def test_get_up_to_date_assembly_annotation_jobs_should_retrieve_all_jobs_in_priority_order(self):
study = mgnify.create_study_obj(study_data)
accessions = ['ERZ795049', 'ERZ795050']
assemblies = []
for accession in accessions:
data = copy.deepcopy(assembly_data)
data['analysis_accession'] = accession
assemblies.append(mgnify.get_or_save_assembly(ena, accession, data, study))
pipeline = Pipeline(version=4.1)
pipeline.save()
pipeline = Pipeline(version=5.0)
pipeline.save()
user = mgnify.create_user(user_data['webin_id'], user_data['email_address'],
user_data['first_name'],
user_data['surname'])
request = mgnify.create_user_request(user, 0, 1)
assert 0 == len(AnnotationJob.objects.all())
mgnify.create_annotation_job(request, assemblies[0], 0, 4.1)
mgnify.create_annotation_job(request, assemblies[1], 1)
up_to_date_assemblies_latest = mgnify.get_up_to_date_assembly_annotation_jobs(
study_data['secondary_study_accession'])
assert 1 == len(up_to_date_assemblies_latest)
up_to_date_assemblies_v4 = mgnify.get_up_to_date_assembly_annotation_jobs(
study_data['secondary_study_accession'], 4.1)
assert 1 == len(up_to_date_assemblies_v4)
up_to_date_assemblies_v5 = mgnify.get_up_to_date_assembly_annotation_jobs(
study_data['secondary_study_accession'], 5)
assert 1 == len(up_to_date_assemblies_v5)
def create_annotation_jobs_without_ena_services(rt_ticket=0, priority=0):
study = mgnify.create_study_obj(study_data)
run_accessions = ['ERR164407', 'ERR164408', 'ERR164409']
for run_acc in run_accessions:
run_data["run_accession"] = run_acc
mgnify.create_run_obj(study, run_data)
pipeline = Pipeline(version=4.1)
pipeline.save()
user = mgnify.create_user(user_data['webin_id'], user_data['email_address'],
user_data['first_name'],
user_data['surname'])
request = mgnify.create_user_request(user, priority, rt_ticket)
runs = []
for run_acc in run_accessions:
run = mgnify.get_backlog_run(run_acc)
runs.append(run)
mgnify.create_annotation_job(request, run, 4)
return study, runs
def test_create_annotation_job_should_create_annotationjob_for_assembly(self):
study = mgnify.create_study_obj(study_data)
assembly = mgnify.create_assembly_obj(ena, study, assembly_data, public=True)
Pipeline(version=4.1).save()
user = User(**user_data)
user.save()
request = UserRequest(user=user, rt_ticket=1234, priority=1)
request.save()
inserted_annotation_job = mgnify.create_annotation_job(request, assembly, 1)
retrieved_annotation_jobs = AnnotationJob.objects.all()
assert len(retrieved_annotation_jobs) == 1
retrieved_annotation_job = retrieved_annotation_jobs[0]
assert inserted_annotation_job.pk == retrieved_annotation_job.pk
related_assemblies = retrieved_annotation_job.assemblyannotationjob_set.all()
assert len(related_assemblies) == 1
assert isinstance(related_assemblies[0].assembly, Assembly)
assert related_assemblies[0].assembly.pk == assembly.pk
def test_create_annotation_job_should_create_annotationjob_for_run(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
Pipeline(version=4.1).save()
user = User(**user_data)
user.save()
request = UserRequest(user=user, rt_ticket=1234, priority=1)
request.save()
inserted_annotation_job = mgnify.create_annotation_job(request, run, 1)
retrieved_annotation_jobs = AnnotationJob.objects.all()
assert len(retrieved_annotation_jobs) == 1
retrieved_annotation_job = retrieved_annotation_jobs[0]
assert inserted_annotation_job.pk == retrieved_annotation_job.pk
related_runs = retrieved_annotation_job.runannotationjob_set.all()
assert len(related_runs) == 1
assert isinstance(related_runs[0].run, Run)
assert related_runs[0].run.pk == run.pk
def test_update_annotation_jobs_should_update_by_pipeline_version_only(self):
rt_ticket = 0
initial_priority = 1
initial_status = AnnotationJobStatus.objects.get(description='SCHEDULED')
final_priority = 2
final_status_description = 'RUNNING'
new_pipeline_version = 5.0
assert len(AnnotationJob.objects.all()) == 0
create_annotation_jobs_using_ena_services(rt_ticket, initial_priority)
assert len(AnnotationJob.objects.all()) == 3
Pipeline(version=new_pipeline_version).save()
request = UserRequest.objects.first()
for run in Run.objects.all():
mgnify.create_annotation_job(request=request, assembly_or_run=run, priority=initial_priority)
assert len(AnnotationJob.objects.all()) == 6
initial_jobs = AnnotationJob.objects.all()
for job in initial_jobs:
assert job.priority == initial_priority
assert job.status == initial_status
mgnify.update_annotation_jobs_from_accessions(priority=final_priority,
status_description=final_status_description,
pipeline_version=new_pipeline_version)
final_jobs = AnnotationJob.objects.all()
assert len(initial_jobs) == len(final_jobs)
for job in final_jobs:
if job.pipeline.version == new_pipeline_version:
assert job.priority == final_priority
assert job.status.description == final_status_description
else:
assert job.priority == initial_priority
assert job.status == initial_status
def create_annotation_jobs_using_ena_services(rt_ticket=0, priority=0, version=4.1):
study = mgnify.create_study_obj(study_data)
accessions = ['ERR164407', 'ERR164408', 'ERR164409']
lineage = 'root:Host-Associated:Human:Digestive System'
runs = [mgnify.get_or_save_run(ena, accession, study=study, lineage=lineage) for accession in
accessions]
versions = [1.0, 2.0, 3.0, 4.0, 4.1, 5.0]
for _version in versions:
Pipeline(version=_version).save()
user = mgnify.create_user(user_data['webin_id'], user_data['email_address'],
user_data['first_name'],
user_data['surname'])
request = mgnify.create_user_request(user, priority, rt_ticket)
assert len(AnnotationJob.objects.all()) == 0
mgnify.create_annotation_job(request, runs[0], priority, version) # 4.1
mgnify.create_annotation_job(request, runs[1], priority, version) # 4.1
mgnify.create_annotation_job(request, runs[2], priority) # latest pipeline version
return study, runs
def test_get_pipeline_by_version_should_return_correct_pipeline(self):
versions = [1.0, 2.0, 3.0, 4.0, 4.1, 5.0]
for version in versions:
Pipeline(version=version).save()
assert mgnify.get_pipeline_by_version(5.0).version == 5.0
def test_get_latest_pipeline_should_return_latest_pipeline(self):
versions = [1.0, 2.0, 3.0, 4.0, 4.1]
for version in versions:
Pipeline(version=version).save()
assert mgnify.get_latest_pipeline().version == max(versions)