def __init__(self, *args, **kwargs):
self.wrapped_instance = None
self.requires_reads = kwargs.pop('requires_reads', False)
self.upload_allowed = get_pangea_config('upload_allowed', True)
self.download_only = get_pangea_config('download_only', False)
self.name_is_uuid = get_pangea_config('name_is_uuid')
self.data_kind = get_pangea_config('data_kind')
self.endpoint = get_pangea_config('pangea_endpoint', PANGEA_URL)
self.knex = Knex(self.endpoint)
self.pipeline_module = None
user = get_pangea_config('user')
if user:
User(self.knex, user, get_pangea_config('password')).login()
if self.name_is_uuid:
self.org_name = None
self.grp_name = None
self.grp = None
else:
self.org_name = get_pangea_config('org_name')
self.grp_name = get_pangea_config('grp_name')
org = Organization(self.knex, self.org_name).get()
self.grp = org.sample_group(self.grp_name).get()
self.wrapped_instance = self.wrapped_type(*args, **kwargs)
def get_pangea_group(org_name,
grp_name,
email=None,
password=None,
endpoint='https://pangea.gimmebio.com'):
knex = Knex()
if email and password:
User(knex, email, password).login()
org = Organization(knex, org_name).get()
grp = org.sample_group(grp_name).get()
return grp
def run_sample(email, password, outdir, group, fasterq_exc, mash_exc,
sample_name):
knex = Knex()
User(knex, email, password).login()
org = Organization(knex, 'MegaGenome').get()
grp = org.sample_group(group).get()
sample = grp.sample(sample_name).get()
makedirs(outdir, exist_ok=True)
process_sample(sample,
outdir=outdir,
fasterq_exc=fasterq_exc,
mash_exc=mash_exc)
def cli_process_tag(log_level, endpoint, email, password, tag_name, strict):
logging.basicConfig(
level=log_level,
format='%(levelname)s: %(message)s',
)
knex = Knex(endpoint)
if email and password:
User(knex, email, password).login()
tag = Tag(knex, tag_name).get()
for pangea_group in tag.get_sample_groups():
logger.info(pangea_group)
process_group(pangea_group, strict=strict)
def create_test_sample():
timestamp = int(time())
knex = Knex(PANGEA_ENDPOINT)
User(knex, PANGEA_USER, PANGEA_PASS).login()
org = Organization(knex, 'MetaSUB Consortium').get()
lib = org.sample_group('CAP2 Test Sandbox').get()
sample = lib.sample(f'CAP2 Test Sample {timestamp}').create()
reads_ar = sample.analysis_result('raw::raw_reads').create()
r1 = reads_ar.field('read_1').create()
r1.upload_file(RAW_READS_1)
r2 = reads_ar.field('read_2').create()
r2.upload_file(RAW_READS_2)
return sample
def run_sample(email, password, outdir, fasterq_exc, mash_exc):
knex = Knex()
User(knex, email, password).login()
tag = Tag(knex, 'MegaGenome').get()
samples = list(tag.get_random_samples())
shuffle(samples)
for sample in samples:
try:
click.echo(sample.name, err=True)
makedirs(outdir, exist_ok=True)
process_sample(sample,
outdir=outdir,
fasterq_exc=fasterq_exc,
mash_exc=mash_exc)
except Exception as e:
if not isinstance(e, HTTPError):
continue
click.echo(f'failed {sample.name}', err=True)
def __init__(self,
sample_name,
email,
password,
endpoint,
org_name,
grp_name,
kind='short_read',
knex=None,
sample=None,
name_is_uuid=False):
if not knex:
knex = Knex(endpoint)
User(knex, email, password).login()
self.sample = sample
if self.sample is None:
if name_is_uuid:
self.sample = sample_from_uuid(knex, sample_name)
else:
org = Organization(knex, org_name).get()
grp = org.sample_group(grp_name).get()
self.sample = grp.sample(sample_name).get()
self.kind = kind
self.name = sample_name
self.sra = f'downloaded_data/{self.name}.sra'
self.r1 = f'downloaded_data/{self.name}.R1.fq.gz'
self.r2 = None
try:
if self.has_reads():
if self.kind == 'short_read':
self.kind = 'single_short_read'
if self.is_paired():
self.kind = 'paired_short_read'
if self.kind == 'paired_short_read':
self.r2 = f'downloaded_data/{self.name}.R2.fq.gz'
self.cap_sample = Sample(self.name,
self.r1,
self.r2,
kind=self.kind)
except CAPSampleError:
self.kind = 'undetermined'
def __init__(self, work_order_uuid, email, password, endpoint):
self.knex = Knex(endpoint)
User(self.knex, email, password).login()
self.wop = WorkOrderProto.from_uuid(self.knex, work_order_uuid)
def __init__(self, tag_name, email, password, endpoint):
self.knex = Knex(endpoint)
User(self.knex, email, password).login()
self.tag = Tag(self.knex, tag_name).get()
self.name = tag_name
def __init__(self, grp_name, email, password, endpoint, org_name):
self.knex = Knex(endpoint)
User(self.knex, email, password).login()
org = Organization(self.knex, org_name).get()
self.grp = org.sample_group(grp_name).get()
self.name = grp_name