def test_no_job_created_when_failed_job_exists(self):
experiment = setup_experiment([], ["GSM001"])
# create a failed job for that experiment
processor_job = ProcessorJob()
processor_job.pipeline_applied = ProcessorPipeline.SALMON
processor_job.ram_amount = 1024
processor_job.success = False
processor_job.retried = False
processor_job.no_retry = False
processor_job.save()
assoc = ProcessorJobOriginalFileAssociation()
assoc.original_file = experiment.samples.first().original_files.first()
assoc.processor_job = processor_job
assoc.save()
# Run command
update_salmon_all_experiments()
dl_jobs = DownloaderJob.objects.all()
self.assertEqual(dl_jobs.count(), 0)
def setup_experiment() -> Dict:
""" Create an experiment with two samples where one of them has a processor job that failed
because Batch restarted it."""
# Create the experiment
experiment_accession = "SRP095529"
experiment = Experiment.objects.create(accession_code=experiment_accession,
technology="RNA-SEQ")
zebrafish = Organism.get_object_for_name("DANIO_RERIO")
accession_code = "S001"
sample = Sample.objects.create(
accession_code=accession_code,
organism=zebrafish,
source_database="SRA",
technology="RNA-SEQ",
platform_accession_code="IlluminaHiSeq1000",
)
ExperimentSampleAssociation.objects.create(experiment=experiment,
sample=sample)
original_file = OriginalFile()
original_file.filename = accession_code + ".SRA"
original_file.source_filename = accession_code + ".SRA"
original_file.save()
OriginalFileSampleAssociation.objects.get_or_create(
original_file=original_file, sample=sample)
accession_code = "S002"
sample = Sample.objects.create(
accession_code=accession_code,
organism=zebrafish,
source_database="SRA",
technology="RNA-SEQ",
platform_accession_code="IlluminaHiSeq1000",
)
ExperimentSampleAssociation.objects.create(experiment=experiment,
sample=sample)
original_file = OriginalFile()
original_file.filename = accession_code + ".SRA"
original_file.source_filename = accession_code + ".SRA"
original_file.save()
OriginalFileSampleAssociation.objects.get_or_create(
original_file=original_file, sample=sample)
# add a failed processor job for the second sample
processor_job = ProcessorJob()
processor_job.start_time = timezone.now()
processor_job.end_time = timezone.now()
processor_job.no_retry = True
processor_job.success = False
processor_job.failure_reason = (
"ProcessorJob has already completed with a fail - why are we here again?"
)
processor_job.save()
processor_assoc = ProcessorJobOriginalFileAssociation()
processor_assoc.original_file = original_file
processor_assoc.processor_job = processor_job
processor_assoc.save()
return experiment