def run( self, trans, workflow_id, payload, **kwd ):
"""
POST /api_internal/workflows/{encoded_workflow_id}/run
Run a workflow with a dictionary of prefixed_name/value pairs e.g.
payload = { inputs: { step_0: { parameter_0|parameter_1 : value_0, ... }, ... } }
"""
workflow = self.__get_stored_accessible_workflow( trans, workflow_id ).latest_workflow
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector( trans )
params, param_keys = expand_workflow_inputs( payload.get( 'inputs', [] ) )
errors = {}
for workflow_args in params:
for step in workflow.steps:
step_args = workflow_args.get( str( step.id ), {} )
step_errors = module_injector.inject( step, step_args )
if step_errors:
errors[ step.id ] = step_errors
if errors:
log.exception( errors )
raise exceptions.MessageException( err_data=errors )
invocations = []
for index, workflow_args in enumerate( params ):
for step in workflow.steps:
step_args = workflow_args.get( str( step.id ), {} )
module_injector.inject( step, step_args )
new_history = None
if 'new_history_name' in payload:
if payload[ 'new_history_name' ]:
nh_name = payload[ 'new_history_name' ]
else:
nh_name = 'History from %s workflow' % workflow.name
if index in param_keys:
ids = param_keys[ index ]
nids = len( ids )
if nids == 1:
nh_name = '%s on %s' % ( nh_name, ids[ 0 ] )
elif nids > 1:
nh_name = '%s on %s and %s' % ( nh_name, ', '.join( ids[ 0:-1 ] ), ids[ -1 ] )
new_history = trans.app.model.History( user=trans.user, name=nh_name )
new_history.copy_tags_from( trans.user, trans.history )
trans.sa_session.add( new_history )
target_history = new_history
elif 'history_id' in payload:
target_history = histories.HistoryManager( trans.app ).get_owned( trans.security.decode_id( payload.get( 'history_id' ), trans.user, current_history=trans.history ) )
else:
target_history = trans.history
run_config = WorkflowRunConfig(
target_history=target_history,
replacement_dict=payload.get( 'replacement_params', {} ),
copy_inputs_to_history=new_history is not None )
invocation = queue_invoke(
trans=trans,
workflow=workflow,
workflow_run_config=run_config,
populate_state=False )
invocations.append({ 'history' : { 'id' : trans.app.security.encode_id( new_history.id ), 'name' : new_history.name } if new_history else None,
'scheduled' : invocation.state == trans.app.model.WorkflowInvocation.states.SCHEDULED })
trans.sa_session.flush()
return invocations
def build_workflow_run_configs(trans, workflow, payload):
app = trans.app
allow_tool_state_corrections = payload.get('allow_tool_state_corrections', False)
use_cached_job = payload.get('use_cached_job', False)
# Sanity checks.
if len(workflow.steps) == 0:
raise exceptions.MessageException("Workflow cannot be run because it does not have any steps")
if workflow.has_cycles:
raise exceptions.MessageException("Workflow cannot be run because it contains cycles")
if 'step_parameters' in payload and 'parameters' in payload:
raise exceptions.RequestParameterInvalidException("Cannot specify both legacy parameters and step_parameters attributes.")
if 'inputs' in payload and 'ds_map' in payload:
raise exceptions.RequestParameterInvalidException("Cannot specify both legacy ds_map and input attributes.")
add_to_history = 'no_add_to_history' not in payload
legacy = payload.get('legacy', False)
already_normalized = payload.get('parameters_normalized', False)
raw_parameters = payload.get('parameters', {})
run_configs = []
unexpanded_param_map = _normalize_step_parameters(workflow.steps, raw_parameters, legacy=legacy, already_normalized=already_normalized)
expanded_params, expanded_param_keys = expand_workflow_inputs(unexpanded_param_map)
for index, param_map in enumerate(expanded_params):
history = _get_target_history(trans, workflow, payload, expanded_param_keys, index)
inputs = payload.get('inputs', None)
inputs_by = payload.get('inputs_by', None)
# New default is to reference steps by index of workflow step
# which is intrinsic to the workflow and independent of the state
# of Galaxy at the time of workflow import.
default_inputs_by = 'step_index|step_uuid'
if inputs is None:
# Default to legacy behavior - read ds_map and reference steps
# by unencoded step id (a raw database id).
inputs = payload.get('ds_map', {})
if legacy:
default_inputs_by = 'step_id|step_uuid'
inputs_by = inputs_by or default_inputs_by
else:
inputs = inputs or {}
inputs_by = inputs_by or default_inputs_by
if inputs or not already_normalized:
normalized_inputs = _normalize_inputs(workflow.steps, inputs, inputs_by)
else:
# Only allow dumping IDs directly into JSON database instead of properly recording the
# inputs with referential integrity if parameters are already normalized (coming from tool form).
normalized_inputs = {}
steps_by_id = workflow.steps_by_id
# Set workflow inputs.
for key, input_dict in normalized_inputs.items():
step = steps_by_id[key]
if step.type == 'parameter_input':
continue
if 'src' not in input_dict:
raise exceptions.RequestParameterInvalidException("Not input source type defined for input '%s'." % input_dict)
if 'id' not in input_dict:
raise exceptions.RequestParameterInvalidException("Not input id defined for input '%s'." % input_dict)
if 'content' in input_dict:
raise exceptions.RequestParameterInvalidException("Input cannot specify explicit 'content' attribute %s'." % input_dict)
input_source = input_dict['src']
input_id = input_dict['id']
try:
if input_source == 'ldda':
ldda = trans.sa_session.query(app.model.LibraryDatasetDatasetAssociation).get(trans.security.decode_id(input_id))
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset)
content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
elif input_source == 'ld':
ldda = trans.sa_session.query(app.model.LibraryDataset).get(trans.security.decode_id(input_id)).library_dataset_dataset_association
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), ldda.dataset)
content = ldda.to_history_dataset_association(history, add_to_history=add_to_history)
elif input_source == 'hda':
# Get dataset handle, add to dict and history if necessary
content = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(trans.security.decode_id(input_id))
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), content.dataset)
elif input_source == 'uuid':
dataset = trans.sa_session.query(app.model.Dataset).filter(app.model.Dataset.uuid == input_id).first()
if dataset is None:
# this will need to be changed later. If federation code is avalible, then a missing UUID
# could be found amoung fereration partners
raise exceptions.RequestParameterInvalidException("Input cannot find UUID: %s." % input_id)
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset(trans.get_current_user_roles(), dataset)
content = history.add_dataset(dataset)
elif input_source == 'hdca':
content = app.dataset_collections_service.get_dataset_collection_instance(trans, 'history', input_id)
else:
raise exceptions.RequestParameterInvalidException("Unknown workflow input source '%s' specified." % input_source)
if add_to_history and content.history != history:
content = content.copy()
if isinstance(content, app.model.HistoryDatasetAssociation):
history.add_dataset(content)
else:
history.add_dataset_collection(content)
input_dict['content'] = content
except AssertionError:
raise exceptions.ItemAccessibilityException("Invalid workflow input '%s' specified" % input_id)
for key in set(normalized_inputs.keys()):
value = normalized_inputs[key]
if isinstance(value, dict) and 'content' in value:
normalized_inputs[key] = value['content']
else:
normalized_inputs[key] = value
resource_params = payload.get('resource_params', {})
if resource_params:
# quick attempt to validate parameters, just handle select options now since is what
# is needed for DTD - arbitrary plugins can define arbitrary logic at runtime in the
# destination function. In the future this should be extended to allow arbitrary
# pluggable validation.
resource_mapper_function = get_resource_mapper_function(trans.app)
# TODO: Do we need to do anything with the stored_workflow or can this be removed.
resource_parameters = resource_mapper_function(trans=trans, stored_workflow=None, workflow=workflow)
for resource_parameter in resource_parameters:
if resource_parameter.get("type") == "select":
name = resource_parameter.get("name")
if name in resource_params:
value = resource_params[name]
valid_option = False
# TODO: How should be handle the case where no selection is made by the user
# This can happen when there is a select on the page but the user has no options to select
# Here I have the validation pass it through. An alternative may be to remove the parameter if
# it is None.
if value is None:
valid_option = True
else:
for option_elem in resource_parameter.get('data'):
option_value = option_elem.get("value")
if value == option_value:
valid_option = True
if not valid_option:
raise exceptions.RequestParameterInvalidException("Invalid value for parameter '%s' found." % name)
run_configs.append(WorkflowRunConfig(
target_history=history,
replacement_dict=payload.get('replacement_params', {}),
inputs=normalized_inputs,
param_map=param_map,
allow_tool_state_corrections=allow_tool_state_corrections,
use_cached_job=use_cached_job,
resource_params=resource_params,
))
return run_configs
def build_workflow_run_configs( trans, workflow, payload ):
app = trans.app
allow_tool_state_corrections = payload.get( 'allow_tool_state_corrections', False )
# Sanity checks.
if len( workflow.steps ) == 0:
raise exceptions.MessageException( "Workflow cannot be run because it does not have any steps" )
if workflow.has_cycles:
raise exceptions.MessageException( "Workflow cannot be run because it contains cycles" )
if 'step_parameters' in payload and 'parameters' in payload:
raise exceptions.RequestParameterInvalidException( "Cannot specify both legacy parameters and step_parameters attributes." )
if 'inputs' in payload and 'ds_map' in payload:
raise exceptions.RequestParameterInvalidException( "Cannot specify both legacy ds_map and input attributes." )
add_to_history = 'no_add_to_history' not in payload
legacy = payload.get( 'legacy', False )
already_normalized = payload.get( 'parameters_normalized', False )
raw_parameters = payload.get( 'parameters', {} )
run_configs = []
unexpanded_param_map = _normalize_step_parameters( workflow.steps, raw_parameters, legacy=legacy, already_normalized=already_normalized )
expanded_params, expanded_param_keys = expand_workflow_inputs( unexpanded_param_map )
for index, param_map in enumerate( expanded_params ):
history = _get_target_history(trans, workflow, payload, expanded_param_keys, index)
inputs = payload.get( 'inputs', None )
inputs_by = payload.get( 'inputs_by', None )
# New default is to reference steps by index of workflow step
# which is intrinsic to the workflow and independent of the state
# of Galaxy at the time of workflow import.
default_inputs_by = 'step_index|step_uuid'
if inputs is None:
# Default to legacy behavior - read ds_map and reference steps
# by unencoded step id (a raw database id).
inputs = payload.get( 'ds_map', {} )
if legacy:
default_inputs_by = 'step_id|step_uuid'
inputs_by = inputs_by or default_inputs_by
else:
inputs = inputs or {}
inputs_by = inputs_by or default_inputs_by
if inputs or not already_normalized:
normalized_inputs = _normalize_inputs( workflow.steps, inputs, inputs_by )
else:
# Only allow dumping IDs directly into JSON database instead of properly recording the
# inputs with referential integrity if parameters are already normalized (coming from tool form).
normalized_inputs = {}
steps_by_id = workflow.steps_by_id
# Set workflow inputs.
for key, input_dict in normalized_inputs.iteritems():
step = steps_by_id[key]
if step.type == 'parameter_input':
continue
if 'src' not in input_dict:
raise exceptions.RequestParameterInvalidException( "Not input source type defined for input '%s'." % input_dict )
if 'id' not in input_dict:
raise exceptions.RequestParameterInvalidException( "Not input id defined for input '%s'." % input_dict )
if 'content' in input_dict:
raise exceptions.RequestParameterInvalidException( "Input cannot specify explicit 'content' attribute %s'." % input_dict )
input_source = input_dict[ 'src' ]
input_id = input_dict[ 'id' ]
try:
if input_source == 'ldda':
ldda = trans.sa_session.query( app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( input_id ) )
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset )
content = ldda.to_history_dataset_association( history, add_to_history=add_to_history )
elif input_source == 'ld':
ldda = trans.sa_session.query( app.model.LibraryDataset ).get( trans.security.decode_id( input_id ) ).library_dataset_dataset_association
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset )
content = ldda.to_history_dataset_association( history, add_to_history=add_to_history )
elif input_source == 'hda':
# Get dataset handle, add to dict and history if necessary
content = trans.sa_session.query( app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( input_id ) )
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset )
elif input_source == 'uuid':
dataset = trans.sa_session.query( app.model.Dataset ).filter( app.model.Dataset.uuid == input_id ).first()
if dataset is None:
# this will need to be changed later. If federation code is avalible, then a missing UUID
# could be found amoung fereration partners
raise exceptions.RequestParameterInvalidException( "Input cannot find UUID: %s." % input_id )
assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), dataset )
content = history.add_dataset( dataset )
elif input_source == 'hdca':
content = app.dataset_collections_service.get_dataset_collection_instance( trans, 'history', input_id )
else:
raise exceptions.RequestParameterInvalidException( "Unknown workflow input source '%s' specified." % input_source )
if add_to_history and content.history != history:
content = content.copy()
if isinstance( content, app.model.HistoryDatasetAssociation ):
history.add_dataset( content )
else:
history.add_dataset_collection( content )
input_dict[ 'content' ] = content
except AssertionError:
raise exceptions.ItemAccessibilityException( "Invalid workflow input '%s' specified" % input_id )
for key in set( normalized_inputs.keys() ):
value = normalized_inputs[ key ]
if isinstance( value, dict ) and 'content' in value:
normalized_inputs[ key ] = value[ 'content' ]
else:
normalized_inputs[ key ] = value
run_configs.append(WorkflowRunConfig(
target_history=history,
replacement_dict=payload.get( 'replacement_params', {} ),
inputs=normalized_inputs,
param_map=param_map,
allow_tool_state_corrections=allow_tool_state_corrections
))
return run_configs
def run(self, trans, workflow_id, payload, **kwd):
"""
POST /api_internal/workflows/{encoded_workflow_id}/run
Run a workflow with a dictionary of prefixed_name/value pairs e.g.
payload = { inputs: { step_0: { parameter_0|parameter_1 : value_0, ... }, ... } }
"""
workflow = self.__get_stored_accessible_workflow(
trans, workflow_id).latest_workflow
trans.workflow_building_mode = workflow_building_modes.USE_HISTORY
module_injector = WorkflowModuleInjector(trans)
params, param_keys = expand_workflow_inputs(payload.get('inputs', []))
errors = {}
for workflow_args in params:
for step in workflow.steps:
step_args = workflow_args.get(str(step.id), {})
step_errors = module_injector.inject(step, step_args)
if step_errors:
errors[step.id] = step_errors
if errors:
log.exception(errors)
raise exceptions.MessageException(err_data=errors)
invocations = []
for index, workflow_args in enumerate(params):
for step in workflow.steps:
step_args = workflow_args.get(str(step.id), {})
module_injector.inject(step, step_args)
new_history = None
if 'new_history_name' in payload:
if payload['new_history_name']:
nh_name = payload['new_history_name']
else:
nh_name = 'History from %s workflow' % workflow.name
if index in param_keys:
ids = param_keys[index]
nids = len(ids)
if nids == 1:
nh_name = '%s on %s' % (nh_name, ids[0])
elif nids > 1:
nh_name = '%s on %s and %s' % (nh_name, ', '.join(
ids[0:-1]), ids[-1])
new_history = trans.app.model.History(user=trans.user,
name=nh_name)
new_history.copy_tags_from(trans.user, trans.history)
trans.sa_session.add(new_history)
target_history = new_history
elif 'history_id' in payload:
target_history = histories.HistoryManager(trans.app).get_owned(
trans.security.decode_id(payload.get('history_id'),
trans.user,
current_history=trans.history))
else:
target_history = trans.history
run_config = WorkflowRunConfig(target_history=target_history,
replacement_dict=payload.get(
'replacement_params', {}),
copy_inputs_to_history=new_history
is not None)
invocation = queue_invoke(trans=trans,
workflow=workflow,
workflow_run_config=run_config,
populate_state=False)
invocations.append({
'history': {
'id': trans.app.security.encode_id(new_history.id),
'name': new_history.name
} if new_history else None,
'scheduled':
invocation.state ==
trans.app.model.WorkflowInvocation.states.SCHEDULED
})
trans.sa_session.flush()
return invocations