Source code for luna.common.utils

from filehash import FileHash
from io import BytesIO
import os, json


def to_sql_field(s):
	filter1 = s.replace(".","_").replace(" ","_")
	filter2 = ''.join(e for e in filter1 if e.isalnum() or e=='_')
	return filter2

def to_sql_value(s):
	if isinstance(s, str): return f"'{s}'"
	if not s==s:  return 'Null'
	if s is None: return 'Null'
	else: return f"{s}"


def clean_nested_colname(s):
	"""
	Removes map name for MapType columns.
	e.g. metadata.SeriesInstanceUID -> SeriesInstanceUID
	"""
	return s[s.find('.')+1:]

def generate_uuid(path, prefix):
	"""
	Returns hash of the file given path, preceded by the prefix.
	:param path: file path e.g. file:/path/to/file
	:param prefix: list e.g. ["SVGEOJSON","default-label"]
	:return: string uuid
	"""
	posix_file_path = path.split(':')[-1]

	rec_hash = FileHash('sha256').hash_file(posix_file_path)
	prefix.append(rec_hash)
	return "-".join(prefix)


def generate_uuid_binary(content, prefix):
	"""
	Returns hash of the binary, preceded by the prefix.
	:param content: binary
	:param prefix: list e.g. ["FEATURE"]
	:return: string uuid
	"""
	content = BytesIO(content)

	import EnsureByteContext
	with EnsureByteContext.EnsureByteContext():
		uuid = FileHash('sha256').hash_file(content)

	prefix.append(uuid)
	return "-".join(prefix)


def generate_uuid_dict(json_str, prefix):
	"""
	Returns hash of the json string, preceded by the prefix.
	:param json_str: str representation of json
	:param prefix: list e.g. ["SVGEOJSON","default-label"]
	:return: v
	"""
	json_bytes = json.dumps(json_str).encode('utf-8')

	import EnsureByteContext
	with EnsureByteContext.EnsureByteContext():
		uuid = FileHash('sha256').hash_file(BytesIO(json_bytes))

	prefix.append(uuid)
	return "-".join(prefix)

def does_not_contain(token, value):
	"""
	Validate that `token` is not a substring of `value`

	:param: token: string e.g. : | .
	:param: value: dictionary, list, or str
	"""
	if isinstance(value, str):
		if token in value:
			raise ValueError(f"{value} cannot contain {token}")

	if isinstance(value, list):
		if any([token in v for v in value]):
			raise ValueError(str(value) + f" cannot contain {token}")

	if isinstance(value, dict):
		if any([isinstance(key, str) and token in key or isinstance(val, str) and token in val for key,val in value.items()]):
			raise ValueError(str(value) + f" cannot contain {token}")

	return True


def replace_token(token, token_replacement, value):
	"""
	Replace `token` with `token_replacement` in `value`

	:param: token: string e.g. : | .
	:param: token_replacement: string e.g. _ -
	:param: value: dictionary, list, or str
	"""
	if isinstance(value, str):
		return value.replace(token, token_replacement)

	if isinstance(value, list):
		new_value = []
		for v in value:
			new_value.append(v.replace(token, token_replacement))
		return new_value

	if isinstance(value, dict):
		new_value = {}
		for key,val in value.items():
			new_key, new_val = key, val
			if isinstance(key, str):
				new_key = key.replace(token, token_replacement)
			if isinstance(val, str):
				new_val = val.replace(token, token_replacement)
			new_value[new_key] = new_val

		return new_value

	return value


def get_method_data(cohort_id, method_id):
    """
    Return method dict

    :param: cohort_id: string
    :param: method_id: string
    """

    method_dir = os.path.join(os.environ['MIND_GPFS_DIR'], "data", cohort_id, "methods")
    with open(os.path.join(method_dir, f'{method_id}.json')) as json_file:
        method_config = json.load(json_file)['params']
    return method_config

def get_absolute_path(module_path, relative_path):
	""" Given the path to a module file and the path, relative to the module file, of another file
	that needs to be referenced in the module, this method returns the absolute path of the file
	that needs to be referenced.

	This method makes it possible to resolve absolute paths to files in any environment a
	module and the referenced files are deployed to.

	:param module_path path to the module. Use '__file__' from the module.
	:param relative_path path to the file that needs to be referenced by the module. The path must
	be relative to the module.
	:return absolute path to file with the specified relative_path
	"""
	path = os.path.join(os.path.dirname(module_path), relative_path)

	# resolve any back-paths with ../ to simplify absolute path
	return os.path.realpath(path)