def config_for_main(event: Dict) -> Dict:
if len(event['Records']) > 1:
raise ValueError(
'main_handler(): trigger for this function should contain only a single record'
)
record = event['Records'][0]
config_str = pipeline_config_s3(record)
config_buf = config_ini_to_buf(config_str)
config = init_config(config_buf)
if len(config.keys()) > 3:
raise ValueError(
'main_handler(): current pipeline supports only technologies with up to 3 FASTQ files per sample'
)
return config
from unittest import TestCase
from scito_count.BUSTools import *
from scito_count.ProcessSettings import *
from scito_count.SeqFile import *
from scito_lambdas.lambda_utils import init_config
conf = init_config(
"/Users/antonogorodnikov/Documents/Work/Python/scito/tests/config_test.ini"
)
s3_set2 = S3Settings(conf, "ATAC ADT R2")
read_set2 = ReadSettings(conf, "ATAC ADT R2")
s3_set3 = S3Settings(conf, "ATAC ADT R3")
read_set3 = ReadSettings(conf, "ATAC ADT R3")
upl_test_s3 = S3Settings(conf, "ATAC ADT R2 UPLOAD TEST")
upl_test_read = ReadSettings(conf, "ATAC ADT R2 UPLOAD TEST")
class TestNativeBusTools(TestCase):
def setUp(self) -> None:
ground = FQFile(s3_settings=upl_test_s3,
read_settings=upl_test_read,
byte_range='0-1000',
qc_scale="phred")
async_file = FQFile(s3_settings=s3_set3,
read_settings=read_set3,
byte_range='0-1000',
qc_scale="phred")
self.sync_two_reads = FQSyncTwoReads((ground, async_file))
self.sync_two_reads.two_read_sync()
from unittest import TestCase
from scito_lambdas.architecture_utils import *
from scito_lambdas.lambda_utils import init_config
from ufixtures.UfixVcr import UfixVcr
from scito_lambdas.lambda_settings import settings_event_source_true_split_lambda
import os
import time
curr_dir = os.path.dirname(os.path.realpath(__file__))
conf = init_config(os.path.join(curr_dir, 'fixtures/test_config.ini'))
class Test(TestCase):
def setUp(self) -> None:
self.sqs_interface = SQSInterface(conf, 'unit_test')
self.ufixtures = UfixVcr(os.path.join(curr_dir, 'fixtures/cassettes'))
self.vcr = self.ufixtures.sanitize(
attributes=['(?i)token', 'Author', 'User'],
targets=[
'arn:aws:sqs:us-west-2:\d+',
'us-west-2.queue.amazonaws.com/\d+', '3A\d+', '2F\d+', ':\d+:',
'\"sg-.*\"', '\"subnet-.*\"', '\"vpc-.*\"'
])
def test_prep_queues(self):
with self.vcr.use_cassette('architecture_utils_prep_queues.yml'):
main_queue = prep_queues(conf, 'unit_test')
main_sqs_exists = self.sqs_interface.queue_exists(
dead_letter=False)
dead_letter_sqs_exists = self.sqs_interface.queue_exists(
dead_letter=True)