,16 @@

 Covers the ``blastxml`` format and the BLAST databases.
 """
-
 import logging
 import os
 from time import sleep

-from galaxy.datatypes.data import get_file_peek
-from galaxy.datatypes.data import Data, Text
-from galaxy.datatypes.xml import GenericXml
+from .data import (
+    Data,
+    get_file_peek,
+    Text
+)
+from .xml import GenericXml

 log = logging.getLogger(__name__)

@@ -1,7 +1,7 @@
 from __future__ import absolute_import

-import galaxy.datatypes.tabular
 import galaxy.datatypes.metadata
+import galaxy.datatypes.tabular
 from galaxy.datatypes.metadata import MetadataElement


@@ -5,18 +5,19 @@ from __future__ import division
 import sys

 from bx.arrays.array_tree import array_tree_dict_from_reader, FileArrayTreeDict
+from six import Iterator

 BLOCK_SIZE = 100


-class BedGraphReader:
+class BedGraphReader(Iterator):
    def __init__( self, f ):
        self.f = f

    def __iter__( self ):
        return self

-    def next( self ):
+    def __next__( self ):
        while True:
            line = self.f.readline()
            if not line:
@@ -46,7 +47,7 @@ def main():
    # Fill array from reader
    d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )

-    for array_tree in d.itervalues():
+    for array_tree in d.values():
        array_tree.root.build_summary()

    FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
@@ -10,9 +10,8 @@
 Input: fasta
 Output: tabular
 """
-
-import sys
 import os
+import sys

 seq_hash = {}

@@ -89,7 +89,7 @@ def main():
    out = open( out_fname, 'w' )
    max_len = 0
    entries = []
-    for name in sorted( name_loc_dict.iterkeys() ):
+    for name in sorted( name_loc_dict.keys() ):
        loc = name_loc_dict[ name ]
        entry = '%s\t%s\t%s' % ( name.lower(), name, '%s:%i-%i' % ( loc[ 'contig' ], loc[ 'start' ], loc[ 'end' ] ) )
        if len( entry ) > max_len:
@@ -3,9 +3,9 @@
 from __future__ import print_function

 import os
+import subprocess
 import sys
 import tempfile
-import subprocess
 import time

 prog = "pbed_ldreduced_converter.py"
@@ -4,9 +4,8 @@ convert a ref.taxonomy file to a seq.taxonomy file
 Usage:
 %python ref_to_seq_taxonomy_converter.py <ref.taxonom> <seq.taxonomy>
 """
-
-import sys
 import re
+import sys

 assert sys.version_info[:2] >= (2, 4)

@@ -5,12 +5,12 @@
 A wrapper script for converting SAM to BAM, with sorting.
 %prog input_filename.sam output_filename.bam
 """
-import os
-import sys
 import optparse
-import tempfile
-import subprocess
+import os
 import shutil
+import subprocess
+import sys
+import tempfile
 from distutils.version import LooseVersion

 CHUNK_SIZE = 2 ** 20  # 1mb
@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-
 """
 Convert from VCF file to interval index file.
 """
@@ -7,9 +6,8 @@ from __future__ import division

 import optparse

-from bx.interval_index_file import Indexes
-
 import galaxy_utils.sequence.vcf
+from bx.interval_index_file import Indexes


 def main():
@@ -20,7 +20,7 @@ def main():
    # Fill array from reader
    d = array_tree_dict_from_reader( reader, {}, block_size=BLOCK_SIZE )

-    for array_tree in d.itervalues():
+    for array_tree in d.values():
        array_tree.root.build_summary()

    FileArrayTreeDict.dict_to_file( d, open( out_fname, "w" ) )
@@ -11,7 +11,10 @@ import sys

 import bx.wiggle

-from galaxy.util.ucsc import UCSCOutWrapper, UCSCLimitException
+from galaxy.util.ucsc import (
+    UCSCLimitException,
+    UCSCOutWrapper
+)


 def stop_err( msg ):
@@ -22,29 +22,6 @@ class LastzCoverage( Tabular ):
    MetadataElement( name="reverseCol", desc="Optional reverse read column", param=metadata.ColumnParameter, optional=True, no_value=0 )
    MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True, visible=False )

-    def get_track_window(self, dataset, data, start, end):
-        """
-        Assumes we have a numpy file.
-        """
-        # Maybe if we import here people will still be able to use Galaxy when numpy kills it
-        import numpy
-
-        range = end - start
-        # Determine appropriate resolution to plot ~1000 points
-        resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
-        # Restrict to valid range
-        resolution = min( resolution, 10000 )
-        resolution = max( resolution, 1 )
-        # Memory map the array (don't load all the data)
-        data = numpy.load( data )
-        # Grab just what we need
-        t_start = math.floor( start / resolution )
-        t_end = math.ceil( end / resolution )
-        x = numpy.arange( t_start, t_end ) * resolution
-        y = data[ t_start : t_end ]
-
-        return zip(x.tolist(), y.tolist())
-
    def get_track_resolution( self, dataset, start, end):
        range = end - start
        # Determine appropriate resolution to plot ~1000 points
@@ -4,16 +4,18 @@ Chunk (N number of bytes at M offset to a source's beginning) provider.
 Primarily for file sources but usable by any iterator that has both
 seek and read( N ).
 """
-import os
 import base64
-import base
-import exceptions
-
 import logging
+import os
+
+from . import (
+    base,
+    exceptions
+)
+
 log = logging.getLogger( __name__ )


-# -----------------------------------------------------------------------------
 class ChunkDataProvider( base.DataProvider ):
    """
    Data provider that yields chunks of data from its file.
@@ -2,9 +2,10 @@
 Providers that provide lists of lists generally where each line of a source
 is further subdivided into multiple data (e.g. columns from a line).
 """
+import logging
+import re

 from six.moves.urllib.parse import unquote_plus
-import re

 from . import line

@@ -15,7 +16,6 @@ TransposedColumnarDataProvider: provides each column as a single array
    - see existing visualizations/dataprovider/basic.ColumnDataProvider
 """

-import logging
 log = logging.getLogger( __name__ )


@@ -5,18 +5,23 @@ Dataproviders that use either:
    - or provide data in some way relevant to bioinformatic data
        (e.g. parsing genomic regions from their source)
 """
-
-
-import base
-import line
-import column
-import external
-from galaxy.util import sqlite
+import logging
 import sys

-from bx import seq as bx_seq
-from bx import wiggle as bx_wig
-from bx import bbi as bx_bbi
+from bx import (
+    bbi as bx_bbi,
+    seq as bx_seq,
+    wiggle as bx_wig
+)
+
+from galaxy.util import sqlite
+
+from . import (
+    base,
+    column,
+    external,
+    line
+)

 _TODO = """
 use bx as much as possible
@@ -25,7 +30,6 @@ gff3 hierarchies
 change SamtoolsDataProvider to use pysam
 """

-import logging
 log = logging.getLogger( __name__ )


@@ -150,7 +154,7 @@ class DatasetDataProvider( base.DataProvider ):
        """
        region_column_names = ( 'chromCol', 'startCol', 'endCol' )
        region_indices = [ self.get_metadata_column_index_by_name( name ) for name in region_column_names ]
-        if check and not all( map( lambda i: i is not None, region_indices) ):
+        if check and not all( _ is not None for _ in region_indices ):
            raise ValueError( "Could not determine proper column indices for chrom, start, end: %s" % ( str( region_indices ) ) )
        return region_indices

@@ -296,7 +300,7 @@ class GenomicRegionDataProvider( column.ColumnarDataProvider ):
        if end_column is None:
            end_column = dataset_source.get_metadata_column_index_by_name( 'endCol' )
        indeces = [ chrom_column, start_column, end_column ]
-        if not all( map( lambda i: i is not None, indeces ) ):
+        if not all( _ is not None for _ in indeces ):
            raise ValueError( "Could not determine proper column indeces for" +
                              " chrom, start, end: %s" % ( str( indeces ) ) )
        kwargs.update({ 'indeces' : indeces })
@@ -14,11 +14,12 @@ DataProvider related decorators.
 # adapted from: http://stackoverflow.com
 #    /questions/14095616/python-can-i-programmatically-decorate-class-methods-from-a-class-instance

-from functools import wraps
-import urllib2
 import copy
-
 import logging
+from functools import wraps
+
+from six.moves.urllib.parse import unquote
+
 log = logging.getLogger( __name__ )

 _DATAPROVIDER_CLASS_MAP_KEY = 'dataproviders'
@@ -65,7 +66,7 @@ def has_dataproviders( cls ):
    # scan for methods with dataprovider names and add them to the map
    # note: this has a 'cascading' effect
    #       where it's possible to override a super's provider with a sub's
-    for attr_key, attr_value in cls.__dict__.iteritems():
+    for attr_key, attr_value in cls.__dict__.items():
        # can't use isinstance( attr_value, MethodType ) bc of wrapping
        if( ( callable( attr_value ) ) and
                ( not attr_key.startswith( "__" ) ) and
@@ -129,7 +130,7 @@ def _parse_query_string_settings( query_kwargs, settings=None ):
        'float' : float,
        'bool'  : bool,
        'list:str'      : lambda s: list_from_query_string( s ),
-        'list:escaped'  : lambda s: [ urllib2.unquote( e ) for e in list_from_query_string( s ) ],
+        'list:escaped'  : lambda s: [ unquote( e ) for e in list_from_query_string( s ) ],
        'list:int'      : lambda s: [ int( i ) for i in list_from_query_string( s ) ],
    }
    settings = settings or {}
@@ -2,14 +2,18 @@
 Data providers that iterate over a source that is not in memory
 or not in a file.
 """
-
-import base
 import gzip
-import line
+import logging
 import subprocess
 import tempfile
-import urllib
-import urllib2
+
+from six.moves.urllib.parse import urlencode
+from six.moves.urllib.request import urlopen
+
+from . import (
+    base,
+    line
+)

 _TODO = """
 YAGNI: ftp, image, cryptos, sockets
@@ -17,7 +21,6 @@ job queue
 admin: admin server log rgx/stats, ps aux
 """

-import logging
 log = logging.getLogger( __name__ )


@@ -105,13 +108,13 @@ class URLDataProvider( base.DataProvider ):
        self.method = method

        self.data = data or {}
-        encoded_data = urllib.urlencode( self.data )
+        encoded_data = urlencode( self.data )

        if method == 'GET':
            self.url += '?%s' % ( encoded_data )
-            opened = urllib2.urlopen( url )
+            opened = urlopen( url )
        elif method == 'POST':
-            opened = urllib2.urlopen( url, encoded_data )
+            opened = urlopen( url, encoded_data )
        else:
            raise ValueError( 'Not a valid method: %s' % ( method ) )

@@ -1,14 +1,17 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
+import logging
+from xml.etree.ElementTree import (
+    Element,
+    iterparse
+)

-import line
-from xml.etree.ElementTree import Element, iterparse
+from . import line

 _TODO = """
 """

-import logging
 log = logging.getLogger( __name__ )


@@ -1,12 +1,12 @@
 """
 Dataproviders that iterate over lines from their sources.
 """
-
 import collections
+import logging
 import re
+
 from . import base

-import logging
 log = logging.getLogger( __name__ )

 _TODO = """
@@ -1,16 +1,24 @@
 # Contains objects for using external display applications
 import logging
-import urllib
-from six import string_types
-from urllib import quote_plus
 from copy import deepcopy

-from galaxy.util import parse_xml, string_as_bool
+from six import string_types
+from six.moves.urllib.parse import quote_plus
+
+from galaxy.util import (
+    parse_xml,
+    string_as_bool
+)
 from galaxy.util.odict import odict
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
-from parameters import DisplayApplicationParameter, DisplayApplicationDataParameter, DEFAULT_DATASET_NAME
-from util import encode_dataset_user
+
+from .parameters import (
+    DEFAULT_DATASET_NAME,
+    DisplayApplicationDataParameter,
+    DisplayApplicationParameter
+)
+from .util import encode_dataset_user

 log = logging.getLogger( __name__ )

@@ -50,8 +58,8 @@ class DisplayApplicationLink( object ):
                        action="display_application",
                        dataset_id=dataset_hash,
                        user_id=user_hash,
-                        app_name=urllib.quote_plus( self.display_application.id ),
-                        link_name=urllib.quote_plus( self.id ),
+                        app_name=quote_plus( self.display_application.id ),
+                        link_name=quote_plus( self.id ),
                        app_action=None )

    def get_inital_values( self, data, trans ):
@@ -60,7 +68,7 @@ class DisplayApplicationLink( object ):
        else:
            rval = odict()
        rval.update( { 'BASE_URL': trans.request.base, 'APP': trans.app } )  # trans automatically appears as a response, need to add properties of trans that we want here
-        for key, value in BASE_PARAMS.iteritems():  # add helper functions/variables
+        for key, value in BASE_PARAMS.items():  # add helper functions/variables
            rval[ key ] = value
        rval[ DEFAULT_DATASET_NAME ] = data  # always have the display dataset name available
        return rval
@@ -70,7 +78,7 @@ class DisplayApplicationLink( object ):
        other_values[ 'DATASET_HASH' ] = dataset_hash
        other_values[ 'USER_HASH' ] = user_hash
        ready = True
-        for name, param in self.parameters.iteritems():
+        for name, param in self.parameters.items():
            assert name not in other_values, "The display parameter '%s' has been defined more than once." % name
            if param.ready( other_values ):
                if name in app_kwds and param.allow_override:
@@ -142,7 +150,7 @@ class DynamicDisplayApplicationBuilder( object ):
        max_col = max( id_col, name_col )
        dynamic_params = {}
        if data_table is not None:
-            max_col = max( [ max_col ] + data_table.columns.values() )
+            max_col = max( [ max_col ] + list(data_table.columns.values()) )
            for key, value in data_table.columns.items():
                dynamic_params[key] = { 'column': value, 'split': False, 'separator': ',' }
        for dynamic_param in elem.findall( 'dynamic_param' ):
@@ -174,7 +182,7 @@ class DynamicDisplayApplicationBuilder( object ):
                new_elem.set( 'id', fields[id_col] )
                new_elem.set( 'name', fields[name_col] )
                dynamic_values = {}
-                for key, attributes in dynamic_params.iteritems():
+                for key, attributes in dynamic_params.items():
                    value = fields[ attributes[ 'column' ] ]
                    if attributes['split']:
                        value = value.split( attributes['separator'] )
@@ -210,7 +218,7 @@ class PopulatedDisplayApplicationLink( object ):

    def preparing_display( self ):
        if not self.ready:
-            return self.link.parameters[ self.parameters.keys()[ -1 ] ].is_preparing( self.parameters )
+            return self.link.parameters[ list(self.parameters.keys())[-1] ].is_preparing( self.parameters )
        return False

    def prepare_display( self ):
@@ -218,8 +226,8 @@ class PopulatedDisplayApplicationLink( object ):
        found_last = False
        if not self.ready and not self.preparing_display():
            other_values = self.parameters
-            for name, param in self.link.parameters.iteritems():
-                if found_last or other_values.keys()[ -1 ] == name:  # found last parameter to be populated
+            for name, param in self.link.parameters.items():
+                if found_last or list(other_values.keys())[-1] == name:  # found last parameter to be populated
                    found_last = True
                    value = param.prepare( other_values, self.dataset_hash, self.user_hash, self.trans )
                    rval.append( { 'name': name, 'value': value, 'param': param } )
@@ -231,7 +239,7 @@ class PopulatedDisplayApplicationLink( object ):

    def get_prepare_steps( self, datasets_only=True ):
        rval = []
-        for name, param in self.link.parameters.iteritems():
+        for name, param in self.link.parameters.items():
            if datasets_only and not isinstance( param, DisplayApplicationDataParameter ):
                continue
            value = self.parameters.get( name, None )
@@ -243,7 +251,7 @@ class PopulatedDisplayApplicationLink( object ):
        return fill_template( self.link.url.text, context=self.parameters )

    def get_param_name_by_url( self, url ):
-        for name, parameter in self.link.parameters.iteritems():
+        for name, parameter in self.link.parameters.items():
            if parameter.build_url( self.parameters ) == url:
                return name
        raise ValueError( "Unknown URL parameter name provided: %s" % url )
@@ -301,7 +309,7 @@ class DisplayApplication( object ):
    def filter_by_dataset( self, data, trans ):
        self._check_and_reload()
        filtered = DisplayApplication( self.id, self.name, self.app, version=self.version )
-        for link_name, link_value in self.links.iteritems():
+        for link_name, link_value in self.links.items():
            if link_value.filter_by_dataset( data, trans ):
                filtered.links[link_name] = link_value
        return filtered
@@ -318,13 +326,11 @@ class DisplayApplication( object ):
        # We will not allow changing the id at this time (we'll need to fix several mappings upstream to handle this case)
        assert attr_dict.get( 'id' ) == self.id, ValueError( "You cannot reload a Display application where the ID has changed. You will need to restart the server instead." )
        # clear old links
-        for key in self.links.keys():
-            del self.links[key]
+        self.links = {}
        # clear data table versions:
-        for key in self._data_table_versions.keys():
-            del self._data_table_versions[ key ]
+        self._data_table_versions = {}
        # Set new attributes
-        for key, value in attr_dict.iteritems():
+        for key, value in attr_dict.items():
            setattr( self, key, value )
        # Load new links
        self._load_links_from_elem( elem )
@@ -334,7 +340,7 @@ class DisplayApplication( object ):
        self._data_table_versions[ table_name ] = version

    def _requires_reload( self ):
-        for key, value in self._data_table_versions.iteritems():
+        for key, value in self._data_table_versions.items():
            table = self.app.tool_data_tables.get( key, None )
            if table and not table.is_current_version( value ):
                return True
@@ -1,10 +1,12 @@
 # Contains parameters that are used in Display Applications
-import urllib
+import mimetypes
+
+from six.moves.urllib.parse import quote_plus
+
 from galaxy.util import string_as_bool
 from galaxy.util.bunch import Bunch
 from galaxy.util.template import fill_template
 from galaxy.web import url_for
-import mimetypes

 DEFAULT_DATASET_NAME = 'dataset'

@@ -110,7 +112,7 @@ class DisplayApplicationDataParameter( DisplayApplicationParameter ):
            if target_ext and not converted_dataset:
                if isinstance( data, DisplayDataValueWrapper ):
                    data = data.value
-                new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()[0]
+                new_data = next(iter(data.datatype.convert_dataset( trans, data, target_ext, return_output=True, visible=False ).values()))
                new_data.hid = data.hid
                new_data.name = data.name
                trans.sa_session.add( new_data )
@@ -193,8 +195,8 @@ class DisplayParameterValueWrapper( object ):
                                   action="display_application",
                                   dataset_id=self._dataset_hash,
                                   user_id=self._user_hash,
-                                   app_name=urllib.quote_plus( self.parameter.link.display_application.id ),
-                                   link_name=urllib.quote_plus( self.parameter.link.id ),
+                                   app_name=quote_plus( self.parameter.link.display_application.id ),
+                                   link_name=quote_plus( self.parameter.link.id ),
                                   app_action=self.action_name,
                                   action_param=self._url ) )

@@ -1,15 +1,17 @@
 """
 Graph content classes.
 """
+import logging

-import data
-import tabular
-import xml
-
-import dataproviders
 from galaxy.util import simplegraph

-import logging
+from . import (
+    data,
+    dataproviders,
+    tabular,
+    xml
+)
+
 log = logging.getLogger( __name__ )


@@ -7,7 +7,6 @@ import os
 import sys
 import tempfile

-import numpy
 from bx.intervals.io import GenomicIntervalReader, ParseError
 from six.moves.urllib.parse import quote_plus

@@ -335,20 +334,6 @@ class Interval( Tabular ):
        except:
            return False

-    def get_track_window(self, dataset, data, start, end):
-        """
-        Assumes the incoming track data is sorted already.
-        """
-        window = list()
-        for record in data:
-            fields = record.rstrip("\n\r").split("\t")
-            record_chrom = fields[dataset.metadata.chromCol - 1]
-            record_start = int(fields[dataset.metadata.startCol - 1])
-            record_end = int(fields[dataset.metadata.endCol - 1])
-            if record_start < end and record_end > start:
-                window.append( (record_chrom, record_start, record_end) )  # Yes I did want to use a generator here, but it doesn't work downstream
-        return window
-
    def get_track_resolution( self, dataset, start, end):
        return None

@@ -1259,26 +1244,6 @@ class Wiggle( Tabular, _RemoteCallMixin ):
        except:
            return False

-    def get_track_window(self, dataset, data, start, end):
-        """
-        Assumes we have a numpy file.
-        """
-        range = end - start
-        # Determine appropriate resolution to plot ~1000 points
-        resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) )
-        # Restrict to valid range
-        resolution = min( resolution, 100000 )
-        resolution = max( resolution, 1 )
-        # Memory map the array (don't load all the data)
-        data = numpy.load( data )
-        # Grab just what we need
-        t_start = math.floor( start / resolution )
-        t_end = math.ceil( end / resolution )
-        x = numpy.arange( t_start, t_end ) * resolution
-        y = data[ t_start : t_end ]
-
-        return list(zip(x.tolist(), y.tolist()))
-
    def get_track_resolution( self, dataset, start, end):
        range = end - start
        # Determine appropriate resolution to plot ~1000 points
@@ -1,17 +1,18 @@
 # -*- coding: utf-8 -*-
-
-from galaxy.datatypes import data
 import logging
-from galaxy.datatypes.sniff import get_headers
-from galaxy.datatypes.data import get_file_peek
-from galaxy.datatypes.tabular import Tabular
-from galaxy.datatypes.binary import Binary
-from galaxy.datatypes.xml import GenericXml
-import subprocess
 import os
+import subprocess

+from galaxy.datatypes import (
+    data,
+    metadata
+)
+from galaxy.datatypes.binary import Binary
+from galaxy.datatypes.data import get_file_peek
 from galaxy.datatypes.metadata import MetadataElement
-from galaxy.datatypes import metadata
+from galaxy.datatypes.sniff import get_headers
+from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.xml import GenericXml

 log = logging.getLogger(__name__)

@@ -2,11 +2,12 @@
 Mothur Metagenomics Datatypes
 """
 import logging
-import sys
 import re
-from galaxy.datatypes.sniff import get_headers
-from galaxy.datatypes.metadata import MetadataElement
+import sys
+
 from galaxy.datatypes.data import Text
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes.sniff import get_headers
 from galaxy.datatypes.tabular import Tabular

 log = logging.getLogger(__name__)
@@ -2,9 +2,9 @@
 Neo4j Composite Dataset
 """
 import logging
-import sys
-import shutil
 import os
+import shutil
+import sys

 from galaxy.datatypes.data import Data
 from galaxy.datatypes.images import Html
@@ -29,7 +29,7 @@ class Neo4j(Html):
            '<html><head><title>Files for Composite Dataset (%s)</title></head><p/>\
            This composite dataset is composed of the following files:<p/><ul>' % (
                self.file_ext)]
-        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():
            opt_text = ''
            if composite_file.optional:
                opt_text = ' (optional)'
@@ -1,9 +1,10 @@
 """
 Qualityscore class
 """
-
-import data
 import logging
+
+from . import data
+
 log = logging.getLogger(__name__)


@@ -3,8 +3,9 @@ File format detector
 """
 from __future__ import absolute_import

-import gzip
 import bz2
+import codecs
+import gzip
 import logging
 import os
 import re
@@ -13,13 +14,13 @@ import sys
 import tempfile
 import zipfile

-from encodings import search_function as encodings_search_function
 from six import text_type

 from galaxy import util
-from galaxy.util import multi_byte
+from galaxy.datatypes.binary import Binary
 from galaxy.util import (
    compression_utils,
+    multi_byte,
    unicodify
 )
 from galaxy.util.checkers import (
@@ -28,7 +29,6 @@ from galaxy.util.checkers import (
    is_bz2,
    is_gzip
 )
-from galaxy.datatypes.binary import Binary

 log = logging.getLogger(__name__)

@@ -48,7 +48,9 @@ def stream_to_open_named_file( stream, fd, filename, source_encoding=None, sourc
    is_compressed = False
    is_binary = False
    is_multi_byte = False
-    if not target_encoding or not encodings_search_function( target_encoding ):
+    try:
+        codecs.lookup(target_encoding)
+    except:
        target_encoding = util.DEFAULT_ENCODING  # utf-8
    if not source_encoding:
        source_encoding = util.DEFAULT_ENCODING  # sys.getdefaultencoding() would mimic old behavior (defaults to ascii)
@@ -1,12 +1,15 @@
 """
 Triple format classes
 """
-import re
-import data
 import logging
-import xml
-import text
-import binary
+import re
+
+from . import (
+    binary,
+    data,
+    text,
+    xml
+)

 log = logging.getLogger(__name__)

@@ -6,6 +6,8 @@ import copy
 from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError
 from bx.tabular.io import Comment, Header

+from six import Iterator
+
 from galaxy.util.odict import odict


@@ -117,7 +119,7 @@ class GFFIntervalToBEDReaderWrapper( NiceReaderWrapper ):
        return interval


-class GFFReaderWrapper( NiceReaderWrapper ):
+class GFFReaderWrapper( Iterator, NiceReaderWrapper ):  # Iterator can be removed after bx-python library is ported to Python3
    """
    Reader wrapper for GFF files.

@@ -149,15 +151,14 @@ class GFFReaderWrapper( NiceReaderWrapper ):
                                self.default_strand, fix_strand=self.fix_strand )
        return interval

-    # For Python3 this needs to be changed to __next__() after bx-python library is ported too
-    def next( self ):
+    def __next__( self ):
        """ Returns next GFFFeature. """

        #
        # Helper function.
        #

-        def handle_parse_error( parse_error ):
+        def handle_parse_error( e ):
            """ Actions to take when ParseError found. """
            if self.outstream:
                if self.print_delegate and hasattr(self.print_delegate, "__call__"):
@@ -434,19 +435,16 @@ def read_unordered_gtf( iterator, strict=False ):
    chroms_features = {}
    for count, intervals in enumerate( feature_intervals.values() ):
        # Sort intervals by start position.
-        intervals.sort( lambda a, b: cmp( a.start, b.start ) )
+        intervals.sort(key=lambda _: _.start)
        feature = GFFFeature( None, intervals=intervals )
        if feature.chrom not in chroms_features:
            chroms_features[ feature.chrom ] = []
        chroms_features[ feature.chrom ].append( feature )

    # Sort features by chrom, start position.
-    chroms_features_sorted = []
-    for chrom_features in chroms_features.values():
-        chroms_features_sorted.append( chrom_features )
-    chroms_features_sorted.sort( lambda a, b: cmp( a[0].chrom, b[0].chrom ) )
+    chroms_features_sorted = sorted(chroms_features.values(), key=lambda _: _[0].chrom)
    for features in chroms_features_sorted:
-        features.sort( lambda a, b: cmp( a.start, b.start ) )
+        features.sort(key=lambda _: _.start)

    # Yield comments first, then features.
    # FIXME: comments can appear anywhere in file, not just the beginning.
@@ -1,10 +1,13 @@
 """
 XML format classes
 """
-import re
-import data
 import logging
-import dataproviders
+import re
+
+from . import (
+    data,
+    dataproviders
+)

 log = logging.getLogger(__name__)

@@ -1,11 +1,11 @@
 """
 Determine what optional dependencies are needed.
 """
-import pkg_resources
-
 from os.path import dirname, join
 from xml.etree import ElementTree

+import pkg_resources
+
 from galaxy.util import asbool
 from galaxy.util.properties import load_app_properties

@@ -2,10 +2,17 @@
 Shared model and mapping code between Galaxy and Tool Shed, trying to
 generalize to generic database connections.
 """
+from inspect import (
+    getmembers,
+    isclass
+)
+
+from sqlalchemy.orm import (
+    scoped_session,
+    sessionmaker
+)

-from sqlalchemy.orm import scoped_session, sessionmaker
 from galaxy.util.bunch import Bunch
-from inspect import getmembers, isclass


 # TODO: Refactor this to be a proper class, not a bunch.
@@ -3,17 +3,21 @@ import copy
 import json
 import logging
 import uuid
-
-from sys import getsizeof
-from itertools import chain
 from collections import deque
+from itertools import chain
+from sys import getsizeof

 import sqlalchemy
+from sqlalchemy.ext.mutable import Mutable
+from sqlalchemy.types import (
+    CHAR,
+    LargeBinary,
+    String,
+    TypeDecorator
+)

 from galaxy import app
 from galaxy.util.aliaspickler import AliasPickleModule
-from sqlalchemy.types import CHAR, LargeBinary, String, TypeDecorator
-from sqlalchemy.ext.mutable import Mutable

 log = logging.getLogger( __name__ )

@@ -234,6 +238,7 @@ def total_size(o, handlers={}, verbose=False):
    """
    def dict_handler(d):
        return chain.from_iterable(d.items())
+
    all_handlers = { tuple: iter,
                     list: iter,
                     deque: iter,
@@ -268,7 +273,7 @@ class MetadataType( JSONType ):
    def process_bind_param(self, value, dialect):
        if value is not None:
            if app.app and app.app.config.max_metadata_value_size:
-                for k, v in value.items():
+                for k, v in list(value.items()):
                    sz = total_size(v)
                    if sz > app.app.config.max_metadata_value_size:
                        del value[k]
@@ -32,12 +32,28 @@ import parsley
 from sqlalchemy import and_
 from sqlalchemy.orm import aliased

-from galaxy.model import (HistoryDatasetAssociation, LibraryDatasetDatasetAssociation,
-                          History, Library, LibraryFolder, LibraryDataset, StoredWorkflowTagAssociation,
-                          StoredWorkflow, HistoryTagAssociation, HistoryDatasetAssociationTagAssociation,
-                          ExtendedMetadata, ExtendedMetadataIndex, HistoryAnnotationAssociation, Job, JobParameter,
-                          JobToInputLibraryDatasetAssociation, JobToInputDatasetAssociation, JobToOutputDatasetAssociation,
-                          Page, PageRevision)
+from galaxy.model import (
+    ExtendedMetadata,
+    ExtendedMetadataIndex,
+    History,
+    HistoryAnnotationAssociation,
+    HistoryDatasetAssociation,
+    HistoryDatasetAssociationTagAssociation,
+    HistoryTagAssociation,
+    Job,
+    JobParameter,
+    JobToInputDatasetAssociation,
+    JobToInputLibraryDatasetAssociation,
+    JobToOutputDatasetAssociation,
+    Library,
+    LibraryDataset,
+    LibraryDatasetDatasetAssociation,
+    LibraryFolder,
+    Page,
+    PageRevision,
+    StoredWorkflow,
+    StoredWorkflowTagAssociation
+)
 from galaxy.model.tool_shed_install import ToolVersion

 log = logging.getLogger( __name__ )
@@ -1,10 +1,12 @@
 import logging
 import os
-from galaxy.util.dictifiable import Dictifiable
-from galaxy.util.bunch import Bunch
+
+from six.moves.urllib.parse import urljoin
+
 from galaxy.util import asbool
+from galaxy.util.bunch import Bunch
+from galaxy.util.dictifiable import Dictifiable
 from tool_shed.util import common_util
-from urlparse import urljoin

 log = logging.getLogger( __name__ )

@@ -1,11 +1,27 @@
+from sqlalchemy import (
+    Boolean,
+    Column,
+    DateTime,
+    ForeignKey,
+    Integer,
+    MetaData,
+    String,
+    Table,
+    TEXT
+)
+from sqlalchemy.orm import (
+    mapper,
+    relation
+)
+
 from galaxy.model import tool_shed_install as install_model
-from sqlalchemy import MetaData
-from sqlalchemy import Boolean, Column, DateTime, ForeignKey, Integer, String, Table, TEXT
-from sqlalchemy.orm import relation, mapper
-from galaxy.model.custom_types import JSONType, TrimmedString
-from galaxy.model.orm.now import now
 from galaxy.model.base import ModelMapping
+from galaxy.model.custom_types import (
+    JSONType,
+    TrimmedString
+)
 from galaxy.model.orm.engine_factory import build_engine
+from galaxy.model.orm.now import now

 metadata = MetaData()

@@ -1,14 +1,17 @@
-import sys
-import os.path
 import logging
+import os.path
+import sys

-# from sqlalchemy import *
-from sqlalchemy import create_engine
-from sqlalchemy import MetaData
-from sqlalchemy import Table
-
+from migrate.versioning import (
+    repository,
+    schema
+)
+from sqlalchemy import (
+    create_engine,
+    MetaData,
+    Table
+)
 from sqlalchemy.exc import NoSuchTableError
-from migrate.versioning import repository, schema

 log = logging.getLogger( __name__ )

@@ -6,7 +6,7 @@ import logging
 import socket
 from datetime import datetime, timedelta

-from sqlalchemy import and_, false, or_, not_
+from sqlalchemy import and_, false, not_, or_
 from sqlalchemy.orm import eagerload_all

 from galaxy.util import listify
@@ -1008,7 +1008,7 @@ class GalaxyRBACAgent( RBACAgent ):
        # Add the new permissions on library_item
        for item_class, permission_class in self.library_item_assocs:
            if isinstance( library_item, item_class ):
-                for action, roles in permissions.items():
+                for action, roles in list(permissions.items()):
                    if isinstance( action, Action ):
                        action = action.action
                    for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]:
@@ -1,10 +1,11 @@
-import hmac
 import hashlib
-from struct import Struct
-from operator import xor
-from itertools import starmap
-from os import urandom
+import hmac
 from base64 import b64encode
+from itertools import starmap
+from operator import xor
+from os import urandom
+from struct import Struct
+
 from galaxy.util import safe_str_cmp

 SALT_LENGTH = 12
@@ -77,6 +78,6 @@ def pbkdf2_bin( data, salt, iterations=1000, keylen=24, hashfunc=None ):
        rv = u = _pseudorandom(salt + _pack_int(block))
        for i in range(iterations - 1):
            u = _pseudorandom(''.join(map(chr, u)))
-            rv = starmap( xor, zip( rv, u ) )  # Python < 2.6.8: starmap requires function inputs to be tuples, so we need to use zip instead of izip
+            rv = starmap( xor, zip( rv, u ) )
        buf.extend(rv)
    return ''.join(map(chr, buf))[:keylen]
@@ -1,10 +1,10 @@
 """
 This module manages loading of Galaxy webhooks.
 """
-
-import os
-import yaml
 import logging
+import os
+
+import yaml

 from galaxy.util import config_directories_from_setting

@@ -1,7 +1,7 @@
 from galaxy.managers.context import (
    ProvidesAppContext,
-    ProvidesUserContext,
-    ProvidesHistoryContext
+    ProvidesHistoryContext,
+    ProvidesUserContext
 )


@@ -3,34 +3,44 @@ Modules used in building workflows
 """
 import logging
 from json import loads
-from xml.etree.ElementTree import Element
-from xml.etree.ElementTree import XML
+from xml.etree.ElementTree import (
+    Element,
+    XML
+)

-from galaxy import exceptions, model, web
-from galaxy.exceptions import ToolMissingException
+from galaxy import (
+    exceptions,
+    model,
+    web
+)
 from galaxy.dataset_collections import matching
+from galaxy.exceptions import ToolMissingException
 from galaxy.jobs.actions.post import ActionBox
 from galaxy.model import PostJobAction
+from galaxy.tools import (
+    DefaultToolState,
+    ToolInputsNotReadyException
+)
 from galaxy.tools.execute import execute
-from galaxy.tools.parameters import check_param
-from galaxy.tools.parameters import params_to_incoming
-from galaxy.tools.parameters import visit_input_values
+from galaxy.tools.parameters import (
+    check_param,
+    params_to_incoming,
+    visit_input_values
+)
 from galaxy.tools.parameters.basic import (
-    parameter_types,
    BooleanToolParameter,
-    TextToolParameter,
-    SelectToolParameter,
    DataCollectionToolParameter,
    DataToolParameter,
+    parameter_types,
    RuntimeValue,
+    SelectToolParameter,
+    TextToolParameter,
    workflow_building_modes
 )
 from galaxy.tools.parameters.wrapped import make_dict_copy
-from galaxy.tools import DefaultToolState
-from galaxy.tools import ToolInputsNotReadyException
-from galaxy.util.odict import odict
 from galaxy.util.bunch import Bunch
 from galaxy.util.json import safe_loads
+from galaxy.util.odict import odict
 from tool_shed.util import common_util

 log = logging.getLogger( __name__ )
@@ -346,7 +356,7 @@ class InputModule( WorkflowModule ):
        # Web controller may set copy_inputs_to_history, API controller always sets
        # inputs.
        if invocation.copy_inputs_to_history:
-            for input_dataset_hda in step_outputs.values():
+            for input_dataset_hda in list(step_outputs.values()):
                content_type = input_dataset_hda.history_content_type
                if content_type == "dataset":
                    new_hda = input_dataset_hda.copy( copy_children=True )
@@ -362,7 +372,7 @@ class InputModule( WorkflowModule ):
        # so do that now so dependent steps can be recalculated. In the future
        # everything should come in from the API and this can be eliminated.
        if not invocation.has_input_for_step( step.id ):
-            content = step_outputs.values()[ 0 ]
+            content = next(iter(step_outputs.values()))
            if content:
                invocation.add_input( content, step.id )
        progress.set_outputs_for_input( step, step_outputs )
@@ -610,7 +620,7 @@ class ToolModule( WorkflowModule ):
        super( ToolModule, self ).save_to_step( step )
        step.tool_id = self.tool_id
        step.tool_version = self.get_version()
-        for k, v in self.post_job_actions.iteritems():
+        for k, v in self.post_job_actions.items():
            pja = self.__to_pja( k, v, step )
            self.trans.sa_session.add( pja )

@@ -666,7 +676,7 @@ class ToolModule( WorkflowModule ):
    def get_data_outputs( self ):
        data_outputs = []
        if self.tool:
-            for name, tool_output in self.tool.outputs.iteritems():
+            for name, tool_output in self.tool.outputs.items():
                extra_kwds = {}
                if tool_output.collection:
                    extra_kwds["collection"] = True
@@ -907,7 +917,7 @@ class ToolModule( WorkflowModule ):
        # job actions for this execution.
        flush_required = False
        effective_post_job_actions = step.post_job_actions[:]
-        for key, value in self.runtime_post_job_actions.iteritems():
+        for key, value in self.runtime_post_job_actions.items():
            effective_post_job_actions.append( self.__to_pja( key, value, None ) )
        for pja in effective_post_job_actions:
            if pja.action_type in ActionBox.immediate_actions:
@@ -96,8 +96,8 @@ class WorkflowCanvas( object ):
            else:
                # Take any key / value pair available in out_conn_index_dict.
                # A problem will result if the dictionary is empty.
-                if out_conn_index_dict.keys():
-                    key = out_conn_index_dict.keys()[0]
+                if out_conn_index_dict:
+                    key = next(iter(out_conn_index_dict.keys()))
                    out_conn_pos = self.out_pos[ out_pos_index ][ key ]
        adjusted = ( out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] )
        self.text.append( svgwrite.shapes.Circle(center=(out_conn_pos[ 0 ] + self.widths[ output_dict[ 'id' ] ] - MARGIN,
@@ -130,7 +130,7 @@ class WorkflowCanvas( object ):
                fill = "#EBD9B2"
            width = self.widths[ step_dict[ 'id' ] ]
            self.add_boxes( step_dict, width, fill )
-            for conn, output_dict in step_dict[ 'input_connections' ].iteritems():
+            for conn, output_dict in step_dict[ 'input_connections' ].items():
                self.add_connection( step_dict, conn, output_dict )

    def populate_data_for_step( self, step, module_name, module_data_inputs, module_data_outputs, tool_errors=None ):
@@ -1,14 +1,15 @@
+import logging
 import uuid

-from galaxy import exceptions
-from galaxy import model
-
+from galaxy import (
+    exceptions,
+    model
+)
 from galaxy.managers import histories
 from galaxy.tools.parameters.meta import expand_workflow_inputs

 INPUT_STEP_TYPES = [ 'data_input', 'data_collection_input', 'parameter_input' ]

-import logging
 log = logging.getLogger( __name__ )


@@ -147,8 +148,7 @@ def _flatten_step_params( param_dict, prefix="" ):
    # a complex value object versus something that maps to child parameters
    # better than the hack or searching for src and id here.
    new_params = {}
-    keys = param_dict.keys()[:]
-    for key in keys:
+    for key in list(param_dict.keys()):
        if prefix:
            effective_key = "%s|%s" % ( prefix, key )
        else:
@@ -244,7 +244,7 @@ def build_workflow_run_configs( trans, workflow, payload ):

        steps_by_id = workflow.steps_by_id
        # Set workflow inputs.
-        for key, input_dict in normalized_inputs.iteritems():
+        for key, input_dict in normalized_inputs.items():
            step = steps_by_id[key]
            if step.type == 'parameter_input':
                continue
@@ -353,13 +353,13 @@ def workflow_run_config_to_request( trans, run_config, workflow ):
            )

    replacement_dict = run_config.replacement_dict
-    for name, value in replacement_dict.iteritems():
+    for name, value in replacement_dict.items():
        add_parameter(
            name=name,
            value=value,
            type=param_types.REPLACEMENT_PARAMETERS,
        )
-    for step_id, content in run_config.inputs.iteritems():
+    for step_id, content in run_config.inputs.items():
        workflow_invocation.add_input( content, step_id )

    add_parameter( "copy_inputs_to_history", "true" if run_config.copy_inputs_to_history else "false", param_types.META_PARAMETERS )
@@ -1,16 +1,14 @@
-import os
-import time
 import logging
+import os
 import threading
-
+import time
 from xml.etree import ElementTree

+import galaxy.workflow.schedulers
 from galaxy import model
 from galaxy.util import plugin_config
 from galaxy.util.handlers import ConfiguresHandlers

-import galaxy.workflow.schedulers
-
 log = logging.getLogger( __name__ )

 DEFAULT_SCHEDULER_ID = "default"  # well actually this should be called DEFAULT_DEFAULT_SCHEDULER_ID...
@@ -77,7 +75,7 @@ class WorkflowSchedulingManager( object, ConfiguresHandlers ):
        return self.__has_handlers.get_handler( None, index=random_index )

    def shutdown( self ):
-        for workflow_scheduler in self.workflow_schedulers.itervalues():
+        for workflow_scheduler in self.workflow_schedulers.values():
            try:
                workflow_scheduler.shutdown()
            except Exception:
@@ -103,7 +101,7 @@ class WorkflowSchedulingManager( object, ConfiguresHandlers ):
        return workflow_invocation

    def __start_schedulers( self ):
-        for workflow_scheduler in self.workflow_schedulers.itervalues():
+        for workflow_scheduler in self.workflow_schedulers.values():
            workflow_scheduler.startup( self.app )

    def __plugins_dict( self ):
@@ -185,7 +183,7 @@ class WorkflowRequestMonitor( object ):
    def __monitor( self ):
        to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
        while self.active:
-            for workflow_scheduler_id, workflow_scheduler in to_monitor.iteritems():
+            for workflow_scheduler_id, workflow_scheduler in to_monitor.items():
                if not self.active:
                    return

@@ -1,9 +1,8 @@
 # override tempfile methods for debugging
-
+import logging
 import tempfile
 import traceback

-import logging
 log = logging.getLogger( __name__ )