[galaxy-commits] commit/galaxy-central: greg: Tool shed import fixes.

18 Jan 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/864e960c5247/
changeset:   864e960c5247
user:        greg
date:        2013-01-18 17:40:29
summary:     Tool shed import fixes.
affected #:  7 files

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/admin.py

--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -1,9 +1,9 @@
-from galaxy.web.base.controller import *
+from galaxy.web.base.controller import BaseUIController
+from galaxy import web, util
 from galaxy.web.base.controllers.admin import Admin
 from galaxy.webapps.community import model
 from galaxy.model.orm import and_
-from galaxy.web.framework.helpers import time_ago, iff, grids
-from galaxy.web.form_builder import SelectField
+from galaxy.web.framework.helpers import time_ago, grids
 from galaxy.util import inflector
 import galaxy.util.shed_util_common as suc
 from repository import RepositoryGrid, CategoryGrid

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -1,10 +1,6 @@
 import logging
 from galaxy.model.item_attrs import UsesItemRatings
 
-from galaxy import eggs
-eggs.require('mercurial')
-from mercurial import hg, ui, commands
-
 log = logging.getLogger( __name__ )
 
 class ItemRatings( UsesItemRatings ):

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/hg.py
--- a/lib/galaxy/webapps/community/controllers/hg.py
+++ b/lib/galaxy/webapps/community/controllers/hg.py
@@ -1,5 +1,6 @@
 import os, logging
-from galaxy.web.base.controller import *
+from galaxy import web
+from galaxy.web.base.controller import BaseUIController
 from galaxy.util.shed_util_common import get_repository_by_name_and_owner, set_repository_metadata
 
 from galaxy import eggs

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/repository_review.py
--- a/lib/galaxy/webapps/community/controllers/repository_review.py
+++ b/lib/galaxy/webapps/community/controllers/repository_review.py
@@ -1,9 +1,9 @@
 import os, logging
-from galaxy import util
-from galaxy.web.base.controller import *
+from galaxy import web, util
+from galaxy.web.base.controller import BaseUIController
 from galaxy.web.form_builder import SelectField, CheckboxField
 from galaxy.webapps.community import model
-from galaxy.web.framework.helpers import time_ago, iff, grids
+from galaxy.web.framework.helpers import grids
 from galaxy.model.orm import and_
 from sqlalchemy.sql.expression import func
 import common

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/controllers/upload.py
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -1,5 +1,6 @@
 import sys, os, shutil, logging, tarfile, tempfile, urllib
-from galaxy.web.base.controller import *
+from galaxy.web.base.controller import BaseUIController
+from galaxy import web, util
 from galaxy.datatypes import checkers
 import galaxy.util.shed_util_common as suc
 

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/community/framework/middleware/hg.py
--- a/lib/galaxy/webapps/community/framework/middleware/hg.py
+++ b/lib/galaxy/webapps/community/framework/middleware/hg.py
@@ -2,7 +2,7 @@
 Middleware for handling hg authentication for users pushing change sets to local repositories.
 """
 import os, logging
-from sqlalchemy import *
+import sqlalchemy
 from paste.auth.basic import AuthBasicAuthenticator
 from paste.httpheaders import REMOTE_USER, AUTH_TYPE
 
@@ -43,7 +43,7 @@
                 username = path_info_components[1]
                 name = path_info_components[2]
                 # Instantiate a database connection
-                engine = create_engine( self.db_url )
+                engine = sqlalchemy.create_engine( self.db_url )
                 connection = engine.connect()
                 result_set = connection.execute( "select id from galaxy_user where username = '%s'" % username.lower() )
                 for row in result_set:
@@ -101,7 +101,7 @@
         return self.__authenticate( username, password )
     def __authenticate( self, username, password ):
         # Instantiate a database connection
-        engine = create_engine( self.db_url )
+        engine = sqlalchemy.create_engine( self.db_url )
         connection = engine.connect()
         result_set = connection.execute( "select email, password from galaxy_user where username = '%s'" % username.lower() )
         for row in result_set:

diff -r add133ca7596281900e31933e6b0748812323517 -r 864e960c52474fe6cb19129196b0ccccf48856bd lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1,15 +1,24 @@
-import urllib2, tempfile
-from admin import *
+import logging, os, shutil, tempfile, urllib2
+from admin import AdminGalaxy
+from galaxy import model, web, util
+from galaxy.web.form_builder import SelectField, CheckboxField
+from galaxy.web.framework.helpers import iff, grids
 from galaxy.util import json
+from galaxy.model.orm import or_
 import galaxy.util.shed_util as shed_util
 import galaxy.util.shed_util_common as suc
 from galaxy.tool_shed import encoding_util
 from galaxy.webapps.community.util import container_util, workflow_util
 from galaxy import eggs, tools
+import pkg_resources
 
 eggs.require( 'mercurial' )
 from mercurial import hg, ui, commands
 
+pkg_resources.require( 'elementtree' )
+from elementtree import ElementTree
+from elementtree.ElementTree import Element
+
 log = logging.getLogger( __name__ )
 
 class InstalledRepositoryGrid( grids.Grid ):
@@ -447,7 +456,7 @@
     @web.require_admin
     def browse_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '/', qualified=True )
+        galaxy_url = web.url_for( '/', qualified=True )
         url = suc.url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) )
         return trans.response.send_redirect( url )
     @web.expose
@@ -469,7 +478,7 @@
         tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository )
         url = suc.url_join( tool_shed_url,
                             'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \
-                            ( url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
+                            ( web.url_for( '/', qualified=True ), repository.name, repository.owner, repository.changeset_revision ) )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
@@ -557,14 +566,14 @@
     @web.require_admin
     def find_tools_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '/', qualified=True )
+        galaxy_url = web.url_for( '/', qualified=True )
         url = suc.url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s' % galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
     @web.require_admin
     def find_workflows_in_tool_shed( self, trans, **kwd ):
         tool_shed_url = kwd[ 'tool_shed_url' ]
-        galaxy_url = url_for( '/', qualified=True )
+        galaxy_url = web.url_for( '/', qualified=True )
         url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url )
         return trans.response.send_redirect( url )
     @web.expose
@@ -993,7 +1002,7 @@
             # Send a request to the tool shed to install the repository.
             url = suc.url_join( tool_shed_url,
                                 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \
-                                ( repository.name, repository.owner, repository.installed_changeset_revision, ( url_for( '/', qualified=True ) ) ) )
+                                ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) )
             return trans.response.send_redirect( url )
         description = util.restore_text( params.get( 'description', repository.description ) )
         shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: greg: Tool shed import fixes.

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