def SQSDatabase(path, name_constraint=''):
"""
Convienence function to create a TinyDB for the SQS database found at `path`.
Parameters
----------
path : path-like of the folder containing the SQS database.
name_constraint : Any name constraint to add into the recursive glob. Not case sensitive. Exact substring.
Returns
-------
TinyDB
Database of abstract SQS.
"""
db = TinyDB(storage=MemoryStorage)
dataset_filenames = recursive_glob(path, '*.json')
dataset_filenames = [
fname for fname in dataset_filenames
if name_constraint.upper() in fname.upper()
]
for fname in dataset_filenames:
with open(fname) as file_:
try:
db.insert(json.load(file_))
except ValueError as e:
raise ValueError('JSON Error in {}: {}'.format(fname, e))
return db
def get_config_file(config_folder=".", queue_script="vaspjob.pbs"):
"""
Get the file name of the config file in config_folder and its sub-folders
Parameter
config_folder: str (path like)
The folder containing the config file or containing config file in its sub-folder
queue_script: str (filename like)
The filename of the queue script
Return
config_file: dict
The dict of the filename(key) and corresponding path(value).
If the config file is not in config_folder, store None.
If more than one file (the same filename), it will store the uppest file [Ref. get_shortest_path]
"""
config_file = {}
required_file = ["db.json", "my_launchpad.yaml"]
option_file = ["FW_config.yaml", "my_fworker.yaml", "my_qadapter.yaml", queue_script]
files = required_file + option_file
for file in files:
file_list = recursive_glob(config_folder, file)
if len(file_list) == 0:
if file in required_file:
raise FileNotFoundError("{} file is required for configuration of dfttk.".format(file))
else:
warnings.warn("{} file does not exist, the default setting will be used.".format(file))
config_file[file] = None
else:
config_file[file] = get_abspath(get_shortest_path(file_list))
return config_file
def get_structure_file(STR_FOLDER=".", RECURSIVE=False, MATCH_PATTERN="*"):
"""
Get all file names in STR_FOLDER path [and its sub-folder (RECURSIVE)] with condition (MATCH_PATTEN)
Parameter
STR_FOLDER: str (path-like)
The path containing files, Default: .
RECURSIVE: bool
Including the sub-folder (True) or not (Default: False)
MATCH_PATTERN: str
The match pattern for the file name
Return
STR_FILES: list[str (filename-like)]
The list of all the filenames matching the conditions
"""
## Get the file name of structure file
STR_FOLDER = get_abspath(STR_FOLDER)
if not os.path.exists(STR_FOLDER):
raise FileNotFoundError(
"The specified folder/file '{}' does not exist.".format(
STR_FOLDER))
if os.path.isfile(STR_FOLDER):
STR_FILES = [STR_FOLDER]
else:
if RECURSIVE:
STR_FILES = recursive_glob(STR_FOLDER, MATCH_PATTERN)
else:
STR_FILES = glob.glob(os.path.join(STR_FOLDER, MATCH_PATTERN))
for file_i in STR_FILES:
if os.path.isdir(file_i):
STR_FILES.remove(file_i)
return STR_FILES
