def handles(self):
'''
Handles files are assumed to reside in a subfolder called "handles"
and have the suffix ".handles.yml".
Returns
-------
List[dict]
name and description for each handles file
'''
handles = list()
for module_file in self.module_files:
name = self._get_module_name_from_file(module_file)
try:
with YamlReader(self._get_handles_file(module_file)) as y:
handles.append({
# FIXME: why not a NamedTuple??
'name': name,
'description': y.read(),
})
except Exception as err:
logging.warning("Cannot read handles file for module `%s`: %s",
name, err)
continue
return handles
def _create_pipe(self):
with YamlReader(self.pipe_file) as f:
content = f.read()
try:
description = PipelineDescription(**content)
except TypeError as err:
raise PipelineDescription('Incorrect pipeline description: %s' %
str(err))
return Pipe(description)
def _create_handles(self):
handles = list()
for name in self._module_names:
h_file = self._get_handles_file(name)
try:
with YamlReader(h_file) as f:
content = f.read()
description = HandleDescriptions(**content)
h = Handles(name, description)
handles.append(h)
except Exception as err:
logger.error("Cannot instanciate module `%s`: %s: %s", name,
err.__class__.__name__, err)
return handles
def _create_handles(self):
handles = list()
for name in self._module_names:
h_file = self._get_handles_file(name)
with YamlReader(h_file) as f:
content = f.read()
try:
description = HandleDescriptions(**content)
except TypeError as err:
raise PipelineDescription(
'Incorrect handles description of module "%s": %s' %
(name, str(err)))
h = Handles(name, description)
handles.append(h)
return handles
def handles(self):
'''
Handles files are assumed to reside in a subfolder called "handles"
and have the suffix ".handles.yml".
Returns
-------
List[dict]
name and description for each handles file
'''
handles = list()
for name in self.module_names:
try:
with YamlReader(self._get_handles_file(name)) as f:
handles.append({'name': name, 'description': f.read()})
except:
continue
return handles
def workflow_description(self):
'''tmlib.workflow.tmaps.description.WorkflowDescription: description
of the workflow
Note
----
When no description is available from file, a default description is
provided. The type of the workflow will be determined based on
:attr:`workflow_type <tmlib.models.experiment.Experiment.workflow_type>`.
'''
if not os.path.exists(self._workflow_descriptor_file):
logger.warn('no persistent workflow description found')
with ExperimentSession(self.id) as session:
exp = session.query(Experiment).get(self.id)
workflow_type = exp.workflow_type
logger.info('create workflow of type "%s"', workflow_type)
workflow_description = WorkflowDescription(workflow_type)
self.persist_workflow_description(workflow_description)
with YamlReader(self._workflow_descriptor_file) as f:
description = f.read()
if not isinstance(description, dict):
raise TypeError('Description must be a mapping.')
if 'type' not in description:
raise KeyError('Workflow description must have key "type".')
if 'stages' not in description:
raise KeyError('Workflow description must have key "stages".')
workflow_description = WorkflowDescription(**description)
def update_choices(arguments):
for arg in arguments.iterargs():
if getattr(arg, 'get_choices', None):
arg.choices = arg.get_choices(self)
for stage in workflow_description.stages:
for step in stage.steps:
update_choices(step.batch_args)
update_choices(step.submission_args)
return workflow_description