Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.webapps.galaxy.controllers.biostar

"""
Controller for integration with the Biostar application
"""

from galaxy.web.base.controller import BaseUIController, error, web
from galaxy.util import biostar


[docs]class BiostarController( BaseUIController ): """ Provides integration with Biostar through external authentication, see: http://liondb.com/help/x/ """
[docs] @web.expose def biostar_redirect( self, trans, payload=None, biostar_action=None ): """ Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and optional information about a specific tool. """ try: url, payload = biostar.get_biostar_url( trans.app, payload=payload, biostar_action=biostar_action ) except Exception as e: return error( str( e ) ) # Only create/log in biostar user if is registered Galaxy user if trans.user: biostar.create_cookie( trans, trans.app.config.biostar_key_name, trans.app.config.biostar_key, trans.user.email ) if payload: return trans.fill_template( "biostar/post_redirect.mako", post_url=url, form_inputs=payload ) return trans.response.send_redirect( url )
[docs] @web.expose def biostar_tool_tag_redirect( self, trans, tool_id=None ): """ Generate a redirect to a Biostar site using tag for tool. """ # tool_id is required if tool_id is None: return error( "No tool_id provided" ) # Load the tool tool_version_select_field, tools, tool = \ self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) # No matching tool, unlikely if not tool: return error( "No tool found matching '%s'" % tool_id ) # Tool specific information for payload payload = biostar.populate_tag_payload( tool=tool ) # Pass on to standard redirect method return self.biostar_redirect( trans, payload=payload, biostar_action='show_tags' )
[docs] @web.expose def biostar_question_redirect( self, trans, payload=None ): """ Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool. """ # Pass on to standard redirect method return self.biostar_redirect( trans, payload=payload, biostar_action='new_post' )
[docs] @web.expose def biostar_tool_question_redirect( self, trans, tool_id=None ): """ Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool. """ # tool_id is required if tool_id is None: return error( "No tool_id provided" ) # Load the tool tool_version_select_field, tools, tool = \ self.app.toolbox.get_tool_components( tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=True ) # No matching tool, unlikely if not tool: return error( "No tool found matching '%s'" % tool_id ) # Tool specific information for payload payload = biostar.populate_tool_payload( tool=tool ) # Pass on to regular question method return self.biostar_question_redirect( trans, payload )
[docs] @web.expose def biostar_tool_bug_report( self, trans, hda=None, email=None, message=None ): """ Generate a redirect to a Biostar site using external authentication to pass Galaxy user information and information about a specific tool error. """ try: error_reporter = biostar.BiostarErrorReporter( hda, trans.app ) payload = error_reporter.send_report( trans.user, email=email, message=message ) except Exception as e: return error( str( e ) ) return self.biostar_redirect( trans, payload=payload, biostar_action='new_post' )
[docs] @web.expose def biostar_logout( self, trans ): """ Log out of biostar """ try: url = biostar.biostar_log_out( trans ) except Exception as e: return error( str( e ) ) if url: return trans.response.send_redirect( url ) return error( "Could not determine Biostar logout URL." )