# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# 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
# limitations under the License.
#
"""
Introspector that looks for all SAS 7BDAT files in a given path
matching a given pattern, reads metadata and generates data model
for each file in YAML format. the data model is written to the common
registry.
"""
import logging
import re
import sys
from typing import List
import yaml
from cms.tools.mcr_registry import MedicareRegistry
from cms.tools.mcr_sas import MedicareSAS
from nsaph.data_model.utils import split
from nsaph.loader.introspector import Introspector
from nsaph.pg_keywords import PG_INT_TYPE, PG_SERIAL_TYPE
[docs]class SASIntrospector(MedicareSAS, MedicareRegistry):
"""
Introspector that looks for all SAS 7BDAT files in a given path
matching a given pattern, reads metadata and generates data model
for each file in YAML format. the data model is written to the common
registry.
"""
[docs] @classmethod
def process(cls, registry_path: str, pattern: str, root_dir:str = '.'):
introspector = SASIntrospector(registry_path, root_dir)
introspector.traverse(pattern)
introspector.save()
yaml.dump(introspector.registry, sys.stdout)
return
def __init__(self, registry_path: str, root_dir: str = '.'):
MedicareSAS.__init__(self, root_dir)
MedicareRegistry.__init__(self, registry_path)
[docs] @classmethod
def matches(cls, s: str, candidates: List[str]):
if s in candidates:
return True
patterns = [c.replace('*', '.*') for c in candidates if '*' in c]
for p in patterns:
if re.fullmatch(p, s):
return True
return False
[docs] def handle(self, table: str, file_path: str, file_type: str, year: int):
if file_type == "denominator":
index_all = True
else:
index_all = False
self.add_sas_table(table, file_path, index_all, year)
return
[docs] def add_sas_table(self, table: str, file_path: str, index_all: bool,
year: int):
introspector = Introspector(file_path)
introspector.introspect()
introspector.append_file_column()
introspector.append_record_column()
columns = introspector.get_columns()
specials = {
"bene_id": (None, ["bene_id", "intbid", "qid", "bid_5333*"]),
"state": (None, ["state", "ssa_state", "state_code",
"bene_rsdnc_ssa_state_cd", "state_cd",
"medpar_bene_rsdnc_ssa_state_cd"]),
"zip": (None, ["zip", "zipcode", "bene_zip_cd", "bene_zip",
"bene_mlg_cntct_zip_cd",
"medpar_bene_mlg_cntct_zip_cd"]),
"year": (None, ["year", "enrolyr", "bene_enrollmt_ref_yr",
"rfrnc_yr"])
}
for column in columns:
cname, c = split(column)
if cname == "year":
yc = cname
is_key = False
for key in specials:
key_column, candidates = specials[key]
if self.matches(cname, candidates):
if key_column is not None:
raise ValueError("Multiple {} columns in {}"
.format(key, file_path))
specials[key] = (column, candidates)
is_key = True
if index_all and not is_key:
c["index"] = "true"
for key in specials:
column, _ = specials[key]
if column is None:
if key == "year":
columns.append(
{
key: {
"type": PG_INT_TYPE,
"index": True,
"source": {
"type": "generated",
"code": "GENERATED ALWAYS AS ({:d}) STORED"
.format(year)
}
}
}
)
logging.warning("Generating year column for " + file_path)
continue
raise ValueError("No {} column in {}".format(key, file_path))
cname, c = split(column)
if key == cname:
c["index"] = "true"
continue
columns.append(
{
key: {
"type": c["type"],
"index": True,
"source": {
"type": "generated",
"code": "GENERATED ALWAYS AS ({}) STORED"
.format(cname)
}
}
}
)
self.registry[self.domain]["tables"][table] = {
"columns": columns,
"primary_key": [
"FILE",
"RECORD"
]
}
if __name__ == '__main__':
SASIntrospector.process(*sys.argv[1:])