def redirect_chunk_stdout_and_stderr(O,
log_format=Auto,
out=Auto,
have_array=False):
if (O.n == 1): return
log_name = None
if (not have_array):
i = O.queuing_system_info
if (i is not None and i.have_array()):
have_array = True
if (have_array):
if (log_format is Auto): log_format="log%%0%dd"
fmt = log_format % max(3, len("%d" % (O.n-1)))
log_name = fmt % O.i
log = open(log_name, "w")
sys.stdout = log
sys.stderr = log
from libtbx.utils import host_and_user
if (out is Auto): out = sys.stdout
if (out is not None):
host_and_user().show(out=out)
print >> out, "chunk.n:", O.n
print >> out, "chunk.i:", O.i
if (log_name is not None):
print >> out, "log_name:", log_name
print >> out
return O
def exercise_misc():
utils.host_and_user().show(prefix="### ")
time_in_seconds = 1.1
for i_trial in xrange(55):
time_in_seconds = time_in_seconds**1.1
time_units, time_unit = utils.human_readable_time(
time_in_seconds=time_in_seconds)
assert approx_equal(
utils.human_readable_time_as_seconds(time_units, time_unit),
time_in_seconds)
#
fts = utils.format_timestamp
f12 = utils.format_timestamp_12_hour
f24 = utils.format_timestamp_24_hour
def check(string, expected):
assert len(string) == len(expected)
check(f12(1280007000), 'Jul 24 2010 02:30 PM')
check(f24(1280007000), 'Jul 24 2010 14:30')
check(f12(1280007000, True), '24-07-10 02:30 PM')
check(f24(1280007000, True), '24-07-10 14:30')
check(fts(1280007000), 'Jul 24 2010 02:30 PM')
#
nfs = utils.number_from_string
for string in ["True", "False"]:
try: nfs(string=string)
except ValueError, e:
assert str(e) == 'Error interpreting "%s" as a numeric expression.' % (
string)
else: raise Exception_expected
def exercise_misc():
utils.host_and_user().show(prefix="### ")
time_in_seconds = 1.1
for i_trial in xrange(55):
time_in_seconds = time_in_seconds**1.1
time_units, time_unit = utils.human_readable_time(
time_in_seconds=time_in_seconds)
assert approx_equal(
utils.human_readable_time_as_seconds(time_units, time_unit),
time_in_seconds)
#
fts = utils.format_timestamp
f12 = utils.format_timestamp_12_hour
f24 = utils.format_timestamp_24_hour
def check(string, expected):
assert len(string) == len(expected)
check(f12(1280007000), 'Jul 24 2010 02:30 PM')
check(f24(1280007000), 'Jul 24 2010 14:30')
check(f12(1280007000, True), '24-07-10 02:30 PM')
check(f24(1280007000, True), '24-07-10 14:30')
check(fts(1280007000), 'Jul 24 2010 02:30 PM')
#
nfs = utils.number_from_string
for string in ["True", "False"]:
try:
nfs(string=string)
except ValueError, e:
assert str(
e) == 'Error interpreting "%s" as a numeric expression.' % (
string)
else:
raise Exception_expected
def redirect_chunk_stdout_and_stderr(O,
log_format=Auto,
out=Auto,
have_array=False):
if (O.n == 1): return
log_name = None
if (not have_array):
i = O.queuing_system_info
if (i is not None and i.have_array()):
have_array = True
if (have_array):
if (log_format is Auto): log_format = "log%%0%dd"
fmt = log_format % max(3, len("%d" % (O.n - 1)))
log_name = fmt % O.i
log = open(log_name, "w")
sys.stdout = log
sys.stderr = log
from libtbx.utils import host_and_user
if (out is Auto): out = sys.stdout
if (out is not None):
host_and_user().show(out=out)
print >> out, "chunk.n:", O.n
print >> out, "chunk.i:", O.i
if (log_name is not None):
print >> out, "log_name:", log_name
print >> out
return O
def abort(self, force=None):
touch_file(self.stop_file)
if (force) and (not None in [self._process_host, self._process_pid]):
info = host_and_user()
if (info.get_host_name() == self._process_host):
os.kill(self._process_pid, signal.SIGTERM)
self.running = False
self.callback_abort()
def abort (self, force=None) :
touch_file(self.stop_file)
if (force) and (not None in [self._process_host, self._process_pid]) :
info = host_and_user()
if (info.get_host_name() == self._process_host) :
os.kill(self._process_pid, signal.SIGTERM)
self.running = False
self.callback_abort()
def callback_start(self, data=None):
info = host_and_user()
assert (info.pid is not None)
f = open(self.start_file, "w")
host_name = info.get_host_name()
if (host_name is None) and (sys.platform == "darwin"):
host_name = os.uname()[1]
f.write("%s %d" % (host_name, info.pid))
f.close()
def callback_start (self, data=None) :
info = host_and_user()
assert (info.pid is not None)
f = open(self.start_file, "w")
host_name = info.get_host_name()
if (host_name is None) and (sys.platform == "darwin") :
host_name = os.uname()[1]
f.write("%s %d" % (host_name, info.pid))
f.close()
def exercise_dir_utils():
dirs = ["tst_utils_1", "tst_utils_2", "tst_utils_45"]
for dir_name in dirs :
if (os.path.isdir(dir_name)) : os.rmdir(dir_name)
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_1")
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_2")
dir_name = utils.create_run_directory("tst_utils", 45)
assert (os.path.basename(dir_name) == "tst_utils_45")
for dir_name in dirs :
os.rmdir(dir_name)
file_name = "/cctbx/%s/%s/XXXX.pdb" % (random.random(), random.random())
try :
utils.check_if_output_directory_exists(file_name)
except utils.Sorry :
pass
else :
raise Exception_expected
dir_name = os.getcwd()
utils.check_if_output_directory_exists(dir_name=dir_name)
dir_created = False
if (not os.path.exists("Dropbox")):
os.mkdir("Dropbox")
dir_created = True
dir_name = os.path.join(os.getcwd(), "Dropbox")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
utils.check_if_output_directory_exists(dir_name=dir_name)
assert len(w) == 1
assert "Dropbox directory" in str(w[-1].message)
if (dir_created):
os.rmdir("Dropbox")
host_info = utils.host_and_user()
assert not utils.allow_delete_directory(host_info.homedir)
target_dir = os.path.join(host_info.homedir, "Downloads")
assert not utils.allow_delete_directory(target_dir)
target_dir = os.path.join(host_info.homedir, "data", "lysozyme")
assert utils.allow_delete_directory(target_dir)
def exercise_dir_utils () :
dirs = ["tst_utils_1", "tst_utils_2", "tst_utils_45"]
for dir_name in dirs :
if (os.path.isdir(dir_name)) : os.rmdir(dir_name)
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_1")
dir_name = utils.create_run_directory("tst_utils")
assert (os.path.basename(dir_name) == "tst_utils_2")
dir_name = utils.create_run_directory("tst_utils", 45)
assert (os.path.basename(dir_name) == "tst_utils_45")
for dir_name in dirs :
os.rmdir(dir_name)
file_name = "/cctbx/%s/%s/XXXX.pdb" % (random.random(), random.random())
try :
utils.check_if_output_directory_exists(file_name)
except utils.Sorry :
pass
else :
raise Exception_expected
dir_name = os.getcwd()
utils.check_if_output_directory_exists(dir_name=dir_name)
dir_created = False
if (not os.path.exists("Dropbox")) :
os.mkdir("Dropbox")
dir_created = True
dir_name = os.path.join(os.getcwd(), "Dropbox")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
utils.check_if_output_directory_exists(dir_name=dir_name)
assert len(w) == 1
assert "Dropbox directory" in str(w[-1].message)
if (dir_created) :
os.rmdir("Dropbox")
host_info = utils.host_and_user()
assert not utils.allow_delete_directory(host_info.homedir)
target_dir = os.path.join(host_info.homedir, "Downloads")
assert not utils.allow_delete_directory(target_dir)
target_dir = os.path.join(host_info.homedir, "data", "lysozyme")
assert utils.allow_delete_directory(target_dir)
def exercise_misc():
utils.host_and_user().show(prefix="### ")
time_in_seconds = 1.1
for i_trial in range(55):
time_in_seconds = time_in_seconds**1.1
time_units, time_unit = utils.human_readable_time(
time_in_seconds=time_in_seconds)
assert approx_equal(
utils.human_readable_time_as_seconds(time_units, time_unit),
time_in_seconds)
#
fts = utils.format_timestamp
f12 = utils.format_timestamp_12_hour
f24 = utils.format_timestamp_24_hour
def check(string, expected):
assert len(string) == len(expected)
check(f12(1280007000), 'Jul 24 2010 02:30 PM')
check(f24(1280007000), 'Jul 24 2010 14:30')
check(f12(1280007000, True), '24-07-10 02:30 PM')
check(f24(1280007000, True), '24-07-10 14:30')
check(fts(1280007000), 'Jul 24 2010 02:30 PM')
#
nfs = utils.number_from_string
for string in ["True", "False"]:
try: nfs(string=string)
except ValueError as e:
assert str(e) == 'Error interpreting "%s" as a numeric expression.' % (
string)
else: raise Exception_expected
assert nfs(string="-42") == -42
assert approx_equal(nfs(string="3.14"), 3.14)
assert approx_equal(nfs(string="cos(0)"), 1)
try: nfs(string="xxx(0)")
except ValueError as e:
assert str(e).startswith(
'Error interpreting "xxx(0)" as a numeric expression: ')
else: raise Exception_expected
#
s = "[0.143139, -0.125121, None, -0.308607]"
assert numstr(values=eval(s)) == s
#
for s,i in {"2000000" : 2000000,
"2k" : 2048,
"2Kb" : 2048,
"2 Kb" : 2048,
"5Mb" : 5*1024*1024,
"2.5Gb" : 2.5*1024*1024*1024,
"1T": 1024*1024*1024*1024,
10000 : 10000,
5.5 : 5.5,
}.items():
assert utils.get_memory_from_string(s) == i
#
assert utils.tupleize(1) == (1,)
assert utils.tupleize("abcde") == ('a', 'b', 'c', 'd', 'e')
assert utils.tupleize([1,2,3]) == (1,2,3)
#
sf = utils.search_for
assert sf(pattern="fox", mode="==", lines=["fox", "foxes"]) \
== ["fox"]
assert sf(pattern="o", mode="find", lines=["fox", "bird", "mouse"]) \
== ["fox", "mouse"]
assert sf(pattern="fox", mode="startswith", lines=["fox", "foxes"]) \
== ["fox", "foxes"]
assert sf(pattern="xes", mode="endswith", lines=["fox", "foxes"]) \
== ["foxes"]
assert sf(pattern="es$", mode="re.search", lines=["geese", "foxes"]) \
== ["foxes"]
assert sf(pattern="ge", mode="re.match", lines=["geese", "angel"]) \
== ["geese"]
#
nd1d = utils.n_dim_index_from_one_dim
for size in range(1,5):
for i1d in range(size):
assert nd1d(i1d=i1d, sizes=(size,)) == [i1d]
for sizes in [(1,1), (1,3), (3,1), (2,3)]:
ni, nj = sizes
for i in range(ni):
for j in range(nj):
i1d = i*nj+j
assert nd1d(i1d=i1d, sizes=sizes) == [i,j]
for sizes in [(1,1,1), (1,3,1), (3,2,1), (4,3,2)]:
ni, nj, nk = sizes
for i in range(ni):
for j in range(nj):
for k in range(nk):
i1d = (i*nj+j)*nk+k
assert nd1d(i1d=i1d, sizes=sizes) == [i,j,k]
#
from libtbx import easy_run
b = easy_run.fully_buffered(
command="libtbx.raise_exception_for_testing")
for lines in [b.stdout_lines, b.stderr_lines]:
assert lines[0].startswith("EXCEPTION_INFO: show_stack(0): ")
assert lines[-1] == "EXCEPTION_INFO: RuntimeError: Just for testing."
b = easy_run.fully_buffered(
command="libtbx.raise_exception_for_testing silent")
b.raise_if_errors_or_output()
#
frange = utils.frange
samples = utils.samples
assert approx_equal([i/10. for i in range(-2,2)], frange(-0.2,0.2,0.1))
assert approx_equal([i/10. for i in range(-2,2+1)], samples(-0.2,0.2,0.1))
assert approx_equal([i/10. for i in range(2,-2,-1)], frange(0.2,-0.2,-0.1))
assert approx_equal([i/10. for i in range(2,-2-1,-1)], samples(0.2,-0.2,-0.1))
assert approx_equal([i/4. for i in range(4,8)], frange(1, 2, 0.25))
assert approx_equal([i/4. for i in range(4,8+1)], samples(1, 2, 0.25))
assert approx_equal([0.2+i/3. for i in range(4)], frange(0.2, 1.3, 1./3))
assert approx_equal([0.2+i/3. for i in range(4)], samples(0.2, 1.3, 1./3))
assert approx_equal(list(range(5)) , frange(5))
assert approx_equal(list(range(5+1)) , samples(5))
assert approx_equal(list(range(-5)), frange(-5))
assert approx_equal(list(range(-5-1)), samples(-5))
assert approx_equal(list(range(1,3)), frange(1, 3))
assert approx_equal(list(range(1,3+1)), samples(1, 3))
assert approx_equal([i/10. for i in range(20,9,-2)], frange(2.0,0.9,-0.2))
assert approx_equal([i/10. for i in range(20,9,-2)], samples(2.0,0.9,-0.2))
#
ff = utils.format_float_with_standard_uncertainty
assert ff(21.234567, 0.0013) == "21.2346(13)"
assert ff(21.234567, 0.0023) == "21.235(2)"
assert ff(12345, 45) == "12350(50)"
assert ff(12.3,1.2) == "12.3(12)"
assert ff(-0.2451, 0.8135) == "-0.2(8)"
assert ff(1.234, 0.196) == "1.2(2)"
assert ff(1.234, 0.193) == "1.23(19)"
#
for n in range(4):
assert len(utils.random_hex_code(number_of_digits=n)) == n
#
print("multiprocessing problem:", utils.detect_multiprocessing_problem())
#
print("base36_timestamp():", utils.base36_timestamp(), "now")
print("base36_timestamp():", utils.base36_timestamp(
seconds_since_epoch=115855*365.2425*24*60*60), "year 115855 CE")
#
print("get_svn_revision():", utils.get_svn_revision())
print("get_build_tag():", utils.get_build_tag())
# concatenate_python_script
# XXX the string concatenation here is required to trick libtbx.find_clutter,
# which will warn about repetition of the future division import.
script = """
from __future__ """ + """import division
import os.path
def foo():
print "bar"
"""
d = tempfile.mkdtemp()
name = os.path.join(d, "tst_libtbx_utils_python_script.py")
name2 = os.path.join(d, "tst_libtbx_utils_python_script2.py")
open(name, "w").write(script)
f = open(name2, "w")
utils.concatenate_python_script(out=f, file_name=name)
f.close()
lines = open(name2).readlines()
have_def = False
for line in lines :
assert (not "__future__" in line)
if line.startswith("def foo"):
have_def = True
assert have_def
def run():
host_and_user().show()
def run(): host_and_user().show()
