Gnumed.business.gmATC

Package Gnumed :: Package business :: Module gmATC |
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# Source Code for Module Gnumed.business.gmATC

      1  # -*- coding: utf-8 -*-
      2  """ATC handling code.
      3
      4  http://who.no
      5
      6  There is no DDD handling because DDD explicitely
      7  does not carry clinical meaning.
      8  """
      9  #============================================================
     10  __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
     11  __license__ = "GPL v2 or later"
     12
     13  import sys
     14  import io
     15  import logging
     16  import csv
     17  import os.path
     18  import re as regex
     19
     20
     21  if __name__ == '__main__':
     22          sys.path.insert(0, '../../')
     23  from Gnumed.pycommon import gmPG2
     24  from Gnumed.pycommon import gmTools
     25  from Gnumed.pycommon import gmCfg2
     26
     27
     28  _log = logging.getLogger('gm.atc')
     29  _cfg = gmCfg2.gmCfgData()
     30
     31
     32  ATC_NICOTINE = 'N07BA01'
     33  ATC_ETHANOL  = 'V03AB16'
     34
     35  #============================================================
     36 -def propagate_atc(substance=None, atc=None, link_obj=None):
     37
     38          _log.debug('substance <%s>, ATC <%s>', substance, atc)
     39
     40          if atc is not None:
     41                  if atc.strip() == '':
     42                          atc = None
     43
     44          if atc is None:
     45                  atcs = text2atc(text = substance, fuzzy = False, link_obj = link_obj)
     46                  if len(atcs) == 0:
     47                          _log.debug('no ATC found, aborting')
     48                          return atc
     49                  if len(atcs) > 1:
     50                          _log.debug('non-unique ATC mapping, aborting')
     51                          return atc
     52                  atc = atcs[0][0].strip()
     53
     54          args = {'atc': atc, 'term': substance.strip()}
     55          queries = [
     56                  {'cmd': "UPDATE ref.substance SET atc = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc IS NULL",
     57                   'args': args},
     58                  {'cmd': "UPDATE ref.drug_product SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL",
     59                   'args': args}
     60          ]
     61          gmPG2.run_rw_queries(link_obj = link_obj, queries = queries)
     62
     63          return atc
     64
     65  #============================================================
     66 -def text2atc(text=None, fuzzy=False, link_obj=None):
     67
     68          text = text.strip()
     69
     70          if fuzzy:
     71                  args = {'term': '%%%s%%' % text}
     72                  cmd = """
     73                          SELECT DISTINCT ON (atc_code) *
     74                          FROM (
     75                                  SELECT atc as atc_code, is_group_code, pk_data_source
     76                                  FROM ref.v_atc
     77                                  WHERE term ilike %(term)s AND atc IS NOT NULL
     78                                          UNION
     79                                  SELECT atc as atc_code, null, null
     80                                  FROM ref.substance
     81                                  WHERE description ilike %(term)s AND atc IS NOT NULL
     82                                          UNION
     83                                  SELECT atc_code, null, null
     84                                  FROM ref.drug_product
     85                                  WHERE description ilike %(term)s AND atc_code IS NOT NULL
     86                          ) as tmp
     87                          ORDER BY atc_code
     88                  """
     89          else:
     90                  args = {'term': text.lower()}
     91                  cmd = """
     92                          SELECT DISTINCT ON (atc_code) *
     93                          FROM (
     94                                  SELECT atc as atc_code, is_group_code, pk_data_source
     95                                  FROM ref.v_atc
     96                                  WHERE lower(term) = lower(%(term)s) AND atc IS NOT NULL
     97                                          UNION
     98                                  SELECT atc as atc_code, null, null
     99                                  FROM ref.substance
    100                                  WHERE lower(description) = lower(%(term)s) AND atc IS NOT NULL
    101                                          UNION
    102                                  SELECT atc_code, null, null
    103                                  FROM ref.drug_product
    104                                  WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
    105                          ) as tmp
    106                          ORDER BY atc_code
    107                  """
    108
    109          rows, idx = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
    110
    111          _log.debug('term: %s => ATCs: %s (fuzzy: %s)', text, rows, fuzzy)
    112
    113          return rows
    114
    115  #============================================================
    116 -def exists_as_atc(substance):
    117          args = {'term': substance}
    118          cmd = 'SELECT EXISTS (SELECT 1 FROM ref.atc WHERE lower(term) = lower(%(term)s))'
    119          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
    120          return rows[0][0]
    121
    122  #============================================================
    123 -def get_reference_atcs(order_by='atc, term, lang'):
    124          cmd = 'SELECT * FROM ref.v_atc ORDER BY %s' % order_by
    125          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = False)
    126          return rows
    127
    128  #============================================================
    129 -def atc_import(cfg_fname=None, conn=None):
    130
    131          # read meta data
    132          _cfg.add_file_source(source = 'atc', file = cfg_fname, encoding = 'utf8')
    133
    134          data_fname = os.path.join (
    135                  os.path.dirname(cfg_fname),
    136                  _cfg.get(group = 'atc', option = 'data file', source_order = [('atc', 'return')])
    137          )                       # must be in same dir as conf file
    138          version = _cfg.get(group = 'atc', option = 'version', source_order = [('atc', 'return')])
    139          lang = _cfg.get(group = 'atc', option = 'language', source_order = [('atc', 'return')])
    140          desc = _cfg.get(group = 'atc', option = 'description', source_order = [('atc', 'return')])
    141          url = _cfg.get(group = 'atc', option = 'url', source_order = [('atc', 'return')])
    142          name_long = _cfg.get(group = 'atc', option = 'long name', source_order = [('atc', 'return')])
    143          name_short = _cfg.get(group = 'atc', option = 'short name', source_order = [('atc', 'return')])
    144
    145          _cfg.remove_source(source = 'atc')
    146
    147          _log.debug('importing ATC version [%s] (%s) from [%s]', version, lang, data_fname)
    148
    149          args = {'ver': version, 'desc': desc, 'url': url, 'name_long': name_long, 'name_short': name_short, 'lang': lang}
    150
    151          # create data source record
    152          queries = [
    153                  {
    154                  'cmd': """delete from ref.data_source where name_short = %(name_short)s and version = %(ver)s""",
    155                  'args': args
    156                  }, {
    157                  'cmd': """
    158  insert into ref.data_source (name_long, name_short, version, description, lang, source) values (
    159          %(name_long)s,
    160          %(name_short)s,
    161          %(ver)s,
    162          %(desc)s,
    163          %(lang)s,
    164          %(url)s
    165  )""",
    166                  'args': args
    167                  }, {
    168                  'cmd': """select pk from ref.data_source where name_short = %(name_short)s and version = %(ver)s""",
    169                  'args': args
    170                  }
    171          ]
    172          rows, idx = gmPG2.run_rw_queries(queries = queries, return_data = True)
    173          data_src_pk = rows[0][0]
    174          _log.debug('ATC data source record created, pk is #%s', data_src_pk)
    175
    176          # import data
    177          csv_file = io.open(data_fname, mode = 'rt', encoding = 'utf8', errors = 'replace')
    178          atc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = ",", quotechar = '"')
    179
    180          # clean out staging area
    181          curs = conn.cursor()
    182          cmd = """delete from ref.atc_staging"""
    183          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
    184          curs.close()
    185          conn.commit()
    186          _log.debug('ATC staging table emptied')
    187
    188          # from file into staging table
    189          curs = conn.cursor()
    190          cmd = """insert into ref.atc_staging values (%s, %s, %s, %s, %s)"""
    191          first = False
    192          for atc_line in atc_reader:
    193                  # skip first
    194                  if not first:
    195                          first = True
    196                          continue
    197
    198                  # skip blanks
    199                  if atc_line[0] + atc_line[1] + atc_line[2] + atc_line[3] + atc_line[4] == '':
    200                          continue
    201
    202                  comment = ''
    203                  unit = ''
    204                  adro = ''
    205
    206                  # "1,1 mg O,P,R,..."
    207                  if regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
    208                          tmp, unit, adro = regex.split('\s', atc_line[4])
    209                  # "1,1 mg O,P,R bezogen auf ..."
    210                  elif regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
    211                          tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
    212                  # "20 mg O"
    213                  elif regex.match('\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
    214                          tmp, unit, adro = regex.split('\s', atc_line[4])
    215                  # "20 mg O bezogen auf ..."
    216                  elif regex.match('\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
    217                          tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
    218                  # "Standarddosis: 1 Tablette oder 30 ml Mixtur"
    219                  else:
    220                          comment = atc_line[4]
    221
    222                  args = [
    223                          atc_line[0].strip(),
    224                          atc_line[2],
    225                          unit,
    226                          adro,
    227                          comment
    228                  ]
    229
    230                  gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd, 'args': args}])
    231
    232          curs.close()
    233          conn.commit()
    234          csv_file.close()
    235          _log.debug('ATC staging table loaded')
    236
    237          # from staging table to real table
    238          curs = conn.cursor()
    239          args = {'src_pk': data_src_pk}
    240          cmd = """
    241  insert into ref.atc (
    242          fk_data_source,
    243          code,
    244          term,
    245          comment,
    246          unit,
    247          administration_route
    248  ) select
    249          %(src_pk)s,
    250          atc,
    251          name,
    252          nullif(comment, ''),
    253          nullif(unit, ''),
    254          nullif(adro, '')
    255
    256  from
    257          ref.atc_staging
    258  """
    259
    260          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd, 'args': args}])
    261
    262          curs.close()
    263          conn.commit()
    264          _log.debug('transfer from ATC staging table to real ATC table done')
    265
    266          # clean out staging area
    267          curs = conn.cursor()
    268          cmd = """delete from ref.atc_staging"""
    269          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
    270          curs.close()
    271          conn.commit()
    272          _log.debug('ATC staging table emptied')
    273
    274          return True
    275
    276  #============================================================
    277  # main
    278  #------------------------------------------------------------
    279  if __name__ == "__main__":
    280
    281          if len(sys.argv) == 1:
    282                  sys.exit()
    283
    284          if sys.argv[1] != 'test':
    285                  sys.exit()
    286
    287          from Gnumed.pycommon import gmLog2
    288          from Gnumed.pycommon import gmI18N
    289
    290          gmI18N.activate_locale()
    291  #       gmDateTime.init()
    292
    293          #--------------------------------------------------------
    294 -        def test_atc_import():
    295                  atc_import(cfg_fname = sys.argv[2], conn = gmPG2.get_connection(readonly = False))
    296          #--------------------------------------------------------
    297 -        def test_text2atc():
    298                  print('searching ATC code for:', sys.argv[2])
    299                  print(' ', text2atc(sys.argv[2]))
    300                  print(' ', text2atc(sys.argv[2], True))
    301          #--------------------------------------------------------
    302 -        def test_get_reference_atcs():
    303                  print("reference_of_atc_codes:")
    304                  for atc in get_reference_atcs():
    305                          print(atc)
    306          #--------------------------------------------------------
    307          #test_atc_import()
    308          #test_text2atc()
    309          test_get_reference_atcs()
    310
    311  #============================================================
    312