Gnumed.business.gmATC

Package Gnumed :: Package business :: Module gmATC |
[frames] | no frames]

# Source Code for Module Gnumed.business.gmATC

      1  # -*- coding: utf8 -*-
      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  license: GPL v2 or later
     10  """
     11  #============================================================
     12  __version__ = "$Revision: 1.7 $"
     13  __author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
     14
     15  import sys, codecs, logging, csv, re as regex, os.path
     16
     17
     18  if __name__ == '__main__':
     19          sys.path.insert(0, '../../')
     20  from Gnumed.pycommon import gmPG2, gmTools, gmCfg2
     21
     22
     23  _log = logging.getLogger('gm.atc')
     24  _log.info(__version__)
     25
     26  _cfg = gmCfg2.gmCfgData()
     27  #============================================================
     28 -def propagate_atc(substance=None, atc=None):
     29
     30          _log.debug('substance <%s>, ATC <%s>', substance, atc)
     31
     32          if atc is not None:
     33                  if atc.strip() == u'':
     34                          atc = None
     35
     36          if atc is None:
     37                  atcs = text2atc(text = substance, fuzzy = False)
     38                  if len(atcs) == 0:
     39                          _log.debug(u'no ATC found, aborting')
     40                          return atc
     41                  if len(atcs) > 1:
     42                          _log.debug(u'non-unique ATC mapping, aborting')
     43                          return atc
     44                  atc = atcs[0][0].strip()
     45
     46          args = {'atc': atc, 'term': substance.strip()}
     47          queries = [
     48                  {'cmd': u"UPDATE ref.consumable_substance SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL",
     49                   'args': args},
     50                  {'cmd': u"UPDATE ref.branded_drug SET atc_code = %(atc)s WHERE lower(description) = lower(%(term)s) AND atc_code IS NULL",
     51                   'args': args}
     52          ]
     53          gmPG2.run_rw_queries(queries = queries)
     54
     55          return atc
     56  #============================================================
     57 -def text2atc(text=None, fuzzy=False):
     58
     59          text = text.strip()
     60
     61          if fuzzy:
     62                  args = {'term': u'%%%s%%' % text}
     63                  cmd = u"""
     64                          SELECT DISTINCT ON (atc_code) *
     65                          FROM (
     66                                  SELECT atc as atc_code, is_group_code, pk_data_source
     67                                  FROM ref.v_atc
     68                                  WHERE term ilike %(term)s AND atc IS NOT NULL
     69                                          UNION
     70                                  SELECT atc_code, null, null
     71                                  FROM ref.consumable_substance
     72                                  WHERE description ilike %(term)s AND atc_code IS NOT NULL
     73                                          UNION
     74                                  SELECT atc_code, null, null
     75                                  FROM ref.branded_drug
     76                                  WHERE description ilike %(term)s AND atc_code IS NOT NULL
     77                          ) as tmp
     78                          ORDER BY atc_code
     79                  """
     80          else:
     81                  args = {'term': text.lower()}
     82                  cmd = u"""
     83                          SELECT DISTINCT ON (atc_code) *
     84                          FROM (
     85                                  SELECT atc as atc_code, is_group_code, pk_data_source
     86                                  FROM ref.v_atc
     87                                  WHERE lower(term) = lower(%(term)s) AND atc IS NOT NULL
     88                                          UNION
     89                                  SELECT atc_code, null, null
     90                                  FROM ref.consumable_substance
     91                                  WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
     92                                          UNION
     93                                  SELECT atc_code, null, null
     94                                  FROM ref.branded_drug
     95                                  WHERE lower(description) = lower(%(term)s) AND atc_code IS NOT NULL
     96                          ) as tmp
     97                          ORDER BY atc_code
     98                  """
     99
    100          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
    101
    102          _log.debug(u'term: %s => ATCs: %s (fuzzy: %s)', text, rows, fuzzy)
    103
    104          return rows
    105
    106  #============================================================
    107 -def get_reference_atcs(order_by=u'atc, term, lang'):
    108          cmd = u'SELECT * FROM ref.v_atc ORDER BY %s' % order_by
    109          rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = False)
    110          return rows
    111
    112  #============================================================
    113 -def atc_import(cfg_fname=None, conn=None):
    114
    115          # read meta data
    116          _cfg.add_file_source(source = 'atc', file = cfg_fname, encoding = 'utf8')
    117
    118          data_fname = os.path.join (
    119                  os.path.dirname(cfg_fname),
    120                  _cfg.get(group = 'atc', option = 'data file', source_order = [('atc', 'return')])
    121          )                       # must be in same dir as conf file
    122          version = _cfg.get(group = 'atc', option = 'version', source_order = [('atc', 'return')])
    123          lang = _cfg.get(group = 'atc', option = 'language', source_order = [('atc', 'return')])
    124          desc = _cfg.get(group = 'atc', option = 'description', source_order = [('atc', 'return')])
    125          url = _cfg.get(group = 'atc', option = 'url', source_order = [('atc', 'return')])
    126          name_long = _cfg.get(group = 'atc', option = 'long name', source_order = [('atc', 'return')])
    127          name_short = _cfg.get(group = 'atc', option = 'short name', source_order = [('atc', 'return')])
    128
    129          _cfg.remove_source(source = 'atc')
    130
    131          _log.debug('importing ATC version [%s] (%s) from [%s]', version, lang, data_fname)
    132
    133          args = {'ver': version, 'desc': desc, 'url': url, 'name_long': name_long, 'name_short': name_short, 'lang': lang}
    134
    135          # create data source record
    136          queries = [
    137                  {
    138                  'cmd': u"""delete from ref.data_source where name_short = %(name_short)s and version = %(ver)s""",
    139                  'args': args
    140                  }, {
    141                  'cmd': u"""
    142  insert into ref.data_source (name_long, name_short, version, description, lang, source) values (
    143          %(name_long)s,
    144          %(name_short)s,
    145          %(ver)s,
    146          %(desc)s,
    147          %(lang)s,
    148          %(url)s
    149  )""",
    150                  'args': args
    151                  }, {
    152                  'cmd': u"""select pk from ref.data_source where name_short = %(name_short)s and version = %(ver)s""",
    153                  'args': args
    154                  }
    155          ]
    156          rows, idx = gmPG2.run_rw_queries(queries = queries, return_data = True)
    157          data_src_pk = rows[0][0]
    158          _log.debug('ATC data source record created, pk is #%s', data_src_pk)
    159
    160          # import data
    161          csv_file = codecs.open(data_fname, 'rU', 'utf8', 'replace')
    162          atc_reader = gmTools.unicode_csv_reader(csv_file, delimiter = ",", quotechar = '"')
    163
    164          # clean out staging area
    165          curs = conn.cursor()
    166          cmd = u"""delete from ref.atc_staging"""
    167          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
    168          curs.close()
    169          conn.commit()
    170          _log.debug('ATC staging table emptied')
    171
    172          # from file into staging table
    173          curs = conn.cursor()
    174          cmd = u"""insert into ref.atc_staging values (%s, %s, %s, %s, %s)"""
    175          first = False
    176          for atc_line in atc_reader:
    177                  # skip first
    178                  if not first:
    179                          first = True
    180                          continue
    181
    182                  # skip blanks
    183                  if atc_line[0] + atc_line[1] + atc_line[2] + atc_line[3] + atc_line[4] == u'':
    184                          continue
    185
    186                  comment = u''
    187                  unit = u''
    188                  adro = u''
    189
    190                  # "1,1 mg O,P,R,..."
    191                  if regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
    192                          tmp, unit, adro = regex.split('\s', atc_line[4])
    193                  # "1,1 mg O,P,R bezogen auf ..."
    194                  elif regex.match('\d{,3},\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
    195                          tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
    196                  # "20 mg O"
    197                  elif regex.match('\d{,3}\s.{1,2}\s.(,.)*$', atc_line[4]):
    198                          tmp, unit, adro = regex.split('\s', atc_line[4])
    199                  # "20 mg O bezogen auf ..."
    200                  elif regex.match('\d{,3}\s.{1,2}\s.(,.)*\s.+$', atc_line[4]):
    201                          tmp, unit, adro, comment = regex.split('\s', atc_line[4], 3)
    202                  # "Standarddosis: 1 Tablette oder 30 ml Mixtur"
    203                  else:
    204                          comment = atc_line[4]
    205
    206                  args = [
    207                          atc_line[0].strip(),
    208                          atc_line[2],
    209                          unit,
    210                          adro,
    211                          comment
    212                  ]
    213
    214                  gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd, 'args': args}])
    215
    216          curs.close()
    217          conn.commit()
    218          csv_file.close()
    219          _log.debug('ATC staging table loaded')
    220
    221          # from staging table to real table
    222          curs = conn.cursor()
    223          args = {'src_pk': data_src_pk}
    224          cmd = u"""
    225  insert into ref.atc (
    226          fk_data_source,
    227          code,
    228          term,
    229          comment,
    230          unit,
    231          administration_route
    232  ) select
    233          %(src_pk)s,
    234          atc,
    235          name,
    236          nullif(comment, ''),
    237          nullif(unit, ''),
    238          nullif(adro, '')
    239
    240  from
    241          ref.atc_staging
    242  """
    243
    244          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd, 'args': args}])
    245
    246          curs.close()
    247          conn.commit()
    248          _log.debug('transfer from ATC staging table to real ATC table done')
    249
    250          # clean out staging area
    251          curs = conn.cursor()
    252          cmd = u"""delete from ref.atc_staging"""
    253          gmPG2.run_rw_queries(link_obj = curs, queries = [{'cmd': cmd}])
    254          curs.close()
    255          conn.commit()
    256          _log.debug('ATC staging table emptied')
    257
    258          return True
    259  #============================================================
    260  # main
    261  #------------------------------------------------------------
    262  if __name__ == "__main__":
    263
    264          if len(sys.argv) == 1:
    265                  sys.exit()
    266
    267          if sys.argv[1] != 'test':
    268                  sys.exit()
    269
    270          from Gnumed.pycommon import gmLog2
    271          from Gnumed.pycommon import gmI18N
    272
    273          gmI18N.activate_locale()
    274  #       gmDateTime.init()
    275
    276          #--------------------------------------------------------
    277 -        def test_atc_import():
    278                  atc_import(cfg_fname = sys.argv[2], conn = gmPG2.get_connection(readonly = False))
    279          #--------------------------------------------------------
    280 -        def test_text2atc():
    281                  print 'searching ATC code for:', sys.argv[2]
    282                  print ' ', text2atc(sys.argv[2])
    283                  print ' ', text2atc(sys.argv[2], True)
    284          #--------------------------------------------------------
    285 -        def test_get_reference_atcs():
    286                  print "reference_of_atc_codes:"
    287                  for atc in get_reference_atcs():
    288                          print atc
    289          #--------------------------------------------------------
    290          #test_atc_import()
    291          #test_text2atc()
    292          test_get_reference_atcs()
    293
    294  #============================================================
    295