Pandas interface to OMOP data stored as local parquet files/folders.
| PARAMETER |
DESCRIPTION |
folder |
absolute path to a folder containing several parquet files with omop data
TYPE:
str
|
Examples:
>>> data = LocalData(folder="/export/home/USER/my_data/")
>>> person = data.person
>>> person.shape
(100, 10)
| ATTRIBUTE |
DESCRIPTION |
person |
Pandas dataframe person. All dataframe attributes are
dynamically generated to match the content of the
selected folder.
TYPE:
pd.DataFrame
|
Source code in edsteva/io/files.py
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79 | class LocalData: # pragma: no cover
"""Pandas interface to OMOP data stored as local parquet files/folders.
Parameters
----------
folder: str
absolute path to a folder containing several parquet files with omop data
Examples
--------
>>> data = LocalData(folder="/export/home/USER/my_data/")
>>> person = data.person
>>> person.shape
(100, 10)
Attributes
----------
person: pd.DataFrame
Pandas dataframe `person`. All dataframe attributes are
dynamically generated to match the content of the
selected folder.
"""
def __init__(
self,
folder: str,
):
(
self.parquet_tables,
self.pickle_tables,
self.available_tables,
self.tables_paths,
) = self.list_available_tables(folder)
@staticmethod
def list_available_tables(folder: str) -> Tuple[List[str], List[str]]:
available_tables = []
pickle_tables = []
parquet_tables = []
tables_paths = {}
for filename in os.listdir(folder):
file = Path(folder) / filename
table_name = file.stem
extension = file.suffix
if extension == ".parquet":
abspath = Path.resolve(file)
tables_paths[table_name] = abspath
parquet_tables.append(table_name)
available_tables.append(table_name)
elif extension == ".pkl" or extension == ".pickle":
abspath = Path.resolve(file)
tables_paths[table_name] = abspath
pickle_tables.append(table_name)
available_tables.append(table_name)
return parquet_tables, pickle_tables, available_tables, tables_paths
def _read_table(self, table_name: str) -> pd.DataFrame:
path = self.tables_paths[table_name]
if table_name in self.parquet_tables:
return pd.read_parquet(path)
return pd.read_pickle(path)
def __getattr__(self, table_name: str) -> pd.DataFrame:
if table_name in self.available_tables:
return self._read_table(table_name)
raise AttributeError(f"Table '{table_name}' is not available in chosen folder.")
def __dir__(self) -> List[str]:
return list(super().__dir__()) + list(self.available_tables)
|