def test_remote_from_samfile(self, platform='in_drop_v2'):
test_name = 'test_remote_%s' % platform
self.check_parameters()
argv = [
'run',
platform,
'-o',
REMOTE_OUTPUT,
'-u',
UPLOAD % (self.bucket, test_name),
'-i',
INDEX,
'-e',
self.email,
'-a',
SAMFILE % platform,
'-k',
self.rsa_key,
'--instance-type',
'r5.2xlarge',
'--debug',
# '--spot-bid', '1.0'
]
if platform != 'drop_seq':
argv += ['--barcode-files', PLATFORM_BARCODES % platform]
main.main(argv)
def test_using_local_dataset(self, platform="ten_x_v2"):
# must NOT end with a slash
file_prefix = "test"
output_prefix = os.path.join(self.path_temp, file_prefix)
params = [
("run", platform),
("--local", ),
("--output-prefix", output_prefix),
("--index", dataset_local.index),
("--barcode-files", dataset_local.barcodes % platform),
("--barcode-fastq", dataset_local.barcode_fastq % platform),
("--genomic-fastq", dataset_local.genomic_fastq % platform),
("--star-args", "runRNGseed=0"),
]
argv = [element for tupl in params for element in tupl]
if platform != "drop_seq":
argv += ["--barcode-files", dataset_local.barcodes % platform]
main.main(argv)
# get output file list
files = get_output_file_list(self.test_id, self.path_temp)
# check if each expected file is found in the list of files generated
for file in expected_output_files(file_prefix):
self.assertIn(file, files)
def test_remote_from_raw_fastq(self, platform='ten_x_v2'):
test_name = 'test_remote_%s' % platform
self.check_parameters()
argv = [
'run', platform, '-o', REMOTE_OUTPUT, '-u',
UPLOAD % (self.bucket, test_name), '-i', INDEX, '-e', self.email,
'-b', BARCODE_FASTQ % platform, '-g', GENOMIC_FASTQ % platform,
'--instance-type', 'c4.large', '--spot-bid', '1.0', '-k',
self.rsa_key, '--debug'
]
if platform != 'drop_seq':
argv += ['--barcode-files', PLATFORM_BARCODES % platform]
main.main(argv)
def test_remote_from_raw_fastq(self, platform="ten_x_v2"):
output_prefix = "from-raw-fastq"
# must end with a slash
test_folder = f"seqc/run-{platform}-{self.test_id}/"
params = [
("run", platform),
("--output-prefix", "from-raw-fastq"),
("--upload-prefix", f"s3://{self.s3_bucket}/{test_folder}"),
("--index", dataset_s3.index),
("--email", self.email),
("--barcode-fastq", dataset_s3.barcode_fastq % platform),
("--genomic-fastq", dataset_s3.genomic_fastq % platform),
("--instance-type", "r5.2xlarge"),
("--spot-bid", "1.0"),
("--rsa-key", self.rsa_key),
("--debug",),
("--remote-update",),
("--ami-id", self.ami_id),
("--user-tags", f"TestID:{self.test_id}"),
]
argv = [element for tupl in params for element in tupl]
if platform != "drop_seq":
argv += ["--barcode-files", dataset_s3.barcodes % platform]
main.main(argv)
# wait until terminated
# get output file list
files = get_output_file_list(self.test_id, self.s3_bucket, test_folder)
# check for the exact same filenames
self.assertSetEqual(files, expected_output_files(output_prefix))
# check for success message in seqc_log.txt
has_success_msg = check_for_success_msg(
s3_seqc_log_uri="s3://{}/{}".format(
self.s3_bucket, os.path.join(test_folder, "seqc_log.txt")
),
path_temp=self.path_temp,
)
self.assertTrue(
has_success_msg, msg="Unable to find the success message in the log"
)
def test_local(self, platform='in_drop_v2'):
"""test seqc after pre-downloading all files"""
with open('seqc_log.txt', 'w') as f:
f.write(
'Dummy log. nose2 captures input, so no log is produced. This causes '
'pipeline errors.\n')
test_name = 'test_no_aws_%s' % platform
makedirs(LOCAL_OUTPUT % test_name)
if self.email is None:
self.email = input(
'please provide an email address for SEQC to mail results: ')
argv = [
'run', platform, '-o', test_name, '-i', INDEX, '-b',
BARCODE_FASTQ % platform, '-g', GENOMIC_FASTQ % platform,
'--barcode-files', PLATFORM_BARCODES % platform, '-e', self.email,
'--local'
]
main.main(argv)
os.remove('./seqc_log.txt') # clean up the dummy log we made.
def test_generate_api(merged_data):
output_stem = os.path.join(tempfile.mkdtemp(), 'test_notebooks')
args = ['notebook', 'generate', '-o', output_stem, '-i', merged_data]
main.main(args)
def test_merge_api(testing_data):
output_filename = os.path.join(tempfile.mkdtemp(), 'test_notebooks.ipynb')
args = ['notebook', 'merge', '-o', output_filename, '-i'] + testing_data
main.main(args)