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 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 create_form_definition( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
self.__imported_from_file = False
if params.get( 'create_form_button', False ):
form_definition, message = self.save_form_definition( trans, form_definition_current_id=None, **kwd )
if not form_definition:
return trans.response.send_redirect( web.url_for( controller='forms',
action='create_form_definition',
message=message,
status='error',
name=util.restore_text( params.get( 'name', '' ) ),
description=util.restore_text( params.get( 'description', '' ) ) ))
if self.__imported_from_file:
return trans.response.send_redirect( web.url_for( controller='forms',
action='edit_form_definition',
id=trans.security.encode_id( form_definition.current.id )) )
else:
return trans.response.send_redirect( web.url_for( controller='forms',
action='edit_form_definition',
id=trans.security.encode_id( form_definition.current.id ),
add_field_button='Add field',
name=form_definition.name,
description=form_definition.desc,
form_type_select_field=form_definition.type ) )
inputs = [ ( 'Name', TextField( 'name', 40, util.restore_text( params.get( 'name', '' ) ) ) ),
( 'Description', TextField( 'description', 40, util.restore_text( params.get( 'description', '' ) ) ) ),
( 'Type', self.__build_form_types_widget( trans, selected=params.get( 'form_type', 'none' ) ) ),
( 'Import from csv file (Optional)', FileField( 'file_data', 40, '' ) ) ]
return trans.fill_template( '/admin/forms/create_form.mako',
inputs=inputs,
message=message,
status=status )
def specified_date_handler( self, trans, **kwd ):
# We add params to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
if 'f-specified_date' in kwd and 'specified_date' not in kwd:
# The user clicked a State link in the Advanced Search box, so 'specified_date'
# will have been eliminated.
pass
elif 'specified_date' not in kwd:
kwd[ 'f-specified_date' ] = 'All'
else:
kwd[ 'f-specified_date' ] = kwd[ 'specified_date' ]
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "workflow_per_month":
# The received id is the stored_workflow id.
return trans.response.send_redirect( web.url_for( controller='workflows',
action='workflow_per_month',
**kwd ) )
elif operation == "user_per_month":
stored_workflow_id = kwd.get( 'id', None )
workflow = get_workflow( trans, stored_workflow_id )
if workflow.user:
kwd[ 'email' ] = workflow.user.email
else:
kwd[ 'email' ] = None # For anonymous users ( shouldn't happen with workflows )
return trans.response.send_redirect( web.url_for( controller='workflows',
action='user_per_month',
**kwd ) )
return self.specified_date_list_grid( trans, **kwd )
def specified_date_handler(self, trans, **kwd):
# We add params to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
if 'f-specified_date' in kwd and 'specified_date' not in kwd:
# The user clicked a State link in the Advanced Search box, so 'specified_date'
# will have been eliminated.
pass
elif 'specified_date' not in kwd:
kwd['f-specified_date'] = 'All'
else:
kwd['f-specified_date'] = kwd['specified_date']
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "workflow_per_month":
# The received id is the stored_workflow id.
return trans.response.send_redirect(
web.url_for(controller='workflows',
action='workflow_per_month',
**kwd))
elif operation == "user_per_month":
stored_workflow_id = kwd.get('id', None)
workflow = get_workflow(trans, stored_workflow_id)
if workflow.user:
kwd['email'] = workflow.user.email
else:
kwd['email'] = None # For anonymous users ( shouldn't happen with workflows )
return trans.response.send_redirect(
web.url_for(controller='workflows',
action='user_per_month',
**kwd))
return self.specified_date_list_grid(trans, **kwd)
def create_form_definition(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
self.__imported_from_file = False
if params.get('create_form_button', False):
form_definition, message = self.save_form_definition(trans, form_definition_current_id=None, **kwd)
if not form_definition:
return trans.response.send_redirect(web.url_for(controller='forms',
action='create_form_definition',
message=message,
status='error',
name=util.restore_text(params.get('name', '')),
description=util.restore_text(params.get('description', ''))))
if self.__imported_from_file:
return trans.response.send_redirect(web.url_for(controller='forms',
action='edit_form_definition',
id=trans.security.encode_id(form_definition.current.id)))
else:
return trans.response.send_redirect(web.url_for(controller='forms',
action='edit_form_definition',
id=trans.security.encode_id(form_definition.current.id),
add_field_button='Add field',
name=form_definition.name,
description=form_definition.desc,
form_type_select_field=form_definition.type))
inputs = [('Name', TextField('name', 40, util.restore_text(params.get('name', '')))),
('Description', TextField('description', 40, util.restore_text(params.get('description', '')))),
('Type', self.__build_form_types_widget(trans, selected=params.get('form_type', 'none'))),
('Import from csv file (Optional)', FileField('file_data', 40, ''))]
return trans.fill_template('/admin/forms/create_form.mako',
inputs=inputs,
message=message,
status=status)
def browse_request_types(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
obj_id = kwd.get('id', None)
if operation == "view_form_definition":
return self.view_form_definition(trans, **kwd)
elif operation == "view_request_type":
return self.view_request_type(trans, **kwd)
elif operation == "use run details template":
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='add_template',
cntrller='requests_admin',
item_type='request_type',
form_type=trans.model.FormDefinition.types.
RUN_DETAILS_TEMPLATE,
request_type_id=obj_id))
elif operation == "edit request type":
return self.view_editable_request_type(trans, **kwd)
elif operation == "delete":
return self.delete_request_type(trans, **kwd)
elif operation == "undelete":
return self.undelete_request_type(trans, **kwd)
elif operation == "edit permissions":
return self.request_type_permissions(trans, **kwd)
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
return self.request_type_grid(trans, **kwd)
def browse_request_types(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
obj_id = kwd.get('id', None)
if operation == "view_form_definition":
return self.view_form_definition(trans, **kwd)
elif operation == "view_request_type":
return self.view_request_type(trans, **kwd)
elif operation == "use run details template":
return trans.response.send_redirect(web.url_for(controller='requests_admin',
action='add_template',
cntrller='requests_admin',
item_type='request_type',
form_type=trans.model.FormDefinition.types.RUN_DETAILS_TEMPLATE,
request_type_id=obj_id))
elif operation == "edit request type":
return self.view_editable_request_type(trans, **kwd)
elif operation == "delete":
return self.delete_request_type(trans, **kwd)
elif operation == "undelete":
return self.undelete_request_type(trans, **kwd)
elif operation == "edit permissions":
return self.request_type_permissions(trans, **kwd)
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
return self.request_type_grid(trans, **kwd)
def specified_date_handler(self, trans, **kwd):
# We add params to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
kwd['sort_id'] = 'default'
kwd['order'] = 'default'
if 'f-specified_date' in kwd and 'specified_date' not in kwd:
# The user clicked a State link in the Advanced Search box, so 'specified_date'
# will have been eliminated.
pass
elif 'specified_date' not in kwd:
kwd['f-specified_date'] = 'All'
else:
kwd['f-specified_date'] = kwd['specified_date']
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "job_info":
return trans.response.send_redirect(
web.url_for(controller='jobs', action='job_info', **kwd))
elif operation == "tool_for_month":
kwd['f-tool_id'] = kwd['tool_id']
elif operation == "tool_per_month":
# The received id is the job id, so we need to get the job's tool_id.
job_id = kwd.get('id', None)
job = get_job(trans, job_id)
kwd['tool_id'] = job.tool_id
return trans.response.send_redirect(
web.url_for(controller='jobs',
action='tool_per_month',
**kwd))
elif operation == "user_for_month":
kwd['f-email'] = util.restore_text(kwd['email'])
elif operation == "user_per_month":
# The received id is the job id, so we need to get the id of the user
# that submitted the job.
job_id = kwd.get('id', None)
job = get_job(trans, job_id)
if job.user:
kwd['email'] = job.user.email
else:
kwd['email'] = None # For anonymous users
return trans.response.send_redirect(
web.url_for(controller='jobs',
action='user_per_month',
**kwd))
elif operation == "specified_date_in_error":
kwd['f-state'] = 'error'
elif operation == "unfinished":
kwd['f-state'] = 'Unfinished'
elif operation == "specified_tool_in_error":
kwd['f-state'] = 'error'
kwd['f-tool_id'] = kwd['tool_id']
return self.specified_date_list_grid(trans, **kwd)
def specified_date_handler( self, trans, **kwd ):
# We add params to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
kwd[ 'sort_id' ] = 'default'
kwd[ 'order' ] = 'default'
if 'f-specified_date' in kwd and 'specified_date' not in kwd:
# The user clicked a State link in the Advanced Search box, so 'specified_date'
# will have been eliminated.
pass
elif 'specified_date' not in kwd:
kwd[ 'f-specified_date' ] = 'All'
else:
kwd[ 'f-specified_date' ] = kwd[ 'specified_date' ]
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "job_info":
return trans.response.send_redirect( web.url_for( controller='jobs',
action='job_info',
**kwd ) )
elif operation == "tool_for_month":
kwd[ 'f-tool_id' ] = kwd[ 'tool_id' ]
elif operation == "tool_per_month":
# The received id is the job id, so we need to get the job's tool_id.
job_id = kwd.get( 'id', None )
job = get_job( trans, job_id )
kwd[ 'tool_id' ] = job.tool_id
return trans.response.send_redirect( web.url_for( controller='jobs',
action='tool_per_month',
**kwd ) )
elif operation == "user_for_month":
kwd[ 'f-email' ] = util.restore_text( kwd[ 'email' ] )
elif operation == "user_per_month":
# The received id is the job id, so we need to get the id of the user
# that submitted the job.
job_id = kwd.get( 'id', None )
job = get_job( trans, job_id )
if job.user:
kwd[ 'email' ] = job.user.email
else:
kwd[ 'email' ] = None # For anonymous users
return trans.response.send_redirect( web.url_for( controller='jobs',
action='user_per_month',
**kwd ) )
elif operation == "specified_date_in_error":
kwd[ 'f-state' ] = 'error'
elif operation == "unfinished":
kwd[ 'f-state' ] = 'Unfinished'
elif operation == "specified_tool_in_error":
kwd[ 'f-state' ] = 'error'
kwd[ 'f-tool_id' ] = kwd[ 'tool_id' ]
return self.specified_date_list_grid( trans, **kwd )
def edit_external_service_form_definition( self, trans, **kwd ):
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 reload_external_service_types(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
external_service_type_id = params.get('external_service_type_id',
'none')
if params.get('reload_external_service_type_button', False):
new_external_service_type = trans.app.external_service_types.reload(
external_service_type_id)
status = 'done'
message = 'Reloaded external service type: %s' % new_external_service_type.name
external_service_type_select_field = self.__build_external_service_type_select_field(
trans,
external_service_type_id,
refresh_on_change=False,
visible_external_service_types_only=False)
if not trans.app.external_service_types.visible_external_service_types:
message = 'There are no visible external service types in the external service types config file.'
status = 'error'
return trans.response.send_redirect(
web.url_for(controller='external_service',
action='browse_external_services',
message=message,
status=status))
return trans.fill_template(
'/admin/external_service/reload_external_service_types.mako',
external_service_type_select_field=
external_service_type_select_field,
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 undelete_form_definition(self, trans, **kwd):
id_list = util.listify(kwd['id'])
for id in id_list:
try:
form_definition_current = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).get(trans.security.decode_id(id))
except:
return trans.response.send_redirect(web.url_for(controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error'))
form_definition_current.deleted = False
trans.sa_session.add(form_definition_current)
trans.sa_session.flush()
return trans.response.send_redirect(web.url_for(controller='forms',
action='browse_form_definitions',
message='%i forms have been undeleted.' % len(id_list),
status='done'))
def create_external_service(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
external_service_type_id = params.get('external_service_type_id',
'none')
widgets = self.__build_external_service_widgets(trans,
external_service=None,
**kwd)
external_service_type = None
error = False
if not trans.app.external_service_types.visible_external_service_types:
error = True
message = 'There are no visible external_service types in the external_service types config file'
elif params.get('create_external_service_button', False):
if external_service_type_id == 'none':
error = True
message = 'Provide an external_service_type_id to create a new external service.'
else:
self.__save_external_service(trans, **kwd)
message = 'The external_service has been created.'
return trans.response.send_redirect(
web.url_for(controller='external_service',
action='browse_external_services',
message=message,
status=status))
elif external_service_type_id != 'none':
# Form submission via refresh_on_change
trans.app.external_service_types.reload(external_service_type_id)
external_service_type = self.get_external_service_type(
trans, external_service_type_id)
widgets.extend(
external_service_type.form_definition.get_widgets(
trans.user, **kwd))
if error:
return trans.response.send_redirect(
web.url_for(controller='external_service',
action='browse_external_services',
message=message,
status='error'))
return trans.fill_template(
'/admin/external_service/create_external_service.mako',
widgets=widgets,
message=message,
status=status,
external_service_type=external_service_type)
def undelete_form_definition( self, trans, **kwd ):
id_list = util.listify( kwd['id'] )
for id in id_list:
try:
form_definition_current = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( trans.security.decode_id(id) )
except:
return trans.response.send_redirect( web.url_for( controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error' ) )
form_definition_current.deleted = False
trans.sa_session.add( form_definition_current )
trans.sa_session.flush()
return trans.response.send_redirect( web.url_for( controller='forms',
action='browse_form_definitions',
message='%i forms have been undeleted.' % len(id_list),
status='done') )
def get_external_service_type(self, trans, external_service_type_id, action='browse_external_services'):
try:
return trans.app.external_service_types.all_external_service_types[ external_service_type_id ]
except KeyError:
message = 'Error in loading external service type: %s' % external_service_type_id
return trans.response.send_redirect( web.url_for( controller='external_service',
action=action,
message=message,
status='error' ) )
def browse_requests(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "edit":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_basic_request_info',
cntrller='requests_admin',
**kwd))
if operation == "add_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='add_samples',
cntrller='requests_admin',
**kwd))
if operation == "edit_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
**kwd))
if operation == "view_request":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request',
cntrller='requests_admin',
**kwd))
if operation == "view_request_history":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request_history',
cntrller='requests_admin',
**kwd))
if operation == "reject":
return self.reject_request(trans, **kwd)
if operation == "view_type":
return trans.response.send_redirect(
web.url_for(controller='request_type',
action='view_request_type',
**kwd))
if operation == "delete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='delete_request',
cntrller='requests_admin',
**kwd))
if operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='undelete_request',
cntrller='requests_admin',
**kwd))
# Render the list view
return self.request_grid(trans, **kwd)
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 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 view_latest_form_definition(self, trans, **kwd):
'''Displays the layout of the latest version of the form definition'''
form_definition_current_id = kwd.get('id', None)
try:
form_definition_current = trans.sa_session.query(trans.app.model.FormDefinitionCurrent) \
.get(trans.security.decode_id(form_definition_current_id))
except:
return trans.response.send_redirect(web.url_for(controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error'))
return trans.fill_template('/admin/forms/view_form_definition.mako',
form_definition=form_definition_current.latest_form)
def view_latest_form_definition( self, trans, **kwd ):
'''Displays the layout of the latest version of the form definition'''
form_definition_current_id = kwd.get( 'id', None )
try:
form_definition_current = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ) \
.get( trans.security.decode_id( form_definition_current_id ) )
except:
return trans.response.send_redirect( web.url_for( controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error' ) )
return trans.fill_template( '/admin/forms/view_form_definition.mako',
form_definition=form_definition_current.latest_form )
def __get_files(self, trans, request, external_service, folder_path):
# Retrieves the filenames to be transferred from the remote host.
ok = True
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
if not scp_configs['host'] or not scp_configs[
'user_name'] or not scp_configs['password']:
status = 'error'
message = "Error in external service login information."
ok = False
def print_ticks(d):
pass
cmd = 'ssh %s@%s "ls -p \'%s\'"' % (scp_configs['user_name'],
scp_configs['host'], folder_path)
# Handle the authentication message if keys are not set - the message is
# something like: "Are you sure you want to continue connecting (yes/no)."
if pexpect is not None:
output = pexpect.run(cmd,
events={
'\(yes\/no\)\.*': 'yes\r\n',
'.ssword:*':
scp_configs['password'] + '\r\n',
pexpect.TIMEOUT: print_ticks
},
timeout=10)
if 'No such file or directory' in output:
status = 'error'
message = "No folder named (%s) exists on the external service." % folder_path
ok = False
else:
status = 'error'
message = PEXPECT_IMPORT_MESSAGE
ok = False
if ok:
if 'assword:' in output:
# Eliminate the output created using ssh from the tree
output_as_list = output.splitlines()[1:]
else:
output_as_list = output.splitlines()
return output_as_list
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='select_datasets_to_transfer',
request_id=trans.security.encode_id(request.id),
external_service_id=trans.security.encode_id(
external_service.id),
status=status,
message=message))
def create_request_type(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
rt_info_widgets, rt_states_widgets = self.__get_populated_request_type_widgets(
trans, **kwd)
external_service_select_fields_list = []
# get all the external services selected till now
external_services_list = self.__get_external_services(trans, **kwd)
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)
if params.get('add_state_button', False):
# Append a new tuple to the set of states which will result in
# empty state name and description TextFields being displayed on
# the form.
rt_states_widgets.append(("", ""))
elif params.get('remove_state_button', False):
index = int(params.get('remove_state_button', '').split(" ")[2])
del rt_states_widgets[index - 1]
elif params.get('add_external_service_button', False):
# create a new one
external_service_select_field = self.__build_external_service_select_field(
trans, 'external_service_id_%i' % len(external_services_list))
external_service_select_fields_list.append(
external_service_select_field)
elif params.get('create_request_type_button', False):
self.__save_request_type(trans,
action='create_request_type',
**kwd)
message = 'The request type has been created.'
return trans.response.send_redirect(
web.url_for(controller='request_type',
action='browse_request_types',
message=message,
status=status))
# A request_type requires at least one possible sample state so that
# it can be used to create a sequencing request
if not len(rt_states_widgets):
rt_states_widgets.append(("New", "First sample state"))
return trans.fill_template(
'/admin/request_type/create_request_type.mako',
rt_info_widgets=rt_info_widgets,
rt_states_widgets=rt_states_widgets,
external_service_select_fields_list=
external_service_select_fields_list,
message=message,
status=status)
def get_external_service_type(self,
trans,
external_service_type_id,
action='browse_external_services'):
try:
return trans.app.external_service_types.all_external_service_types[
external_service_type_id]
except KeyError:
message = 'Error in loading external service type: %s' % external_service_type_id
return trans.response.send_redirect(
web.url_for(controller='external_service',
action=action,
message=message,
status='error'))
def edit_external_service_form_definition(self, trans, **kwd):
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 create_external_service( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
external_service_type_id = params.get( 'external_service_type_id', 'none' )
widgets = self.__build_external_service_widgets( trans, external_service=None, **kwd )
external_service_type = None
error = False
if not trans.app.external_service_types.visible_external_service_types:
error = True
message = 'There are no visible external_service types in the external_service types config file'
elif params.get( 'create_external_service_button', False ):
if external_service_type_id == 'none':
error = True
message = 'Provide an external_service_type_id to create a new external service.'
else:
self.__save_external_service( trans, **kwd )
message = 'The external_service has been created.'
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status=status ) )
elif external_service_type_id != 'none':
# Form submission via refresh_on_change
trans.app.external_service_types.reload( external_service_type_id )
external_service_type = self.get_external_service_type( trans, external_service_type_id )
widgets.extend( external_service_type.form_definition.get_widgets( trans.user, **kwd ) )
if error:
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status='error' ) )
return trans.fill_template( '/admin/external_service/create_external_service.mako',
widgets=widgets,
message=message,
status=status,
external_service_type=external_service_type )
def __import_fields(self, trans, csv_file, form_type):
'''
"company","name of the company", "True", "required", "TextField",,
"due date","turnaround time", "True", "optional", "SelectField","24 hours, 1 week, 1 month"
'''
import csv
fields = []
layouts = set()
try:
reader = csv.reader(csv_file.file)
index = 1
for row in reader:
if len(row) < 7: # ignore bogus rows
continue
options = row[5].split(',')
if len(row) >= 8:
fields.append({
'name': '%i_field_name' % index,
'label': row[0],
'helptext': row[1],
'visible': row[2],
'required': row[3],
'type': row[4],
'selectlist': options,
'layout': row[6],
'default': row[7]
})
layouts.add(row[6])
else:
fields.append({
'name': '%i_field_name' % index,
'label': row[0],
'helptext': row[1],
'visible': row[2],
'required': row[3],
'type': row[4],
'selectlist': options,
'default': row[6]
})
index = index + 1
except:
return trans.response.send_redirect(
web.url_for(controller='forms',
action='create_form',
status='error',
message='Error in importing <b>%s</b> file' %
csv_file.file))
self.__imported_from_file = True
return fields, list(layouts)
def browse_requests( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "edit":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='edit_basic_request_info',
cntrller='requests_admin',
**kwd ) )
if operation == "add_samples":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='add_samples',
cntrller='requests_admin',
**kwd ) )
if operation == "edit_samples":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
**kwd ) )
if operation == "view_request":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request',
cntrller='requests_admin',
**kwd ) )
if operation == "view_request_history":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='view_request_history',
cntrller='requests_admin',
**kwd ) )
if operation == "reject":
return self.reject_request( trans, **kwd )
if operation == "view_type":
return trans.response.send_redirect( web.url_for( controller='request_type',
action='view_request_type',
**kwd ) )
if operation == "delete":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='delete_request',
cntrller='requests_admin',
**kwd ) )
if operation == "undelete":
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='undelete_request',
cntrller='requests_admin',
**kwd ) )
# Render the list view
return self.request_grid( trans, **kwd )
def delete_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 = True
trans.sa_session.add( external_service )
trans.sa_session.flush()
message = '%i external services has been deleted' % len( external_service_id_list )
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status='done' ) )
def delete_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 = True
trans.sa_session.add(request_type)
trans.sa_session.flush()
message = '%i request types has been deleted' % len(request_type_id_list)
return trans.response.send_redirect(web.url_for(controller='request_type',
action='browse_request_types',
message=message,
status='done'))
def update_external_service_form_definition( self, trans, **kwd ):
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 browse_form_definitions(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if not kwd.get('id', None):
return trans.response.send_redirect(web.url_for(controller='forms',
action='browse_form_definitions',
status='error',
message="Invalid form ID"))
if operation == "view_latest_form_definition":
return self.view_latest_form_definition(trans, **kwd)
elif operation == "delete":
return self.delete_form_definition(trans, **kwd)
elif operation == "undelete":
return self.undelete_form_definition(trans, **kwd)
elif operation == "edit":
return self.edit_form_definition(trans, **kwd)
return self.forms_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:
message = "Message queue transfer is no longer supported, please set enable_beta_job_managers = True in galaxy.ini"
status = "error"
return trans.response.send_redirect(web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
message=message,
status=status))
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:
message = "Message queue transfer is no longer supported, please set enable_beta_job_managers = True in galaxy.ini"
status = "error"
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id( sample.id ),
message=message,
status=status ) )
def browse_form_definitions( self, trans, **kwd ):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if not kwd.get( 'id', None ):
return trans.response.send_redirect( web.url_for( controller='forms',
action='browse_form_definitions',
status='error',
message="Invalid form ID") )
if operation == "view_latest_form_definition":
return self.view_latest_form_definition( trans, **kwd )
elif operation == "delete":
return self.delete_form_definition( trans, **kwd )
elif operation == "undelete":
return self.undelete_form_definition( trans, **kwd )
elif operation == "edit":
return self.edit_form_definition( trans, **kwd )
return self.forms_grid( trans, **kwd )
def __import_fields( self, trans, csv_file, form_type ):
'''
"company","name of the company", "True", "required", "TextField",,
"due date","turnaround time", "True", "optional", "SelectField","24 hours, 1 week, 1 month"
'''
import csv
fields = []
layouts = set()
try:
reader = csv.reader(csv_file.file)
index = 1
for row in reader:
if len(row) < 7: # ignore bogus rows
continue
options = row[5].split(',')
if len(row) >= 8:
fields.append( { 'name': '%i_field_name' % index,
'label': row[0],
'helptext': row[1],
'visible': row[2],
'required': row[3],
'type': row[4],
'selectlist': options,
'layout': row[6],
'default': row[7] } )
layouts.add(row[6])
else:
fields.append( { 'name': '%i_field_name' % index,
'label': row[0],
'helptext': row[1],
'visible': row[2],
'required': row[3],
'type': row[4],
'selectlist': options,
'default': row[6] } )
index = index + 1
except:
return trans.response.send_redirect( web.url_for( controller='forms',
action='create_form',
status='error',
message='Error in importing <b>%s</b> file' % csv_file.file))
self.__imported_from_file = True
return fields, list(layouts)
def create_request_type(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
rt_info_widgets, rt_states_widgets = self.__get_populated_request_type_widgets(trans, **kwd)
external_service_select_fields_list = []
# get all the external services selected till now
external_services_list = self.__get_external_services(trans, **kwd)
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)
if params.get('add_state_button', False):
# Append a new tuple to the set of states which will result in
# empty state name and description TextFields being displayed on
# the form.
rt_states_widgets.append(("", ""))
elif params.get('remove_state_button', False):
index = int(params.get('remove_state_button', '').split(" ")[2])
del rt_states_widgets[index - 1]
elif params.get('add_external_service_button', False):
# create a new one
external_service_select_field = self.__build_external_service_select_field(trans,
'external_service_id_%i' % len(external_services_list))
external_service_select_fields_list.append(external_service_select_field)
elif params.get('create_request_type_button', False):
self.__save_request_type(trans, action='create_request_type', **kwd)
message = 'The request type has been created.'
return trans.response.send_redirect(web.url_for(controller='request_type',
action='browse_request_types',
message=message,
status=status))
# A request_type requires at least one possible sample state so that
# it can be used to create a sequencing request
if not len(rt_states_widgets):
rt_states_widgets.append(("New", "First sample state"))
return trans.fill_template('/admin/request_type/create_request_type.mako',
rt_info_widgets=rt_info_widgets,
rt_states_widgets=rt_states_widgets,
external_service_select_fields_list=external_service_select_fields_list,
message=message,
status=status)
def __get_files( self, trans, request, external_service, folder_path ):
# Retrieves the filenames to be transferred from the remote host.
ok = True
external_service.load_data_transfer_settings( trans )
scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ]
if not scp_configs[ 'host' ] or not scp_configs[ 'user_name' ] or not scp_configs[ 'password' ]:
status = 'error'
message = "Error in external service login information."
ok = False
def print_ticks( d ):
pass
cmd = 'ssh %s@%s "ls -p \'%s\'"' % ( scp_configs[ 'user_name' ], scp_configs[ 'host' ], folder_path )
# Handle the authentication message if keys are not set - the message is
# something like: "Are you sure you want to continue connecting (yes/no)."
if pexpect is not None:
output = pexpect.run( cmd,
events={ '\(yes\/no\)\.*' : 'yes\r\n',
'.ssword:*' : scp_configs[ 'password' ] + '\r\n',
pexpect.TIMEOUT : print_ticks },
timeout=10 )
if 'No such file or directory' in output:
status = 'error'
message = "No folder named (%s) exists on the external service." % folder_path
ok = False
else:
status = 'error'
message = PEXPECT_IMPORT_MESSAGE
ok = False
if ok:
if 'assword:' in output:
# Eliminate the output created using ssh from the tree
output_as_list = output.splitlines()[ 1: ]
else:
output_as_list = output.splitlines()
return output_as_list
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='select_datasets_to_transfer',
request_id=trans.security.encode_id( request.id ),
external_service_id=trans.security.encode_id( external_service.id ),
status=status,
message=message ) )
def update_external_service_form_definition(self, trans, **kwd):
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 reload_external_service_types( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
external_service_type_id = params.get( 'external_service_type_id', 'none' )
if params.get( 'reload_external_service_type_button', False ):
new_external_service_type = trans.app.external_service_types.reload( external_service_type_id )
status = 'done'
message = 'Reloaded external service type: %s' % new_external_service_type.name
external_service_type_select_field = self.__build_external_service_type_select_field( trans,
external_service_type_id,
refresh_on_change=False,
visible_external_service_types_only=False )
if not trans.app.external_service_types.visible_external_service_types:
message = 'There are no visible external service types in the external service types config file.'
status = 'error'
return trans.response.send_redirect( web.url_for( controller='external_service',
action='browse_external_services',
message=message,
status=status ) )
return trans.fill_template( '/admin/external_service/reload_external_service_types.mako',
external_service_type_select_field=external_service_type_select_field,
message=message,
status=status )
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')
# When this method is called due to a grid operation, the sample ID
# will be in the param 'id'. But when this method is called via a
# redirect from another method, the ID will be in 'sample_id'. So,
# check for 'id' if 'sample_id' is not provided.
sample_id = params.get('sample_id', None)
if sample_id is None:
sample_id = params.get('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)
class RequestsAdmin(BaseUIController, UsesFormDefinitionsMixin):
request_grid = AdminRequestsGrid()
datatx_grid = DataTransferGrid()
@web.expose
@web.require_admin
def index(self, trans):
return trans.fill_template("/admin/requests/index.mako")
@web.expose
@web.require_admin
def browse_requests(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "edit":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_basic_request_info',
cntrller='requests_admin',
**kwd))
if operation == "add_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='add_samples',
cntrller='requests_admin',
**kwd))
if operation == "edit_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
**kwd))
if operation == "view_request":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request',
cntrller='requests_admin',
**kwd))
if operation == "view_request_history":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request_history',
cntrller='requests_admin',
**kwd))
if operation == "reject":
return self.reject_request(trans, **kwd)
if operation == "view_type":
return trans.response.send_redirect(
web.url_for(controller='request_type',
action='view_request_type',
**kwd))
if operation == "delete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='delete_request',
cntrller='requests_admin',
**kwd))
if operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='undelete_request',
cntrller='requests_admin',
**kwd))
# Render the list view
return self.request_grid(trans, **kwd)
@web.expose
@web.require_admin
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))
# Data transfer from sequencer/external_service
@web.expose
@web.require_admin
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')
# When this method is called due to a grid operation, the sample ID
# will be in the param 'id'. But when this method is called via a
# redirect from another method, the ID will be in 'sample_id'. So,
# check for 'id' if 'sample_id' is not provided.
sample_id = params.get('sample_id', None)
if sample_id is None:
sample_id = params.get('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)
@web.expose
@web.require_admin
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))
@web.expose
@web.require_admin
def select_datasets_to_transfer(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_id = kwd.get('request_id', None)
external_service_id = kwd.get('external_service_id', None)
request = trans.sa_session.query(trans.model.Request).get(
trans.security.decode_id(request_id))
external_service = trans.sa_session.query(
trans.model.ExternalService).get(
trans.security.decode_id(external_service_id))
# Load the data transfer settings
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
selected_datasets_to_transfer = util.restore_text(
params.get('selected_datasets_to_transfer', ''))
if selected_datasets_to_transfer:
selected_datasets_to_transfer = selected_datasets_to_transfer.split(
',')
else:
selected_datasets_to_transfer = []
sample_id = kwd.get('sample_id', 'none')
sample_id_select_field = self.__build_sample_id_select_field(
trans, request, sample_id)
if sample_id != 'none':
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
else:
sample = None
# The __get_files() method redirects here with a status of 'error' and a message if there
# was a problem retrieving the files.
if params.get('select_datasets_to_transfer_button', False):
# Get the sample that was sequenced to produce these datasets.
if sample_id == 'none':
del kwd['select_datasets_to_transfer_button']
message = 'Select the sample that was sequenced to produce the datasets you want to transfer.'
kwd['message'] = message
kwd['status'] = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='select_datasets_to_transfer',
**kwd))
if not sample.library:
# Display an error if a sample has been selected that
# has not yet been associated with a destination library.
message = 'Select a target data library and folder for the sample before selecting the datasets.'
status = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
id=trans.security.encode_id(request.id),
status=status,
message=message))
# Save the sample datasets
sample_dataset_file_names = self.__create_sample_datasets(
trans, sample, selected_datasets_to_transfer, external_service)
if sample_dataset_file_names:
message = 'Datasets (%s) have been selected for sample (%s)' % \
( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name )
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
request_id=request_id,
sample_id=sample_id,
message=message,
status=status))
return trans.fill_template(
'/admin/requests/select_datasets_to_transfer.mako',
cntrller='requests_admin',
request=request,
external_service=external_service,
scp_configs=scp_configs,
sample=sample,
sample_id_select_field=sample_id_select_field,
status=status,
message=message)
@web.json
def get_file_details(self, trans, request_id, external_service_id,
folder_path):
def print_ticks(d):
# pexpect timeout method
pass
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
if pexpect is None:
return PEXPECT_IMPORT_MESSAGE
external_service = trans.sa_session.query(
trans.model.ExternalService).get(
trans.security.decode_id(external_service_id))
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
cmd = 'ssh %s@%s "ls -oghp \'%s\'"' % (
scp_configs['user_name'], scp_configs['host'], folder_path)
# Handle the authentication message if ssh keys are not set - the message is
# something like: "Are you sure you want to continue connecting (yes/no)."
output = pexpect.run(cmd,
events={
'\(yes\/no\)\.*': 'yes\r\n',
'.ssword:*': scp_configs['password'] + '\r\n',
pexpect.TIMEOUT: print_ticks
},
timeout=10)
for password_str in ['Password:\r\n', 'password:\r\n']:
# Eliminate the output created using ssh from the tree
if password_str in output:
output = output.replace(password_str, '')
return unicode(output.replace('\r\n', '<br/>'))
@web.json
def open_folder(self, trans, request_id, external_service_id, key):
# Avoid caching
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
request = trans.sa_session.query(trans.model.Request).get(
trans.security.decode_id(request_id))
external_service = trans.sa_session.query(
trans.model.ExternalService).get(
trans.security.decode_id(external_service_id))
folder_path = key
files_list = self.__get_files(trans, request, external_service,
folder_path)
folder_contents = []
for filename in files_list:
is_folder = False
if filename and filename[-1] == os.sep:
is_folder = True
if filename:
full_path = os.path.join(folder_path, filename)
node = {
"title": filename,
"isFolder": is_folder,
"isLazy": is_folder,
"tooltip": full_path,
"key": full_path
}
folder_contents.append(node)
return folder_contents
def __get_files(self, trans, request, external_service, folder_path):
# Retrieves the filenames to be transferred from the remote host.
ok = True
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
if not scp_configs['host'] or not scp_configs[
'user_name'] or not scp_configs['password']:
status = 'error'
message = "Error in external service login information."
ok = False
def print_ticks(d):
pass
cmd = 'ssh %s@%s "ls -p \'%s\'"' % (scp_configs['user_name'],
scp_configs['host'], folder_path)
# Handle the authentication message if keys are not set - the message is
# something like: "Are you sure you want to continue connecting (yes/no)."
if pexpect is not None:
output = pexpect.run(cmd,
events={
'\(yes\/no\)\.*': 'yes\r\n',
'.ssword:*':
scp_configs['password'] + '\r\n',
pexpect.TIMEOUT: print_ticks
},
timeout=10)
if 'No such file or directory' in output:
status = 'error'
message = "No folder named (%s) exists on the external service." % folder_path
ok = False
else:
status = 'error'
message = PEXPECT_IMPORT_MESSAGE
ok = False
if ok:
if 'assword:' in output:
# Eliminate the output created using ssh from the tree
output_as_list = output.splitlines()[1:]
else:
output_as_list = output.splitlines()
return output_as_list
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='select_datasets_to_transfer',
request_id=trans.security.encode_id(request.id),
external_service_id=trans.security.encode_id(
external_service.id),
status=status,
message=message))
def __create_sample_datasets(self, trans, sample,
selected_datasets_to_transfer,
external_service):
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
sample_dataset_file_names = []
if selected_datasets_to_transfer:
for filepath in selected_datasets_to_transfer:
# FIXME: handle folder selection - ignore folders for now
if filepath[-1] != os.sep:
name = self.__rename_dataset(sample,
filepath.split('/')[-1],
scp_configs)
status = trans.app.model.SampleDataset.transfer_status.NOT_STARTED
size = sample.get_untransferred_dataset_size(
filepath, scp_configs)
sample_dataset = trans.model.SampleDataset(
sample=sample,
file_path=filepath,
status=status,
name=name,
error_msg='',
size=size,
external_service=external_service)
trans.sa_session.add(sample_dataset)
trans.sa_session.flush()
sample_dataset_file_names.append(str(sample_dataset.name))
return sample_dataset_file_names
def __rename_dataset(self, sample, filepath, scp_configs):
name = filepath.split('/')[-1]
options = sample.request.type.rename_dataset_options
option = scp_configs.get('rename_dataset', options.NO)
if option == options.SAMPLE_NAME:
new_name = sample.name + '_' + name
if option == options.EXPERIMENT_AND_SAMPLE_NAME:
new_name = sample.request.name + '_' + sample.name + '_' + name
if option == options.EXPERIMENT_NAME:
new_name = sample.request.name + '_' + name
else:
new_name = name
return util.sanitize_for_filename(new_name)
def __ensure_library_add_permission(self, trans, target_library,
target_folder):
"""
Ensures the current admin user has ADD_LIBRARY permission on the target data library and folder.
"""
current_user_roles = trans.user.all_roles()
current_user_private_role = trans.app.security_agent.get_private_user_role(
trans.user)
flush_needed = False
if not trans.app.security_agent.can_add_library_item(
current_user_roles, target_library):
lp = trans.model.LibraryPermissions(
trans.app.security_agent.permitted_actions.LIBRARY_ADD.action,
target_library, current_user_private_role)
trans.sa_session.add(lp)
flush_needed = True
if not trans.app.security_agent.can_add_library_item(
current_user_roles, target_folder):
lfp = trans.model.LibraryFolderPermissions(
trans.app.security_agent.permitted_actions.LIBRARY_ADD.action,
target_folder, current_user_private_role)
trans.sa_session.add(lfp)
flush_needed = True
if flush_needed:
trans.sa_session.flush()
def __create_data_transfer_messages(self, trans, sample,
selected_sample_datasets):
"""
Creates the xml messages to send to the rabbitmq server. It returns a dictionary of messages
keyed by the external service used to transfer the datasets
"""
# Create the xml message based on the following template
xml = \
''' <data_transfer>
<galaxy_host>%(GALAXY_HOST)s</galaxy_host>
<api_key>%(API_KEY)s</api_key>
<data_host>%(DATA_HOST)s</data_host>
<data_user>%(DATA_USER)s</data_user>
<data_password>%(DATA_PASSWORD)s</data_password>
<request_id>%(REQUEST_ID)s</request_id>
<sample_id>%(SAMPLE_ID)s</sample_id>
<library_id>%(LIBRARY_ID)s</library_id>
<folder_id>%(FOLDER_ID)s</folder_id>
%(DATASETS)s
</data_transfer>'''
dataset_xml = \
'''<dataset>
<dataset_id>%(ID)s</dataset_id>
<name>%(NAME)s</name>
<file>%(FILE)s</file>
</dataset>'''
# Here we group all the sample_datasets by the external service used to transfer them.
# The idea is to bundle up the sample_datasets which uses the same external service and
# send a single AMQP message to the galaxy_listener
dataset_elements = {}
for sample_dataset in selected_sample_datasets:
external_service = sample_dataset.external_service
if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED:
if external_service not in dataset_elements:
dataset_elements[external_service] = ''
dataset_elements[external_service] += dataset_xml % dict(
ID=str(sample_dataset.id),
NAME=sample_dataset.name,
FILE=sample_dataset.file_path)
# update the dataset transfer status
sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE
trans.sa_session.add(sample_dataset)
trans.sa_session.flush()
# Finally prepend the external service info to the sets of sample datasets
messages = []
for external_service, dataset_elem in dataset_elements.items():
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
# Check data transfer settings
err_msg = self.__validate_data_transfer_settings(
trans, sample.request.type, scp_configs)
if err_msg:
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
status='error',
message=err_msg))
message = xml % dict(GALAXY_HOST=trans.request.host,
API_KEY=trans.user.api_keys[0].key,
DATA_HOST=scp_configs['host'],
DATA_USER=scp_configs['user_name'],
DATA_PASSWORD=scp_configs['password'],
REQUEST_ID=str(sample.request.id),
SAMPLE_ID=str(sample.id),
LIBRARY_ID=str(sample.library.id),
FOLDER_ID=str(sample.folder.id),
DATASETS=dataset_elem)
messages.append(message.replace('\n', '').replace('\r', ''))
return messages
def __validate_data_transfer_settings(self, trans, request_type,
scp_configs):
err_msg = ''
# check the external service login info
if not scp_configs.get( 'host', '' ) or \
not scp_configs.get( 'user_name', '' ) or \
not scp_configs.get( 'password', '' ):
err_msg += "Error in external service login information. "
if not trans.user.api_keys:
err_msg += "Set your API Key in your User Preferences to transfer datasets. "
# Check if library_import_dir is set
if not trans.app.config.library_import_dir:
err_msg = "'The library_import_dir' setting is not correctly set in the Galaxy config file. "
# Check the RabbitMQ server settings in the config file
for k, v in trans.app.config.amqp.items():
if not v:
err_msg += 'Set RabbitMQ server settings in the "galaxy_amqp" section of the Galaxy config file, specifically "%s" is not set.' % k
break
return err_msg
@web.expose
@web.require_admin
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'])
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"
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
message=message,
status=status))
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' )
# When this method is called due to a grid operation, the sample ID
# will be in the param 'id'. But when this method is called via a
# redirect from another method, the ID will be in 'sample_id'. So,
# check for 'id' if 'sample_id' is not provided.
sample_id = params.get( 'sample_id', None )
if sample_id is None:
sample_id = params.get( '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 handle_error( **kwd ):
kwd[ 'status' ] = 'error'
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
**kwd ) )
def select_datasets_to_transfer( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
request_id = kwd.get( 'request_id', None )
external_service_id = kwd.get( 'external_service_id', None )
request = trans.sa_session.query( trans.model.Request ).get( trans.security.decode_id( request_id ) )
external_service = trans.sa_session.query( trans.model.ExternalService ).get( trans.security.decode_id( external_service_id ) )
# Load the data transfer settings
external_service.load_data_transfer_settings( trans )
scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ]
selected_datasets_to_transfer = util.restore_text( params.get( 'selected_datasets_to_transfer', '' ) )
if selected_datasets_to_transfer:
selected_datasets_to_transfer = selected_datasets_to_transfer.split(',')
else:
selected_datasets_to_transfer = []
sample_id = kwd.get( 'sample_id', 'none' )
sample_id_select_field = self.__build_sample_id_select_field( trans, request, sample_id )
if sample_id != 'none':
sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) )
else:
sample = None
# The __get_files() method redirects here with a status of 'error' and a message if there
# was a problem retrieving the files.
if params.get( 'select_datasets_to_transfer_button', False ):
# Get the sample that was sequenced to produce these datasets.
if sample_id == 'none':
del kwd[ 'select_datasets_to_transfer_button' ]
message = 'Select the sample that was sequenced to produce the datasets you want to transfer.'
kwd[ 'message' ] = message
kwd[ 'status' ] = 'error'
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='select_datasets_to_transfer',
**kwd ) )
if not sample.library:
# Display an error if a sample has been selected that
# has not yet been associated with a destination library.
message = 'Select a target data library and folder for the sample before selecting the datasets.'
status = 'error'
return trans.response.send_redirect( web.url_for( controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
id=trans.security.encode_id( request.id ),
status=status,
message=message ) )
# Save the sample datasets
sample_dataset_file_names = self.__create_sample_datasets( trans, sample, selected_datasets_to_transfer, external_service )
if sample_dataset_file_names:
message = 'Datasets (%s) have been selected for sample (%s)' % \
( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name )
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
request_id=request_id,
sample_id=sample_id,
message=message,
status=status ) )
return trans.fill_template( '/admin/requests/select_datasets_to_transfer.mako',
cntrller='requests_admin',
request=request,
external_service=external_service,
scp_configs=scp_configs,
sample=sample,
sample_id_select_field=sample_id_select_field,
status=status,
message=message )
def browse_requests(self, trans, **kwd):
if "operation" in kwd:
operation = kwd["operation"].lower()
if operation == "edit":
return trans.response.send_redirect(
web.url_for(
controller="requests_common", action="edit_basic_request_info", cntrller="requests", **kwd
)
)
if operation == "add_samples":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="add_samples", cntrller="requests", **kwd)
)
if operation == "edit_samples":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="edit_samples", cntrller="requests", **kwd)
)
if operation == "view_request":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="view_request", cntrller="requests", **kwd)
)
if operation == "delete":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="delete_request", cntrller="requests", **kwd)
)
if operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="undelete_request", cntrller="requests", **kwd)
)
if operation == "view_request_history":
return trans.response.send_redirect(
web.url_for(controller="requests_common", action="view_request_history", cntrller="requests", **kwd)
)
# If there are requests that have been rejected, show a message as a reminder to the user
rejected = 0
for request in (
trans.sa_session.query(trans.app.model.Request)
.filter(trans.app.model.Request.table.c.deleted == false())
.filter(trans.app.model.Request.table.c.user_id == trans.user.id)
):
if request.is_rejected:
rejected = rejected + 1
if rejected:
status = "warning"
message = (
"%d requests (highlighted in red) were rejected. Click on the request name for details." % rejected
)
kwd["status"] = status
kwd["message"] = message
# Allow the user to create a new request only if they have permission to access a request type.
accessible_request_types = trans.app.security_agent.get_accessible_request_types(trans, trans.user)
if accessible_request_types:
self.request_grid.global_actions = [
grids.GridAction(
"Create new request",
dict(controller="requests_common", action="create_request", cntrller="requests"),
)
]
else:
self.request_grid.global_actions = []
# Render the list view
return self.request_grid(trans, **kwd)
def browse_requests(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "edit":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_basic_request_info',
cntrller='requests',
**kwd))
if operation == "add_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='add_samples',
cntrller='requests',
**kwd))
if operation == "edit_samples":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_samples',
cntrller='requests',
**kwd))
if operation == "view_request":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request',
cntrller='requests',
**kwd))
if operation == "delete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='delete_request',
cntrller='requests',
**kwd))
if operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='undelete_request',
cntrller='requests',
**kwd))
if operation == "view_request_history":
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='view_request_history',
cntrller='requests',
**kwd))
# If there are requests that have been rejected, show a message as a reminder to the user
rejected = 0
for request in trans.sa_session.query( trans.app.model.Request ) \
.filter( trans.app.model.Request.table.c.deleted == false() ) \
.filter( trans.app.model.Request.table.c.user_id == trans.user.id ):
if request.is_rejected:
rejected = rejected + 1
if rejected:
status = 'warning'
message = "%d requests (highlighted in red) were rejected. Click on the request name for details." % rejected
kwd['status'] = status
kwd['message'] = message
# Allow the user to create a new request only if they have permission to access a request type.
accessible_request_types = trans.app.security_agent.get_accessible_request_types(
trans, trans.user)
if accessible_request_types:
self.request_grid.global_actions = [
grids.GridAction(
"Create new request",
dict(controller='requests_common',
action='create_request',
cntrller='requests'))
]
else:
self.request_grid.global_actions = []
# Render the list view
return self.request_grid(trans, **kwd)
def handle_error(**kwd):
kwd['status'] = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
**kwd))
def __create_data_transfer_messages( self, trans, sample, selected_sample_datasets ):
"""
Creates the xml messages to send to the rabbitmq server. It returns a dictionary of messages
keyed by the external service used to transfer the datasets
"""
# Create the xml message based on the following template
xml = \
''' <data_transfer>
<galaxy_host>%(GALAXY_HOST)s</galaxy_host>
<api_key>%(API_KEY)s</api_key>
<data_host>%(DATA_HOST)s</data_host>
<data_user>%(DATA_USER)s</data_user>
<data_password>%(DATA_PASSWORD)s</data_password>
<request_id>%(REQUEST_ID)s</request_id>
<sample_id>%(SAMPLE_ID)s</sample_id>
<library_id>%(LIBRARY_ID)s</library_id>
<folder_id>%(FOLDER_ID)s</folder_id>
%(DATASETS)s
</data_transfer>'''
dataset_xml = \
'''<dataset>
<dataset_id>%(ID)s</dataset_id>
<name>%(NAME)s</name>
<file>%(FILE)s</file>
</dataset>'''
# Here we group all the sample_datasets by the external service used to transfer them.
# The idea is to bundle up the sample_datasets which uses the same external service and
# send a single AMQP message to the galaxy_listener
dataset_elements = {}
for sample_dataset in selected_sample_datasets:
external_service = sample_dataset.external_service
if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED:
if external_service not in dataset_elements:
dataset_elements[ external_service ] = ''
dataset_elements[ external_service ] += dataset_xml % dict( ID=str( sample_dataset.id ),
NAME=sample_dataset.name,
FILE=sample_dataset.file_path )
# update the dataset transfer status
sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE
trans.sa_session.add( sample_dataset )
trans.sa_session.flush()
# Finally prepend the external service info to the sets of sample datasets
messages = []
for external_service, dataset_elem in dataset_elements.items():
external_service.load_data_transfer_settings( trans )
scp_configs = external_service.data_transfer[ trans.model.ExternalService.data_transfer_protocol.SCP ]
# Check data transfer settings
err_msg = self.__validate_data_transfer_settings( trans, sample.request.type, scp_configs )
if err_msg:
return trans.response.send_redirect( web.url_for( controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id( sample.id ),
status='error',
message=err_msg ) )
message = xml % dict( GALAXY_HOST=trans.request.host,
API_KEY=trans.user.api_keys[0].key,
DATA_HOST=scp_configs[ 'host' ],
DATA_USER=scp_configs[ 'user_name' ],
DATA_PASSWORD=scp_configs[ 'password' ],
REQUEST_ID=str( sample.request.id ),
SAMPLE_ID=str( sample.id ),
LIBRARY_ID=str( sample.library.id ),
FOLDER_ID=str( sample.folder.id ),
DATASETS=dataset_elem )
messages.append( message.replace( '\n', '' ).replace( '\r', '' ) )
return messages
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')
# 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 'state_name_%i' % i in kwd:
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 edit_form_definition(self, trans, response_redirect=None, **kwd):
'''
This callback method is for handling form editing. The value of response_redirect
should be an URL that is defined by the caller. This allows for redirecting as desired
when the form changes have been saved. For an example of how this works, see the
edit_template() method in the base controller.
'''
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
try:
form_definition_current = trans.sa_session.query(
trans.app.model.FormDefinitionCurrent).get(
trans.security.decode_id(kwd['id']))
except:
return trans.response.send_redirect(
web.url_for(controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error'))
form_definition = form_definition_current.latest_form
# TODO: eliminate the need for this refresh param.
if params.get('refresh', False):
# Refresh
current_form = self.get_current_form(trans, **kwd)
else:
# Show the saved form for editing
current_form = self.get_saved_form(form_definition)
# Save changes
if params.get('save_changes_button', False):
new_form_definition, message = self.save_form_definition(
trans,
form_definition_current_id=form_definition.
form_definition_current.id,
**kwd)
# if validation error encountered while saving the form, show the
# unsaved form, with the error message
if not new_form_definition:
status = 'error'
else:
# everything went fine. form saved successfully. Show the saved form or redirect
# to response_redirect if appropriate.
if response_redirect:
return trans.response.send_redirect(response_redirect)
form_definition = new_form_definition
current_form = self.get_saved_form(form_definition)
message = "The form '%s' has been updated with the changes." % form_definition.name
# Add a layout grid
elif params.get('add_layout_grid_button', False):
current_form['layout'].append('')
# Delete a layout grid
elif params.get('remove_layout_grid_button', False):
index = int(kwd['remove_layout_grid_button'].split(' ')[2]) - 1
del current_form['layout'][index]
# Add a field
elif params.get('add_field_button', False):
field_index = len(current_form['fields']) + 1
self.empty_field['name'] = '%i_field_name' % field_index
self.empty_field['label'] = 'Field label %i' % field_index
current_form['fields'].append(self.empty_field)
# Delete a field
elif params.get('remove_button', False):
# find the index of the field to be removed from the remove button label
index = int(kwd['remove_button'].split(' ')[2]) - 1
del current_form['fields'][index]
# Add SelectField option
elif 'Add' in kwd.values():
current_form, status, message = self.__add_select_field_option(
trans=trans, current_form=current_form, **kwd)
# Remove SelectField option
elif 'Remove' in kwd.values():
current_form, status, message = self.__remove_select_field_option(
trans=trans, current_form=current_form, **kwd)
return self.show_editable_form_definition(
trans=trans,
form_definition=form_definition,
current_form=current_form,
message=message,
status=status,
response_redirect=response_redirect,
**kwd)
def select_datasets_to_transfer(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
request_id = kwd.get('request_id', None)
external_service_id = kwd.get('external_service_id', None)
request = trans.sa_session.query(trans.model.Request).get(
trans.security.decode_id(request_id))
external_service = trans.sa_session.query(
trans.model.ExternalService).get(
trans.security.decode_id(external_service_id))
# Load the data transfer settings
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
selected_datasets_to_transfer = util.restore_text(
params.get('selected_datasets_to_transfer', ''))
if selected_datasets_to_transfer:
selected_datasets_to_transfer = selected_datasets_to_transfer.split(
',')
else:
selected_datasets_to_transfer = []
sample_id = kwd.get('sample_id', 'none')
sample_id_select_field = self.__build_sample_id_select_field(
trans, request, sample_id)
if sample_id != 'none':
sample = trans.sa_session.query(trans.model.Sample).get(
trans.security.decode_id(sample_id))
else:
sample = None
# The __get_files() method redirects here with a status of 'error' and a message if there
# was a problem retrieving the files.
if params.get('select_datasets_to_transfer_button', False):
# Get the sample that was sequenced to produce these datasets.
if sample_id == 'none':
del kwd['select_datasets_to_transfer_button']
message = 'Select the sample that was sequenced to produce the datasets you want to transfer.'
kwd['message'] = message
kwd['status'] = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='select_datasets_to_transfer',
**kwd))
if not sample.library:
# Display an error if a sample has been selected that
# has not yet been associated with a destination library.
message = 'Select a target data library and folder for the sample before selecting the datasets.'
status = 'error'
return trans.response.send_redirect(
web.url_for(controller='requests_common',
action='edit_samples',
cntrller='requests_admin',
id=trans.security.encode_id(request.id),
status=status,
message=message))
# Save the sample datasets
sample_dataset_file_names = self.__create_sample_datasets(
trans, sample, selected_datasets_to_transfer, external_service)
if sample_dataset_file_names:
message = 'Datasets (%s) have been selected for sample (%s)' % \
( str( sample_dataset_file_names )[1:-1].replace( "'", "" ), sample.name )
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
request_id=request_id,
sample_id=sample_id,
message=message,
status=status))
return trans.fill_template(
'/admin/requests/select_datasets_to_transfer.mako',
cntrller='requests_admin',
request=request,
external_service=external_service,
scp_configs=scp_configs,
sample=sample,
sample_id_select_field=sample_id_select_field,
status=status,
message=message)
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')
# 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 'state_name_%i' % i in kwd:
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 __create_data_transfer_messages(self, trans, sample,
selected_sample_datasets):
"""
Creates the xml messages to send to the rabbitmq server. It returns a dictionary of messages
keyed by the external service used to transfer the datasets
"""
# Create the xml message based on the following template
xml = \
''' <data_transfer>
<galaxy_host>%(GALAXY_HOST)s</galaxy_host>
<api_key>%(API_KEY)s</api_key>
<data_host>%(DATA_HOST)s</data_host>
<data_user>%(DATA_USER)s</data_user>
<data_password>%(DATA_PASSWORD)s</data_password>
<request_id>%(REQUEST_ID)s</request_id>
<sample_id>%(SAMPLE_ID)s</sample_id>
<library_id>%(LIBRARY_ID)s</library_id>
<folder_id>%(FOLDER_ID)s</folder_id>
%(DATASETS)s
</data_transfer>'''
dataset_xml = \
'''<dataset>
<dataset_id>%(ID)s</dataset_id>
<name>%(NAME)s</name>
<file>%(FILE)s</file>
</dataset>'''
# Here we group all the sample_datasets by the external service used to transfer them.
# The idea is to bundle up the sample_datasets which uses the same external service and
# send a single AMQP message to the galaxy_listener
dataset_elements = {}
for sample_dataset in selected_sample_datasets:
external_service = sample_dataset.external_service
if sample_dataset.status == trans.app.model.SampleDataset.transfer_status.NOT_STARTED:
if external_service not in dataset_elements:
dataset_elements[external_service] = ''
dataset_elements[external_service] += dataset_xml % dict(
ID=str(sample_dataset.id),
NAME=sample_dataset.name,
FILE=sample_dataset.file_path)
# update the dataset transfer status
sample_dataset.status = trans.app.model.SampleDataset.transfer_status.IN_QUEUE
trans.sa_session.add(sample_dataset)
trans.sa_session.flush()
# Finally prepend the external service info to the sets of sample datasets
messages = []
for external_service, dataset_elem in dataset_elements.items():
external_service.load_data_transfer_settings(trans)
scp_configs = external_service.data_transfer[
trans.model.ExternalService.data_transfer_protocol.SCP]
# Check data transfer settings
err_msg = self.__validate_data_transfer_settings(
trans, sample.request.type, scp_configs)
if err_msg:
return trans.response.send_redirect(
web.url_for(controller='requests_admin',
action='manage_datasets',
sample_id=trans.security.encode_id(sample.id),
status='error',
message=err_msg))
message = xml % dict(GALAXY_HOST=trans.request.host,
API_KEY=trans.user.api_keys[0].key,
DATA_HOST=scp_configs['host'],
DATA_USER=scp_configs['user_name'],
DATA_PASSWORD=scp_configs['password'],
REQUEST_ID=str(sample.request.id),
SAMPLE_ID=str(sample.id),
LIBRARY_ID=str(sample.library.id),
FOLDER_ID=str(sample.folder.id),
DATASETS=dataset_elem)
messages.append(message.replace('\n', '').replace('\r', ''))
return messages
def edit_form_definition( self, trans, response_redirect=None, **kwd ):
'''
This callback method is for handling form editing. The value of response_redirect
should be an URL that is defined by the caller. This allows for redirecting as desired
when the form changes have been saved. For an example of how this works, see the
edit_template() method in the base controller.
'''
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
try:
form_definition_current = trans.sa_session.query( trans.app.model.FormDefinitionCurrent ).get( trans.security.decode_id(kwd['id']) )
except:
return trans.response.send_redirect( web.url_for( controller='forms',
action='browse_form_definitions',
message='Invalid form',
status='error' ) )
form_definition = form_definition_current.latest_form
# TODO: eliminate the need for this refresh param.
if params.get( 'refresh', False ):
# Refresh
current_form = self.get_current_form( trans, **kwd )
else:
# Show the saved form for editing
current_form = self.get_saved_form( form_definition )
# Save changes
if params.get( 'save_changes_button', False ):
new_form_definition, message = self.save_form_definition( trans, form_definition_current_id=form_definition.form_definition_current.id, **kwd )
# if validation error encountered while saving the form, show the
# unsaved form, with the error message
if not new_form_definition:
status = 'error'
else:
# everything went fine. form saved successfully. Show the saved form or redirect
# to response_redirect if appropriate.
if response_redirect:
return trans.response.send_redirect( response_redirect )
form_definition = new_form_definition
current_form = self.get_saved_form( form_definition )
message = "The form '%s' has been updated with the changes." % form_definition.name
# Add a layout grid
elif params.get( 'add_layout_grid_button', False ):
current_form[ 'layout' ].append( '' )
# Delete a layout grid
elif params.get( 'remove_layout_grid_button', False ):
index = int( kwd[ 'remove_layout_grid_button' ].split( ' ' )[2] ) - 1
del current_form[ 'layout' ][index]
# Add a field
elif params.get( 'add_field_button', False ):
field_index = len( current_form[ 'fields' ] ) + 1
self.empty_field[ 'name' ] = '%i_field_name' % field_index
self.empty_field[ 'label' ] = 'Field label %i' % field_index
current_form[ 'fields' ].append( self.empty_field )
# Delete a field
elif params.get( 'remove_button', False ):
# find the index of the field to be removed from the remove button label
index = int( kwd[ 'remove_button' ].split( ' ' )[2] ) - 1
del current_form[ 'fields' ][ index ]
# Add SelectField option
elif 'Add' in kwd.values():
current_form, status, message = self.__add_select_field_option( trans=trans,
current_form=current_form,
**kwd)
# Remove SelectField option
elif 'Remove' in kwd.values():
current_form, status, message = self.__remove_select_field_option( trans=trans,
current_form=current_form,
**kwd)
return self.show_editable_form_definition( trans=trans,
form_definition=form_definition,
current_form=current_form,
message=message,
status=status,
response_redirect=response_redirect,
**kwd )
