def request_type_permissions( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
request_type_id = kwd.get( 'id', '' )
try:
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' )
roles = trans.sa_session.query( trans.model.Role ) \
.filter( trans.model.Role.table.c.deleted==False ) \
.order_by( trans.model.Role.table.c.name )
if params.get( 'update_roles_button', False ):
permissions = {}
for k, v in trans.model.RequestType.permitted_actions.items():
in_roles = [ trans.sa_session.query( trans.model.Role ).get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ]
permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles
trans.app.security_agent.set_request_type_permissions( request_type, permissions )
trans.sa_session.refresh( request_type )
message = "Permissions updated for request type '%s'" % request_type.name
return trans.fill_template( '/admin/request_type/request_type_permissions.mako',
request_type=request_type,
roles=roles,
status=status,
message=message )
def view_editable_request_type( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
request_type_id = params.get( 'id', None )
try:
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' )
# See if we have any associated templates
widgets = request_type.get_template_widgets( trans )
widget_fields_have_contents = self.widget_fields_have_contents( widgets )
# get all the external services selected till now
external_service_select_fields_list = []
for index, external_service in enumerate( request_type.external_services ):
external_service_select_field = self.__build_external_service_select_field( trans,
'external_service_id_%i' % index,
external_service )
external_service_select_fields_list.append( external_service_select_field )
return trans.fill_template( '/admin/request_type/edit_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
external_service_select_fields_list=external_service_select_fields_list,
message=message,
status=status )
def reject_request( self, trans, **kwd ):
params = util.Params( kwd )
request_id = params.get( 'id', '' )
status = params.get( 'status', 'done' )
message = params.get( 'message', 'done' )
if params.get( 'cancel_reject_button', False ):
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id ) )
try:
request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', request_id )
# Validate
comment = util.restore_text( params.get( 'comment', '' ) )
if not comment:
status='error'
message='A reason for rejecting the request is required.'
return trans.fill_template( '/admin/requests/reject.mako',
cntrller='requests_admin',
request=request,
status=status,
message=message )
# Create an event with state 'Rejected' for this request
event_comment = "Sequencing request marked rejected by %s. Reason: %s " % ( trans.user.email, comment )
event = trans.model.RequestEvent( request, request.states.REJECTED, event_comment )
trans.sa_session.add( event )
trans.sa_session.flush()
message='Sequencing request (%s) has been rejected.' % request.name
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='browse_requests',
status=status,
message=message,
**kwd ) )
def view_form_definition( self, trans, **kwd ):
form_definition_id = kwd.get( 'id', None )
try:
form_definition = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( form_definition_id ) )
except:
return invalid_id_redirect( trans, 'request_type', form_definition_id, 'form definition', action='browse_request_types' )
return trans.fill_template( '/admin/forms/view_form_definition.mako',
form_definition=form_definition )
def view_external_service( self, trans, **kwd ):
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service_type = self.get_external_service_type( trans, external_service.external_service_type_id )
return trans.fill_template( '/admin/external_service/view_external_service.mako',
external_service=external_service,
external_service_type=external_service_type )
def view_external_service( self, trans, **kwd ):
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service_type = self.get_external_service_type( trans, external_service.external_service_type_id )
return trans.fill_template( '/admin/external_service/view_external_service.mako',
external_service=external_service,
external_service_type=external_service_type )
def edit_external_service_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
vars = dict( id=trans.security.encode_id( external_service.form_definition.form_definition_current_id ),
response_redirect=web.url_for( controller='external_service',
action='update_external_service_form_definition',
**kwd ) )
return trans.response.send_redirect( web.url_for( controller='forms', action='edit_form_definition', **vars ) )
def edit_external_service_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
vars = dict( id=trans.security.encode_id( external_service.form_definition.form_definition_current_id ),
response_redirect=web.url_for( controller='external_service',
action='update_external_service_form_definition',
**kwd ) )
return trans.response.send_redirect( web.url_for( controller='forms', action='edit_form_definition', **vars ) )
def rename_datasets( self, trans, **kwd ):
# This method is called from the DataTransferGrid when a user is renaming 1 or more
# SampleDatasets.
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
sample_id = kwd.get( 'sample_id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' )
# id_list is list of SampleDataset ids, which is a subset of all
# of the SampleDatasets associated with the Sample. The user may
# or may not have selected all of the SampleDatasets for renaming.
id_list = util.listify( kwd.get( 'id_list', [] ) )
# Get all of the SampleDatasets
sample_datasets = []
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query( trans.app.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
sample_datasets.append( sample_dataset )
if params.get( 'rename_datasets_button', False ):
incorrect_dataset_names = []
for sample_dataset in sample_datasets:
encoded_id = trans.security.encode_id( sample_dataset.id )
selected_option = util.restore_text( params.get( 'rename_datasets_for_sample_%s' % encoded_id, '' ) )
new_name = util.restore_text( params.get( 'new_name_%s' % encoded_id, '' ) )
if not new_name:
incorrect_dataset_names.append( sample_dataset.name )
continue
new_name = util.sanitize_for_filename( new_name )
if selected_option == 'none':
sample_dataset.name = new_name
else:
sample_dataset.name = '%s_%s' % ( selected_option, new_name )
trans.sa_session.add( sample_dataset )
trans.sa_session.flush()
if len( sample_datasets ) == len( incorrect_dataset_names ):
status = 'error'
message = 'All datasets renamed incorrectly.'
elif len( incorrect_dataset_names ):
status = 'done'
message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str( incorrect_dataset_names )
else:
message = 'Changes saved successfully.'
return trans.fill_template( '/admin/requests/rename_datasets.mako',
sample=sample,
id_list=id_list,
message=message,
status=status )
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=sample_id ) )
def __get_external_services(self, trans, request_type=None, **kwd):
params = util.Params( kwd )
external_services_list = []
i = 0
while True:
if kwd.has_key( 'external_service_id_%i' % i ):
id = params.get( 'external_service_id_%i' % i, '' )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( id ) )
except:
return invalid_id_redirect( trans, 'request_type', id, 'external service', action='browse_request_types' )
external_services_list.append( external_service )
i += 1
else:
break
return external_services_list
def update_external_service_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service.form_definition = external_service.form_definition.current.latest_form
trans.sa_session.add( external_service )
trans.sa_session.flush()
message = "The form definition for the '%s' external service has been updated with your changes." % external_service.name
return trans.response.send_redirect( web.url_for( controller='external_service',
action='edit_external_service',
message=message,
status='done',
**kwd ) )
def update_external_service_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
external_service_id = kwd.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service.form_definition = external_service.form_definition.current.latest_form
trans.sa_session.add( external_service )
trans.sa_session.flush()
message = "The form definition for the '%s' external service has been updated with your changes." % external_service.name
return trans.response.send_redirect( web.url_for( controller='external_service',
action='edit_external_service',
message=message,
status='done',
**kwd ) )
def undelete_external_service( self, trans, **kwd ):
external_service_id = kwd.get( 'id', '' )
external_service_id_list = util.listify( external_service_id )
for external_service_id in external_service_id_list:
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service.deleted = False
trans.sa_session.add( external_service )
trans.sa_session.flush()
status = 'done'
message = '%i external services have been undeleted' % len( external_service_id_list )
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status=status ) )
def undelete_external_service( self, trans, **kwd ):
external_service_id = kwd.get( 'id', '' )
external_service_id_list = util.listify( external_service_id )
for external_service_id in external_service_id_list:
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
external_service.deleted = False
trans.sa_session.add( external_service )
trans.sa_session.flush()
status = 'done'
message = '%i external services have been undeleted' % len( external_service_id_list )
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status=status ) )
def undelete_request_type( self, trans, **kwd ):
request_type_id = kwd.get( 'id', '' )
request_type_id_list = util.listify( request_type_id )
for request_type_id in request_type_id_list:
try:
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' )
request_type.deleted = False
trans.sa_session.add( request_type )
trans.sa_session.flush()
status = 'done'
message = '%i request types have been undeleted' % len( request_type_id_list )
return trans.response.send_redirect( web.url_for( controller='request_type',
action='browse_request_types',
message=message,
status=status ) )
def view_request_type( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
request_type_id = kwd.get( 'id', None )
try:
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' )
# See if we have any associated templates
widgets = request_type.get_template_widgets( trans )
widget_fields_have_contents = self.widget_fields_have_contents( widgets )
return trans.fill_template( '/admin/request_type/view_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
message=message,
status=status )
def reject_request(self, trans, **kwd):
params = util.Params(kwd)
request_id = params.get('id', '')
status = params.get('status', 'done')
message = params.get('message', 'done')
if params.get('cancel_reject_button', False):
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id))
try:
request = trans.sa_session.query(trans.model.Request).get(
trans.security.decode_id(request_id))
except:
return invalid_id_redirect(trans, 'requests_admin', request_id)
# Validate
comment = util.restore_text(params.get('comment', ''))
if not comment:
status = 'error'
message = 'A reason for rejecting the request is required.'
return trans.fill_template('/admin/requests/reject.mako',
cntrller='requests_admin',
request=request,
status=status,
message=message)
# Create an event with state 'Rejected' for this request
event_comment = "Sequencing request marked rejected by %s. Reason: %s " % (
trans.user.email, comment)
event = trans.model.RequestEvent(request, request.states.REJECTED,
event_comment)
trans.sa_session.add(event)
trans.sa_session.flush()
message = 'Sequencing request (%s) has been rejected.' % request.name
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='browse_requests',
status=status,
message=message,
**kwd))
def edit_external_service( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
external_service_id = params.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
if params.get( 'edit_external_service_button', False ):
external_service = self.__save_external_service( trans, **kwd )
trans.sa_session.refresh( external_service )
message = 'Changes made to external service (%s) have been saved' % external_service.name
widgets = self.__build_external_service_widgets( trans, external_service, **kwd )
widgets.extend( external_service.form_definition.get_widgets( trans.user, external_service.form_values.content, **kwd ) )
external_service_type = self.get_external_service_type( trans, external_service.external_service_type_id )
return trans.fill_template( '/admin/external_service/edit_external_service.mako',
external_service=external_service,
widgets=widgets,
message=message,
status=status,
external_service_type=external_service_type )
def edit_external_service( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
external_service_id = params.get( 'id', None )
try:
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
except:
return invalid_id_redirect( trans, 'external_service', external_service_id, 'external_service', action='browse_external_services' )
if params.get( 'edit_external_service_button', False ):
external_service = self.__save_external_service( trans, **kwd )
trans.sa_session.refresh( external_service )
message = 'Changes made to external service (%s) have been saved' % external_service.name
widgets = self.__build_external_service_widgets( trans, external_service, **kwd )
widgets.extend( external_service.form_definition.get_widgets( trans.user, external_service.form_values.content, **kwd ) )
external_service_type = self.get_external_service_type( trans, external_service.external_service_type_id )
return trans.fill_template( '/admin/external_service/edit_external_service.mako',
external_service=external_service,
widgets=widgets,
message=message,
status=status,
external_service_type=external_service_type )
def edit_request_type( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
request_type_id = params.get( 'id', None )
try:
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'request type', action='browse_request_types' )
# See if we have any associated templates
widgets = request_type.get_template_widgets( trans )
widget_fields_have_contents = self.widget_fields_have_contents( widgets )
# get all the external services selected till now
external_service_select_fields_list = []
external_services_list = self.__get_external_services( trans, request_type, **kwd )
if params.get( 'edit_request_type_button', False ):
request_type = self.__save_request_type( trans, action='edit_request_type', **kwd )
message = 'Changes made to request type (%s) have been saved' % request_type.name
elif params.get( 'add_external_service_button', False ):
external_services_list.append( None )
elif params.get( 'remove_external_service_button', False ):
index = int( kwd[ 'remove_external_service_button' ].split(' ')[3] ) - 1
del external_services_list[index]
#if external_services_list
for index, external_service in enumerate( external_services_list ):
external_service_select_field = self.__build_external_service_select_field( trans,
'external_service_id_%i' % index,
external_service )
external_service_select_fields_list.append( external_service_select_field )
return trans.fill_template( '/admin/request_type/edit_request_type.mako',
request_type=request_type,
widgets=widgets,
widget_fields_have_contents=widget_fields_have_contents,
external_service_select_fields_list=external_service_select_fields_list,
message=message,
status=status )
def __save_request_type( self, trans, action, **kwd ):
# Here we save a newly created request_type or save changed
# attributes of an existing request_type.
params = util.Params( kwd )
request_type_id = params.get( 'id', None )
name = util.restore_text( params.get( 'name', '' ) )
desc = util.restore_text( params.get( 'desc', '' ) )
request_form_id = params.get( 'request_form_id', 'none' )
sample_form_id = params.get( 'sample_form_id', 'none' )
external_service_id = params.get( 'external_service_id', 'none' )
# validate
if not name or request_form_id == 'none' or sample_form_id == 'none':
message = 'Enter the name, request form, sample form and at least one sample state associated with this request type.'
return trans.response.send_redirect( web.url_for( controller='request_type',
action=action,
message=message,
status='error' ) )
try:
request_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( request_form_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'form definition', action='browse_request_types' )
try:
sample_form = trans.sa_session.query( trans.model.FormDefinition ).get( trans.security.decode_id( sample_form_id ) )
except:
return invalid_id_redirect( trans, 'request_type', request_type_id, 'form definition', action='browse_request_types' )
if request_type_id:
# We're saving changed attributes of an existing request_type.
request_type = trans.sa_session.query( trans.model.RequestType ).get( trans.security.decode_id( request_type_id ) )
request_type.name = name
request_type.desc = desc
request_type.request_form = request_form
request_type.sample_form = sample_form
for sample_state in request_type.states:
sample_state_id = trans.security.encode_id( sample_state.id )
name = util.restore_text( params.get( 'state_name_%s' % sample_state_id, '' ) )
desc = util.restore_text( params.get( 'state_desc_%s' % sample_state_id, '' ) )
sample_state.name = name
sample_state.desc = desc
trans.sa_session.add( sample_state )
trans.sa_session.flush()
trans.sa_session.add( request_type )
trans.sa_session.flush()
else:
# We're saving a newly created request_type
request_type = trans.model.RequestType( name=name,
desc=desc,
request_form=request_form,
sample_form=sample_form )
trans.sa_session.add( request_type )
trans.sa_session.flush()
i = 0
while True:
if kwd.has_key( 'state_name_%i' % i ):
name = util.restore_text( params.get( 'state_name_%i' % i, '' ) )
desc = util.restore_text( params.get( 'state_desc_%i' % i, '' ) )
sample_state = trans.model.SampleState( name, desc, request_type )
trans.sa_session.add( sample_state )
trans.sa_session.flush()
i += 1
else:
break
# delete existing associations
request_type.delete_external_service_associations( trans )
# save the external services associated with this request_type
external_services_list = self.__get_external_services( trans, **kwd )
for external_service in external_services_list:
request_type.add_external_service_association( trans, external_service )
return request_type
def initiate_data_transfer(self,
trans,
sample_id,
sample_datasets=[],
sample_dataset_id=''):
# Initiate the transfer of the datasets from the external service to the target Galaxy data library.
# The admin user must have LIBRARY_ADD permission for the target library and folder
try:
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
except:
return invalid_id_redirect(trans, 'requests_admin', sample_id,
'sample')
message = ""
status = "done"
# Make sure the current admin user has LIBRARY_ADD permission on the target data library and folder.
self.__ensure_library_add_permission(trans, sample.library,
sample.folder)
if sample_dataset_id and not sample_datasets:
# Either a list of SampleDataset objects or a comma-separated string of
# encoded SampleDataset ids can be received. If the latter, parse the
# sample_dataset_id string to build the list of sample_datasets.
id_list = util.listify(sample_dataset_id)
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query(
trans.model.SampleDataset).get(
trans.security.decode_id(sample_dataset_id))
sample_datasets.append(sample_dataset)
if trans.app.config.enable_beta_job_managers:
# For now, assume that all SampleDatasets use the same external service ( this may not be optimal ).
if sample_datasets:
external_service_type_id = sample_datasets[
0].external_service.external_service_type_id
# Here external_service_type_id will be something like '454_life_sciences'
external_service = sample.request.type.get_external_service(
external_service_type_id)
external_service_type = external_service.get_external_service_type(
trans)
external_service.load_data_transfer_settings(trans)
# For now only scp is supported.
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
if not scp_configs['automatic_transfer']:
deferred_plugin = 'ManualDataTransferPlugin'
else:
raise Exception(
"Automatic data transfer using scp is not yet supported."
)
trans.app.job_manager.deferred_job_queue.plugins[
deferred_plugin].create_job(
trans,
sample=sample,
sample_datasets=sample_datasets,
external_service=external_service,
external_service_type=external_service_type)
else:
# TODO: Using RabbitMq for now, but eliminate this entire block when we replace RabbitMq with Galaxy's
# own messaging engine. We're holding off on using the new way to transfer files manually until we
# implement a Galaxy-proprietary messaging engine because the deferred job plugins currently perform
# constant db hits to check for deferred jobs that are not in a finished state.
# Create the message
messages = self.__create_data_transfer_messages(
trans, sample, sample_datasets)
# Send the messages
for rmq_msg in messages:
try:
conn = amqp.Connection(
host=trans.app.config.amqp['host'] + ":" +
trans.app.config.amqp['port'],
userid=trans.app.config.amqp['userid'],
password=trans.app.config.amqp['password'],
virtual_host=trans.app.config.amqp['virtual_host'],
insist=False)
chan = conn.channel()
msg = amqp.Message(
rmq_msg,
content_type='text/plain',
application_headers={'msg_type': 'data_transfer'})
msg.properties["delivery_mode"] = 2
chan.basic_publish(
msg,
exchange=trans.app.config.amqp['exchange'],
routing_key=trans.app.config.amqp['routing_key'])
chan.close()
conn.close()
except Exception, e:
message = "Error sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(
e)
status = "error"
if not message:
message = "%i datasets have been queued for transfer from the external service." % len(
sample_datasets)
status = "done"
def rename_datasets(self, trans, **kwd):
# This method is called from the DataTransferGrid when a user is renaming 1 or more
# SampleDatasets.
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
sample_id = kwd.get('sample_id', None)
try:
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
except:
return invalid_id_redirect(trans, 'requests_admin', sample_id,
'sample')
# id_list is list of SampleDataset ids, which is a subset of all
# of the SampleDatasets associated with the Sample. The user may
# or may not have selected all of the SampleDatasets for renaming.
id_list = util.listify(kwd.get('id_list', []))
# Get all of the SampleDatasets
sample_datasets = []
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query(
trans.app.model.SampleDataset).get(
trans.security.decode_id(sample_dataset_id))
sample_datasets.append(sample_dataset)
if params.get('rename_datasets_button', False):
incorrect_dataset_names = []
for sample_dataset in sample_datasets:
encoded_id = trans.security.encode_id(sample_dataset.id)
selected_option = util.restore_text(
params.get('rename_datasets_for_sample_%s' % encoded_id,
''))
new_name = util.restore_text(
params.get('new_name_%s' % encoded_id, ''))
if not new_name:
incorrect_dataset_names.append(sample_dataset.name)
continue
new_name = util.sanitize_for_filename(new_name)
if selected_option == 'none':
sample_dataset.name = new_name
else:
sample_dataset.name = '%s_%s' % (selected_option, new_name)
trans.sa_session.add(sample_dataset)
trans.sa_session.flush()
if len(sample_datasets) == len(incorrect_dataset_names):
status = 'error'
message = 'All datasets renamed incorrectly.'
elif len(incorrect_dataset_names):
status = 'done'
message = 'Changes saved successfully. The following datasets were renamed incorrectly: %s.' % str(
incorrect_dataset_names)
else:
message = 'Changes saved successfully.'
return trans.fill_template('/admin/requests/rename_datasets.mako',
sample=sample,
id_list=id_list,
message=message,
status=status)
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=sample_id))
def manage_datasets(self, trans, **kwd):
def handle_error(**kwd):
kwd['status'] = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
**kwd))
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
sample_id = params.get('sample_id', None)
try:
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
except:
return invalid_id_redirect(trans, 'requests_admin', sample_id,
'sample')
if 'operation' in kwd:
operation = kwd['operation'].lower()
sample_dataset_id = params.get('id', None)
if not sample_dataset_id:
message = 'Select at least 1 dataset to %s.' % operation
kwd['message'] = message
del kwd['operation']
handle_error(**kwd)
id_list = util.listify(sample_dataset_id)
selected_sample_datasets = []
for sample_dataset_id in id_list:
try:
sample_dataset = trans.sa_session.query(
trans.model.SampleDataset).get(
trans.security.decode_id(sample_dataset_id))
except:
return invalid_id_redirect(trans, 'requests_admin',
sample_dataset_id,
'sample dataset')
selected_sample_datasets.append(sample_dataset)
if operation == "view":
return trans.fill_template(
'/admin/requests/view_sample_dataset.mako',
cntrller='requests_admin',
sample_dataset=selected_sample_datasets[0])
elif operation == "delete":
not_deleted = []
for sample_dataset in selected_sample_datasets:
# Make sure the dataset has been transferred before deleting it.
if sample_dataset in sample_dataset.sample.untransferred_dataset_files:
# Save the sample dataset
sample = sample_dataset.sample
trans.sa_session.delete(sample_dataset)
trans.sa_session.flush()
else:
not_deleted.append(sample_dataset.name)
message = '%i datasets have been deleted.' % (len(id_list) -
len(not_deleted))
if not_deleted:
status = 'warning'
message = message + ' %s could not be deleted because their transfer status is not "Not Started". ' % str(
not_deleted)
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
status=status,
message=message))
elif operation == "rename":
# If one of the selected sample datasets is in the NOT_STARTED state,
# then display an error message. A NOT_STARTED state implies the dataset
# has not yet been transferred.
no_datasets_transferred = True
for selected_sample_dataset in selected_sample_datasets:
if selected_sample_dataset in selected_sample_dataset.sample.untransferred_dataset_files:
no_datasets_transferred = False
break
if no_datasets_transferred:
status = 'error'
message = 'A dataset can be renamed only if it has been transferred.'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(
selected_sample_datasets[0].sample.id),
status=status,
message=message))
return trans.fill_template(
'/admin/requests/rename_datasets.mako',
sample=selected_sample_datasets[0].sample,
id_list=id_list)
elif operation == "transfer":
self.initiate_data_transfer(
trans,
trans.security.encode_id(
selected_sample_datasets[0].sample.id),
sample_datasets=selected_sample_datasets)
elif operation == "view_external_service":
return trans.response.send_redirect(
web.url_for(controller='external_service',
action='view_external_service',
**kwd))
# Render the grid view
request_id = trans.security.encode_id(sample.request.id)
library_id = trans.security.encode_id(sample.library.id)
self.datatx_grid.title = 'Manage "%s" datasets' % sample.name
self.datatx_grid.global_actions = [
grids.GridAction(
"Browse target data library",
dict(controller='library_common',
action='browse_library',
cntrller='library_admin',
id=library_id)),
grids.GridAction(
"Browse this request",
dict(controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id))
]
return self.datatx_grid(trans, **kwd)
def initiate_data_transfer( self, trans, sample_id, sample_datasets=[], sample_dataset_id='' ):
# Initiate the transfer of the datasets from the external service to the target Galaxy data library.
# The admin user must have LIBRARY_ADD permission for the target library and folder
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' )
message = ""
status = "done"
# Make sure the current admin user has LIBRARY_ADD permission on the target data library and folder.
self.__ensure_library_add_permission( trans, sample.library, sample.folder )
if sample_dataset_id and not sample_datasets:
# Either a list of SampleDataset objects or a comma-separated string of
# encoded SampleDataset ids can be received. If the latter, parse the
# sample_dataset_id string to build the list of sample_datasets.
id_list = util.listify( sample_dataset_id )
for sample_dataset_id in id_list:
sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
sample_datasets.append( sample_dataset )
if trans.app.config.enable_beta_job_managers:
# For now, assume that all SampleDatasets use the same external service ( this may not be optimal ).
if sample_datasets:
external_service_type_id = sample_datasets[0].external_service.external_service_type_id
# Here external_service_type_id will be something like '454_life_sciences'
external_service = sample.request.type.get_external_service( external_service_type_id )
external_service_type = external_service.get_external_service_type( trans )
external_service.load_data_transfer_settings( trans )
# For now only scp is supported.
scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ]
if not scp_configs[ 'automatic_transfer' ]:
deferred_plugin = 'ManualDataTransferPlugin'
else:
raise Exception( "Automatic data transfer using scp is not yet supported." )
trans.app.job_manager.deferred_job_queue.plugins[ deferred_plugin ].create_job( trans,
sample=sample,
sample_datasets=sample_datasets,
external_service=external_service,
external_service_type=external_service_type )
else:
# TODO: Using RabbitMq for now, but eliminate this entire block when we replace RabbitMq with Galaxy's
# own messaging engine. We're holding off on using the new way to transfer files manually until we
# implement a Galaxy-proprietary messaging engine because the deferred job plugins currently perform
# constant db hits to check for deferred jobs that are not in a finished state.
# Create the message
messages = self.__create_data_transfer_messages( trans, sample, sample_datasets )
# Send the messages
for rmq_msg in messages:
try:
conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ],
userid=trans.app.config.amqp[ 'userid' ],
password=trans.app.config.amqp[ 'password' ],
virtual_host=trans.app.config.amqp[ 'virtual_host' ],
insist=False )
chan = conn.channel()
msg = amqp.Message( rmq_msg,
content_type='text/plain',
application_headers={ 'msg_type': 'data_transfer' } )
msg.properties[ "delivery_mode" ] = 2
chan.basic_publish( msg,
exchange=trans.app.config.amqp[ 'exchange' ],
routing_key=trans.app.config.amqp[ 'routing_key' ] )
chan.close()
conn.close()
except Exception, e:
message = "Error sending the data transfer message to the Galaxy AMQP message queue:<br/>%s" % str(e)
status = "error"
if not message:
message = "%i datasets have been queued for transfer from the external service." % len( sample_datasets )
status = "done"
def manage_datasets( self, trans, **kwd ):
def handle_error( **kwd ):
kwd[ 'status' ] = 'error'
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
**kwd ) )
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
sample_id = params.get( 'sample_id', None )
try:
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' )
if 'operation' in kwd:
operation = kwd[ 'operation' ].lower()
sample_dataset_id = params.get( 'id', None )
if not sample_dataset_id:
message = 'Select at least 1 dataset to %s.' % operation
kwd[ 'message' ] = message
del kwd[ 'operation' ]
handle_error( **kwd )
id_list = util.listify( sample_dataset_id )
selected_sample_datasets = []
for sample_dataset_id in id_list:
try:
sample_dataset = trans.sa_session.query( trans.model.SampleDataset ).get( trans.security.decode_id( sample_dataset_id ) )
except:
return invalid_id_redirect( trans, 'requests_admin', sample_dataset_id, 'sample dataset' )
selected_sample_datasets.append( sample_dataset )
if operation == "view":
return trans.fill_template( '/admin/requests/view_sample_dataset.mako',
cntrller='requests_admin',
sample_dataset=selected_sample_datasets[0] )
elif operation == "delete":
not_deleted = []
for sample_dataset in selected_sample_datasets:
# Make sure the dataset has been transferred before deleting it.
if sample_dataset in sample_dataset.sample.untransferred_dataset_files:
# Save the sample dataset
sample = sample_dataset.sample
trans.sa_session.delete( sample_dataset )
trans.sa_session.flush()
else:
not_deleted.append( sample_dataset.name )
message = '%i datasets have been deleted.' % ( len( id_list ) - len( not_deleted ) )
if not_deleted:
status = 'warning'
message = message + ' %s could not be deleted because their transfer status is not "Not Started". ' % str( not_deleted )
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id( sample.id ),
status=status,
message=message ) )
elif operation == "rename":
# If one of the selected sample datasets is in the NOT_STARTED state,
# then display an error message. A NOT_STARTED state implies the dataset
# has not yet been transferred.
no_datasets_transferred = True
for selected_sample_dataset in selected_sample_datasets:
if selected_sample_dataset in selected_sample_dataset.sample.untransferred_dataset_files:
no_datasets_transferred = False
break
if no_datasets_transferred:
status = 'error'
message = 'A dataset can be renamed only if it has been transferred.'
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id( selected_sample_datasets[0].sample.id ),
status=status,
message=message ) )
return trans.fill_template( '/admin/requests/rename_datasets.mako',
sample=selected_sample_datasets[0].sample,
id_list=id_list )
elif operation == "transfer":
self.initiate_data_transfer( trans,
trans.security.encode_id( selected_sample_datasets[0].sample.id ),
sample_datasets=selected_sample_datasets )
elif operation == "view_external_service":
return trans.response.send_redirect( web.url_for( controller='external_service',
action='view_external_service',
**kwd ) )
# Render the grid view
request_id = trans.security.encode_id( sample.request.id )
library_id = trans.security.encode_id( sample.library.id )
self.datatx_grid.title = 'Manage "%s" datasets' % sample.name
self.datatx_grid.global_actions = [ grids.GridAction( "Browse target data library",
dict( controller='library_common',
action='browse_library',
cntrller='library_admin',
id=library_id ) ),
grids.GridAction( "Browse this request",
dict( controller='requests_common',
action='view_request',
cntrller='requests_admin',
id=request_id ) ) ]
return self.datatx_grid( trans, **kwd )
