def history_set_default_permissions( self, trans, id=None, **kwd ): """Sets the permissions on a history. """ # TODO: unencoded id if trans.user: if 'update_roles_button' in kwd: history = None if id: try: id = int( id ) except: id = None if id: history = trans.sa_session.query( trans.app.model.History ).get( id ) if not history: # If we haven't retrieved a history, use the current one history = trans.get_history() p = Params( kwd ) permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): in_roles = p.get( k + '_in', [] ) if not isinstance( in_roles, list ): in_roles = [ in_roles ] in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ] 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 ) return trans.show_ok_message( 'Default history permissions have been changed.' ) return trans.fill_template( 'history/permissions.mako' ) else: # user not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change a history's default permissions." )
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. NOTE: No longer accepts "id" or "template" options for security reasons. """ if as_xml: return self.history_as_xml( trans, show_deleted=string_as_bool( show_deleted ), show_hidden=string_as_bool( show_hidden ) ) # get all datasets server-side, client-side will get flags and render appropriately show_deleted = string_as_bool_or_none( show_deleted ) show_purged = show_deleted show_hidden = string_as_bool_or_none( show_hidden ) params = Params( kwd ) message = params.get( 'message', '' ) #TODO: ugh... message = message if message != 'None' else '' status = params.get( 'status', 'done' ) if trans.app.config.require_login and not trans.user: return trans.fill_template( '/no_access.mako', message = 'Please log in to access Galaxy histories.' ) def err_msg( where=None ): where = where if where else 'getting the history data from the server' err_msg = ( 'An error occurred %s. ' + 'Please contact a Galaxy administrator if the problem persists.' ) %( where ) return err_msg, 'error' history_dictionary = {} hda_dictionaries = [] try: history = trans.get_history( create=True ) hdas = self.get_history_datasets( trans, history, show_deleted=True, show_hidden=True, show_purged=True ) for hda in hdas: try: hda_dictionaries.append( self.get_hda_dict( trans, hda ) ) except Exception, exc: # don't fail entire list if hda err's, record and move on log.error( 'Error bootstrapping hda %d: %s', hda.id, str( exc ), exc_info=True ) hda_dictionaries.append( self.get_hda_dict_with_error( trans, hda, str( exc ) ) ) # re-use the hdas above to get the history data... history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries )
def index(self, trans, tool_id=None, data_secret=None, **kwd): """Manages ascynchronous connections""" if tool_id is None: return "tool_id argument is required" tool_id = str(tool_id) # redirect to main when getting no parameters if not kwd: return trans.response.send_redirect("/index") history = trans.get_history(create=True) params = Params(kwd, sanitize=False) STATUS = params.STATUS URL = params.URL data_id = params.data_id log.debug('async dataid -> %s' % data_id) trans.log_event('Async dataid -> %s' % str(data_id)) # initialize the tool toolbox = self.get_toolbox() tool = toolbox.get_tool(tool_id) if not tool: return "Tool with id %s not found" % tool_id # # we have an incoming data_id # if data_id: if not URL: return "No URL parameter was submitted for data %s" % data_id data = trans.sa_session.query( trans.model.HistoryDatasetAssociation).get(data_id) if not data: return "Data %s does not exist or has already been deleted" % data_id if STATUS == 'OK': key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) if key != data_secret: return "You do not have permission to alter data %s." % data_id # push the job into the queue data.state = data.blurb = data.states.RUNNING log.debug('executing tool %s' % tool.id) trans.log_event('Async executing tool %s' % tool.id, tool_id=tool.id) galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key) galaxy_url = params.get("GALAXY_URL", galaxy_url) params = dict(URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext) # Assume there is exactly one output file possible params[tool.outputs.keys()[0]] = data.id tool.execute(trans, incoming=params) else: log.debug('async error -> %s' % STATUS) trans.log_event('Async error -> %s' % STATUS) data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) else: # # no data_id must be parameter submission # if params.data_type: GALAXY_TYPE = params.data_type elif params.galaxyFileFormat == 'wig': # this is an undocumented legacy special case GALAXY_TYPE = 'wig' else: GALAXY_TYPE = params.GALAXY_TYPE or tool.outputs.values( )[0].format GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or '' GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?' # data = datatypes.factory(ext=GALAXY_TYPE)() # data.ext = GALAXY_TYPE # data.name = GALAXY_NAME # data.info = GALAXY_INFO # data.dbkey = GALAXY_BUILD # data.state = jobs.JOB_OK # history.datasets.add_dataset( data ) data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE) trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history)) data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO trans.sa_session.add( data ) # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW open(data.file_name, 'wb').close() # create the file trans.history.add_dataset(data, genome_build=GALAXY_BUILD) trans.sa_session.add(trans.history) trans.sa_session.flush() trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id), tool_id=tool_id) try: key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key) params.update({'GALAXY_URL': galaxy_url}) params.update({'data_id': data.id}) # Use provided URL or fallback to tool action url = URL or tool.action # Does url already have query params? if '?' in url: url_join_char = '&' else: url_join_char = '?' url = "%s%s%s" % (url, url_join_char, urllib.urlencode(params.flatten())) log.debug("connecting to -> %s" % url) trans.log_event("Async connecting to -> %s" % url) text = urllib.urlopen(url).read(-1) text = text.strip() if not text.endswith('OK'): raise Exception(text) data.state = data.blurb = data.states.RUNNING except Exception, e: data.info = str(e) data.state = data.blurb = data.states.ERROR trans.sa_session.flush()
def index(self, trans, tool_id=None, data_secret=None, **kwd): """Manages ascynchronous connections""" if tool_id is None: return "tool_id argument is required" tool_id=str(tool_id) #log.debug('async params -> %s' % kwd) # redirect to main when getting no parameters if not kwd: return trans.response.send_redirect( "/index" ) history = trans.get_history( create=True ) params = Params(kwd, sanitize=False) STATUS = params.STATUS URL = params.URL data_id = params.data_id log.debug('async dataid -> %s' % data_id) trans.log_event( 'Async dataid -> %s' % str(data_id) ) # initialize the tool toolbox = self.get_toolbox() tool = toolbox.get_tool( tool_id ) if not tool: return "Tool with id %s not found" % tool_id # # we have an incoming data_id # if data_id: if not URL: return "No URL parameter was submitted for data %s" % data_id data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( data_id ) if not data: return "Data %s does not exist or has already been deleted" % data_id if STATUS == 'OK': key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) ) if key != data_secret: return "You do not have permission to alter data %s." % data_id # push the job into the queue data.state = data.blurb = data.states.RUNNING log.debug('executing tool %s' % tool.id) trans.log_event( 'Async executing tool %s' % tool.id, tool_id=tool.id ) galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) galaxy_url = params.get("GALAXY_URL",galaxy_url) params = dict( URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext ) # Assume there is exactly one output file possible params[tool.outputs.keys()[0]] = data.id tool.execute( trans, incoming=params ) else: log.debug('async error -> %s' % STATUS) trans.log_event( 'Async error -> %s' % STATUS ) data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) else: # # no data_id must be parameter submission # if params.data_type: GALAXY_TYPE = params.data_type elif params.galaxyFileFormat == 'wig': #this is an undocumented legacy special case GALAXY_TYPE = 'wig' else: GALAXY_TYPE = params.GALAXY_TYPE or tool.outputs.values()[0].format GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or '' GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?' #data = datatypes.factory(ext=GALAXY_TYPE)() #data.ext = GALAXY_TYPE #data.name = GALAXY_NAME #data.info = GALAXY_INFO #data.dbkey = GALAXY_BUILD #data.state = jobs.JOB_OK #history.datasets.add_dataset( data ) data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE ) trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history ) ) data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO trans.sa_session.add( data ) #Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) trans.sa_session.add( trans.history ) trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) try: key = hmac_new( trans.app.config.tool_secret, "%d:%d" % ( data.id, data.history_id ) ) galaxy_url = trans.request.base + '/async/%s/%s/%s' % ( tool_id, data.id, key ) params.update( { 'GALAXY_URL' :galaxy_url } ) params.update( { 'data_id' :data.id } ) url = tool.action + '?' + urllib.urlencode( params.flatten() ) log.debug("connecting to -> %s" % url) trans.log_event( "Async connecting to -> %s" % url ) text = urllib.urlopen(url).read(-1) text = text.strip() if not text.endswith('OK'): raise Exception, text data.state = data.blurb = data.states.RUNNING except Exception, e: data.info = str(e) data.state = data.blurb = data.states.ERROR trans.sa_session.flush()
def index(self, trans, tool_id=None, data_secret=None, **kwd): """Manages ascynchronous connections""" if tool_id is None: return "tool_id argument is required" tool_id = str(tool_id) # redirect to main when getting no parameters if not kwd: return trans.response.send_redirect("/index") params = Params(kwd, sanitize=False) STATUS = params.STATUS URL = params.URL data_id = params.data_id log.debug('async dataid -> %s' % data_id) trans.log_event('Async dataid -> %s' % str(data_id)) # initialize the tool toolbox = self.get_toolbox() tool = toolbox.get_tool(tool_id) if not tool: return "Tool with id %s not found" % tool_id # # we have an incoming data_id # if data_id: if not URL: return "No URL parameter was submitted for data %s" % data_id data = trans.sa_session.query( trans.model.HistoryDatasetAssociation).get(data_id) if not data: return "Data %s does not exist or has already been deleted" % data_id if STATUS == 'OK': key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) if key != data_secret: return "You do not have permission to alter data %s." % data_id # push the job into the queue data.state = data.blurb = data.states.RUNNING log.debug('executing tool %s' % tool.id) trans.log_event('Async executing tool %s' % tool.id, tool_id=tool.id) galaxy_url = trans.request.base + f'/async/{tool_id}/{data.id}/{key}' galaxy_url = params.get("GALAXY_URL", galaxy_url) params = dict(URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext) # Assume there is exactly one output file possible TOOL_OUTPUT_TYPE = None for key, obj in tool.outputs.items(): try: TOOL_OUTPUT_TYPE = obj.format params[key] = data.id break except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption continue if TOOL_OUTPUT_TYPE is None: raise Exception("Error: ToolOutput object not found") original_history = trans.sa_session.query( trans.app.model.History).get(data.history_id) tool.execute(trans, incoming=params, history=original_history) else: log.debug('async error -> %s' % STATUS) trans.log_event('Async error -> %s' % STATUS) data.state = data.blurb = "error" data.info = "Error -> %s" % STATUS trans.sa_session.flush() return f"Data {data_id} with status {STATUS} received. OK" else: # # no data_id must be parameter submission # GALAXY_TYPE = None if params.data_type: GALAXY_TYPE = params.data_type elif params.galaxyFileFormat == 'wig': # this is an undocumented legacy special case GALAXY_TYPE = 'wig' elif params.GALAXY_TYPE: GALAXY_TYPE = params.GALAXY_TYPE else: # Assume there is exactly one output outputs_count = 0 for obj in tool.outputs.values(): try: GALAXY_TYPE = obj.format outputs_count += 1 except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption # a collection object does not have the 'format' attribute, so it will throw an exception continue if outputs_count > 1: raise Exception( "Error: the tool should have just one output") if GALAXY_TYPE is None: raise Exception("Error: ToolOutput object not found") GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or '' GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?' # data = datatypes.factory(ext=GALAXY_TYPE)() # data.ext = GALAXY_TYPE # data.name = GALAXY_NAME # data.info = GALAXY_INFO # data.dbkey = GALAXY_BUILD # data.state = jobs.JOB_OK # history.datasets.add_dataset( data ) data = trans.app.model.HistoryDatasetAssociation( create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE) trans.app.security_agent.set_all_dataset_permissions( data.dataset, trans.app.security_agent.history_get_default_permissions( trans.history)) data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO trans.sa_session.add( data ) # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW trans.history.add_dataset(data, genome_build=GALAXY_BUILD) trans.sa_session.add(trans.history) trans.sa_session.flush() # Need to explicitly create the file data.dataset.object_store.create(data) trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id), tool_id=tool_id) try: key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) galaxy_url = trans.request.base + f'/async/{tool_id}/{data.id}/{key}' params.update({'GALAXY_URL': galaxy_url}) params.update({'data_id': data.id}) # Use provided URL or fallback to tool action url = URL or tool.action # Does url already have query params? if '?' in url: url_join_char = '&' else: url_join_char = '?' url = "{}{}{}".format(url, url_join_char, urlencode(params.flatten())) log.debug("connecting to -> %s" % url) trans.log_event("Async connecting to -> %s" % url) text = requests.get(url).text.strip() if not text.endswith('OK'): raise Exception(text) data.state = data.blurb = data.states.RUNNING except Exception as e: data.info = unicodify(e) data.state = data.blurb = data.states.ERROR trans.sa_session.flush() return trans.fill_template('root/tool_runner.mako', out_data={}, num_jobs=1, job_errors=[])
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. NOTE: No longer accepts "id" or "template" options for security reasons. """ if as_xml: return self.history_as_xml( trans, show_deleted=string_as_bool(show_deleted), show_hidden=string_as_bool(show_hidden)) # get all datasets server-side, client-side will get flags and render appropriately show_deleted = string_as_bool_or_none(show_deleted) show_purged = show_deleted show_hidden = string_as_bool_or_none(show_hidden) params = Params(kwd) message = params.get('message', '') #TODO: ugh... message = message if message != 'None' else '' status = params.get('status', 'done') if trans.app.config.require_login and not trans.user: return trans.fill_template( '/no_access.mako', message='Please log in to access Galaxy histories.') def err_msg(where=None): where = where if where else 'getting the history data from the server' err_msg = ( 'An error occurred %s. ' + 'Please contact a Galaxy administrator if the problem persists.' ) % (where) return err_msg, 'error' history_dictionary = {} hda_dictionaries = [] try: history = trans.get_history(create=True) hdas = self.get_history_datasets(trans, history, show_deleted=True, show_hidden=True, show_purged=True) for hda in hdas: try: hda_dictionaries.append(self.get_hda_dict(trans, hda)) except Exception, exc: # don't fail entire list if hda err's, record and move on log.error('Error bootstrapping hda %d: %s', hda.id, str(exc), exc_info=True) hda_dictionaries.append( self.get_hda_dict_with_error(trans, hda, str(exc))) # re-use the hdas above to get the history data... history_dictionary = self.get_history_dict( trans, history, hda_dictionaries=hda_dictionaries)
def index(self, trans, tool_id=None, data_secret=None, **kwd): """Manages ascynchronous connections""" if tool_id is None: return "tool_id argument is required" tool_id = str(tool_id) # redirect to main when getting no parameters if not kwd: return trans.response.send_redirect("/index") params = Params(kwd, sanitize=False) STATUS = params.STATUS URL = params.URL data_id = params.data_id log.debug('async dataid -> %s' % data_id) trans.log_event('Async dataid -> %s' % str(data_id)) # initialize the tool toolbox = self.get_toolbox() tool = toolbox.get_tool(tool_id) if not tool: return "Tool with id %s not found" % tool_id # # we have an incoming data_id # if data_id: if not URL: return "No URL parameter was submitted for data %s" % data_id data = trans.sa_session.query(trans.model.HistoryDatasetAssociation).get(data_id) if not data: return "Data %s does not exist or has already been deleted" % data_id if STATUS == 'OK': key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) if key != data_secret: return "You do not have permission to alter data %s." % data_id # push the job into the queue data.state = data.blurb = data.states.RUNNING log.debug('executing tool %s' % tool.id) trans.log_event('Async executing tool %s' % tool.id, tool_id=tool.id) galaxy_url = trans.request.base + '/async/%s/%s/%s' % (tool_id, data.id, key) galaxy_url = params.get("GALAXY_URL", galaxy_url) params = dict(URL=URL, GALAXY_URL=galaxy_url, name=data.name, info=data.info, dbkey=data.dbkey, data_type=data.ext) # Assume there is exactly one output file possible TOOL_OUTPUT_TYPE = None for key, obj in tool.outputs.items(): try: TOOL_OUTPUT_TYPE = obj.format params[key] = data.id break except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption continue if TOOL_OUTPUT_TYPE is None: raise Exception("Error: ToolOutput object not found") original_history = trans.sa_session.query(trans.app.model.History).get(data.history_id) tool.execute(trans, incoming=params, history=original_history) else: log.debug('async error -> %s' % STATUS) trans.log_event('Async error -> %s' % STATUS) data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) else: # # no data_id must be parameter submission # GALAXY_TYPE = None if params.data_type: GALAXY_TYPE = params.data_type elif params.galaxyFileFormat == 'wig': # this is an undocumented legacy special case GALAXY_TYPE = 'wig' elif params.GALAXY_TYPE: GALAXY_TYPE = params.GALAXY_TYPE else: # Assume there is exactly one output outputs_count = 0 for obj in tool.outputs.values(): try: GALAXY_TYPE = obj.format outputs_count += 1 except Exception: # exclude outputs different from ToolOutput (e.g. collections) from the previous assumption # a collection object does not have the 'format' attribute, so it will throw an exception continue if outputs_count > 1: raise Exception("Error: the tool should have just one output") if GALAXY_TYPE is None: raise Exception("Error: ToolOutput object not found") GALAXY_NAME = params.name or params.GALAXY_NAME or '%s query' % tool.name GALAXY_INFO = params.info or params.GALAXY_INFO or params.galaxyDescription or '' GALAXY_BUILD = params.dbkey or params.GALAXY_BUILD or params.galaxyFreeze or '?' # data = datatypes.factory(ext=GALAXY_TYPE)() # data.ext = GALAXY_TYPE # data.name = GALAXY_NAME # data.info = GALAXY_INFO # data.dbkey = GALAXY_BUILD # data.state = jobs.JOB_OK # history.datasets.add_dataset( data ) data = trans.app.model.HistoryDatasetAssociation(create_dataset=True, sa_session=trans.sa_session, extension=GALAXY_TYPE) trans.app.security_agent.set_all_dataset_permissions(data.dataset, trans.app.security_agent.history_get_default_permissions(trans.history)) data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO trans.sa_session.add(data) # Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW open(data.file_name, 'wb').close() # create the file trans.history.add_dataset(data, genome_build=GALAXY_BUILD) trans.sa_session.add(trans.history) trans.sa_session.flush() trans.log_event("Added dataset %d to history %d" % (data.id, trans.history.id), tool_id=tool_id) try: key = hmac_new(trans.app.config.tool_secret, "%d:%d" % (data.id, data.history_id)) galaxy_url = trans.request.base + '/async/%s/%s/%s' % (tool_id, data.id, key) params.update({'GALAXY_URL': galaxy_url}) params.update({'data_id': data.id}) # Use provided URL or fallback to tool action url = URL or tool.action # Does url already have query params? if '?' in url: url_join_char = '&' else: url_join_char = '?' url = "%s%s%s" % (url, url_join_char, urlencode(params.flatten())) log.debug("connecting to -> %s" % url) trans.log_event("Async connecting to -> %s" % url) text = requests.get(url).text.strip() if not text.endswith('OK'): raise Exception(text) data.state = data.blurb = data.states.RUNNING except Exception as e: data.info = str(e) data.state = data.blurb = data.states.ERROR trans.sa_session.flush() return trans.fill_template('root/tool_runner.mako', out_data={}, num_jobs=1, job_errors=[])