def __init__(self, app):
super(HistoryContentsController, self).__init__(app)
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.folder_manager = folders.FolderManager()
self.hda_serializer = hdas.HDASerializer(app)
self.hda_deserializer = hdas.HDADeserializer(app)
def _get_target_history(trans, workflow, payload, param_keys=None, index=0):
param_keys = param_keys or []
history_name = payload.get('new_history_name', None)
history_id = payload.get('history_id', None)
history_param = payload.get('history', None)
if [history_name, history_id, history_param].count(None) < 2:
raise exceptions.RequestParameterInvalidException("Specified workflow target history multiple ways - at most one of 'history', 'history_id', and 'new_history_name' may be specified.")
if history_param:
if history_param.startswith('hist_id='):
history_id = history_param[8:]
else:
history_name = history_param
if history_id:
history_manager = histories.HistoryManager(trans.app)
target_history = history_manager.get_owned(trans.security.decode_id(history_id), trans.user, current_history=trans.history)
else:
if history_name:
nh_name = history_name
else:
nh_name = 'History from %s workflow' % workflow.name
if len(param_keys) <= index:
raise exceptions.MessageException("Incorrect expansion of workflow batch parameters.")
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)
trans.sa_session.add(new_history)
target_history = new_history
return target_history
def __init__(self, app):
super(HistoriesController, self).__init__(app)
self.citations_manager = citations.CitationsManager(app)
self.user_manager = users.UserManager(app)
self.history_manager = histories.HistoryManager(app)
self.history_serializer = histories.HistorySerializer(app)
self.history_deserializer = histories.HistoryDeserializer(app)
self.history_filters = histories.HistoryFilters(app)
def __init__( self, app ):
self.type_registry = DatasetCollectionTypesRegistry( app )
self.collection_type_descriptions = CollectionTypeDescriptionFactory( self.type_registry )
self.model = app.model
self.security = app.security
self.hda_manager = hdas.HDAManager()
self.history_manager = histories.HistoryManager()
self.tag_manager = tags.TagsManager( app )
self.ldda_manager = lddas.LDDAManager( )
def __init__(self, app):
super(HistoriesController, self).__init__(app)
self.citations_manager = citations.CitationsManager(app)
self.user_manager = users.UserManager(app)
self.workflow_manager = workflows.WorkflowsManager(app)
self.manager = histories.HistoryManager(app)
self.serializer = histories.HistorySerializer(app)
self.deserializer = histories.HistoryDeserializer(app)
self.filters = histories.HistoryFilters(app)
def __init__(self, app):
self.type_registry = DATASET_COLLECTION_TYPES_REGISTRY
self.collection_type_descriptions = COLLECTION_TYPE_DESCRIPTION_FACTORY
self.model = app.model
self.security = app.security
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.tag_handler = tags.GalaxyTagHandler(app.model.context)
self.ldda_manager = lddas.LDDAManager(app)
def __init__(self, app):
super().__init__(app)
self.citations_manager = citations.CitationsManager(app)
self.user_manager = users.UserManager(app)
self.workflow_manager = workflows.WorkflowsManager(app)
self.manager = histories.HistoryManager(app)
self.history_export_view = histories.HistoryExportView(app)
self.serializer = histories.HistorySerializer(app)
self.deserializer = histories.HistoryDeserializer(app)
self.filters = histories.HistoryFilters(app)
def __init__(self, app):
super(WorkflowsAPIController, self).__init__(app)
self.history_manager = histories.HistoryManager(app)
self.workflow_manager = workflows.WorkflowsManager(app)
self.workflow_contents_manager = workflows.WorkflowContentsManager()
def build_workflow_run_config(trans, workflow, payload):
app = trans.app
history_manager = histories.HistoryManager(app)
# Pull other parameters out of payload.
param_map = payload.get('parameters', {})
param_map = normalize_step_parameters(workflow.steps, param_map)
inputs = payload.get('inputs', None)
inputs_by = payload.get('inputs_by', None)
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', {})
inputs_by = inputs_by or 'step_id|step_uuid'
else:
inputs = inputs or {}
# 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.
inputs_by = inputs_by or 'step_index|step_uuid'
add_to_history = 'no_add_to_history' not in payload
history_param = payload.get('history', '')
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 workflow.has_errors:
message = "Workflow cannot be run because of validation errors in some steps"
raise exceptions.MessageException(message)
# Get target history.
if history_param.startswith('hist_id='):
# Passing an existing history to use.
encoded_history_id = history_param[8:]
history_id = __decode_id(trans,
encoded_history_id,
model_type="history")
history = history_manager.get_owned(history_id,
trans.user,
current_history=trans.history)
else:
# Send workflow outputs to new history.
history = app.model.History(name=history_param, user=trans.user)
trans.sa_session.add(history)
trans.sa_session.flush()
# Set workflow inputs.
for input_dict in inputs.itervalues():
if 'src' not in input_dict:
message = "Not input source type defined for input '%s'." % input_dict
raise exceptions.RequestParameterInvalidException(message)
if 'id' not in input_dict:
message = "Not input id defined for input '%s'." % input_dict
raise exceptions.RequestParameterInvalidException(message)
if 'content' in input_dict:
message = "Input cannot specify explicit 'content' attribute %s'." % input_dict
raise exceptions.RequestParameterInvalidException(message)
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
message = "Input cannot find UUID: %s." % input_id
raise exceptions.RequestParameterInvalidException(message)
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:
message = "Unknown workflow input source '%s' specified." % input_source
raise exceptions.RequestParameterInvalidException(message)
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:
message = "Invalid workflow input '%s' specified" % input_id
raise exceptions.ItemAccessibilityException(message)
normalized_inputs = normalize_inputs(workflow.steps, inputs, inputs_by)
# Run each step, connecting outputs to inputs
replacement_dict = payload.get('replacement_params', {})
run_config = WorkflowRunConfig(
target_history=history,
replacement_dict=replacement_dict,
inputs=normalized_inputs,
param_map=param_map,
allow_tool_state_corrections=allow_tool_state_corrections)
return run_config
def __init__(self, app):
super(HistoriesController, self).__init__(app)
self.citations_manager = citations.CitationsManager(app)
self.mgrs = util.bunch.Bunch(histories=histories.HistoryManager())
def set_up_managers(self):
super(CurrentUserSerializerTestCase, self).set_up_managers()
self.history_manager = histories.HistoryManager(self.app)
self.user_serializer = users.CurrentUserSerializer(self.app)
def __init__(self, app):
super(PluginsController, self).__init__(app)
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
def __init__(self, app):
super(HistoryContentsController, self).__init__(app)
self.mgrs = util.bunch.Bunch(histories=histories.HistoryManager(),
hdas=hdas.HDAManager())
def __init__(self):
"""
Set up and initialize other managers needed by hdas.
"""
self.histories_mgr = history_manager.HistoryManager()
def __init__(self, app):
super().__init__(app)
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
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