def test_generic_codes_prw(): gmPG2.get_connection() app = wx.PyWidgetTester(size = (500, 40)) pw = cGenericCodesPhraseWheel(app.frame, -1) #pw.set_context(context = u'zip', val = u'04318') app.frame.Show(True) app.MainLoop()
def create_vaccine(pk_drug_product=None, product_name=None, indications=None, is_live=None):
assert (is_live is not None), '<is_live> must not be <None>'
conn = gmPG2.get_connection(readonly = False)
if pk_drug_product is None:
#prep = _('vaccine')
prep = 'vaccine'
_log.debug('creating vaccine drug product [%s %s]', product_name, prep)
vacc_prod = gmMedication.create_drug_product (
product_name = product_name,
preparation = prep,
return_existing = True,
# indications are ref.dose rows
doses = indications,
link_obj = conn
)
#conn.commit()
vacc_prod['atc'] = 'J07'
vacc_prod.save(conn = conn)
pk_drug_product = vacc_prod['pk_drug_product']
cmd = 'INSERT INTO ref.vaccine (fk_drug_product, is_live) values (%(pk_drug_product)s, %(live)s) RETURNING pk'
queries = [{'cmd': cmd, 'args': {'pk_drug_product': pk_drug_product, 'live': is_live}}]
rows, idx = gmPG2.run_rw_queries(link_obj = conn, queries = queries, get_col_idx = False, return_data = True, end_tx = True)
conn.close()
return cVaccine(aPK_obj = rows[0]['pk'])
def set(self, workplace = None, cookie = None, option = None, value = None):
"""Set (insert or update) option value in database.
Any parameter that is None will be set to the database default.
Note: you can't change the type of a parameter once it has been
created in the backend. If you want to change the type you will
have to delete the parameter and recreate it using the new type.
"""
# sanity checks
if None in [option, value]:
raise ValueError('invalid arguments (option=<%s>, value=<%s>)' % (option, value))
rw_conn = gmPG2.get_connection(readonly=False)
alias = self.__make_alias(workplace, 'CURRENT_USER', cookie, option)
opt_value = value
sql_type_cast = u''
if isinstance(value, basestring):
sql_type_cast = u'::text'
elif isinstance(value, types.BooleanType):
opt_value = int(opt_value)
elif isinstance(value, (types.FloatType, types.IntType, types.LongType, decimal.Decimal, types.BooleanType)):
sql_type_cast = u'::numeric'
elif isinstance(value, types.ListType):
# there can be different syntaxes for list types so don't try to cast them
pass
elif isinstance(value, types.BufferType):
# can go directly into bytea
pass
else:
try:
opt_value = gmPG2.dbapi.Binary(pickle.dumps(value))
sql_type_cast = '::bytea'
except pickle.PicklingError:
_log.error("cannot pickle option of type [%s] (key: %s, value: %s)", type(value), alias, str(value))
raise
except:
_log.error("don't know how to store option of type [%s] (key: %s, value: %s)", type(value), alias, str(value))
raise
cmd = u'select cfg.set_option(%%(opt)s, %%(val)s%s, %%(wp)s, %%(cookie)s, NULL)' % sql_type_cast
args = {
'opt': option,
'val': opt_value,
'wp': workplace,
'cookie': cookie
}
try:
rows, idx = gmPG2.run_rw_queries(link_obj=rw_conn, queries=[{'cmd': cmd, 'args': args}], return_data=True)
result = rows[0][0]
except:
_log.exception('cannot set option')
result = False
rw_conn.commit() # will rollback if transaction failed
rw_conn.close()
return result
def test(): conn = gmPG2.get_connection() app = wx.PyWidgetTester(size = (600, 600)) dlg = cOrganizationManagerDlg(app.frame, -1, size = (600, 600)) dlg.SetSize((600, 600)) dlg.ShowModal() # app.SetWidget(dlg, -1) app.MainLoop()
def add_items(self, items=None): """Requires no pending changes within the bill itself.""" # should check for item consistency first conn = gmPG2.get_connection(readonly = False) for item in items: item['pk_bill'] = self._payload[self._idx['pk_bill']] item.save(conn = conn) conn.commit() self.refetch_payload() # make sure aggregates are re-filled from view
def get_hints_for_patient(pk_identity=None, include_suppressed_needing_invalidation=False):
conn = gmPG2.get_connection()
curs = conn.cursor()
curs.callproc('clin.get_hints_for_patient', [pk_identity])
rows = curs.fetchall()
idx = gmPG2.get_col_indices(curs)
curs.close()
conn.rollback()
if not include_suppressed_needing_invalidation:
return [ cDynamicHint(row = {'data': r, 'idx': idx, 'pk_field': 'pk_auto_hint'}) for r in rows if r['rationale4suppression'] != 'magic_tag::please_invalidate_suppression' ]
return [ cDynamicHint(row = {'data': r, 'idx': idx, 'pk_field': 'pk_auto_hint'}) for r in rows ]
def get_dbowner_connection(procedure=None, dbo_password=None, dbo_account='gm-dbo'):
if procedure is None:
procedure = _('<restricted procedure>')
# 1) get password for gm-dbo
if dbo_password is None:
dbo_password = wx.GetPasswordFromUser (
message = _("""
[%s]
This is a restricted procedure. We need the
current password for the GNUmed database owner.
Please enter the current password for <%s>:""") % (
procedure,
dbo_account
),
caption = procedure
)
if dbo_password == '':
return None
gmLog2.add_word2hide(dbo_password)
# 2) connect as gm-dbo
login = gmPG2.get_default_login()
dsn = gmPG2.make_psycopg2_dsn (
database = login.database,
host = login.host,
port = login.port,
user = dbo_account,
password = dbo_password
)
try:
conn = gmPG2.get_connection (
dsn = dsn,
readonly = False,
verbose = True,
pooled = False
)
except:
_log.exception('cannot connect')
gmGuiHelpers.gm_show_error (
aMessage = _('Cannot connect as the GNUmed database owner <%s>.') % dbo_account,
aTitle = procedure
)
gmPG2.log_database_access(action = 'failed to connect as database owner for [%s]' % procedure)
return None
return conn
def create_progress_note(soap=None, episode_id=None, encounter_id=None, link_obj=None):
"""Create clinical narrative entries.
<soap>
must be a dict, the keys being SOAP categories (including U and
None=admin) and the values being text (possibly multi-line)
Existing but empty ('' or None) categories are skipped.
"""
if soap is None:
return True
if not gmSoapDefs.are_valid_soap_cats(soap.keys(), allow_upper = True):
raise ValueError('invalid SOAP category in <soap> dictionary: %s', soap)
if link_obj is None:
link_obj = gmPG2.get_connection(readonly = False)
conn_rollback = link_obj.rollback
conn_commit = link_obj.commit
conn_close = link_obj.close
else:
conn_rollback = lambda x:x
conn_commit = lambda x:x
conn_close = lambda x:x
instances = {}
for cat in soap:
val = soap[cat]
if val is None:
continue
if ''.join([ v.strip() for v in val ]) == '':
continue
instance = create_narrative_item (
narrative = '\n'.join([ v.strip() for v in val ]),
soap_cat = cat,
episode_id = episode_id,
encounter_id = encounter_id,
link_obj = link_obj
)
if instance is None:
continue
instances[cat] = instance
conn_commit()
conn_close()
return instances
def connect_to_database(max_attempts=3,
expected_version=None,
require_version=True):
"""Display the login dialog and try to log into the backend.
- up to max_attempts times
- returns True/False
"""
# force programmer to set a valid expected_version
gmPG2.known_schema_hashes[expected_version]
client_version = _cfg.get(option='client_version')
global current_db_name
current_db_name = 'gnumed_v%s' % expected_version
attempt = 0
dlg = cLoginDialog(None, -1, client_version=client_version)
dlg.Centre(wx.BOTH)
while attempt < max_attempts:
_log.debug('login attempt %s of %s', (attempt + 1), max_attempts)
connected = False
dlg.ShowModal()
login = dlg.panel.GetLoginInfo()
if login is None:
_log.info("user cancelled login dialog")
break
# obscure unconditionally, it could be a valid password
gmLog2.add_word2hide(login.password)
# try getting a connection to verify the parameters do work
creds = gmConnectionPool.cPGCredentials()
creds.database = login.database
creds.host = login.host
creds.port = login.port
creds.user = login.user
creds.password = login.password
pool = gmConnectionPool.gmConnectionPool()
pool.credentials = creds
try:
conn = gmPG2.get_raw_connection(verbose=True, readonly=True)
_log.info('successfully connected: %s', conn)
connected = True
except gmPG2.cAuthenticationError as exc:
_log.exception('login attempt failed')
gmPG2.log_pg_exception_details(exc)
attempt += 1
if attempt < max_attempts:
if ('host=127.0.0.1' in ('%s' % exc)) or ('host='
not in ('%s' % exc)):
msg = msg_auth_error_local
else:
msg = msg_auth_error
msg = msg % exc
msg = regex.sub(
r'password=[^\s]+',
'password=%s' % gmTools.u_replacement_character, msg)
gmGuiHelpers.gm_show_error(msg, _('Connecting to backend'))
del exc
continue
except gmPG2.dbapi.OperationalError as exc:
_log.exception('login attempt failed')
gmPG2.log_pg_exception_details(exc)
msg = msg_login_problem_generic % exc
msg = regex.sub(r'password=[^\s]+',
'password=%s' % gmTools.u_replacement_character,
msg)
gmGuiHelpers.gm_show_error(msg, _('Connecting to backend'))
del exc
continue
conn.close()
if not __database_is_acceptable_for_use(
require_version=require_version,
expected_version=expected_version,
login=login):
_log.info('database not suitable for use')
connected = False
break
dlg.panel.save_state()
gmExceptionHandlingWidgets.set_is_public_database(
_cfg.get(option='is_public_db'))
gmExceptionHandlingWidgets.set_helpdesk(_cfg.get(option='helpdesk'))
_log.debug('establishing DB listener connection')
conn = gmPG2.get_connection(
verbose=True,
connection_name='GNUmed-[DbListenerThread]',
pooled=False)
gmBackendListener.gmBackendListener(conn=conn)
break
dlg.DestroyLater()
return connected
def __import_single_PID_hl7_file(filename, emr=None):
"""Assumes single-PID/single-MSH HL7 file."""
_log.debug('importing single-PID single-MSH HL7 data from [%s]', filename)
# read the file
MSH_file = io.open(filename, mode = 'rt', encoding = 'utf-8-sig', newline = '')
HL7 = pyhl7.parse(MSH_file.read(1024 * 1024 * 5)) # 5 MB max
MSH_file.close()
# sanity checks
if len(HL7.segments('MSH')) != 1:
_log.error('more than one MSH segment')
return False
if len(HL7.segments('PID')) != 1:
_log.error('more than one PID segment')
return False
# ensure lab is in database
hl7_lab = HL7.extract_field('MSH', field_num = MSH_field__sending_lab)
gm_lab = __find_or_create_lab(hl7_lab)
# ensure test types exist
conn = gmPG2.get_connection(readonly = False)
__ensure_hl7_test_types_exist_in_gnumed(link_obj = conn, hl7_data = HL7, pk_test_org = gm_lab['pk_test_org'])
# find patient
if emr is None:
#PID = HL7.segment('PID')
pats = __PID2dto(HL7 = HL7)
if len(pats) == 0:
conn.rollback()
return False
if len(pats) > 1:
conn.rollback()
return False
emr = pats[0].emr
# import values: loop over segments
when_list = {}
current_result = None
previous_segment = None
had_errors = False
msh_seen = False
#pid_seen = False
last_obr = None
obr = {}
for seg_idx in range(len(HL7)):
seg = HL7[seg_idx]
seg_type = seg[0][0]
_log.debug('processing line #%s = segment of type <%s>', seg_idx, seg_type)
if seg_type == 'MSH':
msh_seen = True
if seg_type == 'PID':
if not msh_seen:
conn.rollback()
_log.error('PID segment before MSH segment')
return False
#pid_seen = True
if seg_type in ['MSH', 'PID']:
_log.info('segment already handled')
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type in ['ORC']:
_log.info('currently ignoring %s segments', seg_type)
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type == 'OBR':
previous_segment = seg_type
last_obr = seg
current_result = None
obr['abbrev'] = ('%s' % seg[OBR_field__service_name][0]).strip()
try:
obr['name'] = ('%s' % seg[OBR_field__service_name][1]).strip()
except IndexError:
obr['name'] = obr['abbrev']
for field_name in [OBR_field__ts_ended, OBR_field__ts_started, OBR_field__ts_specimen_received, OBR_field__ts_requested]:
obr['clin_when'] = seg[field_name][0].strip()
if obr['clin_when'] != '':
break
continue
if seg_type == 'OBX':
current_result = None
# determine value
val_alpha = seg[OBX_field__value][0].strip()
is_num, val_num = gmTools.input2decimal(initial = val_alpha)
if is_num:
val_alpha = None
else:
val_num = None
val_alpha = val_alpha.replace('\.br\\', '\n')
# determine test type
unit = seg[OBX_field__unit][0].strip()
if unit == '':
if is_num:
unit = '1/1'
else:
unit = None
test_type = __find_or_create_test_type (
loinc = '%s' % seg[OBX_field__type][0][OBX_component__loinc-1],
name = '%s' % seg[OBX_field__type][0][OBX_component__name-1],
pk_lab = gm_lab['pk_test_org'],
unit = unit,
link_obj = conn
)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
current_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_num = val_num,
val_alpha = val_alpha,
unit = unit
)
# handle range information et al
ref_range = seg[OBX_field__range][0].strip()
if ref_range != '':
current_result.reference_range = ref_range
flag = seg[OBX_field__abnormal_flag][0].strip()
if flag != '':
current_result['abnormality_indicator'] = flag
current_result['status'] = seg[OBX_field__status][0].strip()
current_result['val_grouping'] = seg[OBX_field__subid][0].strip()
current_result['source_data'] = ''
if last_obr is not None:
current_result['source_data'] += str(last_obr)
current_result['source_data'] += '\n'
current_result['source_data'] += str(seg)
clin_when = seg[OBX_field__timestamp][0].strip()
if clin_when == '':
_log.warning('no <Observation timestamp> in OBX, trying OBR timestamp')
clin_when = obr['clin_when']
try:
clin_when = __hl7dt2pydt(clin_when)
except ValueError:
_log.exception('clin_when from OBX or OBR not useable, assuming <today>')
if clin_when is not None:
current_result['clin_when'] = clin_when
current_result.save(conn = conn)
when_list[gmDateTime.pydt_strftime(current_result['clin_when'], '%Y %b %d')] = 1
previous_segment = seg_type
continue
if seg_type == 'NTE':
note = seg[NET_field__note][0].strip().replace('\.br\\', '\n')
if note == '':
_log.debug('empty NTE segment')
previous_segment = seg_type # maybe not ? (HL7 providers happen to use empty NTE segments to "structure" raw HL7 |-)
continue
# if this is an NTE following an OBR (IOW an order-related
# comment): make this a test result all of its own :-)
if previous_segment == 'OBR':
_log.debug('NTE following OBR: general note, using OBR timestamp [%s]', obr['clin_when'])
current_result = None
name = obr['name']
if name == '':
name = _('Comment')
# FIXME: please suggest a LOINC for "order comment"
test_type = __find_or_create_test_type(name = name, pk_lab = gm_lab['pk_test_org'], abbrev = obr['abbrev'], link_obj = conn)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
nte_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_alpha = note
)
#nte_result['val_grouping'] = seg[OBX_field__subid][0].strip()
nte_result['source_data'] = str(seg)
try:
nte_result['clin_when'] = __hl7dt2pydt(obr['clin_when'])
except ValueError:
_log.exception('no .clin_when from OBR for NTE pseudo-OBX available')
nte_result.save(conn = conn)
continue
if (previous_segment == 'OBX') and (current_result is not None):
current_result['source_data'] += '\n'
current_result['source_data'] += str(seg)
current_result['note_test_org'] = gmTools.coalesce (
current_result['note_test_org'],
note,
'%%s\n%s' % note
)
current_result.save(conn = conn)
previous_segment = seg_type
continue
_log.error('unexpected NTE segment')
had_errors = True
break
_log.error('unknown segment, aborting')
_log.debug('line: %s', seg)
had_errors = True
break
if had_errors:
conn.rollback()
return False
conn.commit()
# record import in chart
try:
no_results = len(HL7.segments('OBX'))
except KeyError:
no_results = '?'
soap = _(
'Imported HL7 file [%s]:\n'
' lab "%s" (%s@%s), %s results (%s)'
) % (
filename,
hl7_lab,
gm_lab['unit'],
gm_lab['organization'],
no_results,
' / '.join(list(when_list))
)
epi = emr.add_episode (
episode_name = 'administrative',
is_open = False,
allow_dupes = False
)
emr.add_clin_narrative (
note = soap,
soap_cat = None,
episode = epi
)
# keep copy of HL7 data in document archive
folder = gmPerson.cPatient(emr.pk_patient).document_folder
hl7_docs = folder.get_documents (
doc_type = 'HL7 data',
pk_episodes = [epi['pk_episode']],
order_by = 'ORDER BY clin_when DESC'
)
if len(hl7_docs) > 0:
# there should only ever be one unless the user manually creates more,
# also, it should always be the latest since "ORDER BY clin_when DESC"
hl7_doc = hl7_docs[0]
else:
hl7_doc = folder.add_document (
document_type = 'HL7 data',
encounter = emr.active_encounter['pk_encounter'],
episode = epi['pk_episode']
)
hl7_doc['comment'] = _('list of imported HL7 data files')
hl7_doc['pk_org_unit'] = gmPraxis.gmCurrentPraxisBranch()['pk_org_unit']
hl7_doc['clin_when'] = gmDateTime.pydt_now_here()
hl7_doc.save()
part = hl7_doc.add_part(file = filename)
part['obj_comment'] = _('Result dates: %s') % ' / '.join(list(when_list))
part.save()
hl7_doc.set_reviewed(technically_abnormal = False, clinically_relevant = False)
return True
def connect_to_database(max_attempts=3,
expected_version=None,
require_version=True):
"""Display the login dialog and try to log into the backend.
- up to max_attempts times
- returns True/False
"""
# force programmer to set a valid expected_version
expected_hash = gmPG2.known_schema_hashes[expected_version]
client_version = _cfg.get(option='client_version')
global current_db_name
current_db_name = 'gnumed_v%s' % expected_version
attempt = 0
dlg = cLoginDialog(None, -1, client_version=client_version)
dlg.Centre(wx.BOTH)
while attempt < max_attempts:
_log.debug('login attempt %s of %s', (attempt + 1), max_attempts)
connected = False
dlg.ShowModal()
login = dlg.panel.GetLoginInfo()
if login is None:
_log.info("user cancelled login dialog")
break
gmLog2.add_word2hide(login.password)
# try getting a connection to verify the parameters work
creds = gmConnectionPool.cPGCredentials()
creds.database = login.database
creds.host = login.host
creds.port = login.port
creds.user = login.user
creds.password = login.password
pool = gmConnectionPool.gmConnectionPool()
pool.credentials = creds
try:
conn = gmPG2.get_raw_connection(verbose=True, readonly=True)
connected = True
except gmPG2.cAuthenticationError as e:
attempt += 1
_log.error("login attempt failed: %s", e)
if attempt < max_attempts:
if ('host=127.0.0.1' in ('%s' % e)) or ('host='
not in ('%s' % e)):
msg = _(
'Unable to connect to database:\n\n'
'%s\n\n'
"Are you sure you have got a local database installed ?\n"
'\n'
"Please retry with proper credentials or cancel.\n"
'\n'
' (for the public and any new GNUmed data-\n'
' bases the default user name and password\n'
' are {any-doc, any-doc})\n'
'\n'
'You may also need to check the PostgreSQL client\n'
'authentication configuration in pg_hba.conf. For\n'
'details see:\n'
'\n'
'wiki.gnumed.de/bin/view/Gnumed/ConfigurePostgreSQL')
else:
msg = _(
"Unable to connect to database:\n\n"
"%s\n\n"
"Please retry with proper credentials or cancel.\n"
"\n"
"For the public and any new GNUmed databases the\n"
"default user name and password are {any-doc, any-doc}.\n"
"\n"
'You may also need to check the PostgreSQL client\n'
'authentication configuration in pg_hba.conf. For\n'
'details see:\n'
'\n'
'wiki.gnumed.de/bin/view/Gnumed/ConfigurePostgreSQL')
msg = msg % e
msg = regex.sub(
r'password=[^\s]+',
'password=%s' % gmTools.u_replacement_character, msg)
gmGuiHelpers.gm_show_error(msg, _('Connecting to backend'))
del e
continue
except gmPG2.dbapi.OperationalError as exc:
_log.exception('login attempt failed')
gmPG2.log_pg_exception_details(exc)
msg = _(
"Unable to connect to database:\n\n"
"%s\n\n"
"Please retry another backend / user / password combination !\n"
"\n"
" (for the public and any new GNUmed databases\n"
" the default user name and password are\n"
" {any-doc, any-doc})\n"
"\n") % exc
msg = regex.sub(r'password=[^\s]+',
'password=%s' % gmTools.u_replacement_character,
msg)
gmGuiHelpers.gm_show_error(msg, _('Connecting to backend'))
del exc
continue
conn.close()
seems_bootstrapped = gmPG2.schema_exists(schema='gm')
if not seems_bootstrapped:
_log.error(
'schema [gm] does not exist - database not bootstrapped ?')
msg = _('The database you connected to does not seem\n'
'to have been boostrapped properly.\n'
'\n'
'Make sure you have run the GNUmed database\n'
'bootstrapper tool to create a new database.\n'
'\n'
'Further help can be found on the website at\n'
'\n'
' http://wiki.gnumed.de\n'
'\n'
'or on the GNUmed mailing list.')
gmGuiHelpers.gm_show_error(msg, _('Verifying database'))
connected = False
break
compatible = gmPG2.database_schema_compatible(version=expected_version)
if compatible or not require_version:
dlg.panel.save_state()
if not compatible:
connected_db_version = gmPG2.get_schema_version()
msg = msg_generic % (client_version, connected_db_version,
expected_version,
gmTools.coalesce(login.host, '<localhost>'),
login.database, login.user)
if require_version:
gmGuiHelpers.gm_show_error(msg + msg_fail,
_('Verifying database version'))
connected = False
continue
gmGuiHelpers.gm_show_info(msg + msg_override,
_('Verifying database version'))
# FIXME: make configurable
max_skew = 1 # minutes
if _cfg.get(option='debug'):
max_skew = 10
if not gmPG2.sanity_check_time_skew(tolerance=(max_skew * 60)):
if _cfg.get(option='debug'):
gmGuiHelpers.gm_show_warning(msg_time_skew_warn % max_skew,
_('Verifying database settings'))
else:
gmGuiHelpers.gm_show_error(msg_time_skew_fail % max_skew,
_('Verifying database settings'))
connected = False
continue
sanity_level, message = gmPG2.sanity_check_database_settings()
if sanity_level != 0:
gmGuiHelpers.gm_show_error((msg_insanity % message),
_('Verifying database settings'))
if sanity_level == 2:
connected = False
continue
gmExceptionHandlingWidgets.set_is_public_database(
_cfg.get(option='is_public_db'))
gmExceptionHandlingWidgets.set_helpdesk(_cfg.get(option='helpdesk'))
gmLog2.log_multiline(logging.DEBUG,
message='fingerprint',
text=gmPG2.get_db_fingerprint(eol='\n'))
conn = gmPG2.get_connection(
verbose=True,
connection_name='GNUmed-[DbListenerThread]',
pooled=False)
listener = gmBackendListener.gmBackendListener(conn=conn)
break
dlg.DestroyLater()
return connected
cmd = """
SELECT
soap_cat,
narrative,
src_table,
(SELECT rank FROM clin.soap_cat_ranks scr WHERE scr.soap_cat = vn4s.soap_cat) AS rank
FROM
clin.v_narrative4search vn4s
WHERE
pk_patient = %(pat)s
ORDER BY
pk_encounter -- sort of chronologically sorted
, pk_health_issue
, pk_episode
, rank
, src_table
"""
conn = gmPG2.get_connection(encoding='utf8')
rows, idx = gmPG2.run_ro_queries(link_obj=conn, queries=[{'cmd': cmd, 'args': {'pat': sys.argv[1]}}])
f = io.open('emr-%s-narrative-dump.txt' % sys.argv[1], mode = 'wt', encoding = 'utf8', errors = 'strict')
for row in rows:
f.write('%s: %s (%s)\n'.encode('utf8') % (row['soap_cat'], row['narrative'], row['src_table']))
f.close()
#============================================================
def set(self, workplace=None, cookie=None, option=None, value=None):
"""Set (insert or update) option value in database.
Any parameter that is None will be set to the database default.
Note: you can't change the type of a parameter once it has been
created in the backend. If you want to change the type you will
have to delete the parameter and recreate it using the new type.
"""
# sanity checks
if None in [option, value]:
raise ValueError('invalid arguments (option=<%s>, value=<%s>)' %
(option, value))
rw_conn = gmPG2.get_connection(readonly=False)
alias = self.__make_alias(workplace, 'CURRENT_USER', cookie, option)
opt_value = value
sql_type_cast = ''
if isinstance(value, str):
sql_type_cast = '::text'
elif isinstance(value, bool):
opt_value = int(opt_value)
elif isinstance(value, (float, int, decimal.Decimal, bool)):
sql_type_cast = '::numeric'
elif isinstance(value, list):
# there can be different syntaxes for list types so don't try to cast them
pass
elif isinstance(value, buffer):
# can go directly into bytea
pass
else:
try:
opt_value = gmPG2.dbapi.Binary(pickle.dumps(value))
sql_type_cast = '::bytea'
except pickle.PicklingError:
_log.error(
"cannot pickle option of type [%s] (key: %s, value: %s)",
type(value), alias, str(value))
raise
except:
_log.error(
"don't know how to store option of type [%s] (key: %s, value: %s)",
type(value), alias, str(value))
raise
cmd = 'select cfg.set_option(%%(opt)s, %%(val)s%s, %%(wp)s, %%(cookie)s, NULL)' % sql_type_cast
args = {
'opt': option,
'val': opt_value,
'wp': workplace,
'cookie': cookie
}
try:
rows, idx = gmPG2.run_rw_queries(link_obj=rw_conn,
queries=[{
'cmd': cmd,
'args': args
}],
return_data=True)
result = rows[0][0]
except:
_log.exception('cannot set option')
result = False
rw_conn.commit() # will rollback if transaction failed
rw_conn.close()
return result
narrative,
src_table,
(SELECT rank FROM clin.soap_cat_ranks scr WHERE scr.soap_cat = vn4s.soap_cat) AS rank
FROM
clin.v_narrative4search vn4s
WHERE
pk_patient = %(pat)s
ORDER BY
pk_encounter -- sort of chronologically sorted
, pk_health_issue
, pk_episode
, rank
, src_table
"""
conn = gmPG2.get_connection(encoding='utf8')
rows, idx = gmPG2.run_ro_queries(link_obj=conn,
queries=[{
'cmd': cmd,
'args': {
'pat': sys.argv[1]
}
}])
f = io.open('emr-%s-narrative-dump.txt' % sys.argv[1],
mode='wt',
encoding='utf8',
errors='strict')
for row in rows:
def __init__(self): self._generate_queries = self._generate_queries_de # make a cursor self.conn = gmPG2.get_connection() self.curs = self.conn.cursor()
def connect_to_database(max_attempts=3, expected_version=None, require_version=True):
"""Display the login dialog and try to log into the backend.
- up to max_attempts times
- returns True/False
"""
# force programmer to set a valid expected_version
expected_hash = gmPG2.known_schema_hashes[expected_version]
client_version = _cfg.get(option = 'client_version')
global current_db_name
current_db_name = 'gnumed_v%s' % expected_version
attempt = 0
dlg = cLoginDialog(None, -1, client_version = client_version)
dlg.Centre(wx.BOTH)
while attempt < max_attempts:
_log.debug('login attempt %s of %s', (attempt+1), max_attempts)
connected = False
dlg.ShowModal()
login = dlg.panel.GetLoginInfo()
if login is None:
_log.info("user cancelled login dialog")
break
gmLog2.add_word2hide(login.password)
# try getting a connection to verify the DSN works
dsn = gmPG2.make_psycopg2_dsn (
database = login.database,
host = login.host,
port = login.port,
user = login.user,
password = login.password
)
try:
conn = gmPG2.get_raw_connection(dsn = dsn, verbose = True, readonly = True)
connected = True
except gmPG2.cAuthenticationError as e:
attempt += 1
_log.error("login attempt failed: %s", e)
if attempt < max_attempts:
if ('host=127.0.0.1' in ('%s' % e)) or ('host=' not in ('%s' % e)):
msg = _(
'Unable to connect to database:\n\n'
'%s\n\n'
"Are you sure you have got a local database installed ?\n"
'\n'
"Please retry with proper credentials or cancel.\n"
'\n'
' (for the public and any new GNUmed data-\n'
' bases the default user name and password\n'
' are {any-doc, any-doc})\n'
'\n'
'You may also need to check the PostgreSQL client\n'
'authentication configuration in pg_hba.conf. For\n'
'details see:\n'
'\n'
'wiki.gnumed.de/bin/view/Gnumed/ConfigurePostgreSQL'
)
else:
msg = _(
"Unable to connect to database:\n\n"
"%s\n\n"
"Please retry with proper credentials or cancel.\n"
"\n"
"For the public and any new GNUmed databases the\n"
"default user name and password are {any-doc, any-doc}.\n"
"\n"
'You may also need to check the PostgreSQL client\n'
'authentication configuration in pg_hba.conf. For\n'
'details see:\n'
'\n'
'wiki.gnumed.de/bin/view/Gnumed/ConfigurePostgreSQL'
)
msg = msg % e
msg = regex.sub(r'password=[^\s]+', 'password=%s' % gmTools.u_replacement_character, msg)
gmGuiHelpers.gm_show_error (
msg,
_('Connecting to backend')
)
del e
continue
except gmPG2.dbapi.OperationalError as exc:
_log.exception('login attempt failed')
gmPG2.log_pg_exception_details(exc)
msg = _(
"Unable to connect to database:\n\n"
"%s\n\n"
"Please retry another backend / user / password combination !\n"
"\n"
" (for the public and any new GNUmed databases\n"
" the default user name and password are\n"
" {any-doc, any-doc})\n"
"\n"
) % exc
msg = regex.sub(r'password=[^\s]+', 'password=%s' % gmTools.u_replacement_character, msg)
gmGuiHelpers.gm_show_error(msg, _('Connecting to backend'))
del exc
continue
conn.close()
# connect was successful
gmPG2.set_default_login(login = login)
gmPG2.set_default_client_encoding(encoding = dlg.panel.backend_profile.encoding)
seems_bootstrapped = gmPG2.schema_exists(schema = 'gm')
if not seems_bootstrapped:
_log.error('schema [gm] does not exist - database not bootstrapped ?')
msg = _(
'The database you connected to does not seem\n'
'to have been boostrapped properly.\n'
'\n'
'Make sure you have run the GNUmed database\n'
'bootstrapper tool to create a new database.\n'
'\n'
'Further help can be found on the website at\n'
'\n'
' http://wiki.gnumed.de\n'
'\n'
'or on the GNUmed mailing list.'
)
gmGuiHelpers.gm_show_error(msg, _('Verifying database'))
connected = False
break
compatible = gmPG2.database_schema_compatible(version = expected_version)
if compatible or not require_version:
dlg.panel.save_state()
if not compatible:
connected_db_version = gmPG2.get_schema_version()
msg = msg_generic % (
client_version,
connected_db_version,
expected_version,
gmTools.coalesce(login.host, '<localhost>'),
login.database,
login.user
)
if require_version:
gmGuiHelpers.gm_show_error(msg + msg_fail, _('Verifying database version'))
connected = False
continue
gmGuiHelpers.gm_show_info(msg + msg_override, _('Verifying database version'))
# FIXME: make configurable
max_skew = 1 # minutes
if _cfg.get(option = 'debug'):
max_skew = 10
if not gmPG2.sanity_check_time_skew(tolerance = (max_skew * 60)):
if _cfg.get(option = 'debug'):
gmGuiHelpers.gm_show_warning(msg_time_skew_warn % max_skew, _('Verifying database settings'))
else:
gmGuiHelpers.gm_show_error(msg_time_skew_fail % max_skew, _('Verifying database settings'))
connected = False
continue
sanity_level, message = gmPG2.sanity_check_database_settings()
if sanity_level != 0:
gmGuiHelpers.gm_show_error((msg_insanity % message), _('Verifying database settings'))
if sanity_level == 2:
connected = False
continue
gmExceptionHandlingWidgets.set_is_public_database(login.public_db)
gmExceptionHandlingWidgets.set_helpdesk(login.helpdesk)
conn = gmPG2.get_connection(verbose = True, connection_name = 'GNUmed-[DbListenerThread]', pooled = False)
listener = gmBackendListener.gmBackendListener(conn = conn)
break
dlg.DestroyLater()
return connected
def test_atc_import(): atc_import(cfg_fname = sys.argv[2], conn = gmPG2.get_connection(readonly = False))
def save_payload(self, conn=None):
"""Store updated values (if any) in database.
Optionally accepts a pre-existing connection
- returns a tuple (<True|False>, <data>)
- True: success
- False: an error occurred
* data is (error, message)
* for error meanings see gmPG2.run_rw_queries()
"""
if not self._is_modified:
return (True, None)
args = {}
for field in self._idx.keys():
args[field] = self._payload[self._idx[field]]
self.modified_payload = args
close_conn = self.__noop
if conn is None:
conn = gmPG2.get_connection(readonly=False)
close_conn = 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
)
# 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 ...
if len(rows) == 0:
return (False, (u'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
row = rows[0]
for key in idx:
try:
self._payload[self._idx[key]] = row[idx[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._idx))
_log.error('XMIN refetch keys: %s' % str(idx))
_log.error(args)
raise
conn.commit()
close_conn()
self._is_modified = False
# update to new "original" payload
self.original_payload = {}
for field in self._idx.keys():
self.original_payload[field] = self._payload[self._idx[field]]
return (True, None)
pass
l = login()
l.database = 'gnumed_v9'
l.host = 'publicdb.gnumed.de'
l.port = '5432'
l.user = '******'
l.password = '******'
gmPG2.set_default_login(l)
gmPG2.set_default_client_timezone(timezone='Asia/Colombo')
gmPG2.set_default_client_timezone(timezone='Asia/Calcutta')
conn = gmPG2.get_connection()
cmd = """select * from dem.v_staff where db_user = CURRENT_USER"""
try:
rows, idx = gmPG2.run_ro_queries(queries=[{'cmd': cmd}], verbose=True)
for row in rows:
_log.info(row)
print rows
print "==> success"
except Exception:
_log.exception('query failed')
gmLog2.log_stack_trace('query failed')
print "==> failure"
# =======================================================================
def __init__(self):
self._generate_queries = self._generate_queries_de
# make a cursor
self.conn = gmPG2.get_connection()
self.curs = self.conn.cursor()
def __init__(self): self.ro_conn = gmPG2.get_connection()
ddl.append('-- ----------------------------------------------')
return ddl
#==================================================================
# main
#------------------------------------------------------------------
if __name__ == "__main__" :
tmp = ''
try:
tmp = raw_input("audit trail parent table [%s]: " % audit_trail_parent_table)
except KeyboardError:
pass
if tmp != '':
audit_trail_parent_table = tmp
conn = gmPG2.get_connection(readonly=False, pooled=False)
curs = conn.cursor()
schema = create_audit_ddl(curs)
curs.close()
conn.close()
if schema is None:
print "error creating schema"
sys.exit(-1)
file = io.open('audit-trail-schema.sql', mode = 'wb', encoding = 'utf8')
for line in schema:
file.write("%s;\n" % line)
file.close()
def save_payload(self, conn=None):
"""Store updated values (if any) in database.
Optionally accepts a pre-existing connection
- returns a tuple (<True|False>, <data>)
- True: success
- False: an error occurred
* data is (error, message)
* for error meanings see gmPG2.run_rw_queries()
"""
if not self._is_modified:
return (True, None)
args = {}
for field in self._idx.keys():
args[field] = self._payload[self._idx[field]]
self.payload_most_recently_attempted_to_store = args
close_conn = self.__noop
if conn is None:
conn = gmPG2.get_connection(readonly=False)
close_conn = 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 idx:
try:
self._payload[self._idx[key]] = row[idx[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._idx))
_log.error('XMIN refetch keys: %s' % str(idx))
_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()
close_conn()
# update to new "original" payload
self.payload_most_recently_fetched = {}
for field in self._idx.keys():
self.payload_most_recently_fetched[field] = self._payload[
self._idx[field]]
return (True, None)
def __import_single_PID_hl7_file(filename, emr=None):
"""Assumes single-PID/single-MSH HL7 file."""
_log.debug('importing single-PID single-MSH HL7 data from [%s]', filename)
# read the file
MSH_file = io.open(filename, mode = 'rt', encoding = 'utf8')
HL7 = pyhl7.parse(MSH_file.read(1024 * 1024 * 5)) # 5 MB max
MSH_file.close()
# sanity checks
if len(HL7.segments('MSH')) != 1:
_log.error('more than one MSH segment')
return False
if len(HL7.segments('PID')) != 1:
_log.error('more than one PID segment')
return False
# ensure lab is in database
hl7_lab = HL7.extract_field('MSH', field_num = MSH_field__sending_lab)
gm_lab = __find_or_create_lab(hl7_lab)
# ensure test types exist
conn = gmPG2.get_connection(readonly = False)
__ensure_hl7_test_types_exist_in_gnumed(link_obj = conn, hl7_data = HL7, pk_test_org = gm_lab['pk_test_org'])
# find patient
if emr is None:
#PID = HL7.segment('PID')
pats = __PID2dto(HL7 = HL7)
if len(pats) == 0:
conn.rollback()
return False
if len(pats) > 1:
conn.rollback()
return False
emr = pats[0].emr
# import values: loop over segments
when_list = {}
current_result = None
previous_segment = None
had_errors = False
msh_seen = False
pid_seen = False
last_obr = None
obr = {}
for seg_idx in range(len(HL7)):
seg = HL7[seg_idx]
seg_type = seg[0][0]
_log.debug('processing line #%s = segment of type <%s>', seg_idx, seg_type)
if seg_type == u'MSH':
msh_seen = True
if seg_type == u'PID':
if not msh_seen:
conn.rollback()
_log.error('PID segment before MSH segment')
return False
pid_seen = True
if seg_type in [u'MSH', u'PID']:
_log.info('segment already handled')
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type in [u'ORC']:
_log.info('currently ignoring %s segments', seg_type)
previous_segment = seg_type
obr = {}
current_result = None
continue
if seg_type == u'OBR':
previous_segment = seg_type
last_obr = seg
current_result = None
obr['abbrev'] = (u'%s' % seg[OBR_field__service_name][0]).strip()
try:
obr['name'] = (u'%s' % seg[OBR_field__service_name][1]).strip()
except IndexError:
obr['name'] = obr['abbrev']
for field_name in [OBR_field__ts_ended, OBR_field__ts_started, OBR_field__ts_specimen_received, OBR_field__ts_requested]:
obr['clin_when'] = seg[field_name][0].strip()
if obr['clin_when'] != u'':
break
continue
if seg_type == u'OBX':
current_result = None
# determine value
val_alpha = seg[OBX_field__value][0].strip()
is_num, val_num = gmTools.input2decimal(initial = val_alpha)
if is_num:
val_alpha = None
else:
val_num = None
val_alpha = val_alpha.replace('\.br\\', u'\n')
# determine test type
unit = seg[OBX_field__unit][0].strip()
if unit == u'':
if is_num:
unit = u'1/1'
else:
unit = None
test_type = __find_or_create_test_type (
loinc = u'%s' % seg[OBX_field__type][0][OBX_component__loinc-1],
name = u'%s' % seg[OBX_field__type][0][OBX_component__name-1],
pk_lab = gm_lab['pk_test_org'],
unit = unit
)
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
current_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_num = val_num,
val_alpha = val_alpha,
unit = unit
)
# handle range information et al
ref_range = seg[OBX_field__range][0].strip()
if ref_range != u'':
current_result.reference_range = ref_range
flag = seg[OBX_field__abnormal_flag][0].strip()
if flag != u'':
current_result['abnormality_indicator'] = flag
current_result['status'] = seg[OBX_field__status][0].strip()
current_result['val_grouping'] = seg[OBX_field__subid][0].strip()
current_result['source_data'] = u''
if last_obr is not None:
current_result['source_data'] += unicode(last_obr)
current_result['source_data'] += u'\n'
current_result['source_data'] += unicode(seg)
clin_when = seg[OBX_field__timestamp][0].strip()
if clin_when == u'':
_log.warning('no <Observation timestamp> in OBX, trying OBR timestamp')
clin_when = obr['clin_when']
try:
clin_when = __hl7dt2pydt(clin_when)
except ValueError:
_log.exception('clin_when from OBX or OBR not useable, assuming <today>')
if clin_when is not None:
current_result['clin_when'] = clin_when
current_result.save(conn = conn)
when_list[gmDateTime.pydt_strftime(current_result['clin_when'], '%Y %b %d')] = 1
previous_segment = seg_type
continue
if seg_type == u'NTE':
note = seg[NET_field__note][0].strip().replace('\.br\\', u'\n')
if note == u'':
_log.debug('empty NTE segment')
previous_segment = seg_type # maybe not ? (HL7 providers happen to use empty NTE segments to "structure" raw HL7 |-)
continue
# if this is an NTE following an OBR (IOW an order-related
# comment): make this a test result all of its own :-)
if previous_segment == u'OBR':
_log.debug('NTE following OBR: general note, using OBR timestamp [%s]', obr['clin_when'])
current_result = None
name = obr['name']
if name == u'':
name = _('Comment')
# FIXME: please suggest a LOINC for "order comment"
test_type = __find_or_create_test_type(name = name, pk_lab = gm_lab['pk_test_org'], abbrev = obr['abbrev'])
# eventually, episode should be read from lab_request
epi = emr.add_episode (
link_obj = conn,
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
nte_result = emr.add_test_result (
link_obj = conn,
episode = epi['pk_episode'],
type = test_type['pk_test_type'],
intended_reviewer = gmStaff.gmCurrentProvider()['pk_staff'],
val_alpha = note
)
#nte_result['val_grouping'] = seg[OBX_field__subid][0].strip()
nte_result['source_data'] = unicode(seg)
try:
nte_result['clin_when'] = __hl7dt2pydt(obr['clin_when'])
except ValueError:
_log.exception('no .clin_when from OBR for NTE pseudo-OBX available')
nte_result.save(conn = conn)
continue
if (previous_segment == u'OBX') and (current_result is not None):
current_result['source_data'] += u'\n'
current_result['source_data'] += unicode(seg)
current_result['note_test_org'] = gmTools.coalesce (
current_result['note_test_org'],
note,
u'%%s\n%s' % note
)
current_result.save(conn = conn)
previous_segment = seg_type
continue
_log.error(u'unexpected NTE segment')
had_errors = True
break
_log.error('unknown segment, aborting')
_log.debug('line: %s', seg)
had_errors = True
break
if had_errors:
conn.rollback()
return False
conn.commit()
# record import in chart
try:
no_results = len(HL7.segments('OBX'))
except KeyError:
no_results = u'?'
soap = _(
'Imported HL7 file [%s]:\n'
' lab "%s" (%s@%s), %s results (%s)'
) % (
filename,
hl7_lab,
gm_lab['unit'],
gm_lab['organization'],
no_results,
u' / '.join(when_list.keys())
)
epi = emr.add_episode (
episode_name = u'administrative',
is_open = False,
allow_dupes = False
)
emr.add_clin_narrative (
note = soap,
soap_cat = None,
episode = epi
)
# keep copy of HL7 data in document archive
folder = gmPerson.cPatient(emr.pk_patient).document_folder
hl7_docs = folder.get_documents (
doc_type = u'HL7 data',
episodes = [epi['pk_episode']],
order_by = u'ORDER BY clin_when DESC'
)
if len(hl7_docs) > 0:
# there should only ever be one unless the user manually creates more,
# also, it should always be the latest since "ORDER BY clin_when DESC"
hl7_doc = hl7_docs[0]
else:
hl7_doc = folder.add_document (
document_type = u'HL7 data',
encounter = emr.active_encounter['pk_encounter'],
episode = epi['pk_episode']
)
hl7_doc['comment'] = _('list of imported HL7 data files')
hl7_doc['clin_when'] = gmDateTime.pydt_now_here()
hl7_doc.save()
part = hl7_doc.add_part(file = filename)
part['obj_comment'] = _('Result dates: %s') % u' / '.join(when_list.keys())
part.save()
hl7_doc.set_reviewed(technically_abnormal = False, clinically_relevant = False)
return True
def test_atc_import():
atc_import(cfg_fname=sys.argv[2],
conn=gmPG2.get_connection(readonly=False))
def __init__(self, *args, **kwargs):
gmPhraseWheel.cPhraseWheel.__init__(self, *args, **kwargs)
mp = gmLOINC.cLOINCMatchProvider()
mp.setThresholds(1, 2, 4)
#mp.print_queries = True
#mp.word_separators = '[ \t:@]+'
self.matcher = mp
self.selection_only = False
self.final_regex = r'\d{1,5}-\d{1}$'
self.SetToolTip(_('Select a LOINC (Logical Observation Identifiers Names and Codes).'))
#================================================================
# main
#----------------------------------------------------------------
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
from Gnumed.pycommon import gmPG2
#----------------------------------------
gmPG2.get_connection()
app = wx.PyWidgetTester(size = (600, 80))
app.SetWidget(cLOINCPhraseWheel, -1)
app.MainLoop()
#==================================================================
# main
#------------------------------------------------------------------
if __name__ == "__main__":
tmp = ''
try:
tmp = raw_input("audit trail parent table [%s]: " %
AUDIT_TRAIL_PARENT_TABLE)
except KeyboardError:
pass
if tmp != '':
AUDIT_TRAIL_PARENT_TABLE = tmp
conn = gmPG2.get_connection(readonly=False, pooled=False)
curs = conn.cursor()
schema = create_audit_ddl(curs)
curs.close()
conn.close()
if schema is None:
print "error creating schema"
sys.exit(-1)
f = io.open('audit-trail-schema.sql', mode='wb', encoding='utf8')
for line in schema:
f.write("%s;\n" % line)
f.close()