Module Gnumed.business.gmATC

# -*- coding: utf-8 -*-
"""ATC handling code.

http://who.no

There is no DDD handling because DDD explicitly
does not carry clinical meaning.
"""
#============================================================
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = "GPL v2 or later"

import sys
import io
import logging
import os.path
import re as regex


if __name__ == '__main__':
        sys.path.insert(0, '../../')
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmCfgINI


_log = logging.getLogger('gm.atc')
_cfg = gmCfgINI.gmCfgData()


ATC_NICOTINE = 'N07BA01'
ATC_ETHANOL  = 'V03AB16'

#============================================================
def propagate_atc(substance=None, atc=None, link_obj=None):

        _log.debug('substance <%s>, ATC <%s>', substance, atc)

        if atc is not None:
                if atc.strip() == '':
                        atc = None

        if atc is None:
                atcs = text2atc(text = substance, fuzzy = False, link_obj = link_obj)
                if len(atcs) == 0:
                        _log.debug('no ATC found, aborting')
                        return atc
                if len(atcs) > 1:
                        _log.debug('non-unique ATC mapping, aborting')
                        return atc
                atc = atcs[0][0].strip()

        args = {'atc': atc, 'term': substance.strip()}
        queries = [
                {'cmd': "UPDATE ref.substance SET atc = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc IS NULL",
                 'args': args},
                {'cmd': "UPDATE ref.drug_product SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL",
                 'args': args}
        ]
        gmPG2.run_rw_queries(link_obj = link_obj, queries = queries)

        return atc

#============================================================
def text2atc(text=None, fuzzy=False, link_obj=None):

        text = text.strip()

        if fuzzy:
                args = {'term': '%%%s%%' % text}
                cmd = """
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE term ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE description ilike %(term)s AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE description ilike %(term)s AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                """
        else:
                args = {'term': text.casefold()}
                cmd = """
                        SELECT DISTINCT ON (atc_code) *
                        FROM (
                                SELECT atc as atc_code, is_group_code, pk_data_source
                                FROM ref.v_atc
                                WHERE lower(term) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc as atc_code, null, null
                                FROM ref.substance
                                WHERE lower(description) = lower(%(term)s) AND atc IS NOT NULL
                                        UNION
                                SELECT atc_code, null, null
                                FROM ref.drug_product
                                WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
                        ) as tmp
                        ORDER BY atc_code
                """

        rows, idx = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)

        _log.debug('term: %s => ATCs: %s (fuzzy: %s)', text, rows, fuzzy)

        return rows

#============================================================
def exists_as_atc(substance):
        args = {'term': substance}
        cmd = 'SELECT EXISTS (SELECT 1 FROM ref.atc WHERE lower(term) = lower(%(term)s))'
        rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
        return rows[0][0]

#============================================================
def get_reference_atcs(order_by='atc, term, lang'):
        cmd = 'SELECT * FROM ref.v_atc ORDER BY %s' % order_by
        rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = False)
        return rows

#============================================================
def atc_import(cfg_fname=None, conn=None):

        # read meta data
        _cfg.add_file_source(source = 'atc', file = cfg_fname, encoding = 'utf8')

        data_fname = os.path.join (
                os.path.dirname(cfg_fname),
                _cfg.get(group = 'atc', option = 'data file', source_order = [('atc', 'return')])
        )                       # must be in same dir as conf file
        version = _cfg.get(group = 'atc', option = 'version', source_order = [('atc', 'return')])
        lang = _cfg.get(group = 'atc', option = 'language', source_order = [('atc', 'return')])
        desc = _cfg.get(group = 'atc', option = 'description', source_order = [('atc', 'return')])
        url = _cfg.get(group = 'atc', option = 'url', source_order = [('atc', 'return')])
        name_long = _cfg.get(group = 'atc', option = 'long name', source_order = [('atc', 'return')])
        name_short = _cfg.get(group = 'atc', option = 'short name', source_order = [('atc', 'return')])

        _cfg.remove_source(source = 'atc')

        _log.debug('importing ATC version [%s] (%s) from [%s]', version, lang, data_fname)

        args = {'ver': version, 'desc': desc, 'url': url, 'name_long': name_long, 'name_short': name_short, 'lang': lang}

        # find or create data source record
        cmd = u"select pk from ref.data_source where name_short = %(name_short)s and version = %(ver)s"
        rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
        if len(rows) > 0:
                data_src_pk = rows[0][0]
                _log.debug('ATC data source record existed, pk is #%s, refreshing fields', data_src_pk)
                # exists - update
                args['pk'] = data_src_pk
                cmd = u"""UPDATE ref.data_source SET
                                name_long = %(name_long)s,
                                description = %(desc)s,
                                lang = %(lang)s,
                                source = %(url)s
                        WHERE
                                pk = %(pk)s
                """
                rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
        else:
                _log.debug('ATC data source record not found, creating')
                # create
                cmd = u"""insert into ref.data_source (name_long, name_short, version, description, lang, source) values (
                        %(name_long)s,
                        %(name_short)s,
                        %(ver)s,
                        %(desc)s,
                        %(lang)s,
                        %(url)s
                ) returning pk"""
                rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
                data_src_pk = rows[0][0]
                _log.debug('ATC data source record created, pk is #%s', data_src_pk)

        # import data
        csv_file = io.open(data_fname, mode = 'rt', encoding = 'utf-8-sig', errors = 'replace')
        atc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = ",", quotechar = '"')

        # clean out staging area
        curs = conn.cursor()
        cmd = """delete from ref.atc_staging"""
        gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
        curs.close()
        conn.commit()
        _log.debug('ATC staging table emptied')

        # from file into staging table
        curs = conn.cursor()
        cmd = """insert into ref.atc_staging values (%s, %s, %s, %s, %s)"""
        first = False
        for atc_line in atc_reader:
                # skip first
                if not first:
                        first = True
                        continue

                # skip blanks
                if atc_line[0] + atc_line[1] + atc_line[2] + atc_line[3] + atc_line[4] == '':
                        continue

                comment = ''
                unit = ''
                adro = ''

                # "1,1 mg O,P,R,..."
                if regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
                        tmp, unit, adro = regex.split('\s', atc_line[4])
                # "1,1 mg O,P,R bezogen auf ..."
                elif regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
                        tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
                # "20 mg O"
                elif regex.match('\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
                        tmp, unit, adro = regex.split('\s', atc_line[4])
                # "20 mg O bezogen auf ..."
                elif regex.match('\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
                        tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
                # "Standarddosis: 1 Tablette oder 30 ml Mixtur"
                else:
                        comment = atc_line[4]

                args = [
                        atc_line[0].strip(),
                        atc_line[2],
                        unit,
                        adro,
                        comment
                ]

                gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd, 'args': args}])

        curs.close()
        conn.commit()
        csv_file.close()
        _log.debug('ATC staging table loaded')

        # from staging table to real table
        args = {'src_pk': data_src_pk}
        queries = []
        # transfer new records
        cmd = u"""
                insert into ref.atc (
                        fk_data_source,
                        code,
                        term,
                        comment,
                        administration_route
                ) select
                        %(src_pk)s,
                        atc,
                        name,
                        nullif(comment, ''),
                        nullif(adro, '')
                FROM
                        ref.atc_staging
                WHERE
                        not exists (
                                select 1 FROM ref.atc WHERE fk_data_source = %(src_pk)s AND code = ref.atc_staging.atc
                        )
        """
        queries.append({'cmd': cmd, 'args': args})
        # update records so pre-existing ones are refreshed
        cmd = u"""
                UPDATE ref.atc SET
                        code = r_as.atc,
                        term = r_as.name,
                        comment = nullif(r_as.comment, ''),
                        administration_route = nullif(r_as.adro, '')
                FROM
                        (SELECT atc, name, comment, adro FROM ref.atc_staging) AS r_as
                WHERE
                        fk_data_source = %(src_pk)s
        """
        queries.append({'cmd': cmd, 'args': args})
        curs = conn.cursor()
        gmPG2.run_rw_queries(link_obj = curs, queries = queries)
        curs.close()
        conn.commit()
        _log.debug('transfer from ATC staging table to real ATC table done')

        # clean out staging area
        curs = conn.cursor()
        cmd = """delete from ref.atc_staging"""
        gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
        curs.close()
        conn.commit()
        _log.debug('ATC staging table emptied')

        return True

#============================================================
# main
#------------------------------------------------------------
if __name__ == "__main__":

        if len(sys.argv) == 1:
                sys.exit()

        if sys.argv[1] != 'test':
                sys.exit()

        from Gnumed.pycommon import gmI18N

        gmI18N.activate_locale()
#       gmDateTime.init()

        #--------------------------------------------------------
        def test_atc_import():
                atc_import(cfg_fname = sys.argv[2], conn = gmPG2.get_connection(readonly = False))
        #--------------------------------------------------------
        def test_text2atc():
                print('searching ATC code for:', sys.argv[2])
                print(' ', text2atc(sys.argv[2]))
                print(' ', text2atc(sys.argv[2], True))
        #--------------------------------------------------------
        def test_get_reference_atcs():
                print("reference_of_atc_codes:")
                for atc in get_reference_atcs():
                        print(atc)
        #--------------------------------------------------------
        #test_atc_import()
        #test_text2atc()
        test_get_reference_atcs()

#============================================================