def test_is_assembly_in_backlog_should_not_find_assembly_version(self):
study = mgnify.create_study_obj(study_data)
status = AssemblyJobStatus(description='pending')
status.save()
run = mgnify.create_run_obj(study, run_data)
mgnify.create_assembly_job(run, '0', status, 'metaspades', '3.12.0')
assert mgnify.is_assembly_job_in_backlog(run_data['run_accession'], 'metaspades', '3.11.1') is None
def test_get_pending_assembly_jobs_should_return_all_pending_jobs(self):
status = AssemblyJobStatus(description='pending')
status.save()
assembler = Assembler(name='metaspades', version='3.12.0')
assembler.save()
assert len(AssemblyJob.objects.all()) == 0
AssemblyJob(directory='/dir', status=status, priority=0, assembler=assembler, input_size=3).save()
AssemblyJob(directory='/dir', status=status, priority=1, assembler=assembler, input_size=4).save()
assert len(mgnify.get_pending_assembly_jobs()) == 2
def test_filter_active_runs_should_return_empty_list(self):
assert len(AssemblyJob.objects.all()) == 0
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
status = AssemblyJobStatus(description='pending')
status.save()
mgnify.create_assembly_job(run, '0', status, 'metaspades', '3.12.0')
assert len(AssemblyJob.objects.all()) == 1
assert len(mgnify.filter_active_runs([run_data], 'metaspades')) == 0
def test_create_assembly_job_should_set_status_from_model(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
_ = Assembler(name='metaspades', version='3.11.1').save()
status = AssemblyJobStatus(description='PENDING')
status.save()
mgnify.create_assembly_job(run, 0, status, 'metaspades')
assembly_jobs = AssemblyJob.objects.all()
assert len(assembly_jobs) == 1
assembly_job = assembly_jobs[0]
assert assembly_job.status.description == status.description
def test_save_assembly_job_should_update_job(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
assembler = Assembler(name='metaspades', version='3.12.0')
assembler.save()
status = AssemblyJobStatus(description='pending')
status.save()
status2 = AssemblyJobStatus(description='running')
status2.save()
assert len(AssemblyJob.objects.all()) == 0
assembly_job = AssemblyJob(input_size=0, assembler=assembler, status=status, priority=0)
assembly_job.save()
RunAssemblyJob(run=run, assembly_job=assembly_job).save()
new_priority = 1
mgnify.save_assembly_job(run, 0, assembler.name, assembler.version, status2, new_priority)
assert len(RunAssemblyJob.objects.all()) == 1
assembly_jobs = AssemblyJob.objects.all()
assert len(assembly_jobs) == 1
updated_assembly_job = assembly_jobs[0]
assert updated_assembly_job.pk == assembly_job.pk
assert updated_assembly_job.status.pk == status2.pk
assert updated_assembly_job.priority == new_priority
def test_save_assembly_job_should_create_new_job(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
status = AssemblyJobStatus(description='pending')
status.save()
job = mgnify.save_assembly_job(run, 1, 'metaspades', '3.12.0', status, 3)
jobs = AssemblyJob.objects.all()
assert len(jobs) == 1
inserted_job = jobs[0]
assert inserted_job.pk == job.pk
assert inserted_job.input_size == 1
assert inserted_job.assembler.name == 'metaspades'
assert inserted_job.assembler.version == '3.12.0'
assert inserted_job.status.pk == status.pk
assert inserted_job.priority == 3
def test_get_pending_assembly_jobs_should_order_jobs_by_decreasing_priority(self):
status = AssemblyJobStatus(description='pending')
status.save()
assembler = Assembler(name='metaspades', version='3.12.0')
assembler.save()
assert len(AssemblyJob.objects.all()) == 0
job1 = AssemblyJob(directory='/dir', status=status, priority=3, assembler=assembler, input_size=3)
job1.save()
job2 = AssemblyJob(directory='/dir', status=status, priority=1, assembler=assembler, input_size=4)
job2.save()
pending_jobs = mgnify.get_pending_assembly_jobs()
assert len(pending_jobs) == 2
assert pending_jobs[0].pk == job1.pk
assert pending_jobs[1].pk == job2.pk
def test_set_assembly_job_running_should_update_existing_assembly_job(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
status = AssemblyJobStatus(description='pending')
status.save()
AssemblyJobStatus(description='running').save()
assembler_name = 'metaspades'
assembler_version = '3.11.1'
inserted_assembly_job = mgnify.create_assembly_job(run, '0', status, assembler_name, assembler_version)
assert len(AssemblyJob.objects.all()) == 1
mgnify.set_assembly_job_running(run_data['run_accession'], assembler_name, assembler_version)
assembly_jobs = AssemblyJob.objects.all()
assert len(assembly_jobs) == 1
assert len(Run.objects.all()) == 1
assert len(Study.objects.all()) == 1
assembly_job = assembly_jobs[0]
assert assembly_job.pk == inserted_assembly_job.pk
assert assembly_job.status.description == 'running'