def setUpClass(cls):
super(ESTestCases, cls).setUpClass(
) # ref https://stackoverflow.com/a/29655301/763705
"""Set up class."""
experiment = Experiment()
experiment.accession_code = "GSE000-X"
experiment.title = "NONONONO"
experiment.description = "Boooooourns. Wasabi."
experiment.technology = "RNA-SEQ"
experiment.save()
experiment = Experiment()
experiment.accession_code = "GSE123-X"
experiment.title = "Hey Ho Let's Go"
experiment.description = (
"This is a very exciting test experiment. Faygo soda. Blah blah blah."
)
experiment.technology = "MICROARRAY"
experiment.num_processed_samples = 1 # added below
experiment.num_total_samples = 1
experiment.num_downloadable_samples = 1
experiment.save()
experiment_annotation = ExperimentAnnotation()
experiment_annotation.data = {"hello": "world", "123": 456}
experiment_annotation.experiment = experiment
experiment_annotation.save()
sample = Sample()
sample.title = "123"
sample.accession_code = "123"
sample.save()
organism = Organism(name="AILUROPODA_MELANOLEUCA",
taxonomy_id=9646,
is_scientific_name=True)
organism.save()
sample = Sample()
sample.title = "789"
sample.accession_code = "789"
sample.is_processed = True
sample.organism = organism
sample.save()
sample_annotation = SampleAnnotation()
sample_annotation.data = {"goodbye": "world", "789": 123}
sample_annotation.sample = sample
sample_annotation.save()
original_file = OriginalFile()
original_file.save()
original_file_sample_association = OriginalFileSampleAssociation()
original_file_sample_association.sample = sample
original_file_sample_association.original_file = original_file
original_file_sample_association.save()
downloader_job = DownloaderJob()
downloader_job.save()
download_assoc = DownloaderJobOriginalFileAssociation()
download_assoc.original_file = original_file
download_assoc.downloader_job = downloader_job
download_assoc.save()
processor_job = ProcessorJob()
processor_job.save()
processor_assoc = ProcessorJobOriginalFileAssociation()
processor_assoc.original_file = original_file
processor_assoc.processor_job = processor_job
processor_assoc.save()
# associate the experiment with the sample
experiment_sample_association = ExperimentSampleAssociation()
experiment_sample_association.sample = sample
experiment_sample_association.experiment = experiment
experiment_sample_association.save()
result = ComputationalResult()
result.save()
# and create a qn tarjet for the sample
computational_result = ComputationalResultAnnotation()
computational_result.result = result
computational_result.data = {
"is_qn": True,
"organism_id": sample.organism.id
}
computational_result.save()
# and associate it with the sample organism
sample.organism.qn_target = result
sample.organism.save()
sra = SampleResultAssociation()
sra.sample = sample
sra.result = result
sra.save()
result = ComputationalResult()
result.save()
sra = SampleResultAssociation()
sra.sample = sample
sra.result = result
sra.save()
# clear default cache and reindex
# otherwise the organisms with qn_targes will be cached.
cache.clear()
call_command("search_index", "--rebuild", "-f")
def setUp(self):
# Saving this for if we have protected endpoints
# self.superuser = User.objects.create_superuser('john', '*****@*****.**', 'johnpassword')
# self.client.login(username='******', password='******')
# self.user = User.objects.create(username="******")
experiment = Experiment()
experiment.accession_code = "GSE000"
experiment.title = "NONONONO"
experiment.description = "Boooooourns. Wasabi."
experiment.technology = "RNA-SEQ"
experiment.save()
experiment = Experiment()
experiment.accession_code = "GSE123"
experiment.title = "Hey Ho Let's Go"
experiment.description = (
"This is a very exciting test experiment. Faygo soda. Blah blah blah."
)
experiment.technology = "MICROARRAY"
experiment.save()
self.experiment = experiment
experiment_annotation = ExperimentAnnotation()
experiment_annotation.data = {"hello": "world", "123": 456}
experiment_annotation.experiment = experiment
experiment_annotation.save()
ailuropoda = Organism(name="AILUROPODA_MELANOLEUCA",
taxonomy_id=9646,
is_scientific_name=True)
ailuropoda.save()
self.homo_sapiens = Organism(name="HOMO_SAPIENS",
taxonomy_id=9606,
is_scientific_name=True)
self.homo_sapiens.save()
self.danio_rerio = Organism(name="DANIO_RERIO",
taxonomy_id=1337,
is_scientific_name=True)
self.danio_rerio.save()
sample = Sample()
sample.title = "123"
sample.accession_code = "123"
sample.is_processed = True
sample.organism = ailuropoda
sample.save()
sample = Sample()
sample.title = "789"
sample.accession_code = "789"
sample.is_processed = True
sample.organism = ailuropoda
sample.save()
self.sample = sample
# add qn target for sample organism
result = ComputationalResult()
result.commands.append("create_qn_target.py")
result.is_ccdl = True
result.is_public = True
result.processor = None
result.save()
cra = ComputationalResultAnnotation()
cra.result = result
cra.data = {"organism_id": ailuropoda.id, "is_qn": True}
cra.save()
ailuropoda.qn_target = result
ailuropoda.save()
sample_annotation = SampleAnnotation()
sample_annotation.data = {"goodbye": "world", "789": 123}
sample_annotation.sample = sample
sample_annotation.save()
original_file = OriginalFile()
original_file.save()
original_file_sample_association = OriginalFileSampleAssociation()
original_file_sample_association.sample = sample
original_file_sample_association.original_file = original_file
original_file_sample_association.save()
downloader_job = DownloaderJob()
downloader_job.save()
download_assoc = DownloaderJobOriginalFileAssociation()
download_assoc.original_file = original_file
download_assoc.downloader_job = downloader_job
download_assoc.save()
processor_job = ProcessorJob()
processor_job.save()
processor_assoc = ProcessorJobOriginalFileAssociation()
processor_assoc.original_file = original_file
processor_assoc.processor_job = processor_job
processor_assoc.save()
experiment_sample_association = ExperimentSampleAssociation()
experiment_sample_association.sample = sample
experiment_sample_association.experiment = experiment
experiment_sample_association.save()
experiment.num_total_samples = 1
experiment.num_processed_samples = 1
experiment.save()
result = ComputationalResult()
result.save()
sra = SampleResultAssociation()
sra.sample = sample
sra.result = result
sra.save()
result = ComputationalResult()
result.save()
sra = SampleResultAssociation()
sra.sample = sample
sra.result = result
sra.save()
processor = Processor()
processor.name = "Salmon Quant"
processor.version = "v9.9.9"
processor.docker_image = "dr_salmon"
processor.environment = '{"some": "environment"}'
processor.save()
computational_result_short = ComputationalResult(processor=processor)
computational_result_short.save()
organism_index = OrganismIndex()
organism_index.index_type = "TRANSCRIPTOME_SHORT"
organism_index.organism = self.danio_rerio
organism_index.result = computational_result_short
organism_index.absolute_directory_path = (
"/home/user/data_store/salmon_tests/TRANSCRIPTOME_INDEX/SHORT")
organism_index.is_public = True
organism_index.s3_url = "not_blank"
organism_index.save()
return
def test_download_multiple_zips(self, mock_send_job):
"""Tests that each sample gets one processor job no matter what.
https://github.com/AlexsLemonade/refinebio/pull/351 deals with
a bug where every file that was extracted to a directory got a
processor job queued for it each time a downloader job ran
which pointed to that directory. This test makes sure this bug
stays squashed.
It does so by running two downloader jobs for the same
experiment which use two different zip files. Before this bug
was squashed this would have resulted in the first sample
getting a second processor job queued for it because the
second downloader job would have found the file in the
directory.
"""
dlj1 = DownloaderJob()
dlj1.accession_code = 'E-MEXP-433'
dlj1.save()
original_file = OriginalFile()
original_file.source_url = "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-433/E-MEXP-433.raw.1.zip"
original_file.source_filename = "Waldhof_020604_R30_01-2753_U133A.CEL"
original_file.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.original_file = original_file
assoc.downloader_job = dlj1
assoc.save()
sample = Sample()
sample.accession_code = 'E-MEXP-433-Waldhof_020604_R30_01-2753_U133A'
sample.technology = "MICROARRAY"
sample.manufacturer = "AFFYMETRIX"
sample.has_raw = True
# This is fake, but we don't currently support any agilent
# platforms so we're using a platform that is supported.
sample.platform_accession_code = "hgu133a"
sample.save()
OriginalFileSampleAssociation.objects.get_or_create(
sample=sample, original_file=original_file)
dlj2 = DownloaderJob()
dlj2.accession_code = 'E-MEXP-433'
dlj2.save()
original_file = OriginalFile()
original_file.source_url = "ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-433/E-MEXP-433.raw.2.zip"
original_file.source_filename = "N08_U133A.CEL"
original_file.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.original_file = original_file
assoc.downloader_job = dlj2
assoc.save()
sample = Sample()
sample.accession_code = 'E-MEXP-433-N08_U133A'
sample.technology = "MICROARRAY"
sample.manufacturer = "AFFYMETRIX"
sample.has_raw = True
# This is fake, but we don't currently support any agilent
# platforms so we're using a platform that is supported.
sample.platform_accession_code = "hgu133a"
sample.save()
OriginalFileSampleAssociation.objects.get_or_create(
sample=sample, original_file=original_file)
array_express.download_array_express(dlj1.id)
array_express.download_array_express(dlj2.id)
self.assertEqual(ProcessorJob.objects.all().count(), 2)