Gnumed.pycommon.gmBusinessDBObject API documentation
Description: GNUmed database object business class …

# Module `Gnumed.pycommon.gmBusinessDBObject`

GNUmed database object business class.

## Overview

This class wraps a source relation (table, view) which represents an entity that makes immediate business sense such as a vaccination or a medical document. In many if not most cases this source relation is a denormalizing view. The data in that view will in most cases, however, originate from several normalized tables. One instance of this class represents one row of said source relation.

Note, however, that this class does not always simply wrap a single table or view. It can also encompass several relations (views, tables, sequences etc) that taken together form an object meaningful to business logic.

## Initialization

There are two ways to initialize an instance with values. One way is to pass a "primary key equivalent" object into init(). Refetch_payload() will then pull the data from the backend. Another way would be to fetch the data outside the instance and pass it in via the argument. In that case the instance will not initially connect to the database which may offer a great boost to performance.

## Values Api

Field values are cached for later access. They can be accessed by a dictionary API, eg:

        old_value = object['field']
        object['field'] = new_value

The field names correspond to the respective column names in the "main" source relation. Accessing non-existent field names will raise an error, so does trying to set fields not listed in self.class._updatable_fields. To actually store updated values in the database one must explicitly call save_payload().

The class will in many cases be enhanced by accessors to related data that is not directly part of the business object itself but are closely related, such as codes linked to a clinical narrative entry (eg a diagnosis). Such accessors in most cases start with get_. Related setters start with set_. The values can be accessed via the object['field'] syntax, too, but they will be cached independently.

## Concurrency Handling

GNUmed connections always run transactions in isolation level "serializable". This prevents transactions happening at the very same time to overwrite each other's data. All but one of them will abort with a concurrency error (eg if a transaction runs a select-for-update later than another one it will hang until the first transaction ends. Then it will succeed or fail depending on what the first transaction did). This is standard transactional behaviour.

However, another transaction may have updated our row between the time we first fetched the data and the time we start the update transaction. This is noticed by getting the XMIN system column for the row when initially fetching the data and using that value as a where condition value when updating the row later. If the row had been updated (xmin changed) or deleted (primary key disappeared) in the meantime the update will touch zero rows (as no row with both PK and XMIN matching is found) even if the query itself syntactically succeeds.

When detecting a change in a row due to XMIN being different one needs to be careful how to represent that to the user. The row may simply have changed but it also might have been deleted and a completely new and unrelated row which happens to have the same primary key might have been created ! This row might relate to a totally different context (eg. patient, episode, encounter).

One can offer all the data to the user:

- self.payload_most_recently_fetched:

contains the data at the last successful refetch

- self.payload_most_recently_attempted_to_store:

contains the modified payload just before the last failure of save_payload() - IOW what is currently in the database

- self._payload:

contains the currently active payload which may or may not contain changes

For discussion on this see the thread starting at:

        <http://archives.postgresql.org/pgsql-general/2004-10/msg01352.php>

and here

        <http://groups.google.com/group/pgsql.general/browse_thread/thread/e3566ba76173d0bf/6cf3c243a86d9233>
        (google for "XMIN semantic at peril")

Problem cases with XMIN:

1) not unlikely:

- a very old row is read with XMIN

- vacuum comes along and sets XMIN to FrozenTransactionId

      * now XMIN changed but the row actually didn't !

- an update with "… where xmin = old_xmin …" fails although there is no need to fail

2) quite unlikely:

- a row is read with XMIN
- a long time passes
- the original XMIN gets frozen to FrozenTransactionId
- another writer comes along and changes the row

- incidentally the exact same old row gets the old XMIN again

      * now XMIN is (again) the same but the data changed !

- a later update fails to detect the concurrent change !!

TODO: The solution is to use our own column for optimistic locking which gets updated by an AFTER UPDATE trigger.

## Classes

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

      class cBusinessDBObject(object):
              """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']
              """
              _cmd_fetch_payload:str = None
              _cmds_store_payload:list[str] = None
              _updatable_fields:list[str] = None
              #--------------------------------------------------------
              def __init__(self, aPK_obj:int|dict=None, row:dict=None, link_obj=None):
                      """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 ]
                      """
                      # initialize those "too early" because sanity checking descendants might
                      # fail which will then call __str__ in stack trace logging if --debug
                      # was given which in turn needs those instance variables
                      self.pk_obj:int|dict = -1
      #               self._idx:dict[str, int|str] = {}
                      self._payload:dict|gmPG2._TRow = {}     # the cache for backend object values (mainly table fields)
                      self._is_modified:bool = False
                      self.original_payload:list = None
                      # only now check child classes
                      assert self.__class__._cmd_fetch_payload is not None, '<_cmd_fetch_payload> undefined'
                      assert self.__class__._cmds_store_payload is not None, '<_cmds_store_payload> undefined'
                      assert self.__class__._updatable_fields is not None, '<_updatable_fields> undefined'

                      if aPK_obj is not None:
                              self.__init_from_pk(aPK_obj = aPK_obj, link_obj = link_obj)
                      else:
                              self.__init_from_row_data(row = row)
                      self._is_modified = False

              #--------------------------------------------------------
              def __init_from_pk(self, aPK_obj:int|dict=None, link_obj=None):
                      """Creates a new clinical item instance by its PK.

                      Args:
                              aPK_obj:

                              * a simple value -> the primary key WHERE condition must be     a simple column
                              * a dictionary of values -> the primary key WHERE condition must be a
                                  subselect consuming the dict and producing the single-value primary key
                      """
                      self.pk_obj = aPK_obj
                      if self.refetch_payload(link_obj = link_obj):
                              self.payload_most_recently_fetched = {}
                              for field in self._payload.keys():
                                      self.payload_most_recently_fetched[field] = self._payload[field]
                              return

                      raise gmExceptions.ConstructorError("[%s:%s]: error loading instance" % (self.__class__.__name__, self.pk_obj))

              #--------------------------------------------------------
              def __init_from_row_data(self, row:dict|gmPG2._TRow=None):
                      """Creates a new clinical item instance given its fields.

                      Args:
                              row: EITHER {'data': ..., 'pk_field': ...}

                                      * data: list of column values for the row selected by the PK (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 passing to cursor.execute(),
                                        holding the primary key values; used for composite PKs

                      Examples:

                                      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 ]

                      Copy/Paste:

                                      row = {
                                              'data': rows[0],
                                              'pk_field': 'pk_XXX (the PK column name)',
                                              #'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
                                      }
                      """
                      assert ('data' in row), "[%s:??]: 'data' missing from <row> argument: %s" % (self.__class__.__name__, row)
                      faulty_pk = (('pk_field' not in row) and ('pk_obj' not in row))
                      assert not faulty_pk, "[%s:??]: either 'pk_field' or 'pk_obj' must exist in <row> argument: %s" % (self.__class__.__name__, row)

                      self._payload = row['data']
                      if 'pk_field' in row:
                              self.pk_obj = self._payload[row['pk_field']]
                      else:
                              self.pk_obj = row['pk_obj']
                      self.payload_most_recently_fetched = {}
                      for field in self._payload.keys():
                              self.payload_most_recently_fetched[field] = self._payload[field]

              #--------------------------------------------------------
              #--------------------------------------------------------
              def __del__(self):
                      if '_is_modified' in self.__dict__:
                              if self._is_modified:
                                      _log.critical('[%s:%s]: losing payload changes' % (self.__class__.__name__, self.pk_obj))
                                      _log.debug('most recently fetched: %s' % self.payload_most_recently_fetched)
                                      _log.debug('modified: %s' % self._payload)

              #--------------------------------------------------------
              def __str__(self):
                      lines = []
                      try:
                              for attr in self._payload.keys():
                                      if self._payload[attr] is None:
                                              lines.append('%s: NULL' % attr)
                                      else:
                                              lines.append('%s [%s]: %s' % (
                                                      attr,
                                                      type(self._payload[attr]),
                                                      self._payload[attr]
                                              ))
                              return '[%s:%s] %s:\n%s' % (
                                      self.__class__.__name__,
                                      self.pk_obj,
                                      self._is_modified,
                                      '\n'.join(lines)
                              )

                      except Exception:
                              return '[%s @ %s], cannot show payload and primary key, nascent ?' % (self.__class__.__name__, id(self))

              #--------------------------------------------------------
              def __getitem__(self, attribute):
                      return self._payload[attribute]

              #--------------------------------------------------------
              def __setitem__(self, attribute, value):
                      assert attribute in self.__class__._updatable_fields, '[%s]: field <%s> not declared updatable' % (self.__class__.__name__, attribute)

                      try:
                              if self._payload[attribute] == value:
                                      return

                      except KeyError:
                              _log.exception('[%s]: cannot set attribute <%s>', self.__class__.__name__, attribute)
                              _log.debug('[%s]: settable attributes: %s', self.__class__.__name__, str(self.__class__._updatable_fields))
                              raise KeyError('[%s]: cannot set [%s]' % (self.__class__.__name__, attribute))

                      self._payload[attribute] = value
                      self._is_modified = True

              #--------------------------------------------------------
              # external API
              #--------------------------------------------------------
              def same_payload(self, another_object:'cBusinessDBObject'=None) -> bool:
                      """Check whether *self* and *another_object* hold the same payload."""
                      raise NotImplementedError('comparison between [%s] and [%s] not implemented' % (self, another_object))

              #--------------------------------------------------------
              def is_modified(self) -> bool:
                      """Whether data in this business object has been modified."""
                      return self._is_modified

              #--------------------------------------------------------
              def get_fields(self) -> list[str]:
                      """Return list of accessible fields."""
                      keys = list(self._payload.keys())
                      if not keys:
                              keys = [
                                      '[%s @ %s]' % (self.__class__.__name__, id(self)),
                                      'no keys, nascent instance ?'
                              ]
                      return keys

              keys = property(get_fields)

              #--------------------------------------------------------
              def get_updatable_fields(self) -> list[str]:
                      """Return a list of fields that can be updated."""
                      return self.__class__._updatable_fields

              #--------------------------------------------------------
              def fields_as_dict(self, date_format:str='%Y %b %d  %H:%M', none_string:str='', escape_style:str=None, bool_strings:list[str]=None) -> dict:
                      """Return field values as a dictionary of strings."""
                      if bool_strings is None:
                              bools = {True: 'True', False: 'False'}
                      else:
                              bools = {True: bool_strings[0], False: bool_strings[1]}
                      data = {}
                      for field in self._payload.keys():
                              # harden against BYTEA fields
                              if isinstance(self._payload[field], memoryview):
                                      val = _('binary data: %s%s (total: %s bytes)') % (
                                              self._payload[field].obj[:10],
                                              u_ellipsis,
                                              self._payload[field].nbytes
                                      )
                              else:
                                      val = self._payload[field]
                              if val is None:
                                      data[field] = none_string
                                      continue
                              if isinstance(val, bool):
                                      data[field] = bools[val]
                                      continue
                              if isinstance(val, datetime.datetime):
                                      if date_format is None:
                                              data[field] = str(val)                  # x-type: ignore [assignment]
                                              continue
                                      data[field] = val.strftime(date_format)
                                      if escape_style in ['latex', 'tex']:
                                              data[field] = tex_escape_string(data[field])
                                      elif escape_style in ['xetex', 'xelatex']:
                                              data[field] = xetex_escape_string(data[field])
                                      continue
                              try:
                                      data[field] = str(val, encoding = 'utf8', errors = 'replace')
                              except TypeError:
                                      try:
                                              data[field] = str(val)
                                      except (UnicodeDecodeError, TypeError):
                                              val = '%s' % str(val)
                                              data[field] = val.decode('utf8', 'replace')
                              if escape_style in ['latex', 'tex']:
                                      data[field] = tex_escape_string(data[field])
                              elif escape_style in ['xetex', 'xelatex']:
                                      data[field] = xetex_escape_string(data[field])
                      return data

              #--------------------------------------------------------
              def get_patient(self):
                      """Get associated patient object."""
                      _log.error('[%s:%s]: forgot to override get_patient()' % (self.__class__.__name__, self.pk_obj))
                      return None

              #--------------------------------------------------------
              def _get_patient_pk(self) -> int:
                      """Get primary key of associated patient if any."""
                      pk_patient = None
                      try:
                              pk_patient = self._payload['pk_patient']
                      except KeyError:
                              pass
                      try:
                              pk_patient = self._payload['pk_identity']
                      except KeyError:
                              pass

                      return pk_patient

              patient_pk = property(_get_patient_pk)

              #--------------------------------------------------------
              def _get_staff_id(self) -> int:
                      """Get staff id of associated staff if any."""
                      try:
                              return self._payload['pk_staff']

                      except KeyError:
                              _log.debug('[%s]: .pk_staff should be added to the view', self.__class__.__name__)
                      try:
                              return self._payload['pk_provider']

                      except KeyError:
                              pass
                      mod_by = None
                      try:
                              mod_by = self._payload['modified_by_raw']
                      except KeyError:
                              _log.debug('[%s]: .modified_by_raw should be added to the view', self.__class__.__name__)
                      if mod_by is not None:
                              # find by DB account
                              args = {'db_u': mod_by}
                              cmd = "SELECT pk FROM dem.staff WHERE db_user = %(db_u)s"
                              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                              if rows:
                                      # logically, they are all the same provider, because they share the DB account
                                      return rows[0]['pk']

                      mod_by = self._payload['modified_by']
                      # is .modified_by a "<DB-account>" ?
                      if mod_by.startswith('<') and mod_by.endswith('>'):
                              # find by DB account
                              args = {'db_u': mod_by.lstrip('<').rstrip('>')}
                              cmd = "SELECT pk FROM dem.staff WHERE db_user = %(db_u)s"
                              rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                              if rows:
                                      # logically, they are all the same provider, because they share the DB account
                                      return rows[0]['pk']

                      # .modified_by is probably dem.staff.short_alias
                      args = {'alias': mod_by}
                      cmd = "SELECT pk FROM dem.staff WHERE short_alias = %(alias)s"
                      rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                      if rows:
                              # logically, they are all the same provider, because they share the DB account
                              return rows[0]['pk']

                      _log.error('[%s]: cannot retrieve staff ID for [%s]', self.__class__.__name__, mod_by)
                      return None

              staff_id = property(_get_staff_id)

              #--------------------------------------------------------
              def format(self, *args, **kwargs) -> list[str]:
                      """Return instance data generically formatted as a table."""
                      return format_dict_like (
                              self.fields_as_dict(none_string = '<?>'),
                              tabular = True,
                              value_delimiters = None
                      ).split('\n')

              #--------------------------------------------------------
              def _get_revision_history(self, query:str, args:dict, title:str) -> list[str]:
                      rows = gmPG2.run_ro_queries(queries = [{'sql': query, 'args': args}])
                      if not rows:
                              return ['%s (no versions)' % title]

                      lines = ['%s (%s versions)' % (title, rows[0]['row_version'] + 1)]
                      column_labels = [ 'rev %s (%s)' % (r['row_version'], pydt_strftime(r['audit__action_when'], format = '%Y %b %d %H:%M', none_str = 'live row')) for r in rows ]
                      lines.extend (dicts2table_columns (
                              rows,
                              left_margin = 1,
                              eol = None,
                              keys2ignore = ['audit__action_when', 'row_version', 'pk_audit'],
                              show_only_changes = True,
                              column_labels = column_labels,
                              date_format = '%Y %b %d %H:%M',
                              equality_value = u_left_arrow
                      ))
                      return lines

              #--------------------------------------------------------
              def refetch_payload(self, ignore_changes:bool=False, link_obj=None) -> bool:
                      """Fetch field values from backend.

                      Args:
                              ignore_changes: True -> loose local changes if data on the backend changed
                      """
                      if self._is_modified:
                              compare_dict_likes(self.original_payload, self.fields_as_dict(date_format = None, none_string = None), 'original payload', 'modified payload')
                              if ignore_changes:
                                      _log.critical('[%s:%s]: losing payload changes' % (self.__class__.__name__, self.pk_obj))
                                      #_log.debug('most recently fetched: %s' % self.payload_most_recently_fetched)
                                      #_log.debug('modified: %s' % self._payload)
                              else:
                                      _log.critical('[%s:%s]: cannot reload, payload changed' % (self.__class__.__name__, self.pk_obj))
                                      return False

                      if isinstance(self.pk_obj, dict):
                              args:dict = self.pk_obj
                      else:
                              args:list = [self.pk_obj]               # type: ignore [no-redef]
                      queries = [{'sql': self.__class__._cmd_fetch_payload, 'args': args}]
                      rows = gmPG2.run_ro_queries (
                              link_obj = link_obj,
                              queries = queries
                      )
                      if len(rows) == 0:
                              _log.error('[%s:%s]: no such instance' % (self.__class__.__name__, self.pk_obj))
                              return False

                      if len(rows) > 1:
                              raise AssertionError('[%s:%s]: %s instances !' % (self.__class__.__name__, self.pk_obj, len(rows)))

                      self._payload = rows[0]
                      return True

              #--------------------------------------------------------
              def save(self, conn:gmPG2.dbapi.extras.DictConnection=None) -> tuple[bool, tuple]:
                      """Just calls save_payload()."""
                      return self.save_payload(conn = conn)

              #--------------------------------------------------------
              def save_payload(self, conn:gmPG2.dbapi.extras.DictConnection=None) -> tuple[bool, tuple]:
                      """Store updated values (if any) into database.

                      Optionally accepts a pre-existing connection

                      Returns:
                              a tuple (True|False, data)
                              True: success
                              False: an error occurred,
                              data: (error, message), for error meanings see gmPG2.run_rw_queries()
                      """
                      if not self._is_modified:
                              return (True, None)

                      args:dict[str, Any] = {}
                      for field in self._payload.keys():
                              args[field] = self._payload[field]
                      self.payload_most_recently_attempted_to_store = args
                      close_conn = lambda : None
                      commit_conn = lambda : None
                      if conn is None:
                              conn = gmPG2.get_connection(readonly=False)
                              close_conn = conn.close
                              commit_conn = conn.commit
                      queries = []
                      for query in self.__class__._cmds_store_payload:
                              queries.append({'sql': query, 'args': args})
                      rows = gmPG2.run_rw_queries (
                              link_obj = conn,
                              queries = queries,
                              return_data = True
                      )
                      # success ?
                      if len(rows) == 0:
                              # nothing updated - this can happen if:
                              # - someone else updated the row so XMIN does not match anymore
                              # - the PK went away (rows were deleted from under us)
                              # - another WHERE condition of the UPDATE did not produce any rows to update
                              # - savepoints are used since subtransactions may relevantly change the xmin/xmax ...
                              return (False, ('cannot update row', _('[%s:%s]: row not updated (nothing returned), row in use ?') % (self.__class__.__name__, self.pk_obj)))

                      # update cached values from should-be-first-and-only
                      # result row of last query,
                      # update all fields returned such that computed
                      # columns see their new values (given they are
                      # returned by the query)
                      row = rows[0]
                      for key in row.keys():
                              try:
                                      self._payload[key] = row[key]
                              except KeyError:
                                      conn.rollback()
                                      close_conn()
                                      _log.error('[%s:%s]: cannot update instance, XMIN-refetch key mismatch on [%s]' % (self.__class__.__name__, self.pk_obj, key))
                                      _log.error('payload keys: %s' % str(self._payload.keys()))
                                      _log.error('XMIN-refetch keys: %s' % str(row.keys()))
                                      _log.error(args)
                                      raise

                      # only at commit time will data actually
                      # get committed (and thusly trigger based notifications
                      # be sent out), so reset the local modification flag
                      # right before that
                      self._is_modified = False
                      commit_conn()
                      close_conn()
                      # update to new "original" payload
                      self.payload_most_recently_fetched = {}
                      for field in self._payload.keys():
                              self.payload_most_recently_fetched[field] = self._payload[field]
                      return (True, None)

  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 ]

  ### Subclasses

  - cAllergy
  - cAllergyState
  - cDynamicHint
  - cSuppressedHint
  - cBill
  - cBillItem
  - cBillable
  - cNarrative
  - cGenericCode
  - cGenericLinkedCode
  - cAddress
  - cCommChannel
  - cOrgCommChannel
  - cPatientAddress
  - cPersonTag
  - cTagImage
  - cDocument
  - cDocumentPart
  - cDocumentType
  - cEncounter
  - cEpisode
  - cExportItem
  - cExternalCareItem
  - cFamilyHistory
  - cFormTemplate
  - cGenderDef
  - cGenericEMRItem
  - cHealthIssue
  - cHospitalStay
  - cIncomingData
  - cKeywordExpansion
  - cDrugComponent
  - cDrugProduct
  - cIntakeRegimen
  - cIntakeWithRegimen
  - cSubstance
  - cSubstanceDose
  - cSubstanceIntakeEntry
  - cOrg
  - cOrgUnit
  - cLabRequest
  - cMeasurementType
  - cMetaTestType
  - cTestOrg
  - cTestPanel
  - cTestResult
  - cPerformedProcedure
  - cPerson
  - cPersonName
  - cPraxisBranch
  - cProblem
  - cInboxMessage
  - cStaff
  - cVaccination
  - cVaccine

  ### Instance variables

  `prop keys : list[str]`
    Expand source code

        def get_fields(self) -> list[str]:
                """Return list of accessible fields."""
                keys = list(self._payload.keys())
                if not keys:
                        keys = [
                                '[%s @ %s]' % (self.__class__.__name__, id(self)),
                                'no keys, nascent instance ?'
                        ]
                return keys

    Return list of accessible fields.

  `prop patient_pk : int`
    Expand source code

        def _get_patient_pk(self) -> int:
                """Get primary key of associated patient if any."""
                pk_patient = None
                try:
                        pk_patient = self._payload['pk_patient']
                except KeyError:
                        pass
                try:
                        pk_patient = self._payload['pk_identity']
                except KeyError:
                        pass

                return pk_patient

    Get primary key of associated patient if any.

  `prop staff_id : int`
    Expand source code

        def _get_staff_id(self) -> int:
                """Get staff id of associated staff if any."""
                try:
                        return self._payload['pk_staff']

                except KeyError:
                        _log.debug('[%s]: .pk_staff should be added to the view', self.__class__.__name__)
                try:
                        return self._payload['pk_provider']

                except KeyError:
                        pass
                mod_by = None
                try:
                        mod_by = self._payload['modified_by_raw']
                except KeyError:
                        _log.debug('[%s]: .modified_by_raw should be added to the view', self.__class__.__name__)
                if mod_by is not None:
                        # find by DB account
                        args = {'db_u': mod_by}
                        cmd = "SELECT pk FROM dem.staff WHERE db_user = %(db_u)s"
                        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                        if rows:
                                # logically, they are all the same provider, because they share the DB account
                                return rows[0]['pk']

                mod_by = self._payload['modified_by']
                # is .modified_by a "<DB-account>" ?
                if mod_by.startswith('<') and mod_by.endswith('>'):
                        # find by DB account
                        args = {'db_u': mod_by.lstrip('<').rstrip('>')}
                        cmd = "SELECT pk FROM dem.staff WHERE db_user = %(db_u)s"
                        rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                        if rows:
                                # logically, they are all the same provider, because they share the DB account
                                return rows[0]['pk']

                # .modified_by is probably dem.staff.short_alias
                args = {'alias': mod_by}
                cmd = "SELECT pk FROM dem.staff WHERE short_alias = %(alias)s"
                rows = gmPG2.run_ro_queries(queries = [{'sql': cmd, 'args': args}])
                if rows:
                        # logically, they are all the same provider, because they share the DB account
                        return rows[0]['pk']

                _log.error('[%s]: cannot retrieve staff ID for [%s]', self.__class__.__name__, mod_by)
                return None

    Get staff id of associated staff if any.

  ### Methods

  `def fields_as_dict(self,
  date_format: str = '%Y %b %d %H:%M',
  none_string: str = '',
  escape_style: str = None,
  bool_strings: list[str] = None) ‑> dict`
    Expand source code

        def fields_as_dict(self, date_format:str='%Y %b %d  %H:%M', none_string:str='', escape_style:str=None, bool_strings:list[str]=None) -> dict:
                """Return field values as a dictionary of strings."""
                if bool_strings is None:
                        bools = {True: 'True', False: 'False'}
                else:
                        bools = {True: bool_strings[0], False: bool_strings[1]}
                data = {}
                for field in self._payload.keys():
                        # harden against BYTEA fields
                        if isinstance(self._payload[field], memoryview):
                                val = _('binary data: %s%s (total: %s bytes)') % (
                                        self._payload[field].obj[:10],
                                        u_ellipsis,
                                        self._payload[field].nbytes
                                )
                        else:
                                val = self._payload[field]
                        if val is None:
                                data[field] = none_string
                                continue
                        if isinstance(val, bool):
                                data[field] = bools[val]
                                continue
                        if isinstance(val, datetime.datetime):
                                if date_format is None:
                                        data[field] = str(val)                  # x-type: ignore [assignment]
                                        continue
                                data[field] = val.strftime(date_format)
                                if escape_style in ['latex', 'tex']:
                                        data[field] = tex_escape_string(data[field])
                                elif escape_style in ['xetex', 'xelatex']:
                                        data[field] = xetex_escape_string(data[field])
                                continue
                        try:
                                data[field] = str(val, encoding = 'utf8', errors = 'replace')
                        except TypeError:
                                try:
                                        data[field] = str(val)
                                except (UnicodeDecodeError, TypeError):
                                        val = '%s' % str(val)
                                        data[field] = val.decode('utf8', 'replace')
                        if escape_style in ['latex', 'tex']:
                                data[field] = tex_escape_string(data[field])
                        elif escape_style in ['xetex', 'xelatex']:
                                data[field] = xetex_escape_string(data[field])
                return data

    Return field values as a dictionary of strings.

  `def format(self, *args, **kwargs) ‑> list[str]`
    Expand source code

        def format(self, *args, **kwargs) -> list[str]:
                """Return instance data generically formatted as a table."""
                return format_dict_like (
                        self.fields_as_dict(none_string = '<?>'),
                        tabular = True,
                        value_delimiters = None
                ).split('\n')

    Return instance data generically formatted as a table.

  `def get_fields(self) ‑> list[str]`
    Expand source code

        def get_fields(self) -> list[str]:
                """Return list of accessible fields."""
                keys = list(self._payload.keys())
                if not keys:
                        keys = [
                                '[%s @ %s]' % (self.__class__.__name__, id(self)),
                                'no keys, nascent instance ?'
                        ]
                return keys

    Return list of accessible fields.

  `def get_patient(self)`
    Expand source code

        def get_patient(self):
                """Get associated patient object."""
                _log.error('[%s:%s]: forgot to override get_patient()' % (self.__class__.__name__, self.pk_obj))
                return None

    Get associated patient object.

  `def get_updatable_fields(self) ‑> list[str]`
    Expand source code

        def get_updatable_fields(self) -> list[str]:
                """Return a list of fields that can be updated."""
                return self.__class__._updatable_fields

    Return a list of fields that can be updated.

  `def is_modified(self) ‑> bool`
    Expand source code

        def is_modified(self) -> bool:
                """Whether data in this business object has been modified."""
                return self._is_modified

    Whether data in this business object has been modified.

  `def refetch_payload(self, ignore_changes: bool = False, link_obj=None) ‑> bool`
    Expand source code

        def refetch_payload(self, ignore_changes:bool=False, link_obj=None) -> bool:
                """Fetch field values from backend.

                Args:
                        ignore_changes: True -> loose local changes if data on the backend changed
                """
                if self._is_modified:
                        compare_dict_likes(self.original_payload, self.fields_as_dict(date_format = None, none_string = None), 'original payload', 'modified payload')
                        if ignore_changes:
                                _log.critical('[%s:%s]: losing payload changes' % (self.__class__.__name__, self.pk_obj))
                                #_log.debug('most recently fetched: %s' % self.payload_most_recently_fetched)
                                #_log.debug('modified: %s' % self._payload)
                        else:
                                _log.critical('[%s:%s]: cannot reload, payload changed' % (self.__class__.__name__, self.pk_obj))
                                return False

                if isinstance(self.pk_obj, dict):
                        args:dict = self.pk_obj
                else:
                        args:list = [self.pk_obj]               # type: ignore [no-redef]
                queries = [{'sql': self.__class__._cmd_fetch_payload, 'args': args}]
                rows = gmPG2.run_ro_queries (
                        link_obj = link_obj,
                        queries = queries
                )
                if len(rows) == 0:
                        _log.error('[%s:%s]: no such instance' % (self.__class__.__name__, self.pk_obj))
                        return False

                if len(rows) > 1:
                        raise AssertionError('[%s:%s]: %s instances !' % (self.__class__.__name__, self.pk_obj, len(rows)))

                self._payload = rows[0]
                return True

    Fetch field values from backend.

    ## Args

    `ignore_changes`
      True -> loose local changes if data on the backend changed
  `def same_payload(self,
  another_object: cBusinessDBObject = None) ‑> bool`
    Expand source code

        def same_payload(self, another_object:'cBusinessDBObject'=None) -> bool:
                """Check whether *self* and *another_object* hold the same payload."""
                raise NotImplementedError('comparison between [%s] and [%s] not implemented' % (self, another_object))

    Check whether self and another_object hold the same payload.

  `def save(self, conn: psycopg2.extras.DictConnection = None) ‑> tuple[bool, tuple]`
    Expand source code

        def save(self, conn:gmPG2.dbapi.extras.DictConnection=None) -> tuple[bool, tuple]:
                """Just calls save_payload()."""
                return self.save_payload(conn = conn)

    Just calls save_payload().

  `def save_payload(self, conn: psycopg2.extras.DictConnection = None) ‑> tuple[bool, tuple]`
    Expand source code

        def save_payload(self, conn:gmPG2.dbapi.extras.DictConnection=None) -> tuple[bool, tuple]:
                """Store updated values (if any) into database.

                Optionally accepts a pre-existing connection

                Returns:
                        a tuple (True|False, data)
                        True: success
                        False: an error occurred,
                        data: (error, message), for error meanings see gmPG2.run_rw_queries()
                """
                if not self._is_modified:
                        return (True, None)

                args:dict[str, Any] = {}
                for field in self._payload.keys():
                        args[field] = self._payload[field]
                self.payload_most_recently_attempted_to_store = args
                close_conn = lambda : None
                commit_conn = lambda : None
                if conn is None:
                        conn = gmPG2.get_connection(readonly=False)
                        close_conn = conn.close
                        commit_conn = conn.commit
                queries = []
                for query in self.__class__._cmds_store_payload:
                        queries.append({'sql': query, 'args': args})
                rows = gmPG2.run_rw_queries (
                        link_obj = conn,
                        queries = queries,
                        return_data = True
                )
                # success ?
                if len(rows) == 0:
                        # nothing updated - this can happen if:
                        # - someone else updated the row so XMIN does not match anymore
                        # - the PK went away (rows were deleted from under us)
                        # - another WHERE condition of the UPDATE did not produce any rows to update
                        # - savepoints are used since subtransactions may relevantly change the xmin/xmax ...
                        return (False, ('cannot update row', _('[%s:%s]: row not updated (nothing returned), row in use ?') % (self.__class__.__name__, self.pk_obj)))

                # update cached values from should-be-first-and-only
                # result row of last query,
                # update all fields returned such that computed
                # columns see their new values (given they are
                # returned by the query)
                row = rows[0]
                for key in row.keys():
                        try:
                                self._payload[key] = row[key]
                        except KeyError:
                                conn.rollback()
                                close_conn()
                                _log.error('[%s:%s]: cannot update instance, XMIN-refetch key mismatch on [%s]' % (self.__class__.__name__, self.pk_obj, key))
                                _log.error('payload keys: %s' % str(self._payload.keys()))
                                _log.error('XMIN-refetch keys: %s' % str(row.keys()))
                                _log.error(args)
                                raise

                # only at commit time will data actually
                # get committed (and thusly trigger based notifications
                # be sent out), so reset the local modification flag
                # right before that
                self._is_modified = False
                commit_conn()
                close_conn()
                # update to new "original" payload
                self.payload_most_recently_fetched = {}
                for field in self._payload.keys():
                        self.payload_most_recently_fetched[field] = self._payload[field]
                return (True, None)

    Store updated values (if any) into database.

    Optionally accepts a pre-existing connection

    ## Returns

    a tuple (True|False, data)
    `True`
      success
    `False`
      an error occurred,
    `data`
      (error, message), for error meanings see gmPG2.run_rw_queries()