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run black and isort
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simonbray committed May 27, 2022
1 parent fcc4c58 commit c04495a
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Showing 2 changed files with 10 additions and 10 deletions.
18 changes: 9 additions & 9 deletions bioblend/_tests/TestGalaxyInvocations.py
Original file line number Diff line number Diff line change
Expand Up @@ -140,25 +140,25 @@ def test_rerun_invocation(self):
history = self.gi.histories.show_history(rerun_invocation["history_id"], contents=True)
self.assertEqual(len(history), 3)

@test_util.skip_unless_galaxy('release_21.05')
@test_util.skip_unless_galaxy("release_21.05")
def test_rerun_and_remap_invocation(self):
path = test_util.get_abspath(os.path.join('data', 'select_first.ga'))
path = test_util.get_abspath(os.path.join("data", "select_first.ga"))
wf = self.gi.workflows.import_workflow_from_local_path(path)
wf_inputs = {
"0": {'src': 'hda', 'id': self.dataset_id},
"0": {"src": "hda", "id": self.dataset_id},
"1": "-1",
}
invocation_id = self.gi.workflows.invoke_workflow(wf['id'], inputs=wf_inputs, history_id=self.history_id)['id']
invocation_id = self.gi.workflows.invoke_workflow(wf["id"], inputs=wf_inputs, history_id=self.history_id)["id"]
self.gi.invocations.wait_for_invocation(invocation_id)
failed_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, name='Select first on data 1')
failed_dataset = self.gi.datasets.wait_for_dataset(failed_datasets[0]['id'], check=False)
self.assertEqual(failed_dataset['state'], 'error')
failed_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, name="Select first on data 1")
failed_dataset = self.gi.datasets.wait_for_dataset(failed_datasets[0]["id"], check=False)
self.assertEqual(failed_dataset["state"], "error")

self.gi.invocations.rerun_invocation(invocation_id, remap=True)
for dataset in self.gi.datasets.get_datasets(history_id=self.history_id):
self.gi.datasets.wait_for_dataset(dataset['id'], check=False)
self.gi.datasets.wait_for_dataset(dataset["id"], check=False)

new_ok_jobs = self.gi.datasets.get_datasets(state='ok', history_id=self.history_id)
new_ok_jobs = self.gi.datasets.get_datasets(state="ok", history_id=self.history_id)
self.assertEqual(len(new_ok_jobs), 3)

def _invoke_workflow(self):
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2 changes: 1 addition & 1 deletion bioblend/galaxy/invocations/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@ def rerun_invocation(
invocation_id: str,
remap: bool = False,
inputs_update: Optional[dict] = None,
params_update: Optional[dict] = None,
params: Optional[dict] = None,
history_id: Optional[str] = None,
history_name: Optional[str] = None,
import_inputs_to_history: bool = False,
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