def check_reference(meta, args):
"""Check and install the needed reference genome"""
print("Checking reference")
plan_data = json.load(open(os.path.join(args.path, "plan.json")))
version, design, meta = ampliseq.handle_versioned_plans(plan_data, meta)
print("Got versioned stuff")
# If we have a genome reference, check to see if it's installed
reference = design.get('genome_reference', None)
print(reference)
if not reference:
return False
try:
url = reference.get('uri')
ref_hash = reference.get('files_md5sum', {}).get('fasta')
short_name = reference.get('short_name')
name = reference.get('name')
notes = reference.get('notes', "AmpliSeq Import")
print("Got various fields")
except KeyError as err:
# If the key does not exist, that's fine, but it can't exist and be corrupt
print("Corrupt genome_reference entry: {0}".format(err))
sys.exit(1)
# The identity_hash matching the files_md5sum.fasta hash determines whether
# or not the genome is installed
print("Checking reference " + ref_hash)
if not models.ReferenceGenome.objects.filter(identity_hash=ref_hash).exists():
reference = models.ReferenceGenome(
enabled = False,
identity_hash = ref_hash,
name = name,
notes = notes,
short_name = short_name,
source = url,
status = "downloading",
index_version = "tmap-f3"
)
reference.save()
print("created new reference")
pub = models.Publisher.objects.get(name='BED')
upload = models.ContentUpload.objects.get(pk=args.upload_id)
# This is a celery subtask that will run the publisher scripts on this upload again
finish_me = run_pub_scripts.si(pub, upload)
print("About t set check point")
set_checkpoint(meta, args)
print("check point set")
# With a status starting with "Waiting" the framework will stop
# after pre_processing, before validate.
upload.status = "Waiting on reference"
upload.save()
# the subtask finish_me will be called at the end of the reference install
# process to restart validation of the upload
start_reference_download(url, reference, callback=finish_me)
print("Started reference download")
return True
print("exiting in shame")
return False
def check_reference(meta, args):
print("Checking reference")
plan_data = json.load(open(os.path.join(args.path, "plan.json")))
version, design, meta = ampliseq.handle_versioned_plans(plan_data, meta)
print("Got versioned stuff")
reference = design.get('genome_reference', None)
print(reference)
if not reference:
return False
try:
url = reference.get('uri')
ref_hash = reference.get('files_md5sum', {}).get('fasta')
short_name = reference.get('short_name')
name = reference.get('name')
notes = reference.get('notes', "AmpliSeq Import")
print("Got various fields")
except KeyError as err:
print("Corrupt genome_reference entry: {0}".format(err))
sys.exit(1)
print("Checking reference " + ref_hash)
if not models.ReferenceGenome.objects.filter(identity_hash=ref_hash).exists():
reference = models.ReferenceGenome(
enabled = False,
identity_hash = ref_hash,
name = name,
notes = notes,
short_name = short_name,
source = url,
status = "downloading",
index_version = "tmap-f3"
)
reference.save()
print("created new reference")
pub = models.Publisher.objects.get(name='BED')
upload = models.ContentUpload.objects.get(pk=args.upload_id)
finish_me = run_pub_scripts.si(pub, upload)
print("About t set check point")
set_checkpoint(meta, args)
print("check point set")
upload.status = "Waiting on reference"
upload.save()
start_reference_download(url, reference, callback=finish_me)
print("Started reference download")
return True
print("exiting in shame")
return False
def check_reference(meta, args):
print("Checking reference")
plan_data = json.load(open(os.path.join(args.path, "plan.json")))
version, design, meta = ampliseq.handle_versioned_plans(plan_data, meta)
print("Got versioned stuff")
reference = design.get('genome_reference', None)
print(reference)
if not reference:
return False
try:
url = reference.get('uri')
ref_hash = reference.get('files_md5sum', {}).get('fasta')
short_name = reference.get('short_name')
name = reference.get('name')
notes = reference.get('notes', "AmpliSeq Import")
print("Got various fields")
except KeyError as err:
print("Corrupt genome_reference entry: {0}".format(err))
sys.exit(1)
print("Checking reference " + ref_hash)
if not models.ReferenceGenome.objects.filter(
identity_hash=ref_hash).exists():
reference = models.ReferenceGenome(enabled=False,
identity_hash=ref_hash,
name=name,
notes=notes,
short_name=short_name,
source=url,
status="downloading",
index_version="tmap-f3")
reference.save()
print("created new reference")
pub = models.Publisher.objects.get(name='BED')
upload = models.ContentUpload.objects.get(pk=args.upload_id)
finish_me = run_pub_scripts.si(pub, upload)
print("About t set check point")
set_checkpoint(meta, args)
print("check point set")
upload.status = "Waiting on reference"
upload.save()
start_reference_download(url, reference, callback=finish_me)
print("Started reference download")
return True
print("exiting in shame")
return False
