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 test5_run_cleanup(self, call_patch, check_call_patch,
check_output_patch):
call_patch.return_value = 0
check_call_patch.return_value = 0
check_output_patch.return_value = b'0'
pwd = os.getcwd()
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_REMOTE_URL"))
asm = sample.assembly()
with self.assertRaisesRegex(
Exception,
"Failed to find 4 mkoutput fasta files. Refusing to remove post assembly files"
):
assembly.run_cleanup(asm)
check_output_patch.return_value = b'a.fasta.gz\na.fasta.gz\na.fasta.gz\na.fasta.gz\n'
err.seek(0, 0)
assembly.run_cleanup(asm)
self.maxDiff = 10000
expected_err = "Cleanup assembly for TESTER ...\nAssembly remote URL: gs://data/TESTER/assembly\nChecking if gsutil is installed...\nRUNNING: which gsutil\nChecking mkfastq files exist.\nRUNNING: gsutil ls gs://data/TESTER/assembly/mkoutput/*fasta.gz\nRemoving ASSEMBLER_CS logs path.\nRUNNING: gsutil -m rm -r gs://data/TESTER/assembly/ASSEMBLER_CS\nMoving outs / assembly / stats to outs.\nRUNNING: gsutil -m mv gs://data/TESTER/assembly/outs/assembly/stats gs://data/TESTER/assembly/outs\nRemoving outs / assembly path\nRUNNING: gsutil -m rm -r gs://data/TESTER/assembly/outs/assembly\nCleanup assembly ... OK\n"
self.assertEqual(err.getvalue(), expected_err)
self.assertEqual(os.getcwd(), pwd)
def test11_is_successful(self):
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
os.makedirs(asm.path)
self.assertFalse(asm.is_successful())
os.makedirs(os.path.join(asm.path, "outs", "assembly"))
self.assertTrue(asm.is_successful())
def setUp(self):
self.temp_d = tempfile.TemporaryDirectory()
sample = TenxSample(name="__SAMPLE__", base_path=self.temp_d.name)
self.asm = sample.assembly()
os.makedirs(os.path.join(self.asm.path))
tenx.app.TenxApp.config = {
"TENX_DATA_PATH":
os.path.join(self.temp_d.name, "__SAMPLE__", "assembly"),
"TENX_REMOTE_URL":
"gs://data",
"TENX_CROMWELL_PATH":
os.path.join(os.path.dirname(__file__), "data", "app"),
}
def test1_run_assemble_fails_without_supernova(self):
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
with self.assertRaisesRegex(Exception, "No such file or directory"):
run_assemble(asm)
self.assertFalse(os.path.exists(sample.path))
expected_err = "Checking if supernova is in PATH...\nRUNNING: supernova --help\n"
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
def test31_run_mkoutput_fails_with_incomplete_assembly(
self, check_call_patch):
check_call_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
with self.assertRaisesRegex(
Exception, "Assembly is not complete! Cannot run mkoutput!"):
assembly.run_mkoutput(asm)
expected_err = "Running mkoutput for TESTER...\n"
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
def test3_run_assemble_success(self, check_call_patch):
check_call_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
os.makedirs(asm.outs_assembly_path)
run_assemble(asm)
self.assertTrue(os.path.exists(sample.path))
expected_err = "Checking if supernova is in PATH...\nRUNNING: supernova --help\nRUNNING: supernova run --id=assembly --fastqs={} --uiport=18080 --nodebugmem --localcores=2 --localmem=2\n".format(
sample.reads_path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
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 test32_run_mkoutput_fails_without_all_fasta_files(
self, check_call_patch):
check_call_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
outs_asm_d = asm.outs_assembly_path
os.makedirs(outs_asm_d)
with self.assertRaisesRegex(
Exception, "Expected 4 assembly fasta.gz files in " +
asm.mkoutput_path + " after running mkoutput, but found 0"):
assembly.run_mkoutput(asm)
expected_err = "Running mkoutput for TESTER...\nChecking if supernova is in PATH...\nRUNNING: supernova --help\nEntering {ASM_D}/mkoutput\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.raw --style=raw\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.megabubbles --style=megabubbles\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.pseudohap2 --style=pseudohap2\n".format(
ASM_D=asm.path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
def test2_run_assemble_fails_when_no_outs_assembly_dir(
self, check_call_patch):
check_call_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
TenxApp.config['TENX_ASM_PARAMS'] = "--maxreads='all'"
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
with self.assertRaisesRegex(
Exception, "Ran supernova script, but {} was not found".format(
asm.outs_assembly_path)):
run_assemble(asm)
self.assertTrue(os.path.exists(sample.path))
expected_err = "Checking if supernova is in PATH...\nRUNNING: supernova --help\nRUNNING: supernova run --id=assembly --fastqs={} --uiport=18080 --nodebugmem --localcores=2 --localmem=2 --maxreads='all'\n".format(
sample.reads_path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
def test33_run_mkoutput_success(self, check_call_patch):
check_call_patch.return_value = '0'
err = io.StringIO()
sys.stderr = err
sample = TenxSample(name="TESTER",
base_path=TenxApp.config.get("TENX_DATA_PATH"))
asm = sample.assembly()
outs_asm_d = asm.outs_assembly_path
os.makedirs(outs_asm_d)
mkoutput_d = asm.mkoutput_path
os.makedirs(mkoutput_d)
for n in range(4):
with open(os.path.join(mkoutput_d, "{}.fasta.gz".format(n)),
"w") as f:
f.write(">SEQ1\nATGC")
f.flush()
assembly.run_mkoutput(asm)
expected_err = "Running mkoutput for TESTER...\nChecking if supernova is in PATH...\nRUNNING: supernova --help\nEntering {ASM_D}/mkoutput\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.raw --style=raw\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.megabubbles --style=megabubbles\nRUNNING: supernova mkoutput --asmdir={ASM_D}/outs/assembly --outprefix=TESTER.pseudohap2 --style=pseudohap2\n".format(
ASM_D=asm.path)
self.assertEqual(err.getvalue(), expected_err)
sys.stderr = sys.__stderr__
def test10_assembly(self):
for base_path in TenxApp.config["TENX_DATA_PATH"], TenxApp.config[
"TENX_REMOTE_URL"]:
sample = TenxSample(name="TESTER", base_path=base_path)
asm = sample.assembly()
self.assertEqual(asm.path, os.path.join(sample.path, "assembly"))
self.assertEqual(asm.path,
os.path.join(base_path, 'TESTER', 'assembly'))
self.assertEqual(
asm.mkoutput_path,
os.path.join(base_path, 'TESTER', 'assembly', 'mkoutput'))
self.assertEqual(
asm.outs_path,
os.path.join(base_path, 'TESTER', 'assembly', 'outs'))
self.assertEqual(
asm.outs_assembly_path,
os.path.join(base_path, 'TESTER', 'assembly', 'outs',
'assembly'))
self.assertEqual(
asm.outs_assembly_stats_path,
os.path.join(base_path, 'TESTER', 'assembly', 'outs',
'assembly', 'stats'))
def asm_pipeline_cmd(sample_name):
"""
Run the Assembly Pipeline with Cromwell
Process includes: downloading reads, running supernova, mkoutput, and then uploading the assembly.
"""
assert bool(TenxApp.config) is True, "Must provide tenx yaml config file!"
sys.stderr.write("Run assembly pipeline for {}\n".format(sample_name))
hostname = socket.gethostname()
notifications.slack("{} START {}".format(sample_name, hostname))
sample = TenxSample(base_path=TenxApp.config["TENX_DATA_PATH"],
name=sample_name)
asm = sample.assembly()
try:
run_pipeline(asm)
except BaseException as ex:
sys.stderr.write("Exception: {}\n".format(ex))
sys.stderr.write(
"Exception encountered, sending notifications if configured...\n")
notifications.slack("{} FAILED {}".format(sample_name,
socket.gethostname()))
raise
notifications.slack("{} SUCCESS {}".format(sample_name, hostname))
class TenxAppTest1(unittest.TestCase):
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 tearDown(self):
TenxApp.config = None
self.temp_d.cleanup()
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 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 test_cromwell_fails(self):
with self.assertRaisesRegex(Exception,
"Tenx config has not been initialized!"):
cromwell = TenxCromwell(entity=self.asm)
TenxApp.config = {
"TENX_CROMWELL_PATH": "/",
}
with self.assertRaisesRegex(
Exception, "Cromwell jar not found at /cromwell.jar!"):
cromwell = TenxCromwell(entity=self.asm)
with self.assertRaisesRegex(Exception, "Unknown entity:"):
cromwell = TenxCromwell(entity=self.sample)
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))
