def test_survey(self, mock_send_task):
"""A Simple test of the ArrayExpress surveyor."""
survey_job = self.create_job_for_accession("E-MTAB-3050")
ae_surveyor = ArrayExpressSurveyor(survey_job)
ae_surveyor.survey()
samples = Sample.objects.all()
downloader_jobs = DownloaderJob.objects.all()
# We are expecting this to discover 5 samples.
self.assertEqual(samples.count(), 5)
# And for one DownloaderJob to be created for all of them.
self.assertEqual(downloader_jobs.count(), 1)
sample = Sample.objects.first()
self.assertTrue(' (hgu95av2)' in sample.pretty_platform)
# Confirm the sample's protocol_info
self.assertEqual(len(sample.protocol_info), 9)
self.assertEqual(sample.protocol_info[0]['Accession'], "P-MTAB-41854")
self.assertEqual(sample.protocol_info[0]['Text'], "Aliquoting of biomaterials.")
self.assertEqual(sample.protocol_info[0]['Type'], "split")
survey_job2 = self.create_job_for_accession("E-GEOD-44719")
ae_surveyor = ArrayExpressSurveyor(survey_job2)
ae_surveyor.survey()
# We are expecting this to discover 77 samples.
self.assertEqual(samples.count(), 77+5)
# And for one DownloaderJob to be created for all of them.
self.assertEqual(downloader_jobs.count(), 2)
def test_survey_with_protocol_list(self):
"""Tests an edge case that came up after months:
https://github.com/AlexsLemonade/refinebio/issues/761
"""
survey_job = self.create_job_for_accession("E-MEXP-2381")
ae_surveyor = ArrayExpressSurveyor(survey_job)
ae_surveyor.survey()
samples = Sample.objects.all()
downloader_jobs = DownloaderJob.objects.all()
# We are expecting this to discover 2 samples.
self.assertEqual(samples.count(), 2)
# And for one DownloaderJob to be created for all of them.
self.assertEqual(downloader_jobs.count(), 1)
def test_survey(self, mock_send_task, mock_get):
"""The 'survey' function generates one Batch per sample.
This test also tests the handle_batches method of ExternalSourceSurveyor
which isn't tested on its own because it is an abstract class.
"""
mock_send_task.return_value = Mock(ok=True)
mock_get.side_effect = mocked_requests_get
ae_surveyor = ArrayExpressSurveyor(self.survey_job)
ae_surveyor.survey()
downloader_jobs = DownloaderJob.objects.all()
mock_send_task.assert_has_calls(
[call(Downloaders.ARRAY_EXPRESS, downloader_jobs[0].id)])
batches = Batch.objects.all()
self.assertEqual(2, len(batches))
self.assertEqual(1, len(downloader_jobs))
batch = batches[0]
self.assertEqual(batch.survey_job.id, self.survey_job.id)
self.assertEqual(batch.source_type, "ARRAY_EXPRESS")
self.assertEqual(batch.pipeline_required, "AFFY_TO_PCL")
self.assertEqual(batch.platform_accession_code, "A-AFFY-1")
self.assertEqual(batch.experiment_accession_code, "E-MTAB-3050")
self.assertEqual(batch.experiment_title,
"Microarray analysis of in vitro differentiation")
self.assertEqual(batch.status, "NEW")
self.assertEqual(batch.release_date, datetime.date(2014, 10, 31))
self.assertEqual(batch.last_uploaded_date, datetime.date(2014, 10, 30))
self.assertEqual(batch.organism_id, 9606)
self.assertEqual(batch.organism_name, "H**O SAPIENS")
file = batch.files[0]
self.assertEqual(file.size_in_bytes, -1)
self.assertEqual(
file.download_url,
"ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-3050/E-MTAB-3050.raw.1.zip"
) # noqa
self.assertEqual(file.raw_format, "CEL")
self.assertEqual(file.processed_format, "PCL")
self.assertEqual(file.name, "C30057.CEL")
self.assertEqual(file.internal_location, "A-AFFY-1/AFFY_TO_PCL")
def test_survey(self, mock_send_task):
"""A Simple test of the ArrayExpress surveyor."""
survey_job = self.create_job_for_accession("E-MTAB-3050")
ae_surveyor = ArrayExpressSurveyor(survey_job)
ae_surveyor.survey()
samples = Sample.objects.all()
downloader_jobs = DownloaderJob.objects.all()
# We are expecting this to discover 5 samples.
self.assertEqual(samples.count(), 5)
# And for one DownloaderJob to be created for all of them.
self.assertEqual(downloader_jobs.count(), 1)
experiment = Experiment.objects.first()
self.assertEqual(experiment.accession_code, "E-MTAB-3050")
self.assertEqual(experiment.source_first_published,
datetime.datetime(2014, 10, 31, tzinfo=timezone.utc))
self.assertEqual(experiment.source_last_modified,
datetime.datetime(2014, 10, 30, tzinfo=timezone.utc))
sample = Sample.objects.first()
self.assertTrue(" (hgu95av2)" in sample.pretty_platform)
# Confirm the sample's protocol_info
self.assertEqual(len(sample.protocol_info), 9)
self.assertEqual(sample.protocol_info[0]["Accession"], "P-MTAB-41854")
self.assertEqual(sample.protocol_info[0]["Text"],
"Aliquoting of biomaterials.")
self.assertEqual(sample.protocol_info[0]["Type"], "split")
survey_job2 = self.create_job_for_accession("E-GEOD-44719")
ae_surveyor = ArrayExpressSurveyor(survey_job2)
ae_surveyor.survey()
# We are expecting this to discover 77 samples.
self.assertEqual(samples.count(), 77 + 5)
# And for one DownloaderJob to be created for all of them.
self.assertEqual(downloader_jobs.count(), 2)