Gnumed.business.gmVaccination API documentation
Description: GNUmed vaccination related business objects.

# Module `Gnumed.business.gmVaccination`

GNUmed vaccination related business objects.

## Functions

`def create_vaccination(encounter: int = None,
episode: int = None,
pk_vaccine: int = None,
batch_no: str = None)`
  Expand source code

      def create_vaccination(encounter:int=None, episode:int=None, pk_vaccine:int=None, batch_no:str=None):
              cmd = """
                      INSERT INTO clin.vaccination (
                              fk_encounter,
                              fk_episode,
                              fk_vaccine,
                              batch_no
                      ) VALUES (
                              %(enc)s,
                              %(epi)s,
                              %(pk_vacc)s,
                              %(batch)s
                      ) RETURNING pk;
              """
              args = {
                      'enc': encounter,
                      'epi': episode,
                      'pk_vacc': pk_vaccine,
                      'batch': batch_no
              }
              rows = gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}], return_data = True)
              return cVaccination(aPK_obj = rows[0][0])

`def create_vaccine(pk_drug_product=None, product_name=None, is_live=None)`
  Expand source code

      def create_vaccine(pk_drug_product=None, product_name=None, is_live=None):
              # force caller to make a decision, which is hoped
              # to bubble up towards the end user ;-)
              assert (is_live is not None), '<is_live> must not be <None>'

              conn = gmPG2.get_connection(readonly = False)
              dose = create_vaccine_dummy_dose(link_obj = conn)
              if not pk_drug_product:
                      if product_name:
                              _log.debug('creating vaccine drug product [%s]', product_name)
                              vacc_prod = gmMedication.create_drug_product (
                                      product_name = product_name,
                                      preparation = 'vaccine',
                                      return_existing = True,
                                      pk_doses = [dose],
                                      link_obj = conn
                              )
                              pk_drug_product = vacc_prod['pk_drug_product']
              if pk_drug_product:
                      SQL = 'INSERT INTO ref.vaccine (fk_drug_product, is_live) values (%(pk_drug_product)s, %(live)s) RETURNING pk'
              else:
                      SQL = 'INSERT INTO ref.vaccine (is_live) values (%(live)s) RETURNING pk'
              args = {
                      'pk_drug_product': pk_drug_product,
                      'live': is_live
              }
              queries = [{'sql': SQL, 'args': args}]
              rows = gmPG2.run_rw_queries(link_obj = conn, queries = queries, return_data = True, end_tx = True)
              return cVaccine(aPK_obj = rows[0]['pk'], link_obj = conn)

`def create_vaccine_dummy_dose(link_obj=None) ‑> int`
  Expand source code

      def create_vaccine_dummy_dose(link_obj=None) -> int:
              # brands require a component, so:
              SQL = """-- INSERT dummy vaccine substance
              INSERT INTO ref.substance (description, atc)
                      SELECT %(subst)s, %(atc)s
                      WHERE NOT EXISTS (
                              SELECT 1 FROM ref.substance WHERE description = %(subst)s AND atc = %(atc)s
                      );
              -- INSERT dummy vaccine dose
              INSERT INTO ref.dose (fk_substance, amount, unit, dose_unit)
                      SELECT
                              (SELECT pk FROM ref.substance WHERE description = %(subst)s AND atc = %(atc)s),
                              1, %(unit)s, %(dose_unit)s
                      WHERE NOT EXISTS (
                              SELECT 1 FROM ref.dose WHERE fk_substance = (
                                      SELECT pk FROM ref.substance WHERE description = %(subst)s AND atc = %(atc)s
                              )
                      );
              SELECT pk FROM ref.dose WHERE fk_substance = (
                      SELECT pk FROM ref.substance WHERE description = %(subst)s AND atc = %(atc)s
              );
              """
              args = {
                      'subst': 'vaccine',
                      'atc': 'J07',
                      'unit': 'dose',
                      'dose_unit': 'shot'
              }
              rows = gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}], link_obj = link_obj, return_data = True)
              return rows[0]['pk']

`def delete_vaccination(vaccination=None)`
  Expand source code

      def delete_vaccination(vaccination=None):
              SQL = 'DELETE FROM clin.vaccination WHERE pk = %(pk)s'
              args = {'pk': vaccination}
              gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])

`def delete_vaccine(pk_vaccine: int = None, also_delete_product: bool = False) ‑> bool`
  Expand source code

      def delete_vaccine(pk_vaccine:int=None, also_delete_product:bool=False) -> bool:
              args = {'pk_vacc': pk_vaccine, 'pk_drug': None}
              if also_delete_product:
                      SQL = 'SELECT fk_drug_product FROM ref.vaccine WHERE pk = %(pk_vacc)s'
                      q = {'sql': SQL, 'args': args}
                      rows = gmPG2.run_ro_queries(queries = [q])
                      if rows:
                              args['pk_drug'] = rows[0]['fk_drug_product']
              queries = []
              SQL = 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_vaccine = %(pk_vacc)s'
              queries.append({'sql': SQL, 'args': args})
              SQL = 'DELETE FROM ref.vaccine WHERE pk = %(pk_vacc)s'
              queries.append({'sql': SQL, 'args': args})
              if args['pk_drug']:
                      SQL = 'DELETE FROM ref.lnk_dose2drug WHERE fk_drug_product = %(pk_drug)s'
                      queries.append({'sql': SQL, 'args': args})
                      SQL = 'DELETE FROM ref.drug_product WHERE pk = %(pk_drug)s'
                      queries.append({'sql': SQL, 'args': args})
              try:
                      gmPG2.run_rw_queries(queries = queries)
              except gmPG2.dbapi.IntegrityError:
                      _log.exception('cannot delete vaccine [#%s]', pk_vaccine)
                      return False

              return True

`def format_latest_vaccinations(output_format='latex', emr=None)`
  Expand source code

      def format_latest_vaccinations(output_format='latex', emr=None):

              _log.debug('formatting latest vaccinations into [%s]', output_format)

              vaccs = emr.get_latest_vaccinations()

              if output_format == 'latex':
                      return __format_latest_vaccinations_latex(vaccinations = vaccs)

              msg = _('unknown vaccinations output format [%s]') % output_format
              _log.error(msg)
              return msg

`def format_vaccinations_by_indication_for_failsafe_output(pk_patient: int, max_width: int = 80) ‑> list[str]`
  Expand source code

      def format_vaccinations_by_indication_for_failsafe_output(pk_patient:int, max_width:int=80) -> list[str]:
              shots = get_vaccinations(pk_identity = pk_patient)
              if not shots:
                      return []

              shots_by_ind:dict[str, list[cVaccination]] = {}
              for shot in shots:
                      inds = shot['indications']
                      for ind in inds:
                              try:
                                      shots_by_ind[ind['l10n_indication']]
                              except KeyError:
                                      shots_by_ind[ind['l10n_indication']] = []
                              shots_by_ind[ind['l10n_indication']].append(shot)
              lines = []
              l10n_inds_sorted = sorted(shots_by_ind.keys(), key = functools.cmp_to_key(locale.strcoll))
              for ind in l10n_inds_sorted:
                      lines.append('')
                      lines.append(_('Indication: %s') % ind)
                      shots4ind = sorted(shots_by_ind[ind], key = lambda d: d['date_given'], reverse = True)
                      for shot in shots4ind:
                              lines.append(gmTools.shorten_text (
                                      '  %s: %s [%s]' % (
                                              shot['date_given'].strftime('%Y %b %d'),
                                              shot['vaccine'],
                                              shot['batch_no']
                                      ),
                                      max_width
                              ))
                              if shot['comment']:
                                      lines.append(gmTools.shorten_text('   ' + shot['comment'], max_width))
                              if shot._payload['reaction']:
                                      lines.append(gmTools.shorten_text('   ' + shot['reaction'], max_width))
              return lines

`def get_vaccination_indications(order_by: str = None)`
  Expand source code

      def get_vaccination_indications(order_by:str=None):
              SQL = 'SELECT * from ref.vacc_indication'
              if order_by:
                      SQL += ' ORDER BY %s' % order_by
              rows = gmPG2.run_ro_query(sql = SQL)
              return rows

`def get_vaccinations(pk_identity=None,
pk_episodes=None,
pk_health_issues=None,
pk_encounters=None,
order_by=None,
return_pks=False)`
  Expand source code

      def get_vaccinations(pk_identity=None, pk_episodes=None, pk_health_issues=None, pk_encounters=None, order_by=None, return_pks=False):

              args = {}
              where_parts = []

              if pk_identity is not None:
                      args = {'pk_identity': pk_identity}
                      where_parts.append('pk_patient = %(pk_identity)s')

              if (pk_episodes is not None) and (len(pk_episodes) > 0):
                      where_parts.append('pk_episode = ANY(%(pk_epis)s)')
                      args['pk_epis'] = pk_episodes

              if (pk_health_issues is not None) and (len(pk_health_issues) > 0):
                      where_parts.append('pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(pk_issues)s))')
                      args['pk_issues'] = pk_health_issues

              if (pk_encounters is not None) and (len(pk_encounters) > 0):
                      where_parts.append('pk_encounter = ANY(%(pk_encs)s)')
                      args['pk_encs'] = pk_encounters

              ORDER_BY = gmTools.coalesce (
                      value2test = order_by,
                      return_instead = '',
                      value2return = 'ORDER BY %s' % order_by
              )
              if len(where_parts) == 0:
                      WHERE = 'True'
              else:
                      WHERE = '\nAND '.join(where_parts)

              SQL = '%s %s' % (
                      _SQL_get_vaccination_fields % WHERE,
                      ORDER_BY
              )
              rows = gmPG2.run_ro_query(sql = SQL, args = args)
              if return_pks:
                      return [ r['pk_vaccination'] for r in rows ]

              vaccs = [ cVaccination(row = {'data': r, 'pk_field': 'pk_vaccination'}) for r in rows ]
              return vaccs

`def get_vaccines(order_by=None, return_pks=False)`
  Expand source code

      def get_vaccines(order_by=None, return_pks=False):

              if order_by is None:
                      cmd = _SQL_get_vaccine_fields % 'TRUE'
              else:
                      cmd = _SQL_get_vaccine_fields % ('TRUE\nORDER BY %s' % order_by)

              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd}])
              if return_pks:
                      return [ r['pk_vaccine'] for r in rows ]
              return [ cVaccine(row = {'data': r, 'pk_field': 'pk_vaccine'}) for r in rows ]

## Classes

`class cVaccination (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      class cVaccination(gmBusinessDBObject.cBusinessDBObject):

              _cmd_fetch_payload = _SQL_get_vaccination_fields % "pk_vaccination = %s"

              _cmds_store_payload = [
                      """UPDATE clin.vaccination SET
                                      soap_cat = %(soap_cat)s,
                                      clin_when = %(date_given)s,
                                      site = gm.nullify_empty_string(%(site)s),
                                      batch_no = gm.nullify_empty_string(%(batch_no)s),
                                      reaction = gm.nullify_empty_string(%(reaction)s),
                                      narrative = gm.nullify_empty_string(%(comment)s),
                                      fk_vaccine = %(pk_vaccine)s,
                                      fk_provider = %(pk_provider)s,
                                      fk_encounter = %(pk_encounter)s,
                                      fk_episode = %(pk_episode)s
                              WHERE
                                      pk = %(pk_vaccination)s
                                              AND
                                      xmin = %(xmin_vaccination)s
                              RETURNING
                                      xmin as xmin_vaccination
                      """
              ]

              _updatable_fields = [
                      'soap_cat',
                      'date_given',
                      'site',
                      'batch_no',
                      'reaction',
                      'comment',
                      'pk_vaccine',
                      'pk_provider',
                      'pk_encounter',
                      'pk_episode'
              ]

              #--------------------------------------------------------
              def format_maximum_information(self, patient=None):
                      return self.format (
                              with_indications = True,
                              with_comment = True,
                              with_reaction = True,
                              date_format = '%Y %b %d'
                      )

              #--------------------------------------------------------
              def format(self, with_indications=False, with_comment=False, with_reaction=False, date_format='%Y-%m-%d'):

                      lines = []

                      lines.append (' %s: %s [%s]%s' % (
                              self._payload['date_given'].strftime(date_format),
                              self._payload['vaccine'],
                              self._payload['batch_no'],
                              gmTools.coalesce(self._payload['site'], '', ' (%s)')
                      ))

                      if with_comment:
                              if self._payload['comment'] is not None:
                                      lines.append('   %s' % self._payload['comment'])

                      if with_reaction:
                              if self._payload['reaction'] is not None:
                                      lines.append('   %s' % self._payload['reaction'])

                      if with_indications:
                              lines.append('   %s' % ' / '.join([ i['l10n_indication'] for i in self._payload['indications'] ]))

                      return lines

              #--------------------------------------------------------
              def format_for_failsafe_output(self, max_width:int=80) -> list[str]:
                      lines = []
                      lines.append(gmTools.shorten_text(
                              '%s: %s [%s]%s' % (
                                      self._payload['date_given'].strftime('%Y %b %d'),
                                      self._payload['vaccine'],
                                      self._payload['batch_no'],
                                      gmTools.coalesce(self._payload['site'], '', ' (%s)')
                              ),
                              max_width
                      ))
                      lines.append('  ' + _('Indications: %s') % ' / '.join([ i['l10n_indication'] for i in self._payload['indications'] ]))
                      if self._payload['comment']:
                              lines.append(gmTools.shorten_text('  ' + self._payload['comment'], max_width))
                      if self._payload['reaction']:
                              lines.append(gmTools.shorten_text('  ' + self._payload['reaction'], max_width))
                      return lines

              #--------------------------------------------------------
              def _get_vaccine(self):
                      return cVaccine(aPK_obj = self._payload['pk_vaccine'])

              vaccine = property(_get_vaccine)

  Represents business objects in the database.

  ## Rules

  - instances ARE ASSUMED TO EXIST in the database
  - PK construction (aPK_obj): DOES verify its existence on instantiation (fetching data fails)
  - Row construction (row): allowed by using a dict of pairs of field name: field value (PERFORMANCE improvement)
  - does NOT verify FK target existence
  - does NOT create new entries in the database
  - does NOT lazy-fetch fields on access

  Class scope SQL commands and variables:

  _cmd_fetch_payload:

  - must return exactly one row
  - WHERE clause argument values are expected in self.pk_obj (taken from init(aPK_obj))
  - must return xmin of all rows that _cmds_store_payload will be updating, so views must support the xmin columns of their underlying tables

  _cmds_store_payload:

  - one or multiple "update … set … where xmin_ = … and pk = …" statements which actually update the database from the data in self._payload,
  - the last query must refetch at least the XMIN values needed to detect concurrent updates, their field names had better be the same as in _cmd_fetch_payload,
  - the last query CAN return other fields which is particularly useful when those other fields are computed in the backend and may thus change upon save but will not have been set by the client code explicitly - this is only really of concern if the saved subclass is to be reused after saving rather than re-instantiated
  - when subclasses tend to live a while after save_payload() was called and they support computed fields (say, _(some_column) you need to return all columns (see cEncounter)

  _updatable_fields:

  - a list of fields available for update via object['field']

  Call init from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend
  - an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
  - a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
  `row`
    must hold the fields
  - data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
  - pk_field: the name of the primary key column OR
  - pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
  - for example:

        row = {
                'data': rows[0],
                'pk_field': 'pk_XXX (the PK column name)',
                'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
        }

        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
        objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]

  ### Ancestors

  - cBusinessDBObject

  ### Instance variables

  `prop vaccine`
    Expand source code

        def _get_vaccine(self):
                return cVaccine(aPK_obj = self._payload['pk_vaccine'])

  ### Methods

  `def format_for_failsafe_output(self, max_width: int = 80) ‑> list[str]`
    Expand source code

        def format_for_failsafe_output(self, max_width:int=80) -> list[str]:
                lines = []
                lines.append(gmTools.shorten_text(
                        '%s: %s [%s]%s' % (
                                self._payload['date_given'].strftime('%Y %b %d'),
                                self._payload['vaccine'],
                                self._payload['batch_no'],
                                gmTools.coalesce(self._payload['site'], '', ' (%s)')
                        ),
                        max_width
                ))
                lines.append('  ' + _('Indications: %s') % ' / '.join([ i['l10n_indication'] for i in self._payload['indications'] ]))
                if self._payload['comment']:
                        lines.append(gmTools.shorten_text('  ' + self._payload['comment'], max_width))
                if self._payload['reaction']:
                        lines.append(gmTools.shorten_text('  ' + self._payload['reaction'], max_width))
                return lines

  `def format_maximum_information(self, patient=None)`
    Expand source code

        def format_maximum_information(self, patient=None):
                return self.format (
                        with_indications = True,
                        with_comment = True,
                        with_reaction = True,
                        date_format = '%Y %b %d'
                )

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`
`class cVaccine (aPK_obj: int | dict = None, row: dict = None, link_obj=None)`
  Expand source code

      class cVaccine(gmBusinessDBObject.cBusinessDBObject):
              """Represents one vaccine."""

              _cmd_fetch_payload = _SQL_get_vaccine_fields % "pk_vaccine = %s"
              _cmds_store_payload = [
                      """UPDATE ref.vaccine SET
                                      is_live = %(is_live)s,
                                      min_age = %(min_age)s,
                                      max_age = %(max_age)s,
                                      comment = gm.nullify_empty_string(%(comment)s),
                                      fk_drug_product = %(pk_drug_product)s,
                                      atc = %(atc_vaccine)s
                              WHERE
                                      pk = %(pk_vaccine)s
                                              AND
                                      xmin = %(xmin_vaccine)s
                              RETURNING
                                      xmin as xmin_vaccine
                      """
              ]
              _updatable_fields = [
                      'is_live',
                      'min_age',
                      'max_age',
                      'comment',
                      'pk_drug_product',
                      'atc_vaccine'
              ]

              #--------------------------------------------------------
              def format(self, *args, **kwargs):
                      lines = []
                      live = gmTools.bool2subst(self._payload['is_live'], _(' (live)'), '', ' <liveness error in DB>')
                      if self._payload['pk_drug_product']:
                              lines.append(_('"%s" [#%s]%s -- #%s') % (
                                      self._payload['vaccine'],
                                      self._payload['pk_vaccine'],
                                      live,
                                      gmTools.coalesce(self._payload['pk_drug_product'], '', '#%s')
                              ))
                      else:
                              lines.append(_('Generic vaccine%s [#%s]%s') % (
                                      gmTools.coalesce(self._payload['atc_vaccine'], '', ' "ATC:%s"'),
                                      self._payload['pk_vaccine'],
                                      live
                              ))
                      lines.append(_(' Targets:'))
                      lines.extend([ '  %s [ATC:%s]' % (i['l10n_indication'], i['atc_indication']) for i in self._payload['indications'] ])
                      if self._payload['pk_drug_product']:
                              lines.append(' %s%s%s' % (
                                      self._payload['l10n_preparation'],
                                      gmTools.coalesce(self._payload['atc_product'], '', ' [ATC:%s]'),
                                      gmTools.coalesce(self._payload['external_code'], '', ' [%s:%%s]' % self._payload['external_code_type'])
                              ))
                      lines.append(_(' Age range: %s - %s') % (
                              gmDateTime.format_interval(interval = self._payload['min_age'], accuracy_wanted = gmDateTime.ACC_MONTHS, none_string = ''),
                              gmDateTime.format_interval(interval = self._payload['max_age'], accuracy_wanted = gmDateTime.ACC_MONTHS, none_string = '')
                      ))
                      if self._payload['comment'] is not None:
                              lines.extend([ ' %s' % l for l in self._payload['comment'].split('\n')] )
                      return lines

              #--------------------------------------------------------
              # properties
              #--------------------------------------------------------
              def _get_product(self):
                      if self._payload['pk_drug_product']:
                              return gmMedication.cDrugProduct(aPK_obj = self._payload['pk_drug_product'])

                      return None

              product = property(_get_product)

              #--------------------------------------------------------
              def _get_is_in_use(self):
                      cmd = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = %(pk)s)'
                      args = {'pk': self._payload['pk_vaccine']}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      return rows[0][0]

              is_in_use = property(_get_is_in_use)

              #--------------------------------------------------------
              # indications handling
              #--------------------------------------------------------
              @staticmethod
              def atcs2indication_pks(atcs:list[str]=None) -> list[int]:
                      query = {
                              'sql': 'SELECT pk FROM ref.vacc_indication WHERE atc = ANY(%(atcs)s)',
                              'args': {'atcs': atcs}
                      }
                      rows = gmPG2.run_ro_queries(queries = [query])
                      if len(atcs) != len(rows):              # all mapped ?
                              _log.error('cannot map all ATCs to vaccine indications')
                              _log.error('ATCs: %s', atcs)
                              return None

                      return [ r['pk'] for r in rows ]

              #--------------------------------------------------------
              @staticmethod
              def targets2indication_pks(targets:list[str]=None) -> list[int]:
                      query = {
                              'sql': 'SELECT pk FROM ref.vacc_indication WHERE atc = ANY(%(targets)s)',
                              'args': {'targets': targets}
                      }
                      rows = gmPG2.run_ro_queries(queries = [query])
                      if len(targets) != len(rows):
                              return None

                      return [ r['pk'] for r in rows ]

              #--------------------------------------------------------
              def add_indication(self, pk_indication:int=None, atc:str=None, indication:str=None):
                      args:dict[str,str]|dict[str,int]
                      if not pk_indication:
                              args = {
                                      'atc': atc,
                                      'indication': indication
                              }
                              if atc:
                                      SQL = 'SELECT pk FROM ref.vacc_indication WHERE atc = %(atc)s'
                              elif indication:
                                      SQL = 'SELECT pk FROM ref.vacc_indication WHERE target = %(indication)s'
                              else:
                                      _log.error('neither <pk_indication>, nor <atc>, nor <indication> given')
                                      return False

                              rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                              if not rows:
                                      _log.error('indication [%s: %s] does not exist', atc, indication)
                                      return False

                              pk_indication = rows[0]['pk']

                      args = {
                              'pk_ind': pk_indication,
                              'pk_vacc': self._payload['pk_vaccine']
                      }
                      SQL = """
                      INSERT INTO ref.lnk_indic2vaccine (fk_indication, fk_vaccine)
                              SELECT %(pk_ind)s, %(pk_vacc)s WHERE NOT EXISTS (
                                      SELECT 1 FROM ref.lnk_indic2vaccine WHERE fk_indication %(pk_ind)s = AND fk_vaccine = %(pk_vacc)s
                              )
                      """
                      gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])
                      return True

              #--------------------------------------------------------
              def remove_indication(self, pk_indication:int=None):
                      args = {
                              'pk_ind': pk_indication,
                              'pk_vacc': self._payload['pk_vaccine']
                      }
                      SQL = 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_indication %(pk_ind)s = AND fk_vaccine = %(pk_vacc)s'
                      gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])

              #--------------------------------------------------------
              def remove_indications(self):
                      args = {'pk_vacc': self._payload['pk_vaccine']}
                      SQL = 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_vaccine = %(pk_vacc)s'
                      gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])

              #--------------------------------------------------------
              def set_indications(self, pk_indications:list[int]=None) -> bool:
                      if not pk_indications:
                              return False

                      if set(pk_indications) == set([ ind['pk_indication'] for ind in self._payload['indications'] ]):
                              # already the same
                              return True

                      queries = [{
                              'sql': 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_vaccine = %(pk_vacc)s',
                              'args': {'pk_vacc': self._payload['pk_vaccine']}
                      }]
                      for pk_ind in set(pk_indications):              # remove dupes
                              queries.append ({
                                      'sql': 'INSERT INTO ref.lnk_indic2vaccine (fk_indication, fk_vaccine) VALUES (%(pk_ind)s, %(pk_vacc)s)',
                                      'args': {'pk_ind': pk_ind, 'pk_vacc': self._payload['pk_vaccine']}
                              })
                      gmPG2.run_rw_queries(queries = queries)
                      self.refetch_payload()
                      return True

  Represents one vaccine.

  Call init from child classes like so:

          super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)

  ## Args

  `aPK_obj`
    retrieve data from backend
  - an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
  - a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
  `row`
    must hold the fields
  - data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
  - pk_field: the name of the primary key column OR
  - pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
  - for example:

        row = {
                'data': rows[0],
                'pk_field': 'pk_XXX (the PK column name)',
                'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
        }

        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
        objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]

  ### Ancestors

  - cBusinessDBObject

  ### Static methods

  `def atcs2indication_pks(atcs: list[str] = None) ‑> list[int]`
    Expand source code

        @staticmethod
        def atcs2indication_pks(atcs:list[str]=None) -> list[int]:
                query = {
                        'sql': 'SELECT pk FROM ref.vacc_indication WHERE atc = ANY(%(atcs)s)',
                        'args': {'atcs': atcs}
                }
                rows = gmPG2.run_ro_queries(queries = [query])
                if len(atcs) != len(rows):              # all mapped ?
                        _log.error('cannot map all ATCs to vaccine indications')
                        _log.error('ATCs: %s', atcs)
                        return None

                return [ r['pk'] for r in rows ]

  `def targets2indication_pks(targets: list[str] = None) ‑> list[int]`
    Expand source code

        @staticmethod
        def targets2indication_pks(targets:list[str]=None) -> list[int]:
                query = {
                        'sql': 'SELECT pk FROM ref.vacc_indication WHERE atc = ANY(%(targets)s)',
                        'args': {'targets': targets}
                }
                rows = gmPG2.run_ro_queries(queries = [query])
                if len(targets) != len(rows):
                        return None

                return [ r['pk'] for r in rows ]

  ### Instance variables

  `prop is_in_use`
    Expand source code

        def _get_is_in_use(self):
                cmd = 'SELECT EXISTS(SELECT 1 FROM clin.vaccination WHERE fk_vaccine = %(pk)s)'
                args = {'pk': self._payload['pk_vaccine']}
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return rows[0][0]

  `prop product`
    Expand source code

        def _get_product(self):
                if self._payload['pk_drug_product']:
                        return gmMedication.cDrugProduct(aPK_obj = self._payload['pk_drug_product'])

                return None

  ### Methods

  `def add_indication(self, pk_indication: int = None, atc: str = None, indication: str = None)`
    Expand source code

        def add_indication(self, pk_indication:int=None, atc:str=None, indication:str=None):
                args:dict[str,str]|dict[str,int]
                if not pk_indication:
                        args = {
                                'atc': atc,
                                'indication': indication
                        }
                        if atc:
                                SQL = 'SELECT pk FROM ref.vacc_indication WHERE atc = %(atc)s'
                        elif indication:
                                SQL = 'SELECT pk FROM ref.vacc_indication WHERE target = %(indication)s'
                        else:
                                _log.error('neither <pk_indication>, nor <atc>, nor <indication> given')
                                return False

                        rows = gmPG2.run_ro_queries(queries = [{'sql': SQL, 'args': args}])
                        if not rows:
                                _log.error('indication [%s: %s] does not exist', atc, indication)
                                return False

                        pk_indication = rows[0]['pk']

                args = {
                        'pk_ind': pk_indication,
                        'pk_vacc': self._payload['pk_vaccine']
                }
                SQL = """
                INSERT INTO ref.lnk_indic2vaccine (fk_indication, fk_vaccine)
                        SELECT %(pk_ind)s, %(pk_vacc)s WHERE NOT EXISTS (
                                SELECT 1 FROM ref.lnk_indic2vaccine WHERE fk_indication %(pk_ind)s = AND fk_vaccine = %(pk_vacc)s
                        )
                """
                gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])
                return True

  `def remove_indication(self, pk_indication: int = None)`
    Expand source code

        def remove_indication(self, pk_indication:int=None):
                args = {
                        'pk_ind': pk_indication,
                        'pk_vacc': self._payload['pk_vaccine']
                }
                SQL = 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_indication %(pk_ind)s = AND fk_vaccine = %(pk_vacc)s'
                gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])

  `def remove_indications(self)`
    Expand source code

        def remove_indications(self):
                args = {'pk_vacc': self._payload['pk_vaccine']}
                SQL = 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_vaccine = %(pk_vacc)s'
                gmPG2.run_rw_queries(queries = [{'sql': SQL, 'args': args}])

  `def set_indications(self, pk_indications: list[int] = None) ‑> bool`
    Expand source code

        def set_indications(self, pk_indications:list[int]=None) -> bool:
                if not pk_indications:
                        return False

                if set(pk_indications) == set([ ind['pk_indication'] for ind in self._payload['indications'] ]):
                        # already the same
                        return True

                queries = [{
                        'sql': 'DELETE FROM ref.lnk_indic2vaccine WHERE fk_vaccine = %(pk_vacc)s',
                        'args': {'pk_vacc': self._payload['pk_vaccine']}
                }]
                for pk_ind in set(pk_indications):              # remove dupes
                        queries.append ({
                                'sql': 'INSERT INTO ref.lnk_indic2vaccine (fk_indication, fk_vaccine) VALUES (%(pk_ind)s, %(pk_vacc)s)',
                                'args': {'pk_ind': pk_ind, 'pk_vacc': self._payload['pk_vaccine']}
                        })
                gmPG2.run_rw_queries(queries = queries)
                self.refetch_payload()
                return True

  ### Inherited members

  - `cBusinessDBObject`:
    - `fields_as_dict`
    - `format`
    - `get_fields`
    - `get_patient`
    - `get_updatable_fields`
    - `is_modified`
    - `keys`
    - `patient_pk`
    - `refetch_payload`
    - `same_payload`
    - `save`
    - `save_payload`
    - `staff_id`