def test_download_file_ncbi(self):
dlj = DownloaderJob()
dlj.accession_code = "SRR9117853"
dlj.save()
og = OriginalFile()
og.source_filename = "SRR9117853.sra"
og.source_url = "[email protected]:/sra/sra-instant/reads/ByRun/sra/SRR/SRR9117/SRR9117853/SRR9117853.sra"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = "SRR9117853"
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
result, downloaded_files = sra.download_sra(dlj.pk)
utils.end_downloader_job(dlj, result)
self.assertTrue(result)
self.assertEqual(downloaded_files[0].sha1, "e7ad484fe6f134ba7d1b2664e58cc15ae5a958cc")
self.assertTrue(os.path.exists(downloaded_files[0].absolute_file_path))
def test_download_file_ncbi(self, mock_send_job):
mock_send_job.return_value = None
dlj = DownloaderJob()
dlj.accession_code = "DRR002116"
dlj.save()
og = OriginalFile()
og.source_filename = "DRR002116.sra"
og.source_url = "[email protected]:/sra/sra-instant/reads/ByRun/sra/DRR/DRR002/DRR002116/DRR002116.sra"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = 'DRR002116'
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
result, downloaded_files = sra.download_sra(dlj.pk)
utils.end_downloader_job(dlj, result)
self.assertTrue(result)
self.assertEqual(downloaded_files[0].sha1, 'd5374e7fe047d4f76b165c3f5148ab2df9d42cea')
self.assertTrue(os.path.exists(downloaded_files[0].absolute_file_path))
def test_download_file(self):
dlj = DownloaderJob()
dlj.accession_code = "ERR036"
dlj.save()
og = OriginalFile()
og.source_filename = "ERR036000.fastq.gz"
og.source_url = "ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036000/ERR036000_1.fastq.gz"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = "ERR036000"
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
result, downloaded_files = sra.download_sra(dlj.pk)
self.assertTrue(result)
self.assertEqual(downloaded_files[0].sha1,
"1dfe5460a4101fe87feeffec0cb2e053f6695961")
self.assertTrue(os.path.exists(downloaded_files[0].absolute_file_path))
def test_download_file(self, mock_send_job):
mock_send_job.return_value = None
dlj = DownloaderJob()
dlj.accession_code = "ERR036"
dlj.save()
og = OriginalFile()
og.source_filename = "ERR036000.fastq.gz"
og.source_url = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036000/ERR036000_1.fastq.gz"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = 'ERR036000'
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
success = sra.download_sra(dlj.pk)
def test_download_file_swapper(self, mock_send_job):
mock_send_job.return_value = None
dlj = DownloaderJob()
dlj.accession_code = "DRR002116"
dlj.save()
og = OriginalFile()
og.source_filename = "DRR002116.sra"
og.source_url = "[email protected]:/sra/sra-instant/reads/ByRun/sra/DRR/DRR002/DRR002116/DRR002116.sra"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = 'DRR002116'
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
result = sra._download_file(og.source_url,
dlj,
"/tmp",
force_ftp=False)
self.assertTrue(result)
def queue_downloader_job_for_original_files(
self,
original_files: List[OriginalFile],
experiment_accession_code: str = None,
is_transcriptome: bool = False,
):
"""Creates a single DownloaderJob with multiple files to download.
"""
# Transcriptome is a special case because there's no sample_object.
# It's alright to re-process transcriptome indices.
if is_transcriptome:
downloader_task = job_lookup.Downloaders.TRANSCRIPTOME_INDEX
else:
source_urls = [
original_file.source_url for original_file in original_files
]
# There is already a downloader job associated with this file.
old_assocs_count = DownloaderJobOriginalFileAssociation.objects.filter(
original_file__source_url__in=source_urls).count()
if old_assocs_count > 0:
logger.debug(
"We found an existing DownloaderJob for these urls.",
source_urls=source_urls)
return False
sample_object = original_files[0].samples.first()
downloader_task = job_lookup.determine_downloader_task(
sample_object)
if downloader_task == job_lookup.Downloaders.NONE:
logger.info(
"No valid downloader task found for sample.",
sample=sample_object.id,
original_file=original_files[0].id,
)
else:
downloader_job = DownloaderJob()
downloader_job.downloader_task = downloader_task.value
downloader_job.accession_code = experiment_accession_code
downloader_job.save()
downloaded_urls = []
for original_file in original_files:
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=downloader_job, original_file=original_file)
downloaded_urls.append(original_file.source_url)
try:
logger.info(
"Queuing downloader job.",
survey_job=self.survey_job.id,
downloader_job=downloader_job.id,
downloaded_urls=downloaded_urls,
)
message_queue.send_job(downloader_task, downloader_job)
except:
# If we fail to queue the job, it will be requeued.
pass
def queue_downloader_job_for_original_files(
self,
original_files: List[OriginalFile],
experiment_accession_code: str = None,
is_transcriptome: bool = False):
"""Creates a single DownloaderJob with multiple files to download.
"""
source_urls = [
original_file.source_url for original_file in original_files
]
# There is already a downloader job associated with this file.
old_assocs = DownloaderJobOriginalFileAssociation.objects.filter(
original_file__source_url__in=source_urls)
if len(old_assocs) > 0:
logger.debug("We found an existing DownloaderJob for these urls.",
source_urls=source_urls)
return False
# Transcriptome is a special case because there's no sample_object.
if is_transcriptome:
downloader_task = job_lookup.Downloaders.TRANSCRIPTOME_INDEX
else:
sample_object = original_files[0].samples.first()
downloader_task = job_lookup.determine_downloader_task(
sample_object)
if downloader_task == job_lookup.Downloaders.NONE:
logger.info("No valid downloader task found for sample.",
sample=sample_object.id,
original_file=original_files[0].id)
else:
downloader_job = DownloaderJob()
downloader_job.downloader_task = downloader_task.value
downloader_job.accession_code = experiment_accession_code
downloader_job.save()
downloaded_urls = []
for original_file in original_files:
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=downloader_job, original_file=original_file)
downloaded_urls.append(original_file.source_url)
try:
logger.info("Queuing downloader job.",
survey_job=self.survey_job.id,
downloader_job=downloader_job.id,
downloaded_urls=downloaded_urls)
message_queue.send_job(downloader_task, downloader_job)
except Exception as e:
# If the task doesn't get sent we don't want the
# downloader_job to be left floating
logger.exception("Failed to enqueue downloader job.",
survey_job=self.survey_job.id,
downloader_job=downloader_job.id,
error=str(e))
downloader_job.success = False
downloader_job.failure_reason = str(e)
downloader_job.save()
def test_jobs_sanity(self):
"""Just makes sure creating Jobs doesn't fail"""
s_job = SurveyJob()
s_job.save()
processor_job = ProcessorJob()
processor_job.pipeline_applied = "test0"
processor_job.save()
dl_job = DownloaderJob()
dl_job.downloader_task = "XYZ"
dl_job.accession_code = "123"
dl_job.save()
def test_download_file_unmated_reads(self):
dlj = DownloaderJob()
dlj.accession_code = "SRR1603661"
dlj.save()
og_1 = OriginalFile()
og_1.source_filename = "SRR1603661_1.fastq.gz"
og_1.source_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR160/001/SRR1603661/SRR1603661_1.fastq.gz"
og_1.expected_md5 = "502a9a482bfa5aa75865ccc0105ad13c"
og_1.expected_size_in_bytes = 6751980628
og_1.is_archive = True
og_1.save()
og_2 = OriginalFile()
og_2.source_filename = "SRR1603661_2.fastq.gz"
og_2.source_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR160/001/SRR1603661/SRR1603661_2.fastq.gz"
og_1.expected_md5 = "fffd24457418d255991f54ec82a39d57"
og_1.expected_size_in_bytes = 6949912932
og_2.is_archive = True
og_2.save()
sample = Sample()
sample.accession_code = "SRR1603661"
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og_1
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og_1
assoc.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og_2
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og_2
assoc.save()
result, downloaded_files = sra.download_sra(dlj.pk)
utils.end_downloader_job(dlj, result)
self.assertTrue(result)
self.assertEqual(downloaded_files[0].sha1,
"52bf22472069d04fa7767429f6ab78ebd10c0152")
self.assertTrue(os.path.exists(downloaded_files[0].absolute_file_path))
def test_no_rnaseq(self):
"""Makes sure that no RNA-Seq data gets downloaded even if there's a job for it.
"""
dlj = DownloaderJob()
dlj.accession_code = 'GSE103217'
dlj.save()
original_file = OriginalFile()
original_file.filename = "GSE103217_family.xml.tgz"
original_file.source_url = "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE103nnn/GSE103217/miniml/GSE103217_family.xml.tgz"
original_file.source_filename = "GSE103217_family.xml.tgz"
original_file.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.original_file = original_file
assoc.downloader_job = dlj
assoc.save()
sample = Sample()
sample.accession_code = 'GSE103217'
sample.technology = "RNA-SEQ"
sample.manufacturer = "ILLUMINA"
sample.platform_accession_code = "Illumina HiSeq 2500"
sample.save()
og_assoc = OriginalFileSampleAssociation()
og_assoc.sample = sample
og_assoc.original_file = original_file
og_assoc.save()
download_result = geo.download_geo(dlj.id)
self.assertFalse(download_result)
dlj.refresh_from_db()
self.assertFalse(dlj.success)
# It's not necessarily that we didn't extract any files, but
# none that were usable so it looks like none.
self.assertEqual(dlj.failure_reason,
"Failed to extract any downloaded files.")
def test_download_file_swapper(self):
dlj = DownloaderJob()
dlj.accession_code = "SRR9117853"
dlj.save()
og = OriginalFile()
og.source_filename = "SRR9117853.sra"
og.source_url = "[email protected]:/sra/sra-instant/reads/ByRun/sra/SRR/SRR9117/SRR9117853/SRR9117853.sra"
og.is_archive = True
og.save()
sample = Sample()
sample.accession_code = "SRR9117853"
sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = sample
assoc.original_file = og
assoc.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = dlj
assoc.original_file = og
assoc.save()
result = sra._download_file(og.source_url, dlj, "/tmp/doomed", force_ftp=False)
self.assertTrue(result)
def test_download_aspera_and_ftp(self):
""" Tests the main 'download_geo' function. """
dlj = DownloaderJob()
dlj.accession_code = 'GSE22427'
dlj.save()
original_file = OriginalFile()
original_file.source_url = "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22427/suppl/GSE22427_non-normalized.txt.gz"
original_file.source_filename = "GSE22427_non-normalized.txt.gz"
original_file.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.original_file = original_file
assoc.downloader_job = dlj
assoc.save()
sample = Sample()
sample.accession_code = 'GSE22427'
sample.save()
sample_annotation = SampleAnnotation()
sample_annotation.sample = sample
sample_annotation.data = {
'label_protocol_ch1': 'Agilent',
'label_protocol_ch2': 'Agilent'
}
sample_annotation.save()
og_assoc = OriginalFileSampleAssociation()
og_assoc.sample = sample
og_assoc.original_file = original_file
og_assoc.save()
LOCAL_ROOT_DIR = "/home/user/data_store"
os.makedirs(LOCAL_ROOT_DIR + '/' + sample.accession_code,
exist_ok=True)
dl_file_path = LOCAL_ROOT_DIR + '/' + sample.accession_code + '/' + original_file.source_url.split(
'/')[-1]
# Aspera
result = geo._download_file(original_file.source_url,
file_path=dl_file_path,
job=dlj,
force_ftp=False)
self.assertTrue(result)
self.assertTrue(os.path.exists(dl_file_path))
os.remove(dl_file_path)
# FTP
result = geo._download_file(original_file.source_url,
file_path=dl_file_path,
job=dlj,
force_ftp=True)
self.assertTrue(result)
self.assertTrue(os.path.exists(dl_file_path))
os.remove(dl_file_path)
# Aspera, fail
result = geo._download_file_aspera("https://rich.zone/cool_horse.jpg",
target_file_path=dl_file_path,
downloader_job=dlj,
attempt=5)
self.assertFalse(result)
self.assertTrue(dlj.failure_reason != None)
def test_download_geo(self, mock_send_task):
""" Tests the main 'download_geo' function. """
dlj = DownloaderJob()
dlj.accession_code = 'GSE22427'
dlj.save()
original_file = OriginalFile()
original_file.filename = "GSE22427_non-normalized.txt.gz"
original_file.source_url = "ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE22nnn/GSE22427/suppl/GSE22427_non-normalized.txt.gz"
original_file.source_filename = "GSE22427_non-normalized.txt.gz"
original_file.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.original_file = original_file
assoc.downloader_job = dlj
assoc.save()
sample = Sample()
sample.accession_code = 'GSE22427'
sample.technology = "MICROARRAY"
sample.manufacturer = "AGILENT"
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 = "Illumina_RatRef-12_V1.0"
sample.save()
sample_annotation = SampleAnnotation()
sample_annotation.sample = sample
sample_annotation.data = {
'label_protocol_ch1': 'Agilent',
'label_protocol_ch2': 'Agilent'
}
sample_annotation.save()
og_assoc = OriginalFileSampleAssociation()
og_assoc.sample = sample
og_assoc.original_file = original_file
og_assoc.save()
download_result = geo.download_geo(dlj.id)
file_assocs = OriginalFileSampleAssociation.objects.filter(
sample=sample)
self.assertEqual(file_assocs.count(), 2)
for file_assoc in file_assocs:
original_file = file_assoc.original_file
if original_file.filename.endswith(".gz"):
# We delete the archive after we extract from it
self.assertFalse(original_file.is_downloaded)
else:
self.assertTrue(original_file.is_downloaded)
# Make sure it worked
self.assertTrue(download_result)
self.assertTrue(dlj.failure_reason is None)
self.assertTrue(len(ProcessorJob.objects.all()) > 0)
self.assertEqual(ProcessorJob.objects.all()[0].pipeline_applied,
"AGILENT_TWOCOLOR_TO_PCL")
self.assertEqual(ProcessorJob.objects.all()[0].ram_amount, 2048)
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)
def create_downloader_job(undownloaded_files: OriginalFile, processor_job_id: int) -> bool:
"""Creates a downloader job to download `undownloaded_files`."""
if not undownloaded_files:
return False
original_downloader_job = None
archive_file = None
for undownloaded_file in undownloaded_files:
try:
original_downloader_job = undownloaded_file.downloader_jobs.latest('id')
# Found the job so we don't need to keep going.
break
except DownloaderJob.DoesNotExist:
# If there's no association between this file and any
# downloader jobs, it's most likely because the original
# file was created after extracting a archive containing
# multiple files worth of data.
# The way to handle this is to find that archive and
# recreate a downloader job FOR THAT. That archive will
# have the same filename as the file at the end of the
# 'source_url' field, because that source URL is pointing
# to the archive we need.
archive_filename = undownloaded_file.source_url.split("/")[-1]
# This file or its job might not exist, but we'll wait
# until we've checked all the files before calling it a
# failure.
try:
archive_file = OriginalFile.objects.filter(filename=archive_filename)
if archive_file.count() > 0:
archive_file = archive_file.first()
else:
# We might need to match these up based on
# source_filenames rather than filenames so just
# try them both.
archive_file = OriginalFile.objects.filter(source_filename=archive_filename).first()
original_downloader_job = DownloaderJobOriginalFileAssociation.objects.filter(
original_file=archive_file
).latest('id').downloader_job
# Found the job so we don't need to keep going.
break
except:
pass
if not original_downloader_job:
sample_object = list(undownloaded_files)[0].samples.first()
if sample_object:
downloader_task = job_lookup.determine_downloader_task(sample_object)
if downloader_task == job_lookup.Downloaders.NONE:
logger.warn(("No valid downloader task found for sample, which is weird"
" because it was able to have a processor job created for it..."),
sample=sample_object.id)
return False
else:
# determine_downloader_task returns an enum object,
# but we wanna set this on the DownloaderJob object so
# we want the actual value.
downloader_task = downloader_task.value
accession_code = sample_object.accession_code
original_files = sample_object.original_files.all()
else:
logger.error(
"Could not find the original DownloaderJob or Sample for these files.",
undownloaded_file=undownloaded_files
)
return False
elif original_downloader_job.was_recreated:
logger.warn(
"Downloader job has already been recreated once, not doing it again.",
original_downloader_job=original_downloader_job,
undownloaded_files=undownloaded_files
)
return False
else:
downloader_task = original_downloader_job.downloader_task
accession_code = original_downloader_job.accession_code
original_files = original_downloader_job.original_files.all()
sample_object = original_files[0].samples.first()
new_job = DownloaderJob()
new_job.downloader_task = downloader_task
new_job.accession_code = accession_code
new_job.was_recreated = True
new_job.ram_amount = 1024
new_job.save()
if archive_file:
# If this downloader job is for an archive file, then the
# files that were passed into this function aren't what need
# to be directly downloaded, they were extracted out of this
# archive. The DownloaderJob will re-extract them and set up
# the associations for the new ProcessorJob.
# So double check that it still needs downloading because
# another file that came out of it could have already
# recreated the DownloaderJob.
if archive_file.needs_downloading(processor_job_id):
if archive_file.is_downloaded:
# If it needs to be downloaded then it's not
# downloaded and the is_downloaded field should stop
# lying about that.
archive_file.is_downloaded = False
archive_file.save()
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=new_job,
original_file=archive_file
)
else:
# We can't just associate the undownloaded files, because
# there's a chance that there is a file which actually is
# downloaded that also needs to be associated with the job.
for original_file in original_files:
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=new_job,
original_file=original_file
)
return True
def test_organism_shepherd_command(self, mock_nomad, mock_send_job,
mock_get_active_volumes):
"""Tests that the organism shepherd requeues jobs in the right order.
The situation we're setting up is basically this:
* There are two experiments.
* One of them has 1/2 samples processed, the other 0/1
* One of them needs a DownloaderJob requeued and the other
needs a ProcessorJob requued.
And what we're going to test for is:
* Both of the jobs that need to be requeued are requeued.
* The experiment with a processed sample is requeued first
because it has a higher completion percentage.
"""
# First, set up our mocks to prevent network calls.
mock_send_job.return_value = True
active_volumes = {"1", "2", "3"}
mock_get_active_volumes.return_value = active_volumes
def mock_init_nomad(host, port=0, timeout=0):
ret_value = MagicMock()
ret_value.jobs = MagicMock()
ret_value.jobs.get_jobs = MagicMock()
ret_value.jobs.get_jobs.side_effect = lambda: []
return ret_value
mock_nomad.side_effect = mock_init_nomad
zebrafish = Organism(name="DANIO_RERIO",
taxonomy_id=1337,
is_scientific_name=True)
zebrafish.save()
# Experiment that is 0% complete.
zero_percent_experiment = Experiment(accession_code='ERP037000')
zero_percent_experiment.technology = 'RNA-SEQ'
zero_percent_experiment.save()
organism_assoc = ExperimentOrganismAssociation.objects.create(
organism=zebrafish, experiment=zero_percent_experiment)
zero_percent = OriginalFile()
zero_percent.filename = "ERR037001.fastq.gz"
zero_percent.source_filename = "ERR037001.fastq.gz"
zero_percent.source_url = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR037/ERR037001/ERR037001_1.fastq.gz"
zero_percent.is_archive = True
zero_percent.save()
zero_percent_sample = Sample()
zero_percent_sample.accession_code = 'ERR037001'
zero_percent_sample.organism = zebrafish
zero_percent_sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = zero_percent_sample
assoc.original_file = zero_percent
assoc.save()
assoc = ExperimentSampleAssociation()
assoc.sample = zero_percent_sample
assoc.experiment = zero_percent_experiment
assoc.save()
# TODO: fix names of all the variables to be appropriate for this test case.
zero_percent_dl_job = DownloaderJob()
zero_percent_dl_job.accession_code = zero_percent_sample.accession_code
zero_percent_dl_job.downloader_task = "SRA"
zero_percent_dl_job.start_time = timezone.now()
zero_percent_dl_job.end_time = timezone.now()
zero_percent_dl_job.success = False
zero_percent_dl_job.save()
assoc = DownloaderJobOriginalFileAssociation()
assoc.downloader_job = zero_percent_dl_job
assoc.original_file = zero_percent
assoc.save()
# Experiment that is 50% complete.
fify_percent_experiment = Experiment(accession_code='ERP036000')
fify_percent_experiment.technology = 'RNA-SEQ'
fify_percent_experiment.save()
organism_assoc = ExperimentOrganismAssociation.objects.create(
organism=zebrafish, experiment=fify_percent_experiment)
## First sample, this one has been processed.
successful_pj = ProcessorJob()
successful_pj.accession_code = "ERR036000"
successful_pj.pipeline_applied = "SALMON"
successful_pj.ram_amount = 12288
successful_pj.start_time = timezone.now()
successful_pj.end_time = timezone.now()
successful_pj.success = True
successful_pj.save()
successful_og = OriginalFile()
successful_og.filename = "ERR036000.fastq.gz"
successful_og.source_filename = "ERR036000.fastq.gz"
successful_og.source_url = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036000/ERR036000_1.fastq.gz"
successful_og.is_archive = True
successful_og.save()
successful_sample = Sample()
successful_sample.accession_code = 'ERR036000'
successful_sample.organism = zebrafish
successful_sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = successful_sample
assoc.original_file = successful_og
assoc.save()
assoc = ProcessorJobOriginalFileAssociation()
assoc.processor_job = successful_pj
assoc.original_file = successful_og
assoc.save()
assoc = ExperimentSampleAssociation()
assoc.sample = successful_sample
assoc.experiment = fify_percent_experiment
assoc.save()
## Second sample, this one hasn't been processed.
fifty_percent_unprocessed_og = OriginalFile()
fifty_percent_unprocessed_og.filename = "ERR036001.fastq.gz"
fifty_percent_unprocessed_og.source_filename = "ERR036001.fastq.gz"
fifty_percent_unprocessed_og.source_url = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR036/ERR036001/ERR036001_1.fastq.gz"
fifty_percent_unprocessed_og.is_archive = True
fifty_percent_unprocessed_og.save()
fifty_percent_unprocessed_sample = Sample()
fifty_percent_unprocessed_sample.accession_code = 'ERR036001'
fifty_percent_unprocessed_sample.organism = zebrafish
fifty_percent_unprocessed_sample.save()
assoc = OriginalFileSampleAssociation()
assoc.sample = fifty_percent_unprocessed_sample
assoc.original_file = fifty_percent_unprocessed_og
assoc.save()
assoc = ExperimentSampleAssociation()
assoc.sample = fifty_percent_unprocessed_sample
assoc.experiment = fify_percent_experiment
assoc.save()
fifty_percent_processor_job = ProcessorJob()
fifty_percent_processor_job.pipeline_applied = "SALMON"
fifty_percent_processor_job.accession_code = fifty_percent_unprocessed_sample.accession_code
fifty_percent_processor_job.ram_amount = 12288
fifty_percent_processor_job.start_time = timezone.now()
fifty_percent_processor_job.end_time = timezone.now()
fifty_percent_processor_job.success = False
fifty_percent_processor_job.save()
assoc = ProcessorJobOriginalFileAssociation()
assoc.processor_job = fifty_percent_processor_job
assoc.original_file = fifty_percent_unprocessed_og
assoc.save()
# Setup is done, actually run the command.
args = []
options = {"organism_name": "DANIO_RERIO"}
call_command("organism_shepherd", *args, **options)
# Verify that the jobs were called in the correct order.
mock_calls = mock_send_job.mock_calls
first_call_job_type = mock_calls[0][1][0]
first_call_job_object = mock_calls[0][2]["job"]
self.assertEqual(first_call_job_type, ProcessorPipeline.SALMON)
self.assertEqual(first_call_job_object.pipeline_applied,
fifty_percent_processor_job.pipeline_applied)
self.assertEqual(first_call_job_object.ram_amount,
fifty_percent_processor_job.ram_amount)
self.assertIn(first_call_job_object.volume_index, active_volumes)
fifty_percent_processor_job.refresh_from_db()
self.assertEqual(first_call_job_object,
fifty_percent_processor_job.retried_job)
second_call_job_type = mock_calls[1][1][0]
second_call_job_object = mock_calls[1][2]["job"]
self.assertEqual(second_call_job_type, Downloaders.SRA)
self.assertEqual(second_call_job_object.accession_code,
zero_percent_dl_job.accession_code)
self.assertEqual(second_call_job_object.downloader_task,
zero_percent_dl_job.downloader_task)
zero_percent_dl_job.refresh_from_db()
self.assertEqual(second_call_job_object,
zero_percent_dl_job.retried_job)
def queue_downloader_jobs(self, experiment: Experiment,
samples: List[Sample]):
"""This enqueues DownloaderJobs on a per-file basis.
There is a complementary function below for enqueueing multi-file
DownloaderJobs.
"""
files_to_download = []
for sample in samples:
files_for_sample = OriginalFile.objects.filter(sample=sample,
is_downloaded=False)
for og_file in files_for_sample:
files_to_download.append(og_file)
download_urls_with_jobs = {}
for original_file in files_to_download:
# We don't need to create multiple downloaders for the same file.
# However, we do want to associate original_files with the
# DownloaderJobs that will download them.
if original_file.source_url in download_urls_with_jobs.keys():
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=download_urls_with_jobs[
original_file.source_url],
original_file=original_file,
)
continue
# There is already a downloader job associated with this file.
old_assocs_count = DownloaderJobOriginalFileAssociation.objects.filter(
original_file__source_url=original_file.source_url).count()
if old_assocs_count > 0:
logger.debug(
"We found an existing DownloaderJob for this file/url.",
original_file_id=original_file.id,
)
continue
sample_object = original_file.samples.first()
downloader_task = determine_downloader_task(sample_object)
if downloader_task == Downloaders.NONE:
logger.info(
"No valid downloader task found for sample.",
sample=sample_object.id,
original_file=original_file.id,
)
else:
downloader_job = DownloaderJob()
downloader_job.downloader_task = downloader_task.value
downloader_job.accession_code = experiment.accession_code
downloader_job.save()
DownloaderJobOriginalFileAssociation.objects.get_or_create(
downloader_job=downloader_job, original_file=original_file)
download_urls_with_jobs[
original_file.source_url] = downloader_job
try:
logger.info(
"Queuing downloader job for URL: " +
original_file.source_url,
survey_job=self.survey_job.id,
downloader_job=downloader_job.id,
)
send_job(downloader_task, downloader_job)
except Exception:
# If we fail to queue the job, it will be requeued.
pass
def test_dharma(self):
dlj1 = DownloaderJob()
dlj1.accession_code = 'D1'
dlj1.worker_id = get_instance_id()
dlj1.start_time = datetime.datetime.now()
dlj1.save()
dlj2 = DownloaderJob()
dlj2.accession_code = 'D2'
dlj2.worker_id = get_instance_id()
dlj2.start_time = datetime.datetime.now()
dlj2.save()
dlj3 = DownloaderJob()
dlj3.accession_code = 'D3'
dlj3.worker_id = get_instance_id()
dlj3.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 = dlj3
assoc.save()
sample = Sample()
sample.accession_code = 'Blahblahblah'
sample.technology = "MICROARRAY"
sample.manufacturer = "AFFYMETRIX"
sample.has_raw = True
sample.platform_accession_code = "hgu133a"
sample.save()
OriginalFileSampleAssociation.objects.get_or_create(
sample=sample, original_file=original_file)
exited = False
try:
utils.start_job(dlj3.id,
max_downloader_jobs_per_node=2,
force_harakiri=True)
except SystemExit as e:
# This is supposed to happen!
self.assertTrue(True)
exited = True
except Exception as e:
# This isn't!
self.assertTrue(False)
self.assertTrue(exited)
exited = False
try:
utils.start_job(dlj3.id,
max_downloader_jobs_per_node=15,
force_harakiri=True)
except SystemExit as e:
# This is not supposed to happen!
self.assertTrue(False)
exited = True
except Exception as e:
# This is!
self.assertTrue(True)
self.assertFalse(exited)