code stringlengths 3 6.57k |
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subworkflow
(type ``subworkflow``) |
pause (type ``pause``) |
__init__(self, step_dict, parent) |
super() |
__init__(step_dict, parent=parent, gi=parent.gi) |
ValueError('not a step dict') |
ValueError(f"Unknown step type: {stype!r}") |
InvocationStep(Wrapper) |
Workflow(Wrapper) |
__init__(self, wf_dict, gi=None) |
super() |
__init__(wf_dict, gi=gi) |
gi.tools.get_previews() |
self.steps.items() |
str(v['id']) |
values() |
str(i['source_step']) |
Step(v, self) |
missing_ids.append(k) |
tool_labels_to_ids.setdefault(step.tool_id, set() |
add(step.id) |
self.inputs.items() |
input_labels_to_ids.setdefault(d['label'], set() |
add(id_) |
object.__setattr__(self, 'input_labels_to_ids', input_labels_to_ids) |
object.__setattr__(self, 'tool_labels_to_ids', tool_labels_to_ids) |
self._get_dag() |
set(dag) |
set(inv_dag) |
object.__setattr__(self, 'dag', dag) |
object.__setattr__(self, 'inv_dag', inv_dag) |
object.__setattr__(self, 'source_ids', heads - tails) |
set(self.inputs) |
object.__setattr__(self, 'sink_ids', tails - heads) |
object.__setattr__(self, 'missing_ids', missing_ids) |
_get_dag(self) |
by (direct) |
by (inverse) |
self.steps.values() |
s.input_steps.values() |
dag.setdefault(head, set() |
add(tail) |
inv_dag.setdefault(tail, set() |
add(head) |
sorted_step_ids(self) |
self.source_ids.copy() |
v.copy() |
self.inv_dag.items() |
source_ids.pop() |
ids.append(head) |
self.dag.get(head, []) |
incoming.remove(head) |
source_ids.add(tail) |
data_input_ids(self) |
self.steps.items() |
data_collection_input_ids(self) |
self.steps.items() |
parameter_input_ids(self) |
self.steps.items() |
tool_ids(self) |
self.steps.items() |
input_labels(self) |
set(self.input_labels_to_ids) |
is_runnable(self) |
convert_input_map(self, input_map) |
self.input_labels_to_ids.items() |
input_map.get(label, []) |
isinstance(datasets, Iterable) |
len(datasets) |
len(slot_ids) |
RuntimeError(f'not enough datasets for "{label}"') |
zip(slot_ids, datasets) |
preview(self) |
getf(published=True) |
ValueError(f"no object for id {self.id}") |
library.get_datasets() |
parameters (see below) |
following (deprecated) |
Finally (again, for backwards compatibility) |
RuntimeError('workflow is not mapped to a Galaxy object') |
join(f"{self.steps[step_id].tool_id}[{step_id}]" for step_id in self.missing_ids) |
RuntimeError(f"workflow has missing tools: {missing_tools_str}") |
self.convert_input_map(input_map or {}) |
isinstance(history, History) |
RuntimeError('history does not have an id') |
isinstance(history, str) |
self.gi.gi.workflows.run_workflow(self.id, **kwargs) |
self.gi.histories.get(res['history']) |
outputs.append(out_hist.get_dataset(output_id) |
outputs.append(out_hist.get_dataset_collection(output_id) |
export(self) |
self.gi.gi.workflows.export_workflow_dict(self.id) |
delete(self) |
self.gi.workflows.delete(id_=self.id) |
self.unmap() |
LibraryDatasetDatasetAssociation (``ldda``) |
LibraryDataset (``ld``) |
HistoryDatasetAssociation (``hda``) |
HistoryDatasetCollectionAssociation (``hdca``) |
parameters (see below) |
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