Source code for cms.mcr_data_loader

#  Copyright (c) 2022. Harvard University
#
#  Developed by Research Software Engineering,
#  Faculty of Arts and Sciences, Research Computing (FAS RC)
#  Author: Michael A Bouzinier
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
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#         http://www.apache.org/licenses/LICENSE-2.0
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#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
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#
import glob
import os
from typing import List, Tuple, Any, Callable

from cms.fts2yaml import mcr_type, MedicareFTS
from nsaph.loader.data_loader import DataLoader
from nsaph_utils.utils.fwf import FWFReader
from nsaph_utils.utils.io_utils import fopen


[docs]class MedicareDataLoader(DataLoader): """ Subclass of generic Data Loader aware of the raw Medicare CMS data structure. Matches FTS and DAT files. """
[docs] @classmethod def dat4fts(cls, fts_path): f, ext = os.path.splitext(fts_path) assert ext.lower() == '.fts' data_files = glob.glob("{}*.dat".format(f)) return data_files
[docs] @classmethod def open(cls, name: str, dat_path: str = None) -> FWFReader: f, ext = os.path.splitext(name) if dat_path is not None: assert ext.lower() == '.fts' fts_path = name elif ext.lower() == ".fts": fts_path = name dat_path = f + ".dat" elif ext.lower() == ".dat": dat_path = name fts_path = f + ".fts" else: dat_path = name + ".dat" fts_path = name + ".fts" basedir, fname = os.path.split(f) t = mcr_type(fname) fts = MedicareFTS(t).init(fts_path) return FWFReader(fts.to_fwf_meta(dat_path))
def __init__(self, context): super().__init__(context)
[docs] def get_files(self) -> List[Tuple[Any, Callable]]: objects = [] for fts_path in self.context.data: dat_files = self.dat4fts(fts_path) for dat_file in dat_files: objects.append((self.open(fts_path, dat_file), fopen)) return objects
if __name__ == '__main__': loader = MedicareDataLoader(None) loader.run()