code stringlengths 3 6.57k |
|---|
actions (see below) |
following (deprecated) |
Finally (again, for backwards compatibility) |
actions (PJAs) |
property
(which is stable across workflow imports) |
self.gi.invocations.get(inv_dict['id']) |
Invocation(Wrapper) |
__init__(self, inv_dict, gi=None) |
super() |
__init__(inv_dict, gi=gi) |
InvocationStep(step, self) |
self.inputs.items() |
sorted_step_ids(self) |
sorted(self.steps, key=lambda step: step.order_index) |
step_states(self) |
number_of_steps(self) |
len(self.steps) |
sorted_steps_by(self, indices=None, states=None, step_ids=None) |
filter(lambda step: step.order_index in indices, steps) |
filter(lambda step: step.state in states, steps) |
filter(lambda step: step.id in step_ids, steps) |
sorted(steps, key=lambda step: step.order_index) |
cancel(self) |
self.gi.gi.invocations.cancel_invocation(self.id) |
self.__init__(inv_dict, gi=self.gi) |
refresh(self) |
self.gi.gi.invocations.show_invocation(self.id) |
self.__init__(inv_dict, gi=self.gi) |
run_step_actions(self, steps, actions) |
len(steps) |
len(actions) |
RuntimeError(f'Different number of ``steps`` ({len(steps) |
len(actions) |
run_step_actions() |
self.gi.gi.invocations.run_invocation_step_action(self.id, step.id, action) |
zip(steps, actions) |
zip(steps, step_dict_list) |
step.__init__(step_dict, parent=self) |
summary(self) |
self.gi.gi.invocations.get_invocation_summary(self.id) |
step_jobs_summary(self) |
self.gi.gi.invocations.get_invocation_step_jobs_summary(self.id) |
report(self) |
self.gi.gi.invocations.get_invocation_report(self.id) |
save_report_pdf(self, file_path, chunk_size=bioblend.CHUNK_SIZE) |
self.gi.gi.invocations.get_invocation_report_pdf(self.id, file_path, chunk_size) |
biocompute_object(self) |
self.gi.gi.invocations.get_invocation_biocompute_object(self.id) |
wait(self, maxwait=12000, interval=3, check=True) |
self.gi.gi.invocations.wait_for_invocation(self.id, maxwait=maxwait, interval=interval, check=check) |
self.__init__(inv_dict, gi=self.gi) |
Dataset(Wrapper, metaclass=abc.ABCMeta) |
__init__(self, ds_dict, container, gi=None) |
super() |
__init__(ds_dict, gi=gi) |
object.__setattr__(self, 'container', container) |
_stream_url(self) |
get_stream(self, chunk_size=bioblend.CHUNK_SIZE) |
isinstance(self, LibraryDataset) |
self.gi.gi.make_get_request(self._stream_url, **kwargs) |
isinstance(self, LibraryDataset) |
self.gi.gi.make_get_request(self._stream_url, **kwargs) |
r.raise_for_status() |
r.iter_content(chunk_size) |
peek(self, chunk_size=bioblend.CHUNK_SIZE) |
next(self.get_stream(chunk_size=chunk_size) |
download(self, file_object, chunk_size=bioblend.CHUNK_SIZE) |
self.get_stream(chunk_size=chunk_size) |
file_object.write(chunk) |
get_contents(self, chunk_size=bioblend.CHUNK_SIZE) |
join(self.get_stream(chunk_size=chunk_size) |
refresh(self) |
getattr(self.gi.gi, self.container.API_MODULE) |
gi_client.show_dataset(self.container.id, self.id) |
self.__init__(ds_dict, self.container, self.gi) |
wait(self, polling_interval=POLLING_INTERVAL, break_on_error=True) |
refreshed (possibly multiple times) |
HistoryDatasetAssociation(Dataset) |
_stream_url(self) |
self.gi.gi.histories._make_url(module_id=self.container.id, contents=True) |
update(self, **kwds) |
build (dbkey) |
self.gi.gi.histories.update_dataset(self.container.id, self.id, **kwds) |
been (un) |
self.container.refresh() |
self.__init__(res, self.container, gi=self.gi) |
delete(self, purge=False) |
purge (permanently delete) |
self.gi.gi.histories.delete_dataset(self.container.id, self.id, purge=purge) |
self.container.refresh() |
self.refresh() |
DatasetCollection(Wrapper, metaclass=abc.ABCMeta) |
__init__(self, dsc_dict, container, gi=None) |
super() |
__init__(dsc_dict, gi=gi) |
object.__setattr__(self, 'container', container) |
refresh(self) |
getattr(self.gi.gi, self.container.API_MODULE) |
gi_client.show_dataset_collection(self.container.id, self.id) |
self.__init__(dsc_dict, self.container, self.gi) |
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