1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/c3a9547df6f1/ changeset: c3a9547df6f1 user: greg date: 2012-10-02 15:47:06 summary: Fixes for tool shed features broken due to the elimination of the ability to use the webapp param. affected #: 33 files

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -138,8 +138,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() @@ -260,7 +259,7 @@ tool_shed_repository, self.app.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) # Get the tool_versions from the tool shed for each tool in the installed change set. - url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + url = '%s/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_url, tool_shed_repository.name, self.repository_owner, installed_changeset_revision ) response = urllib2.urlopen( url ) text = response.read()

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -30,7 +30,7 @@ tool_dependencies_dict = {} repository_name = elem.get( 'name' ) changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager' % \ + url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&from_install_manager=True' % \ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) try: response = urllib2.urlopen( url )

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/tool_shed/update_manager.py --- a/lib/galaxy/tool_shed/update_manager.py +++ b/lib/galaxy/tool_shed/update_manager.py @@ -34,7 +34,7 @@ log.info( 'Transfer job restarter shutting down...' ) def check_for_update( self, repository ): tool_shed_url = get_url_from_repository_tool_shed( self.app, repository ) - url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&webapp=update_manager' % \ + url = '%s/repository/check_for_updates?name=%s&owner=%s&changeset_revision=%s&from_update_manager=True' % \ ( tool_shed_url, repository.name, repository.owner, repository.changeset_revision ) try: response = urllib2.urlopen( url )

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -297,7 +297,7 @@ # tag for any tool in the repository. break return can_generate_dependency_metadata -def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files, webapp='galaxy' ): +def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): """ Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make sure the files exist. @@ -602,7 +602,7 @@ tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, webapp='galaxy' ): + resetting_all_metadata_on_repository=False, updating_installed_repository=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -695,7 +695,7 @@ if not valid: invalid_file_tups.append( ( name, error_message ) ) else: - invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths, webapp=webapp ) + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_file_metadata_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: @@ -1115,7 +1115,7 @@ return manifest_ctx, ctx_file return None, None def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): - url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % ( name, owner, changeset_revision ) ) + url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) ctx_rev = response.read() response.close()

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -69,7 +69,7 @@ columns = [ UserLoginColumn( "Email", key="email", - link=( lambda item: dict( operation="information", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="information", id=item.id ) ), attach_popup=True, filterable="advanced" ), UserNameColumn( "User Name", @@ -93,18 +93,18 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Create new user", - dict( controller='admin', action='users', operation='create', webapp="community" ) ) + dict( controller='admin', action='users', operation='create' ) ) ] operations = [ grids.GridOperation( "Manage Roles and Groups", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="manage_roles_and_groups_for_user" ) ), + url_args=dict( action="manage_roles_and_groups_for_user" ) ), grids.GridOperation( "Reset Password", condition=( lambda item: not item.deleted ), allow_multiple=True, allow_popup=False, - url_args=dict( webapp="community", action="reset_user_password" ) ) + url_args=dict( action="reset_user_password" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -119,8 +119,7 @@ return trans.user

class RoleListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): return role.name @@ -156,7 +155,7 @@ columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), attach_popup=True, filterable="advanced" ), DescriptionColumn( "Description", @@ -183,24 +182,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new role", - dict( controller='admin', action='roles', operation='create', webapp="community" ) ) + dict( controller='admin', action='roles', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_role" ) ), + url_args=dict( action="rename_role" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_role_deleted" ) ), + url_args=dict( action="mark_role_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_role" ) ), + url_args=dict( action="undelete_role" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_role" ) ) ] + url_args=dict( action="purge_role" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -213,8 +212,7 @@ return query.filter( model.Role.type != model.Role.types.PRIVATE )

class GroupListGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same - # in the galaxy webapp. + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, group ): return group.name @@ -242,7 +240,7 @@ columns = [ NameColumn( "Name", #key="name", - link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), attach_popup=True #filterable="advanced" ), @@ -262,24 +260,24 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new group", - dict( controller='admin', action='groups', operation='create', webapp="community" ) ) + dict( controller='admin', action='groups', operation='create' ) ) ] operations = [ grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( webapp="community", action="rename_group" ) ), + url_args=dict( action="rename_group" ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="mark_group_deleted" ) ), + url_args=dict( action="mark_group_deleted" ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="undelete_group" ) ), + url_args=dict( action="undelete_group" ) ), grids.GridOperation( "Purge", condition=( lambda item: item.deleted ), allow_multiple=True, - url_args=dict( webapp="community", action="purge_group" ) ) ] + url_args=dict( action="purge_group" ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -294,12 +292,12 @@ # Override the NameColumn to include an Edit link columns[ 0 ] = CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id ) ), model_class=model.Category, attach_popup=False ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create' ) ) ]

class AdminRepositoryListGrid( RepositoryListGrid ): @@ -377,9 +375,7 @@ NameColumn( "Name", key="name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository_revision", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), attach_popup=True ), RevisionColumn( "Revision", attach_popup=False ), @@ -716,7 +712,6 @@ "repository" ) ) trans.response.send_redirect( web.url_for( controller='admin', action='browse_repository_metadata', - webapp='community', message=util.sanitize_text( message ), status=status ) ) else:

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -612,8 +612,7 @@ repo_files_dir, tool_config_filename, tool, - sample_files, - webapp='community' ) + sample_files ) if invalid_files_and_errors_tups: message2 = generate_message_for_invalid_tools( invalid_files_and_errors_tups, repository, @@ -753,8 +752,7 @@ relative_install_dir=repo_dir, repository_files_dir=work_dir, resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -829,8 +827,7 @@ relative_install_dir=repo_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='community' ) + updating_installed_repository=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -49,7 +49,7 @@ columns = [ NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="repositories_by_category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_category", id=item.id ) ), attach_popup=False ), DescriptionColumn( "Description", key="Category.description", @@ -87,7 +87,7 @@ columns = [ CategoryListGrid.NameColumn( "Name", key="Category.name", - link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id, webapp="galaxy" ) ), + link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ), attach_popup=False ), CategoryListGrid.DescriptionColumn( "Description", key="Category.description", @@ -136,7 +136,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s&webapp=community">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -173,8 +173,7 @@ NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", key="description", @@ -187,7 +186,7 @@ attach_popup=False ), UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), grids.CommunityRatingColumn( "Average Rating", key="rating" ), @@ -231,15 +230,14 @@ RepositoryListGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + id=item.id ) ), attach_popup=False ), RepositoryListGrid.DescriptionColumn( "Synopsis", key="description", attach_popup=False ), RepositoryListGrid.UserColumn( "Owner", model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), @@ -254,7 +252,7 @@ condition=( lambda item: not item.deleted ), async_compatible=False ) ] global_actions = [ - grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) + grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) ]

class WritableRepositoryListGrid( RepositoryListGrid ): @@ -285,7 +283,7 @@ rval = '<ul>' if repository.categories: for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s&webapp=galaxy">%s</a></li>' \ + rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \ % ( trans.security.encode_id( rca.category.id ), rca.category.name ) else: rval += '<li>not set</li>' @@ -372,9 +370,7 @@ default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="community" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), DescriptionColumn( "Synopsis", attach_popup=False ), @@ -414,9 +410,7 @@ columns = [ col for col in MatchedRepositoryListGrid.columns ] # Override the NameColumn columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", - link=( lambda item: dict( operation="view_or_manage_repository", - id=item.id, - webapp="galaxy" ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False )

class RepositoryController( BaseUIController, ItemRatings ): @@ -481,7 +475,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) cntrller = params.get( 'cntrller', 'repository' ) is_admin = trans.user_is_admin() invalid_tools_dict = odict() @@ -514,15 +507,12 @@ return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, - webapp=webapp, message=message, status=status ) @web.expose def browse_repositories( self, trans, **kwd ): # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. - if 'webapp' not in kwd: - kwd[ 'webapp' ] = get_webapp( trans, **kwd ) if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": @@ -606,7 +596,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) @@ -619,7 +608,6 @@ metadata=metadata, commit_message=commit_message, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -631,7 +619,7 @@ if 'f-free-text-search' in kwd: if kwd[ 'f-free-text-search' ] == 'All': # The user performed a search, then clicked the "x" to eliminate the search criteria. - new_kwd = dict( webapp='galaxy' ) + new_kwd = {} return self.valid_category_list_grid( trans, **new_kwd ) # Since we are searching valid repositories and not categories, redirect to browse_valid_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: @@ -656,7 +644,6 @@ return self.valid_category_list_grid( trans, **kwd ) @web.expose def browse_valid_repositories( self, trans, **kwd ): - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if 'f-free-text-search' in kwd: if 'f-Category.name' in kwd: @@ -676,7 +663,6 @@ latest_installable_changeset_revision = repository_metadata.changeset_revision return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id, changeset_revision=latest_installable_changeset_revision ) ) elif operation == "valid_repositories_by_category": @@ -700,12 +686,10 @@ if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', - webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', - webapp=webapp, repository_id=repository_id ) self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", url_args=url_args, @@ -745,10 +729,7 @@ shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) @web.expose def check_for_updates( self, trans, **kwd ): - """ - Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' UpdateManager, the value of 'webapp' - will be 'update_manager'. - """ + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -757,14 +738,13 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) # Default to the current changeset revision. update_to_ctx = get_changectx_for_changeset( repo, changeset_revision ) latest_changeset_revision = changeset_revision - from_update_manager = webapp == 'update_manager' + from_update_manager = kwd.get( 'from_update_manager', False ) if from_update_manager: update = 'true' no_update = 'false' @@ -923,7 +903,6 @@ message = "Repository '%s' has been created." % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', - webapp='community', message=message, id=trans.security.encode_id( repository.id ) ) ) return trans.fill_template( '/webapps/community/repository/create_repository.mako', @@ -939,7 +918,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository, tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) @@ -952,12 +930,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) except Exception, e: message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -996,7 +973,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1012,7 +988,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1048,16 +1024,16 @@ if ok: kwd[ 'match_tuples' ] = match_tuples # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_categories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_categories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_tools' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1071,7 +1047,6 @@ status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_tools.mako', - webapp=webapp, tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1083,7 +1058,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -1099,7 +1073,7 @@ repository = get_repository( trans, repository_id ) kwd[ 'id' ] = repository_id kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision - if webapp == 'community' and ( is_admin or repository.user == trans.user ): + if trans.webapp.name == 'community' and ( is_admin or repository.user == trans.user ): a = 'manage_repository' else: a = 'view_repository' @@ -1136,17 +1110,16 @@ ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples - # Render the list view - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': # Our initial request originated from a Galaxy instance. global_actions = [ grids.GridAction( "Browse valid repositories", - dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + dict( controller='repository', action='browse_valid_repositories' ) ), grids.GridAction( "Search for valid tools", - dict( controller='repository', action='find_tools', webapp=webapp ) ), + dict( controller='repository', action='find_tools' ) ), grids.GridAction( "Search for workflows", - dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + dict( controller='repository', action='find_workflows' ) ) ] self.install_matched_repository_list_grid.global_actions = global_actions - install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + install_url_args = dict( controller='repository', action='find_workflows' ) operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] self.install_matched_repository_list_grid.operations = operations return self.install_matched_repository_list_grid( trans, **kwd ) @@ -1163,7 +1136,6 @@ workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) return trans.fill_template( '/webapps/community/repository/find_workflows.mako', - webapp=webapp, workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1234,8 +1206,7 @@ return '' @web.expose def get_tool_dependencies( self, trans, **kwd ): - # Handle a request from a local Galaxy instance. If the request originated with the Galaxy instances' InstallManager, the value of 'webapp' - # will be 'install_manager'. + """Handle a request from a local Galaxy instance.""" params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1244,14 +1215,14 @@ name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = get_webapp( trans, **kwd ) repository = get_repository_by_name_and_owner( trans, name, owner ) for downloadable_revision in repository.downloadable_revisions: if downloadable_revision.changeset_revision == changeset_revision: break metadata = downloadable_revision.metadata tool_dependencies = metadata.get( 'tool_dependencies', '' ) - if webapp == 'install_manager': + from_install_manager = kwd.get( 'from_install_manager', False ) + if from_install_manager: if tool_dependencies: return tool_shed_encode( tool_dependencies ) return '' @@ -1450,7 +1421,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - webapp = get_webapp( trans, **kwd ) repository_clone_url = generate_clone_url( trans, repository_id ) repository, tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) @@ -1461,8 +1431,7 @@ repository.repo_path, tool_config, tool, - [], - webapp=webapp ) + [] ) if invalid_file_tups: message = generate_message_for_invalid_tools( invalid_file_tups, repository, {}, as_html=True, displaying_invalid_tool=True ) elif error_message: @@ -1474,12 +1443,11 @@ tool=tool, tool_state=tool_state, is_malicious=is_malicious, - webapp=webapp, message=message, status='error' ) except Exception, e: message = "Exception thrown attempting to display tool: %s." % str( e ) - if webapp == 'galaxy': + if trans.webapp.name == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -1535,7 +1503,6 @@ if user.email in repository.email_alerts: email_alert_repositories.append( repository ) return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", - webapp='community', new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -1573,7 +1540,6 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, - webapp='community', message=message, status='error' ) ) if description != repository.description: @@ -1713,8 +1679,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - if 'webapp' not in kwd: - kwd[ 'webapp' ] = 'community' if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "receive email alerts": @@ -1753,7 +1717,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) @@ -1776,7 +1739,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - webapp=webapp, message=message, status=status ) @web.expose @@ -2218,7 +2180,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) cntrller = params.get( 'cntrller', 'repository' ) - webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, id ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) metadata = repository_metadata.metadata @@ -2236,7 +2197,6 @@ changeset_revision=changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2245,7 +2205,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) - webapp = get_webapp( trans, **kwd ) repo = hg.repository( get_configured_ui(), repository.repo_path ) avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model ) changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) ) @@ -2307,7 +2266,6 @@ changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, is_malicious=is_malicious, - webapp=webapp, message=message, status=status ) @web.expose @@ -2315,7 +2273,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) @@ -2376,7 +2333,6 @@ revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, - webapp=webapp, message=message, status=status )

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -19,7 +19,7 @@

class UploadController( BaseUIController ): @web.expose - @web.require_login( 'upload', use_panels=True, webapp='community' ) + @web.require_login( 'upload', use_panels=True ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -161,7 +161,6 @@ action='browse_repository', id=repository_id, commit_message='Deleted selected files', - webapp='community', message=message, status=status ) ) else:

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -141,7 +141,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -152,11 +151,10 @@ repository_metadata_id=repository_metadata_id, workflow_name=workflow_name, metadata=repository_metadata, - webapp=webapp, message=message, status=status ) @web.expose - def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name ): repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) repository_id = trans.security.encode_id( repository_metadata.repository_id ) changeset_revision = repository_metadata.changeset_revision @@ -388,7 +386,6 @@ workflow_name = kwd.get( 'workflow_name', '' ) if workflow_name: workflow_name = tool_shed_decode( workflow_name ) - webapp = kwd.get( 'webapp', 'community' ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) @@ -404,8 +401,8 @@ to_file.write( to_json_string( workflow_data ) ) return open( tmp_fname ) galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \ + ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ) ) return trans.response.send_redirect( url ) return trans.response.send_redirect( web.url_for( controller='workflow', action='view_workflow',

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c 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 @@ -65,7 +65,7 @@ key="name", link=( lambda item: iff( item.status in [ model.ToolShedRepository.installation_status.CLONING ], None, - dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ) ), + dict( operation="manage_repository", id=item.id ) ) ), attach_popup=True ), DescriptionColumn( "Description" ), OwnerColumn( "Owner" ), @@ -410,7 +410,7 @@ def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s&webapp=galaxy' % ( galaxy_url ) ) + url = url_join( tool_shed_url, 'repository/browse_valid_categories?galaxy_url=%s' % ( galaxy_url ) ) return trans.response.send_redirect( url ) @web.expose @web.require_admin @@ -419,7 +419,6 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', - webapp='galaxy', message=message, status='error' ) @web.expose @@ -429,7 +428,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + '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 ) ) return trans.response.send_redirect( url ) @web.expose @@ -507,14 +506,14 @@ def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) - url = url_join( tool_shed_url, 'repository/find_tools?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = 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 ) - url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s&webapp=galaxy' % galaxy_url ) + url = url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) def generate_tool_path( self, repository_clone_url, changeset_revision ): """ @@ -676,7 +675,7 @@ trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, tool_shed_repository ) url = url_join( tool_shed_url, - '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -731,8 +730,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -806,7 +804,7 @@ # Send a request to the tool shed to install the repository. tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s&webapp=galaxy' % \ + 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision, @@ -1030,7 +1028,7 @@ changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. url = url_join( tool_shed_url, - 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % \ + 'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s' % \ ( repository_ids, changeset_revisions ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1175,7 +1173,7 @@ repo_info_tuple = repo_info_dict[ name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1350,7 +1348,7 @@ # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. url = url_join( tool_shed_url, - 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/previous_changeset_revisions?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( url_for( '/', qualified=True ), repository_name, repository_owner, changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1413,7 +1411,7 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True ) if metadata and 'readme' in metadata: url = url_join( tool_shed_url, - 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_readme?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) response = urllib2.urlopen( url ) raw_text = response.read() @@ -1448,8 +1446,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - webapp='galaxy' ) + updating_installed_repository=False ) repository.metadata = metadata_dict trans.sa_session.add( repository ) trans.sa_session.flush() @@ -1506,7 +1503,7 @@ repository = get_repository( trans, kwd[ 'id' ] ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) url = url_join( tool_shed_url, - 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \ + 'repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.changeset_revision ) ) response = urllib2.urlopen( url ) text = response.read() @@ -1625,8 +1622,7 @@ relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - webapp='galaxy' ) + updating_installed_repository=True ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision @@ -1676,7 +1672,6 @@ changeset_revision=repository.changeset_revision, readme_text=readme_text, is_malicious=is_malicious, - webapp='galaxy', message=message, status=status ) @web.expose @@ -1685,7 +1680,6 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) repository_metadata = repository.metadata tool_metadata = {}

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1026,7 +1026,6 @@ """ url = kwd.get( 'url', '' ) workflow_text = kwd.get( 'workflow_text', '' ) - webapp = get_webapp( trans, **kwd ) message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) import_button = kwd.get( 'import_button', False ) @@ -1056,8 +1055,8 @@ import_button = True if tool_shed_url and not import_button: # Use urllib (send another request to the tool shed) to retrieve the workflow. - workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ) ) response = urllib2.urlopen( workflow_url ) workflow_text = response.read() response.close() @@ -1137,7 +1136,7 @@ for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) - url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '/', qualified=True ), webapp ) + url = '%s/repository/find_tools?galaxy_url=%s' % ( shed_url, url_for( '/', qualified=True ) ) if missing_tool_tups: url += '&tool_id=' for missing_tool_tup in missing_tool_tups: @@ -1155,7 +1154,6 @@ action = 'index' return trans.response.send_redirect( web.url_for( controller='admin', action=action, - webapp='galaxy', message=message, status=status ) ) else: @@ -1164,8 +1162,8 @@ if tool_shed_url: # We've received the textual representation of a workflow from a Galaxy tool shed. message = "Workflow <b>%s</b> imported successfully." % workflow.name - url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ - ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), message ) return trans.response.send_redirect( url ) elif installed_repository_file: # The workflow was read from a file included with an installed tool shed repository.

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ b/templates/webapps/community/admin/index.mako @@ -48,19 +48,19 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories', webapp='community' )}">Browse all repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories', webapp='community' )}">Reset selected metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}">Reset selected metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata', webapp='community' )}">Browse metadata</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin', webapp='community' )}">Browse invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a></div></div></div> @@ -70,7 +70,7 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a></div></div></div> @@ -81,13 +81,13 @@ <div class="toolSectionBody"><div class="toolSectionBg"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a></div></div></div> @@ -95,7 +95,7 @@ Statistics </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}">View shed statistics</a> + <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a></div></div></div> @@ -104,7 +104,7 @@

<%def name="center_panel()"><% - center_url = h.url_for( action='center', webapp='community' ) + center_url = h.url_for( action='center' ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ b/templates/webapps/community/admin/statistics.mako @@ -7,7 +7,7 @@

<div class="toolForm"><div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics', webapp='community' )}" method="post" > + <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" ><div class="form-row"><table class="grid"><tr>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -64,10 +64,10 @@ </%def>

## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index', webapp='community' ) )} + ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )}

## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} + ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )}

## Help tab. <% @@ -85,9 +85,9 @@ ## User tabs. <% # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login', webapp='community' ), "galaxy_main" ] ] + menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) extra_class = "loggedout-only" visible = ( trans.user == None ) tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) @@ -101,12 +101,12 @@ if app.config.remote_user_logout_href: menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='community' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout', webapp='community' ) + menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) + logout_url = h.url_for( controller='/user', action='logout' ) menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='community' ), "galaxy_main" ] ) + menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] )

extra_class = "loggedin-only" visible = ( trans.user != None )

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/common/view_readme.mako --- a/templates/webapps/community/common/view_readme.mako +++ b/templates/webapps/community/common/view_readme.mako @@ -3,7 +3,7 @@ <%namespace file="/webapps/community/common/common.mako" import="render_readme" /><% - if webapp == 'community': + if trans.webapp.name == 'community': is_admin = trans.user_is_admin() is_new = repository.is_new can_contact_owner = trans.user and trans.user != repository.user @@ -22,43 +22,43 @@

<br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %else: %if cntrller=='repository': - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Preview tools for install</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', operation='preview_tools_in_changeset', id=trans.security.encode_id( repository.id ) )}">Preview tools for install</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ b/templates/webapps/community/index.mako @@ -50,10 +50,10 @@ </div><div class="toolSectionBody"><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools', webapp='community' )}">Search for valid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows', webapp='community' )}">Search for workflows</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> %endif @@ -62,7 +62,7 @@ All Repositories </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories', webapp='community' )}">Browse by category</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a></div> %if trans.user: <div class="toolSectionPad"></div> @@ -70,20 +70,20 @@ My Repositories and Tools </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own', webapp='community' )}">Repositories I own</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories', webapp='community' )}">My writable repositories</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='writable_repositories' )}">My writable repositories</a></div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository', webapp='community' )}">My invalid tools</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a></div><div class="toolSectionPad"></div><div class="toolSectionTitle"> Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository', webapp='community' )}">Create new repository</a> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a></div> %else: <div class="toolSectionPad"></div> @@ -91,7 +91,7 @@ Available Actions </div><div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to create a repository</a> + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a></div> %endif </div> @@ -102,9 +102,9 @@ <%def name="center_panel()"><% if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status, webapp='community' ) + center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ b/templates/webapps/community/repository/browse_invalid_tools.mako @@ -20,7 +20,7 @@ <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %><tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ b/templates/webapps/community/repository/browse_repository.mako @@ -65,23 +65,23 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -83,7 +83,7 @@ hg clone <a href="${clone_str}">${clone_str}</a></%def>

-<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )"> +<%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False )"><% from galaxy.tool_shed.encoding_util import tool_shed_encode %> %if metadata or can_set_metadata: <p/> @@ -184,10 +184,10 @@ <tr><td><div style="float:left;" class="menubutton split popup" id="tool-${index}-popup"> - <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_dict[ 'name' ]}</a> + <a class="view-info" href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_dict[ 'name' ]}</a></div><div popupmenu="tool-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ], webapp=webapp )}">View tool metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision, tool_id=tool_dict[ 'id' ] )}">View tool metadata</a></div></td><td>${tool_dict[ 'description' ]}</td> @@ -232,7 +232,7 @@ %for invalid_tool_config in invalid_tool_configs: <tr><td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision, webapp=webapp )}"> + <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> ${invalid_tool_config} </a></td> @@ -274,7 +274,7 @@ %><tr><td> - <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">${workflow_name}</a> + <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">${workflow_name}</a></td><td> %if steps:

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/contact_owner.mako --- a/templates/webapps/community/repository/contact_owner.mako +++ b/templates/webapps/community/repository/contact_owner.mako @@ -31,26 +31,26 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ) )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ) )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_tools.mako --- a/templates/webapps/community/repository/find_tools.mako +++ b/templates/webapps/community/repository/find_tools.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/>

-%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></li></ul> %endif

@@ -32,7 +32,7 @@ strings if these types of search strings are entered in more than one field. </div><div style="clear: both"></div> - <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}" method="post" > + <form name="find_tools" id="find_tools" action="${h.url_for( controller='repository', action='find_tools' )}" method="post" ><div class="form-row"><label>Tool id:</label><input name="tool_id" type="textfield" value="${tool_id}" size="40"/>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/find_workflows.mako --- a/templates/webapps/community/repository/find_workflows.mako +++ b/templates/webapps/community/repository/find_workflows.mako @@ -10,11 +10,11 @@ %><%inherit file="${inherit(context)}"/>

-%if webapp == 'galaxy': +%if trans.webapp.name == 'galaxy': <br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a></li> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> + <li><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a></li> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a></ul> %endif

@@ -30,7 +30,7 @@ Comma-separated strings may be entered to expand search criteria. </div><div style="clear: both"></div> - <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}" method="post" > + <form name="find_workflows" id="find_workflows" action="${h.url_for( controller='repository', action='find_workflows' )}" method="post" ><div style="clear: both"></div><div class="form-row"><label>Workflow name:</label>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/manage_repository.mako --- a/templates/webapps/community/repository/manage_repository.mako +++ b/templates/webapps/community/repository/manage_repository.mako @@ -42,30 +42,30 @@ <br/><br/><ul class="manage-table-actions"> %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_reset_all_metadata: - <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ), webapp='community' )}">Reset all repository metadata</a> + <a class="action-button" href="${h.url_for( controller='repository', action='reset_all_metadata', id=trans.security.encode_id( repository.id ) )}">Reset all repository metadata</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -276,7 +276,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp='community' )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -303,7 +303,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp='community' )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/preview_tools_in_changeset.mako --- a/templates/webapps/community/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako @@ -36,15 +36,15 @@

<br/><br/><ul class="manage-table-actions"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></ul>

@@ -79,4 +79,4 @@ </div></div><p/> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )}

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/rate_repository.mako --- a/templates/webapps/community/repository/rate_repository.mako +++ b/templates/webapps/community/repository/rate_repository.mako @@ -72,29 +72,29 @@ <br/><br/><ul class="manage-table-actions"> %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -121,46 +121,46 @@

<br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -50,13 +50,13 @@ %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">Browse or delete repository files</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse or delete repository files</a> %endif </div></ul>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changelog.mako --- a/templates/webapps/community/repository/view_changelog.mako +++ b/templates/webapps/community/repository/view_changelog.mako @@ -45,24 +45,24 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_changeset.mako --- a/templates/webapps/community/repository/view_changeset.mako +++ b/templates/webapps/community/repository/view_changeset.mako @@ -46,27 +46,27 @@ <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, file_type='gz' )}">Download as a .tar.gz file</a>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_repository.mako --- a/templates/webapps/community/repository/view_repository.mako +++ b/templates/webapps/community/repository/view_repository.mako @@ -11,8 +11,8 @@ can_rate = not is_new and trans.user and repository.user != trans.user can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new - can_view_change_log = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -37,44 +37,44 @@

<br/><br/><ul class="manage-table-actions"> - %if webapp == 'community': + %if trans.webapp.name == 'community': %if is_new and can_upload: - <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a></li> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">Rate repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz', webapp=webapp )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2', webapp=webapp )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip', webapp=webapp )}">Download as a zip file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> %endif </div> %endif %else: - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -87,7 +87,7 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><% if changeset_revision == repository.tip: @@ -117,7 +117,7 @@ <div class="form-row"><label>Name:</label> %if can_browse_contents: - <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${repository.name}</a> + <a href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${repository.name}</a> %else: ${repository.name} %endif @@ -132,7 +132,7 @@ <div class="form-row"><label>Revision:</label> %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${revision_label}</a> + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> %else: ${revision_label} %endif @@ -157,7 +157,7 @@ %endif </div></div> -${render_repository_items( repository_metadata_id, metadata, webapp=webapp )} +${render_repository_items( repository_metadata_id, metadata )} %if repository.categories: <p/><div class="toolForm"> @@ -172,12 +172,12 @@ </div></div> %endif -%if webapp == 'community' and trans.user and trans.app.config.smtp_server: +%if trans.webapp.name == 'community' and trans.user and trans.app.config.smtp_server: <p/><div class="toolForm"><div class="toolFormTitle">Notification on update</div><div class="toolFormBody"> - <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), webapp=webapp )}" method="post" > + <form name="receive_email_alerts" id="receive_email_alerts" action="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ) )}" method="post" ><div class="form-row"><label>Receive email alerts:</label> ${alerts_check_box.get_html()} @@ -214,7 +214,7 @@ <div class="toolFormBody"> %if display_reviews: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False, webapp=webapp )}"><label>Hide Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=False )}"><label>Hide Reviews</label></a></div><table class="grid"><thead> @@ -241,7 +241,7 @@ </table> %else: <div class="form-row"> - <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True, webapp=webapp )}"><label>Display Reviews</label></a> + <a href="${h.url_for( controller='repository', action='view_repository', id=trans.security.encode_id( repository.id ), display_reviews=True )}"><label>Display Reviews</label></a></div> %endif </div>

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -12,10 +12,10 @@ can_push = trans.app.security_agent.can_push( trans.user, repository ) can_upload = can_push can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = webapp == 'community' and not is_new + can_browse_contents = trans.webapp.name == 'community' and not is_new can_rate = repository.user != trans.user can_manage = is_admin or repository.user == trans.user - can_view_change_log = webapp == 'community' and not is_new + can_view_change_log = trans.webapp.name == 'community' and not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: @@ -34,43 +34,43 @@

<br/><br/><ul class="manage-table-actions"> - %if webapp == 'galaxy': + %if trans.webapp.name == 'galaxy': <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="tool_shed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %else: %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> %endif %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp=webapp )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp=webapp )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp=webapp )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp=webapp )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -126,7 +126,7 @@ </div><div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_metadata_dict[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision )}">${tool_metadata_dict[ 'name' ]}</a><div style="clear: both"></div></div> %if 'description' in tool_metadata_dict:

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -7,7 +7,7 @@ from galaxy.web.framework.helpers import time_ago from galaxy.tool_shed.encoding_util import tool_shed_encode

- in_tool_shed = webapp == 'community' + in_tool_shed = trans.webapp.name == 'community' is_admin = trans.user_is_admin() is_new = repository.is_new can_manage = is_admin or trans.user == repository.user @@ -34,8 +34,8 @@ %><%inherit file="${inherit(context)}"/>

-<%def name="render_workflow( repository_metadata_id, workflow_name, webapp )"> - <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp ) %> +<%def name="render_workflow( repository_metadata_id, workflow_name )"> + <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def>

@@ -43,32 +43,32 @@ <ul class="manage-table-actions"> %if in_tool_shed: %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ), webapp='community' )}">Upload files to repository</a> + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %endif %if can_manage: <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">Manage repository</a> %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip, webapp='community' )}">View repository</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip )}">View repository</a> %endif %if has_readme: - <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, webapp='community' )}">View README</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_readme', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View README</a> %endif %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">View change log</a> + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> %endif %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ), webapp='community' )}">${browse_label}</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> %endif %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ), webapp='community' )}">Contact repository owner</a> + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> @@ -80,14 +80,14 @@ %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">Import workflow to local Galaxy</a></li> + <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li></div><li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="toolshed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories', webapp=webapp )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools', webapp=webapp )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows', webapp=webapp )}">Search for workflows</a> + <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> + <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div> %endif </ul> @@ -105,4 +105,4 @@ </div><br clear="left"/>

-${render_workflow( repository_metadata_id, workflow_name, webapp )} +${render_workflow( repository_metadata_id, workflow_name )}

diff -r 4bdb9214efd6ec510f2cc6e00224a467d36ba721 -r c3a9547df6f1ea1f7db1f5ae8ba30b6ae113c97c templates/webapps/community/user/manage_email_alerts.mako --- a/templates/webapps/community/user/manage_email_alerts.mako +++ b/templates/webapps/community/user/manage_email_alerts.mako @@ -4,10 +4,10 @@ <br/><br/><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository', webapp=webapp )}">Manage repository alerts</a> + <a class="action-button" href="${h.url_for( controller='repository', action='multi_select_email_alerts', cntrller='repository' )}">Manage repository alerts</a></li><li> - <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository', webapp=webapp )}">User preferences</a> + <a class="action-button" href="${h.url_for( controller='user', action='index', cntrller='repository' )}">User preferences</a></li></ul>

@@ -17,7 +17,7 @@

<div class="toolForm"><div class="toolFormTitle">Email alerts for new repositories</div> - <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts', webapp=webapp )}" method="post" > + <form name="new_repo_alert" id="new_repo_alert" action="${h.url_for( controller='repository', action='manage_email_alerts' )}" method="post" ><div class="form-row"><label>New repository alert:</label> ${new_repo_alert_check_box.get_html()}

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

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