def create_inbox_message(message_type=None, subject=None, patient=None, staff=None, message_category='clinical'):
success, pk_type = gmTools.input2int(initial = message_type)
if not success:
pk_type = create_inbox_item_type(message_type = message_type, category = message_category)
cmd = """
INSERT INTO dem.message_inbox (
fk_staff,
fk_patient,
fk_inbox_item_type,
comment
) VALUES (
%(staff)s,
%(pat)s,
%(type)s,
gm.nullify_empty_string(%(subject)s)
)
RETURNING pk
"""
args = {
'staff': staff,
'pat': patient,
'type': pk_type,
'subject': subject
}
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
return cInboxMessage(aPK_obj = rows[0]['pk'])
def create_inbox_item_type(message_type=None, category=u'clinical'):
# determine category PK
success, pk_cat = gmTools.input2int(initial=category)
if not success:
args = {u'cat': category}
cmd = u"""SELECT COALESCE (
(SELECT pk FROM dem.inbox_item_category WHERE _(description) = %(cat)s),
(SELECT pk FROM dem.inbox_item_category WHERE description = %(cat)s)
) AS pk"""
rows, idx = gmPG2.run_ro_queries(queries=[{'cmd': cmd, 'args': args}])
if rows[0]['pk'] is None:
cmd = u"INSERT INTO dem.inbox_item_category (description) VALUES (%(cat)s) RETURNING pk"
rows, idx = gmPG2.run_rw_queries(queries=[{
'cmd': cmd,
'args': args
}],
return_data=True)
pk_cat = rows[0]['pk']
else:
pk_cat = rows[0]['pk']
# find type PK or create type
args = {u'pk_cat': pk_cat, u'type': message_type}
cmd = u"""SELECT COALESCE (
(SELECT pk FROM dem.inbox_item_type where fk_inbox_item_category = %(pk_cat)s AND _(description) = %(type)s),
(SELECT pk FROM dem.inbox_item_type where fk_inbox_item_category = %(pk_cat)s AND description = %(type)s)
) AS pk"""
rows, idx = gmPG2.run_ro_queries(queries=[{'cmd': cmd, 'args': args}])
if rows[0]['pk'] is None:
cmd = u"""
INSERT INTO dem.inbox_item_type (
fk_inbox_item_category,
description,
is_user
) VALUES (
%(pk_cat)s,
%(type)s,
TRUE
) RETURNING pk"""
rows, idx = gmPG2.run_rw_queries(queries=[{
'cmd': cmd,
'args': args
}],
return_data=True)
return rows[0]['pk']
def create_inbox_item_type(message_type=None, category='clinical'):
# determine category PK
success, pk_cat = gmTools.input2int(initial = category)
if not success:
args = {'cat': category}
cmd = """SELECT COALESCE (
(SELECT pk FROM dem.inbox_item_category WHERE _(description) = %(cat)s),
(SELECT pk FROM dem.inbox_item_category WHERE description = %(cat)s)
) AS pk"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if rows[0]['pk'] is None:
cmd = "INSERT INTO dem.inbox_item_category (description) VALUES (%(cat)s) RETURNING pk"
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
pk_cat = rows[0]['pk']
else:
pk_cat = rows[0]['pk']
# find type PK or create type
args = {'pk_cat': pk_cat, 'type': message_type}
cmd = """SELECT COALESCE (
(SELECT pk FROM dem.inbox_item_type where fk_inbox_item_category = %(pk_cat)s AND _(description) = %(type)s),
(SELECT pk FROM dem.inbox_item_type where fk_inbox_item_category = %(pk_cat)s AND description = %(type)s)
) AS pk"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if rows[0]['pk'] is None:
cmd = """
INSERT INTO dem.inbox_item_type (
fk_inbox_item_category,
description,
is_user
) VALUES (
%(pk_cat)s,
%(type)s,
TRUE
) RETURNING pk"""
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
return rows[0]['pk']
def set_active_patient(patient=None, forced_reload=False):
# already active ?
if isinstance(patient, gmPerson.gmCurrentPatient):
return True
if isinstance(patient, gmPerson.cPatient):
if patient['is_deleted']:
_log.error('patient is disabled, will not use as active patient: %s', patient)
return False
elif isinstance(patient, gmPerson.cPerson):
if patient['is_deleted']:
_log.error('patient is disabled, will not use as active patient: %s', patient)
return False
patient = patient.as_patient
elif patient == -1:
pass
else:
# maybe integer ?
success, pk = gmTools.input2int(initial = patient, minval = 1)
if not success:
raise ValueError('<patient> must be either -1, >0, or a cPatient, cPerson or gmCurrentPatient instance, is: %s' % patient)
# but also valid patient ID ?
try:
patient = gmPerson.cPatient(aPK_obj = pk)
except Exception:
_log.exception('error changing active patient to [%s]' % patient)
return False
if not _verify_staff_chart_access(patient = patient):
return False
success = gmPerson.set_active_patient(patient = patient, forced_reload = forced_reload)
if not success:
return False
wx.CallAfter(_do_after_setting_active_patient, patient)
return True
def create_inbox_message(message_type=None,
subject=None,
patient=None,
staff=None,
message_category=u'clinical'):
success, pk_type = gmTools.input2int(initial=message_type)
if not success:
pk_type = create_inbox_item_type(message_type=message_type,
category=message_category)
cmd = u"""
INSERT INTO dem.message_inbox (
fk_staff,
fk_patient,
fk_inbox_item_type,
comment
) VALUES (
%(staff)s,
%(pat)s,
%(type)s,
gm.nullify_empty_string(%(subject)s)
)
RETURNING pk
"""
args = {
u'staff': staff,
u'pat': patient,
u'type': pk_type,
u'subject': subject
}
rows, idx = gmPG2.run_rw_queries(queries=[{
'cmd': cmd,
'args': args
}],
return_data=True,
get_col_idx=False)
return cInboxMessage(aPK_obj=rows[0]['pk'])
def set_active_patient(patient=None, forced_reload=False):
# already active ?
if isinstance(patient, gmPerson.gmCurrentPatient):
return True
if isinstance(patient, gmPerson.cPatient):
if patient['is_deleted']:
_log.error('patient is disabled, will not use as active patient: %s', patient)
return False
elif isinstance(patient, gmPerson.cPerson):
if patient['is_deleted']:
_log.error('patient is disabled, will not use as active patient: %s', patient)
return False
patient = patient.as_patient
elif patient == -1:
pass
else:
# maybe integer ?
success, pk = gmTools.input2int(initial = patient, minval = 1)
if not success:
raise ValueError('<patient> must be either -1, >0, or a cPatient, cPerson or gmCurrentPatient instance, is: %s' % patient)
# but also valid patient ID ?
try:
patient = gmPerson.cPatient(aPK_obj = pk)
except:
_log.exception('error changing active patient to [%s]' % patient)
return False
if not _verify_staff_chart_access(patient = patient):
return False
success = gmPerson.set_active_patient(patient = patient, forced_reload = forced_reload)
if not success:
return False
wx.CallAfter(_do_after_setting_active_patient, patient)
return True
def load_data_packs_list():
dbcfg = gmCfg.cCfgSQL()
dpl_url = dbcfg.get2 (
option = dpl_url_option,
workplace = gmPraxis.gmCurrentPraxisBranch().active_workplace,
bias = 'workplace',
default = default_dpl_url
)
items = []
data = []
dpl_fname = gmNetworkTools.download_data_packs_list(dpl_url)
if dpl_fname is None:
return (items, data)
try:
_cfg.add_file_source(source = 'data-packs', file = dpl_fname)
except (UnicodeDecodeError):
_log.exception("cannot read data pack list from [%s]", dpl_fname)
return (items, data)
packs = _cfg.get('data packs', 'data packs', source_order = [('data-packs', 'return')])
if packs is None:
_log.info('no data packs listed in data packs list file')
_cfg.remove_source('data-packs')
return (items, data)
for pack in packs:
_log.debug('reading pack [%s] metadata', pack)
pack_group = u'pack %s' % pack
name = _cfg.get(pack_group, u'name', source_order = [('data-packs', 'return')])
pack_url = _cfg.get(pack_group, u'URL', source_order = [('data-packs', 'return')])
md5_url = pack_url + u'.md5'
db_min = _cfg.get(pack_group, u'minimum database version', source_order = [('data-packs', 'return')])
converted, db_min = gmTools.input2int (
db_min,
# here we introduced data packs:
#16,
0,
# no use looking at data packs requiring a database > the current database:
_cfg.get(option = 'database_version')
)
if not converted:
_log.error('cannot convert minimum database version [%s]', db_min)
continue
db_max = _cfg.get(pack_group, u'maximum database version', source_order = [('data-packs', 'return')])
if db_max is None:
db_max = sys.maxint
converted, db_max = gmTools.input2int (
db_max,
db_min # max version must be at least db_min
)
if not converted:
_log.error('cannot convert maximum database version [%s]', db_max)
continue
if _cfg.get(option = 'database_version') < db_min:
_log.error('ignoring data pack: current database version (%s) < minimum required database version (%s)', _cfg.get(option = 'database_version'), db_min)
continue
if _cfg.get(option = 'database_version') > db_max:
_log.error('ignoring data pack: current database version (%s) > maximum allowable database version (%s)', _cfg.get(option = 'database_version'), db_max)
continue
items.append([name, u'v%s' % db_min, u'v%s' % db_max, pack_url])
data.append ({
'name': name,
'pack_url': pack_url,
'md5_url': md5_url,
'db_min': db_min,
'db_max': db_max
})
_cfg.remove_source('data-packs')
return (items, data)
def process_options():
if _cfg.get(option='-h', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option='-?', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option='--help', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
file2import = _cfg.get(option='--file2import',
source_order=[('cli', 'return')])
if file2import is None:
exit_with_message('ERROR: option --file2import missing')
if file2import is True:
exit_with_message('ERROR: data file missing in option --file2import=')
try:
open(file2import).close()
except IOError:
_log.exception('cannot open data file')
exit_with_message(
'ERROR: cannot open data file in option --file2import=%s' %
file2import)
datatype = _cfg.get(option='--data-type', source_order=[('cli', 'return')])
if datatype is None:
exit_with_message('ERROR: option --data-type missing')
if datatype is True:
exit_with_message('ERROR: data type missing in option --data-type=')
if datatype.strip() == '':
exit_with_message(
'ERROR: invalid data type in option --data-type=>>>%s<<<' %
datatype)
db_user = _cfg.get(option='--user', source_order=[('cli', 'return')])
if db_user is None:
exit_with_message('ERROR: option --user missing')
if db_user is True:
exit_with_message('ERROR: user name missing in option --user='******'':
exit_with_message(
'ERROR: invalid user name in option --user=>>>%s<<<' % db_user)
db_host = _cfg.get(option='--host', source_order=[('cli', 'return')])
if db_host is None:
_log.debug(
'option --host not set, using <UNIX domain socket> on <localhost>')
elif db_host is True:
exit_with_message('ERROR: host name missing in option --host=')
elif db_host.strip() == '':
_log.debug(
'option --host set to "", using <UNIX domain socket> on <localhost>'
)
db_host = None
db_port = _cfg.get(option='--port', source_order=[('cli', 'return')])
if db_port is None:
_log.debug(
'option --port not set, using <UNIX domain socket> on <localhost>')
elif db_port is True:
exit_with_message('ERROR: port value missing in option --port=')
elif db_port.strip() == '':
_log.debug(
'option --port set to "", using <UNIX domain socket> on <localhost>'
)
db_port = None
else:
converted, db_port = gmTools.input2int(initial=db_port,
minval=1024,
maxval=65535)
if not converted:
exit_with_message(
'ERROR: invalid port in option --port=%s (must be 1024...65535)'
% db_port)
gmPG2.log_auth_environment()
dsn = gmPG2.make_psycopg2_dsn(
database=gmPG2.default_database,
host=db_host,
port=db_port,
user=db_user,
password=
None # None = force not-required (TRUST/IDENT/PEER) or use-.pgpass-or-$PGPASSFILE
)
gmPG2._default_dsn = dsn
return datatype, file2import
def process_options():
if _cfg.get(option = '-h', source_order = [('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option = '-?', source_order = [('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option = '--help', source_order = [('cli', 'return')]):
show_usage()
sys.exit(0)
file2import = _cfg.get(option = '--file2import', source_order = [('cli', 'return')])
if file2import is None:
exit_with_message('ERROR: option --file2import missing')
if file2import is True:
exit_with_message('ERROR: data file missing in option --file2import=')
try:
open(file2import).close()
except IOError:
_log.exception('cannot open data file')
exit_with_message('ERROR: cannot open data file in option --file2import=%s' % file2import)
datatype = _cfg.get(option = '--data-type', source_order = [('cli', 'return')])
if datatype is None:
exit_with_message('ERROR: option --data-type missing')
if datatype is True:
exit_with_message('ERROR: data type missing in option --data-type=')
if datatype.strip() == '':
exit_with_message('ERROR: invalid data type in option --data-type=>>>%s<<<' % datatype)
db_user = _cfg.get(option = '--user', source_order = [('cli', 'return')])
if db_user is None:
exit_with_message('ERROR: option --user missing')
if db_user is True:
exit_with_message('ERROR: user name missing in option --user='******'':
exit_with_message('ERROR: invalid user name in option --user=>>>%s<<<' % db_user)
db_host = _cfg.get(option = '--host', source_order = [('cli', 'return')])
if db_host is None:
_log.debug('option --host not set, using <UNIX domain socket> on <localhost>')
elif db_host is True:
exit_with_message('ERROR: host name missing in option --host=')
elif db_host.strip() == '':
_log.debug('option --host set to "", using <UNIX domain socket> on <localhost>')
db_host = None
db_port = _cfg.get(option = '--port', source_order = [('cli', 'return')])
if db_port is None:
_log.debug('option --port not set, using <UNIX domain socket> on <localhost>')
elif db_port is True:
exit_with_message('ERROR: port value missing in option --port=')
elif db_port.strip() == '':
_log.debug('option --port set to "", using <UNIX domain socket> on <localhost>')
db_port = None
else:
converted, db_port = gmTools.input2int(initial = db_port, minval = 1024, maxval = 65535)
if not converted:
exit_with_message('ERROR: invalid port in option --port=%s (must be 1024...65535)' % db_port)
gmPG2.log_auth_environment()
dsn = gmPG2.make_psycopg2_dsn (
database = gmPG2.default_database,
host = db_host,
port = db_port,
user = db_user,
password = None # None = force not-required (TRUST/IDENT/PEER) or use-.pgpass-or-$PGPASSFILE
)
gmPG2._default_dsn = dsn
return datatype, file2import
def load_data_packs_list():
dbcfg = gmCfg.cCfgSQL()
dpl_url = dbcfg.get2(
option=dpl_url_option,
workplace=gmPraxis.gmCurrentPraxisBranch().active_workplace,
bias='workplace',
default=default_dpl_url)
items = []
data = []
dpl_fname = gmNetworkTools.download_data_packs_list(dpl_url)
if dpl_fname is None:
return (items, data)
try:
_cfg.add_file_source(source='data-packs', file=dpl_fname)
except (UnicodeDecodeError):
_log.exception("cannot read data pack list from [%s]", dpl_fname)
return (items, data)
packs = _cfg.get('data packs',
'data packs',
source_order=[('data-packs', 'return')])
if packs is None:
_log.info('no data packs listed in data packs list file')
_cfg.remove_source('data-packs')
return (items, data)
for pack in packs:
_log.debug('reading pack [%s] metadata', pack)
pack_group = u'pack %s' % pack
name = _cfg.get(pack_group,
u'name',
source_order=[('data-packs', 'return')])
pack_url = _cfg.get(pack_group,
u'URL',
source_order=[('data-packs', 'return')])
md5_url = pack_url + u'.md5'
db_min = _cfg.get(pack_group,
u'minimum database version',
source_order=[('data-packs', 'return')])
converted, db_min = gmTools.input2int(
db_min,
# here we introduced data packs:
#16,
0,
# no use looking at data packs requiring a database > the current database:
_cfg.get(option='database_version'))
if not converted:
_log.error('cannot convert minimum database version [%s]', db_min)
continue
db_max = _cfg.get(pack_group,
u'maximum database version',
source_order=[('data-packs', 'return')])
if db_max is None:
db_max = sys.maxint
converted, db_max = gmTools.input2int(
db_max,
db_min # max version must be at least db_min
)
if not converted:
_log.error('cannot convert maximum database version [%s]', db_max)
continue
if _cfg.get(option='database_version') < db_min:
_log.error(
'ignoring data pack: current database version (%s) < minimum required database version (%s)',
_cfg.get(option='database_version'), db_min)
continue
if _cfg.get(option='database_version') > db_max:
_log.error(
'ignoring data pack: current database version (%s) > maximum allowable database version (%s)',
_cfg.get(option='database_version'), db_max)
continue
items.append([name, u'v%s' % db_min, u'v%s' % db_max, pack_url])
data.append({
'name': name,
'pack_url': pack_url,
'md5_url': md5_url,
'db_min': db_min,
'db_max': db_max
})
_cfg.remove_source('data-packs')
return (items, data)
def process_options():
if _cfg.get(option='-h', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option='-?', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
if _cfg.get(option='--help', source_order=[('cli', 'return')]):
show_usage()
sys.exit(0)
file2import = _cfg.get(option='--file2import',
source_order=[('cli', 'return')])
if file2import is None:
exit_with_message('ERROR: option --file2import missing')
if file2import is True:
exit_with_message('ERROR: data file missing in option --file2import=')
try:
open(file2import).close()
except IOError:
_log.exception('cannot open data file')
exit_with_message(
'ERROR: cannot open data file in option --file2import=%s' %
file2import)
datatype = _cfg.get(option='--data-type', source_order=[('cli', 'return')])
if datatype is None:
exit_with_message('ERROR: option --data-type missing')
if datatype is True:
exit_with_message('ERROR: data type missing in option --data-type=')
if datatype.strip() == '':
exit_with_message(
'ERROR: invalid data type in option --data-type=>>>%s<<<' %
datatype)
db_user = _cfg.get(option='--user', source_order=[('cli', 'return')])
if db_user is None:
exit_with_message('ERROR: option --user missing')
if db_user is True:
exit_with_message('ERROR: user name missing in option --user='******'':
exit_with_message(
'ERROR: invalid user name in option --user=>>>%s<<<' % db_user)
db_host = _cfg.get(option='--host', source_order=[('cli', 'return')])
if db_host is None:
_log.debug(
'option --host not set, using <UNIX domain socket> on <localhost>')
elif db_host is True:
exit_with_message('ERROR: host name missing in option --host=')
elif db_host.strip() == '':
_log.debug(
'option --host set to "", using <UNIX domain socket> on <localhost>'
)
db_host = None
db_port = _cfg.get(option='--port', source_order=[('cli', 'return')])
if db_port is None:
_log.debug(
'option --port not set, using <UNIX domain socket> on <localhost>')
elif db_port is True:
exit_with_message('ERROR: port value missing in option --port=')
elif db_port.strip() == '':
_log.debug(
'option --port set to "", using <UNIX domain socket> on <localhost>'
)
db_port = None
else:
converted, db_port = gmTools.input2int(initial=db_port,
minval=1024,
maxval=65535)
if not converted:
exit_with_message(
'ERROR: invalid port in option --port=%s (must be 1024...65535)'
% db_port)
return datatype, file2import
