def addpackage(sitedir, pthfile, known_dirs=None):
"""
Wrapper for site.addpackage
Try and work out which directories are added by
the .pth and add them to the known_dirs set
"""
known_dirs = set(known_dirs or [])
with open(join(sitedir, pthfile)) as f:
for n, line in enumerate(f):
if line.startswith("#"):
continue
line = line.rstrip()
if line:
if line.startswith(("import ", "import\t")):
exec (line, globals(), locals())
continue
else:
p_rel = join(sitedir, line)
p_abs = abspath(line)
if isdir(p_rel):
os.environ['PATH'] += env_t(os.pathsep + p_rel)
sys.path.append(p_rel)
added_dirs.add(p_rel)
elif isdir(p_abs):
os.environ['PATH'] += env_t(os.pathsep + p_abs)
sys.path.append(p_abs)
added_dirs.add(p_abs)
if isfile(pthfile):
site.addpackage(sitedir, pthfile, known_dirs)
else:
logging.debug("pth file '%s' not found")
def del_prefix_2_subfolders(self, dir_path, prefix='tmp_'):
'''This function rename all the folders inside a path.
Here we remove the prefix to the subfolders.For example:
current folder
my_folder:
tmp_10
tmp_20
tmp_30
The result will be
my_folder:
1
2
3
'''
print('\n Rename all subfolders inside: {}'.format(dir_path))
prefix_len = len(prefix)
for f in listdir(dir_path):
src = join(dir_path, f)
if isdir(src):
try:
print(src)
if f.startswith(prefix):
new_file_name = f[prefix_len:]
tar = join(dir_path, new_file_name)
os.rename(src, tar)
except Exception as e:
print('error: {}'.format(e))
def rename_subfolders(self, dir_path, delta):
'''This function rename all the folders inside a path.
The folders names are integers. for example:
my_folder:
1
2
3
The new names will have a prefix "tmp_" and the integer number will increase summing delta.
If delta = 10. So the result will be
my_folder:
tmp_10
tmp_20
tmp_30
'''
print('\n Rename all subfolders inside: {}'.format(dir_path))
for f in listdir(dir_path):
src = join(dir_path, f)
if isdir(src):
try:
print(src)
n = str(int(f) + delta)
tar = join(dir_path, 'tmp_' + n)
os.rename(src, tar)
except Exception as e:
print('error: {}'.format(e))
def get_subfolders(self, dir_path):
print('\n List folder: {}'.format(dir_path))
for file_name in listdir(dir_path):
file_path = join(dir_path, file_name)
if isdir(file_path):
print(file_path)
def get_package_dir():
"""
Get the directory in which packages are installed if not overridden on project level.
"""
envpath = getenv('NOTEX_PACKAGE_DIR', '')
if isdir(envpath):
return envpath
defpath = user_data_dir('ntp')
if not isdir(defpath):
stderr.write((
'package path not set in NOTEX_PACKAGE_DIR and default location does not exist at "{0:s}"; '
+
'it will be created (this is normal if you\'re running for the first time)'
).format(defpath))
makedirs(defpath)
return defpath
def clean_log_history(dir):
for f1 in os.listdir(dir):
path = os.path.join(dir, f1)
if isdir(path):
clean_log_history(path)
else:
os.remove(path)
def load_music_lists(music_path):
music_list_dir = os.listdir(music_path)
return [
MusicLoader.list_all_files(join(music_path, music_list))
for music_list in music_list_dir
if isdir(join(music_path, music_list))
]
def add_resource(mt_file, ref, cache):
"""Add a resources entry, downloading the intuiting the file, replacing entries with
the same reference"""
from metatab.util import enumerate_contents
if isinstance(mt_file, MetatabDoc):
doc = mt_file
else:
doc = MetatabDoc(mt_file)
if not 'Resources' in doc:
doc.new_section('Resources')
doc['Resources'].args = [e for e in set(doc['Resources'].args + ['Name', 'StartLine', 'HeaderLines', 'Encoding']) if
e]
seen_names = set()
if isdir(ref):
for f in find_files(ref, DATA_FORMATS):
if f.endswith(DEFAULT_METATAB_FILE):
continue
if doc.find_first('Root.Datafile', value=f):
prt("Datafile exists for '{}', ignoring".format(f))
else:
add_single_resource(doc, f, cache=cache, seen_names=seen_names)
else:
for c in enumerate_contents(ref, cache=cache, callback=prt):
add_single_resource(doc, c.rebuild_url(), cache=cache, seen_names=seen_names)
write_doc(doc, mt_file)
def setUp(self):
self.testConfPath = os.path.join(os.environ["HOME"], ".cpc/test")
if isdir(self.testConfPath):
shutil.rmtree(self.testConfPath)
self.serverConfs = dict()
os.makedirs(self.testConfPath)
def setUp(self):
self.testConfPath = os.path.join(os.environ["HOME"], ".cpc/test")
if isdir(self.testConfPath):
shutil.rmtree(self.testConfPath)
self.serverConfs = dict()
os.makedirs(self.testConfPath)
def getPaths(basePath, pathsVector):
thisDirPaths = [basePath + "/" + x for x in listdir(basePath) if isdir(basePath + "/" + x)]
for path in thisDirPaths:
pathsVector.append(path)
getPaths(path, pathsVector)
return pathsVector
def do_process(self, request, response, abspath):
if isdir(abspath):
if(not request.path.endswith('/')):
response.redirect(request.path + '/')
else:
self.process_dir(request, response, abspath)
else:
self.process_file(request, response, abspath)
def ensure_directory(directory):
"""
Create the directory if it does not exist
:param str directory: Directory to create
:return None:
"""
if not isdir(directory):
makedirs(directory)
def listdir(path):
listfile=[]
if isdir(path):
lf =os.listdir(path)
for i in lf:
listfile.append(listdir(os.path.join(path,i)))
listfile.append(path)
return listfile
def getPaths(basePath, pathsVector):
thisDirPaths = [basePath + "/" + x for x in listdir(basePath) if isdir(basePath + "/" + x)]
for path in thisDirPaths:
pathsVector.append(path)
getPaths(path, pathsVector)
return pathsVector
def delete_cache():
for f in os.listdir(SERIAL_DIR):
path = os.path.join(SERIAL_DIR, f)
if isdir(path):
shutil.rmtree(path)
else:
os.remove(path)
print("Serialzed data folder purged!")
def index_image_folder(folder_path):
for f in listdir(folder_path):
path = join(folder_path, f)
if isfile(path):
is_image = any(path.endswith("." + ext) for ext in config.IMAGE_EXTENSIONS)
if is_image: # check extension, only index images
index_image(folder_path=folder_path, file_name=f)
elif isdir(path):
index_image_folder(path)
def __init__(self):
assert isinstance(self.dumpRequestsSize, int), 'Invalid dump size %s' % self.dumpRequestsSize
assert isinstance(self.dumpRequestsPath, str), 'Invalid dump path %s' % self.dumpRequestsPath
self.dumpRequestsPath = normOSPath(self.dumpRequestsPath)
if not os.path.exists(self.dumpRequestsPath): os.makedirs(self.dumpRequestsPath)
assert isdir(self.dumpRequestsPath) and os.access(self.dumpRequestsPath, os.W_OK), \
'Unable to access the dump directory %s' % self.dumpRequestsPath
super().__init__()
self._count = 0
def conan_builds(self, conan_reference):
""" Returns a list of package ids from a local cache build folder """
assert isinstance(conan_reference, ConanFileReference)
builds_dir = self.builds(conan_reference)
try:
builds = [dirname for dirname in os.listdir(builds_dir)
if isdir(os.path.join(builds_dir, dirname))]
except: # if there isn't any package folder
builds = []
return builds
def conan_packages(self, conan_reference):
""" Returns a list of package_id from a local cache package folder """
assert isinstance(conan_reference, ConanFileReference)
packages_dir = self.packages(conan_reference)
try:
packages = [dirname for dirname in os.listdir(packages_dir)
if isdir(os.path.join(packages_dir, dirname))]
except: # if there isn't any package folder
packages = []
return packages
def raise_error_if_no_such_directory(directory):
"""
Raise a RuntimeError if the directory does not exist
:param str directory: Directory to check
:return None:
"""
if not isdir(directory):
raise RuntimeError(
"Directory {} does not exists! Perhaps you meant to specify a "
"different directory. Can't start the Vagrant.".format(directory))
def index_image_folder(folder_path):
for f in listdir(folder_path):
path = join(folder_path, f)
if isfile(path):
is_image = any(
path.endswith("." + ext) for ext in config.IMAGE_EXTENSIONS)
if is_image: # check extension, only index images
index_image(folder_path=folder_path, file_name=f)
elif isdir(path):
index_image_folder(path)
def conan_packages(self, conan_reference):
""" Returns a list of package_id from a local cache package folder """
assert isinstance(conan_reference, ConanFileReference)
packages_dir = self.packages(conan_reference)
try:
packages = [dirname for dirname in os.listdir(packages_dir)
if isdir(os.path.join(packages_dir, dirname))]
except: # if there isn't any package folder
packages = []
return packages
def conan_builds(self, conan_reference):
""" Returns a list of package ids from a local cache build folder """
assert isinstance(conan_reference, ConanFileReference)
builds_dir = self.builds(conan_reference)
try:
builds = [dirname for dirname in os.listdir(builds_dir)
if isdir(os.path.join(builds_dir, dirname))]
except: # if there isn't any package folder
builds = []
return builds
def ignored(path, only_hidden=False):
"""if path is in the ignorelist return True
ignore list includes hidden files and git or annex maintained folders
when only_hidden set, only ignores hidden files and folders not git or annex
maintained folders
"""
if isdir(opj(path, ".git")) and not only_hidden:
return True
return '.' == leaf_name(path)[0] or leaf_name(path) == 'index.html'
def __init__(self):
assert isinstance(self.locale_dir_path, str), 'Invalid locale directory %s' % self.locale_dir_path
assert isinstance(self.catalog_config, dict), 'Invalid catalog configurations %s' % self.catalog_config
assert isinstance(self.write_po_config, dict), 'Invalid write PO configurations %s' % self.write_po_config
assert isinstance(self.messageService, IMessageService), 'Invalid message service %s' % self.messageService
assert isinstance(self.sourceService, ISourceService), 'Invalid source file service %s' % self.sourceService
if not os.path.exists(self.locale_dir_path): os.makedirs(self.locale_dir_path)
if not isdir(self.locale_dir_path) or not os.access(self.locale_dir_path, os.W_OK):
raise IOError('Unable to access the locale directory %s' % self.locale_dir_path)
def ignored(path, only_hidden=False):
"""if path is in the ignorelist return True
ignore list includes hidden files and git or annex maintained folders
when only_hidden set, only ignores hidden files and folders not git or annex
maintained folders
"""
if isdir(opj(path, ".git")) and not only_hidden:
return True
return '.' == leaf_name(path)[0] or leaf_name(path) == 'index.html'
def raise_error_if_no_such_directory(directory):
"""
Raise a RuntimeError if the directory does not exist
:param str directory: Directory to check
:return None:
"""
if not isdir(directory):
raise RuntimeError(
"Directory {} does not exists! Perhaps you meant to specify a "
"different directory. Can't start the Vagrant.".format(directory)
)
def init_path():
"""
Add any new modules that are directories to the PATH
"""
sitedirs = getsyssitepackages()
for sitedir in sitedirs:
env_path = os.environ['PATH'].split(os.pathsep)
for module in allowed_modules:
p = join(sitedir, module)
if isdir(p) and not p in env_path:
os.environ['PATH'] += env_t(os.pathsep + p)
def init_path():
"""
Add any new modules that are directories to the PATH
"""
sitedirs = getsyssitepackages()
for sitedir in sitedirs:
env_path = os.environ['PATH'].split(os.pathsep)
for module in allowed_modules:
p = join(sitedir, module)
if isdir(p) and not p in env_path:
os.environ['PATH'] += env_t(os.pathsep + p)
def process_transcoding((flac_file, flac_root_path, mp3_target_path)):
try:
target_mp3_file = get_mp3_filename(mp3_target_path, flac_root_path, flac_file)
if not isdir(dirname(target_mp3_file)):
try:
os.makedirs(dirname(target_mp3_file))
except OSError:
pass # other thread might have been faster
transcode(flac_file, target_mp3_file)
except Exception as e:
LOGGER.error('error during the transcoding of %r : %s' % (flac_file, e))
def scanDir(l, root, folder=None):
if not folder is None:
root = os.path.join(root, folder)
for f in os.listdir(root):
path = os.path.join(root, f)
if isdir(path):
scanDir(l, root, f)
else:
l.append({"filename": f,
"folder": folder,
"from_root": None if root == VIEW.showLocation else os.path.relpath(root, VIEW.showLocation)})
def __scan_dlls(self):
# Scan DLLs separately since we need to build them as their own thing
dll_dirs = [dir for dir in glob.glob("src/dlls/*") if isdir(dir)]
to_compile: "set[str]" = set()
for dir in dll_dirs:
dir_parts = dir.split("/")
number = dir_parts[-1]
# Skip if this DLL is configured to use the original DLL instead of recompiling
if not self.__should_compile_dll(Path(dir), number):
continue
c_paths = [
Path(path)
for path in glob.glob(f"{dir}/**/*.c", recursive=True)
]
asm_paths = [
Path(path)
for path in glob.glob(f"{dir}/**/*.s", recursive=True)
]
asm_paths.extend([
Path(path) for path in glob.glob(
f"asm/nonmatchings/dlls/{number}/data/*.s")
])
files: "list[BuildFile]" = []
for src_path in c_paths:
obj_path = self.__make_obj_path(src_path)
opt = self.__get_optimization_level(src_path)
files.append(
BuildFile(str(src_path), obj_path, BuildFileType.C, opt))
for src_path in asm_paths:
obj_path = self.__make_obj_path(src_path)
files.append(
BuildFile(str(src_path), obj_path, BuildFileType.ASM))
self.dlls.append(DLL(number, dir, files))
to_compile.add(number)
# Scan for leftover DLLs that haven't been decompiled yet
paths = [
Path(path)
for path in glob.glob("bin/assets/dlls/*.dll", recursive=True)
]
for src_path in paths:
number = src_path.name.split(".")[0]
if number in to_compile:
continue
obj_path = f"$BUILD_DIR/{src_path.with_suffix('.dll')}"
self.leftover_dlls.append(
BuildFile(str(src_path), obj_path, BuildFileType.BIN))
def synchronizeURIToDir(path, dirPath):
'''
Publishes the entire contents from the URI path to the provided directory path.
@param path: string
The path to a resource: a file system path, a ZIP path
@param dirPath: string
The directory path to synchronize with.
'''
assert isinstance(path, str) and path, 'Invalid content path %s' % path
assert isinstance(dirPath, str), 'Invalid directory path value %s' % dirPath
if not isdir(path):
# not a directory, see if it's a entry in a zip file
zipFilePath, inDirPath = getZipFilePath(path)
zipFile = ZipFile(zipFilePath)
if not inDirPath.endswith(ZIPSEP): inDirPath = inDirPath + ZIPSEP
tmpDir = TemporaryDirectory()
lenPath, zipTime = len(inDirPath), datetime.fromtimestamp(stat(zipFilePath).st_mtime)
for zipInfo in zipFile.filelist:
assert isinstance(zipInfo, ZipInfo), 'Invalid zip info %s' % zipInfo
if zipInfo.filename.startswith(inDirPath):
if zipInfo.filename[0] == '/': dest = zipInfo.filename[1:]
else: dest = zipInfo.filename
dest = normpath(join(dirPath, dest[lenPath:]))
if exists(dest) and zipTime <= datetime.fromtimestamp(stat(dest).st_mtime): continue
destDir = dirname(dest)
if not exists(destDir): makedirs(destDir)
zipFile.extract(zipInfo.filename, tmpDir.name)
move(join(tmpDir.name, normOSPath(zipInfo.filename)), dest)
if zipInfo.filename.endswith('.exe'): os.chmod(dest, stat(dest).st_mode | S_IEXEC)
return
path = normpath(path)
assert os.access(path, os.R_OK), 'Unable to read the directory path %s' % path
lenPath = len(path) + 1
for root, _dirs, files in os.walk(path):
for file in files:
src, dest = join(root, file), join(dirPath, root[lenPath:], file)
if exists(dest) and \
datetime.fromtimestamp(stat(src).st_mtime) <= datetime.fromtimestamp(stat(dest).st_mtime): continue
destDir = dirname(dest)
if not exists(destDir): makedirs(destDir)
copy(src, dest)
if file.endswith('.exe'): os.chmod(dest, stat(dest).st_mode | S_IEXEC)
def __init__(self):
assert isinstance(self.dumpRequestsSize,
int), 'Invalid dump size %s' % self.dumpRequestsSize
assert isinstance(self.dumpRequestsPath,
str), 'Invalid dump path %s' % self.dumpRequestsPath
self.dumpRequestsPath = normOSPath(self.dumpRequestsPath)
if not os.path.exists(self.dumpRequestsPath):
os.makedirs(self.dumpRequestsPath)
assert isdir(self.dumpRequestsPath) and os.access(self.dumpRequestsPath, os.W_OK), \
'Unable to access the dump directory %s' % self.dumpRequestsPath
super().__init__()
self._count = 0
def initList(self):
if not self.location:
return
self.table.clearContents()
self.list.clear()
for f in os.listdir(self.location):
dir = os.path.join(str(self.location), f)
if isdir(dir):
item = QtGui.QListWidgetItem(self.list)
item.setText(f)
self.list.sortItems()
def getType(self, path):
"""
Metoda vraca tip fajla koji se nalazi na zadatoj putanji
Args:
path putanja do fajla
"""
if isdir(path):
return "FOLDER "
if isfile(path):
return "FILE "
else:
return "INVALID"
def listSubfolders(folder, sort=True, shuffle=False, seed=None):
'''
:param sort: if true, sort subfolders by name
:param shuffle: if true, shuffle subfolders in random order
:return: a list of full paths to subfolders of given folder.
'''
subfolders = [
join(folder, f) for f in listdir(folder) if isdir(join(folder, f))
]
if sort or shuffle: subfolders.sort()
if shuffle:
if seed: random.seed(seed)
random.shuffle(subfolders)
return subfolders
def load_specs():
bad_specs = set()
last_error = None
for fn in spec_files():
logger.debug("load spec: %s", fn)
if fn in bad_specs:
# Don't try and load the same bad spec twice
continue
try:
spec = open_spec(open(fn))
for module in spec['modules']:
logger.debug("allow module: %s", module)
allowed_modules.add(module)
for path_name in spec.get('extra_paths', []):
extra_path = get_extra_path(path_name)
if isdir(extra_path):
os.environ['PATH'] += env_t(os.pathsep + extra_path)
sys.path.append(extra_path)
added_dirs.add(extra_path)
else:
logger.warn(
"Could not add extra path: {0}".format(extra_path))
sys_sitedirs = getsyssitepackages()
for sys_sitedir in sys_sitedirs:
with fixup_paths():
for pth in [pth for pth in spec['pths'] or [] if pth]:
try:
logger.debug("open pth: %s", pth)
pth_file = join(sys_sitedir, pth)
addpackage(sys_sitedir, pth_file, added_dirs)
init_path() # TODO
except IOError as e:
# Path files are optional..
logging.debug('No pth found at %s', pth_file)
pass
except Exception as e:
bad_specs.add(fn)
err_msg = 'error loading spec %s: %s' % (fn, e)
if last_error != err_msg:
logging.error(err_msg)
last_error = err_msg
if bad_specs:
raise VextError('Error loading spec files: %s' % ', '.join(bad_specs))
def process_transcoding((flac_file, flac_root_path, mp3_target_path)):
try:
target_mp3_file = get_mp3_filename(mp3_target_path, flac_root_path, flac_file)
if not isdir(dirname(target_mp3_file)):
try:
os.makedirs(dirname(target_mp3_file))
except OSError:
pass # other thread might have been faster
if isfile(target_mp3_file) and tags_are_equals(flac_file, target_mp3_file):
LOGGER.info('skipping %r as target mp3 file exists and seems to have the same tags', flac_file)
else:
transcode(flac_file, target_mp3_file)
except Exception as e:
LOGGER.exception('error during the transcoding of %r : %s' % (flac_file, e))
def add_directory_csv_files(dir_path, paths=None):
if not paths:
paths = []
for p in listdir(dir_path):
path = join(dir_path, p)
if isdir(path):
# call recursively for each dir
paths = add_directory_csv_files(path, paths)
elif isfile(path) and path.endswith('.csv'):
# add every file to the list
paths.append(path)
return paths
def subfolders(self, sort=True, shuffle=False, seed=0, abspath=True):
'''
Return the list of locations's subfolders
:param sort: if true, sort subfolders by name
:param shuffle: if true, shuffle subfolders in random order
:return: a list of full paths to subfolders of given folder.
'''
folder = lambda f: join(self._root, f) if abspath else f
subfolders = [
folder(f) for f in listdir(self._root)
if isdir(join(self._root, f))
]
if sort or shuffle: self.__sortShuffle(subfolders, shuffle, seed)
return subfolders
def _foreach_cluster_root_dir(self, cluster_home_dir, action):
results = []
cluster_home_dir = path_join(self.path, cluster_home_dir)
if isdir(cluster_home_dir):
cluster_member_dirs = listdir(cluster_home_dir)
for cluster_member_dir in cluster_member_dirs:
neo4j_dirs = listdir(path_join(cluster_home_dir, cluster_member_dir))
for neo4j_dir in neo4j_dirs:
if neo4j_dir.startswith("neo4j"):
neo4j_path = path_join(cluster_home_dir, cluster_member_dir, neo4j_dir)
result = action(neo4j_path)
results.append(result)
break
return results
def _foreach_cluster_root_dir(self, cluster_home_dir, action):
results = []
cluster_home_dir = path_join(self.path, cluster_home_dir)
if isdir(cluster_home_dir):
cluster_member_dirs = listdir(cluster_home_dir)
for cluster_member_dir in cluster_member_dirs:
neo4j_dirs = listdir(path_join(cluster_home_dir, cluster_member_dir))
for neo4j_dir in neo4j_dirs:
if neo4j_dir.startswith("neo4j"):
neo4j_path = path_join(cluster_home_dir, cluster_member_dir, neo4j_dir)
result = action(neo4j_path)
results.append(result)
break
return results
def test_isdir(self):
self.assertIs(genericpath.isdir(support.TESTFN), False)
f = open(support.TESTFN, "wb")
try:
f.write(b"foo")
f.close()
self.assertIs(genericpath.isdir(support.TESTFN), False)
os.remove(support.TESTFN)
os.mkdir(support.TESTFN)
self.assertIs(genericpath.isdir(support.TESTFN), True)
os.rmdir(support.TESTFN)
finally:
if not f.close():
f.close()
try:
os.remove(support.TESTFN)
except os.error:
pass
try:
os.rmdir(support.TESTFN)
except os.error:
pass
self.assertRaises(TypeError, genericpath.isdir)
def addpackage(sys_sitedir, pthfile, known_dirs):
"""
Wrapper for site.addpackage
Try and work out which directories are added by
the .pth and add them to the known_dirs set
:param sys_sitedir: system site-packages directory
:param pthfile: path file to add
:param known_dirs: set of known directories
"""
with open(join(sys_sitedir, pthfile)) as f:
for n, line in enumerate(f):
if line.startswith("#"):
continue
line = line.rstrip()
if line:
if line.startswith(("import ", "import\t")):
exec(line, globals(), locals())
continue
else:
p_rel = join(sys_sitedir, line)
p_abs = abspath(line)
if isdir(p_rel):
os.environ['PATH'] += env_t(os.pathsep + p_rel)
sys.path.append(p_rel)
added_dirs.add(p_rel)
elif isdir(p_abs):
os.environ['PATH'] += env_t(os.pathsep + p_abs)
sys.path.append(p_abs)
added_dirs.add(p_abs)
if isfile(pthfile):
site.addpackage(sys_sitedir, pthfile, known_dirs)
else:
logging.debug("pth file '%s' not found")
def test_isdir(self):
self.assertIs(genericpath.isdir(support.TESTFN), False)
f = open(support.TESTFN, "wb")
try:
f.write(b"foo")
f.close()
self.assertIs(genericpath.isdir(support.TESTFN), False)
os.remove(support.TESTFN)
os.mkdir(support.TESTFN)
self.assertIs(genericpath.isdir(support.TESTFN), True)
os.rmdir(support.TESTFN)
finally:
if not f.close():
f.close()
try:
os.remove(support.TESTFN)
except os.error:
pass
try:
os.rmdir(support.TESTFN)
except os.error:
pass
self.assertRaises(TypeError, genericpath.isdir)
def load_specs():
bad_specs = set()
last_error = None
for fn in spec_files():
logger.debug("load spec: %s", fn)
if fn in bad_specs:
# Don't try and load the same bad spec twice
continue
try:
spec = open_spec(open(fn))
for module in spec['modules']:
logger.debug("allow module: %s", module)
allowed_modules.add(module)
for path_name in spec.get('extra_paths', []):
extra_path = get_extra_path(path_name)
if isdir(extra_path):
os.environ['PATH'] += env_t(os.pathsep + extra_path)
sys.path.append(extra_path)
added_dirs.add(extra_path)
else:
logger.warn("Could not add extra path: {0}".format(extra_path))
sys_sitedirs = getsyssitepackages()
for sys_sitedir in sys_sitedirs:
for pth in [pth for pth in spec['pths'] or [] if pth]:
try:
logger.debug("open pth: %s", pth)
pth_file = join(sys_sitedir, pth)
addpackage(sys_sitedir, pth_file, added_dirs)
init_path() # TODO
except IOError as e:
# Path files are optional..
logging.debug('No pth found at %s', pth_file)
pass
except Exception as e:
bad_specs.add(fn)
err_msg = 'error loading spec %s: %s' % (fn, e)
if last_error != err_msg:
logging.error(err_msg)
last_error = err_msg
if bad_specs:
raise VextError('Error loading spec files: %s' % ', '.join(bad_specs))
def RepositoryIterator(root, depth=1):
"""
Ordered iterator over the filesystem, returning only files from
the fourth directory level, corresponding to the data files in
the repository.
"""
root = canonify(root)
files = sorted(listdir(root))
for file in files:
path = join(root, file)
if isdir(path) and depth < 4:
# cannot use 'yield from' as 3to2 doesn't translate it
for path in RepositoryIterator(path, depth=depth + 1):
yield path
elif depth == 4:
yield path
def private():
'''Private dotfiles'''
name = 'dotfiles_secrets'
print_section('Clone repo')
repo = f'https://github.com/davidkristoffersen/{name}.git'
if not isdir(f'{DOTFILES_PRIVATE}/{name}'):
bash_cmd(f'git clone {repo} "{DOTFILES_PRIVATE}/{name}"')
print_section('Link repo')
link_dir(f'{DOTFILES_PRIVATE}/{name}', name)
print_section('Shell source')
secret_body = '#!/usr/bin/env bash\n\n'
secret_body += f'. \\"\\$DOTFILES_PRIVATE/{name}/.bashrc\\"'
write(f'{DOTFILES_SHELL}/.bash.d/.90-secrets.bash', secret_body)
def generate(self):
"""
Procedure - generation folder structure
"""
for item in os.listdir(self.fullpath()):
# if it's a folder than calculate and generate subfolder structure
if isdir(self.fullpath() + item):
self._folders_count += 1
# for each folder create FolderTree object
f = FolderTree(item, self)
# save child object
self._items.append(f)
# generate folder structure for child
f.generate()
# if it's a file than calculate
elif isfile(self.fullpath() + item):
self._files_count += 1
return self
def copy2remote():
webhdfs = WebHdfs()
base_path = "/home/work/data/collie/local_projects/"
dirs = [f for f in listdir(base_path) if isdir(join(base_path, f))]
for dr in dirs:
try:
project_version = int(dr)
print "processing version %d" % project_version
project_file_path = join(base_path, dr)
files = [
f for f in listdir(project_file_path)
if isfile(join(project_file_path, f))
]
if len(files) <= 0:
continue
if len(files) > 1:
print "ERROR!!!"
file_name = files[0]
local_path = join(project_file_path, file_name)
# local_path_new = join(project_file_path, str(project_version) + ".zip")
# os.rename(local_path, local_path_new)
remote_path = "/user/h_sns/collie/projects/"
webhdfs.copyFromLocal(local_path, remote_path)
print "local copied from %s to %s" % (local_path, remote_path)
version = ProjectVersions.objects.filter(
project_version=project_version)[:1].get()
version.hdfs_path = join(remote_path, file_name)
version.save()
print "saved version %d, path %s" % (project_version,
version.hdfs_path)
except IOError:
print "Error!!"
continue
except OSError:
print "Error!!"
continue
def getPaths(basePath, pathsVector):
'''
Insert a complete list of sub-dirs for a path in
a vector of paths
@param basePath: the base path to search into
@type basePath: string
@param pathsVector: the sub-path vector
@type pathsVector: list
@rtype: list
'''
thisDirPaths = [basePath + "/" + x for x in listdir(basePath) if isdir(basePath + "/" + x)]
for path in thisDirPaths:
if exists(path + "/functions.json"):
pathsVector.append(path)
else:
# search inside
getPaths(path, pathsVector)
return pathsVector
def __init__(self):
assert isinstance(self.image_dir_path, str), 'Invalid image directory %s' % self.image_dir_path
assert isinstance(self.format_file_name, str), 'Invalid format file name %s' % self.format_file_name
assert isinstance(self.default_file_name, str), 'Invalid default file name %s' % self.default_file_name
assert isinstance(self.imageTypeKey, str), 'Invalid meta type image key %s' % self.imageTypeKey
assert isinstance(self.thumbnailSizes, dict), 'Invalid thumbnail sizes %s' % self.thumbnailSizes
assert isinstance(self.cdmImages, ICDM), 'Invalid image CDM %s' % self.cdmImages
assert isinstance(self.cdmThumbnails, ICDM), 'Invalid image thumbnail CDM %s' % self.cdmThumbnails
SessionSupport.__init__(self)
if not os.path.exists(self.image_dir_path): os.makedirs(self.image_dir_path)
if not isdir(self.image_dir_path) or not os.access(self.image_dir_path, os.W_OK):
raise IOError('Unable to access the repository directory %s' % self.image_dir_path)
# We order the thumbnail sizes in descending order
thumbnailSizes = [(key, sizes) for key, sizes in self.thumbnailSizes.items()]
thumbnailSizes.sort(key=lambda pack: pack[1][0] * pack[1][1])
self.thumbnailSizes = OrderedDict(thumbnailSizes)
self._metaTypeId = None
def main_loop():
GAMES_DIR = os.getcwd()+'/../games/'
print "GAMES_DIR: ", GAMES_DIR
print
games = [x for x in os.listdir(GAMES_DIR) if isdir(GAMES_DIR + "/" + x) and isfile(GAMES_DIR+"/"+x+"/"+"package.json")]
if len(games) < 1:
print "Non ho trovato nessun gioco. Ciao ciao...."
return False
while True:
print "Questi sono i giochi che ho trovato:"
for i, game in enumerate(games):
print "\t"+str(i)+") "+str(game)
print "\t.) Qualsiasi altra selezione per uscire"
try:
choosed = int(raw_input('Cosa vuoi che risolva? '))
print "Hai scelto: "+str(games[choosed])
print
print "--------------------------------"
try:
solve_game(GAMES_DIR+"/"+games[choosed]+"/")
except Exception:
traceback.print_exc(file=sys.stdout)
print "--------------------------------"
print
except ValueError:
print "...Ciao Ciao..."
return True
def __buildFileListToSend(self, path):
fileListToSend = []
fullPath = os.path.join(self.__repositoryPath, path)
if isfile(fullPath):
file = open(fullPath, mode='rb')
fileInfo = {'file' : file
,'fileName' : path}
fileListToSend.append(fileInfo)
elif isdir(fullPath):
filesUnderPath = os.path.join(fullPath, '*' )
it = iter(glob.iglob(filesUnderPath))
for filePath in it:
if isfile(filePath) :
file = open(filePath, mode='rb')
fileName = filePath.replace(self.__repositoryPath, '')
fileInfo = {'file' : file
,'fileName' : fileName}
fileListToSend.append(fileInfo)
return fileListToSend
def check_dir(dirpath):
if dirpath:
if not exists(dirpath):
arg_parse_error('Directory ' + dirpath + ' does not exist.')
if not isdir(dirpath):
arg_parse_error(dirpath + ' is a file.')
def _update(self, locale, messages, poFile, path, pathMO, isGlobal=True):
assert isinstance(locale, Locale), 'Invalid locale %s' % locale
assert isinstance(messages, Iterable), 'Invalid messages %s' % messages
assert isinstance(poFile, IInputStream), 'Invalid file object %s' % poFile
assert isinstance(path, str), 'Invalid path %s' % path
assert isinstance(pathMO, str), 'Invalid path MO %s' % pathMO
assert isinstance(isGlobal, bool), 'Invalid is global flag %s' % isGlobal
catalog = read_po(poFile, locale=locale)
assert isinstance(catalog, Catalog), 'Invalid catalog %s' % catalog
if not catalog:
# The catalog has no messages, no need for updating.
return
if not isGlobal:
pathGlobal = self._filePath(locale)
pathGlobalMO = self._filePath(locale, format=FORMAT_MO)
if isfile(pathGlobal):
with open(pathGlobal) as fObj: catalogGlobal = read_po(fObj, locale)
self._processCatalog(catalogGlobal, self.messageService.getMessages())
else:
isGlobal, path, pathMO = True, pathGlobal, pathGlobalMO
messages = self.messageService.getMessages()
self._processCatalog(catalog, messages)
if isfile(path):
with open(path) as fObj: catalogOld = read_po(fObj, locale)
for msg in catalog:
msgO = catalogOld.get(msgId(msg), msg.context)
if not isMsgTranslated(msg) and msgO and isMsgTranslated(msgO):
msg.string = msgO.string
catalog.creation_date = catalogOld.creation_date
else:
pathDir = dirname(path)
if not isdir(pathDir): os.makedirs(pathDir)
catalog.creation_date = datetime.now()
if not isGlobal:
# We remove all the messages that are not translated or have the same translation as in the global locale
# or are the only plugin that makes use of the message in the global.
updatedGlobal = False
for msg in list(catalog):
id = msgId(msg)
if not id: continue
if not isMsgTranslated(msg):
catalog.delete(id, msg.context)
else:
msgG = catalogGlobal.get(id, msg.context)
if not msgG or msgG.string == msg.string:
catalog.delete(id, msg.context)
elif not isMsgTranslated(msgG) or msgG.locations == msg.locations:
copyTranslation(msg, msgG)
catalog.delete(id, msg.context)
updatedGlobal = True
if updatedGlobal:
# We remove all the messages that are not translated.
for msg in list(catalogGlobal):
if not isMsgTranslated(msg):
catalogGlobal.delete(msgId(msg), msg.context)
catalogGlobal.revision_date = datetime.now()
os.makedirs(dirname(pathGlobal), exist_ok=True)
with open(pathGlobal, 'wb') as fObj: write_po(fObj, catalogGlobal, **self.write_po_config)
os.makedirs(dirname(pathGlobalMO), exist_ok=True)
with open(pathGlobalMO, 'wb') as fObj: write_mo(fObj, catalogGlobal)
else:
# We remove all the messages that are not translated.
for msg in list(catalog):
if not isMsgTranslated(msg):
catalog.delete(msgId(msg), msg.context)
catalog.revision_date = datetime.now()
os.makedirs(dirname(path), exist_ok=True)
with open(path, 'wb') as fObj: write_po(fObj, catalog, **self.write_po_config)
os.makedirs(dirname(pathMO), exist_ok=True)
with open(pathMO, 'wb') as fObj: write_mo(fObj, catalog)
def main(args):
cnf, options = common_main(
'targetcov',
opts=[
(['--bam'], 'align.bam', {
'dest': 'bam',
'help': 'used to generate some annotations by GATK'}),
(['--capture', '--bed'], 'capture.bed', {
'dest': 'capture',
'help': ''}),
(['--genes', '--genes'], 'genes.bed', {
'dest': 'genes',
'help': ''}),
(['--exons', '--exons'], 'exons.bed', {
'dest': 'exons',
'help': ''}),
(['--padding'], '250', {
'dest': 'padding',
'help': '',
'default': 250}),
])
genes_bed = options.get('genes') or cnf.get('genes') or cnf['genome'].get('genes')
exons_bed = options.get('exons') or cnf.get('exons') or expanduser(cnf['genome'].get('exons'))
chr_len_fpath = cnf.get('chr_lengths') or cnf['genome'].get('chr_lengths')
capture_bed = options.get('capture') or cnf.get('capture')
bam = options.get('bam') or cnf.get('bam')
genes_bed = expanduser(genes_bed)
exons_bed = expanduser(exons_bed)
chr_len_fpath = expanduser(chr_len_fpath)
bam = expanduser(bam)
capture_bed = expanduser(capture_bed)
if not genes_bed:
critical('Specify sorted genes bed file in system info or in run info.')
if not exons_bed:
critical('Specify sorted exons bed file in system info or in run info.')
if not chr_len_fpath:
critical('Specify chromosome lengths for the genome'
' in system info or in run info.')
if not bam:
critical('Specify bam file by --bam option or in run_config.')
if not capture_bed:
critical('Specify capture file by --capture option or in run_config.')
print('using genes ' + genes_bed)
print('using exons ' + exons_bed)
print('using chr lengths ' + chr_len_fpath)
print('using bam ' + bam)
print('using capture panel ' + capture_bed)
if not verify_file(genes_bed): exit()
if not verify_file(exons_bed): exit()
if not verify_file(chr_len_fpath): exit()
if not verify_file(bam): exit()
if not verify_file(capture_bed): exit()
depth_thresholds = cnf['depth_thresholds']
padding = options.get('padding', cnf.get('padding', 250))
output_dir = expanduser(options.get('output_dir', cnf.get('output_dir', os.getcwd())))
work_dir = join(output_dir, 'work')
if isdir(work_dir):
rmtree(work_dir)
os.makedirs(work_dir)
run_header_report(output_dir, work_dir, capture_bed, bam, chr_len_fpath, depth_thresholds, padding)
run_cov_report(output_dir, work_dir, capture_bed, bam, depth_thresholds)
run_cov_report(output_dir, work_dir, capture_bed, bam, depth_thresholds, genes_bed, exons_bed)
def fs_traverse(path, repo, parent=None,
subdatasets=None,
render=True,
recurse_datasets=False,
recurse_directories=False,
json=None, basepath=None):
"""Traverse path through its nodes and returns a dictionary of relevant
attributes attached to each node
Parameters
----------
path: str
Path to the directory to be traversed
repo: AnnexRepo or GitRepo
Repo object the directory belongs too
parent: dict
Extracted info about parent directory
recurse_directories: bool
Recurse into subdirectories (note that subdatasets are not traversed)
render: bool
To render from within function or not. Set to false if results to be
manipulated before final render
Returns
-------
list of dict
extracts and returns a (recursive) list of directory info at path
does not traverse into annex, git or hidden directories
"""
subdatasets = subdatasets or []
fs = fs_extract(path, repo, basepath=basepath or path)
dataset = Dataset(repo.path)
submodules = {sm.path: sm
for sm in repo.get_submodules()}
# TODO: some submodules might not even have a local empty directory
# (git doesn't care about those), so us relying on listdir here and
# for _traverse_handle_subds might not work out.
# E.g. create-sibling --ui true ... --existing=reconfigure
# causes removal of those empty ones on the remote end
if isdir(path): # if node is a directory
children = [fs.copy()] # store its info in its children dict too (Yarik is not sure why, but I guess for .?)
# ATM seems some pieces still rely on having this duplication, so left as is
# TODO: strip away
for node in listdir(path):
nodepath = opj(path, node)
# Might contain subdatasets, so we should analyze and prepare entries
# to pass down... in theory we could just pass full paths may be? strip
node_subdatasets = []
is_subdataset = False
if isdir(nodepath):
node_sep = with_pathsep(node)
for subds in subdatasets:
if subds == node:
# it is the subdataset
is_subdataset = True
else:
# use path_is_subdir
if subds.startswith(node_sep):
node_subdatasets += [subds[len(node_sep):]]
# TODO: it might be a subdir which is non-initialized submodule!
# if not ignored, append child node info to current nodes dictionary
if is_subdataset:
# repo.path is real, so we are doomed (for now at least)
# to resolve nodepath as well to get relpath for it
node_relpath = relpath(realpath(nodepath), repo.path)
subds = _traverse_handle_subds(
node_relpath,
dataset,
recurse_datasets=recurse_datasets,
recurse_directories=recurse_directories,
json=json
)
# Enhance it with external url if available
submod_url = submodules[node_relpath].url
if submod_url and is_datalad_compat_ri(submod_url):
subds['url'] = submod_url
children.append(subds)
elif not ignored(nodepath):
# if recursive, create info dictionary (within) each child node too
if recurse_directories:
subdir = fs_traverse(nodepath,
repo,
subdatasets=node_subdatasets,
parent=None, # children[0],
recurse_datasets=recurse_datasets,
recurse_directories=recurse_directories,
json=json,
basepath=basepath or path)
subdir.pop('nodes', None)
else:
# read child metadata from its metadata file if it exists
subdir_json = metadata_locator(path=node, ds_path=basepath or path)
if exists(subdir_json):
with open(subdir_json) as data_file:
subdir = js.load(data_file)
subdir.pop('nodes', None)
# else extract whatever information you can about the child
else:
# Yarik: this one is way too lean...
subdir = fs_extract(nodepath,
repo,
basepath=basepath or path)
# append child metadata to list
children.extend([subdir])
# sum sizes of all 1st level children
children_size = {}
for node in children[1:]:
for size_type, child_size in node['size'].items():
children_size[size_type] = children_size.get(size_type, 0) + machinesize(child_size)
# update current node sizes to the humanized aggregate children size
fs['size'] = children[0]['size'] = \
{size_type: humanize.naturalsize(child_size)
for size_type, child_size in children_size.items()}
children[0]['name'] = '.' # replace current node name with '.' to emulate unix syntax
if parent:
parent['name'] = '..' # replace parent node name with '..' to emulate unix syntax
children.insert(1, parent) # insert parent info after current node info in children dict
fs['nodes'] = children # add children info to main fs dictionary
if render: # render directory node at location(path)
fs_render(fs, json=json, ds_path=basepath or path)
lgr.info('Directory: %s' % path)
return fs