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Commit 5e1fdfc4 authored by mjbonifa's avatar mjbonifa
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refactored files into the module acmc and sorted all the imports

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from acmc.main import main
if __name__ == "__main__":
main()
\ No newline at end of file
import pandas as pd
import os
from acmc import logging_config
logger = logging_config.setup_logger()
class bcolors: #for printing coloured text
HEADER = '\033[95m'
OKBLUE = '\033[94m'
......
File moved
......@@ -3,13 +3,10 @@ import logging
from pathlib import Path
# acmc imports
import trud
import omop
import phen
from acmc import trud, omop, phen, logging_config as lc
# setup logging
import logging_config
logger = logging_config.setup_logger()
logger = lc.setup_logger()
BUILD_PATH = Path('build')
......
......@@ -6,9 +6,8 @@ import json
import logging
from pathlib import Path
# setup logging
from logging_config import setup_logger
logger = setup_logger()
from acmc import logging_config
logger = logging_config.setup_logger()
OMOP_DB_DIR = Path('./build/omop')
OMOP_DB_PATH = OMOP_DB_DIR / 'omop_54.sqlite'
......
import pandas as pd
import numpy as np
import os
import trud
# setup logging
import logging_config
logger = logging_config.setup_logger()
# acmc imports
from acmc import trud, logging_config as lc
from acmc.base import log_invalid_code, bcolors, raise_
from base import log_invalid_code
from base import bcolors
from base import raise_
logger = lc.setup_logger()
def in_database(codes, db, col):
return codes.isin(db[col])
......
......@@ -14,15 +14,14 @@ from pathlib import Path
from urllib.parse import urlparse, urlunparse
# acmc imports
import trud
import omop
from base import log_invalid_code, bcolors, raise_
from parse import Read2, Read3, Icd10, Snomed, Opcs4, Atc, code_types, vocab_types
from omop import publish_concept_sets, setup
from acmc import trud, omop
from acmc.base import log_invalid_code, bcolors, raise_
from acmc.parse import Read2, Read3, Icd10, Snomed, Opcs4, Atc, code_types, vocab_types
from acmc.omop import publish_concept_sets, setup
# setup logging
from logging_config import setup_logger
logger = setup_logger()
import acmc.logging_config as lc
logger = lc.setup_logger()
pd.set_option("mode.chained_assignment", None)
......
......@@ -10,11 +10,11 @@ import pandas as pd
import simpledbf
from pathlib import Path
# setup logging
import logging_config
logger = logging_config.setup_logger()
from acmc.base import bcolors
from base import bcolors
# setup logging
import acmc.logging_config as lc
logger = lc.setup_logger()
# Constants
FQDN = "isd.digital.nhs.uk"
......
......@@ -5,14 +5,10 @@ import shutil
import logging
from pathlib import Path
import trud
import omop
import phen
import main
from acmc import trud, omop, main, logging_config as lc
# setup logging
from logging_config import setup_logger
logger = setup_logger()
logger = lc.setup_logger()
@pytest.fixture
def tmp_dir():
......
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