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