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/ -- This is a commit notification from bitbucket.org. 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