def build_from_current_history(self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None):
user = trans.get_user()
history = trans.get_history()
if not user:
return trans.show_error_message("Must be logged in to create workflows")
if (job_ids is None and dataset_ids is None) or workflow_name is None:
jobs, warnings = summarize(trans)
# Render
return trans.fill_template(
"workflow/build_from_current_history.mako",
jobs=jobs,
warnings=warnings,
history=history
)
else:
# If there is just one dataset name selected or one dataset collection, these
# come through as string types instead of lists. xref #3247.
dataset_names = util.listify(dataset_names)
dataset_collection_names = util.listify(dataset_collection_names)
stored_workflow = extract_workflow(
trans,
user=user,
job_ids=job_ids,
dataset_ids=dataset_ids,
dataset_collection_ids=dataset_collection_ids,
workflow_name=workflow_name,
dataset_names=dataset_names,
dataset_collection_names=dataset_collection_names
)
# Index page with message
workflow_id = trans.security.encode_id(stored_workflow.id)
return trans.show_message('Workflow "%s" created from current history. '
'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
% (escape(workflow_name), url_for(controller='workflow', action='editor', id=workflow_id),
url_for(controller='workflows', action='run', id=workflow_id)))
def build_from_current_history(self, trans, job_ids=None, dataset_ids=None, dataset_collection_ids=None, workflow_name=None, dataset_names=None, dataset_collection_names=None):
user = trans.get_user()
history = trans.get_history()
if not user:
return trans.show_error_message("Must be logged in to create workflows")
if (job_ids is None and dataset_ids is None) or workflow_name is None:
jobs, warnings = summarize(trans)
# Render
return trans.fill_template(
"workflow/build_from_current_history.mako",
jobs=jobs,
warnings=warnings,
history=history
)
else:
# If there is just one dataset name selected or one dataset collection, these
# come through as string types instead of lists. xref #3247.
dataset_names = util.listify(dataset_names)
dataset_collection_names = util.listify(dataset_collection_names)
stored_workflow = extract_workflow(
trans,
user=user,
job_ids=job_ids,
dataset_ids=dataset_ids,
dataset_collection_ids=dataset_collection_ids,
workflow_name=workflow_name,
dataset_names=dataset_names,
dataset_collection_names=dataset_collection_names
)
# Index page with message
workflow_id = trans.security.encode_id(stored_workflow.id)
return trans.show_message('Workflow "%s" created from current history. '
'You can <a href="%s" target="_parent">edit</a> or <a href="%s" target="_parent">run</a> the workflow.'
% (escape(workflow_name), url_for(controller='workflow', action='editor', id=workflow_id),
url_for(controller='workflows', action='run', id=workflow_id)))
def test_implicit_map_job_hdca(self):
creating_job = model.Job()
hdca = MockHdca(implicit_output_name="out1", job=creating_job)
self.history.active_datasets.append(hdca)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
job = next(iter(job_dict.keys()))
assert job is creating_job
def test_implicit_map_job_hdca(self):
creating_job = model.Job()
hdca = MockHdca(implicit_output_name="out1", job=creating_job)
self.history.active_datasets.append(hdca)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
job = job_dict.keys()[0]
assert job is creating_job
def test_fake_job_hdca(self):
hdca = MockHdca()
self.history.active_datasets.append(hdca)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = next(iter(job_dict.keys()))
assert fake_job.id.startswith("fake_")
assert fake_job.is_fake
content_instances = next(iter(job_dict.values()))
assert content_instances == [(None, hdca)]
def test_finds_original_job_if_copied(self):
hda = MockHda()
derived_hda_1 = MockHda()
derived_hda_1.copied_from_history_dataset_association = hda
derived_hda_2 = MockHda()
derived_hda_2.copied_from_history_dataset_association = derived_hda_1
self.history.active_datasets.append(derived_hda_2)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
self.assertEqual(job_dict[hda.job], [('out1', derived_hda_2)])
def test_fake_job_hdca(self):
hdca = MockHdca()
self.history.active_datasets.append(hdca)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = job_dict.keys()[0]
assert fake_job.id.startswith("fake_")
assert fake_job.is_fake
content_instances = next(iter(job_dict.values()))
assert content_instances == [(None, hdca)]
def test_finds_original_job_if_copied(self):
hda = MockHda()
derived_hda_1 = MockHda()
derived_hda_1.copied_from_history_dataset_association = hda
derived_hda_2 = MockHda()
derived_hda_2.copied_from_history_dataset_association = derived_hda_1
self.history.active_datasets.append(derived_hda_2)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
self.assertEqual(job_dict[hda.job], [('out1', derived_hda_2)])
def test_fake_job_hda_name_guess(self):
hda_from_history = MockHda(job=UNDEFINED_JOB)
hda_from_history.copied_from_history_dataset_association = MockHda(
job=UNDEFINED_JOB)
self.history.active_datasets.append(hda_from_history)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = next(iter(job_dict.keys()))
assert "History" in fake_job.name
self.history.active_datasets.remove(hda_from_history)
hda_from_library = MockHda(job=UNDEFINED_JOB)
hda_from_library.copied_from_library_dataset_dataset_association = MockHda(
job=UNDEFINED_JOB)
self.history.active_datasets.append(hda_from_library)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = next(iter(job_dict.keys()))
assert "Library" in fake_job.name
def test_fake_job_hda(self):
""" Fakes job if creating_job_associations is empty.
"""
hda = MockHda(job=UNDEFINED_JOB)
self.history.active_datasets.append(hda)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = next(iter(job_dict.keys()))
assert fake_job.id.startswith("fake_")
datasets = next(iter(job_dict.values()))
assert datasets == [(None, hda)]
def test_fake_job_hda(self):
""" Fakes job if creating_job_associations is empty.
"""
hda = MockHda(job=UNDEFINED_JOB)
self.history.active_datasets.append(hda)
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert len(job_dict) == 1
fake_job = job_dict.keys()[0]
assert fake_job.id.startswith("fake_")
datasets = list(job_dict.values())[0]
assert datasets == [(None, hda)]
def get_workflow(this):
from galaxy import util
from galaxy.webapps.galaxy.controllers.workflow import WorkflowController
from galaxy.workflow.extract import extract_workflow
from galaxy.workflow.extract import summarize
tmpuser = this.user
if not this.user:
tmpusername = os.getenv('GALAXY_DEFAULT_WORKFLOWGENERATOR_USER', os.environ['GALAXY_DEFAULT_ADMIN_USER'])
if not tmpusername:
tmpuser = UserManager(this.trans.app).admins()[0]
tmpuser = this.trans.sa_session.query(this.trans.app.model.User).filter_by(username=tmpusername,deleted=False).all()[0]
#html = WorkflowController(this.trans.app).build_from_current_history(this.trans)
#use reimplementation since controller does user=trans.get_user() || error
jobs, warnings = summarize(this.trans)
html = this.trans.fill_template("workflow/build_from_current_history.mako", jobs=jobs, warnings=warnings, history=this.history)
job_ids = re.findall('job_ids.+value="([^"]+)',html)
dataset_ids = re.findall('dataset_ids.+value="([^"]+)',html)
dataset_names = re.findall('dataset_names.+value="([^"]+)',html)
dataset_collection_ids = re.findall('dataset_collection_ids.+value="(\d+)',html)
dataset_collection_names = re.findall('dataset_collection_names.+value="(\d+)',html)
dataset_names = util.listify(dataset_names)
dataset_collection_names = util.listify(dataset_collection_names)
stored = extract_workflow(
this.trans,
user=tmpuser,
job_ids=job_ids,
dataset_ids=dataset_ids,
dataset_collection_ids=dataset_collection_ids,
workflow_name='de.STAIR Guide Workflow',
dataset_names=dataset_names,
dataset_collection_names=dataset_collection_names
)
this.workflow = WorkflowController(this.trans.app)._workflow_to_dict(this.trans, stored)
# reimplement deletion which originally makes use of get_stored_workflow which failes in case of anon user
stored.deleted = True
tmpuser.stored_workflow_menu_entries = [entry for entry in tmpuser.stored_workflow_menu_entries if entry.stored_workflow != stored]
this.trans.sa_session.add(stored)
this.trans.sa_session.flush()
return {
'workflow': this.workflow
}
def test_summarize_returns_name_and_dataset_list(self):
# Create two jobs and three datasets, test they are groupped
# by job correctly with correct output names.
hda1 = MockHda()
self.history.active_datasets.append(hda1)
hda2 = MockHda(job=hda1.job, output_name="out2")
self.history.active_datasets.append(hda2)
hda3 = MockHda(output_name="out3")
self.history.active_datasets.append(hda3)
job_dict, warnings = extract.summarize(trans=self.trans)
assert len(job_dict) == 2
assert not warnings
self.assertEqual(job_dict[hda1.job], [('out1', hda1), ('out2', hda2)])
self.assertEqual(job_dict[hda3.job], [('out3', hda3)])
def test_summarize_returns_name_and_dataset_list(self):
# Create two jobs and three datasets, test they are groupped
# by job correctly with correct output names.
hda1 = MockHda()
self.history.active_datasets.append(hda1)
hda2 = MockHda(job=hda1.job, output_name="out2")
self.history.active_datasets.append(hda2)
hda3 = MockHda(output_name="out3")
self.history.active_datasets.append(hda3)
job_dict, warnings = extract.summarize(trans=self.trans)
assert len(job_dict) == 2
assert not warnings
self.assertEqual(job_dict[hda1.job], [('out1', hda1), ('out2', hda2)])
self.assertEqual(job_dict[hda3.job], [('out3', hda3)])
def test_empty_history(self):
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert not job_dict
def test_warns_and_skips_datasets_if_not_finished(self):
hda = MockHda(state='queued')
self.history.active_datasets.append(hda)
job_dict, warnings = extract.summarize(trans=self.trans)
assert warnings
assert len(job_dict) == 0
def test_empty_history(self):
job_dict, warnings = extract.summarize(trans=self.trans)
assert not warnings
assert not job_dict
def test_warns_and_skips_datasets_if_not_finished(self):
hda = MockHda(state='queued')
self.history.active_datasets.append(hda)
job_dict, warnings = extract.summarize(trans=self.trans)
assert warnings
assert len(job_dict) == 0
