1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1fae66a5a9b6/ Changeset: 1fae66a5a9b6 User: greg Date: 2013-06-19 18:12:59 Summary: Eliminate the use of util.params from all methods in Galaxy's admin_toolshed controller. Affected #: 1 file diff -r 170dd4c157b8b5e010804ba4a1ef3b5da08fa49d -r 1fae66a5a9b668ebec6de47906ca89b438f38340 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 @@ -73,9 +73,8 @@ @web.expose @web.require_admin def browse_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, @@ -154,9 +153,8 @@ @web.expose @web.require_admin def browse_tool_dependency( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) tool_dependency = tool_dependency_util.get_tool_dependency( trans, kwd[ 'id' ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " @@ -186,9 +184,8 @@ @web.expose @web.require_admin def browse_tool_sheds( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', message=message, status='error' ) @@ -197,8 +194,7 @@ @web.require_admin def check_for_updates( self, trans, **kwd ): """Send a request to the relevant tool shed to see if there are any updates.""" - params = util.Params( kwd ) - repository_id = params.get( 'id', None ) + repository_id = kwd.get( 'id', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, repository.tool_shed ) url = suc.url_join( tool_shed_url, @@ -215,10 +211,9 @@ is because it becomes a bit complex to determine if other installed repositories include tools that require the same entry. For now we'll never delete entries from config.shed_tool_data_table_config, but we may choose to do so in the future if it becomes necessary. """ - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - remove_from_disk = params.get( 'remove_from_disk', '' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + remove_from_disk = kwd.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) @@ -229,7 +224,7 @@ else: repository_install_dir = None errors = '' - if params.get( 'deactivate_or_uninstall_repository_button', False ): + if kwd.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. tool_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) @@ -387,9 +382,8 @@ @web.require_admin def import_workflow( self, trans, workflow_name, repository_id, **kwd ): """Import a workflow contained in an installed tool shed repository into the Galaxy instance.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) @@ -486,12 +480,11 @@ @web.expose @web.require_admin def install_tool_dependencies( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - tool_dependency_ids = util.listify( params.get( 'tool_dependency_ids', None ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) if not tool_dependency_ids: - tool_dependency_ids = util.listify( params.get( 'id', None ) ) + tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) @@ -554,9 +547,8 @@ @web.expose @web.require_admin def manage_repository( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] operation = kwd.get( 'operation', None ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) @@ -574,7 +566,7 @@ 'repository/install_repositories_by_revision?name=%s&owner=%s&changeset_revisions=%s&galaxy_url=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision, ( web.url_for( '/', qualified=True ) ) ) ) return trans.response.send_redirect( url ) - description = util.restore_text( params.get( 'description', repository.description ) ) + description = kwd.get( 'description', repository.description ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, repository.name ) ) @@ -588,7 +580,7 @@ elif repository.can_install: message = "This repository is not installed. You can install it by choosing <b>Install</b> from the <b>Repository Actions</b> menu." status = "error" - elif params.get( 'edit_repository_button', False ): + elif kwd.get( 'edit_repository_button', False ): if description != repository.description: repository.description = description trans.sa_session.add( repository ) @@ -611,13 +603,12 @@ @web.expose @web.require_admin def manage_repositories( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - tsrid = params.get( 'tool_shed_repository_id', None ) - tsridslist = util.listify( params.get( 'tool_shed_repository_ids', None ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + tsrid = kwd.get( 'tool_shed_repository_id', None ) + tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) ) if not tsridslist: - tsridslist = util.listify( params.get( 'id', None ) ) + tsridslist = util.listify( kwd.get( 'id', None ) ) if tsrid and tsrid not in tsridslist: tsridslist.append( tsrid ) if 'operation' in kwd: @@ -650,7 +641,7 @@ kwd[ 'message' ] = 'All selected tool shed repositories are already uninstalled.' kwd[ 'status' ] = 'error' elif operation == "install": - reinstalling = util.string_as_bool( params.get( 'reinstalling', False ) ) + reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) ) encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] @@ -686,9 +677,8 @@ @web.expose @web.require_admin def manage_tool_dependencies( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) # We need a tool_shed_repository, so get it from one of the tool_dependencies. tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) @@ -766,11 +756,10 @@ @web.expose @web.require_admin def monitor_repository_installation( self, trans, **kwd ): - params = util.Params( kwd ) - tsrid = params.get( 'tool_shed_repository_id', None ) - tsridslist = util.listify( params.get( 'tool_shed_repository_ids', None ) ) + tsrid = kwd.get( 'tool_shed_repository_id', None ) + tsridslist = util.listify( kwd.get( 'tool_shed_repository_ids', None ) ) if not tsridslist: - tsridslist = util.listify( params.get( 'id', None ) ) + tsridslist = util.listify( kwd.get( 'id', None ) ) if tsrid and tsrid not in tsridslist: tsridslist.append( tsrid ) if not tsridslist: @@ -1298,7 +1287,7 @@ if 'reset_metadata_on_selected_repositories_button' in kwd: message, status = metadata_util.reset_metadata_on_selected_repositories( trans, **kwd ) else: - message = util.restore_text( kwd.get( 'message', '' ) ) + message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repositories_select_field = suc.build_repository_ids_select_field( trans ) return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', @@ -1431,12 +1420,11 @@ @web.expose @web.require_admin def uninstall_tool_dependencies( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - tool_dependency_ids = util.listify( params.get( 'tool_dependency_ids', None ) ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + tool_dependency_ids = util.listify( kwd.get( 'tool_dependency_ids', None ) ) if not tool_dependency_ids: - tool_dependency_ids = util.listify( params.get( 'id', None ) ) + tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) @@ -1476,15 +1464,14 @@ @web.require_admin def update_to_changeset_revision( self, trans, **kwd ): """Update a cloned repository to the latest revision possible.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) tool_shed_url = kwd[ 'tool_shed_url' ] - name = params.get( 'name', None ) - owner = params.get( 'owner', None ) - changeset_revision = params.get( 'changeset_revision', None ) - latest_changeset_revision = params.get( 'latest_changeset_revision', None ) - latest_ctx_rev = params.get( 'latest_ctx_rev', None ) + name = kwd.get( 'name', None ) + owner = kwd.get( 'owner', None ) + changeset_revision = kwd.get( 'changeset_revision', None ) + latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) + latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: @@ -1568,9 +1555,8 @@ @web.expose @web.require_admin def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) @@ -1601,9 +1587,8 @@ @web.require_admin def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ): """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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