def run_server_in_temp_folder(files=[], port=8999):
"""
Set up a server with some known files to run captures against. Example:
with run_server_in_temp_folder(['test/assets/test.html','test/assets/test.pdf']):
assert(requests.get("http://localhost/test.html") == contents_of_file("test.html"))
"""
# Run in temp dir.
# We have to (implicitly) cwd to this so SimpleHTTPRequestHandler serves the files for us.
old_cwd = os.getcwd()
with tempdir.in_tempdir():
# Copy over files to current temp dir, stripping paths.
for file in files:
shutil.copyfile(os.path.join(old_cwd, file),
os.path.basename(file))
# start server
httpd = HTTPServer(('', port), SimpleHTTPRequestHandler)
httpd._BaseServer__is_shut_down = multiprocessing.Event()
server_thread = Process(target=httpd.serve_forever)
server_thread.start()
try:
# run body of `with` block
yield
finally:
# shut down server
server_thread.terminate()
def test_hello_world(self):
with tempdir.in_tempdir():
with tempfile.NamedTemporaryFile() as fasta:
with tempfile.NamedTemporaryFile() as tax:
fasta.write(Tests.extra_mcra_fasta)
fasta.flush()
tax.write(Tests.extra_mcra_taxonomy)
tax.flush()
prev_path = os.path.join(path_to_data,'mcrA.10seqs.gpkg')
cmd1 = "%s update --graftm_package %s --sequences %s --taxonomy %s --output %s" %(
path_to_script,
prev_path,
fasta.name,
tax.name,
'updated.gpkg')
extern.run(cmd1)
prev = GraftMPackage.acquire(prev_path)
up = GraftMPackage.acquire('updated.gpkg')
prevhash = prev.taxonomy_hash()
taxhash = up.taxonomy_hash()
self.assertEqual(len(prevhash)+1,
len(taxhash))
self.assertEqual(['mcrA','Euryarchaeota_mcrA','Methanofastidiosa'],
taxhash['KYC55281.1'])
self.assertEqual(prevhash['638165755'],
taxhash['638165755'])
seqio = SequenceIO()
self.assertEqual(
len(seqio.read_fasta_file(prev.unaligned_sequence_database_path()))+1,
len(seqio.read_fasta_file(up.unaligned_sequence_database_path())))
def run_server_in_temp_folder(files=[], port=8999):
"""
Set up a server with some known files to run captures against. Example:
with run_server_in_temp_folder(['test/assets/test.html','test/assets/test.pdf']):
assert(requests.get("http://localhost/test.html") == contents_of_file("test.html"))
"""
# Run in temp dir.
# We have to (implicitly) cwd to this so SimpleHTTPRequestHandler serves the files for us.
old_cwd = os.getcwd()
with tempdir.in_tempdir():
# Copy over files to current temp dir, stripping paths.
for file in files:
shutil.copyfile(os.path.join(old_cwd, file), os.path.basename(file))
# start server
httpd = HTTPServer(('', port), SimpleHTTPRequestHandler)
httpd._BaseServer__is_shut_down = multiprocessing.Event()
server_thread = Process(target=httpd.serve_forever)
server_thread.start()
try:
# run body of `with` block
yield
finally:
# shut down server
server_thread.terminate()
def test_autodecorate(self):
with tempdir.in_tempdir():
with tempfile.NamedTemporaryFile() as fasta:
fasta.write(Tests.extra_mcra_fasta)
fasta.flush()
prev_path = os.path.join(path_to_data,'mcrA.10seqs.gpkg')
update = Update(prerequisites)
update.update(
input_sequence_path = fasta.name,
input_graftm_package_path = prev_path,
output_graftm_package_path = 'updated.gpkg')
prev = GraftMPackage.acquire(prev_path)
up = GraftMPackage.acquire('updated.gpkg')
prevhash = prev.taxonomy_hash()
taxhash = up.taxonomy_hash()
self.assertEqual(11, len(taxhash)) #hard-code 11 because of
#https://github.com/geronimp/graftM/issues/204
self.assertEqual(['mcrA','Euryarchaeota_mcrA', 'Methanomicrobia'],
taxhash['KYC55281.1'])
self.assertEqual(prevhash['638165755'],
taxhash['638165755'])
seqio = SequenceIO()
self.assertEqual(
len(seqio.read_fasta_file(prev.unaligned_sequence_database_path()))+1,
len(seqio.read_fasta_file(up.unaligned_sequence_database_path())))
def test_autodecorate(self):
with tempdir.in_tempdir():
with tempfile.NamedTemporaryFile() as fasta:
fasta.write(Tests.extra_mcra_fasta)
fasta.flush()
prev_path = os.path.join(path_to_data,'mcrA.10seqs.gpkg')
update = Update(prerequisites)
update.update(
input_sequence_path = fasta.name,
input_graftm_package_path = prev_path,
output_graftm_package_path = 'updated.gpkg')
prev = GraftMPackage.acquire(prev_path)
up = GraftMPackage.acquire('updated.gpkg')
prevhash = prev.taxonomy_hash()
taxhash = up.taxonomy_hash()
self.assertEqual(11, len(taxhash)) #hard-code 11 because of
#https://github.com/geronimp/graftM/issues/204
self.assertEqual(['mcrA','Euryarchaeota_mcrA', 'Methanomicrobia'],
taxhash['KYC55281.1'])
self.assertEqual(prevhash['638165755'],
taxhash['638165755'])
seqio = SequenceIO()
self.assertEqual(
len(seqio.read_fasta_file(prev.unaligned_sequence_database_path()))+1,
len(seqio.read_fasta_file(up.unaligned_sequence_database_path())))
def test_hello_world(self):
with tempdir.in_tempdir():
with tempfile.NamedTemporaryFile() as fasta:
with tempfile.NamedTemporaryFile() as tax:
fasta.write(Tests.extra_mcra_fasta)
fasta.flush()
tax.write(Tests.extra_mcra_taxonomy)
tax.flush()
prev_path = os.path.join(path_to_data,'mcrA.10seqs.gpkg')
cmd1 = "%s update --graftm_package %s --sequences %s --taxonomy %s --output %s" %(
path_to_script,
prev_path,
fasta.name,
tax.name,
'updated.gpkg')
extern.run(cmd1)
prev = GraftMPackage.acquire(prev_path)
up = GraftMPackage.acquire('updated.gpkg')
prevhash = prev.taxonomy_hash()
taxhash = up.taxonomy_hash()
self.assertEqual(len(prevhash)+1,
len(taxhash))
self.assertEqual(['mcrA','Euryarchaeota_mcrA','Methanofastidiosa'],
taxhash['KYC55281.1'])
self.assertEqual(prevhash['638165755'],
taxhash['638165755'])
seqio = SequenceIO()
self.assertEqual(
len(seqio.read_fasta_file(prev.unaligned_sequence_database_path()))+1,
len(seqio.read_fasta_file(up.unaligned_sequence_database_path())))
def test_get_writer_container(self):
if not self.ref.container_format:
return
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, self.reader.n_atoms)
def test_get_writer_container(self):
if not self.ref.container_format:
return
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, self.reader.n_atoms)
def test_xtc_striding():
"""testing MDAnalysis.analysis.helanal xtc striding: Check for resolution of Issue #188."""
u = MDAnalysis.Universe(GRO, XTC)
u.trajectory[1]
with tempdir.in_tempdir():
assert_raises(FinishTimeException,
MDAnalysis.analysis.helanal.helanal_trajectory,
u, selection="name CA", finish=5)
def test_create_protein_pkg(self):
with tempdir.in_tempdir():
PackageCreator().create(input_graftm_package=os.path.join(
path_to_data, '4.11.22seqs.gpkg.spkg', '4.11.22seqs'),
output_singlem_package='protein.spkg',
hmm_position=76,
force=False)
self.assertTrue(os.path.isdir('protein.spkg'))
j = json.load(open('protein.spkg/CONTENTS.json'))
self.assertEqual(76, j['singlem_hmm_position'])
def test_create_nuc_pkg(self):
with tempdir.in_tempdir():
PackageCreator().create(input_graftm_package=os.path.join(
path_to_data, '61_otus.v3.gpkg.spkg', '61_otus.v3'),
output_singlem_package='nuc.spkg',
hmm_position=888,
force=False)
self.assertTrue(os.path.isdir('nuc.spkg'))
j = json.load(open('nuc.spkg/CONTENTS.json'))
self.assertEqual(888, j['singlem_hmm_position'])
def test_get_writer(self):
with tempdir.in_tempdir():
self.outfile = 'test-trz-writer.trz'
W = self.trz.Writer(self.outfile)
assert_equal(isinstance(W, mda.coordinates.TRZ.TRZWriter), True)
assert_equal(W.n_atoms, self.trz.n_atoms)
try:
os.unlink(self.outfile)
except OSError:
pass
def test_xtc_striding():
"""testing MDAnalysis.analysis.helanal xtc striding: Check for resolution of Issue #188."""
u = MDAnalysis.Universe(GRO, XTC)
u.trajectory[1]
with tempdir.in_tempdir():
assert_raises(FinishTimeException,
MDAnalysis.analysis.helanal.helanal_trajectory,
u,
selection="name CA",
finish=5)
def run_calc(*funcargs, basedir='.'):
'''
:param funcargs: of tuples of function, **kwargs
'''
results = list()
with in_tempdir(basedir=basedir):
for f, a in funcargs:
if isinstance(a, dict):
results.append(f(**a))
else:
results.append(f(*a))
return results
def test_create_protein_pkg(self):
with tempdir.in_tempdir():
PackageCreator().create(
input_graftm_package = os.path.join(
path_to_data, '4.11.22seqs.gpkg.spkg', '4.11.22seqs'),
output_singlem_package = 'protein.spkg',
hmm_position = 76,
window_size = 63,
force = False)
self.assertTrue(os.path.isdir('protein.spkg'))
j = json.load(open('protein.spkg/CONTENTS.json'))
self.assertEqual(76, j['singlem_hmm_position'])
self.assertEqual(63, j['singlem_window_size'])
def test_create_nuc_pkg(self):
with tempdir.in_tempdir():
PackageCreator().create(
input_graftm_package = os.path.join(
path_to_data, '61_otus.v3.gpkg.spkg', '61_otus.v3'),
output_singlem_package = 'nuc.spkg',
hmm_position = 888,
window_size = 57,
force = False)
self.assertTrue(os.path.isdir('nuc.spkg'))
j = json.load(open('nuc.spkg/CONTENTS.json'))
self.assertEqual(888, j['singlem_hmm_position'])
self.assertEqual(57, j['singlem_window_size'])
def test_writer_trz_from_other(self):
with tempdir.in_tempdir():
outfile = 'trz-writer-2.trz'
W = mda.coordinates.TRZ.TRZWriter(outfile,
n_atoms=len(self.u.atoms))
W.write(self.u.trajectory.ts)
W.close()
u2 = mda.Universe(two_water_gro, outfile)
assert_array_almost_equal(self.u.atoms.positions,
u2.atoms.positions, 3)
def test_helanal_trajectory(reference=HELANAL_BENDING_MATRIX,
outfile="helanal_bending_matrix.dat"):
u = mda.Universe(PSF, DCD)
with tempdir.in_tempdir():
# Helix 8: 161 - 187 http://www.rcsb.org/pdb/explore.do?structureId=4AKE
MDAnalysis.analysis.helanal.helanal_trajectory(u,
selection="name CA and resnum 161-187")
bendingmatrix = read_bending_matrix(outfile)
ref = read_bending_matrix(reference)
assert_equal(sorted(bendingmatrix.keys()), sorted(ref.keys()),
err_msg="different contents in bending matrix data file")
for label in ref.keys():
assert_array_almost_equal(bendingmatrix[label], ref[label],
err_msg="bending matrix stats for {0} mismatch".format(label))
def test_01(self):
with tempdir.in_tempdir() as td:
os.mkdir('src')
os.mkdir('dst')
with open(os.path.join('src', 'Moby Dick.txt'), 'wb') as w:
w.write(TEST_FILES['Moby Dick.txt'])
with open(os.path.join('src', 'Great Expectations.txt'), 'wb') as w:
w.write(TEST_FILES['Great Expectations.txt'])
pycopy.pycopy('src', 'dst')
self.assertTrue(os.path.exists(os.path.join('dst',
'Moby Dick.txt'
)))
self.assertTrue(os.path.exists(os.path.join('dst',
'Great Expectations.txt')))
def test_01(self):
with tempdir.in_tempdir() as td:
os.mkdir('src')
os.mkdir('dst')
with open(os.path.join('src', 'Moby Dick.txt'), 'wb') as w:
w.write(TEST_FILES['Moby Dick.txt'])
with open(os.path.join('src', 'Great Expectations.txt'),
'wb') as w:
w.write(TEST_FILES['Great Expectations.txt'])
pycopy.pycopy('src', 'dst')
self.assertTrue(
os.path.exists(os.path.join('dst', 'Moby Dick.txt')))
self.assertTrue(
os.path.exists(os.path.join('dst', 'Great Expectations.txt')))
def test_conect_bonds_conect(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'test-pdb-hbonds.pdb'
self.conect.atoms.write(outfile, bonds="conect")
u1 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u1.atoms), 1890)
assert_equal(len(u1.bonds), 1922)
def test_conect_bonds_conect(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'test-pdb-hbonds.pdb'
self.conect.atoms.write(outfile, bonds="conect")
u1 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u1.atoms), 1890)
assert_equal(len(u1.bonds), 1922)
def test_conect_bonds_all(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'pdb-connect-bonds.pdb'
self.conect.atoms.write(outfile, bonds="all")
u2 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u2.atoms), 1890)
assert_equal(len([b for b in u2.bonds if not b.is_guessed]), 1922)
def test_conect_bonds_all(self):
conect = self.conect
assert_equal(len(conect.atoms), 1890)
assert_equal(len(conect.bonds), 1922)
with tempdir.in_tempdir():
try:
outfile = 'pdb-connect-bonds.pdb'
self.conect.atoms.write(outfile, bonds="all")
u2 = mda.Universe(outfile, guess_bonds=True)
finally:
os.unlink(outfile)
assert_equal(len(u2.atoms), 1890)
assert_equal(len([b for b in u2.bonds if not b.is_guessed]), 1922)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--config-file', default='backup.yml')
parser.add_argument('--output-dir', default=None)
parser.add_argument('--upload', default=False, action='store_true')
parser.add_argument('--quiet', default=False, action='store_true')
parser.add_argument('--debug', default=False, action='store_true')
opts = parser.parse_args()
if not os.path.exists(opts.config_file):
sys.exit("The specified config file does not exist!")
if not opts.quiet:
if opts.debug:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.ERROR)
config = None
if opts.output_dir:
opts.output_dir = os.path.abspath(opts.output_dir)
with open(opts.config_file) as fp:
logging.debug("Loading config from {0}".format(opts.config_file))
config = yaml.safe_load(fp)
config['quiet'] = opts.quiet
with tempdir.in_tempdir() as dir_path:
logging.debug("Chdir to {0}".format(dir_path))
backup_folder = datetime.datetime.utcnow().strftime(
config['output_prefix'])
logging.info("Creating backup folder: {0}".format(backup_folder))
os.mkdir(backup_folder, 0o700)
os.chdir(backup_folder)
_backup_db(config)
_backup_files(config)
logging.debug("Chdir to {0}".format(dir_path))
os.chdir(dir_path)
archive_name = _create_archive(backup_folder, config)
enc_archive_name = _encrypt_file(archive_name, config)
if opts.upload:
_upload_file(enc_archive_name, config)
if opts.output_dir:
shutil.move(enc_archive_name, opts.output_dir)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--config-file', default='backup.yml')
parser.add_argument('--output-dir', default=None)
parser.add_argument('--upload', default=False, action='store_true')
parser.add_argument('--quiet', default=False, action='store_true')
parser.add_argument('--debug', default=False, action='store_true')
opts = parser.parse_args()
if not os.path.exists(opts.config_file):
sys.exit("The specified config file does not exist!")
if not opts.quiet:
if opts.debug:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
else:
logging.basicConfig(level=logging.ERROR)
config = None
if opts.output_dir:
opts.output_dir = os.path.abspath(opts.output_dir)
with open(opts.config_file) as fp:
logging.debug("Loading config from {0}".format(opts.config_file))
config = yaml.safe_load(fp)
config['quiet'] = opts.quiet
with tempdir.in_tempdir() as dir_path:
logging.debug("Chdir to {0}".format(dir_path))
backup_folder = datetime.datetime.utcnow().strftime(
config['output_prefix'])
logging.info("Creating backup folder: {0}".format(backup_folder))
os.mkdir(backup_folder, 0o700)
os.chdir(backup_folder)
_backup_db(config)
_backup_files(config)
logging.debug("Chdir to {0}".format(dir_path))
os.chdir(dir_path)
archive_name = _create_archive(backup_folder, config)
enc_archive_name = _encrypt_file(archive_name, config)
if opts.upload:
_upload_file(enc_archive_name, config)
if opts.output_dir:
shutil.move(enc_archive_name, opts.output_dir)
def check_density_from_Universe(self, atomselection,
ref_meandensity, **kwargs):
import MDAnalysis.analysis.density
with tempdir.in_tempdir():
D = MDAnalysis.analysis.density.density_from_Universe(
self.universe, atomselection=atomselection,
delta=self.delta, **kwargs)
assert_almost_equal(D.grid.mean(), ref_meandensity,
err_msg="mean density does not match")
D.export(self.outfile)
D2 = MDAnalysis.analysis.density.Density(self.outfile)
assert_almost_equal(D.grid, D2.grid, decimal=self.precision,
err_msg="DX export failed: different grid sizes")
def check_density_from_Universe(self, atomselection,
ref_meandensity, **kwargs):
import MDAnalysis.analysis.density
with tempdir.in_tempdir():
D = MDAnalysis.analysis.density.density_from_Universe(
self.universe, atomselection=atomselection,
delta=self.delta, **kwargs)
assert_almost_equal(D.grid.mean(), ref_meandensity,
err_msg="mean density does not match")
D.export(self.outfile)
D2 = MDAnalysis.analysis.density.Density(self.outfile)
assert_almost_equal(D.grid, D2.grid, decimal=self.precision,
err_msg="DX export failed: different grid sizes")
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
try:
obj = open(outfile, "w")
ns = util.NamedStream(obj, outfile, close=True)
ns.writelines(self.text)
ns.close()
text = open(outfile).readlines()
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
finally:
ns.close()
obj.close()
def test_helanal_trajectory(reference=HELANAL_BENDING_MATRIX,
outfile="helanal_bending_matrix.dat"):
u = mda.Universe(PSF, DCD)
with tempdir.in_tempdir():
# Helix 8: 161 - 187 http://www.rcsb.org/pdb/explore.do?structureId=4AKE
MDAnalysis.analysis.helanal.helanal_trajectory(
u, selection="name CA and resnum 161-187")
bendingmatrix = read_bending_matrix(outfile)
ref = read_bending_matrix(reference)
assert_equal(sorted(bendingmatrix.keys()),
sorted(ref.keys()),
err_msg="different contents in bending matrix data file")
for label in ref.keys():
assert_array_almost_equal(
bendingmatrix[label],
ref[label],
err_msg="bending matrix stats for {0} mismatch".format(label))
def test_File_write(self):
with tempdir.in_tempdir():
outfile = "lookingglas.txt"
try:
obj = open(outfile, "w")
ns = util.NamedStream(obj, outfile, close=True)
ns.writelines(self.text)
ns.close()
text = open(outfile).readlines()
assert_equal(ns.name, outfile)
assert_equal(str(ns), outfile)
assert_equal(len(text), len(self.text))
assert_equal("".join(text), "".join(self.text))
finally:
ns.close()
obj.close()
def extract(self, archive_path, output_package_path, **kwargs):
'''Extract an archived GraftM package.
Parameters
----------
archive_path: str
path to archive
output_package_path: str
path to where to put the extracted file
kwargs:
force: bool
overwrite an existing directory
'''
force = kwargs.pop('force', ArchiveDefaultOptions.force)
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
logging.info("Un-archiving GraftM package '%s' from '%s'" %
(output_package_path, archive_path))
archive = os.path.abspath(archive_path)
output = os.path.abspath(output_package_path)
self._setup_output(output, force)
with tempdir.in_tempdir():
with tarfile.open(archive) as tar:
tar.extractall()
for tarinfo in tar:
folder = os.path.dirname(tarinfo.name)
break
# recreate diamond file
gpkg = GraftMPackage.acquire(folder)
if gpkg.version != 3:
raise Exception(
"Encountered an archived gpkg of unexpected version: %d" %
gpkg.version)
if gpkg.diamond_database_path():
logging.debug("Creating diamond DB")
gpkg.create_diamond_db()
shutil.move(folder, output)
logging.info("Archive successfully extracted")
def test_hole_module_fd_closure(self):
"""MDAnalysis.analysis.hole: Issue 129: ensure low level file descriptors to PDB files used by Hole program are properly closed"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
try:
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
resource.setrlimit(resource.RLIMIT_NOFILE,
(64, self.hard_max_open_files))
except ImportError:
raise NotImplementedError(
"Test cannot be run without the resource module.")
with tempdir.in_tempdir():
try:
# will need to have the 'hole' command available in the path
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
except OSError as err:
if err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in xrange(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError(
"HOLEtraj does not close file descriptors (Issue 129)")
elif err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def test_hole_module_fd_closure(self):
"""MDAnalysis.analysis.hole: Issue 129: ensure low level file descriptors to PDB files used by Hole program are properly closed"""
# If Issue 129 isn't resolved, this function will produce an OSError on
# the system, and cause many other tests to fail as well.
#
# Successful test takes ~10 s, failure ~2 s.
try:
# Hasten failure by setting "ulimit -n 64" (can't go too low because of open modules etc...)
import resource
resource.setrlimit(resource.RLIMIT_NOFILE, (64, self.hard_max_open_files))
except ImportError:
raise NotImplementedError("Test cannot be run without the resource module.")
with tempdir.in_tempdir():
try:
# will need to have the 'hole' command available in the path
H = HOLEtraj(self.universe, cvect=[0, 1, 0], sample=20.0)
except OSError as err:
if err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
self._restore_rlimits()
# pretty unlikely that the code will get through 2 rounds if the MDA
# issue 129 isn't fixed, although this depends on the file descriptor
# open limit for the machine in question
try:
for i in xrange(2):
# will typically get an OSError for too many files being open after
# about 2 seconds if issue 129 isn't resolved
H.run()
except OSError as err:
if err.errno == errno.EMFILE:
raise AssertionError("HOLEtraj does not close file descriptors (Issue 129)")
elif err.errno == errno.ENOENT:
raise OSError(errno.ENOENT, "HOLE binary not found")
raise
finally:
# make sure to restore open file limit !!
self._restore_rlimits()
def extract(self, archive_path, output_package_path, **kwargs):
'''Extract an archived GraftM package.
Parameters
----------
archive_path: str
path to archive
output_package_path: str
path to where to put the extracted file
kwargs:
force: bool
overwrite an existing directory
'''
force = kwargs.pop('force', ArchiveDefaultOptions.force)
if len(kwargs) > 0:
raise Exception("Unexpected arguments detected: %s" % kwargs)
logging.info("Un-archiving GraftM package '%s' from '%s'" % (output_package_path, archive_path))
archive = os.path.abspath(archive_path)
output = os.path.abspath(output_package_path)
self._setup_output(output, force)
with tempdir.in_tempdir():
with tarfile.open(archive) as tar:
tar.extractall()
for tarinfo in tar:
folder = os.path.dirname(tarinfo.name)
break
# recreate diamond file
gpkg = GraftMPackage.acquire(folder)
if gpkg.version != 3:
raise Exception("Encountered an archived gpkg of unexpected version: %d" % gpkg.version)
if gpkg.diamond_database_path():
logging.debug("Creating diamond DB")
gpkg.create_diamond_db()
shutil.move(folder, output)
logging.info("Archive successfully extracted")
def test_round_trip(self):
with tempdir.in_tempdir():
archiver = Archive()
ingpkg = os.path.join(path_to_data, 'mcrA.gpkg')
arc = 'compressed.gpkg.tar.gz'
out = 'reconstituted.gpkg'
archiver.create(ingpkg, arc)
archiver.extract(arc, out)
file_list = ['CONTENTS.json', 'mcrA.faa', 'mcrA.hmm']
dmnd = 'mcra.faa.dmnd'
refpkg = 'mcrA.refpkg'
for f in file_list:
self.assertTrue(
filecmp.cmp(os.path.join(ingpkg, f), os.path.join(out, f)))
self.assertTrue(
filecmp.dircmp(os.path.join(ingpkg, refpkg),
os.path.join(out, refpkg)))
# Do not test actual equality of diamond DB because this changes
# dependant on diamond version.
self.assertTrue(os.path.exists(os.path.join(out, dmnd)))
self.assertEquals(sorted(file_list + [dmnd, refpkg]),
sorted(os.listdir(out)))
def test_round_trip(self):
with tempdir.in_tempdir():
archiver = Archive()
ingpkg = os.path.join(path_to_data, 'mcrA.gpkg')
arc = 'compressed.gpkg.tar.gz'
out = 'reconstituted.gpkg'
archiver.create(ingpkg, arc)
archiver.extract(arc, out)
file_list = ['CONTENTS.json', 'mcrA.faa', 'mcrA.hmm']
dmnd = 'mcra.faa.dmnd'
refpkg = 'mcrA.refpkg'
for f in file_list:
self.assertTrue(filecmp.cmp(
os.path.join(ingpkg, f),
os.path.join(out, f)))
self.assertTrue(filecmp.dircmp(
os.path.join(ingpkg, refpkg),
os.path.join(out, refpkg)))
# Do not test actual equality of diamond DB because this changes
# dependant on diamond version.
self.assertTrue(os.path.exists(os.path.join(out, dmnd)))
self.assertEquals(
sorted(file_list+[dmnd, refpkg]),
sorted(os.listdir(out)))
def in_tmpexport(commit):
with in_tempdir() as tmpdir:
commit.export_to(tmpdir)
yield tmpdir
def test_no_container(self):
with tempdir.in_tempdir():
if self.ref.container_format:
self.ref.writer('foo')
else:
assert_raises(TypeError, self.ref.writer, 'foo')
def test_get_writer(self):
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile, n_atoms=100) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, 100)
def test_startframe(self):
"""test_startframe: TestContactAnalysis1: start frame set to 0 (resolution of Issue #624)"""
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1()
self.assertEqual(CA1.timeseries.shape[1], self.universe.trajectory.n_frames)
def test_no_container(self):
with tempdir.in_tempdir():
if self.ref.container_format:
self.ref.writer('foo')
else:
assert_raises(TypeError, self.ref.writer, 'foo')
def test_get_writer(self):
with tempdir.in_tempdir():
self.outfile = 'test-writer' + self.ref.ext
with self.reader.Writer(self.outfile, n_atoms=100) as W:
assert_equal(isinstance(W, self.ref.writer), True)
assert_equal(W.n_atoms, 100)
def test_end_zero(self):
"""test_end_zero: TestContactAnalysis1: stop frame 0 is not ignored"""
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1(stop=0)
self.assertEqual(len(CA1.timeseries), 0)
def test_slicing(self):
start, stop, step = 10, 30, 5
with tempdir.in_tempdir():
CA1 = self._run_ContactAnalysis1(start=start, stop=stop, step=step)
frames = np.arange(self.universe.trajectory.n_frames)[start:stop:step]
self.assertEqual(CA1.timeseries.shape[1], len(frames))
