def test_can_serialize_work_unit(self):
"""
A regular WorkUnit has an ID and an entry in the database.
"""
sample = ExampleSample(name="S1")
sample.save()
work_unit = WorkUnit()
work_unit.tracked_object = sample
work_unit.save()
result = WorkUnitSerializer(work_unit).data
assert result['id'] == work_unit.id
assert result['tracked_object']['id'] == sample.id
def test_can_serialize_external_work_unit(self):
"""
WorkUnits can be external only. In this case they only exist in the external
workflow engine, as the system hasn't picked them up yet.
"""
sample = ExampleSample(name="S1")
sample.save()
work_unit = WorkUnit(external_work_unit_id="abc",
external_workflow_instance_id="123")
work_unit.tracked_object = sample
result = WorkUnitSerializer(work_unit).data
assert result['id'] == work_unit.id
assert result['tracked_object']['id'] == sample.id
def test_can_assign_substances(self):
"""
Tests an entire path in the workflow: assigning samples, starting a workbatch and
closing the workbatch
"""
# Create a handler so we model the highest level of interacting with the API, the same
# way plugin developers would interact with it:
sample_count = 5
self.toggle_log_level()
cont = ExamplePlate(name="cont1")
for x in range(1, sample_count + 1):
sample = ExampleSample(name="sample-{}".format(x))
cont.append(sample)
cont.save()
workflow = SequenceSimple()
workflow.comment = "Let's sequence some stuff"
workflow.assign(cont)
# We should see one assignment per sample
samples_created = set([x.id for x in cont.contents])
delivered = SubstanceAssignment.objects.filter(status=SubstanceAssignment.STATUS_DELIVERED)
assigned_samples = set([x.substance.id for x in delivered])
assert samples_created == assigned_samples
work_units = workflow.wait_for_work_units("DataEntry", 5)
tracked_objects_in_workflow_engine = [w.tracked_object.id for w in work_units]
assert len(tracked_objects_in_workflow_engine) == sample_count
def bootstrap(self):
self.sample1 = ExampleSample(name="Sample:{}".format(uuid4()))
self.sample1.save()
self.cont1 = PandorasBox(name="Container:{}".format(uuid4()))
self.cont1["a1"] = self.sample1
self.cont1.save()
self.cont2 = PandorasBox(name="Container:{}".format(uuid4()))
self.cont2.save()
self.workbatch = ExampleWorkBatch(name="WorkBatch:{}".format(uuid4()))
self.workbatch.save()
self.url = reverse(WorkBatchTransitionsEndpoint.name,
args=(self.cont1.organization.name,
self.workbatch.id))
self.login_as(self.user)
def create_available_work(count):
# Makes sure we have some work that's available, i.e. start workflow and then
# wait until the workflow is waiting for user intervention
cont = ExamplePlate(name="cont1")
for x in range(1, count + 1):
sample = ExampleSample(name="sample-{}".format(x))
cont.append(sample)
cont.save()
workflow = SequenceSimple()
workflow.comment = "Let's sequence some stuff"
workflow.assign(cont)
def test_get(self):
# 1. Create some work:
count = 3
cont = ExamplePlate(name="cont1")
for x in range(1, count + 1):
sample = ExampleSample(name="sample-{}".format(x))
cont.append(sample)
cont.save()
created_samples_ids = {s.id for s in cont.contents}
workflow = SequenceSimple()
workflow.comment = "Let's sequence some stuff"
workflow.assign(cont)
# 2. Wait for the work to be ready:
self.login_as(self.user)
work_def_id = "clims.plugins.demo.dnaseq.workflows.sequence.SequenceSimple:DataEntry"
url = reverse(WorkUnitsByWorkDefinitionEndpoint.name, args=(work_def_id, ))
response = self.wait_for_endpoint_list(url, 3)
assert response.status_code == 200
data = response.json()
assert len(data) == count
for entry in data:
assert len(entry) == 6
assert entry["workflow_provider"] == "camunda"
assert len(entry["external_work_unit_id"]) == 36 # expecting guid string
assert entry["work_type"] == "clims.plugins.demo.dnaseq.workflows.sequence.DataEntry"
assert entry["external_workflow_instance_id"]
tracked_object_id = entry["tracked_object"]["id"]
created_samples_ids.remove(int(tracked_object_id))
# Make sure we can do a second successful query. This is because getting fresh work units
# for the first time will save them locally, so the state has changed in the meantime
response = self.wait_for_endpoint_list(url, 3)
assert response.status_code == 200
def test_post(self):
# TODO: Fix this test, or an equivalent one.
self.login_as(self.user)
sample_count = 3
cont = ExamplePlate(name="cont1")
for x in range(1, sample_count + 1):
sample = ExampleSample(name="sample-{}".format(x))
cont.append(sample)
cont.save()
workflow = SequenceSimple()
workflow.comment = "Let's sequence some stuff"
workflow.assign(cont)
# Wait until the work unit enpoint returns these items:
work_units_url = reverse(WorkUnitsEndpoint.name,
args=(self.organization.name, ))
# Wait for getting a large enough response from the endpoint
resp = self.wait_for_endpoint_list(work_units_url, sample_count)
data = resp.json()
ids = [entry["id"] for entry in data]
data = {
"work_units": ids,
}
work_batch_url = reverse(WorkBatchEndpoint.name,
args=(self.organization.name, ))
response = self.client.post(
path=work_batch_url,
data=json.dumps(data),
content_type='application/json',
)
assert response.status_code == 201
def test_creates_assignment_entries(self):
workflow = SequenceSimple()
sample = ExampleSample(name="SomeSample")
sample.save()
workflow.assign(sample)
def test_can_not_assign_non_existing_substances(self):
with pytest.raises(self.app.workflows.AssignmentError):
workflow = SequenceSimple()
sample = ExampleSample()
workflow.assign(sample)
class TestWorkBatchTransitions(APITestCase):
def setUp(self):
self.has_context()
# so we can use the domain classes defined in the demo plugin, e.g. StuffoMagico
self.install_main_demo_plugin()
# TODO: Add a DELETE method too. It will be used when
# the frontend component needs to cancel some of those
# transitions. It will also have to remove the sample
# from the container it created. Note that if the user
# goes back and forths with this a lot it can generate
# a significant amount of data, so such samples should
# be soft deleted too so they can be removed in a cleanup
# job if users want that.
@pytest.mark.xfail
def test_delete(self):
raise NotImplementedError()
def bootstrap(self):
self.sample1 = ExampleSample(name="Sample:{}".format(uuid4()))
self.sample1.save()
self.cont1 = PandorasBox(name="Container:{}".format(uuid4()))
self.cont1["a1"] = self.sample1
self.cont1.save()
self.cont2 = PandorasBox(name="Container:{}".format(uuid4()))
self.cont2.save()
self.workbatch = ExampleWorkBatch(name="WorkBatch:{}".format(uuid4()))
self.workbatch.save()
self.url = reverse(WorkBatchTransitionsEndpoint.name,
args=(self.cont1.organization.name,
self.workbatch.id))
self.login_as(self.user)
def test_post(self):
self.bootstrap()
payload = {
"transitions": [{
"type": "move",
"source_position": {
"container_id": self.cont1.id,
"index": "a1"
},
"target_position": {
"container_id": self.cont2.id,
"index": "b2"
},
}]
}
response = self.client.post(
path=self.url,
data=json.dumps(payload),
content_type='application/json',
)
assert response.status_code == status.HTTP_201_CREATED
def test_post__invalid(self):
self.bootstrap()
payload = {
"transitions": [{
"type": "move",
"source_position": {
"container_id": self.cont1.id,
"index": "z100"
},
"target_position": {
"container_id": self.cont2.id,
"index": "b2"
},
}]
}
response = self.client.post(
path=self.url,
data=json.dumps(payload),
content_type='application/json',
)
# TODO: this should be HTTP_400_BAD_REQUEST
assert response.status_code == status.HTTP_500_INTERNAL_SERVER_ERROR
def test_post__invalid_source_substance(self):
self.bootstrap()
payload = {
"transitions": [{
"type": "move",
"source_position": {
"container_id": self.cont1.id,
"index": "c1"
},
"target_position": {
"container_id": self.cont2.id,
"index": "c2"
},
}]
}
response = self.client.post(
path=self.url,
data=json.dumps(payload),
content_type='application/json',
)
# TODO: this should be HTTP_400_BAD_REQUEST
assert response.status_code == status.HTTP_500_INTERNAL_SERVER_ERROR