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 setUp(self):
self.data_dn = os.path.join(os.path.dirname(__file__), "data", "app")
self.temp_d = tempfile.TemporaryDirectory()
self.sample = TenxSample(name="__TEST__", base_path=self.temp_d.name)
self.asm = self.sample.assembly()
self.ref = TenxReference(name="__REF__")
self.aln = self.sample.alignment(ref=self.ref)
TenxApp.config = None
def aln_align_cmd(sample_name, ref_name):
"""
Create alignments with longranger.
"""
assert bool(TenxApp.config) is True, "Must provide tenx yaml config file!"
sample = TenxSample(name=sample_name, base_path=TenxApp.config["TENX_DATA_PATH"])
ref = TenxReference(name=ref_name)
aln = sample.alignment(ref=ref)
alignment.run_align(aln)
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
sample = TenxSample(name="__SAMPLE__", base_path=self.temp_d.name)
ref = TenxReference(name="__REF__")
self.aln = sample.alignment(ref=ref)
os.makedirs(os.path.join(self.aln.path))
tenx.app.TenxApp.config = {
"TENX_DATA_PATH":
os.path.join(self.temp_d.name),
"TENX_REMOTE_URL":
"gs://data",
"TENX_REMOTE_REFSU_URL":
"gs://resources/refs",
"TENX_CROMWELL_PATH":
os.path.join(os.path.dirname(__file__), "data", "app"),
}
def test1_aln_asm(self):
base_path = TenxApp.config.get("TENX_DATA_PATH")
sample = TenxSample(base_path=base_path, name="TEST-001")
ref = TenxReference(name='refdata-GRCh38-2.1.0')
aln = sample.alignment(ref=ref)
self.assertTrue(bool(aln))
self.assertEqual(aln.__class__.__name__, "TenxAlignment")
self.assertEqual(os.path.join(sample.path, "alignment"), aln.path)
self.assertEqual(sample, aln.sample)
self.assertEqual(ref, aln.ref)
asm = sample.assembly()
self.assertTrue(bool(asm))
self.assertEqual(asm.__class__.__name__, "TenxAssembly")
self.assertEqual(os.path.join(sample.path, "assembly"), asm.path)
self.assertEqual(sample, asm.sample)
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 ref_download(ref_name):
"""
Download reference sequences from cloud storage to local disk.
"""
assert bool(TenxApp.config) is True, "Must provide tenx yaml config file!"
download(TenxReference(name=ref_name))
def test_cromwell(self):
TenxApp.config = {
"TENX_CROMWELL_PATH": self.data_dn,
}
ref = TenxReference(name="__REF__")
test_params = [
{
"pipeline": "supernova",
"entity": self.asm,
"inputs": {
"SAMPLE_NAME": self.asm.sample.name
},
},
{
"pipeline": "longranger",
"entity": self.aln,
"inputs": {
"SAMPLE_NAME": self.aln.sample.name,
"REF_NAME": self.aln.ref.name
},
},
]
for p in test_params:
pipeline_name = p["pipeline"]
entity = p["entity"]
cromwell = TenxCromwell(entity=entity)
self.assertTrue(cromwell)
self.assertEqual(cromwell.entity, entity)
self.assertEqual(cromwell.pipeline_name, pipeline_name)
templates_dn = cromwell.templates_dn
self.assertTrue(templates_dn)
cromwell_dn = cromwell.cromwell_dn
self.assertEqual(cromwell_dn,
TenxApp.config.get("TENX_CROMWELL_PATH"))
self.assertEqual(cromwell.cromwell_jar,
os.path.join(cromwell_dn, "cromwell.jar"))
inputs_bn = ".".join([pipeline_name, "inputs", "json"])
self.assertEqual(cromwell.inputs_bn, inputs_bn)
wdl_bn = ".".join([pipeline_name, "gcloud", "wdl"])
self.assertEqual(cromwell.wdl_bn, wdl_bn)
conf_bn = ".".join([pipeline_name, "conf"])
self.assertEqual(cromwell.conf_bn, conf_bn)
self.assertDictEqual(cromwell.inputs_for_entity(), p["inputs"])
conf_fn = os.path.join(cromwell.pipeline_dn, conf_bn)
inputs_fn = os.path.join(cromwell.pipeline_dn, inputs_bn)
wdl_fn = os.path.join(cromwell.pipeline_dn, wdl_bn)
cmd = cromwell.command()
expected_cmd = [
"java", "-Dconfig={}".format(conf_fn), "-jar",
cromwell.cromwell_jar, wdl_fn, "-i", inputs_fn
]
self.assertTrue(os.path.exists(conf_fn))
self.assertTrue(os.path.exists(inputs_fn))
self.assertTrue(os.path.exists(wdl_fn))
class TenxAlignmentTest(unittest.TestCase):
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 tearDown(self):
self.temp_d.cleanup()
TenxApp.config = None
def test10_alignment(self):
sample = TenxSample(name="TESTER",
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment(self.ref)
self.assertEqual(aln.ref, self.ref)
self.assertEqual(os.path.join(sample.path, "alignment"), aln.path)
self.assertEqual(os.path.join(aln.path, "outs"), aln.outs_path)
def test11_is_successful(self):
sample = TenxSample(name="TEST_SUCCESS",
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment()
os.makedirs(os.path.join(aln.outs_path))
with open(os.path.join(aln.outs_path, "summary.csv"), "w") as f:
f.write("SUCCESS!")
self.assertTrue(aln.is_successful())
sample = TenxSample(name="TEST_FAIL",
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment()
os.makedirs(aln.path)
self.assertFalse(aln.is_successful())
@patch('subprocess.check_call')
def test2_run_align(self, test_patch):
test_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TEST_SUCCESS",
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment(self.ref)
os.makedirs(os.path.join(aln.path, "outs"))
with open(os.path.join(aln.path, "outs", "summary.csv"), "w") as f:
f.write("SUCCESS!")
alignment.run_align(aln)
expected_err = "Creating alignments for TEST_SUCCESS\nEntering {}\nRunning longranger wgs --id=alignment --sample=TEST_SUCCESS --reference={} --fastqs={} --vcmode=freebayes --disable-ui --jobmode=local --localmem=6 --localcores=1 ...\n".format(
aln.sample.path, self.ref.directory(), aln.sample.reads_path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
@patch('subprocess.check_call')
@patch('tenx.util.verify_upload')
def test4_run_upload(self, upload_patch, verify_patch):
sys.stderr = io.StringIO()
sample = TenxSample(name='TEST_FAIL',
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment()
rsample = TenxSample(name='TEST_FAIL',
base_path=TenxApp.config['TENX_REMOTE_URL'])
raln = rsample.alignment()
os.makedirs(os.path.join(aln.outs_path))
with self.assertRaisesRegex(
Exception, "Refusing to upload an unsuccessful alignment"):
alignment.run_upload(aln, raln)
upload_patch.return_value = "0"
verify_patch.return_value = "1"
sample = TenxSample(name='TEST_SUCCESS',
base_path=TenxApp.config['TENX_DATA_PATH'])
aln = sample.alignment()
os.makedirs(os.path.join(aln.path, "outs"))
with open(os.path.join(aln.path, "outs", "summary.csv"), "w") as f:
f.write("SUCCESS!")
rsample = TenxSample(name='TEST_SUCCESS',
base_path=TenxApp.config['TENX_DATA_PATH'])
raln = rsample.alignment()
err = io.StringIO()
sys.stderr = err
alignment.run_upload(aln, raln)
expected_err = f"Upload TEST_SUCCESS alignment...\nLocal path: {aln.path}\nEntering {aln.path} ...\nUploading to: {raln.path}\nVerify upload alignment...\nUpload alignment...OK\n".format(
aln.path, raln.path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__