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Source code for galaxy.webapps.galaxy.controllers.tool_runner

"""
Controller handles external tool related requests
"""
import logging

from markupsafe import escape

import galaxy.util
from galaxy import web
from galaxy.tools import DataSourceTool
from galaxy.web import error, url_for
from galaxy.web.base.controller import BaseUIController

log = logging.getLogger( __name__ )


[docs]class ToolRunner( BaseUIController ): # Hack to get biomart to work, ideally, we could pass tool_id to biomart and receive it back
[docs] @web.expose def biomart(self, trans, tool_id='biomart', **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd)
# test to get hapmap to work, ideally, we could pass tool_id to hapmap biomart and receive it back
[docs] @web.expose def hapmapmart(self, trans, tool_id='hapmapmart', **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd)
[docs] @web.expose def default(self, trans, tool_id=None, **kwd): """Catches the tool id and redirects as needed""" return self.index(trans, tool_id=tool_id, **kwd)
def __get_tool( self, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ): tool_version_select_field, tools, tool = self.get_toolbox().get_tool_components( tool_id, tool_version, get_loaded_tools_by_lineage, set_selected ) return tool
[docs] @web.expose def index( self, trans, tool_id=None, from_noframe=None, **kwd ): def __tool_404__(): log.error( 'index called with tool id \'%s\' but no such tool exists', tool_id ) trans.log_event( 'Tool id \'%s\' does not exist' % tool_id ) trans.response.status = 404 return trans.show_error_message('Tool \'%s\' does not exist.' % ( escape(tool_id) )) # tool id not available, redirect to main page if tool_id is None: return trans.response.send_redirect( url_for( controller='root', action='welcome' ) ) tool = self.__get_tool( tool_id ) # tool id is not matching, display an error if not tool: return __tool_404__() if tool.require_login and not trans.user: redirect = url_for( controller='tool_runner', action='index', tool_id=tool_id, **kwd ) return trans.response.send_redirect( url_for( controller='user', action='login', cntrller='user', status='info', message='You must be logged in to use this tool.', redirect=redirect ) ) if not tool.allow_user_access( trans.user ): return __tool_404__() if tool.tool_type == 'default': return trans.response.send_redirect( url_for( controller='root', tool_id=tool_id ) ) # execute tool without displaying form (used for datasource tools) params = galaxy.util.Params( kwd, sanitize=False ) # do param translation here, used by datasource tools if tool.input_translator: tool.input_translator.translate( params ) if 'runtool_btn' not in params.__dict__ and 'URL' not in params.__dict__: error( 'Tool execution through the `tool_runner` requires a `runtool_btn` flag or `URL` parameter.' ) # We may be visiting Galaxy for the first time ( e.g., sending data from UCSC ), # so make sure to create a new history if we've never had one before. history = tool.get_default_history_by_trans( trans, create=True ) try: vars = tool.handle_input( trans, params.__dict__, history=history ) except Exception as e: error( str( e ) ) if len( params ) > 0: trans.log_event( 'Tool params: %s' % ( str( params ) ), tool_id=tool_id ) return trans.fill_template( 'root/tool_runner.mako', **vars )
[docs] @web.expose def rerun( self, trans, id=None, job_id=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in. """ if job_id is None: if not id: error( "'id' parameter is required" ) try: id = int( id ) except: # it's not an un-encoded id, try to parse as encoded try: id = trans.security.decode_id( id ) except: error( "Invalid value for 'id' parameter" ) # Get the dataset object data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) # only allow rerunning if user is allowed access to the dataset. if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): error( "You are not allowed to access this dataset" ) # Get the associated job, if any. job = data.creating_job if job: job_id = trans.security.encode_id( job.id ) else: raise Exception("Failed to get job information for dataset hid %d" % data.hid) return trans.response.send_redirect( url_for( controller="root", job_id=job_id ) )
[docs] @web.expose def data_source_redirect( self, trans, tool_id=None ): """ Redirects a user accessing a Data Source tool to its target action link. This method will subvert mix-mode content blocking in several browsers when accessing non-https data_source tools from an https galaxy server. Tested as working on Safari 7.0 and FireFox 26 Subverting did not work on Chrome 31 """ if tool_id is None: return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) tool = self.__get_tool( tool_id ) # No tool matching the tool id, display an error (shouldn't happen) if not tool: log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) trans.response.status = 404 return trans.show_error_message("Tool '%s' does not exist." % ( escape(tool_id) )) if isinstance( tool, DataSourceTool ): link = url_for( tool.action, **tool.get_static_param_values( trans ) ) else: link = url_for( controller='tool_runner', tool_id=tool.id ) return trans.response.send_redirect( link )
[docs] @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: return trans.show_error_message( "Required URL for redirection missing" ) trans.log_event( "Redirecting to: %s" % redirect_url ) return trans.fill_template( 'root/redirect.mako', redirect_url=redirect_url )