def __to_pja( self, key, value, step ):
if 'output_name' in value:
output_name = value['output_name']
else:
output_name = None
if 'action_arguments' in value:
action_arguments = value['action_arguments']
else:
action_arguments = None
return PostJobAction(value['action_type'], step, output_name, action_arguments)
def save_to_step( self, step ):
step.type = self.type
step.tool_id = self.tool_id
if self.tool:
step.tool_version = self.get_tool_version()
step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
else:
step.tool_version = None
step.tool_inputs = None
step.tool_errors = self.errors
for k, v in self.post_job_actions.iteritems():
# Must have action_type, step. output and a_args are optional.
if 'output_name' in v:
output_name = v['output_name']
else:
output_name = None
if 'action_arguments' in v:
action_arguments = v['action_arguments']
else:
action_arguments = None
n_p = PostJobAction(v['action_type'], step, output_name, action_arguments)
def _create(self, trans: GalaxyWebTransaction, payload, **kwd):
action = payload.get('action')
if action == 'rerun':
raise Exception("'rerun' action has been deprecated")
# Get tool.
tool_version = payload.get('tool_version')
tool_id = payload.get('tool_id')
tool_uuid = payload.get('tool_uuid')
get_kwds = dict(
tool_id=tool_id,
tool_uuid=tool_uuid,
tool_version=tool_version,
)
if tool_id is None and tool_uuid is None:
raise exceptions.RequestParameterMissingException("Must specify either a tool_id or a tool_uuid.")
tool = trans.app.toolbox.get_tool(**get_kwds)
if not tool:
log.debug(f"Not found tool with kwds [{get_kwds}]")
raise exceptions.ToolMissingException('Tool not found.')
if not tool.allow_user_access(trans.user):
raise exceptions.ItemAccessibilityException('Tool not accessible.')
if trans.app.config.user_activation_on:
if not trans.user:
log.warning("Anonymous user attempts to execute tool, but account activation is turned on.")
elif not trans.user.active:
log.warning(f"User \"{trans.user.email}\" attempts to execute tool, but account activation is turned on and user account is not active.")
# Set running history from payload parameters.
# History not set correctly as part of this API call for
# dataset upload.
history_id = payload.get('history_id')
if history_id:
decoded_id = self.decode_id(history_id)
target_history = self.history_manager.get_owned(decoded_id, trans.user, current_history=trans.history)
else:
target_history = None
# Set up inputs.
inputs = payload.get('inputs', {})
if not isinstance(inputs, dict):
raise exceptions.RequestParameterInvalidException(f"inputs invalid {inputs}")
# Find files coming in as multipart file data and add to inputs.
for k, v in payload.items():
if k.startswith('files_') or k.startswith('__files_'):
inputs[k] = v
# for inputs that are coming from the Library, copy them into the history
self._patch_library_inputs(trans, inputs, target_history)
# TODO: encode data ids and decode ids.
# TODO: handle dbkeys
params = util.Params(inputs, sanitize=False)
incoming = params.__dict__
# use_cached_job can be passed in via the top-level payload or among the tool inputs.
# I think it should be a top-level parameter, but because the selector is implemented
# as a regular tool parameter we accept both.
use_cached_job = payload.get('use_cached_job', False) or util.string_as_bool(inputs.get('use_cached_job', 'false'))
input_format = str(payload.get('input_format', 'legacy'))
vars = tool.handle_input(trans, incoming, history=target_history, use_cached_job=use_cached_job, input_format=input_format)
# TODO: check for errors and ensure that output dataset(s) are available.
output_datasets = vars.get('out_data', [])
rval: Dict[str, Any] = {'outputs': [], 'output_collections': [], 'jobs': [], 'implicit_collections': []}
rval['produces_entry_points'] = tool.produces_entry_points
job_errors = vars.get('job_errors', [])
if job_errors:
# If we are here - some jobs were successfully executed but some failed.
rval['errors'] = job_errors
outputs = rval['outputs']
# TODO:?? poss. only return ids?
for output_name, output in output_datasets:
output_dict = output.to_dict()
# add the output name back into the output data structure
# so it's possible to figure out which newly created elements
# correspond with which tool file outputs
output_dict['output_name'] = output_name
outputs.append(trans.security.encode_dict_ids(output_dict, skip_startswith="metadata_"))
new_pja_flush = False
for job in vars.get('jobs', []):
rval['jobs'].append(self.encode_all_ids(trans, job.to_dict(view='collection'), recursive=True))
if inputs.get('send_email_notification', False):
# Unless an anonymous user is invoking this via the API it
# should never be an option, but check and enforce that here
if trans.user is None:
raise exceptions.ToolExecutionError("Anonymously run jobs cannot send an email notification.")
else:
job_email_action = PostJobAction('EmailAction')
job.add_post_job_action(job_email_action)
new_pja_flush = True
if new_pja_flush:
trans.sa_session.flush()
for output_name, collection_instance in vars.get('output_collections', []):
history = target_history or trans.history
output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history)
output_dict['output_name'] = output_name
rval['output_collections'].append(output_dict)
for output_name, collection_instance in vars.get('implicit_collections', {}).items():
history = target_history or trans.history
output_dict = dictify_dataset_collection_instance(collection_instance, security=trans.security, parent=history)
output_dict['output_name'] = output_name
rval['implicit_collections'].append(output_dict)
return rval
def _create(self, trans: GalaxyWebTransaction, payload, **kwd):
if trans.user_is_bootstrap_admin:
raise exceptions.RealUserRequiredException(
"Only real users can execute tools or run jobs.")
action = payload.get('action')
if action == 'rerun':
raise Exception("'rerun' action has been deprecated")
# Get tool.
tool_version = payload.get('tool_version')
tool_id = payload.get('tool_id')
tool_uuid = payload.get('tool_uuid')
get_kwds = dict(
tool_id=tool_id,
tool_uuid=tool_uuid,
tool_version=tool_version,
)
if tool_id is None and tool_uuid is None:
raise exceptions.RequestParameterMissingException(
"Must specify either a tool_id or a tool_uuid.")
tool = trans.app.toolbox.get_tool(**get_kwds)
if not tool:
log.debug(f"Not found tool with kwds [{get_kwds}]")
raise exceptions.ToolMissingException('Tool not found.')
if not tool.allow_user_access(trans.user):
raise exceptions.ItemAccessibilityException('Tool not accessible.')
if trans.app.config.user_activation_on:
if not trans.user:
log.warning(
"Anonymous user attempts to execute tool, but account activation is turned on."
)
elif not trans.user.active:
log.warning(
f"User \"{trans.user.email}\" attempts to execute tool, but account activation is turned on and user account is not active."
)
# Set running history from payload parameters.
# History not set correctly as part of this API call for
# dataset upload.
history_id = payload.get('history_id')
if history_id:
decoded_id = self.decode_id(history_id)
target_history = self.history_manager.get_owned(
decoded_id, trans.user, current_history=trans.history)
else:
target_history = None
# Set up inputs.
inputs = payload.get('inputs', {})
if not isinstance(inputs, dict):
raise exceptions.RequestParameterInvalidException(
f"inputs invalid {inputs}")
# Find files coming in as multipart file data and add to inputs.
for k, v in payload.items():
if k.startswith('files_') or k.startswith('__files_'):
inputs[k] = v
# for inputs that are coming from the Library, copy them into the history
self._patch_library_inputs(trans, inputs, target_history)
# TODO: encode data ids and decode ids.
# TODO: handle dbkeys
params = util.Params(inputs, sanitize=False)
incoming = params.__dict__
# use_cached_job can be passed in via the top-level payload or among the tool inputs.
# I think it should be a top-level parameter, but because the selector is implemented
# as a regular tool parameter we accept both.
use_cached_job = payload.get('use_cached_job',
False) or util.string_as_bool(
inputs.get('use_cached_job', 'false'))
input_format = str(payload.get('input_format', 'legacy'))
vars = tool.handle_input(trans,
incoming,
history=target_history,
use_cached_job=use_cached_job,
input_format=input_format)
new_pja_flush = False
for job in vars.get('jobs', []):
if inputs.get('send_email_notification', False):
# Unless an anonymous user is invoking this via the API it
# should never be an option, but check and enforce that here
if trans.user is None:
raise exceptions.ToolExecutionError(
"Anonymously run jobs cannot send an email notification."
)
else:
job_email_action = PostJobAction('EmailAction')
job.add_post_job_action(job_email_action)
new_pja_flush = True
if new_pja_flush:
trans.sa_session.flush()
return self._handle_inputs_output_to_api_response(
trans, tool, target_history, vars)
