Gnumed.business.gmGenericEMRItem API documentation
Description: GNUmed clinical business object in generic form …

# Module `Gnumed.business.gmGenericEMRItem`

GNUmed clinical business object in generic form.

license: GPL v2 or later

## Functions

`def generic_item_type_str(table)`
  Expand source code

      def generic_item_type_str(table):
              try:
                      return _MAP_generic_emr_item_table2type_str[table]
              except KeyError:
                      return _('unmapped entry type from table [%s]') % table

`def get_generic_emr_items(encounters=None,
episodes=None,
issues=None,
patient=None,
soap_cats=None,
time_range=None,
order_by=None,
active_encounter=None,
return_pks=False)`
  Expand source code

      def get_generic_emr_items(encounters=None, episodes=None, issues=None, patient=None, soap_cats=None, time_range=None, order_by=None, active_encounter=None, return_pks=False):

              faulty_args = (
                      (patient is None) and
                      (encounters is None) and
                      (episodes is None) and
                      (issues is None) and
                      (active_encounter is None)
              )
              assert not faulty_args, 'one of <patient>, <episodes>, <issues>, <active_encounter> must not be None'

              if (patient is not None) and (active_encounter is not None):
                      if patient != active_encounter['pk_patient']:
                              raise AssertionError('<patient> (%s) and <active_encounter>["pk_patient"] (%s) must match, if both given', patient, active_encounter['pk_patient'])

              if order_by is None:
                      order_by = 'ORDER BY clin_when, pk_episode, scr, modified_when, src_table'
              else:
                      order_by = 'ORDER BY %s' % order_by

              if (patient is None) and (active_encounter is not None):
                      patient = active_encounter['pk_patient']

              where_parts = []
              args = {}

              if patient is not None:
                      where_parts.append('c_vej.pk_patient = %(pat)s')
                      args['pat'] = patient
              if soap_cats is not None:
                      # work around bug in psycopg2 not being able to properly
                      # adapt None to NULL inside tuples
                      if None in soap_cats:
                              where_parts.append('((c_vej.soap_cat = ANY(%(soap_cat)s)) OR (c_vej.soap_cat IS NULL))')
                              soap_cats.remove(None)
                      else:
                              where_parts.append('c_vej.soap_cat = ANY(%(soap_cat)s)')
                      args['soap_cat'] = soap_cats
              if time_range is not None:
                      where_parts.append("c_vej.clin_when > (now() - '%s days'::interval)" % time_range)
              if encounters is not None:
                      where_parts.append("c_vej.pk_encounter = ANY(%(encs)s)")
                      args['encs'] = encounters
              if episodes is not None:
                      where_parts.append("c_vej.pk_episode = ANY(%(epis)s)")
                      args['epis'] = episodes
              if issues is not None:
                      where_parts.append("c_vej.pk_health_issue = ANY(%(issues)s)")
                      args['issues'] = issues

              cmd_journal = _SQL_get_generic_emr_items
              if len(where_parts) > 0:
                      cmd_journal += '\nWHERE\n\t'
                      cmd_journal += '\t\tAND\t'.join(where_parts)

              if active_encounter is None:
                      cmd = cmd_journal + '\n' + order_by
              else:
                      args['pk_enc'] = active_encounter['pk_encounter']
                      args['enc_start'] = active_encounter['started']
                      args['enc_last_affirmed'] = active_encounter['last_affirmed']
                      args['enc_type'] = active_encounter['l10n_type']
                      args['enc_pat'] = active_encounter['pk_patient']
                      cmd = __SQL_union % (
                              cmd_journal,
                              _SQL_get_hints_as_generic_emr_items
                      ) + '\n' + order_by

              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
              if return_pks:
                      return [ {
                              'src_table': r['src_table'],
                              'src_pk': r['src_pk']
                      } for r in rows ]

              return [ cGenericEMRItem(row = {
                      'data': r,
                      'pk_obj': {'src_table': r['src_table'], 'src_pk': r['src_pk']}
              } ) for r in rows ]

## Classes

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

      class cGenericEMRItem(gmBusinessDBObject.cBusinessDBObject):
              """Represents an entry in clin.v_emr_journal."""

              _cmd_fetch_payload:str = _SQL_get_generic_emr_items + "WHERE src_table = %(src_table)s AND src_pk = %(src_pk)s"
              _cmds_store_payload:list = []
              _updatable_fields:list = ['']

              #--------------------------------------------------------
              def format(self, eol=None):
                      lines = self.formatted_header
                      lines.append(gmTools.u_box_horiz_4dashes * 40)
                      lines.extend(self._payload['narrative'].strip().split('\n'))
                      lines.append('')
                      lines.append(_('                        rev %s (%s) by %s in <%s>') % (
                              self._payload['row_version'],
                              self._payload['date_modified'],
                              self._payload['modified_by'],
                              self._payload['src_table']
                      ))
                      if eol is None:
                              return lines
                      return eol.join(lines)

              #--------------------------------------------------------
              def format_header(self, eol=None):
                      lines = []
                      lines.append(_('Chart entry (%s): %s       [#%s in %s]') % (
                              self.i18n_soap_cat,
                              self.item_type_str,
                              self._payload['src_pk'],
                              self._payload['src_table']
                      ))
                      lines.append(_(' Modified: %s by %s (%s rev %s)') % (
                              self._payload['date_modified'],
                              self._payload['modified_by'],
                              gmTools.u_arrow2right,
                              self._payload['row_version']
                      ))
                      lines.append('')
                      if self._payload['health_issue'] is None:
                              issue_info = gmTools.u_diameter
                      else:
                              issue_info = '%s%s' % (
                                      self._payload['health_issue'],
                                      gmTools.bool2subst(self._payload['issue_active'], ' (' + _('active') + ')', ' (' + _('inactive') + ')', '')
                              )
                      lines.append(_('Health issue: %s') % issue_info)
                      if self._payload['episode'] is None:
                              episode_info = gmTools.u_diameter
                      else:
                              episode_info = '%s%s' % (
                                      self._payload['episode'],
                                      gmTools.bool2subst(self._payload['episode_open'], ' (' +  _('open') + ')', ' (' +  _('closed') + ')', '')
                              )
                      lines.append(_('Episode: %s') % episode_info)
                      if self._payload['encounter_started'] is None:
                              enc_info = gmTools.u_diameter
                      else:
                              enc_info = '%s - %s (%s)' % (
                                      self._payload['encounter_started'].strftime('%Y %b %d  %H:%M'),
                                      self._payload['encounter_last_affirmed'].strftime('%H:%M'),
                                      self._payload['encounter_l10n_type']
                              )
                      lines.append(_('Encounter: %s') % enc_info)
                      lines.append(_('Event: %s') % self._payload['clin_when'].strftime('%Y %b %d  %H:%M'))
                      if eol is None:
                              return lines

                      return eol.join(lines)

              formatted_header = property(format_header)

              #--------------------------------------------------------
              def __get_item_type_str(self):
                      try:
                              return _MAP_generic_emr_item_table2type_str[self._payload['src_table']]
                      except KeyError:
                              return '[%s:%s]' % (
                                      self._payload['src_table'],
                                      self._payload['src_pk']
                              )

              item_type_str = property(__get_item_type_str)

              #--------------------------------------------------------
              def __get_i18n_soap_cat(self):
                      return gmSoapDefs.soap_cat2l10n[self._payload['soap_cat']]

              i18n_soap_cat = property(__get_i18n_soap_cat)

              #--------------------------------------------------------
              def __get_specialized_item(self):
                      item_class = _MAP_generic_emr_item_table2class[self._payload['src_table']]
                      return item_class(aPK_obj = self._payload['src_pk'])

              specialized_item = property(__get_specialized_item)

  Represents an entry in clin.v_emr_journal.

  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 formatted_header`
    Expand source code

        def format_header(self, eol=None):
                lines = []
                lines.append(_('Chart entry (%s): %s       [#%s in %s]') % (
                        self.i18n_soap_cat,
                        self.item_type_str,
                        self._payload['src_pk'],
                        self._payload['src_table']
                ))
                lines.append(_(' Modified: %s by %s (%s rev %s)') % (
                        self._payload['date_modified'],
                        self._payload['modified_by'],
                        gmTools.u_arrow2right,
                        self._payload['row_version']
                ))
                lines.append('')
                if self._payload['health_issue'] is None:
                        issue_info = gmTools.u_diameter
                else:
                        issue_info = '%s%s' % (
                                self._payload['health_issue'],
                                gmTools.bool2subst(self._payload['issue_active'], ' (' + _('active') + ')', ' (' + _('inactive') + ')', '')
                        )
                lines.append(_('Health issue: %s') % issue_info)
                if self._payload['episode'] is None:
                        episode_info = gmTools.u_diameter
                else:
                        episode_info = '%s%s' % (
                                self._payload['episode'],
                                gmTools.bool2subst(self._payload['episode_open'], ' (' +  _('open') + ')', ' (' +  _('closed') + ')', '')
                        )
                lines.append(_('Episode: %s') % episode_info)
                if self._payload['encounter_started'] is None:
                        enc_info = gmTools.u_diameter
                else:
                        enc_info = '%s - %s (%s)' % (
                                self._payload['encounter_started'].strftime('%Y %b %d  %H:%M'),
                                self._payload['encounter_last_affirmed'].strftime('%H:%M'),
                                self._payload['encounter_l10n_type']
                        )
                lines.append(_('Encounter: %s') % enc_info)
                lines.append(_('Event: %s') % self._payload['clin_when'].strftime('%Y %b %d  %H:%M'))
                if eol is None:
                        return lines

                return eol.join(lines)

  `prop i18n_soap_cat`
    Expand source code

        def __get_i18n_soap_cat(self):
                return gmSoapDefs.soap_cat2l10n[self._payload['soap_cat']]

  `prop item_type_str`
    Expand source code

        def __get_item_type_str(self):
                try:
                        return _MAP_generic_emr_item_table2type_str[self._payload['src_table']]
                except KeyError:
                        return '[%s:%s]' % (
                                self._payload['src_table'],
                                self._payload['src_pk']
                        )

  `prop specialized_item`
    Expand source code

        def __get_specialized_item(self):
                item_class = _MAP_generic_emr_item_table2class[self._payload['src_table']]
                return item_class(aPK_obj = self._payload['src_pk'])

  ### Methods

  `def format_header(self, eol=None)`
    Expand source code

        def format_header(self, eol=None):
                lines = []
                lines.append(_('Chart entry (%s): %s       [#%s in %s]') % (
                        self.i18n_soap_cat,
                        self.item_type_str,
                        self._payload['src_pk'],
                        self._payload['src_table']
                ))
                lines.append(_(' Modified: %s by %s (%s rev %s)') % (
                        self._payload['date_modified'],
                        self._payload['modified_by'],
                        gmTools.u_arrow2right,
                        self._payload['row_version']
                ))
                lines.append('')
                if self._payload['health_issue'] is None:
                        issue_info = gmTools.u_diameter
                else:
                        issue_info = '%s%s' % (
                                self._payload['health_issue'],
                                gmTools.bool2subst(self._payload['issue_active'], ' (' + _('active') + ')', ' (' + _('inactive') + ')', '')
                        )
                lines.append(_('Health issue: %s') % issue_info)
                if self._payload['episode'] is None:
                        episode_info = gmTools.u_diameter
                else:
                        episode_info = '%s%s' % (
                                self._payload['episode'],
                                gmTools.bool2subst(self._payload['episode_open'], ' (' +  _('open') + ')', ' (' +  _('closed') + ')', '')
                        )
                lines.append(_('Episode: %s') % episode_info)
                if self._payload['encounter_started'] is None:
                        enc_info = gmTools.u_diameter
                else:
                        enc_info = '%s - %s (%s)' % (
                                self._payload['encounter_started'].strftime('%Y %b %d  %H:%M'),
                                self._payload['encounter_last_affirmed'].strftime('%H:%M'),
                                self._payload['encounter_l10n_type']
                        )
                lines.append(_('Encounter: %s') % enc_info)
                lines.append(_('Event: %s') % self._payload['clin_when'].strftime('%Y %b %d  %H:%M'))
                if eol is None:
                        return lines

                return eol.join(lines)

  ### 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`