commit/galaxy-central: carlfeberhard: controllers/root: remove methods my_data, dataset_state, dataset_code; add documentation; clean imports
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1829e8c8f8bb/ Changeset: 1829e8c8f8bb User: carlfeberhard Date: 2013-04-05 02:08:58 Summary: controllers/root: remove methods my_data, dataset_state, dataset_code; add documentation; clean imports Affected #: 1 file diff -r a64e43d6d4d52f17b53a4ceac07d48105defdc9c -r 1829e8c8f8bb632b8fd1c9224dd3da6849246568 lib/galaxy/webapps/galaxy/controllers/root.py --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -3,25 +3,30 @@ """ import os import urllib -from cgi import escape, FieldStorage +import cgi -from galaxy import util, datatypes, jobs, web, util -from galaxy.web.base.controller import * +from galaxy.web.base.controller import BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin +from galaxy.model.item_attrs import UsesAnnotations +from galaxy import util, web from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.orm import * -from galaxy.model.item_attrs import UsesAnnotations +#from galaxy.model.orm import * import logging log = logging.getLogger( __name__ ) class RootController( BaseUIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesAnnotations ): + """Controller class that maps to the url root of Galaxy (i.e. '/').""" @web.expose def default(self, trans, target1=None, target2=None, **kwd): + """Called on any url that does not match a controller method. + """ return 'This link may not be followed from within Galaxy.' @web.expose def index(self, trans, id=None, tool_id=None, mode=None, workflow_id=None, m_c=None, m_a=None, **kwd): + """Called on the root url to display the main Galaxy page. + """ return trans.fill_template( "root/index.mako", tool_id=tool_id, workflow_id=workflow_id, @@ -31,6 +36,8 @@ ## ---- Tool related ----------------------------------------------------- @web.expose def tool_menu( self, trans ): + """Renders the tool panel of the Galaxy UI. + """ if trans.app.config.require_login and not trans.user: return trans.fill_template( '/no_access.mako', message='Please log in to access Galaxy tools.' ) toolbox = self.get_toolbox() @@ -51,6 +58,11 @@ @web.json def tool_search( self, trans, **kwd ): + """Searches the tool database and returns data for any tool + whose text matches the query. + + Data are returned in JSON format. + """ query = kwd.get( 'query', '' ) tags = util.listify( kwd.get( 'tags[]', [] ) ) trans.log_action( trans.get_user(), "tool_search.search", "", { "query" : query, "tags" : tags } ) @@ -77,11 +89,13 @@ @web.expose def tool_help( self, trans, id ): - """Return help page for tool identified by 'id' if available""" + """Return help page for tool identified by 'id' if available + """ toolbox = self.get_toolbox() tool = toolbox.get_tool( id ) yield "<html><body>" if not tool: + #TODO: arent tool ids strings now? yield "Unknown tool id '%d'" % id elif tool.help: yield tool.help @@ -91,13 +105,6 @@ ## ---- Root history display --------------------------------------------- @web.expose - def my_data( self, trans, **kwd ): - """ - Display user's data. - """ - return trans.fill_template_mako( "/my_data.mako" ) - - @web.expose def history( self, trans, as_xml=False, show_deleted=None, show_hidden=None, hda_id=None, **kwd ): """Display the current history, creating a new history if necessary. @@ -167,38 +174,13 @@ ## ---- Dataset display / editing ---------------------------------------- @web.expose - def dataset_state ( self, trans, id=None, stamp=None ): - if id is not None: - try: - data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) - except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) - trans.response.headers['X-Dataset-State'] = data.state - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - return data.state - else: - return trans.show_error_message( "Must specify a dataset id.") + def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): + """Returns data directly into the browser. - @web.expose - def dataset_code( self, trans, id=None, hid=None, stamp=None ): - if id is not None: - try: - data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) - except: - return trans.show_error_message( "Unable to check dataset %s." %str( id ) ) - trans.response.headers['Pragma'] = 'no-cache' - trans.response.headers['Expires'] = '0' - return trans.fill_template("root/history_item.mako", data=data, hid=hid) - else: - return trans.show_error_message( "Must specify a dataset id.") - - @web.expose - def display( self, trans, id=None, hid=None, tofile=None, toext=".txt", **kwd ): + Sets the mime-type according to the extension. """ - Returns data directly into the browser. - Sets the mime-type according to the extension - """ + #TODO: unused? + #TODO: unencoded id if hid is not None: try: hid = int( hid ) @@ -241,9 +223,9 @@ @web.expose def display_child(self, trans, parent_id=None, designation=None, tofile=None, toext=".txt"): + """Returns child data directly into the browser, based upon parent_id and designation. """ - Returns child data directly into the browser, based upon parent_id and designation. - """ + #TODO: unencoded id try: data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( parent_id ) if data: @@ -260,7 +242,9 @@ @web.expose def display_as( self, trans, id=None, display_app=None, **kwd ): - """Returns a file in a format that can successfully be displayed in display_app""" + """Returns a file in a format that can successfully be displayed in display_app. + """ + #TODO: unencoded id data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) authz_method = 'rbac' if 'authz_method' in kwd: @@ -283,7 +267,10 @@ @web.expose def peek(self, trans, id=None): - """Returns a 'peek' at the data""" + """Returns a 'peek' at the data. + """ + #TODO: unused? + #TODO: unencoded id data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) if data: yield "<html><body><pre>" @@ -295,20 +282,23 @@ ## ---- History management ----------------------------------------------- @web.expose def history_options( self, trans ): - """Displays a list of history related actions""" + """Displays a list of history related actions. + """ return trans.fill_template( "/history/options.mako", user=trans.get_user(), history=trans.get_history( create=True ) ) @web.expose def history_delete( self, trans, id ): + """Backward compatibility with check_galaxy script. """ - Backward compatibility with check_galaxy script. - """ + #TODO: unused? return trans.webapp.controllers['history'].list( trans, id, operation='delete' ) @web.expose def clear_history( self, trans ): - """Clears the history for a user""" + """Clears the history for a user. + """ + #TODO: unused? (seems to only be used in TwillTestCase) history = trans.get_history() for dataset in history.datasets: dataset.deleted = True @@ -319,6 +309,8 @@ @web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): + #TODO: unused? + #TODO: unencoded id msg = "" user = trans.get_user() user_history = trans.get_history() @@ -375,13 +367,19 @@ @web.expose def history_new( self, trans, name=None ): + """Create a new history with the given name + and refresh the history panel. + """ trans.new_history( name=name ) trans.log_event( "Created new History, id: %s." % str(trans.history.id) ) return trans.show_message( "New history created", refresh_frames=['history'] ) @web.expose - def history_add_to( self, trans, history_id=None, file_data=None, name="Data Added to History", info=None, ext="txt", dbkey="?", copy_access_from=None, **kwd ): - """Adds a POSTed file to a History""" + def history_add_to( self, trans, history_id=None, file_data=None, + name="Data Added to History", info=None, ext="txt", dbkey="?", copy_access_from=None, **kwd ): + """Adds a POSTed file to a History. + """ + #TODO: unencoded id try: history = trans.sa_session.query( trans.app.model.History ).get( history_id ) data = trans.app.model.HistoryDatasetAssociation( name=name, @@ -414,12 +412,16 @@ trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id)) return trans.show_ok_message( "Dataset " + str(data.hid) + " added to history " + str(history_id) + "." ) except Exception, e: - trans.log_event( "Failed to add dataset to history: %s" % ( e ) ) + msg = "Failed to add dataset to history: %s" % ( e ) + log.error( msg ) + trans.log_event( msg ) return trans.show_error_message("Adding File to History has Failed") @web.expose def history_set_default_permissions( self, trans, id=None, **kwd ): - """Sets the permissions on a history""" + """Sets the permissions on a history. + """ + #TODO: unencoded id if trans.user: if 'update_roles_button' in kwd: history = None @@ -443,7 +445,8 @@ permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles dataset = 'dataset' in kwd bypass_manage_permission = 'bypass_manage_permission' in kwd - trans.app.security_agent.history_set_default_permissions( history, permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission ) + trans.app.security_agent.history_set_default_permissions( history, permissions, + dataset=dataset, bypass_manage_permission=bypass_manage_permission ) return trans.show_ok_message( 'Default history permissions have been changed.' ) return trans.fill_template( 'history/permissions.mako' ) else: @@ -452,7 +455,10 @@ @web.expose def dataset_make_primary( self, trans, id=None): - """Copies a dataset and makes primary""" + """Copies a dataset and makes primary. + """ + #TODO: unused? + #TODO: unencoded id try: old_data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) new_data = old_data.copy() @@ -477,23 +483,25 @@ # ---- Debug methods ---------------------------------------------------- @web.expose def echo(self, trans, **kwd): - """Echos parameters (debugging)""" + """Echos parameters (debugging). + """ rval = "" for k in trans.request.headers: rval += "%s: %s <br/>" % ( k, trans.request.headers[k] ) for k in kwd: rval += "%s: %s <br/>" % ( k, kwd[k] ) - if isinstance( kwd[k], FieldStorage ): + if isinstance( kwd[k], cgi.FieldStorage ): rval += "-> %s" % kwd[k].file.read() return rval @web.json def echo_json( self, trans, **kwd ): - """Echos parameters as JSON (debugging) + """Echos parameters as JSON (debugging). Attempts to parse values passed as boolean, float, then int. Defaults to string. Non-recursive (will not parse lists). """ + #TODO: use simplejson or json rval = {} for k in kwd: rval[ k ] = kwd[k] @@ -508,4 +516,6 @@ @web.expose def generate_error( self, trans ): + """Raises an exception (debugging). + """ raise Exception( "Fake error!" ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
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