def test_connecting_with_compression(self):
try:
import snappy
except ImportError:
if hasattr(unittest, 'skipTest'):
unittest.skipTest('Snappy compression not available')
else:
return
conn = cql.connect(TEST_HOST, TEST_NATIVE_PORT, native=True, compression=True)
self.assertEqual(conn.compressor, snappy.compress)
self.try_basic_stuff(conn)
def test_connecting_with_compression(self):
try:
import snappy
except ImportError:
if hasattr(unittest, 'skipTest'):
unittest.skipTest('Snappy compression not available')
else:
return
conn = cql.connect(TEST_HOST, TEST_NATIVE_PORT, native=True, compression=True)
self.assertEqual(conn.compressor, snappy.compress)
self.try_basic_stuff(conn)
def test_ccscheck_numerrors(self):
if self.ref_fasta is None:
raise unittest.SkipTest("Comparison FASTA file not specified")
elif self.ref_csv is None:
raise unittest.skipTest("No CSV file defined")
elif not op.isfile(op.realpath(self.ref_fasta)):
self.fail("{f} is not a file".format(f=self.ref_fasta))
ref_lines = {}
with open(self.ref_csv) as csv_ref:
c = csv.reader(csv_ref, delimiter=',')
for row in c:
if row[0] != "Movie":
ref_lines[(row[0], row[1])] = row
for i_file, file_name in enumerate(self.ccs_ds.toExternalFiles()):
out_dir = op.join(self.run_dir, "out_{i}".format(i=i_file))
args = ["ccscheck", file_name, out_dir, self.ref_fasta]
assert subprocess.call(args) == 0, \
"cmd '{a}' failed".format(a=" ".join(args))
csv_file = op.join(out_dir, "zmws.csv")
with open(csv_file) as f:
c = csv.reader(f, delimiter=',')
for row in c:
if row[0] != "Movie":
csv_ref = ref_lines.get((row[0], row[1]), None)
if csv_ref is None:
log.warn("{m}/{z} not found".format(m=row[0],
z=row[1]))
else:
self.assertEqual(row, csv_ref)
def test_ccscheck_numerrors(self):
if self.ref_fasta is None:
raise unittest.SkipTest("Comparison FASTA file not specified")
elif self.ref_csv is None:
raise unittest.skipTest("No CSV file defined")
elif not op.isfile(op.realpath(self.ref_fasta)):
self.fail("{f} is not a file".format(f=self.ref_fasta))
ref_lines = {}
with open(self.ref_csv) as csv_ref:
c = csv.reader(csv_ref, delimiter=',')
for row in c:
if row[0] != "Movie":
ref_lines[(row[0],row[1])] = row
for i_file, file_name in enumerate(self.ccs_ds.toExternalFiles()):
out_dir = op.join(self.run_dir, "out_{i}".format(i=i_file))
args = ["ccscheck", file_name, out_dir, self.ref_fasta]
assert subprocess.call(args) == 0, \
"cmd '{a}' failed".format(a=" ".join(args))
csv_file = op.join(out_dir, "zmws.csv")
with open(csv_file) as f:
c = csv.reader(f, delimiter=',')
for row in c:
if row[0] != "Movie":
csv_ref = ref_lines.get((row[0], row[1]), None)
if csv_ref is None:
log.warn("{m}/{z} not found".format(
m=row[0], z=row[1]))
else:
self.assertEqual(row, csv_ref)
def test_combine_dimensional_operators_0(self):
if self.F.operators[0].solve_banded_offsets[1] != 2:
unittest.skipTest(
"Using first order boundary approximation. Top is tridiag.")
oldL1 = self.L1_.copy()
oldL1 = scipy.sparse.dia_matrix(oldL1.todense())
oldL1.data = oldL1.data[::-1]
oldL1.offsets = oldL1.offsets[::-1]
# high, low = 2, -2
# m = tuple(oldL1.offsets).index(0)
# oldL1.data = oldL1.data[m-high:m-low+1]
# oldL1.offsets = oldL1.offsets[m-high:m-low+1]
oldR1 = self.R1_.T.flatten()
L1 = self.F.operators[0]
# oldL1.data = oldL1.data[:-1]
# oldL1.offsets = oldL1.offsets[:-1]
# print "offsets"
# print oldL1.offsets, L1.D.offsets
# print "old"
# fp(oldL1.data)
# print
# print "new"
# fp(L1.D.data)
# print
# print "diff"
# fp(L1.D.data - oldL1.data)
# print
# print "old"
# fp(oldL1.todense())
# print
# print "new"
# fp(L1.D.todense())
# print
# print "diff"
# fp(oldL1.todense() - L1.D.todense())
# npt.assert_allclose(L1.D.todense(), oldL1.todense())
# npt.assert_allclose(L1.D.data, oldL1.data)
# print "old"
# print oldR1
# print
# print "new"
# print L1.R
npt.assert_allclose(L1.R, oldR1)
def test_combine_dimensional_operators_0(self):
if self.F.operators[0].solve_banded_offsets[1] != 2:
unittest.skipTest("Using first order boundary approximation. Top is tridiag.")
oldL1 = self.L1_.copy()
oldL1 = scipy.sparse.dia_matrix(oldL1.todense())
oldL1.data = oldL1.data[::-1]
oldL1.offsets = oldL1.offsets[::-1]
# high, low = 2, -2
# m = tuple(oldL1.offsets).index(0)
# oldL1.data = oldL1.data[m-high:m-low+1]
# oldL1.offsets = oldL1.offsets[m-high:m-low+1]
oldR1 = self.R1_.T.flatten()
L1 = self.F.operators[0]
# oldL1.data = oldL1.data[:-1]
# oldL1.offsets = oldL1.offsets[:-1]
# print "offsets"
# print oldL1.offsets, L1.D.offsets
# print "old"
# fp(oldL1.data)
# print
# print "new"
# fp(L1.D.data)
# print
# print "diff"
# fp(L1.D.data - oldL1.data)
# print
# print "old"
# fp(oldL1.todense())
# print
# print "new"
# fp(L1.D.todense())
# print
# print "diff"
# fp(oldL1.todense() - L1.D.todense())
# npt.assert_allclose(L1.D.todense(), oldL1.todense())
# npt.assert_allclose(L1.D.data, oldL1.data)
# print "old"
# print oldR1
# print
# print "new"
# print L1.R
npt.assert_allclose(L1.R, oldR1)
def get_real_credentials(self):
dir_name = os.path.dirname(__file__)
file_name = "test.conf.json"
try:
with open(os.path.join(dir_name, file_name), "r") as handler:
return json.load(handler)
except IOError:
raise unittest.skipTest(
"For all tests implying a real connection to the Project Euler "
"website, please create a file named {} in {} which is a json "
"file containing something like : "
"""{"username": "******", "password": "******"}"""
)
def setUpClass(cls):
super(TestAccuracy, cls).setUpClass()
ref_fasta = cls.test_values["ccs"].get("reference", None)
cls.ref_csv = cls.test_values["ccs"].get("ccscheck_out", None)
if cls.ref_csv is None:
raise unittest.skipTest("No CSV file defined")
ref_dir = op.dirname(ref_fasta)
cls.run_dir = tempfile.mkdtemp()
tmp_ref_fasta = op.join(cls.run_dir, op.basename(ref_fasta))
shutil.copyfile(ref_fasta, tmp_ref_fasta)
cls.ref_fasta = tmp_ref_fasta
pysam.faidx(tmp_ref_fasta)
cls.final_ccs_file = None
for file_id, file_info in cls.datastore.get_file_dict().iteritems():
if file_info.is_chunked:
continue
if file_info.file_type_id == FileTypes.DS_CCS.file_type_id:
cls.final_ccs_file = file_info.path
break
cls.ccs_ds = ConsensusReadSet(cls.final_ccs_file)
def setUpClass(cls):
super(TestAccuracy, cls).setUpClass()
ref_fasta = cls.test_values["ccs"].get("reference", None)
cls.ref_csv = cls.test_values["ccs"].get("ccscheck_out", None)
if cls.ref_csv is None:
raise unittest.skipTest("No CSV file defined")
ref_dir = op.dirname(ref_fasta)
cls.run_dir = tempfile.mkdtemp()
tmp_ref_fasta = op.join(cls.run_dir, op.basename(ref_fasta))
shutil.copyfile(ref_fasta, tmp_ref_fasta)
cls.ref_fasta = tmp_ref_fasta
pysam.faidx(tmp_ref_fasta)
cls.final_ccs_file = None
for file_id, file_info in cls.datastore.get_file_dict().iteritems():
if file_info.is_chunked:
continue
if file_info.file_type_id == FileTypes.DS_CCS.file_type_id:
cls.final_ccs_file = file_info.path
break
cls.ccs_ds = ConsensusReadSet(cls.final_ccs_file)
import unittest
import os
import requests
import datetime
import time
skipSeleniumTests = None
try:
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
except ImportError:
skipSeleniumTests = lambda: unittest.skipTest(
"Selenium not installed.")
import utils
import sdk
class Link(unittest.TestCase):
def setUp(self):
self.test_file = utils.create_test_file(self.account)
self.link = self.account.links.create(data={'file_id': self.test_file.id})
def tearDown(self):
self.link.delete()
def test_create_link(self):
self.assertEqual(self.link.file_id, self.test_file.id)
def test_create_direct_link(self):
self.link2 = self.account.links.create(data={
import unittest
import os
import requests
import datetime
import time
skipSeleniumTests = None
try:
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
except ImportError:
skipSeleniumTests = lambda: unittest.skipTest("Selenium not installed.")
import utils
import sdk
class Link(unittest.TestCase):
def setUp(self):
self.test_file = utils.create_test_file(self.account)
self.link = self.account.links.create(
data={'file_id': self.test_file.id})
def tearDown(self):
self.link.delete()
def test_create_link(self):
self.assertEqual(self.link.file_id, self.test_file.id)
def test_create_direct_link(self):
self.link2 = self.account.links.create(data={
def setUp(self):
setup_logger()
if os.environ.get("CIRCLECI"):
unittest.skipTest("Require COCO data and model zoo.")
def setUp(self):
try:
subprocess.call(['mpirun', '--version'])
except FileNotFoundError:
unittest.skipTest('mpirun not found, skipping tests')