def make_analyses_with_single_dataset(number_to_create, user_instance):
"""Create some minimal Analyses"""
instance = GalaxyInstanceFactory()
workflow_engine = WorkflowEngineFactory(instance=instance)
workflow = WorkflowFactory(uuid=str(uuid_builtin.uuid4()),
workflow_engine=workflow_engine)
project = ProjectFactory(is_catch_all=True)
dataset = create_dataset_with_necessary_models()
while number_to_create:
analysis_uuid = str(uuid_builtin.uuid4())
AnalysisFactory(uuid=analysis_uuid,
name="Test Analysis - {}".format(analysis_uuid),
project=project,
data_set=dataset,
workflow=workflow)
number_to_create -= 1
for dataset in DataSet.objects.all():
dataset.set_owner(user_instance)
dataset.save()
for analysis in Analysis.objects.all():
analysis.set_owner(user_instance)
analysis.save()
def setUp(self):
self.GALAXY_HISTORY_ID = str(uuid.uuid4())
self.GALAXY_DATASET_ID = str(uuid.uuid4())
self.GALAXY_DATASET_FILESIZE = 1024
self.MISCELLANEOUS_STRING = "Coffee is tasty"
self.galaxy_instance = GalaxyInstanceFactory(api_key=str(uuid.uuid4()))
self.show_history_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_history").start()
self.show_dataset_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_dataset").start()
self.history_content_entry = {
"name": "Test History Content Entry",
"url": "www.example.com/history_content_entry",
"type": "file",
"id": self.GALAXY_DATASET_ID
}
def make_analyses_with_single_dataset(number_to_create, user_instance):
"""Create some minimal Analyses"""
instance = GalaxyInstanceFactory()
workflow_engine = WorkflowEngineFactory(instance=instance)
workflow = WorkflowFactory(uuid=str(uuid_builtin.uuid4()),
workflow_engine=workflow_engine)
project = ProjectFactory(is_catch_all=True)
dataset = create_dataset_with_necessary_models(user=user_instance)
while number_to_create:
create_analysis(project, dataset, workflow, user_instance)
number_to_create -= 1
return Analysis.objects.all(), dataset
def setUp(self):
self.galaxy_instance = GalaxyInstanceFactory()
self.workflow_engine = WorkflowEngine.objects.create(
instance=self.galaxy_instance)
self.workflow = Workflow.objects.create(
is_active=True, workflow_engine=self.workflow_engine)
self.user = get_anonymous_user()
project = Project.objects.create(name="Catch-All Project",
is_catch_all=True)
project.set_owner(self.user)
self.user.profile.catch_all_project = project
self.user.profile.save()
self.dataset = create_dataset_with_necessary_models()
self.study = self.dataset.get_latest_study()
self.assay = Assay.objects.create(study=self.study)
def setUp(self):
self.GALAXY_HISTORY_ID = str(uuid.uuid4())
self.GALAXY_DATASET_ID = str(uuid.uuid4())
self.GALAXY_DATASET_FILESIZE = 1024
self.MISCELLANEOUS_STRING = "Coffee is tasty"
self.galaxy_instance = GalaxyInstanceFactory(api_key=str(uuid.uuid4()))
self.show_history_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_history"
).start()
self.show_dataset_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_dataset"
).start()
self.history_content_entry = {
"name": "Test History Content Entry",
"url": "www.example.com/history_content_entry",
"type": "file",
"id": self.GALAXY_DATASET_ID
}
def setUp(self):
self.username = '******'
self.password = '******'
self.user = User.objects.create_user(self.username,
'*****@*****.**',
self.password)
self.project = Project.objects.create()
self.galaxy_instance = GalaxyInstanceFactory()
self.workflow_engine = WorkflowEngine.objects.create(
instance=self.galaxy_instance
)
self.workflow = Workflow.objects.create(
workflow_engine=self.workflow_engine
)
# Create Datasets
self.data_set = DataSet.objects.create(name="coffee data_set")
self.data_set.set_owner(self.user)
# Create Investigation/InvestigationLinks for the DataSets
self.investigation = Investigation.objects.create()
InvestigationLink.objects.create(data_set=self.data_set,
investigation=self.investigation,
version=1)
# Create Studys and Assays
self.study = Study.objects.create(investigation=self.investigation)
self.assay = Assay.objects.create(study=self.study)
# Create Analyses
self.analysis = Analysis.objects.create(
name='Coffee Analysis',
summary='coffee',
project=self.project,
data_set=self.data_set,
workflow=self.workflow,
time_start=timezone.now()
)
self.analysis.set_owner(self.user)
self.serializer = AnalysisSerializer(self.analysis)
class GalaxyInstanceTests(TestCase):
def setUp(self):
self.GALAXY_HISTORY_ID = str(uuid.uuid4())
self.GALAXY_DATASET_ID = str(uuid.uuid4())
self.GALAXY_DATASET_FILESIZE = 1024
self.MISCELLANEOUS_STRING = "Coffee is tasty"
self.galaxy_instance = GalaxyInstanceFactory(api_key=str(uuid.uuid4()))
self.show_history_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_history").start()
self.show_dataset_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_dataset").start()
self.history_content_entry = {
"name": "Test History Content Entry",
"url": "www.example.com/history_content_entry",
"type": "file",
"id": self.GALAXY_DATASET_ID
}
def tearDown(self):
mock.patch.stopall()
def test_get_history_file_list_with_populated_dataset_dict(self):
self.show_history_mock.return_value = [self.history_content_entry]
self.show_dataset_mock.return_value = {
"file_ext": "bam",
"state": "ok",
"id": self.GALAXY_DATASET_ID,
"file_size": self.GALAXY_DATASET_FILESIZE,
"visible": True,
"file_name": "Cool bam file",
"genome_build": "hg19",
"misc_info": self.MISCELLANEOUS_STRING,
"misc_blurb": self.MISCELLANEOUS_STRING,
}
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID)
self.assertEqual(len(history_file_list), 1)
history_file = history_file_list[0]
self.assertEqual(history_file["type"], "bam")
self.assertEqual(history_file["state"], "ok")
self.assertEqual(history_file["dataset_id"], self.GALAXY_DATASET_ID)
self.assertEqual(history_file["file_size"],
self.GALAXY_DATASET_FILESIZE)
self.assertTrue(history_file["visible"])
self.assertEqual(history_file["file_name"], "Cool bam file")
self.assertEqual(history_file["genome_build"], "hg19")
self.assertEqual(history_file["misc_info"], self.MISCELLANEOUS_STRING)
self.assertEqual(history_file["misc_blurb"], self.MISCELLANEOUS_STRING)
def test_get_history_file_list_with_unpopulated_dataset_dict(self):
self.show_history_mock.return_value = [self.history_content_entry]
self.show_dataset_mock.return_value = {}
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID)
self.assertEqual(len(history_file_list), 1)
history_file = history_file_list[0]
self.assertIsNone(history_file["type"])
self.assertIsNone(history_file["state"])
self.assertIsNone(history_file["dataset_id"])
self.assertIsNone(history_file["file_size"])
self.assertIsNone(history_file["visible"])
self.assertIsNone(history_file["file_name"])
self.assertIsNone(history_file["genome_build"])
self.assertIsNone(history_file["misc_info"])
self.assertIsNone(history_file["misc_blurb"])
def test_no_history_files_if_history_content_entry_has_no_type(self):
del self.history_content_entry["type"]
self.show_history_mock.return_value = [self.history_content_entry]
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID)
self.assertEqual(len(history_file_list), 0)
def test_no_history_files_if_history_content_entry_isnt_a_file(self):
self.history_content_entry["type"] = "not a file"
self.show_history_mock.return_value = [self.history_content_entry]
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID)
self.assertEqual(len(history_file_list), 0)
def test_create_workflow_engine_bad_group_name(self):
galaxy_instance = GalaxyInstanceFactory()
with self.assertRaises(CommandError):
call_command("create_workflowengine", str(galaxy_instance.id),
"non-existent group name")
def test_create_workflow_engine(self):
galaxy_instance = GalaxyInstanceFactory()
call_command("create_workflowengine", str(galaxy_instance.id),
ExtendedGroup.objects.public_group().name)
self.assertIsNotNone(
WorkflowEngine.objects.get(instance=galaxy_instance))
class GalaxyInstanceTests(TestCase):
def setUp(self):
self.GALAXY_HISTORY_ID = str(uuid.uuid4())
self.GALAXY_DATASET_ID = str(uuid.uuid4())
self.GALAXY_DATASET_FILESIZE = 1024
self.MISCELLANEOUS_STRING = "Coffee is tasty"
self.galaxy_instance = GalaxyInstanceFactory(api_key=str(uuid.uuid4()))
self.show_history_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_history"
).start()
self.show_dataset_mock = mock.patch.object(
galaxy.histories.HistoryClient, "show_dataset"
).start()
self.history_content_entry = {
"name": "Test History Content Entry",
"url": "www.example.com/history_content_entry",
"type": "file",
"id": self.GALAXY_DATASET_ID
}
def tearDown(self):
mock.patch.stopall()
def test_get_history_file_list_with_populated_dataset_dict(self):
self.show_history_mock.return_value = [self.history_content_entry]
self.show_dataset_mock.return_value = {
"file_ext": "bam",
"state": "ok",
"id": self.GALAXY_DATASET_ID,
"file_size": self.GALAXY_DATASET_FILESIZE,
"visible": True,
"file_name": "Cool bam file",
"genome_build": "hg19",
"misc_info": self.MISCELLANEOUS_STRING,
"misc_blurb": self.MISCELLANEOUS_STRING,
}
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID
)
self.assertEqual(len(history_file_list), 1)
history_file = history_file_list[0]
self.assertEqual(history_file["type"], "bam")
self.assertEqual(history_file["state"], "ok")
self.assertEqual(history_file["dataset_id"], self.GALAXY_DATASET_ID)
self.assertEqual(history_file["file_size"],
self.GALAXY_DATASET_FILESIZE)
self.assertTrue(history_file["visible"])
self.assertEqual(history_file["file_name"], "Cool bam file")
self.assertEqual(history_file["genome_build"], "hg19")
self.assertEqual(history_file["misc_info"], self.MISCELLANEOUS_STRING)
self.assertEqual(history_file["misc_blurb"], self.MISCELLANEOUS_STRING)
def test_get_history_file_list_with_unpopulated_dataset_dict(self):
self.show_history_mock.return_value = [self.history_content_entry]
self.show_dataset_mock.return_value = {}
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID
)
self.assertEqual(len(history_file_list), 1)
history_file = history_file_list[0]
self.assertIsNone(history_file["type"])
self.assertIsNone(history_file["state"])
self.assertIsNone(history_file["dataset_id"])
self.assertIsNone(history_file["file_size"])
self.assertIsNone(history_file["visible"])
self.assertIsNone(history_file["file_name"])
self.assertIsNone(history_file["genome_build"])
self.assertIsNone(history_file["misc_info"])
self.assertIsNone(history_file["misc_blurb"])
def test_no_history_files_if_history_content_entry_has_no_type(self):
del self.history_content_entry["type"]
self.show_history_mock.return_value = [self.history_content_entry]
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID
)
self.assertEqual(len(history_file_list), 0)
def test_no_history_files_if_history_content_entry_isnt_a_file(self):
self.history_content_entry["type"] = "not a file"
self.show_history_mock.return_value = [self.history_content_entry]
history_file_list = self.galaxy_instance.get_history_file_list(
self.GALAXY_HISTORY_ID
)
self.assertEqual(len(history_file_list), 0)