def test_calls_survey(self, mock_get):
"""If source_type is supported calls the appropriate survey method."""
mock_get.side_effect = mocked_requests_get
# Prevent a call being made to NCBI's API to determine
# organism name/id.
organism = Organism(name="H**O SAPIENS", taxonomy_id=9606, is_scientific_name=True)
organism.save()
survey_job = SurveyJob(source_type="ARRAY_EXPRESS")
survey_job.save()
key_value_pair = SurveyJobKeyValue(survey_job=survey_job,
key="experiment_accession_code",
value="E-GEOD-22166")
key_value_pair.save()
surveyor.run_job(survey_job)
logger.info("Started Survey Job %d, waiting for it to complete.", survey_job.id)
survey_job = wait_for_job(survey_job, SurveyJob)
self.assertTrue(survey_job.success)
batch = Batch.objects.all()[0]
batch = Batch.objects.filter(survey_job=survey_job).get()
downloader_job = batch.downloaderjob_set.get()
logger.info("Survey Job finished, waiting for Downloader Job %d to complete.",
downloader_job.id)
downloader_job = wait_for_job(downloader_job, DownloaderJob)
self.assertTrue(downloader_job.success)
processor_job = batch.processorjob_set.get()
logger.info("Downloader Job finished, waiting for processor Job %d to complete.",
processor_job.id)
processor_job = wait_for_job(processor_job, ProcessorJob)
self.assertTrue(processor_job.success)
def test_run_unsupported_source(self):
"""If source_type is unsupported the job still is started and ended."""
job = SurveyJob(source_type="UNSUPPORTED")
job.save()
surveyor.run_job(job)
self.assertIsInstance(job.start_time, datetime.datetime)
self.assertIsInstance(job.end_time, datetime.datetime)
self.assertFalse(job.success)
def test_calls_survey(self, survey_method):
"""If source_type is supported calls the appropriate survey method."""
survey_method.return_value = True
job = SurveyJob(source_type="ARRAY_EXPRESS")
job.save()
surveyor.run_job(job)
self.assertEqual(len(survey_method.mock_calls), 1)
self.assertIsInstance(job.start_time, datetime.datetime)
self.assertIsInstance(job.end_time, datetime.datetime)
self.assertTrue(job.success)
def test_nonexistant_srp_survey(self):
"""Try surveying an accession that does not exist
"""
survey_job = SurveyJob(source_type="SRA")
survey_job.save()
key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="experiment_accession_code", value="ERP006216"
)
key_value_pair.save()
run_job(survey_job)
survey_job.refresh_from_db()
self.assertFalse(survey_job.success)
self.assertEqual(survey_job.failure_reason, "No experiment found.")
def handle(self, *args, **options):
if options["file"] is None and options[
"accession"] is None and options["job_id"] is None:
logger.error("You must specify an accession or file or job ID.")
return "1"
if options["file"]:
if "s3://" in options["file"]:
bucket, key = parse_s3_url(options["file"])
s3 = boto3.resource("s3")
try:
filepath = "/tmp/input_" + str(uuid.uuid4()) + ".txt"
s3.Bucket(bucket).download_file(key, filepath)
except botocore.exceptions.ClientError as e:
if e.response["Error"]["Code"] == "404":
logger.error("The remote file does not exist.")
raise
else:
raise
else:
filepath = options["file"]
with open(filepath) as accession_file:
for i, accession in enumerate(accession_file):
if i < options["offset"]:
continue
accession = accession.strip()
try:
run_surveyor_for_accession(accession)
except Exception as e:
logger.exception(e)
if options["accession"]:
accession = options["accession"]
try:
run_surveyor_for_accession(accession)
except Exception as e:
logger.exception(e)
if options["job_id"]:
job_id = options["job_id"]
try:
survey_job = SurveyJob.objects.get(id=job_id)
surveyor.run_job(survey_job)
except Exception as e:
logger.exception(e)