def test_assign_and_update(client, auth):
# Test that user cannot edit sample after being assigned
# Setup
helper = Helper(client)
helper.reset_db()
s_lims.import_steps([dt.steps[0][0]])
s_lims.import_workflow(dt.workflows[0])
workflow_name = dt.workflows[0]['name']
# upload samples
auth.login("*****@*****.**", "supplying lab")
helper.submit_samples(dt.samplesheets_success)
auth.logout()
auth.login()
helper.assign_samples(dt.barcodes[0], workflow_name, "batch1")
auth.logout()
auth.login("*****@*****.**", "supplying lab")
#Test
json_body = {"barcode": "ABC", "species": "Salmonella enterica", "group": "FBI", "name": "testsample1", "archived": "true", "submitted_on": None, "priority": "1", "batch": "Unassigned", "genome_size": 5000000}
response = client.post(
'/samples/data-source/update',
data=json.dumps(json_body),
content_type="application/json;charset=UTF-8",
)
assert response.json == {'errors': {'sample_assigned': ['This sample has already been assigned. Please contact an admin to request changes.']}}
def test_unassign_samples(client, auth):
helper = Helper(client)
helper.reset_db()
#import steps and workflow
steps = [s[0] for s in dt.steps]
s_lims.import_steps(steps)
s_lims.import_workflow(dt.workflows[0])
sample_barcodes = dt.barcodes[0]
samplesheet = dt.samplesheets_success
status = dt.status_ok
assign_data = dt.assign_samples[0]
workflow_name = dt.workflows[0]['name']
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, dt.batch_name)
response = client.put(
'/samples/unassign',
data=json.dumps({"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, dt.batch_name),
}),
content_type="application/json;charset=UTF-8",
)
print(response.json)
assert response.json["status"] == status
# Test if sample assigned
for sample in samplesheet:
sample_db = Sample.objects.get({"barcode": sample["barcode"]})
assert sample_db.batches[0].workflow.name == dt.workflows[0]["name"]
assert sample_db.batches[0].step_cat == "root"
assert sample_db.batches[0].archived is True
def test_start_step_and_cancel(client, auth):
helper = Helper(client)
helper.reset_db()
# Test variables
steps = (dt.steps[0], dt.steps[2])
step_names = [s[0] for s in steps]
workflow = dt.workflows[2]
sample_barcodes = dt.barcodes[0]
#needed
s_lims.import_steps(step_names)
s_lims.import_workflow(workflow)
workflow_name = workflow['name']
batch_name = dt.batch_name
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
# Step 1 start
end_step_1_data = dt.attached['in1']
step_name = steps[0][0]
step_cat = steps[0][1]
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
response = helper.start_step(step_name, step_data)
step_instance_id = response.json["data"]["step_instance_id"]
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# Cancel test
response = client.post(
'/stepinstance/{}/cancel'.format(step_instance_id),
content_type="application/json;charset=UTF-8",
)
assert response.json["status"] == "Cancelled"
step_i = Step_instance.objects.get({"_id": ObjectId(step_instance_id)})
assert step_i.status == "cancelled"
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert len(sample_o.workflows[workflow_name][step_cat]) == 0
def test_step(client, auth, sample_barcodes, step, workflow, step_end_data,
expected_values):
helper = Helper(client)
helper.reset_db()
#needed
s_lims.import_steps([step[0]])
s_lims.import_workflow(workflow)
workflow_name = workflow['name']
batch_name = dt.batch_name
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
step_name = step[0]
step_cat = step[1]
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
helper.end_step(str(step_i.pk), step_end_data)
finished_step_i = Step_instance.objects.get({
"_id": step_i.pk,
"status": "finished",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
if step_name == "submit_to_bifrost":
assert finished_step_i.result_all["samplesheet_csv"]
assert finished_step_i.result_all["run_metadata"]
def test_except_missing_params(client, auth):
helper = Helper(client)
helper.reset_db()
step = dt.steps[0][0]
step_cat = dt.steps[0][1]
workflow = dt.workflows[0]
sample_barcodes = dt.barcodes[0]
step_end_data = dt.attached['none']
#needed
s_lims.import_steps([step])
s_lims.import_workflow(workflow)
workflow_name = workflow['name']
batch_name = dt.batch_name
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
step_name = step
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# for value, subdoc in expected_values:
# if not value in getattr(step_i, subdoc):
# raise ValueError("Missing expected value {} in {}".format(value, subdoc))
response = client.post('/stepinstance/{}/end'.format(str(step_i.pk)),
data=step_end_data,
content_type='multipart/form-data',
follow_redirects=True)
assert response.json["status"] == "Fail"
assert response.json["errors"] == ["Missing or incorrect param in1"]
def test_add_workflow():
helper = Helper(None)
helper.reset_db()
steps = [s[0] for s in dt.steps]
#needed
s_lims.import_steps(steps)
s_lims.import_workflow(dt.workflows[0])
workflow_db = Workflow.objects.get({
"name": dt.workflows[0]["name"]
}).to_son().to_dict()
assert workflow_db["name"] == dt.workflows[0]["name"]
assert len(workflow_db["steps"]) == len(dt.workflows[0]["steps"])
def test_assign_samples(client, auth, samplesheet, status, assign_data):
auth.login()
Sample.objects.delete()
Step.objects.delete()
Workflow.objects.delete()
steps = [s[0] for s in dt.steps]
#import steps and workflow
retrieved = s_lims.import_steps(steps)
s_lims.import_workflow(dt.workflows[0])
# import samples
response = client.post(
'/samples/submit',
data=json.dumps(samplesheet),
content_type="application/json;charset=UTF-8",
)
# Assign sample to workflow
response = client.post(
'/samples/assign-api',
data=json.dumps(assign_data),
content_type="application/json;charset=UTF-8",
)
assert response.json["status"] == status
# Test if sample assigned
for sample in samplesheet:
sample_db = Sample.objects.get({"barcode":sample["barcode"]})
assert sample_db.batches[0].workflow.name == dt.workflows[0]["name"]
assert sample_db.batches[0].step_cat == "root"
def test_create_and_save_step():
helper = Helper(None)
helper.reset_db()
steps = [s[0] for s in dt.steps]
retrieved = s_lims.import_steps(steps)
for step in retrieved:
assert Step.objects.get({"name": step.name}) is not None
def test_delete_step(client, auth):
helper = Helper(client)
helper.reset_db()
# Test variables
steps = (dt.steps[0], dt.steps[2])
step_names = [s[0] for s in steps]
workflow = dt.workflows[2]
sample_barcodes = dt.barcodes[0]
batch_name = dt.batch_name
#needed
s_lims.import_steps(step_names)
s_lims.import_workflow(workflow)
workflow_name = workflow['name']
batch_name = dt.batch_name
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
# Step 1 start
end_step_1_data = dt.attached['in1']
step_name = steps[0][0]
step_cat = steps[0][1]
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# for value, subdoc in expected_values:
# if not value in getattr(step_i, subdoc):
# raise ValueError("Missing expected value {} in {}".format(value, subdoc))
helper.end_step(str(step_i.pk), end_step_1_data)
finished_step_i = Step_instance.objects.get({
"_id": step_i.pk,
"status": "finished",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# Now step 2
step_name = steps[1][0]
step_cat = steps[1][1]
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
helper.end_step(str(step_i.pk), {})
finished_step_i = Step_instance.objects.get({
"_id": step_i.pk,
"status": "finished",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# So far the same as test_two_steps. Now delete the step
response = client.post(
'/stepinstance/{}/delete'.format(step_i.pk),
content_type="application/json;charset=UTF-8",
)
print(response)
print(response.data)
assert response.json["status"] == "Deleted"
# Test that step is deleted and that samples don't have it
query_count = Step_instance.objects.raw({"_id": step_i.pk}).count()
assert query_count == 0
sample = Sample.objects.get({"barcode": sample_barcodes[0]})
assert len(sample.workflows[workflow_name][step_i.step.name]) == 0
def test_two_workflows_parallel(client, auth):
helper = Helper(client)
helper.reset_db()
workflow_1 = dt.workflows[0]
workflow_2 = dt.workflows[1]
sample_barcodes = dt.barcodes[0]
auth.login()
#needed
s_lims.import_steps([dt.steps[0][0], dt.steps[1][0]])
s_lims.import_workflow(workflow_1)
s_lims.import_workflow(workflow_2)
helper.submit_samples(dt.samplesheets_success)
# Workflow 1 assign
end_step_1_data = dt.attached['in1']
workflow_name = workflow_1['name']
batch_name = dt.batch_name
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
# Workflow 2 assign
helper.assign_samples(sample_barcodes, workflow_2['name'], batch_name)
# Workflow 1 step
step_name = dt.steps[0][0]
step_cat = dt.steps[0][1]
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({"barcode": sample_barcodes[0]})
assert sample_o.workflows[
workflow_1['name']][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
helper.end_step(str(step_i.pk), end_step_1_data)
# Workflow 2 step
step_name = dt.steps[1][0]
step_cat = dt.steps[1][1]
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[
workflow_2['name']][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
helper.end_step(str(step_i.pk), dt.attached['illu3'])
def test_two_steps(client, auth):
helper = Helper(client)
helper.reset_db()
# Test variables
steps = (dt.steps[0], dt.steps[2])
step_names = [s[0] for s in steps]
workflow = dt.workflows[2]
sample_barcodes = dt.barcodes[0]
#needed
s_lims.import_steps(step_names)
s_lims.import_workflow(workflow)
workflow_name = workflow['name']
batch_name = dt.batch_name
auth.login()
helper.submit_samples(dt.samplesheets_success)
helper.assign_samples(sample_barcodes, workflow_name, batch_name)
# Step 1 start
end_step_1_data = dt.attached['in1']
step_name = steps[0][0]
step_cat = steps[0][1]
step_data = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_data)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# for value, subdoc in expected_values:
# if not value in getattr(step_i, subdoc):
# raise ValueError("Missing expected value {} in {}".format(value, subdoc))
helper.end_step(str(step_i.pk), end_step_1_data)
finished_step_i = Step_instance.objects.get({
"_id": step_i.pk,
"status": "finished",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
# Now step 2
step_name = steps[1][0]
step_cat = steps[1][1]
step_starts = {
"sample_barcodes": sample_barcodes,
"workflow_batch": "{}: {}".format(workflow_name, batch_name)
}
helper.start_step(step_name, step_starts)
sample_o = Sample.objects.get({
"barcode": sample_barcodes[0],
})
assert sample_o.workflows[workflow_name][step_cat][0].status == "started"
# This query will raise DoesNotExist if missing.
step = Step.objects.get({"name": step_name})
step_i = Step_instance.objects.get({
"step": step.pk,
"status": "started",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
helper.end_step(str(step_i.pk), {})
finished_step_i = Step_instance.objects.get({
"_id": step_i.pk,
"status": "finished",
"result_samples.{}".format(sample_barcodes[0]): {
"$exists": True
}
})
