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 create_assembly_job(self,
run,
total_size,
status,
assembler_name,
assembler_version=None,
priority=0):
try:
if not assembler_version:
assembler_version = self.get_latest_assembler_version(
assembler_name)
assembler = Assembler.objects.using(self.database).get(
name=assembler_name, version=assembler_version)
except ObjectDoesNotExist:
assembler = Assembler(name=assembler_name,
version=assembler_version)
assembler.save(using=self.database)
if isinstance(status, str):
status = AssemblyJobStatus.objects.using(
self.database).get(description=status)
job = AssemblyJob(assembler=assembler,
status=status,
input_size=total_size,
priority=priority)
job.save(using=self.database)
RunAssemblyJob(assembly_job=job, run=run).save(using=self.database)
return job
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_create_assembly_job_should_set_latest_assembler(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
latest_version = '3.12.0'
_ = Assembler(name='metaspades', version='3.11.1').save()
_ = Assembler(name='metaspades', version=latest_version).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.assembler.version == latest_version
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_create_assembly_job_should_set_status_from_string_arg(self):
study = mgnify.create_study_obj(study_data)
run = mgnify.create_run_obj(study, run_data)
description = 'PENDING'
_ = Assembler(name='metaspades', version='3.11.1').save()
_ = AssemblyJobStatus(description=description).save()
mgnify.create_assembly_job(run, 0, description, 'metaspades')
assembly_jobs = AssemblyJob.objects.all()
assert len(assembly_jobs) == 1
assembly_job = assembly_jobs[0]
assert assembly_job.status.description == description
def test_get_latest_assembler_version_should_return_latest_version(self):
assembler_name = 'metaspades'
versions = ['3.10.0', '3.11.1', '3.12.0']
for version in versions:
Assembler(name=assembler_name, version=version).save()
assert mgnify.get_latest_assembler_version(assembler_name) == '3.12.0'