def test_fetch_objects_required_for_analyses_bad_workflow(self):
with self.assertRaises(RuntimeError) as context:
fetch_objects_required_for_analysis({
"studyUuid": self.study.uuid,
"user_id": self.user.id,
"workflowUuid": "COFFEE"
})
self.assertIn("Couldn't fetch Workflow", context.exception.message)
def test_fetch_objects_required_for_analyses_bad_user(self):
with self.assertRaises(RuntimeError) as context:
fetch_objects_required_for_analysis(
{
"studyUuid": self.study.uuid,
"user_id": 400,
"workflowUuid": self.workflow.uuid
}
)
self.assertIn("Couldn't fetch User", context.exception.message)
def test_fetch_objects_required_for_analyses_bad_user(self):
with self.assertRaises(RuntimeError) as context:
fetch_objects_required_for_analysis(
{
"study_uuid": self.study.uuid,
"user_id": 400,
"workflow_uuid": self.workflow.uuid
}
)
self.assertIn("Couldn't fetch User", context.exception.message)
def test_fetch_objects_required_for_analyses_bad_workflow(self):
with self.assertRaises(RuntimeError) as context:
fetch_objects_required_for_analysis(
{
"study_uuid": self.study.uuid,
"user_id": self.user.id,
"workflow_uuid": "COFFEE"
}
)
self.assertIn("Couldn't fetch Workflow", context.exception.message)
def test_fetch_objects_required_for_analyses_bad_dataset(self):
self.dataset.delete()
with self.assertRaises(RuntimeError) as context:
fetch_objects_required_for_analysis(
{
"studyUuid": self.study.uuid,
"user_id": self.user.id,
"workflowUuid": self.workflow.uuid
}
)
self.assertIn("Couldn't fetch DataSet", context.exception.message)
def create_tool_analysis(validated_analysis_config):
"""
Create an Analysis instance from a validated analysis config with
Tool information
:param validated_analysis_config: a dict including the necessary
information to create an Analysis that has been validated prior by
`analysis_manager.utils.validate_analysis_config`
:return: an Analysis instance
:raises: RuntimeError
"""
# Input list for running analysis
common_analysis_objects = (
fetch_objects_required_for_analysis(validated_analysis_config))
name = validated_analysis_config["name"]
current_workflow = common_analysis_objects["current_workflow"]
data_set = common_analysis_objects["data_set"]
user = common_analysis_objects["user"]
try:
tool = Tool.objects.get(uuid=validated_analysis_config["toolUuid"])
except (Tool.DoesNotExist, Tool.MultipleObjectsReturned) as e:
raise RuntimeError("Couldn't fetch Tool from UUID: {}".format(e))
analysis = AnalysisFactory(summary="Analysis run for: {}".format(tool),
name=name,
project=user.profile.catch_all_project,
data_set=data_set,
workflow=current_workflow,
time_start=timezone.now())
analysis.set_owner(user)
return analysis
def test_fetch_objects_required_for_analyses(self):
self.assertEqual(
fetch_objects_required_for_analysis({
"studyUuid":
self.study.uuid,
"user_id":
self.user.id,
"workflowUuid":
self.workflow.uuid
}), {
"user": self.user,
"current_workflow": self.workflow,
"data_set": self.dataset,
})
def test_fetch_objects_required_for_analyses(self):
self.assertEqual(
fetch_objects_required_for_analysis(
{
"study_uuid": self.study.uuid,
"user_id": self.user.id,
"workflow_uuid": self.workflow.uuid
}
),
{
"user": self.user,
"current_workflow": self.workflow,
"data_set": self.dataset,
}
)
def create_tool_analysis(validated_analysis_config):
"""
Create an Analysis instance from a validated analysis config with
Tool information
:param validated_analysis_config: a dict including the necessary
information to create an Analysis that has been validated prior by
`analysis_manager.utils.validate_analysis_config`
:return: an Analysis instance
:raises: RuntimeError
"""
common_analysis_objects = (
fetch_objects_required_for_analysis(validated_analysis_config)
)
current_workflow = common_analysis_objects["current_workflow"]
data_set = common_analysis_objects["data_set"]
user = common_analysis_objects["user"]
try:
tool = WorkflowTool.objects.get(
uuid=validated_analysis_config["toolUuid"]
)
except (WorkflowTool.DoesNotExist,
WorkflowTool.MultipleObjectsReturned) as e:
raise RuntimeError("Couldn't fetch Tool from UUID: {}".format(e))
analysis = AnalysisFactory(
uuid=str(uuid.uuid4()),
summary="Galaxy workflow execution for: {}".format(tool.name),
name="{} - {} - {}".format(
tool.get_tool_name(),
get_aware_local_time().strftime("%Y/%m/%d %H:%M:%S"),
tool.get_owner_username().title()
),
project=user.profile.catch_all_project,
data_set=data_set,
workflow=current_workflow,
time_start=timezone.now()
)
analysis.set_owner(user)
return analysis
