Gnumed.business.gmATC API documentation
Description: ATC handling code …

# Module `Gnumed.business.gmATC`

ATC handling code.

http://who.no

There is no DDD handling because DDD explicitly does not carry clinical meaning.

Expand source code

    # -*- 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 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 = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}])

            _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 = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
            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 = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
            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 = 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 = 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 = 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 = 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(r'\d{,3},\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
                            tmp, unit, adro = regex.split(r'\s', atc_line[4])
                    # "1,1 mg O,P,R bezogen auf ..."
                    elif regex.match(r'\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
                            tmp, unit, adro, comment = regex.split(r'\s', atc_line[4], 3)
                    # "20 mg O"
                    elif regex.match(r'\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
                            tmp, unit, adro = regex.split(r'\s', atc_line[4])
                    # "20 mg O bezogen auf ..."
                    elif regex.match(r'\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
                            tmp, unit, adro, comment = regex.split(r'\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()

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

## Functions

`def atc_import(cfg_fname=None, conn=None)`
  Expand source code

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

`def exists_as_atc(substance)`
  Expand source code

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

`def get_reference_atcs(order_by='atc, term, lang')`
  Expand source code

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

`def propagate_atc(substance=None, atc=None, link_obj=None)`
  Expand source code

      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)`
  Expand source code

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

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

              return rows