Gnumed.business.gmPerformedProcedure API documentation
Description: GNUmed performed-procedure business object …

# Module `Gnumed.business.gmPerformedProcedure`

GNUmed performed-procedure business object.

license: GPL v2 or later

## Functions

`def create_performed_procedure(encounter=None, episode=None, location=None, hospital_stay=None, procedure=None)`
  Expand source code

      def create_performed_procedure(encounter=None, episode=None, location=None, hospital_stay=None, procedure=None):

              queries = [{
                      'sql': """
                              INSERT INTO clin.procedure (
                                      fk_encounter,
                                      fk_episode,
                                      soap_cat,
                                      fk_org_unit,
                                      fk_hospital_stay,
                                      narrative
                              ) VALUES (
                                      %(enc)s,
                                      %(epi)s,
                                      'p',
                                      %(loc)s,
                                      %(stay)s,
                                      gm.nullify_empty_string(%(proc)s)
                              )
                              RETURNING pk""",
                      'args': {'enc': encounter, 'epi': episode, 'loc': location, 'stay': hospital_stay, 'proc': procedure}
              }]

              rows = gmPG2.run_rw_queries(queries = queries, return_data = True)

              return cPerformedProcedure(aPK_obj = rows[0][0])

`def delete_performed_procedure(procedure=None)`
  Expand source code

      def delete_performed_procedure(procedure=None):
              cmd = 'delete from clin.procedure where pk = %(pk)s'
              args = {'pk': procedure}
              gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
              return True

`def get_latest_performed_procedure(patient=None)`
  Expand source code

      def get_latest_performed_procedure(patient=None):
              queries = [{
                      'sql': 'select * FROM clin.v_procedures WHERE pk_patient = %(pat)s ORDER BY clin_when DESC LIMIT 1',
                      'args': {'pat': patient}
              }]
              rows = gmPG2.run_ro_queries(queries = queries)
              if len(rows) == 0:
                      return None

              return cPerformedProcedure(row = {'data': rows[0], 'pk_field': 'pk_procedure'})

`def get_performed_procedures(patient=None, return_pks=False)`
  Expand source code

      def get_performed_procedures(patient=None, return_pks=False):
              queries = [{
                      'sql': 'SELECT * FROM clin.v_procedures WHERE pk_patient = %(pat)s ORDER BY clin_when',
                      'args': {'pat': patient}
              }]
              rows = gmPG2.run_ro_queries(queries = queries)
              if return_pks:
                      return [ r['pk_procedure'] for r in rows ]
              return [ cPerformedProcedure(row = {'data': r, 'pk_field': 'pk_procedure'})  for r in rows ]

`def get_procedures4document(pk_document=None, return_pks=False)`
  Expand source code

      def get_procedures4document(pk_document=None, return_pks=False):
              args = {'pk_doc': pk_document}
              cmd = _SQL_get_procedures % 'pk_doc = %(pk_doc)s'
              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
              if return_pks:
                      return [ r['pk_procedure'] for r in rows ]
              return [ cPerformedProcedure(row = {'data': r, 'pk_field': 'pk_procedure'})  for r in rows ]

## Classes

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

      class cPerformedProcedure(gmBusinessDBObject.cBusinessDBObject):

              _cmd_fetch_payload = _SQL_get_procedures % "pk_procedure = %s"
              _cmds_store_payload = [
                      """UPDATE clin.procedure SET
                                      soap_cat = 'p',
                                      clin_when = %(clin_when)s,
                                      clin_end = %(clin_end)s,
                                      is_ongoing = %(is_ongoing)s,
                                      narrative = gm.nullify_empty_string(%(performed_procedure)s),
                                      fk_hospital_stay = %(pk_hospital_stay)s,
                                      fk_org_unit = (CASE
                                              WHEN %(pk_hospital_stay)s IS NULL THEN %(pk_org_unit)s
                                              ELSE NULL
                                      END)::integer,
                                      fk_episode = %(pk_episode)s,
                                      fk_encounter = %(pk_encounter)s,
                                      fk_doc = %(pk_doc)s,
                                      comment = gm.nullify_empty_string(%(comment)s)
                              WHERE
                                      pk = %(pk_procedure)s AND
                                      xmin = %(xmin_procedure)s
                              RETURNING xmin as xmin_procedure"""
              ]
              _updatable_fields = [
                      'clin_when',
                      'clin_end',
                      'is_ongoing',
                      'performed_procedure',
                      'pk_hospital_stay',
                      'pk_org_unit',
                      'pk_episode',
                      'pk_encounter',
                      'pk_doc',
                      'comment'
              ]
              #-------------------------------------------------------
              def __setitem__(self, attribute, value):

                      if (attribute == 'pk_hospital_stay') and (value is not None):
                              gmBusinessDBObject.cBusinessDBObject.__setitem__(self, 'pk_org_unit', None)

                      if (attribute == 'pk_org_unit') and (value is not None):
                              gmBusinessDBObject.cBusinessDBObject.__setitem__(self, 'pk_hospital_stay', None)

                      gmBusinessDBObject.cBusinessDBObject.__setitem__(self, attribute, value)

              #--------------------------------------------------------
              def format_maximum_information(self, left_margin=0, patient=None):
                      return self.format (
                              left_margin = left_margin,
                              include_episode = True,
                              include_codes = True,
                              include_address = True,
                              include_comm = True,
                              include_doc = True
                      ).split('\n')

              #-------------------------------------------------------
              def format(self, left_margin=0, include_episode=True, include_codes=False, include_address=False, include_comm=False, include_doc=False):

                      if self._payload['is_ongoing']:
                              end = _(' (ongoing)')
                      else:
                              end = self._payload['clin_end']
                              if end is None:
                                      end = ''
                              else:
                                      end = ' - %s' % end.strftime('%Y %b %d')

                      line = '%s%s%s: %s%s [%s @ %s]' % (
                              (' ' * left_margin),
                              self._payload['clin_when'].strftime('%Y %b %d'),
                              end,
                              self._payload['performed_procedure'],
                              gmTools.bool2str(include_episode, ' (%s)' % self._payload['episode'], ''),
                              self._payload['unit'],
                              self._payload['organization']
                      )

                      line += gmTools.coalesce(self._payload['comment'], '', '\n' + (' ' * left_margin) + _('Comment: ') + '%s')

                      if include_comm:
                              for channel in self.org_unit.comm_channels:
                                      line += ('\n%(comm_type)s: %(url)s' % channel)

                      if include_address:
                              adr = self.org_unit.address
                              if adr is not None:
                                      line += '\n'
                                      line += '\n'.join(adr.format(single_line = False, show_type = False))
                                      line += '\n'

                      if include_doc:
                              doc = self.doc
                              if doc is not None:
                                      line += '\n'
                                      line += _('Document') + ': ' + doc.format(single_line = True)
                                      line += '\n'

                      if include_codes:
                              codes = self.generic_codes
                              if len(codes) > 0:
                                      line += '\n'
                              for c in codes:
                                      line += '%s  %s: %s (%s - %s)\n' % (
                                              (' ' * left_margin),
                                              c['code'],
                                              c['term'],
                                              c['name_short'],
                                              c['version']
                                      )
                              del codes

                      return line

              #--------------------------------------------------------
              def add_code(self, pk_code=None):
                      """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
                      cmd = "INSERT INTO clin.lnk_code2procedure (fk_item, fk_generic_code) values (%(issue)s, %(code)s)"
                      args = {
                              'issue': self._payload['pk_procedure'],
                              'code': pk_code
                      }
                      gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                      return True

              #--------------------------------------------------------
              def remove_code(self, pk_code=None):
                      """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
                      cmd = "DELETE FROM clin.lnk_code2procedure WHERE fk_item = %(issue)s AND fk_generic_code = %(code)s"
                      args = {
                              'issue': self._payload['pk_procedure'],
                              'code': pk_code
                      }
                      gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                      return True

              #--------------------------------------------------------
              # properties
              #--------------------------------------------------------
              def _get_stay(self):
                      if self._payload['pk_hospital_stay'] is None:
                              return None

                      return gmHospitalStay.cHospitalStay(aPK_obj = self._payload['pk_hospital_stay'])

              hospital_stay = property(_get_stay)

              #--------------------------------------------------------
              def _get_org_unit(self):
                      return gmOrganization.cOrgUnit(self._payload['pk_org_unit'])

              org_unit = property(_get_org_unit)

              #--------------------------------------------------------
              def _get_doc(self):
                      if self._payload['pk_doc'] is None:
                              return None
                      return gmDocuments.cDocument(aPK_obj = self._payload['pk_doc'])

              doc = property(_get_doc)

              #--------------------------------------------------------
              def _get_generic_codes(self):
                      if len(self._payload['pk_generic_codes']) == 0:
                              return []

                      cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)'
                      args = {'pks': self._payload['pk_generic_codes']}
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ]

              def _set_generic_codes(self, pk_codes):
                      queries = []
                      # remove all codes
                      if len(self._payload['pk_generic_codes']) > 0:
                              queries.append ({
                                      'sql': 'DELETE FROM clin.lnk_code2procedure WHERE fk_item = %(proc)s AND fk_generic_code = ANY(%(codes)s)',
                                      'args': {
                                              'proc': self._payload['pk_procedure'],
                                              'codes': self._payload['pk_generic_codes']
                                      }
                              })
                      # add new codes
                      for pk_code in pk_codes:
                              queries.append ({
                                      'sql': 'INSERT INTO clin.lnk_code2procedure (fk_item, fk_generic_code) VALUES (%(proc)s, %(pk_code)s)',
                                      'args': {
                                              'proc': self._payload['pk_procedure'],
                                              'pk_code': pk_code
                                      }
                              })
                      if len(queries) == 0:
                              return
                      # run it all in one transaction
                      gmPG2.run_rw_queries(queries = queries)
                      return

              generic_codes = property(_get_generic_codes, _set_generic_codes)

  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 doc`
    Expand source code

        def _get_doc(self):
                if self._payload['pk_doc'] is None:
                        return None
                return gmDocuments.cDocument(aPK_obj = self._payload['pk_doc'])

  `prop generic_codes`
    Expand source code

        def _get_generic_codes(self):
                if len(self._payload['pk_generic_codes']) == 0:
                        return []

                cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)'
                args = {'pks': self._payload['pk_generic_codes']}
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ]

  `prop hospital_stay`
    Expand source code

        def _get_stay(self):
                if self._payload['pk_hospital_stay'] is None:
                        return None

                return gmHospitalStay.cHospitalStay(aPK_obj = self._payload['pk_hospital_stay'])

  `prop org_unit`
    Expand source code

        def _get_org_unit(self):
                return gmOrganization.cOrgUnit(self._payload['pk_org_unit'])

  ### Methods

  `def add_code(self, pk_code=None)`
    Expand source code

        def add_code(self, pk_code=None):
                """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
                cmd = "INSERT INTO clin.lnk_code2procedure (fk_item, fk_generic_code) values (%(issue)s, %(code)s)"
                args = {
                        'issue': self._payload['pk_procedure'],
                        'code': pk_code
                }
                gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                return True

    must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)

  `def format_maximum_information(self, left_margin=0, patient=None)`
    Expand source code

        def format_maximum_information(self, left_margin=0, patient=None):
                return self.format (
                        left_margin = left_margin,
                        include_episode = True,
                        include_codes = True,
                        include_address = True,
                        include_comm = True,
                        include_doc = True
                ).split('\n')

  `def remove_code(self, pk_code=None)`
    Expand source code

        def remove_code(self, pk_code=None):
                """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
                cmd = "DELETE FROM clin.lnk_code2procedure WHERE fk_item = %(issue)s AND fk_generic_code = %(code)s"
                args = {
                        'issue': self._payload['pk_procedure'],
                        'code': pk_code
                }
                gmPG2.run_rw_queries(queries = [{'sql': cmd, 'args': args}])
                return True

    must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)

  ### 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`