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.

lib/galaxy/datatypes/coverage.py

@@ -5,7 +5,7 @@ Coverage datatypes
 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 *

lib/galaxy/datatypes/data.py

@@ -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

lib/galaxy/datatypes/genetics.py

@@ -12,7 +12,7 @@ ross lazarus for rgenetics
 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

lib/galaxy/datatypes/interval.py

@@ -5,7 +5,7 @@ Interval datatypes
 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 *

lib/galaxy/model/__init__.py

@@ -5,8 +5,7 @@ Naming: try to use class names that have a distinct plural form so that
 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 tempfile
 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 @@ class User( object ):
         
     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 ]:

lib/galaxy/tools/__init__.py

@@ -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
@@ -27,6 +25,12 @@ 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__ )
 
 class ToolNotFoundException( Exception ):
@@ -211,7 +215,10 @@ class DefaultToolState( object ):
         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 @@ class DefaultToolState( object ):
         # 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 @@ class Tool:
             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 ):
         """

lib/galaxy/web/controllers/admin.py

@@ -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 @@ class Admin( BaseController ):
                         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 @@ class Admin( BaseController ):
                         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 ):

lib/galaxy/web/controllers/async.py

@@ -6,8 +6,13 @@ from galaxy.web.base.controller import *
 
 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 @@ class ASync( BaseController ):
                 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 @@ class ASync( BaseController ):
             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 } )

lib/galaxy/web/controllers/dataset.py

@@ -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

lib/galaxy/web/controllers/genetrack.py

@@ -1,12 +1,16 @@
-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
     pkg_resources.require("GeneTrack")
@@ -265,7 +269,10 @@ class WebRoot(BaseController):
         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]))

lib/galaxy/web/controllers/root.py

@@ -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 @@ class RootController( BaseController ):
             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 ) \

lib/galaxy/web/controllers/tool_runner.py

@@ -117,7 +117,6 @@ class ToolRunner( BaseController ):
         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 @@ class ToolRunner( BaseController ):
         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 ):
         """

lib/galaxy/web/framework/__init__.py

@@ -93,8 +93,8 @@ class MessageException( Exception ):
     """
     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 @@ class WebApplication( base.WebApplication ):
         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 )

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

@@ -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 ):

tools/data_source/genbank.py

@@ -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 )
 

tools/data_source/ucsc_proxy.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 import urllib
-import sys, os, sets
+import sys, os
 
 assert sys.version_info[:2] >= ( 2, 4 )
 

tools/new_operations/get_flanks.py

@@ -9,7 +9,7 @@ usage: %prog input out_file size direction region
    -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

tools/new_operations/operation_filter.py

@@ -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 @@ from galaxy.tools.parameters import DataToolParameter
 #        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 ):

tools/new_operations/subtract_query.py

@@ -5,13 +5,17 @@
 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 )
 
 def get_lines(fname, begin_col='', end_col=''):

tools/regVariation/windowSplitter.py

@@ -7,7 +7,7 @@ usage: %prog input size out_file
    -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" )

tools/stats/column_maker.py

@@ -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

tools/stats/filtering.py

@@ -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 @@ def get_operands( filter_condition ):
     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 ):

tools/stats/grouping.py

@@ -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):

tools/stats/gsummary.py

@@ -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 @@ def main():
     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 ) )

tools/visualization/build_ucsc_custom_track_code.py

@@ -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()

tools/visualization/genetrack_code.py

@@ -1,4 +1,4 @@
-import sets, os
+import os
 from galaxy import eggs
 from galaxy import jobs
 from galaxy.tools.parameters import DataToolParameter