Gnumed.exporters.export_immunization_metadata

Package Gnumed :: Package exporters :: Module export_immunization_metadata |
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# Source Code for Module Gnumed.exporters.export_immunization_metadata

      1  # GNUmed vaccination metadata exporter
      2  #============================================================
      3  __author__ = "Karsten Hilbert"
      4  __license__ = 'GPL'
      5
      6  from Gnumed.pycommon import gmPG
      7  #============================================================
      8  # connect to database
      9  pool = gmPG.ConnectionPool()
     10
     11  filename = 'immunization-data.txt'
     12  print "Writing immunization metadata to:", filename
     13  f = open(filename, 'w')
     14
     15  vaccine_template = """
     16  Vaccine "%s" (%s)
     17    comment  : %s
     18    given via: %s (%s = %s)
     19    age range: %s days - %s days
     20  """
     21
     22  schedule_template = """
     23  Schedule "%s" (%s)
     24    indication : %s (%s)
     25    start @ age: %s days
     26    # of shots : %s
     27    comment    : %s
     28  """
     29
     30  #===========================
     31  # export vaccine information
     32  #===========================
     33
     34  # retrieve vaccines
     35  cmd = "select * from clin.v_vaccine"
     36  vaccine_rows, idx = gmPG.run_ro_query (
     37          link_obj = 'clinical',
     38          aQuery = cmd,
     39          get_col_idx = True
     40  )
     41  # error
     42  if vaccine_rows is None:
     43          print "error retrieving vaccine data"
     44  # display vaccine data
     45  else:
     46          f.write('Vaccines in the GNUmed database\n')
     47          f.write('-------------------------------\n')
     48          for vacc in vaccine_rows:
     49                  f.write(vaccine_template % (
     50                          vacc[idx['trade_name']],
     51                          vacc[idx['short_name']],
     52                          vacc[idx['comment']],
     53                          vacc[idx['l10n_route_description']],
     54                          vacc[idx['route_abbreviation']],
     55                          vacc[idx['route_description']],
     56                          vacc[idx['min_age']].day,
     57                          vacc[idx['max_age']].day
     58                  ))
     59                  if vacc[idx['is_live']] is None:
     60                          f.write("  type of vaccine not known\n")
     61                  elif vacc[idx['is_live']]:
     62                          f.write("  Cave: live vaccine\n")
     63                  else:
     64                          f.write("  non-live vaccine\n")
     65                  # get indications for this vaccine
     66                  cmd = """select * from clin.v_inds4vaccine where pk_vaccine = %s"""
     67                  indication_rows, ind_idx = gmPG.run_ro_query (
     68                          'clinical',
     69                          cmd,
     70                          True,
     71                          vacc[idx['pk_vaccine']]
     72                  )
     73                  # error
     74                  if indication_rows is None:
     75                          print "error retrieving vaccine indication data"
     76                  # display them
     77                  else:
     78                          f.write('  Indications:\n')
     79                          for ind in indication_rows:
     80                                  f.write('  - %s (%s)\n' % (ind[ind_idx['l10n_indication']], ind[ind_idx['indication']]))
     81
     82  #=============================
     83  # export vaccination schedules
     84  #=============================
     85
     86  # retrieve schedules
     87  cmd = "select * from clin.v_vacc_regimes"
     88  schedule_rows, idx = gmPG.run_ro_query (
     89          'clinical',
     90          cmd,
     91          True
     92  )
     93  if schedule_rows is None:
     94          print "error retrieving vaccination schedules"
     95  else:
     96          f.write('\n\nVaccination schedules in the GNUmed database\n')
     97          f.write(    '--------------------------------------------\n')
     98          for sched in schedule_rows:
     99                  if sched[idx['is_active']]:
    100                          act = 'active'
    101                  else:
    102                          act = 'inactive'
    103                  f.write(schedule_template % (
    104                          sched[idx['regime']],
    105                          act,
    106                          sched[idx['l10n_indication']],
    107                          sched[idx['indication']],
    108                          sched[idx['min_age_due']],
    109                          sched[idx['shots']],
    110                          sched[idx['comment']]
    111                  ))
    112                  # get shots for this schedule
    113                  cmd = "select * from clin.v_vacc_defs4reg where pk_regime=%s order by vacc_seq_no"
    114                  shot_rows, shots_idx = gmPG.run_ro_query (
    115                          'clinical',
    116                          cmd,
    117                          True,
    118                          sched[idx['pk_regime']]
    119                  )
    120                  if shot_rows is None:
    121                          print "error retrieving shots for regime"
    122                  else:
    123                          f.write('  Shots defined for this schedule:\n')
    124                          for shot in shot_rows:
    125                                  if shot[shots_idx['is_booster']]:
    126                                          f.write('  booster) start %s - %s days of age, refresh after %s (%s)\n' % (
    127                                                  shot[shots_idx['age_due_min']].day,
    128                                                  shot[shots_idx['age_due_max']].day,
    129                                                  shot[shots_idx['min_interval']].day,
    130                                                  shot[shots_idx['vacc_comment']]
    131                                          ))
    132                                  elif shot[shots_idx['vacc_seq_no']] == 1:
    133                                          f.write('  shot #%s) due between day %s and %s (%s)\n' % (
    134                                                  shot[shots_idx['vacc_seq_no']],
    135                                                  shot[shots_idx['age_due_min']].day,
    136                                                  shot[shots_idx['age_due_max']].day,
    137                                                  shot[shots_idx['vacc_comment']]
    138                                          ))
    139                                  else:
    140                                          f.write('  shot #%s) due between day %s and %s, minimum %s day after previous (%s)\n' % (
    141                                                  shot[shots_idx['vacc_seq_no']],
    142                                                  shot[shots_idx['age_due_min']].day,
    143                                                  shot[shots_idx['age_due_max']].day,
    144                                                  shot[shots_idx['min_interval']].day,
    145                                                  shot[shots_idx['vacc_comment']]
    146                                          ))
    147                  # get vaccines suitable for this schedule
    148                  cmd = """
    149  select trade_name, short_name
    150  from ref.vaccine
    151  where
    152          select () = ()
    153  """
    154
    155  f.close()
    156