def copy_files(cls,
scene_nums,
cam_num,
src_patterns,
dst_pattern,
src_dir,
dst_dir,
src2dst_list,
dst_start_num=None):
for scene_num in scene_nums:
for c, pattern in zip(cam_num, src_patterns):
src_final_format = pattern.replace('([0-9]*)', scene_num)
src_final_format = src_final_format.replace('\\', '')
src_image_file, src_txt_file = get_img_label_path(
src_dir, src_final_format)
if (dst_start_num != -1):
dst_final_format = dst_pattern % (cls, c, dst_start_num)
dst_image_file, dst_txt_file = get_img_label_path(
dst_dir, dst_final_format)
else:
dst_image_file, dst_txt_file = get_img_label_path(
dst_dir, src_final_format)
src2dst_list.append([src_image_file, dst_image_file])
copy_file(src_image_file, dst_image_file)
copy_file(src_txt_file, dst_txt_file)
if (dst_start_num != -1):
dst_start_num += 1
def train(args):
base_dir = args.base_dir
dirs = init_dir(base_dir)
init_log(dirs['log'])
config_dir = args.config_dir
copy_file(config_dir, dirs['data'])
config = configparser.ConfigParser()
config.read(config_dir)
# init env
env = init_env(config['ENV_CONFIG'])
logging.info('Training: a dim %r, agent dim: %d' % (env.n_a_ls, env.n_agent))
# init step counter
total_step = int(config.getfloat('TRAIN_CONFIG', 'total_step'))
test_step = int(config.getfloat('TRAIN_CONFIG', 'test_interval'))
log_step = int(config.getfloat('TRAIN_CONFIG', 'log_interval'))
global_counter = Counter(total_step, test_step, log_step)
# init centralized or multi agent
seed = config.getint('ENV_CONFIG', 'seed')
model = init_agent(env, config['MODEL_CONFIG'], total_step, seed)
# disable multi-threading for safe SUMO implementation
summary_writer = tf.summary.FileWriter(dirs['log'])
trainer = Trainer(env, model, global_counter, summary_writer, output_path=dirs['data'])
trainer.run()
# save model
final_step = global_counter.cur_step
logging.info('Training: save final model at step %d ...' % final_step)
model.save(dirs['model'], final_step)
def cl_news_util(arguments, cache):
if not cache:
htmlfile = utils.get_html_file('http://news.ycombinator.com')
storylinks = re.findall(r'href="(.+)" class="storylink">(.+)</a><span',
htmlfile)
else:
storylinks = cache
if len(arguments) > 1:
if arguments[1] == '--headlines' or arguments[1] == '-h':
utils.hn_headlines(storylinks)
return storylinks
if arguments[1] == '--open' or arguments[1] == '-o':
if len(arguments) > 2:
index = int(arguments[2])
openpage(storylinks, index)
return storylinks
if arguments[1] == '--copy' or arguments[1] == '-cp':
if len(arguments) > 2:
utils.copy_file(arguments[2], htmlfile)
return storylinks
utils.handle_error('hn_error')
def mount(mountTo):
try:
assert path.isdir('/etc/cryptmount/keys/')
except Exception as e:
print(
'You might need to install the actual program and convert this USB to load it.'
)
exit()
key_fp = path.join('/etc/cryptmount/keys/', NAME + '.key')
try:
assert path.isfile(key_fp)
except Exception as e:
print('No key Found.')
raise e
if not path.isdir(mountTo):
mkdir(mountTo)
copy_file(CMTAB_FP, path.join(TARGET, 'cmtab.bak'))
system('echo "%s" > /etc/cryptmount/cmtab' %
cmtab(mountTo, ENCRYPTED_DEV, NAME, key_fp).make())
system('chown -R %s:%s %s' % (getlogin(), getlogin(), mountTo))
system('chmod 0700 %s' % mountTo)
with open(path.join(TARGET, 'tempSave.tmp'), 'w') as f:
f.write(mountTo)
assert system('cryptmount ' + NAME) == 0
return True
def backup_skinshortcuts_properties(propertiesfile, dest_path):
'''parse skinshortcuts properties file and translate images'''
# look for any backgrounds and translate them
propfile = xbmcvfs.File(propertiesfile)
data = propfile.read()
propfile.close()
allprops = eval(data) if data else []
for count, prop in enumerate(allprops):
if prop[2] == "background":
background = prop[3] if prop[3] else ""
defaultid = prop[1]
if background.endswith(".jpg") or background.endswith(
".png") or background.endswith(".gif"):
background = get_clean_image(background)
extension = background.split(".")[-1]
newthumb = os.path.join(
dest_path, "%s-background-%s.%s" %
(xbmc.getSkinDir(), normalize_string(defaultid),
extension))
newthumb_vfs = "special://profile/addon_data/script.skinshortcuts/%s-background-%s.%s" % (
xbmc.getSkinDir(), normalize_string(defaultid),
extension)
if xbmcvfs.exists(background):
copy_file(background, newthumb)
allprops[count] = [
prop[0], prop[1], prop[2], newthumb_vfs
]
# write updated properties file
propfile = xbmcvfs.File(propertiesfile, "w")
propfile.write(repr(allprops))
propfile.close()
def pre_load(source_dic, CACHE_PATH, TMP_PATH, update_types):
'''
检查icd_name是否更新，若更新，重新生成cache文件，并更新tmp文件
:param source_dic: {LC:国家临床版,GB:国家版}
:return:
'''
for file_pre, file_name in source_dic.iteritems():
f1_path = CACHE_PATH + file_pre + '_icd_name.csv'
f2_path = TMP_PATH + file_pre + '_icd_name_shoushu.csv'
if not utils.file_compare(f1_path, f2_path):
# 文件改变，重新生成cache
build_icd_norm(CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icd_norm.csv",
utils.SERVICE_URL_SS)
for type, name in update_types.iteritems():
build_icd_type_norm(
CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icd_" + type + ".csv", name,
file_name)
build_icd_code_dict(CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icdcode_dict.csv",
file_name, 2)
# 更新tmp文件
utils.copy_file(f1_path, f2_path)
def run_previous_uninstaller(self):
if not self.info.previous_uninstaller_path \
or not os.path.isfile(self.info.previous_uninstaller_path):
return
previous_uninstaller = self.info.previous_uninstaller_path.lower()
uninstaller = self.info.previous_uninstaller_path
command = [uninstaller, "--uninstall"]
# Propagate noninteractive mode to the uninstaller
if self.info.non_interactive:
command.append("--noninteractive")
if 0 and previous_uninstaller.lower() == self.info.original_exe.lower():
# This block is disabled as the functionality is achived via pylauncher
if self.info.original_exe.lower().startswith(self.info.previous_target_dir.lower()):
log.debug("Copying uninstaller to a temp directory, so that we can delete the containing directory")
uninstaller = tempfile.NamedTemporaryFile()
uninstaller.close()
uninstaller = uninstaller.name
copy_file(self.info.previous_uninstaller_path, uninstaller)
log.info("Launching asynchronously previous uninstaller %s" % uninstaller)
run_nonblocking_command(command, show_window=True)
return True
elif get_file_hash(self.info.original_exe) == get_file_hash(self.info.previous_uninstaller_path):
log.info("This is the uninstaller running")
else:
log.info("Launching previous uninestaller %s" % uninstaller)
subprocess.call(command)
# Note: the uninstaller is now non-blocking so we can just as well quit this running version
# TBD: make this call synchronous by waiting for the children process of the uninstaller
self.application.quit()
return True
def backup_skinshortcuts(self, dest_path):
'''backup skinshortcuts including images'''
source_path = u'special://profile/addon_data/script.skinshortcuts/'
if not xbmcvfs.exists(dest_path):
xbmcvfs.mkdir(dest_path)
for file in xbmcvfs.listdir(source_path)[1]:
file = file.decode("utf-8")
sourcefile = source_path + file
destfile = dest_path + file
if xbmc.getCondVisibility(
"SubString(Skin.String(skinshortcuts-sharedmenu),false)"):
# User is not sharing menu, so strip the skin name out of the destination file
destfile = destfile.replace("%s." % (xbmc.getSkinDir()), "")
if (file.endswith(".DATA.xml") and
(not xbmc.getCondVisibility(
"SubString(Skin.String(skinshortcuts-sharedmenu),false)")
or file.startswith(xbmc.getSkinDir()))):
xbmcvfs.copy(sourcefile, destfile)
# parse shortcuts file and look for any images - if found copy them to addon folder
self.backup_skinshortcuts_images(destfile, dest_path)
elif file.endswith(".properties") and xbmc.getSkinDir() in file:
if xbmc.getSkinDir() in file:
destfile = dest_path + file.replace(
xbmc.getSkinDir(), "SKINPROPERTIES")
copy_file(sourcefile, destfile)
self.backup_skinshortcuts_properties(destfile, dest_path)
else:
# just copy the remaining files
copy_file(sourcefile, destfile)
def run_previous_uninstaller(self):
if not self.info.previous_uninstaller_path \
or not os.path.isfile(self.info.previous_uninstaller_path):
return
previous_uninstaller = self.info.previous_uninstaller_path.lower()
uninstaller = self.info.previous_uninstaller_path
if 0 and previous_uninstaller.lower() == self.info.original_exe.lower():
# This block is disabled as the functionality is achived via pylauncher
if self.info.original_exe.lower().startswith(self.info.previous_target_dir.lower()):
log.debug("Copying uninstaller to a temp directory, so that we can delete the containing directory")
uninstaller = tempfile.NamedTemporaryFile()
uninstaller.close()
uninstaller = uninstaller.name
copy_file(self.info.previous_uninstaller_path, uninstaller)
log.info("Launching asynchronously previous uninstaller %s" % uninstaller)
run_nonblocking_command([uninstaller, "--uninstall"], show_window=True)
return True
elif get_file_md5(self.info.original_exe) == get_file_md5(self.info.previous_uninstaller_path):
log.info("This is the uninstaller running")
else:
log.info("Launching previous uninestaller %s" % uninstaller)
subprocess.call([uninstaller, "--uninstall"])
# Note: the uninstaller is now non-blocking so we can just as well quit this running version
# TBD: make this call synchronous by waiting for the children process of the uninstaller
self.application.quit()
return True
def build_source(source_path, target_path):
tsconfig_path = join(source_path, "tsconfig.json")
if isfile(join(source_path, ".includes")):
params = read_params_from_includes(source_path)
files = read_files_from_includes(source_path)
elif not isfile(tsconfig_path):
params = COMPILER_OPTIONS.copy()
files = [file for file in glob.glob(
f"{source_path}/**/*", recursive=True)]
else:
# if there isn't .includes but there is tsconfig.json
result = build_tsconfig(tsconfig_path)
if result != 0:
return 1
with open(tsconfig_path) as tsconfig:
config = json.load(tsconfig)
library_path = normpath(
join(source_path, config["compilerOptions"]["outFile"]))
copy_file(library_path, target_path)
declaration_path = f"{splitext(library_path)[0]}.d.ts"
if(isfile(declaration_path)):
copy_file(declaration_path, join(make_config.get_path(
"toolchain/build/typescript-headers"), basename(declaration_path)))
return 0
# decode params
params["checkJs"] = not params.pop("nocheck")
params["declaration"] = params.pop("declarations")
params["experimentalDecorators"] = params.pop("decorators")
# actually there is two directories with *.d.ts files: toolchain/jslibs (for default headers) & toolchain/build/typescript-headers (for additional libraries)
headers = glob.glob(relpath(make_config.get_path(
"toolchain/**/*.d.ts"), source_path), recursive=True)
template = {
"compilerOptions": {
"target": "ES5",
"lib": ["ESNext"],
"allowJs": True,
"downlevelIteration": True,
"outFile": target_path
},
"exclude": [
"**/node_modules/*",
"dom"
],
"include": files,
"files": headers
}
for key, value in params.items():
template["compilerOptions"][key] = value
with open(tsconfig_path, "w") as tsconfig:
json.dump(template, tsconfig, indent="\t")
return build_tsconfig(tsconfig_path)
def create(self, session):
ices_tmp_conf = None
try:
ices_conf_name = '%s_ices.xml' % self.id
ices_tmp_conf = copy_file(config.ICES_BASE_CONFIG_PATH,
config.TMP_FOLDER, ices_conf_name)
self.fill_ices_config(ices_tmp_conf)
ices_conf_perm_path = config.ICES_CONFIGS_PATH + ices_conf_name
move_file(ices_tmp_conf, ices_conf_perm_path)
copy_file(config.ICES_PYTHON_BASE_MODULE_PATH,
config.ICES_PYTHON_MODULES_PATH,
"playlist_%s.py" % self.id)
session.commit()
if self.active:
self.start_ices()
if not self.running:
msg = "Ices station was saved and configured, " \
"but can't run. Please see logs"
flash(msg)
raise IcesException(msg)
except Exception as e:
session.rollback()
try:
# Delete all created files if something went wrong
self.delete_ices_from_file_system(ices_tmp_conf)
except OSError:
pass
finally:
raise Exception(e)
def build(self, target_path):
temp_path = join(temp_directory, basename(target_path))
result = 0
self.create_tsconfig(temp_path)
if storage.is_path_changed(self.directory):
import datetime
print(
f"building {basename(target_path)} from {self.includes_file}")
start_time = datetime.datetime.now()
result = self.build_source(temp_path)
end_time = datetime.datetime.now()
diff = end_time - start_time
print(
f"completed {basename(target_path)} build in {round(diff.total_seconds(), 2)}s with result {result} - {'OK' if result == 0 else 'ERROR'}"
)
if result != 0:
return result
storage.save()
else:
print(f"{basename(target_path)} is not changed")
copy_file(temp_path, target_path)
return result
def _storage_image(self, image, id, path, width):
if not image:
return
ids = (id % 1000, id)
origin_path = join("user", path, "%d/%d.jpg" % ids)
media_root = settings.MEDIA_ROOT
try:
os.makedirs(dirname(join(media_root, origin_path)))
except OSError:
pass
origin_fd = file(os.path.join(media_root, origin_path), "w+")
utils.copy_file(src, origin_fd)
origin_fd.seek(0)
original = PIL.Image.open(origin_fd)
w, h = original.size
if not "JPEG" == original.format:
original.save(origin_fd.name, "JPEG")
origin_fd.close()
for i in width:
self._storage_image_thumbnail(image, id, path, i)
src.close()
origin_fd.close()
def main(args):
for failure in utils.find_all_failures(args.design):
print "Failure", failure
ordered_suspectz = []
for i in range(1, 100):
log_file = failure + args.suffix + ".vennsawork/logs/abr%s/vdb.log" % (
str(i).zfill(3))
# print log_file
ordered_suspectz_file = parse_suspects_from_log(log_file)
ordered_suspectz = merge_suspect_lists(ordered_suspectz,
ordered_suspectz_file)
log_file = failure + args.suffix + ".vennsawork/logs/vdb/vdb.log"
ordered_suspectz_file = parse_suspects_from_log(log_file)
ordered_suspectz = merge_suspect_lists(ordered_suspectz,
ordered_suspectz_file)
print "Number of suspects found by solver:", len(ordered_suspectz)
# add suspects from vennsa.stdb.gz of base debugging instance in case some are missed.
stdb_suspects = utils.parse_suspects(failure)
print "Suspects in %s.vennsawork/vennsa.stdb.gz: %i" % (
failure, len(stdb_suspects))
merge_suspect_lists(ordered_suspectz, stdb_suspects)
print "Total number of suspects:", len(ordered_suspectz)
with open("suspects.txt", "w") as f:
for s in ordered_suspectz:
f.write(s + "\n")
utils.copy_file("suspects.txt",
failure.replace("designs", "suspect_lists") +
"_suspects.txt",
verbose=False)
def preprocess(self):
"""Preprocess the attribute file."""
file_name_list = os.listdir(self.image_dir)
random.seed(1234)
random.shuffle(file_name_list)
for i, d in enumerate(self.domains):
self.attr2idx[d] = i
for i, file_name in enumerate(file_name_list):
if (file_name.startswith('X_')):
continue
parts = file_name.split("-")
label = int(parts[0])
if label not in self.domains:
continue
img_name = file_name
count = self.get_sample_count(label)
if count < self.valid_set_size:
# create holdout set on the fly
utils.copy_file(self.image_dir, self.valid_set_dir, img_name)
else:
self.dataset.append([img_name, self.attr2idx[label]])
self.increment_sample_count(label)
print("Sample count per domain: " + str(self.sample_count) +
" (including holdout set, holdout size per domain is: " +
str(self.valid_set_size) + ")")
print('Finished preprocessing the dataset...')
def pre_load(source_dic):
'''
检查icd_name是否更新，若更新，重新生成cache文件，并更新tmp文件
:param source_dic: {LC:国家临床版,GB:国家版}
:return:
'''
for file_pre, file_name in source_dic.iteritems():
f1_path = CACHE_PATH + file_pre + '_icd_name.csv'
f2_path = TMP_PATH + file_pre + '_icd_name.csv'
if not utils.file_compare(f1_path, f2_path):
# 文件改变，重新生成cache
build_icd_norm(CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icd_norm.csv")
for type, name in {
"region": "部位",
"core": "中心词",
"type": "特征词",
"others": "其他",
"unknown": "未知"
}.iteritems():
build_icd_type_norm(
CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icd_" + type + ".csv", name,
file_name)
build_icd_code_dict(CACHE_PATH + file_pre + "_icd_name.csv",
CACHE_PATH + file_pre + "_icdcode_dict.csv",
file_name)
# 更新tmp文件
utils.copy_file(f1_path, f2_path)
def build_script(source, target):
if os.path.isfile(source):
ensure_file_dir(target)
copy_file(source, target)
return 0
else:
if os.path.isfile(os.path.join(source, ".includes")):
return build_includes_dir(source, target)
def test_copy_file(shell_mock, level_mock):
level_mock.return_value = log.DEBUG
fle = "asdf"
dest = "wtf"
utils.copy_file(fle, dest)
shell_mock.assert_called_with(
['rsync', '-a', '-vv', fle, dest]
)
def test_copy_file(self):
import tempfile
dest = tempfile.NamedTemporaryFile("w")
src = file("resources/10x10.png", "r")
utils.copy_file(src, dest)
self.assertEquals(os.stat(src.name).st_size, os.stat(dest.name).st_size)
dest.close()
src.close()
def copy_supporting_files(start_path, destination):
for file in list_files(start_path):
if not (file.startswith("_") or file.startswith(".")):
print("copying: %s to: %s" % (file, destination))
copy_file(path.join(start_path, file), path.join(destination, file))
for dir in list_dirs(start_path):
if not (dir.startswith("_") or dir.startswith(".")):
print("copying: %s to: %s" % (dir, destination))
copy_tree(path.join(start_path, dir), path.join(destination, dir))
def restore():
log.info('Restoring app store preferences (.plist)...')
source = get_app_store_preferences_backup_dir()
dest = get_app_store_preferences_dir()
for f in listdir(source):
domain = f.split('.plist')[0]
dest_path = path.join(dest, domain, 'Data/Library/Preferences')
ensure_exists(dest_path)
source_file = path.join(source, f)
copy_file(source_file, dest_path)
def copy_eggs(source_dir):
log.debug("Copying eggs from '%s'..." % source_dir)
for name in os.listdir(source_dir):
if name.endswith('.egg'):
if PLATFORM_SUBDIR == 'linux' and name.startswith(
'setuptools-0.6c11'):
continue
else:
utils.copy_file(source_path=os.path.join(source_dir, name),
target_path=TEMP_LIB_EGG_DIR)
def perform_build(target_dir, plugin_package, install_type, python_version,
python_executable):
log.info("Target directory: %s" % target_dir)
log.info("Plug-in package: %r" % plugin_package)
log.info("Python version: %s" % python_version)
log.info("Python executable: %s" % python_executable)
# Retrieve dependencies to the correct location
retrieve_dep_eggs(plugin_package)
# Install the dependencies locally using either local copies or downloading from PyPi
deps = ['Jinja2', 'lxml']
for dep in deps:
command = [
'easy_install-%s' % python_version,
'--find-links install-temp/dep-eggs'
]
command.append(dep)
command = ' '.join(command)
log.debug(command)
ok = utils.run_command(command)
if not ok:
print "Warning: failed to run easy_install to install %s." % dep
# Find paths to the sources to install
source_paths = find_cone_egg_sources(plugin_package)
log.info("Creating install directory...")
if not os.path.exists(target_dir):
os.makedirs(target_dir)
if install_type == 'build':
build_cone_eggs(source_paths, python_executable)
if install_type == 'install':
build_cone_eggs(source_paths, python_executable)
install_cone_eggs(target_dir, python_version)
else:
develop_install_cone_sources(source_paths, target_dir, python_version,
python_executable)
# Copy RELEASE.txt
utils.copy_file(source_path=os.path.join(SOURCE_ROOT, '..', 'RELEASE.TXT'),
target_path=os.path.join(target_dir, INSTALL_SUBDIR,
'RELEASE.TXT'))
# Copy cone.cmd or cone.sh, depending on the platform
if sys.platform == "win32":
sourcefile = targetfile = "cone.cmd"
else:
sourcefile = "cone.sh"
targetfile = "cone"
log.info("Copying %s" % sourcefile)
utils.copy_file(source_path=os.path.join(SOURCE_ROOT, sourcefile),
target_path=os.path.join(target_dir, targetfile))
def copy_files(num_list, cam_num, list_format, src_dir, dst_dir):
for num in num_list:
for c in cam_num:
final_format = list_format % (c, num)
image_file = src_dir + final_format
txt_file = image_file.replace('.jpg', '.txt')
txt_file = txt_file.replace('images', 'labels')
print(image_file)
print(txt_file)
copy_file(image_file, dst_dir)
copy_file(txt_file, dst_dir)
def build(self, target_path):
temp_path = declarations_name = join(temp_directory,
basename(target_path))
result = 0
self.create_tsconfig(temp_path)
if self.is_source_changed(temp_path):
print(f"building {basename(target_path)}")
result = self.build_source(temp_path)
else:
print(f"{basename(target_path)} is not changed")
copy_file(temp_path, target_path)
return result
def task_build_info():
import json
config = get_make_config()
out_dir = os.path.join("output/debug", config.get_mod_dir())
with open(config.get_path(os.path.join(out_dir, "mod.info")), "w") as info_file:
info = dict(config.get_value("global.info", fallback={"name": "No was provided"}))
if "icon" in info:
del info["icon"]
info_file.write(json.dumps(info, indent=" " * 4))
icon_path = config.get_value("global.info.icon")
if icon_path is not None:
copy_file(config.get_path(icon_path, True), config.get_path(os.path.join(out_dir, "mod_icon.png")))
return 0
def run(self):
"""The actual thread code"""
self._running = True
self._started = True
self._log.debug('Starting %s ' % self.name)
while True:
# Assume USB flash drive is powered up and mounted.
# If necessary, create the USB flash destination dir.
dest_dir = self._get_dest_dir(self._dest_file_name)
utils.make_dirs(dest_dir, self._log)
comp_ratio = 1.0
if self._compress:
compressed_path = self._src_path + '.gz'
if not self._compress_file(self._src_path, compressed_path):
self._log.error('Error: file compression failed on %s' % \
self._src_path)
utils.delete_file(self._src_path, self._log)
utils.delete_file(compressed_path, self._log)
return False
orig_bytes = float(utils.get_file_size(self._src_path))
comp_bytes = float(utils.get_file_size(compressed_path))
comp_ratio = orig_bytes/comp_bytes
from_path = compressed_path
to_path = ''.join((dest_dir, '/', self._dest_file_name, '.gz'))
else:
from_path = self._src_path
to_path = ''.join((dest_dir, '/', self._dest_file_name))
self._log.info('Storing %s' % to_path)
self._log.info(' Compression ratio was %.2f to 1' % comp_ratio)
try:
utils.copy_file(from_path, to_path, self._log)
except Exception:
self._log.info('Error: write to %s failed' % to_path)
# Delete the temp files
try:
utils.delete_file(self._src_path, self._log)
except Exception:
self._log.info('Error: could not delete %s' % self._src_path)
if self._compress:
try:
utils.delete_file(compressed_path, self._log)
except Exception:
self._log.error('Could not delete %s' % compressed_path)
break
self._running = False
if self._exit_callback:
self._exit_callback(self)
self._log.debug('Exiting %s ' % self.name)
def restore(self, filename="", silent=False):
'''restore skin settings from file'''
if not filename:
filename = self.get_restorefilename()
progressdialog = None
if not silent:
progressdialog = xbmcgui.DialogProgress(
self.addon.getLocalizedString(32006))
progressdialog.create(self.addon.getLocalizedString(32007))
if filename and xbmcvfs.exists(filename):
# create temp path
temp_path = self.create_temp()
if not filename.endswith("zip"):
# assume that passed filename is actually a skinsettings file
skinsettingsfile = filename
else:
# copy zip to temp directory and unzip
skinsettingsfile = temp_path + "guisettings.txt"
if progressdialog:
progressdialog.update(0, "unpacking backup...")
zip_temp = u'%sskinbackup-%s.zip' % (
ADDON_DATA, datetime.now().strftime('%Y-%m-%d-%H-%M'))
copy_file(filename, zip_temp, True)
unzip_fromfile(zip_temp, temp_path)
delete_file(zip_temp)
# copy skinshortcuts preferences
self.restore_skinshortcuts(temp_path)
# restore any custom skin images or themes
for directory in ["custom_images/", "themes/"]:
custom_images_folder = u"special://profile/addon_data/%s/%s" % (
xbmc.getSkinDir(), directory)
custom_images_folder_temp = temp_path + directory
if xbmcvfs.exists(custom_images_folder_temp):
for file in xbmcvfs.listdir(
custom_images_folder_temp)[1]:
xbmcvfs.copy(custom_images_folder_temp + file,
custom_images_folder + file)
# restore guisettings
if xbmcvfs.exists(skinsettingsfile):
self.restore_guisettings(skinsettingsfile, progressdialog)
# cleanup temp
recursive_delete_dir(temp_path)
progressdialog.close()
if not silent:
xbmcgui.Dialog().ok(self.addon.getLocalizedString(32006),
self.addon.getLocalizedString(32009))
def copy_additionals(source, destination):
global root_files
files = os.listdir(source)
for f in files:
if f in root_files:
continue
src = os.path.join(source, f)
dest = os.path.join(destination, "src", "assets", "root")
if (os.path.isfile(src)):
copy_file(src, os.path.join(dest, f))
elif (os.path.isdir(src)):
copy_file(src, os.path.join(dest, f))
def task_build_scripts():
import json
config = get_make_config()
with open(config.get_path("output/mod.info"), "w") as info_file:
info = dict(config.get_value("global.info",
fallback={"name": "No was provided"}))
if "icon" in info:
del info["icon"]
info_file.write(json.dumps(info, indent=" " * 4))
icon_path = config.get_value("global.info.icon")
if icon_path is not None:
copy_file(config.get_path(icon_path),
config.get_path("output/mod_icon.png"))
return 0
def build_snpeff_db(reference, gff, snpeff_config, snpeff_db):
"""
build SnpEff database for a reference genome
:param: snpeff_config
:param snpeff_db:
:param reference:
:param gff:
:return:
"""
# locate the executable
snpeff = find_executable(['snpEff'])
snpeff_db = os.path.abspath(snpeff_db)
# create SnpEff database
prefix = os.path.join(os.path.abspath(os.path.dirname(reference)),
os.path.splitext(os.path.basename(reference))[0])
index_base = os.path.basename(prefix)
snpeff_data_dir = os.path.join(snpeff_db, 'data')
snpeff_genes_dir = os.path.join(snpeff_data_dir, index_base)
mkdir(snpeff_data_dir)
mkdir(snpeff_genes_dir)
# copy the files
copy_file(src=gff, dest=os.path.join(snpeff_genes_dir, 'genes.gff'))
copy_file(src=reference,
dest=os.path.join(snpeff_genes_dir, 'sequences.fa'))
# Add a genome to the configuration file
snpeff_config = os.path.join(snpeff_db, 'snpeff.config')
with open(snpeff_config, 'w') as f_obj:
f_obj.write('{}.genome : {}\n'.format(index_base, index_base))
# check if db exists and build if not
db_bin = os.path.join(snpeff_genes_dir, 'snpEffectPredictor.bin')
if os.path.exists(db_bin):
logging.critical("SnpEff database exist for {}".format(index_base))
else:
# build db
call = [
"{} build -config {} -dataDir {} -gff3 -v {}".format(
snpeff, snpeff_config, snpeff_data_dir, index_base)
]
cmd = " ".join(call)
logging.info("building SnpEFF database: {}".format(gff))
run_shell_command(cmd=cmd, raise_errors=False, extra_env=None)
return snpeff_config, snpeff_data_dir
def restore_skinshortcuts(temp_path):
'''restore skinshortcuts files'''
source_path = temp_path + u"skinshortcuts/"
if xbmcvfs.exists(source_path):
dest_path = u'special://profile/addon_data/script.skinshortcuts/'
for filename in xbmcvfs.listdir(source_path)[1]:
filename = filename.decode("utf-8")
sourcefile = source_path + filename
destfile = dest_path + filename
if filename == "SKINPROPERTIES.properties":
destfile = dest_path + filename.replace(
"SKINPROPERTIES", xbmc.getSkinDir())
elif xbmc.getCondVisibility(
"SubString(Skin.String(skinshortcuts-sharedmenu),false)"
):
destfile = "%s-" % (xbmc.getSkinDir())
copy_file(sourcefile, destfile)
def test(self, testing_data_dir, result_dir, test_saver, n_cores, num_test=False):
print('Start Testing')
tmp_list = search_wav(testing_data_dir)
if num_test:
test_list = np.random.choice(tmp_list, num_test)
else:
test_list = tmp_list
print('All testing data number:', len(test_list))
REG_dir = join(result_dir, 'REG')
Noisy_write_dir = join(result_dir, 'Source')
Clean_write_dir = join(result_dir, 'Target')
if not os.path.exists(result_dir):
os.makedirs(result_dir)
os.makedirs(REG_dir)
os.makedirs(Noisy_write_dir)
os.makedirs(Clean_write_dir)
with tf.Session(config=self.config) as sess:
self.saver.restore(sess=sess, save_path=test_saver)
for file in tqdm(test_list):
hop_length = 256
file_name = file.split('/')[-1]
try:
snr, noise_name, clean_name1, clean_neme2 = file.split(
'/')[-1].split('_')
clean_file = join(testing_data_dir, '_'.join(
['0dB', 'n0', clean_name1, clean_neme2]))
noisy_file = file
except:
snr, noise_name, clean_name = file.split(
'/')[-1].split('_')
noisy_file = join(testing_data_dir, file_name)
REG_file = join(REG_dir, file_name)
Noisy_file = join(Noisy_write_dir, file_name)
Clean_file = join(Clean_write_dir, file_name)
X_in_seq = wav2spec(noisy_file, sr=16000,
forward_backward=True, SEQUENCE=False, norm=True, hop_length=hop_length)
re_reg = sess.run([self.reg_layer],
feed_dict={self.x_noisy: X_in_seq})[:][0]
spec2wav(noisy_file, 16000, REG_file,
re_reg, hop_length=hop_length)
copy_file(noisy_file, Noisy_file)
copy_file(clean_file, Clean_file)
def calc_labels_avg(events_id, tmin, inverse_method='dSPM', do_plot=False):
d = np.load(op.join(LOCAL_ROOT_DIR, 'fsaverage_labels_indices.npz'))
labels_vertices, labels_names = d['labels_vertices'], d['labels_names']
if do_plot:
plt.close('all')
plt.figure()
res_fol = op.join(LOCAL_ROOT_DIR, 'permutation_ttest_results')
for cond_id, cond_name in enumerate(events_id.keys()):
for patient in get_patients():
blender_fol = blender_template.format(patient=patient, cond_name=cond_name)
results_file_name = op.join(res_fol, '{}_{}_{}.npz'.format(patient, cond_name, inverse_method))
clusters_file_name = op.join(res_fol, '{}_{}_{}_clusters.npy'.format(patient, cond_name, inverse_method))
if op.isfile(results_file_name) and op.isfile(clusters_file_name):
print('{}, {}'.format(patient, cond_name))
clusters = np.load(clusters_file_name)
ttest_res = np.load(results_file_name)
for data, data_name in zip([ttest_res['T_obs'].T, clusters], ['ttest_res', 'clusters']):
fsave_vertices = utils.fsaverage_vertices()
stc = _make_stc(data, fsave_vertices, tmin=tmin, tstep=tstep, subject='fsaverage')
labels_data = np.zeros((len(labels_vertices), stc.data.shape[1], 2))
for ind, (vertidx, label_name) in enumerate(zip(labels_vertices, labels_names)):
if vertidx is not None:
labels_data[ind] = utils.get_max_min(stc.data[vertidx, :])
if do_plot:
plt.plot(labels_data[ind, :, 0], label='{} p<c'.format(label_name))
plt.plot(labels_data[ind, :, 1], label='{} p>c'.format(label_name))
for hemi in ['rh', 'lh']:
indices = [ind for ind, l in enumerate(labels_names) if hemi in l]
labels = [str(l) for l in labels_names if hemi in l]
np.savez(op.join(blender_fol, 'labels_data_{}_{}.npz'.format(hemi, data_name)),
data=labels_data[indices], names=labels, conditions=['p<c', 'p>c'])
if do_plot:
plt.legend()
plt.xlabel('time (ms)')
plt.title('{} {}'.format(patient, cond_name))
plt.show()
print('show!')
# Make clusters to be the default files for blender
for hemi in ['rh', 'lh']:
utils.copy_file(op.join(blender_fol, 'labels_data_{}_clusters.npz'.format(hemi)),
op.join(blender_fol, 'labels_data_{}.npz'.format(hemi)))
def deploy_repo_attempt(self, deploy_path):
LOG.info(utils.configure_env(self.base_path))
manage_files = utils.search_file(deploy_path, 'manage.py')
if not manage_files:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
manage_paths = [os.path.dirname(manage_file) for manage_file in manage_files]
base_dir = next(name for name in manage_paths if 'lib/python2.7/site-packages/' not in name)
manage_path = next(name for name in manage_paths if name.startswith(base_dir))
LOG.info('manage.py path: {}'.format(manage_path))
with open(os.path.join(manage_path, 'manage.py'), 'r') as manage_file:
s = re.search('os.environ.setdefault\("DJANGO_SETTINGS_MODULE", "(.*)"\)', manage_file.read())
if s:
setting_path = s.group(1)
else:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
setting_path = setting_path.replace('.', '/')
if os.path.isdir(os.path.join(manage_path, setting_path)):
setting_path = os.path.join(manage_path, setting_path)
for setting_file in sorted(os.listdir(setting_path)):
if os.path.isfile(os.path.join(setting_path, setting_file)):
setting_path = os.path.join(setting_path, setting_file)
break
self.setting_path = setting_path
elif os.path.isfile(os.path.join(manage_path, setting_path + '.py')):
setting_path = os.path.join(manage_path, setting_path + '.py')
self.setting_path = setting_path
else:
for candidate_setting_files in utils.search_file_regex(deploy_path, '^settings.*\.py$'):
setting_path = os.path.join(manage_path, setting_path + '.py')
utils.copy_file(candidate_setting_files, setting_path)
self.setting_path = setting_path
break
if self.setting_path == None:
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
LOG.info('setting.py path: {}'.format(setting_path))
requirement_files = utils.search_file(deploy_path, 'requirements.txt')
if requirement_files:
LOG.info('requirements.txt path: {}'.format(requirement_files))
return self.try_deploy(manage_path, requirement_files)
def create_preseed_diskimage(self):
source = join_path(self.info.data_dir, 'preseed.disk')
template = read_file(source)
password = md5_password(self.info.password)
dic = dict(
timezone = self.info.timezone,
password = password,
keyboard_variant = self.info.keyboard_variant,
keyboard_layout = self.info.keyboard_layout,
locale = self.info.locale,
user_full_name = self.info.user_full_name,
username = self.info.username)
for k,v in dic.items():
k = "$(%s)" % k
template = template.replace(k, v)
preseed_file = join_path(self.info.install_dir, "preseed.cfg")
write_file(preseed_file, template)
source = join_path(self.info.data_dir, "wubildr-disk.cfg")
target = join_path(self.info.install_dir, "wubildr-disk.cfg")
copy_file(source, target)
def test_6_extensions_directory_autoload(self):
utils.copy_file(test_base.ARGS.build + "/osquery/example_extension.ext",
test_base.CONFIG_DIR)
loader = test_base.Autoloader([test_base.CONFIG_DIR])
daemon = self._run_daemon({
"disable_watchdog": True,
"extensions_timeout": EXTENSION_TIMEOUT,
"extensions_autoload": loader.path,
})
self.assertTrue(daemon.isAlive())
# Get a python-based thrift client
client = test_base.EXClient(daemon.options["extensions_socket"])
self.assertTrue(client.open(timeout=EXTENSION_TIMEOUT))
em = client.getEM()
# The waiting extension should have connected to the daemon.
result = test_base.expect(em.extensions, 1)
self.assertEqual(len(result), 1)
client.close()
daemon.kill(True)
def build_files(root=u'.', dest=u'_site', pattern=u'**/*.html',
exclude=u'_*/**', watch=False, force=False):
try:
os.stat(os.path.join(root, 'index.html'))
except OSError:
if not force:
msg = "Oops, we can't find an index.html in the source folder.\n"+\
"If you want to build this folder anyway, use the --force\n"+\
"option."
print(msg)
sys.exit(1)
print("Building site from '{0}' into '{1}'".format(root, dest))
exclude = exclude or os.path.join(dest, u'**')
for filename in utils.walk_folder(root or '.'):
included = utils.matches_pattern(pattern, filename)
excluded = utils.matches_pattern(exclude, filename)
destfile = os.path.join(dest, filename)
if included and not excluded:
build_file(filename, destfile, root=root)
elif not excluded:
filepath = os.path.join(root, filename)
destpath = os.path.join(dest, filename)
utils.copy_file(filepath, destpath)
if watch:
observer = _watch(root=root,
dest=dest,
pattern=pattern,
exclude=exclude)
if not observer:
return
try:
while True:
time.sleep(1)
except KeyboardInterrupt:
observer.stop()
observer.join()
def deploy_repo_attempt(self, deploy_path):
rake_files = utils.search_file(deploy_path, 'Rakefile')
if not rake_files:
LOG.error('No rakefile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
rakefile_paths = [os.path.dirname(rake_file) for rake_file in rake_files]
gem_files = utils.search_file(deploy_path, 'Gemfile')
if not gem_files:
LOG.error('No gemfile found!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
gemfile_paths = [os.path.dirname(gem_file) for gem_file in gem_files]
base_dirs = sorted(set.intersection(set(rakefile_paths), set(gemfile_paths)))
if not base_dirs:
LOG.error('Can not find base directory!')
return ATTEMPT_STATUS_MISSING_REQUIRED_FILES
base_dir = next(iter(base_dirs))
config_files = utils.search_file_regex(os.path.join(base_dir, 'config'), '.*yml.*')
for config_file in config_files:
if '.example' in config_file:
new_config_file = config_file.replace('.example', '')
utils.copy_file(config_file, new_config_file)
elif '/example' in config_file:
new_config_file = config_file.replace('/example', '')
utils.copy_file(config_file, new_config_file)
elif '-sample' in config_file:
new_config_file = config_file.replace('-sample', '')
utils.copy_file(config_file, new_config_file)
elif '.tmpl' in config_file:
new_config_file = config_file.replace('.tmpl', '')
utils.copy_file(config_file, new_config_file)
self.setting_path = base_dir
return self.try_deploy(base_dir)
def handle_file(self, source_path, dest_path):
copy_file(source_path, dest_path)
print 'Copied {0} to {1}'.format(source_path, dest_path)
def create_preseed_cdboot(self):
source = join_path(self.info.data_dir, 'preseed.cdboot')
target = join_path(self.info.custominstall, "preseed.cfg")
copy_file(source, target)
def setUp(self):
copy_file(
THIS_TEST_DIR + "/Biblioteca.gbs",
TEST_DIR + "/examples/Biblioteca.gbs"
)
def build_fs_tree(src_path, dst_path, lib_path):
"""Build FS tree"""
# Rdf imports
sys.path.append(lib_path)
from rdf import RDFReader
from utils import copy_file
print "Build filesystem data in %s from %s" % (src_path, dst_path)
sys_encoding = sys.getfilesystemencoding()
# Store rdf files
# List of dictionnary {'field': ..., 'uid': ...}
rdf_files = []
# Walk into filesystem
for root, dirs, files in os.walk(src_path):
if root == src_path:
# Loop on files
for item in files:
match = SEARCH_RDF_RE.match(item)
if match is None:
continue
# Get field name and content uid
uid = match.group('uid')
field = match.group('field')
rdf_files.append({'uid': uid, 'field': field})
# Processing collected rdf files
print "Processing %s rdf files" % str(len(rdf_files))
file_paths = []
for rdf_file in rdf_files:
uid = rdf_file['uid']
field = rdf_file['field']
# Get RDF file
rdf_filename = '%s_%s.rdf' % (uid, field)
rdf_path = os.path.join(src_path, rdf_filename)
rdf_file = StringIO()
rdf_text = ''
try:
copy_file(rdf_path, rdf_file)
rdf_file.seek(0)
rdf_text = rdf_file.getvalue()
finally:
rdf_file.close()
# Read RDF properties
try:
rdf_reader = RDFReader(rdf_text)
except:
try:
# XXX known bug to fix
rdf_text = rdf_text.replace('&', '&')
rdf_reader = RDFReader(rdf_text)
except:
print rdf_path
print rdf_text
raise
field_url = rdf_reader.getFieldUrl()
field_url = field_url.encode(sys_encoding, 'replace')
# Create tree directories
content_path_array = field_url.split('/')[:-2]
content_path = dst_path
for content_dir in content_path_array:
content_path = os.path.join(content_path, content_dir)
if os.path.exists(content_path):
continue
print "Create path: %s" % content_path
os.mkdir(content_path)
# Get source file
src_filename = '%s_%s' % (uid, field)
src_file_path = os.path.join(src_path, src_filename)
if not os.path.exists(src_file_path):
print "Source file doesn't exist, we continue: %s" % src_file_path
continue
# Get destination file
dst_filename = field
dst_filenames = rdf_reader.getFieldProperty('fss:filename')
if dst_filenames:
dst_filename = dst_filenames[0]
if not dst_filename:
dst_filename = field
else:
dst_filename = dst_filename.encode(sys_encoding, 'replace')
dst_file_path = os.path.join(content_path, dst_filename)
# In some cases, you can have a content having 2 fss fields with
# 2 files with the same name
orig_dst_filename = dst_filename
dst_file_path_ok = False
index = 0
while not dst_file_path_ok:
if dst_file_path not in file_paths:
dst_file_path_ok = True
file_paths.append(dst_file_path)
else:
index += 1
dst_filename = '%s-%s' % (str(index), orig_dst_filename)
print dst_filename
dst_file_path = os.path.join(content_path, dst_filename)
print "Create file: %s" % dst_file_path
copy_file(src_file_path, dst_file_path)
print "Create RDF file: %s.rdf" % dst_file_path
copy_file(rdf_path, dst_file_path + '.rdf')
print "Filesystem data built complete"
