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
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.
Expand source code
"""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 <row> 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.
"""
#============================================================
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = "GPL v2 or later"
import sys
import logging
import datetime
from typing import Any
if __name__ == '__main__':
sys.path.insert(0, '../../')
_ = lambda x:x
from Gnumed.pycommon import gmExceptions
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon.gmDateTime import pydt_strftime
from Gnumed.pycommon.gmTools import tex_escape_string
from Gnumed.pycommon.gmTools import xetex_escape_string
from Gnumed.pycommon.gmTools import compare_dict_likes
from Gnumed.pycommon.gmTools import format_dict_like
from Gnumed.pycommon.gmTools import dicts2table
from Gnumed.pycommon.gmTools import u_left_arrow
_log = logging.getLogger('gm.db')
#============================================================
# business object template
#------------------------------------------------------------
__TEMPLATE = """
#------------------------------------------------------------
from Gnumed.pycommon import gmBusinessDBObject
from Gnumed.pycommon import gmPG2
#============================================================
# short description
#------------------------------------------------------------
# search/replace "" " -> 3 "s
#
# search-replace get_XXX, use plural form
_SQL_get_XXX = u"" "
SELECT *, (xmin AS xmin_XXX)
FROM XXX.v_XXX
WHERE %s
"" "
class cXxxXxx(gmBusinessDBObject.cBusinessDBObject):
"" "Represents ..."" "
_cmd_fetch_payload = _SQL_get_XXX % u"pk_XXX = %s"
_cmds_store_payload = [
u"" "
-- typically the underlying table name
UPDATE xxx.xxx SET
-- typically "table_col = % (view_col)s"
xxx = %(xxx)s,
xxx = gm.nullify_empty_string(%(xxx)s)
WHERE
pk = %(pk_XXX)s
AND
xmin = %(xmin_XXX)s
RETURNING
xmin AS xmin_XXX
-- also return columns which are calculated in the view used by
-- the initial SELECT such that they will further on contain their
-- updated value:
--, ...
--, ...
"" "
]
# view columns that can be updated:
_updatable_fields = [
'xxx',
'xxx'
]
#--------------------------------------------------------
# def format(self):
# return '%s' % self
#------------------------------------------------------------
def get_XXX(order_by=None):
if order_by is None:
order_by = u'true'
else:
order_by = u'true ORDER BY %s' % order_by
cmd = _SQL_get_XXX % order_by
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd}], get_col_idx = True)
return [ cXxxXxx(row = {'data': r, 'idx': idx, 'pk_field': 'pk_XXX'}) for r in rows ]
#------------------------------------------------------------
def create_xxx(xxx1=None, xxx2=None):
args = {
u'xxx1': xxx1,
u'xxx2': xxx2
}
cmd = u"" "
INSERT INTO xxx.xxx (
xxx1,
xxx2,
xxx
) VALUES (
%(xxx1)s,
%(xxx2)s,
gm.nullify_empty_string(%(xxx)s)
)
RETURNING pk
--RETURNING *
"" "
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
#rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = True)
return cXxxXxx(aPK_obj = rows[0]['pk'])
#return cXxxXxx(row = {'data': r, 'idx': idx, 'pk_field': 'pk_XXX'})
#------------------------------------------------------------
def delete_xxx(pk_XXX=None):
args = {'pk': pk_XXX}
cmd = u"DELETE FROM xxx.xxx WHERE pk = %(pk)s"
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#------------------------------------------------------------
#------------------------------------------------------------
# widget code
#------------------------------------------------------------
#def edit_xxx(parent=None, xxx=None, single_entry=False, presets=None):
# pass
#------------------------------------------------------------
#def delete_xxx():
# pass
#------------------------------------------------------------
#def manage_xxx():
# pass
#------------------------------------------------------------
# remember to add in clinical item generic workflows and generic clinical item formatting
"""
#============================================================
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
* 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
row: must hold the fields
* idx: a dict mapping field names to position
* data: the field values in a list (as returned by cursor.fetchone() in the DB-API)
* pk_field: the name of the primary key field
OR
* pk_obj: a dictionary suitable for passed to cursor.execute
and holding the primary key values, used for composite PKs
* for example:
row = {
'data': rows[0],
'idx': idx,
'pk_field': 'pk_XXX (the PK column name)',
'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val}
}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
objects = [ cChildClass(row = {'data': r, 'idx': idx, '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] = {}
self._payload:dict|'gmPG2.dbapi.extras.DictRow' = {} # the cache for backend object values (mainly table fields)
self._ext_cache:dict = {} # the cache for extended method's results
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.dbapi.extras.DictRow=None):
"""Creates a new clinical item instance given its fields.
Args:
row: EITHER {'idx': ..., 'data': ..., 'pk_field': ...}
* idx: a dict mapping field names to list position inside row['data']
* data: the field values in a list (as returned by cursor.fetchone() in the DB-API)
* pk_field: the name of the primary key field
OR
* pk_obj: a dictionary suitable for passing to cursor.execute(),
holding the primary key values; used for composite PKs
Examples:
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]
Copy/Paste:
row = {
'data': rows[0],
'idx': idx,
'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']
try:
self._idx = row['idx']
assert len(row['idx']) == len(row['data']), "[%s:??]: 'idx'<->'data' field count mismatch: %s" % (self.__class__.__name__, row)
except KeyError:
self._idx = self._payload.keys()
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."""
try:
return self._payload.keys()
except AttributeError:
return [
'[%s @ %s]' % (self.__class__.__name__, id(self)),
'cannot return keys, nascent ?'
]
#--------------------------------------------------------
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():
# FIXME: harden against BYTEA fields
#if type(self._payload[self._idx[field]]) == ...
# data[field] = _('<%s bytes of binary data>') % len(self._payload[self._idx[field]])
# continue
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] = val # type: ignore [assignment]
continue
data[field] = pydt_strftime(val, format = 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
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, idx = gmPG2.run_ro_queries(queries = [{'cmd': query, 'args': args}], get_col_idx = True)
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 (
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]
rows, self._idx = gmPG2.run_ro_queries (
link_obj = link_obj,
queries = [{'cmd': self.__class__._cmd_fetch_payload, 'args': args}],
get_col_idx = True
)
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
conn_close = lambda : None
if conn is None:
conn = gmPG2.get_connection(readonly=False)
conn_close = conn.close
queries = []
for query in self.__class__._cmds_store_payload:
queries.append({'cmd': query, 'args': args})
rows, idx = gmPG2.run_rw_queries (
link_obj = conn,
queries = queries,
return_data = True,
get_col_idx = 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()
conn_close()
_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 conn.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
conn.commit()
conn_close()
# 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)
#============================================================
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
#--------------------------------------------------------
class cTestObj(cBusinessDBObject):
_cmd_fetch_payload = ''
_cmds_store_payload:list[str] = []
_updatable_fields = ['test']
#----------------------------------------------------
def get_something(self):
pass
#----------------------------------------------------
def set_something(self):
pass
#--------------------------------------------------------
from Gnumed.pycommon import gmI18N
gmI18N.activate_locale()
gmI18N.install_domain()
db_row = {'bogus_pk': -1, 'bogus_field': 'bogus_data', 'bogus_date': datetime.datetime.now(), 'test': -1}
db_idx = {'bogus_pk': 0, 'bogus_field': 1, 'bogus_date': 2, 'test': 3}
row_data = {
'pk_field': 'bogus_pk',
#'idx': db_idx,
'data': db_row
}
obj = cTestObj(row = row_data)
print('format():', obj.format())
print('as_dict():', obj.fields_as_dict())
print('test:', obj['test'])
obj['test'] = 'test'
print('test:', obj['test'])
#print(obj['wrong_field'])
#obj['wrong_field'] = 1
#print(obj['wrong_field'])
#============================================================Classes
class cBusinessDBObject (aPK_obj: int | dict = None, row: dict = None, link_obj=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
- 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
row- must hold the fields
- idx: a dict mapping field names to position
- data: the field values in a list (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key field OR
- pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]
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 * 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 row: must hold the fields * idx: a dict mapping field names to position * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs * for example: row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, '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] = {} self._payload:dict|'gmPG2.dbapi.extras.DictRow' = {} # the cache for backend object values (mainly table fields) self._ext_cache:dict = {} # the cache for extended method's results 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.dbapi.extras.DictRow=None): """Creates a new clinical item instance given its fields. Args: row: EITHER {'idx': ..., 'data': ..., 'pk_field': ...} * idx: a dict mapping field names to list position inside row['data'] * data: the field values in a list (as returned by cursor.fetchone() in the DB-API) * pk_field: the name of the primary key field OR * pk_obj: a dictionary suitable for passing to cursor.execute(), holding the primary key values; used for composite PKs Examples: rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ] Copy/Paste: row = { 'data': rows[0], 'idx': idx, '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'] try: self._idx = row['idx'] assert len(row['idx']) == len(row['data']), "[%s:??]: 'idx'<->'data' field count mismatch: %s" % (self.__class__.__name__, row) except KeyError: self._idx = self._payload.keys() 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.""" try: return self._payload.keys() except AttributeError: return [ '[%s @ %s]' % (self.__class__.__name__, id(self)), 'cannot return keys, nascent ?' ] #-------------------------------------------------------- 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(): # FIXME: harden against BYTEA fields #if type(self._payload[self._idx[field]]) == ... # data[field] = _('<%s bytes of binary data>') % len(self._payload[self._idx[field]]) # continue 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] = val # type: ignore [assignment] continue data[field] = pydt_strftime(val, format = 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': query, 'args': args}], get_col_idx = True) 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 ( 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] rows, self._idx = gmPG2.run_ro_queries ( link_obj = link_obj, queries = [{'cmd': self.__class__._cmd_fetch_payload, 'args': args}], get_col_idx = True ) 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 conn_close = lambda : None if conn is None: conn = gmPG2.get_connection(readonly=False) conn_close = conn.close queries = [] for query in self.__class__._cmds_store_payload: queries.append({'cmd': query, 'args': args}) rows, idx = gmPG2.run_rw_queries ( link_obj = conn, queries = queries, return_data = True, get_col_idx = 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() conn_close() _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 conn.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 conn.commit() conn_close() # 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)Subclasses
- cAllergy
- cAllergyState
- cDynamicHint
- cSuppressedHint
- cBill
- cBillItem
- cBillable
- cNarrative
- cGenericCode
- cGenericLinkedCode
- cAddress
- cCommChannel
- cOrgCommChannel
- cPatientAddress
- cPersonTag
- cTagImage
- cDocument
- cDocumentPart
- cDocumentType
- cEncounter
- cEpisode
- cHealthIssue
- cHospitalStay
- cPerformedProcedure
- cProblem
- cExportItem
- cExternalCareItem
- cFamilyHistory
- cFormTemplate
- cGenericEMRItem
- cIncomingData
- cKeywordExpansion
- cDrugComponent
- cDrugProduct
- cIntakeRegimen
- cSubstance
- cSubstanceDose
- cSubstanceIntakeEntry
- cOrg
- cOrgUnit
- cLabRequest
- cMeasurementType
- cMetaTestType
- cTestOrg
- cTestPanel
- cTestResult
- cPerson
- cPersonName
- cPraxisBranch
- cInboxMessage
- cStaff
- cVaccination
- cVaccine
Instance variables
var patient_pk : int-
Get primary key of associated patient if any.
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 var staff_id : int-
Get staff id of associated staff if any.
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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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) 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
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-
Return field values as a dictionary of strings.
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(): # FIXME: harden against BYTEA fields #if type(self._payload[self._idx[field]]) == ... # data[field] = _('<%s bytes of binary data>') % len(self._payload[self._idx[field]]) # continue 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] = val # type: ignore [assignment] continue data[field] = pydt_strftime(val, format = 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 format(self, *args, **kwargs) ‑> list[str]-
Return instance data generically formatted as a table.
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') def get_fields(self) ‑> list[str]-
Return list of accessible fields.
Expand source code
def get_fields(self) -> list[str]: """Return list of accessible fields.""" try: return self._payload.keys() except AttributeError: return [ '[%s @ %s]' % (self.__class__.__name__, id(self)), 'cannot return keys, nascent ?' ] def get_patient(self)-
Get associated patient object.
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 def get_updatable_fields(self) ‑> list[str]-
Return a list of fields that can be updated.
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def get_updatable_fields(self) -> list[str]: """Return a list of fields that can be updated.""" return self.__class__._updatable_fields def is_modified(self) ‑> bool-
Whether data in this business object has been modified.
Expand source code
def is_modified(self) -> bool: """Whether data in this business object has been modified.""" return self._is_modified 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
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] rows, self._idx = gmPG2.run_ro_queries ( link_obj = link_obj, queries = [{'cmd': self.__class__._cmd_fetch_payload, 'args': args}], get_col_idx = True ) 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 same_payload(self, another_object: cBusinessDBObject = None) ‑> bool-
Check whether self and another_object hold the same payload.
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)) def save(self, conn: psycopg2.extras.DictConnection = None) ‑> tuple[bool, tuple]-
Just calls save_payload().
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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: psycopg2.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()
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 conn_close = lambda : None if conn is None: conn = gmPG2.get_connection(readonly=False) conn_close = conn.close queries = [] for query in self.__class__._cmds_store_payload: queries.append({'cmd': query, 'args': args}) rows, idx = gmPG2.run_rw_queries ( link_obj = conn, queries = queries, return_data = True, get_col_idx = 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() conn_close() _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 conn.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 conn.commit() conn_close() # 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)