exporter-diagnosis.py

#!/usr/bin/python3
# vim:ts=8:sw=8:tw=0:noet

import pprint
import re
import argparse
import logging as log
from builtins import str, isinstance, len, set, int
from typing import List

import pandas as pd

from directory import Directory
from orphacodes import OrphaCodes
from icd10codeshelper import ICD10CodesHelper

cachesList = ['directory', 'emails', 'geocoding', 'URLs']

pp = pprint.PrettyPrinter(indent=4)


class ExtendAction(argparse.Action):

    def __call__(self, parser, namespace, values, option_string=None):
        from builtins import getattr, setattr
        items = getattr(namespace, self.dest) or []
        items.extend(values)
        setattr(namespace, self.dest, items)


parser = argparse.ArgumentParser()
parser.register('action', 'extend', ExtendAction)
parser.add_argument('-v', '--verbose', dest='verbose', action='store_true',
                    help='verbose information on progress of the data checks')
parser.add_argument('-d', '--debug', dest='debug', action='store_true',
                    help='debug information on progress of the data checks')
parser.add_argument('-X', '--output-XLSX', dest='outputXLSX', nargs=1,
                    help='output of results into XLSX with filename provided as parameter')
parser.add_argument('-O', '--orphacodes-mapfile', dest='orphacodesfile', nargs=1,
                    help='file name of Orpha code mappings from http://www.orphadata.org/cgi-bin/ORPHAnomenclature.html')
parser.add_argument('-N', '--output-no-stdout', dest='nostdout', action='store_true',
                    help='no output of results into stdout (default: enabled)')
parser.add_argument('--purge-all-caches', dest='purgeCaches', action='store_const', const=cachesList,
                    help='disable all long remote checks (email address testing, geocoding, URLs')
parser.add_argument('--purge-cache', dest='purgeCaches', nargs='+', action='extend', choices=cachesList,
                    help='disable particular long remote checks')
parser.set_defaults(disableChecksRemote=[], disablePlugins=[], purgeCaches=[])
args = parser.parse_args()

if args.debug:
    log.basicConfig(format="%(levelname)s: %(message)s", level=log.DEBUG)
elif args.verbose:
    log.basicConfig(format="%(levelname)s: %(message)s", level=log.INFO)
else:
    log.basicConfig(format="%(levelname)s: %(message)s")

# Main code

dir = Directory(purgeCaches=args.purgeCaches, debug=args.debug, pp=pp)

log.info('Total biobanks: ' + str(dir.getBiobanksCount()))
log.info('Total collections: ' + str(dir.getCollectionsCount()))

orphacodes = OrphaCodes(args.orphacodesfile)

cancerExistingDiagnosed = []
cancerOnlyExistingDiagnosed = []
cancerExistingControls = []
cancerProspective = []
cancerBiobanksExistingDiagnosed = set()
cancerOnlyBiobanksExistingDiagnosed = set()
cancerBiobanksExistingControls = set()
cancerBiobanksProspective = set()
cancerBiobanks = set()
cancerCollectionSamplesExplicit = 0
cancerCollectionDonorsExplicit = 0
cancerCollectionSamplesIncOoM = 0
cancerOnlyCollectionSamplesExplicit = 0
cancerOnlyCollectionDonorsExplicit = 0
cancerOnlyCollectionSamplesIncOoM = 0

for collection in dir.getCollections():
    log.debug("Analyzing collection " + collection['id'])
    biobankId = dir.getCollectionBiobankId(collection['id'])
    biobank = dir.getBiobankById(biobankId)
    biobank_capabilities = []
    if 'capabilities' in biobank:
        for c in biobank['capabilities']:
            biobank_capabilities.append(c['id'])
    biobank_covid = []
    if 'covid19biobank' in biobank:
        for c in biobank['covid19biobank']:
            biobank_covid.append(c['id'])
    biobank_networks = []
    if 'network' in biobank:
        for n in biobank['network']:
            biobank_networks.append(n['id'])

    OoM = collection['order_of_magnitude']['id']

    materials = []
    if 'materials' in collection:
        for m in collection['materials']:
            materials.append(m['id'])

    data_categories = []
    if 'data_categories' in collection:
        for c in collection['data_categories']:
            data_categories.append(c['id'])

    types = []
    if 'type' in collection:
        for t in collection['type']:
            types.append(t['id'])
    log.debug("Types: " + str(types))

    diags = []
    diag_ranges = []
    cancer_diag = False
    cancer_control = False
    cancer_prospective = False
    non_cancer = False

    for d in collection['diagnosis_available']:
        if re.search('-', d['id']):
            diag_ranges.append(d['id'])
        else:
            diags.append(d['id'])

    if diag_ranges:
        log.warning("There are diagnosis ranges provided for collection " + collection['id'] + ": " + str(diag_ranges))

    log.debug(str(collection['diagnosis_available']))