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def _check_dataset(self, hda):
self.assertIsInstance(hda, wrappers.HistoryDatasetAssociation)
self.assertIs(hda.container, self.hist)
self.assertEqual(len(self.hist.dataset_ids), 1)
self.assertEqual(self.hist.dataset_ids[0], hda.id)
def test_get(self):
job_prevs = self.gi.jobs.get_previews()
if len(job_prevs) > 0:
job_prev = job_prevs[0]
self.assertIsInstance(job_prev, wrappers.JobPreview)
job = self.gi.jobs.get(job_prev.id)
self.assertIsInstance(job, wrappers.Job)
self.assertEqual(job.id, job_prev.id)
for job in self.gi.jobs.list():
self.assertIsInstance(job, wrappers.Job)
def _check_and_del_workflow(self, wf, check_is_public=False):
# Galaxy appends additional text to imported workflow names
self.assertTrue(wf.name.startswith('paste_columns'))
self.assertEqual(len(wf.steps), 3)
for step_id, step in wf.steps.items():
self.assertIsInstance(step, wrappers.Step)
self.assertEqual(step_id, step.id)
self.assertIsInstance(step.tool_inputs, dict)
if step.type == 'tool':
self.assertIsNotNone(step.tool_id)
self.assertIsNotNone(step.tool_version)
self.assertIsInstance(step.input_steps, dict)
elif step.type in ('data_collection_input', 'data_input'):
self.assertIsNone(step.tool_id)
self.assertIsNone(step.tool_version)
self.assertEqual(step.input_steps, {})
wf_ids = {_.id for _ in self.gi.workflows.list()}
self.assertIn(wf.id, wf_ids)
if check_is_public:
self.assertTrue(wf.published)
wf.delete()
def get_previews(self, name=None, deleted=False):
dicts = self.gi.libraries.get_libraries(name=name, deleted=deleted)
return [wrappers.LibraryPreview(_, gi=self.obj_gi) for _ in dicts]
def get(self, id_):
"""
Retrieve the data library corresponding to the given id.
:rtype: :class:`~.wrappers.Library`
:return: the library corresponding to ``id_``
"""
return self._get_container(id_, wrappers.Library)
def get(self, id_):
"""
Retrieve the history corresponding to the given id.
:rtype: :class:`~.wrappers.History`
:return: the history corresponding to ``id_``
"""
return self._get_container(id_, wrappers.History)
def get_previews(self, name=None, trackster=None):
"""
Get the list of tools installed on the Galaxy instance.
:type name: str
:param name: return only tools with this name
:type trackster: bool
:param trackster: if True, only tools that are compatible with
Trackster are returned
:rtype: list of :class:`~.wrappers.Tool`
"""
dicts = self.gi.tools.get_tools(name=name, trackster=trackster)
return [wrappers.Tool(_, gi=self.obj_gi) for _ in dicts]
def get_previews(self):
dicts = self.gi.jobs.get_jobs()
return [wrappers.JobPreview(_, gi=self.obj_gi) for _ in dicts]