def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
os.chdir(self.temp_d.name)
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.temp_d.name
TenxApp.config['TENX_ASM_CORES'] = "2"
TenxApp.config['TENX_ASM_MEM'] = "2"
def test1_script_template(self):
with self.assertRaisesRegex(
Exception,
"Scripts directory \(TENX_SCRIPTS_PATH\) is not set in tenx config!"
):
TenxApp.load_script_template('blah')
TenxApp.config['TENX_SCRIPTS_PATH'] = self.scripts_path.name
with self.assertRaisesRegex(
Exception, "Failed to find script template file: {}".format(
os.path.join(TenxApp.config['TENX_SCRIPTS_PATH'],
'blah.jinja'))):
TenxApp.load_script_template('blah')
script_template = TenxApp.load_script_template('foo')
self.assertIsNotNone(script_template)
def test1_slack(self, test_patch):
TenxApp()
TenxApp.config['TENX_NOTIFICATIONS_SLACK'] = "https://slack.com"
notok_response = NotificationsTest.Response(ok=False)
test_patch.return_value = notok_response
with self.assertRaisesRegex(Exception, 'Slack POST failed for {}'.format(TenxApp.config['TENX_NOTIFICATIONS_SLACK'])):
notifications.slack(message="Hello World!")
ok_response = NotificationsTest.Response(ok=True)
test_patch.return_value = ok_response
notifications.slack(message="Hello World!")
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
self.rurl = "gs://data"
os.chdir(self.temp_d.name)
sample = TenxSample(name='TESTER', base_path=self.temp_d.name)
self.asm = sample.assembly()
rsample = TenxSample(name='TESTER', base_path=self.rurl)
self.remote_asm = rsample.assembly()
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.temp_d.name
TenxApp.config['TENX_REMOTE_URL'] = self.rurl
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
self.ref = TenxReference(name='refdata-GRCh38-2.1.0')
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.temp_d.name
TenxApp.config['TENX_REMOTE_URL'] = 'gs://data'
TenxApp.config['TENX_REMOTE_REFS_URL'] = 'gs://data/references'
TenxApp.config['TENX_ALN_MODE'] = 'local'
TenxApp.config['TENX_ALN_CORES'] = '1'
TenxApp.config['TENX_ALN_MEM'] = '6'
TenxApp.config['TENX_ALN_VCMODE'] = 'freebayes'
def test_init(self):
# init w/o config
tenxapp = TenxApp()
self.assertIsNotNone(TenxApp.config)
# re-init w/ config
TenxApp.config = None
self.assertIsNone(TenxApp.config)
conf_f = tempfile.NamedTemporaryFile()
config = {
"environment": "test",
"TENX_SCRIPTS_PATH": "tests/test_app",
"TENX_NOTIFICATIONS_SLACK": "https://slack.com",
}
conf_f.write(yaml.dump(config).encode())
conf_f.flush()
tenxapp = TenxApp(conf_f.name)
self.assertIsNotNone(tenxapp)
self.assertDictEqual(tenxapp.config, config)
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.temp_d.name
TenxApp.config['TENX_REMOTE_URL'] = 'gs://data'
self.lsample = TenxSample(
base_path=TenxApp.config.get("TENX_DATA_PATH"), name='TEST-001')
os.makedirs(self.lsample.reads_path)
with open(os.path.join(self.lsample.reads_path, 'read1.fastq'),
'w') as f:
f.write("FASTQ\n") # a fastq file
self.rsample = TenxSample(
base_path=TenxApp.config.get("TENX_REMOTE_URL"), name='TEST-001')
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
if TenxApp.config is None: TenxApp()
TenxApp.config = {
"TENX_DATA_PATH": self.temp_d.name,
"TENX_REMOTE_URL": "gs://data",
"TENX_REMOTE_REFS_URL": "gs://data/refs",
"TENX_ALN_VCMODE": "freebayes",
"TENX_ALN_MODE": "wgs",
"TENX_ALN_MEM": "1",
"TENX_ALN_CORES": "1",
}
sample = TenxSample(name="__SAMPLE__", base_path=TenxApp.config["TENX_DATA_PATH"])
ref = TenxReference(name="__REF__")
self.aln= sample.alignment(ref)
rsample = TenxSample(name="__SAMPLE__", base_path=TenxApp.config["TENX_REMOTE_URL"])
self.raln = rsample.alignment(ref)
os.chdir(self.temp_d.name)
os.makedirs(self.aln.outs_path)
os.makedirs(os.path.join(TenxApp.config["TENX_DATA_PATH"], "references"))
def setUp(self):
TenxApp()
TenxApp.config = {"TENX_REMOTE_URL": "gs://data"}
def test_init_fails(self):
if TenxApp.config is None: TenxApp()
TenxApp.config = None
with self.assertRaisesRegex(IOError, "No such file or directory"):
TenxApp("/tenx.yaml")
def setUp(self):
TenxApp()
self.scripts_path = tempfile.TemporaryDirectory()
with open(os.path.join(self.scripts_path.name, "foo.jinja"), "w") as f:
f.write("FOO JINJA TEMPLATE")
def setUp(self):
self.tempdir = tempfile.mkdtemp()
os.chdir(self.tempdir)
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.tempdir
TenxApp.config['TENX_REMOTE_REFS_URL'] = 'gs://data/references'
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = self.temp_d.name
TenxApp.config['TENX_REMOTE_URL'] = 'gs://data'
def setUp(self):
if TenxApp.config is None: TenxApp()
TenxApp.config['TENX_DATA_PATH'] = "/mnt/disks/data"
TenxApp.config['TENX_REMOTE_URL'] = "gs://data"
def cli():
"""
10X CLI
"""
TenxApp(os.environ.get('TENX_CONFIG_FILE', None))
pass