details: http://www.bx.psu.edu/hg/galaxy/rev/2ae19c12114c changeset: 2565:2ae19c12114c user: Greg Von Kuster <greg@bx.psu.edu> date: Fri Aug 14 15:37:31 2009 -0400 description: Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made. 26 file(s) affected in this change: lib/galaxy/datatypes/coverage.py lib/galaxy/datatypes/data.py lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/interval.py lib/galaxy/model/__init__.py lib/galaxy/tools/__init__.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/async.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/genetrack.py lib/galaxy/web/controllers/root.py lib/galaxy/web/controllers/tool_runner.py lib/galaxy/web/framework/__init__.py lib/galaxy/webapps/reports/controllers/root.py tools/data_source/genbank.py tools/data_source/ucsc_proxy.py tools/new_operations/get_flanks.py tools/new_operations/operation_filter.py tools/new_operations/subtract_query.py tools/regVariation/windowSplitter.py tools/stats/column_maker.py tools/stats/filtering.py tools/stats/grouping.py tools/stats/gsummary.py tools/visualization/build_ucsc_custom_track_code.py tools/visualization/genetrack_code.py diffs (587 lines): diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/datatypes/coverage.py --- a/lib/galaxy/datatypes/coverage.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/datatypes/coverage.py Fri Aug 14 15:37:31 2009 -0400 @@ -5,7 +5,7 @@ import pkg_resources pkg_resources.require( "bx-python" ) -import logging, os, sys, time, sets, tempfile, shutil +import logging, os, sys, time, tempfile, shutil import data from galaxy import util from galaxy.datatypes.sniff import * diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,4 +1,4 @@ -import logging, os, sys, time, sets, tempfile +import logging, os, sys, time, tempfile from galaxy import util from galaxy.util.odict import odict from galaxy.util.bunch import Bunch diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Fri Aug 14 15:37:31 2009 -0400 @@ -12,7 +12,7 @@ august 20 2007 """ -import logging, os, sys, time, sets, tempfile, shutil +import logging, os, sys, time, tempfile, shutil import data from galaxy import util from cgi import escape diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Aug 14 15:37:31 2009 -0400 @@ -5,7 +5,7 @@ import pkg_resources pkg_resources.require( "bx-python" ) -import logging, os, sys, time, sets, tempfile, shutil +import logging, os, sys, time, tempfile, shutil import data from galaxy import util from galaxy.datatypes.sniff import * diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/model/__init__.py Fri Aug 14 15:37:31 2009 -0400 @@ -5,8 +5,7 @@ the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno -import sha +import os.path, os, errno, sys import galaxy.datatypes from galaxy.util.bunch import Bunch from galaxy import util @@ -14,8 +13,11 @@ import galaxy.datatypes.registry from galaxy.datatypes.metadata import MetadataCollection from galaxy.security import RBACAgent, get_permitted_actions - - +using_24 = sys.version_info[:2] < ( 2, 5 ) +if using_24: + import sha +else: + import hashlib import logging log = logging.getLogger( __name__ ) @@ -40,10 +42,16 @@ def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" - self.password = sha.new( cleartext ).hexdigest() + if using_24: + self.password = sha.new( cleartext ).hexdigest() + else: + self.password = hashlib.sha1( cleartext ).hexdigest() def check_password( self, cleartext ): """Check if 'cleartext' matches 'self.password' when hashed.""" - return self.password == sha.new( cleartext ).hexdigest() + if using_24: + return self.password == sha.new( cleartext ).hexdigest() + else: + return self.password == hashlib.sha1( cleartext ).hexdigest() def all_roles( self ): roles = [ ura.role for ura in self.roles ] for group in [ uga.group for uga in self.groups ]: diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,15 +1,13 @@ """ Classes encapsulating galaxy tools and tool configuration. """ - import pkg_resources; pkg_resources.require( "simplejson" ) import logging, os, string, sys, tempfile, glob, shutil import simplejson -import sha, hmac, binascii - +import hmac, binascii from UserDict import DictMixin from galaxy.util.odict import odict from galaxy.util.bunch import Bunch @@ -26,6 +24,12 @@ from galaxy.util.none_like import NoneDataset from galaxy.datatypes import sniff from cgi import FieldStorage + +using_24 = sys.version_info[:2] < ( 2, 5 ) +if using_24: + import sha +else: + import hashlib log = logging.getLogger( __name__ ) @@ -211,7 +215,10 @@ value["__page__"] = self.page value = simplejson.dumps( value ) # Make it secure - a = hmac.new( app.config.tool_secret, value, sha ).hexdigest() + if using_24: + a = hmac.new( app.config.tool_secret, value, sha ).hexdigest() + else: + a = hmac.new( app.config.tool_secret, value, hashlib.sha1 ).hexdigest() b = binascii.hexlify( value ) return "%s:%s" % ( a, b ) def decode( self, value, tool, app ): @@ -221,7 +228,10 @@ # Extract and verify hash a, b = value.split( ":" ) value = binascii.unhexlify( b ) - test = hmac.new( app.config.tool_secret, value, sha ).hexdigest() + if using_24: + test = hmac.new( app.config.tool_secret, value, sha ).hexdigest() + else: + test = hmac.new( app.config.tool_secret, value, hashlib.sha1 ).hexdigest() assert a == test # Restore from string values = json_fix( simplejson.loads( value ) ) @@ -453,7 +463,6 @@ self.tests = None # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible() - def parse_inputs( self, root ): """ diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,9 +1,14 @@ -import shutil, StringIO, operator, urllib, gzip, tempfile, sets, string, sys +import shutil, StringIO, operator, urllib, gzip, tempfile, string, sys from datetime import datetime, timedelta from galaxy import util, datatypes from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.web.controllers.forms import get_all_forms, get_form_widgets +# Older py compatibility +try: + set() +except: + from sets import Set as set import logging log = logging.getLogger( __name__ ) @@ -1236,16 +1241,16 @@ if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: if len( in_roles ) > 1: # Get the set of all users that are being associated with the dataset - in_roles_set = sets.Set() + in_roles_set = set() for role in in_roles: in_roles_set.add( role ) - users_set = sets.Set() + users_set = set() for role in in_roles: for ura in role.users: users_set.add( ura.user ) # Make sure that at least 1 user has every role being associated with the dataset for user in users_set: - user_roles_set = sets.Set() + user_roles_set = set() for ura in user.roles: user_roles_set.add( ura.role ) if in_roles_set.issubset( user_roles_set ): @@ -1421,16 +1426,16 @@ if v == trans.app.security_agent.permitted_actions.DATASET_ACCESS: if len( in_roles ) > 1: # Get the set of all users that are being associated with the dataset - in_roles_set = sets.Set() + in_roles_set = set() for role in in_roles: in_roles_set.add( role ) - users_set = sets.Set() + users_set = set() for role in in_roles: for ura in role.users: users_set.add( ura.user ) # Make sure that at least 1 user has every role being associated with the dataset for user in users_set: - user_roles_set = sets.Set() + user_roles_set = set() for ura in user.roles: user_roles_set.add( ura.role ) if in_roles_set.issubset( user_roles_set ): diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/async.py Fri Aug 14 15:37:31 2009 -0400 @@ -6,8 +6,13 @@ from galaxy import jobs, util, datatypes, web -import logging, urllib -import sha, hmac +import logging, urllib, hmac, sys + +using_24 = sys.version_info[:2] < ( 2, 5 ) +if using_24: + import sha +else: + import hashlib log = logging.getLogger( __name__ ) @@ -58,7 +63,10 @@ return "Data %s does not exist or has already been deleted" % data_id if STATUS == 'OK': - key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), sha ).hexdigest() + if using_24: + key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), sha ).hexdigest() + else: + key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), hashlib.sha1 ).hexdigest() if key != data_secret: return "You do not have permission to alter data %s." % data_id # push the job into the queue @@ -116,7 +124,10 @@ trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) try: - key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), sha ).hexdigest() + if using_24: + key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), sha ).hexdigest() + else: + key = hmac.new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id), hashlib.sha1 ).hexdigest() galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) params.update( { 'GALAXY_URL' :galaxy_url } ) params.update( { 'data_id' :data.id } ) diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,4 +1,4 @@ -import logging, os, sets, string, shutil, re, socket, mimetypes, smtplib, urllib +import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib from galaxy.web.base.controller import * from galaxy import util, datatypes, jobs, web, model diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/genetrack.py --- a/lib/galaxy/web/controllers/genetrack.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/genetrack.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,11 +1,15 @@ -import time, glob, os +import time, glob, os, sys from itertools import cycle -import sha - from mako import exceptions from mako.template import Template from mako.lookup import TemplateLookup from galaxy.web.base.controller import * + +using_24 = sys.version_info[:2] < ( 2, 5 ) +if using_24: + import sha +else: + import hashlib try: import pkg_resources @@ -265,7 +269,10 @@ tmpl_name, track_maker = conf.PLOT_MAPPER[param.plot] # check against a hash, display an image that already exists if it was previously created. - hash = sha.new() + if using_24: + hash = sha.new() + else: + hash = hashlib.sha1() hash.update(str(dataset_id)) for key in sorted(kwds.keys()): hash.update(str(kwds[key])) diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,7 +1,7 @@ """ Contains the main interface in the Universe class """ -import logging, os, sets, string, shutil, urllib, re, socket +import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage from galaxy import util, datatypes, jobs, web, util from galaxy.web.base.controller import * @@ -60,7 +60,6 @@ trans.response.set_content_type('text/xml') return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) else: - template = "root/history.mako" show_deleted = util.string_as_bool( show_deleted ) query = trans.sa_session.query( model.HistoryDatasetAssociation ) \ .filter( model.HistoryDatasetAssociation.history == history ) \ diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Fri Aug 14 15:37:31 2009 -0400 @@ -117,7 +117,6 @@ tool_state_string = util.object_to_string(state.encode(tool, trans.app)) # Setup context for template history = trans.get_history() - template = "tool_form.mako" vars = dict( tool_state=state, errors = {} ) # Is the "add frame" stuff neccesary here? add_frame = AddFrameData() @@ -125,17 +124,13 @@ if from_noframe is not None: add_frame.wiki_url = trans.app.config.wiki_url add_frame.from_noframe = True - return trans.fill_template( template, history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) - - + return trans.fill_template( "tool_form.mako", history=history, toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: return trans.show_error_message( "Required URL for redirection missing" ) trans.log_event( "Redirecting to: %s" % redirect_url ) return trans.fill_template( 'root/redirect.mako', redirect_url=redirect_url ) - - @web.json def upload_async_create( self, trans, tool_id=None, **kwd ): """ diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Aug 14 15:37:31 2009 -0400 @@ -93,8 +93,8 @@ """ Exception to make throwing errors from deep in controllers easier """ - def __init__( self, message, type="info" ): - self.message = message + def __init__( self, err_msg, type="info" ): + self.err_msg = err_msg self.type = type def error( message ): @@ -117,7 +117,7 @@ self.security = galaxy_app.security def handle_controller_exception( self, e, trans, **kwargs ): if isinstance( e, MessageException ): - return trans.show_message( e.message, e.type ) + return trans.show_message( e.err_msg, e.type ) def make_body_iterable( self, trans, body ): if isinstance( body, FormBuilder ): body = trans.show_form( body ) diff -r eb1244477b90 -r 2ae19c12114c lib/galaxy/webapps/reports/controllers/root.py --- a/lib/galaxy/webapps/reports/controllers/root.py Fri Aug 14 12:17:45 2009 -0400 +++ b/lib/galaxy/webapps/reports/controllers/root.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,8 +1,8 @@ -import sys, os, operator, sets, string, shutil, re, socket, urllib +import sys, os, operator, string, shutil, re, socket, urllib, time from galaxy import web from cgi import escape, FieldStorage from galaxy.webapps.reports.base.controller import * -import logging, sets, time +import logging log = logging.getLogger( __name__ ) class Report( BaseController ): diff -r eb1244477b90 -r 2ae19c12114c tools/data_source/genbank.py --- a/tools/data_source/genbank.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/data_source/genbank.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python from Bio import GenBank -import sys, os, sets, textwrap +import sys, os, textwrap assert sys.version_info[:2] >= ( 2, 4 ) diff -r eb1244477b90 -r 2ae19c12114c tools/data_source/ucsc_proxy.py --- a/tools/data_source/ucsc_proxy.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/data_source/ucsc_proxy.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python import urllib -import sys, os, sets +import sys, os assert sys.version_info[:2] >= ( 2, 4 ) diff -r eb1244477b90 -r 2ae19c12114c tools/new_operations/get_flanks.py --- a/tools/new_operations/get_flanks.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/new_operations/get_flanks.py Fri Aug 14 15:37:31 2009 -0400 @@ -9,7 +9,7 @@ -o, --off=N: Offset """ -import sys, sets, re, os +import sys, re, os from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse diff -r eb1244477b90 -r 2ae19c12114c tools/new_operations/operation_filter.py --- a/tools/new_operations/operation_filter.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/new_operations/operation_filter.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,8 +1,13 @@ # runs after the job (and after the default post-filter) -import sets, os +import os from galaxy import eggs from galaxy import jobs from galaxy.tools.parameters import DataToolParameter +# Older py compatibility +try: + set() +except: + from sets import Set as set #def exec_before_process(app, inp_data, out_data, param_dict, tool=None): # """Sets the name of the data""" @@ -11,8 +16,8 @@ # raise Exception, '<p><font color="yellow">Both Queries must be from the same genome build</font></p>' def validate_input( trans, error_map, param_values, page_param_map ): - dbkeys = sets.Set() - data_param_names = sets.Set() + dbkeys = set() + data_param_names = set() data_params = 0 for name, param in page_param_map.iteritems(): if isinstance( param, DataToolParameter ): diff -r eb1244477b90 -r 2ae19c12114c tools/new_operations/subtract_query.py --- a/tools/new_operations/subtract_query.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/new_operations/subtract_query.py Fri Aug 14 15:37:31 2009 -0400 @@ -5,12 +5,16 @@ Subtract an entire query from another query usage: %prog in_file_1 in_file_2 begin_col end_col output """ - -import sys, sets, re - +import sys, re from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse + +# Older py compatibility +try: + set() +except: + from sets import Set as set assert sys.version_info[:2] >= ( 2, 4 ) diff -r eb1244477b90 -r 2ae19c12114c tools/regVariation/windowSplitter.py --- a/tools/regVariation/windowSplitter.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/regVariation/windowSplitter.py Fri Aug 14 15:37:31 2009 -0400 @@ -7,7 +7,7 @@ -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file """ -import sys, sets, re, os +import sys, re, os from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) diff -r eb1244477b90 -r 2ae19c12114c tools/stats/column_maker.py --- a/tools/stats/column_maker.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/stats/column_maker.py Fri Aug 14 15:37:31 2009 -0400 @@ -2,7 +2,7 @@ # This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of # a computation performed on every row in the original file. The tool will skip over invalid lines within the file, # informing the user about the number of lines skipped. -import sys, sets, re, os.path +import sys, re, os.path from galaxy import eggs from galaxy.tools import validation from galaxy.datatypes import metadata diff -r eb1244477b90 -r 2ae19c12114c tools/stats/filtering.py --- a/tools/stats/filtering.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/stats/filtering.py Fri Aug 14 15:37:31 2009 -0400 @@ -2,8 +2,13 @@ # This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties. # The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. -import sys, sets, re, os.path +import sys, re, os.path from galaxy import eggs +# Older py compatibility +try: + set() +except: + from sets import Set as set assert sys.version_info[:2] >= ( 2, 4 ) @@ -13,7 +18,7 @@ for item in items_to_strip: if filter_condition.find( item ) >= 0: filter_condition = filter_condition.replace( item, ' ' ) - operands = sets.Set( filter_condition.split( ' ' ) ) + operands = set( filter_condition.split( ' ' ) ) return operands def stop_err( msg ): diff -r eb1244477b90 -r 2ae19c12114c tools/stats/grouping.py --- a/tools/stats/grouping.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/stats/grouping.py Fri Aug 14 15:37:31 2009 -0400 @@ -3,7 +3,7 @@ """ This tool provides the SQL "group by" functionality. """ -import sys, string, re, commands, tempfile, random, sets +import sys, string, re, commands, tempfile, random from rpy import * def stop_err(msg): diff -r eb1244477b90 -r 2ae19c12114c tools/stats/gsummary.py --- a/tools/stats/gsummary.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/stats/gsummary.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,7 +1,12 @@ #!/usr/bin/python -import sys, sets, re, tempfile +import sys, re, tempfile from rpy import * +# Older py compatibility +try: + set() +except: + from sets import Set as set assert sys.version_info[:2] >= ( 2, 4 ) @@ -33,7 +38,7 @@ for word in re.compile( '[a-zA-Z]+' ).findall( expression ): if word and not word in math_allowed: stop_err( "Invalid expression '%s': term '%s' is not recognized or allowed" %( expression, word ) ) - symbols = sets.Set() + symbols = set() for symbol in re.compile( '[^a-z0-9\s]+' ).findall( expression ): if symbol and not symbol in ops_allowed: stop_err( "Invalid expression '%s': operator '%s' is not recognized or allowed" % ( expression, symbol ) ) diff -r eb1244477b90 -r 2ae19c12114c tools/visualization/build_ucsc_custom_track_code.py --- a/tools/visualization/build_ucsc_custom_track_code.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/visualization/build_ucsc_custom_track_code.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,6 +1,10 @@ # runs after the job (and after the default post-filter) -from sets import Set as set +# Older py compatibility +try: + set() +except: + from sets import Set as set def validate_input( trans, error_map, param_values, page_param_map ): dbkeys = set() diff -r eb1244477b90 -r 2ae19c12114c tools/visualization/genetrack_code.py --- a/tools/visualization/genetrack_code.py Fri Aug 14 12:17:45 2009 -0400 +++ b/tools/visualization/genetrack_code.py Fri Aug 14 15:37:31 2009 -0400 @@ -1,4 +1,4 @@ -import sets, os +import os from galaxy import eggs from galaxy import jobs from galaxy.tools.parameters import DataToolParameter