Module Gnumed.business.gmClinicalRecord
GNUmed clinical patient record.
Expand source code
# -*- coding: utf-8 -*-
"""GNUmed clinical patient record."""
#============================================================
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = "GPL v2 or later"
# standard libs
import sys
import logging
import datetime as pydt
if __name__ == '__main__':
sys.path.insert(0, '../../')
from Gnumed.pycommon import gmI18N
from Gnumed.pycommon import gmDateTime
if __name__ == '__main__':
_ = lambda x:x
gmI18N.activate_locale()
gmI18N.install_domain()
gmDateTime.init()
from Gnumed.pycommon import gmExceptions
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmDispatcher
from Gnumed.pycommon import gmCfgDB
from Gnumed.pycommon import gmTools
from Gnumed.business import gmGenericEMRItem
from Gnumed.business import gmAllergy
from Gnumed.business import gmPathLab
from Gnumed.business import gmLOINC
from Gnumed.business import gmClinNarrative
from Gnumed.business import gmSoapDefs
from Gnumed.business import gmEMRStructItems
from Gnumed.business import gmMedication
from Gnumed.business import gmVaccination
from Gnumed.business import gmFamilyHistory
from Gnumed.business import gmExternalCare
from Gnumed.business import gmOrganization
from Gnumed.business import gmAutoHints
from Gnumed.business.gmDemographicRecord import get_occupations
_log = logging.getLogger('gm.emr')
_here = None
#============================================================
# helper functions
#------------------------------------------------------------
#_func_ask_user = None
#
#def set_func_ask_user(a_func = None):
# if not callable(a_func):
# _log.error('[%] not callable, not setting _func_ask_user', a_func)
# return False
#
# _log.debug('setting _func_ask_user to [%s]', a_func)
#
# global _func_ask_user
# _func_ask_user = a_func
#============================================================
from Gnumed.business.gmDocuments import cDocument
from Gnumed.business.gmProviderInbox import cInboxMessage
_map_table2class = {
'clin.encounter': gmEMRStructItems.cEncounter,
'clin.episode': gmEMRStructItems.cEpisode,
'clin.health_issue': gmEMRStructItems.cHealthIssue,
'clin.external_care': gmExternalCare.cExternalCareItem,
'clin.vaccination': gmVaccination.cVaccination,
'clin.clin_narrative': gmClinNarrative.cNarrative,
'clin.test_result': gmPathLab.cTestResult,
'clin.substance_intake': gmMedication.cSubstanceIntakeEntry,
'clin.intake_regimen': gmMedication.cIntakeRegimen,
'clin.hospital_stay': gmEMRStructItems.cHospitalStay,
'clin.procedure': gmEMRStructItems.cPerformedProcedure,
'clin.allergy': gmAllergy.cAllergy,
'clin.allergy_state': gmAllergy.cAllergyState,
'clin.family_history': gmFamilyHistory.cFamilyHistory,
'clin.suppressed_hint': gmAutoHints.cSuppressedHint,
'blobs.doc_med': cDocument,
'dem.message_inbox': cInboxMessage,
'ref.auto_hint': gmAutoHints.cDynamicHint
}
def instantiate_clin_root_item(table, pk):
try:
item_class = _map_table2class[table]
except KeyError:
_log.error('unmapped clin_root_item entry [%s], cannot instantiate', table)
return None
return item_class(aPK_obj = pk)
#------------------------------------------------------------
def format_clin_root_item(table, pk, patient=None):
instance = instantiate_clin_root_item(table, pk)
if instance is None:
return _('cannot instantiate clinical root item <%s(%s)>' % (table, pk))
# if patient is not None:
# if patient.ID != instance['pk_patient']:
# raise ValueError(u'patient passed in: [%s], but instance is: [%s:%s:%s]' % (patient.ID, table, pk, instance['pk_patient']))
if hasattr(instance, 'format_maximum_information'):
return '\n'.join(instance.format_maximum_information(patient = patient))
if hasattr(instance, 'format'):
try:
formatted = instance.format(patient = patient)
except TypeError:
formatted = instance.format()
if type(formatted) == type([]):
return '\n'.join(formatted)
return formatted
d = instance.fields_as_dict (
date_format = '%Y %b %d %H:%M',
none_string = gmTools.u_diameter,
escape_style = None,
bool_strings = [_('True'), _('False')]
)
return gmTools.format_dict_like(d, tabular = True, value_delimiters = None)
#============================================================
def __noop_delayed_execute(*args, **kwargs):
pass
_delayed_execute = __noop_delayed_execute
def set_delayed_executor(executor):
if not callable(executor):
raise TypeError('executor <%s> is not callable' % executor)
global _delayed_execute
_delayed_execute = executor
_log.debug('setting delayed executor to <%s>', executor)
#------------------------------------------------------------
class cClinicalRecord(object):
def __init__(self, aPKey=None):#, allow_user_interaction=True, encounter=None):
"""Fails if
- no connection to database possible
- patient referenced by aPKey does not exist
"""
self.pk_patient = aPKey # == identity.pk == primary key
self.gender = None
self.dob = None
from Gnumed.business import gmPraxis
global _here
if _here is None:
_here = gmPraxis.gmCurrentPraxisBranch()
self.__encounter = None
self.__setup_active_encounter()
# register backend notification interests
# (keep this last so we won't hang on threads when
# failing this constructor for other reasons ...)
if not self._register_interests():
raise gmExceptions.ConstructorError("cannot register signal interests")
self.__calculator = None
_log.debug('Instantiated clinical record for patient [%s].' % self.pk_patient)
#--------------------------------------------------------
def cleanup(self):
_log.debug('cleaning up after clinical record for patient [%s]' % self.pk_patient)
if self.__encounter is not None:
self.__encounter.unlock(exclusive = False)
return True
#--------------------------------------------------------
def log_access(self, action=None):
if action is None:
action = 'EMR access for pk_identity [%s]' % self.pk_patient
args = {'action': action}
cmd = 'SELECT gm.log_access2emr(%(action)s)'
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#--------------------------------------------------------
def _get_calculator(self):
if self.__calculator is None:
from Gnumed.business.gmClinicalCalculator import cClinicalCalculator
self.__calculator = cClinicalCalculator()
from Gnumed.business.gmPerson import gmCurrentPatient
curr_pat = gmCurrentPatient()
if curr_pat.ID == self.pk_patient:
self.__calculator.patient = curr_pat
else:
from Gnumed.business.gmPerson import cPatient
self.__calculator.patient = cPatient(self.pk_patient)
return self.__calculator
calculator = property(_get_calculator)
#--------------------------------------------------------
# messaging
#--------------------------------------------------------
def _register_interests(self):
gmDispatcher.connect(signal = 'gm_table_mod', receiver = self.db_modification_callback)
return True
#--------------------------------------------------------
def db_modification_callback(self, **kwds):
if kwds['table'] != 'clin.encounter':
return True
if self.current_encounter is None:
_log.debug('locally no encounter current, ignoring encounter modification signal')
return True
if int(kwds['pk_of_row']) != self.current_encounter['pk_encounter']:
_log.debug('DB reported modification of encounter: #%s', kwds['pk_of_row'])
_log.debug('our locally active encounter is: #%s', self.current_encounter['pk_encounter'])
_log.debug('modified encounter != our encounter, ignoring')
return True
_log.debug('remote modification of our encounter signalled (local: #%s, remote: #%s)', self.current_encounter['pk_encounter'], kwds['pk_of_row'])
# did someone delete the current encounter from under our feet ?
if kwds['operation'] == 'DELETE':
_log.error('local encounter has been DELETEd remotely, trying to get now-active encounter from database')
if self.current_encounter.is_modified():
_log.error('local encounter instance has .is_modified()=True, losing local changes')
_log.error('this hints at an error in .is_modified handling')
# dirty fix: get now-active encounter
self.current_encounter.unlock(exclusive = False)
self.__encounter = None
self.__setup_active_encounter()
gmDispatcher.send('current_encounter_switched')
return True
# get the current encounter as an extra instance
# from the database to check for changes
curr_enc_in_db = gmEMRStructItems.cEncounter(aPK_obj = self.current_encounter['pk_encounter'])
# the encounter just retrieved and the active encounter
# have got the same transaction ID so there's no change
# in the database, there could be a local change in
# the active encounter but that doesn't matter because
# no one else can have written to the DB so far (XMIN match)
if curr_enc_in_db['xmin_encounter'] == self.current_encounter['xmin_encounter']:
_log.debug('in-client and in-DB instance of encounter #%s have matching XMINs (%s), DB has NOT been written to since we last loaded the encounter, checking:', self.current_encounter['pk_encounter'], self.current_encounter['xmin_encounter'])
if self.current_encounter.is_modified():
_log.error('encounter modification signalled from DB, with same XMIN as in local in-client instance of encounter, BUT local instance ALSO has .is_modified()=True')
_log.error('this may hint at an error with .is_modified handling')
gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB')
# here we might want to ask the user for advice on how to proceed
else:
_log.debug('locally not flagged as modified')
return True
# there must have been a change to the active encounter
# committed to the database from elsewhere (different XMIN),
# we must deny to propagate the change, however, if
# there are pending local changes, or, rather, we should ask
# the user for advice
if self.current_encounter.is_modified():
gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB')
raise ValueError('unsaved changes in locally active encounter [%s], cannot switch to DB state of encounter [%s]' % (
self.current_encounter['pk_encounter'],
curr_enc_in_db['pk_encounter']
))
# don't do this, because same_payload() does not compare _all_
# fields so we can get into a reality disconnect if we
# don't announce the modification
# if self.current_encounter.same_payload(another_object = curr_enc_in_db):
# _log.debug('clin.encounter_mod_db received but no change to active encounter payload')
# return True
# there was a change in the database from elsewhere;
# locally, however, we don't have any pending changes;
# therefore we can propagate the remote change locally
# without losing anything;
# this really should be the standard case
gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB')
_log.debug('active encounter modified remotely, no locally pending changes, reloading from DB and locally announcing the remote modification')
self.current_encounter.refetch_payload()
gmDispatcher.send('current_encounter_modified')
return True
#--------------------------------------------------------
# API: family history
#--------------------------------------------------------
def get_family_history(self, episodes=None, issues=None, encounters=None):
fhx = gmFamilyHistory.get_family_history (
order_by = 'l10n_relation, condition',
patient = self.pk_patient
)
if episodes is not None:
fhx = [ f for f in fhx if f['pk_episode'] in episodes ]
if issues is not None:
fhx = [ f for f in fhx if f['pk_health_issue'] in issues ]
if encounters is not None:
fhx = [ f for f in fhx if f['pk_encounter'] in encounters ]
return fhx
#--------------------------------------------------------
def add_family_history(self, episode=None, condition=None, relation=None):
return gmFamilyHistory.create_family_history (
encounter = self.current_encounter['pk_encounter'],
episode = episode,
condition = condition,
relation = relation
)
#--------------------------------------------------------
# API: pregnancy
#--------------------------------------------------------
def _get_gender(self):
if self.__gender is not None:
return self.__gender
cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s'
args = {'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
self.__gender = rows[0]['gender']
self.__dob = rows[0]['dob']
def _set_gender(self, gender):
self.__gender = gender
gender = property(_get_gender, _set_gender)
#--------------------------------------------------------
def _get_dob(self):
if self.__dob is not None:
return self.__dob
cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s'
args = {'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
self.__gender = rows[0]['gender']
self.__dob = rows[0]['dob']
def _set_dob(self, dob):
self.__dob = dob
dob = property(_get_dob, _set_dob)
#--------------------------------------------------------
def _get_EDC(self):
cmd = 'SELECT edc FROM clin.patient WHERE fk_identity = %(pat)s'
args = {'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
if len(rows) == 0:
return None
return rows[0]['edc']
def _set_EDC(self, edc):
cmd = """
INSERT INTO clin.patient (fk_identity, edc) SELECT
%(pat)s,
%(edc)s
WHERE NOT EXISTS (
SELECT 1 FROM clin.patient WHERE fk_identity = %(pat)s
)
RETURNING pk"""
args = {'pat': self.pk_patient, 'edc': edc}
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False, return_data = True)
if len(rows) == 0:
cmd = 'UPDATE clin.patient SET edc = %(edc)s WHERE fk_identity = %(pat)s'
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
EDC = property(_get_EDC, _set_EDC)
#--------------------------------------------------------
def _EDC_is_fishy(self):
edc = self.EDC
if edc is None:
return False
if self.gender != 'f':
return True
now = gmDateTime.pydt_now_here()
# mother too young
if (self.dob + pydt.timedelta(weeks = 5 * 52)) > now:
return True
# mother too old
if (self.dob + pydt.timedelta(weeks = 55 * 52)) < now:
return True
# Beulah Hunter, 375 days (http://www.reference.com/motif/health/longest-human-pregnancy-on-record)
# EDC too far in the future
if (edc - pydt.timedelta(days = 380)) > now:
return True
# even if the pregnancy would have *started* when it
# was documented to *end* it would be over by now by
# all accounts
# EDC too far in the past
if edc < (now - pydt.timedelta(days = 380)):
return True
EDC_is_fishy = property(_EDC_is_fishy)
#--------------------------------------------------------
# API: performed procedures
#--------------------------------------------------------
def get_performed_procedures(self, episodes=None, issues=None):
procs = gmEMRStructItems.get_performed_procedures(patient = self.pk_patient)
if episodes is not None:
procs = [ p for p in procs if p['pk_episode'] in episodes ]
if issues is not None:
procs = [ p for p in procs if p['pk_health_issue'] in issues ]
return procs
performed_procedures = property(get_performed_procedures)
#--------------------------------------------------------
def get_latest_performed_procedure(self):
return gmEMRStructItems.get_latest_performed_procedure(patient = self.pk_patient)
#--------------------------------------------------------
def add_performed_procedure(self, episode=None, location=None, hospital_stay=None, procedure=None):
return gmEMRStructItems.create_performed_procedure (
encounter = self.current_encounter['pk_encounter'],
episode = episode,
location = location,
hospital_stay = hospital_stay,
procedure = procedure
)
#--------------------------------------------------------
def get_procedure_locations_as_org_units(self):
where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_procedures_not_at_hospital WHERE pk_patient = %(pat)s)'
args = {'pat': self.pk_patient}
cmd = gmOrganization._SQL_get_org_unit % where
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
#--------------------------------------------------------
# API: hospitalizations
#--------------------------------------------------------
def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False):
stays = gmEMRStructItems.get_patient_hospital_stays(patient = self.pk_patient, ongoing_only = ongoing_only)
if episodes is not None:
stays = [ s for s in stays if s['pk_episode'] in episodes ]
if issues is not None:
stays = [ s for s in stays if s['pk_health_issue'] in issues ]
return stays
hospital_stays = property(get_hospital_stays)
#--------------------------------------------------------
def get_latest_hospital_stay(self):
return gmEMRStructItems.get_latest_patient_hospital_stay(patient = self.pk_patient)
#--------------------------------------------------------
def add_hospital_stay(self, episode=None, fk_org_unit=None):
return gmEMRStructItems.create_hospital_stay (
encounter = self.current_encounter['pk_encounter'],
episode = episode,
fk_org_unit = fk_org_unit
)
#--------------------------------------------------------
def get_hospital_stay_stats_by_hospital(self, cover_period=None):
args = {'pat': self.pk_patient, 'range': cover_period}
where_parts = ['pk_patient = %(pat)s']
if cover_period is not None:
where_parts.append('discharge > (now() - %(range)s)')
cmd = """
SELECT hospital, COUNT(*) AS frequency
FROM clin.v_hospital_stays
WHERE
%s
GROUP BY hospital
ORDER BY frequency DESC
""" % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return rows
#--------------------------------------------------------
def get_attended_hospitals_as_org_units(self):
where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s)'
args = {'pat': self.pk_patient}
cmd = gmOrganization._SQL_get_org_unit % where
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
#--------------------------------------------------------
# API: narrative
#--------------------------------------------------------
def add_notes(self, notes=None, episode=None, encounter=None):
enc = gmTools.coalesce (
encounter,
self.current_encounter['pk_encounter']
)
for note in notes:
gmClinNarrative.create_narrative_item (
narrative = note[1],
soap_cat = note[0],
episode_id = episode,
encounter_id = enc
)
return True
#--------------------------------------------------------
def add_clin_narrative(self, note='', soap_cat='s', episode=None, link_obj=None):
if note.strip() == '':
_log.info('will not create empty clinical note')
return None
if isinstance(episode, gmEMRStructItems.cEpisode):
episode = episode['pk_episode']
instance = gmClinNarrative.create_narrative_item (
link_obj = link_obj,
narrative = note,
soap_cat = soap_cat,
episode_id = episode,
encounter_id = self.current_encounter['pk_encounter']
)
return instance
#--------------------------------------------------------
def get_clin_narrative(self, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None):
"""Get SOAP notes pertinent to this encounter.
encounters
- list of encounters the narrative of which are to be retrieved
episodes
- list of episodes the narrative of which are to be retrieved
issues
- list of health issues the narrative of which are to be retrieved
soap_cats
- list of SOAP categories of the narrative to be retrieved
"""
where_parts = ['pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if issues is not None:
where_parts.append('pk_health_issue = ANY(%(issues)s)')
if len(issues) == 0:
args['issues'] = []
else:
if isinstance(issues[0], gmEMRStructItems.cHealthIssue):
args['issues'] = [ i['pk_health_issue'] for i in issues ]
elif isinstance(issues[0], int):
args['issues'] = issues
else:
raise ValueError('<issues> must be list of type int (=pk) or cHealthIssue, but 1st issue is: %s' % issues[0])
if episodes is not None:
where_parts.append('pk_episode = ANY(%(epis)s)')
if len(episodes) == 0:
args['epis'] = []
else:
if isinstance(episodes[0], gmEMRStructItems.cEpisode):
args['epis'] = [ e['pk_episode'] for e in episodes ]
elif isinstance(episodes[0], int):
args['epis'] = episodes
else:
raise ValueError('<episodes> must be list of type int (=pk) or cEpisode, but 1st episode is: %s' % episodes[0])
if encounters is not None:
where_parts.append('pk_encounter = ANY(%(encs)s)')
if len(encounters) == 0:
args['encs'] = []
else:
if isinstance(encounters[0], gmEMRStructItems.cEncounter):
args['encs'] = [ e['pk_encounter'] for e in encounters ]
elif isinstance(encounters[0], int):
args['encs'] = encounters
else:
raise ValueError('<encounters> must be list of type int (=pk) or cEncounter, but 1st encounter is: %s' % encounters[0])
if soap_cats is not None:
where_parts.append('c_vn.soap_cat = ANY(%(cats)s)')
args['cats'] = gmSoapDefs.soap_cats_str2list(soap_cats)
if providers is not None:
where_parts.append('c_vn.modified_by = ANY(%(docs)s)')
args['docs'] = providers
cmd = """
SELECT
c_vn.*,
c_scr.rank AS soap_rank
FROM
clin.v_narrative c_vn
LEFT JOIN clin.soap_cat_ranks c_scr on c_vn.soap_cat = c_scr.soap_cat
WHERE %s
ORDER BY date, soap_rank
""" % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmClinNarrative.cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ]
#--------------------------------------------------------
def search_narrative_simple(self, search_term=''):
search_term = search_term.strip()
if search_term == '':
return []
cmd = """
SELECT
*,
coalesce((SELECT description FROM clin.episode WHERE pk = vn4s.pk_episode), vn4s.src_table)
as episode,
coalesce((SELECT description FROM clin.health_issue WHERE pk = vn4s.pk_health_issue), vn4s.src_table)
as health_issue,
(SELECT started FROM clin.encounter WHERE pk = vn4s.pk_encounter)
as encounter_started,
(SELECT last_affirmed FROM clin.encounter WHERE pk = vn4s.pk_encounter)
as encounter_ended,
(SELECT _(description) FROM clin.encounter_type WHERE pk = (SELECT fk_type FROM clin.encounter WHERE pk = vn4s.pk_encounter))
as encounter_type
FROM clin.v_narrative4search vn4s
WHERE
pk_patient = %(pat)s and
vn4s.narrative ~ %(term)s
order by
encounter_started
""" # case sensitive
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient, 'term': search_term}}])
return rows
#--------------------------------------------------------
def get_patient_ID(self):
return self.pk_patient
#--------------------------------------------------------
def get_statistics(self):
union_query = '\n union all\n'.join ([
"""
SELECT ((
-- all relevant health issues + active episodes WITH health issue
SELECT COUNT(*)
FROM clin.v_problem_list
WHERE
pk_patient = %(pat)s
AND
pk_health_issue is not null
) + (
-- active episodes WITHOUT health issue
SELECT COUNT(*)
FROM clin.v_problem_list
WHERE
pk_patient = %(pat)s
AND
pk_health_issue is null
))""",
'SELECT COUNT(*) FROM clin.encounter WHERE fk_patient = %(pat)s',
'SELECT COUNT(*) FROM clin.v_pat_items WHERE pk_patient = %(pat)s',
'SELECT COUNT(*) FROM blobs.v_doc_med WHERE pk_patient = %(pat)s',
'SELECT COUNT(*) FROM clin.v_test_results WHERE pk_patient = %(pat)s',
'SELECT COUNT(*) FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s',
'SELECT COUNT(*) FROM clin.v_procedures WHERE pk_patient = %(pat)s',
"""
SELECT COUNT(*)
FROM clin.v_intakes
WHERE
pk_patient = %(pat)s
AND
use_type IS NOT NULL
""",
'SELECT COUNT(*) FROM clin.v_vaccinations WHERE pk_patient = %(pat)s'
])
rows, idx = gmPG2.run_ro_queries (
queries = [{'cmd': union_query, 'args': {'pat': self.pk_patient}}],
get_col_idx = False
)
stats = dict (
problems = rows[0][0],
encounters = rows[1][0],
items = rows[2][0],
documents = rows[3][0],
results = rows[4][0],
stays = rows[5][0],
procedures = rows[6][0],
active_drugs = rows[7][0],
vaccinations = rows[8][0]
)
return stats
#--------------------------------------------------------
def format_statistics(self):
return _(
'Medical problems: %(problems)s\n'
'Total encounters: %(encounters)s\n'
'Total EMR entries: %(items)s\n'
'Active medications: %(active_drugs)s\n'
'Documents: %(documents)s\n'
'Test results: %(results)s\n'
'Hospitalizations: %(stays)s\n'
'Procedures: %(procedures)s\n'
'Vaccinations: %(vaccinations)s'
) % self.get_statistics()
#--------------------------------------------------------
def format_summary(self) -> str:
cmd = "SELECT dob FROM dem.v_all_persons WHERE pk_identity = %(pk)s"
args = {'pk': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
dob = rows[0]['dob']
stats = self.get_statistics()
first = self.get_first_encounter()
last = self.get_last_encounter()
probs = self.get_problems()
txt = ''
if len(probs) > 0:
txt += _(' %s known problems, clinically relevant thereof:\n') % stats['problems']
else:
txt += _(' %s known problems\n') % stats['problems']
for prob in probs:
if not prob['clinically_relevant']:
continue
txt += ' \u00BB%s\u00AB (%s)\n' % (
prob['problem'],
gmTools.bool2subst(prob['problem_active'], _('active'), _('inactive'))
)
txt += '\n'
txt += _(' %s encounters from %s to %s\n') % (
stats['encounters'],
gmDateTime.pydt_strftime(first['started'], '%Y %b %d'),
gmDateTime.pydt_strftime(last['started'], '%Y %b %d')
)
txt += _(' %s active medications\n') % stats['active_drugs']
txt += _(' %s documents\n') % stats['documents']
txt += _(' %s test results\n') % stats['results']
txt += _(' %s hospitalizations') % stats['stays']
if stats['stays'] == 0:
txt += '\n'
else:
txt += _(', most recently:\n%s\n') % self.get_latest_hospital_stay().format(left_margin = 3)
# FIXME: perhaps only count "ongoing ones"
txt += _(' %s performed procedures') % stats['procedures']
if stats['procedures'] == 0:
txt += '\n'
else:
txt += _(', most recently:\n%s\n') % self.get_latest_performed_procedure().format(left_margin = 3)
txt += '\n'
txt += _('Allergies and Intolerances\n')
allg_state = self.allergy_state
txt += ' '
if allg_state:
txt += allg_state.state_string
if allg_state['last_confirmed']:
txt += _(' (last confirmed %s)') % gmDateTime.pydt_strftime(allg_state['last_confirmed'], '%Y %b %d')
txt += '\n'
txt += gmTools.coalesce(allg_state['comment'], '', ' %s\n')
else:
txt += _('allergy state not acquired')
txt += '\n'
for allg in self.get_allergies():
txt += ' %s: %s\n' % (
allg['descriptor'],
gmTools.coalesce(allg['reaction'], _('unknown reaction'))
)
meds = self.get_current_medications(order_by = 'substance')
if len(meds) > 0:
txt += '\n'
txt += _('Medications and Substances')
txt += '\n'
for m in meds:
txt += '%s\n' % m.format_as_single_line(left_margin = 1)
fhx = self.get_family_history()
if len(fhx) > 0:
txt += '\n'
txt += _('Family History')
txt += '\n'
for f in fhx:
txt += '%s\n' % f.format(left_margin = 1)
jobs = get_occupations(pk_identity = self.pk_patient)
if len(jobs) > 0:
txt += '\n'
txt += _('Occupations')
txt += '\n'
for job in jobs:
txt += ' %s%s\n' % (
job['l10n_occupation'],
gmTools.coalesce(job['activities'], '', ': %s')
)
vaccs = self.get_latest_vaccinations()
if len(vaccs) > 0:
txt += '\n'
txt += _('Vaccinations')
txt += '\n'
inds = sorted(vaccs)
for ind in inds:
ind_count, vacc = vaccs[ind]
if dob is None:
age_given = ''
else:
age_given = ' @ %s' % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age (
start = dob,
end = vacc['date_given']
))
since = _('%s ago') % gmDateTime.format_interval_medically(vacc['interval_since_given'])
txt += ' %s (%s%s): %s%s (%s %s%s%s)\n' % (
ind,
gmTools.u_sum,
ind_count,
#gmDateTime.pydt_strftime(vacc['date_given'], '%b %Y'),
since,
age_given,
vacc['vaccine'],
gmTools.u_left_double_angle_quote,
vacc['batch_no'],
gmTools.u_right_double_angle_quote
)
care = self.get_external_care_items(order_by = 'issue, organization, unit, provider', exclude_inactive = True)
if len(care) > 0:
txt += '\n'
txt += _('External care')
txt += '\n'
for item in care:
txt += ' %s: %s\n' % (
item['issue'],
gmTools.coalesce (
item['provider'],
'%s@%s' % (item['unit'], item['organization']),
'%%s (%s@%s)' % (item['unit'], item['organization'])
)
)
return txt
#--------------------------------------------------------
def format_as_journal(self, left_margin=0, patient=None):
txt = ''
for enc in self.get_encounters(skip_empty = True):
txt += gmTools.u_box_horiz_4dashes * 70 + '\n'
txt += enc.format (
episodes = None, # means: each touched upon
left_margin = left_margin,
patient = patient,
fancy_header = False,
with_soap = True,
with_docs = True,
with_tests = True,
with_vaccinations = True,
with_co_encountlet_hints = False, # irrelevant
with_rfe_aoe = True,
with_family_history = True,
by_episode = True
)
return txt
#--------------------------------------------------------
def get_as_journal(self, since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None):
return gmClinNarrative.get_as_journal (
patient = self.pk_patient,
since = since,
until = until,
encounters = encounters,
episodes = episodes,
issues = issues,
soap_cats = soap_cats,
providers = providers,
order_by = order_by,
time_range = time_range,
active_encounter = self.active_encounter
)
#------------------------------------------------------------------
def get_generic_emr_items(self, pk_encounters=None, pk_episodes=None, pk_health_issues=None, use_active_encounter=False, order_by=None):
if use_active_encounter:
active_encounter = self.active_encounter
else:
active_encounter = None
return gmGenericEMRItem.get_generic_emr_items (
patient = self.pk_patient,
encounters = pk_encounters,
episodes = pk_episodes,
issues = pk_health_issues,
active_encounter = active_encounter,
order_by = order_by
)
#--------------------------------------------------------
# API: allergy
#--------------------------------------------------------
def get_allergies(self, remove_sensitivities=False, since=None, until=None, encounters=None, episodes=None, issues=None, ID_list=None):
"""Retrieves patient allergy items.
remove_sensitivities
- retrieve real allergies only, without sensitivities
since
- initial date for allergy items
until
- final date for allergy items
encounters
- list of encounters whose allergies are to be retrieved
episodes
- list of episodes whose allergies are to be retrieved
issues
- list of health issues whose allergies are to be retrieved
"""
cmd = "SELECT * FROM clin.v_pat_allergies WHERE pk_patient=%s order by descriptor"
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}], get_col_idx = True)
filtered_allergies = []
for r in rows:
filtered_allergies.append(gmAllergy.cAllergy(row = {'data': r, 'idx': idx, 'pk_field': 'pk_allergy'}))
# ok, let's constrain our list
if ID_list is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_allergy'] in ID_list ]
if len(filtered_allergies) == 0:
_log.error('no allergies of list [%s] found for patient [%s]' % (str(ID_list), self.pk_patient))
# better fail here contrary to what we do elsewhere
return None
else:
return filtered_allergies
if remove_sensitivities:
filtered_allergies = [ allg for allg in filtered_allergies if allg['type'] == 'allergy' ]
if since is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] >= since ]
if until is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] < until ]
if issues is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_health_issue'] in issues ]
if episodes is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_episode'] in episodes ]
if encounters is not None:
filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_encounter'] in encounters ]
return filtered_allergies
#--------------------------------------------------------
def add_allergy(self, allergene=None, allg_type=None, encounter_id=None, episode_id=None):
if encounter_id is None:
encounter_id = self.current_encounter['pk_encounter']
if episode_id is None:
issue = self.add_health_issue(issue_name = _('Allergies/Intolerances'))
epi = self.add_episode(episode_name = _('Allergy detail: %s') % allergene, pk_health_issue = issue['pk_health_issue'])
episode_id = epi['pk_episode']
new_allergy = gmAllergy.create_allergy (
allergene = allergene,
allg_type = allg_type,
encounter_id = encounter_id,
episode_id = episode_id
)
return new_allergy
#--------------------------------------------------------
def delete_allergy(self, pk_allergy=None):
cmd = 'delete FROM clin.allergy WHERE pk=%(pk_allg)s'
args = {'pk_allg': pk_allergy}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#--------------------------------------------------------
def is_allergic_to(self, atcs=None, inns=None, product_name=None):
"""Cave: only use with one potential allergic agent
otherwise you won't know which of the agents the allergy is to."""
# not state acquired
if not self.allergy_state:
return None
# we don't know the state
if self.allergy_state['has_allergy'] is None:
return None
# we know there's no allergies
if self.allergy_state['has_allergy'] == 0:
return False
args = {
'atcs': atcs,
'inns': inns,
'prod_name': product_name,
'pat': self.pk_patient
}
allergenes = []
where_parts = []
if len(atcs) == 0:
atcs = None
if atcs is not None:
where_parts.append('atc_code = ANY(%(atcs)s)')
if len(inns) == 0:
inns = None
if inns is not None:
where_parts.append('generics = ANY(%(inns)s)')
allergenes.extend(inns)
if product_name is not None:
where_parts.append('substance = %(prod_name)s')
allergenes.append(product_name)
if len(allergenes) != 0:
where_parts.append('allergene = ANY(%(allgs)s)')
args['allgs'] = allergenes
cmd = """
SELECT * FROM clin.v_pat_allergies
WHERE
pk_patient = %%(pat)s
AND ( %s )""" % ' OR '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
if len(rows) == 0:
return False
return gmAllergy.cAllergy(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_allergy'})
#--------------------------------------------------------
def ensure_has_allergy_state(self) -> gmAllergy.cAllergyState:
return gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter'])
#--------------------------------------------------------
def _set_allergy_state(self, state):
if state not in gmAllergy.ALLERGY_STATES:
raise ValueError('[%s].__set_allergy_state(): <state> must be one of %s' % (self.__class__.__name__, gmAllergy.ALLERGY_STATES))
allg_state = gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter'])
allg_state['has_allergy'] = state
allg_state.save_payload()
return True
def _get_allergy_state(self) -> gmAllergy.cAllergyState:
return gmAllergy.get_allergy_state(pk_encounter = self.current_encounter['pk_encounter'])
allergy_state = property(_get_allergy_state, _set_allergy_state)
#--------------------------------------------------------
# API: external care
#--------------------------------------------------------
def get_external_care_items(self, order_by=None, exclude_inactive=False):
return gmExternalCare.get_external_care_items (
pk_identity = self.pk_patient,
order_by = order_by,
exclude_inactive = exclude_inactive
)
external_care_items = property(get_external_care_items)
#--------------------------------------------------------
# API: episodes
#--------------------------------------------------------
def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False):
"""Fetches from backend patient episodes.
id_list - Episodes' PKs list
issues - Health issues' PKs list to filter episodes by
open_status - return all (None) episodes, only open (True) or closed (False) one(s)
"""
if (unlinked_only is True) and (issues is not None):
raise ValueError('<unlinked_only> cannot be TRUE if <issues> is not None')
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
args = {
'pat': self.pk_patient,
'open': open_status
}
where_parts = ['pk_patient = %(pat)s']
if open_status is not None:
where_parts.append('episode_open IS %(open)s')
if unlinked_only:
where_parts.append('pk_health_issue is NULL')
if issues is not None:
where_parts.append('pk_health_issue = ANY(%(issues)s)')
args['issues'] = issues
if id_list is not None:
where_parts.append('pk_episode = ANY(%(epis)s)')
args['epis'] = id_list
cmd = "SELECT * FROM clin.v_pat_episodes WHERE %s %s" % (
' AND '.join(where_parts),
order_by
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmEMRStructItems.cEpisode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_episode'}) for r in rows ]
episodes = property(get_episodes)
#------------------------------------------------------------------
def get_unlinked_episodes(self, open_status=None, order_by=None):
return self.get_episodes(open_status = open_status, order_by = order_by, unlinked_only = True)
unlinked_episodes = property(get_unlinked_episodes)
#------------------------------------------------------------------
def get_episodes_by_encounter(self, pk_encounter=None):
cmd = """SELECT distinct pk_episode
from clin.v_pat_items
WHERE pk_encounter=%(enc)s and pk_patient=%(pat)s"""
args = {
'enc': gmTools.coalesce(pk_encounter, self.current_encounter['pk_encounter']),
'pat': self.pk_patient
}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return []
epis = []
for row in rows:
epis.append(row[0])
return self.get_episodes(id_list=epis)
#------------------------------------------------------------------
def add_episode(self, episode_name=None, pk_health_issue=None, is_open=False, allow_dupes=False, link_obj=None):
"""Add episode 'episode_name' for a patient's health issue.
- silently returns if episode already exists
"""
episode = gmEMRStructItems.create_episode (
link_obj = link_obj,
pk_health_issue = pk_health_issue,
episode_name = episode_name,
is_open = is_open,
encounter = self.current_encounter['pk_encounter'],
allow_dupes = allow_dupes
)
return episode
#--------------------------------------------------------
def get_most_recent_episode(self, issue=None):
# try to find the episode with the most recently modified clinical item
issue_where = gmTools.coalesce (
value2test = issue,
return_instead = '',
value2return = 'and pk_health_issue = %(issue)s'
)
cmd = """
SELECT pk
from clin.episode
WHERE pk = (
SELECT distinct on(pk_episode) pk_episode
from clin.v_pat_items
WHERE
pk_patient = %%(pat)s
and
modified_when = (
SELECT max(vpi.modified_when)
from clin.v_pat_items vpi
WHERE vpi.pk_patient = %%(pat)s
)
%s
-- guard against several episodes created at the same moment of time
limit 1
)""" % issue_where
rows, idx = gmPG2.run_ro_queries(queries = [
{'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}}
])
if len(rows) != 0:
return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0])
# no clinical items recorded, so try to find
# the youngest episode for this patient
cmd = """
SELECT vpe0.pk_episode
from
clin.v_pat_episodes vpe0
WHERE
vpe0.pk_patient = %%(pat)s
and
vpe0.episode_modified_when = (
SELECT max(vpe1.episode_modified_when)
from clin.v_pat_episodes vpe1
WHERE vpe1.pk_episode = vpe0.pk_episode
)
%s""" % issue_where
rows, idx = gmPG2.run_ro_queries(queries = [
{'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}}
])
if len(rows) != 0:
return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0])
return None
#--------------------------------------------------------
def episode2problem(self, episode=None):
return gmEMRStructItems.episode2problem(episode=episode)
#--------------------------------------------------------
# API: problems
#--------------------------------------------------------
def get_problems(self, episodes=None, issues=None, include_closed_episodes=False, include_irrelevant_issues=False):
"""Retrieve a patient's problems.
"Problems" are the UNION of:
- issues which are .clinically_relevant
- episodes which are .is_open
Therefore, both an issue and the open episode
thereof can each be listed as a problem.
include_closed_episodes/include_irrelevant_issues will
include those -- which departs from the definition of
the problem list being "active" items only ...
episodes - episodes' PKs to filter problems by
issues - health issues' PKs to filter problems by
"""
# FIXME: this could use a good measure of streamlining, probably
args = {'pat': self.pk_patient}
cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_problem_list WHERE pk_patient = %(pat)s ORDER BY problem"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
# Instantiate problem items
problems = []
for row in rows:
pk_args = {
'pk_patient': self.pk_patient,
'pk_health_issue': row['pk_health_issue'],
'pk_episode': row['pk_episode']
}
problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = False))
# include non-problems ?
other_rows = []
if include_closed_episodes:
cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'episode'"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
other_rows.extend(rows)
if include_irrelevant_issues:
cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'health issue'"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
other_rows.extend(rows)
if len(other_rows) > 0:
for row in other_rows:
pk_args = {
'pk_patient': self.pk_patient,
'pk_health_issue': row['pk_health_issue'],
'pk_episode': row['pk_episode']
}
problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = True))
# filter
if issues is not None:
problems = [ p for p in problems if p['pk_health_issue'] in issues ]
if episodes is not None:
problems = [ p for p in problems if p['pk_episode'] in episodes ]
return problems
#--------------------------------------------------------
def reclass_problem(self, problem):
return gmEMRStructItems.reclass_problem(problem = problem)
#--------------------------------------------------------
def get_candidate_diagnoses(self):
cmd = "SELECT * FROM clin.v_candidate_diagnoses WHERE pk_patient = %(pat)s"
rows, idx = gmPG2.run_ro_queries (
queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}],
get_col_idx = False
)
return rows
candidate_diagnoses = property(get_candidate_diagnoses)
#--------------------------------------------------------
# API: health issues
#--------------------------------------------------------
def get_health_issues(self, id_list = None):
cmd = "SELECT *, xmin_health_issue FROM clin.v_health_issues WHERE pk_patient = %(pat)s ORDER BY description"
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = True)
issues = [ gmEMRStructItems.cHealthIssue(row = {'idx': idx, 'data': r, 'pk_field': 'pk_health_issue'}) for r in rows ]
if id_list is None:
return issues
if len(id_list) == 0:
raise ValueError('id_list to filter by is empty, most likely a programming error')
filtered_issues = []
for issue in issues:
if issue['pk_health_issue'] in id_list:
filtered_issues.append(issue)
return filtered_issues
health_issues = property(get_health_issues)
#------------------------------------------------------------------
def add_health_issue(self, issue_name=None):
"""Adds patient health issue."""
return gmEMRStructItems.create_health_issue (
description = issue_name,
encounter = self.current_encounter['pk_encounter'],
patient = self.pk_patient
)
#--------------------------------------------------------
def health_issue2problem(self, issue=None):
return gmEMRStructItems.health_issue2problem(health_issue = issue)
#--------------------------------------------------------
# API: substance intake
#--------------------------------------------------------
def get_current_medications(self, include_inactive=True, order_by=None, episodes=None, issues=None):
return self._get_current_substance_intakes (
include_inactive = include_inactive,
order_by = order_by,
episodes = episodes,
issues = issues,
exclude_medications = False,
exclude_potential_abuses = True
)
#--------------------------------------------------------
def _get_abused_substances(self, order_by=None):
return self._get_current_substance_intakes (
include_inactive = True,
order_by = order_by,
episodes = None,
issues = None,
exclude_medications = True,
exclude_potential_abuses = False
)
abused_substances = property(_get_abused_substances)
#--------------------------------------------------------
def _get_current_substance_intakes(self, include_inactive=True, order_by=None, episodes=None, issues=None, exclude_potential_abuses=False, exclude_medications=False):
where_parts = ['pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if include_inactive:
table = 'clin.v_intakes'
else:
table = 'clin.v_intakes__active'
if exclude_potential_abuses:
where_parts.append('use_type IS NULL')
if exclude_medications:
where_parts.append('use_type IS NOT NULL')
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
cmd = "SELECT * FROM %s WHERE %s %s" % (
table,
'\nAND '.join(where_parts),
order_by
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
intakes = [ gmMedication.cSubstanceIntakeEntry(row = {'idx': idx, 'data': r, 'pk_field': 'pk_intake'}) for r in rows ]
if episodes is not None:
intakes = [ i for i in intakes if i['pk_episode'] in episodes ]
if issues is not None:
intakes = [ i for i in intakes if i ['pk_health_issue'] in issues ]
return intakes
#--------------------------------------------------------
def add_substance_intake(self, pk_component=None, pk_episode=None, pk_drug_product=None, pk_health_issue=None):
pk_enc = self.current_encounter['pk_encounter']
if pk_episode is None:
pk_episode = gmMedication.create_default_medication_history_episode (
pk_health_issue = pk_health_issue,
encounter = pk_enc
)
return gmMedication.create_substance_intake (
pk_component = pk_component,
pk_encounter = pk_enc,
pk_episode = pk_episode,
pk_drug_product = pk_drug_product
)
#--------------------------------------------------------
def substance_intake_exists(self, pk_component=None, pk_substance=None, pk_drug_product=None):
return gmMedication.substance_intake_exists (
pk_component = pk_component,
pk_substance = pk_substance,
pk_identity = self.pk_patient,
pk_drug_product = pk_drug_product
)
#--------------------------------------------------------
# API: vaccinations
#--------------------------------------------------------
def add_vaccination(self, episode=None, vaccine=None, batch_no=None):
return gmVaccination.create_vaccination (
encounter = self.current_encounter['pk_encounter'],
episode = episode,
vaccine = vaccine,
batch_no = batch_no
)
#--------------------------------------------------------
def get_latest_vaccinations(self, episodes=None, issues=None, atc_indications=None):
"""Returns latest given vaccination for each vaccinated indication.
as a dict {'l10n_indication': cVaccination instance}
Note that this will produce duplicate vaccination instances on combi-indication vaccines !
"""
args = {'pat': self.pk_patient}
where_parts = ['c_v_shots.pk_patient = %(pat)s']
if (episodes is not None) and (len(episodes) > 0):
where_parts.append('c_v_shots.pk_episode = ANY(%(epis)s)')
args['epis'] = episodes
if (issues is not None) and (len(issues) > 0):
where_parts.append('c_v_shots.pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(issues)s))')
args['issues'] = issues
if (atc_indications is not None) and (len(atc_indications) > 0):
where_parts.append('c_v_plv4i.atc_indication = ANY(%(atc_inds)s)')
args['atc_inds'] = atc_indications
# find the shots
cmd = """
SELECT
c_v_shots.*,
c_v_plv4i.l10n_indication,
c_v_plv4i.no_of_shots
FROM
clin.v_vaccinations c_v_shots
JOIN clin.v_pat_last_vacc4indication c_v_plv4i ON (c_v_shots.pk_vaccination = c_v_plv4i.pk_vaccination)
WHERE %s
""" % '\nAND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
# none found
if len(rows) == 0:
return {}
# turn them into vaccinations
# (idx is constant)
vaccs = {}
for shot_row in rows:
vaccs[shot_row['l10n_indication']] = (
shot_row['no_of_shots'],
gmVaccination.cVaccination(row = {'idx': idx, 'data': shot_row, 'pk_field': 'pk_vaccination'})
)
return vaccs
#--------------------------------------------------------
def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None):
return gmVaccination.get_vaccinations (
pk_identity = self.pk_patient,
pk_episodes = episodes,
pk_health_issues = issues,
pk_encounters = encounters,
order_by = order_by,
return_pks = False
)
vaccinations = property(get_vaccinations)
#------------------------------------------------------------------
# API: encounters
#------------------------------------------------------------------
def _get_current_encounter(self):
return self.__encounter
def _set_current_encounter(self, encounter):
# first ever setting ? -> fast path
if self.__encounter is None:
_log.debug('first setting of active encounter in this clinical record instance')
encounter.lock(exclusive = False) # lock new
self.__encounter = encounter
gmDispatcher.send('current_encounter_switched')
return True
# real switch -> slow path
_log.debug('switching of active encounter')
# fail if the currently active encounter has unsaved changes
if self.__encounter.is_modified():
gmTools.compare_dict_likes(self.__encounter, encounter, 'modified enc in client', 'enc to switch to')
_log.error('current in client: %s', self.__encounter)
raise ValueError('unsaved changes in active encounter [%s], cannot switch to another one [%s]' % (
self.__encounter['pk_encounter'],
encounter['pk_encounter']
))
prev_enc = self.__encounter
encounter.lock(exclusive = False) # lock new
self.__encounter = encounter
prev_enc.unlock(exclusive = False) # unlock old
gmDispatcher.send('current_encounter_switched')
return True
current_encounter = property(_get_current_encounter, _set_current_encounter)
active_encounter = property(_get_current_encounter, _set_current_encounter)
#--------------------------------------------------------
def __setup_active_encounter(self):
_log.debug('setting up active encounter for identity [%s]', self.pk_patient)
# log access to patient record (HIPAA, for example)
_delayed_execute(self.log_access, action = 'setting up active encounter for identity [%s]' % self.pk_patient)
# cleanup (not async, because we don't want recent encounters
# to become the active one just because they are recent)
self.remove_empty_encounters()
# activate very recent encounter if available
if self.__activate_very_recent_encounter():
return
fairly_recent_enc = self.__get_fairly_recent_encounter()
# create new encounter for the time being
self.start_new_encounter()
if fairly_recent_enc is None:
return
# but check whether user wants to continue a "fairly recent" one
gmDispatcher.send (
signal = 'ask_for_encounter_continuation',
new_encounter = self.__encounter,
fairly_recent_encounter = fairly_recent_enc
)
#------------------------------------------------------------------
def __activate_very_recent_encounter(self):
"""Try to attach to a "very recent" encounter if there is one.
returns:
False: no "very recent" encounter
True: success
"""
min_ttl = gmCfgDB.get4user (
option = 'encounter.minimum_ttl',
workplace = _here.active_workplace,
default = '1 hour 30 minutes'
)
cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = (
SELECT pk_encounter
FROM clin.v_most_recent_encounters
WHERE
pk_patient = %s
and
last_affirmed > (now() - %s::interval)
ORDER BY
last_affirmed DESC
LIMIT 1
)"""
enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, min_ttl]}], get_col_idx = True)
# none found
if len(enc_rows) == 0:
_log.debug('no <very recent> encounter (younger than [%s]) found' % min_ttl)
return False
_log.debug('"very recent" encounter [%s] found and re-activated' % enc_rows[0]['pk_encounter'])
# attach to existing
self.current_encounter = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
return True
#------------------------------------------------------------------
def __get_fairly_recent_encounter(self):
min_ttl = gmCfgDB.get4user (
option = 'encounter.minimum_ttl',
workplace = _here.active_workplace,
default = '1 hour 30 minutes'
)
max_ttl = gmCfgDB.get4user (
option = 'encounter.maximum_ttl',
workplace = _here.active_workplace,
default = '6 hours'
)
# do we happen to have a "fairly recent" candidate ?
cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = (
SELECT pk_encounter
FROM clin.v_most_recent_encounters
WHERE
pk_patient=%s
AND
last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval)
ORDER BY
last_affirmed DESC
LIMIT 1
)"""
enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True)
# none found
if len(enc_rows) == 0:
_log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl))
return None
_log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter'])
return gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
# #------------------------------------------------------------------
# def __check_for_fairly_recent_encounter(self):
#
# min_ttl = gmCfgDB.get4user (
# option = u'encounter.minimum_ttl',
# workplace = _here.active_workplace,
# default = u'1 hour 30 minutes'
# )
# max_ttl = gmCfgDB.get4user (
# option = u'encounter.maximum_ttl',
# workplace = _here.active_workplace,
# default = u'6 hours'
# )
#
# # do we happen to have a "fairly recent" candidate ?
# cmd = gmEMRStructItems.SQL_get_encounters % u"""pk_encounter = (
# SELECT pk_encounter
# FROM clin.v_most_recent_encounters
# WHERE
# pk_patient=%s
# AND
# last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval)
# ORDER BY
# last_affirmed DESC
# LIMIT 1
# )"""
# enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True)
#
# # none found
# if len(enc_rows) == 0:
# _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl))
# return
#
# _log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter'])
# fairly_recent_enc = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
# gmDispatcher.send(u'ask_for_encounter_continuation', current = self.__encounter, fairly_recent_encounter = fairly_recent_enc)
# #------------------------------------------------------------------
# def __activate_fairly_recent_encounter(self, allow_user_interaction=True):
# """Try to attach to a "fairly recent" encounter if there is one.
#
# returns:
# False: no "fairly recent" encounter, create new one
# True: success
# """
# if _func_ask_user is None:
# _log.debug('cannot ask user for guidance, not looking for fairly recent encounter')
# return False
#
# if not allow_user_interaction:
# _log.exception('user interaction not desired, not looking for fairly recent encounter')
# return False
#
# min_ttl = gmCfgDB.get4user (
# option = u'encounter.minimum_ttl',
# workplace = _here.active_workplace,
# default = u'1 hour 30 minutes'
# )
# max_ttl = gmCfgDB.get4user (
# option = u'encounter.maximum_ttl',
# workplace = _here.active_workplace,
# default = u'6 hours'
# )
# cmd = u"""
# SELECT pk_encounter
# FROM clin.v_most_recent_encounters
# WHERE
# pk_patient=%s
# AND
# last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval)
# ORDER BY
# last_affirmed DESC"""
# enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}])
# # none found
# if len(enc_rows) == 0:
# _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl))
# return False
#
# _log.debug('"fairly recent" encounter [%s] found', enc_rows[0][0])
#
# encounter = gmEMRStructItems.cEncounter(aPK_obj=enc_rows[0][0])
# # ask user whether to attach or not
# cmd = u"""
# SELECT title, firstnames, lastnames, gender, dob
# FROM dem.v_all_persons WHERE pk_identity=%s"""
# pats, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}])
# pat = pats[0]
# pat_str = u'%s %s %s (%s), %s [#%s]' % (
# gmTools.coalesce(pat[0], u'')[:5],
# pat[1][:15],
# pat[2][:15],
# pat[3],
# gmDateTime.pydt_strftime(pat[4], '%Y %b %d'),
# self.pk_patient
# )
# msg = _(
# '%s\n'
# '\n'
# "This patient's chart was worked on only recently:\n"
# '\n'
# ' %s %s - %s (%s)\n'
# '\n'
# ' Reason for Encounter:\n'
# ' %s\n'
# ' Assessment of Encounter:\n'
# ' %s\n'
# '\n'
# 'Do you want to continue that consultation\n'
# 'or do you want to start a new one ?\n'
# ) % (
# pat_str,
# gmDateTime.pydt_strftime(encounter['started'], '%Y %b %d'),
# gmDateTime.pydt_strftime(encounter['started'], '%H:%M'), gmDateTime.pydt_strftime(encounter['last_affirmed'], '%H:%M'),
# encounter['l10n_type'],
# gmTools.coalesce(encounter['reason_for_encounter'], _('none given')),
# gmTools.coalesce(encounter['assessment_of_encounter'], _('none given')),
# )
# attach = False
# try:
# attach = _func_ask_user(msg = msg, caption = _('Starting patient encounter'), encounter = encounter)
# except Exception:
# _log.exception('cannot ask user for guidance, not attaching to existing encounter')
# return False
# if not attach:
# return False
#
# # attach to existing
# self.current_encounter = encounter
# _log.debug('"fairly recent" encounter re-activated')
# return True
#------------------------------------------------------------------
def start_new_encounter(self):
enc_type = gmCfgDB.get4user (
option = 'encounter.default_type',
workplace = _here.active_workplace
)
if enc_type is None:
enc_type = gmEMRStructItems.get_most_commonly_used_encounter_type()
if enc_type is None:
enc_type = 'in surgery'
enc = gmEMRStructItems.create_encounter(fk_patient = self.pk_patient, enc_type = enc_type)
enc['pk_org_unit'] = _here['pk_org_unit']
enc.save()
self.current_encounter = enc
_log.debug('new encounter [%s] activated', enc['pk_encounter'])
#------------------------------------------------------------------
def get_encounters(self, since=None, until=None, id_list=None, episodes=None, issues=None, skip_empty=False, order_by=None, max_encounters=None):
"""Retrieves patient's encounters.
id_list - PKs of encounters to fetch
since - initial date for encounter items, DateTime instance
until - final date for encounter items, DateTime instance
episodes - PKs of the episodes the encounters belong to (many-to-many relation)
issues - PKs of the health issues the encounters belong to (many-to-many relation)
skip_empty - do NOT return those which do not have any of documents/clinical items/RFE/AOE
NOTE: if you specify *both* issues and episodes
you will get the *aggregate* of all encounters even
if the episodes all belong to the health issues listed.
IOW, the issues broaden the episode list rather than
the episode list narrowing the episodes-from-issues
list.
Rationale: If it was the other way round it would be
redundant to specify the list of issues at all.
"""
# if issues are given, translate them to their episodes
if (issues is not None) and (len(issues) > 0):
# - find episodes corresponding to the health issues in question
cmd = "SELECT distinct pk_episode FROM clin.v_pat_episodes WHERE pk_health_issue = ANY(%(issue_pks)s) AND pk_patient = %(pat)s"
args = {'issue_pks': issues, 'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
epis4issues_pks = [ r['pk_episode'] for r in rows ]
if episodes is None:
episodes = []
episodes.extend(epis4issues_pks)
if (episodes is not None) and (len(episodes) > 0):
# since the episodes to filter by belong to the patient in question so will
# the encounters found with them - hence we don't need a WHERE on the patient ...
# but, better safe than sorry ...
args = {'epi_pks': episodes, 'pat': self.pk_patient}
cmd = "SELECT DISTINCT fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter = ANY(SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)"
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
encs4epis_pks = [ r['fk_encounter'] for r in rows ]
if id_list is None:
id_list = []
id_list.extend(encs4epis_pks)
where_parts = ['c_vpe.pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if skip_empty:
where_parts.append("""NOT (
gm.is_null_or_blank_string(c_vpe.reason_for_encounter)
AND
gm.is_null_or_blank_string(c_vpe.assessment_of_encounter)
AND
NOT EXISTS (
SELECT 1 FROM clin.v_pat_items c_vpi WHERE c_vpi.pk_patient = %(pat)s AND c_vpi.pk_encounter = c_vpe.pk_encounter
UNION ALL
SELECT 1 FROM blobs.v_doc_med b_vdm WHERE b_vdm.pk_patient = %(pat)s AND b_vdm.pk_encounter = c_vpe.pk_encounter
))""")
if since is not None:
where_parts.append('c_vpe.started >= %(start)s')
args['start'] = since
if until is not None:
where_parts.append('c_vpe.last_affirmed <= %(end)s')
args['end'] = since
if (id_list is not None) and (len(id_list) > 0):
where_parts.append('c_vpe.pk_encounter = ANY(%(enc_pks)s)')
args['enc_pks'] = id_list
if order_by is None:
order_by = 'c_vpe.started'
if max_encounters is None:
limit = ''
else:
limit = 'LIMIT %s' % max_encounters
cmd = """
SELECT * FROM clin.v_pat_encounters c_vpe
WHERE
%s
ORDER BY %s %s
""" % (
' AND '.join(where_parts),
order_by,
limit
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
encounters = [ gmEMRStructItems.cEncounter(row = {'data': r, 'idx': idx, 'pk_field': 'pk_encounter'}) for r in rows ]
# we've got the encounters, start filtering
filtered_encounters = []
filtered_encounters.extend(encounters)
if (episodes is not None) and (len(episodes) > 0):
# since the episodes to filter by belong to the patient in question so will
# the encounters found with them - hence we don't need a WHERE on the patient ...
# but, better safe than sorry ...
args = {'epi_pks': episodes, 'pat': self.pk_patient}
cmd = "SELECT distinct fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)"
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
encs4epis_pks = [ r['fk_encounter'] for r in rows ]
filtered_encounters = [ enc for enc in filtered_encounters if enc['pk_encounter'] in encs4epis_pks ]
return filtered_encounters
#--------------------------------------------------------
def get_first_encounter(self, issue_id=None, episode_id=None):
"""Retrieves first encounter for a particular issue and/or episode.
issue_id - First encounter associated health issue
episode - First encounter associated episode
"""
if issue_id is None:
issues = None
else:
issues = [issue_id]
if episode_id is None:
episodes = None
else:
episodes = [episode_id]
encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started', max_encounters = 1)
if len(encounters) == 0:
return None
return encounters[0]
first_encounter = property(get_first_encounter)
#--------------------------------------------------------
def get_earliest_care_date(self):
args = {'pat': self.pk_patient}
cmd = """
SELECT MIN(earliest) FROM (
(
SELECT MIN(episode_modified_when) AS earliest FROM clin.v_pat_episodes WHERE pk_patient = %(pat)s
) UNION ALL (
SELECT MIN(modified_when) AS earliest FROM clin.v_health_issues WHERE pk_patient = %(pat)s
) UNION ALL (
SELECT MIN(modified_when) AS earliest FROM clin.encounter WHERE fk_patient = %(pat)s
) UNION ALL (
SELECT MIN(started) AS earliest FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s
) UNION ALL (
SELECT MIN(modified_when) AS earliest FROM clin.v_pat_items WHERE pk_patient = %(pat)s
) UNION ALL (
SELECT MIN(modified_when) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s
) UNION ALL (
SELECT MIN(last_confirmed) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s
)
) AS candidates"""
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return rows[0][0]
earliest_care_date = property(get_earliest_care_date)
#--------------------------------------------------------
def get_most_recent_care_date(self):
encounters = self.get_encounters(order_by = 'started DESC', max_encounters = 1)
if len(encounters) == 0:
return None
return encounters[0]['last_affirmed']
most_recent_care_date = property(get_most_recent_care_date)
#--------------------------------------------------------
def get_last_encounter(self, issue_id=None, episode_id=None):
"""Retrieves last encounter for a concrete issue and/or episode
issue_id - Last encounter associated health issue
episode_id - Last encounter associated episode
"""
if issue_id is None:
issues = None
else:
issues = [issue_id]
if episode_id is None:
episodes = None
else:
episodes = [episode_id]
encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started DESC', max_encounters = 1)
if len(encounters) == 0:
return None
return encounters[0]
last_encounter = property(get_last_encounter)
#------------------------------------------------------------------
def get_encounter_stats_by_type(self, cover_period=None):
args = {'pat': self.pk_patient, 'range': cover_period}
where_parts = ['pk_patient = %(pat)s']
if cover_period is not None:
where_parts.append('last_affirmed > now() - %(range)s')
cmd = """
SELECT l10n_type, COUNT(*) AS frequency
FROM clin.v_pat_encounters
WHERE
%s
GROUP BY l10n_type
ORDER BY frequency DESC
""" % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return rows
#------------------------------------------------------------------
def get_last_but_one_encounter(self, issue_id=None, episode_id=None):
args = {'pat': self.pk_patient}
if (issue_id is None) and (episode_id is None):
cmd = """
SELECT * FROM clin.v_pat_encounters
WHERE pk_patient = %(pat)s
ORDER BY started DESC
LIMIT 2
"""
else:
where_parts = []
if issue_id is not None:
where_parts.append('pk_health_issue = %(issue)s')
args['issue'] = issue_id
if episode_id is not None:
where_parts.append('pk_episode = %(epi)s')
args['epi'] = episode_id
cmd = """
SELECT *
FROM clin.v_pat_encounters
WHERE
pk_patient = %%(pat)s
AND
pk_encounter IN (
SELECT distinct pk_encounter
FROM clin.v_narrative
WHERE
%s
)
ORDER BY started DESC
LIMIT 2
""" % ' AND '.join(where_parts)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
if len(rows) == 0:
return None
# just one encounter within the above limits
if len(rows) == 1:
# is it the current encounter ?
if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']:
# yes
return None
# no
return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
# more than one encounter
if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']:
return gmEMRStructItems.cEncounter(row = {'data': rows[1], 'idx': idx, 'pk_field': 'pk_encounter'})
return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'})
last_but_one_encounter = property(get_last_but_one_encounter)
#------------------------------------------------------------------
def remove_empty_encounters(self):
_log.debug('removing empty encounters for pk_identity [%s]', self.pk_patient)
ttl = gmCfgDB.get4user (
option = 'encounter.ttl_if_empty',
workplace = _here.active_workplace,
default = '1 week'
)
# # FIXME: this should be done async
cmd = "SELECT clin.remove_old_empty_encounters(%(pat)s::INTEGER, %(ttl)s::INTERVAL)"
args = {'pat': self.pk_patient, 'ttl': ttl}
try:
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
except Exception:
_log.exception('error deleting empty encounters')
return False
if not rows[0][0]:
_log.debug('no encounters deleted (less than 2 exist)')
return True
#------------------------------------------------------------------
# API: measurements / test results
#------------------------------------------------------------------
def get_most_recent_results_for_patient(self, no_of_results=1):
return gmPathLab.get_most_recent_results_for_patient (
no_of_results = no_of_results,
patient = self.pk_patient
)
#------------------------------------------------------------------
def get_most_recent_results_in_loinc_group(self, loincs=None, max_no_of_results=1, consider_indirect_matches=False):
return gmPathLab.get_most_recent_results_in_loinc_group (
loincs = loincs,
max_no_of_results = max_no_of_results,
patient = self.pk_patient,
consider_indirect_matches = consider_indirect_matches
)
#------------------------------------------------------------------
def get_most_recent_results_for_test_type(self, test_type=None, max_no_of_results=1):
return gmPathLab.get_most_recent_results_for_test_type (
test_type = test_type,
max_no_of_results = max_no_of_results,
patient = self.pk_patient
)
#------------------------------------------------------------------
def get_most_recent_result_for_test_types(self, pk_test_types=None):
return gmPathLab.get_most_recent_result_for_test_types (
pk_test_types = pk_test_types,
pk_patient = self.pk_patient
)
#------------------------------------------------------------------
def get_result_at_timestamp(self, timestamp=None, test_type=None, loinc=None, tolerance_interval='12 hours'):
return gmPathLab.get_result_at_timestamp (
timestamp = timestamp,
test_type = test_type,
loinc = loinc,
tolerance_interval = tolerance_interval,
patient = self.pk_patient
)
#------------------------------------------------------------------
def get_results_for_day(self, timestamp=None, order_by=None):
return gmPathLab.get_results_for_day (
timestamp = timestamp,
patient = self.pk_patient,
order_by = order_by
)
#------------------------------------------------------------------
def get_results_for_issue(self, pk_health_issue=None, order_by=None):
return gmPathLab.get_results_for_issue (
pk_health_issue = pk_health_issue,
order_by = order_by
)
#------------------------------------------------------------------
def get_results_for_episode(self, pk_episode=None):
return gmPathLab.get_results_for_episode(pk_episode = pk_episode)
#------------------------------------------------------------------
def get_unsigned_results(self, order_by=None):
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %%(pat)s
AND
reviewed IS FALSE
%s""" % order_by
args = {'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ]
#------------------------------------------------------------------
# FIXME: use psyopg2 dbapi extension of named cursors - they are *server* side !
def get_test_types_for_results(self, order_by=None, unique_meta_types=False):
"""Retrieve data about test types for which this patient has results."""
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
if unique_meta_types:
cmd = """
SELECT * FROM clin.v_test_types c_vtt
WHERE c_vtt.pk_test_type IN (
SELECT DISTINCT ON (c_vtr1.pk_meta_test_type) c_vtr1.pk_test_type
FROM clin.v_test_results c_vtr1
WHERE
c_vtr1.pk_patient = %%(pat)s
AND
c_vtr1.pk_meta_test_type IS NOT NULL
UNION ALL
SELECT DISTINCT ON (c_vtr2.pk_test_type) c_vtr2.pk_test_type
FROM clin.v_test_results c_vtr2
WHERE
c_vtr2.pk_patient = %%(pat)s
AND
c_vtr2.pk_meta_test_type IS NULL
)
%s""" % order_by
else:
cmd = """
SELECT * FROM clin.v_test_types c_vtt
WHERE c_vtt.pk_test_type IN (
SELECT DISTINCT ON (c_vtr.pk_test_type) c_vtr.pk_test_type
FROM clin.v_test_results c_vtr
WHERE c_vtr.pk_patient = %%(pat)s
)
%s""" % order_by
args = {'pat': self.pk_patient}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmPathLab.cMeasurementType(row = {'pk_field': 'pk_test_type', 'idx': idx, 'data': r}) for r in rows ]
#------------------------------------------------------------------
def get_dates_for_results(self, tests=None, reverse_chronological=True):
"""Get the dates for which we have results."""
where_parts = ['pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if tests is not None:
where_parts.append('pk_test_type = ANY(%(epi_pks)s)')
args['tests'] = tests
cmd = """
SELECT DISTINCT ON (clin_when_day)
clin_when_day,
is_reviewed
FROM (
SELECT
date_trunc('day', clin_when)
AS clin_when_day,
bool_and(reviewed)
AS is_reviewed
FROM (
SELECT
clin_when,
reviewed,
pk_patient,
pk_test_result
FROM clin.v_test_results
WHERE %s
)
AS patient_tests
GROUP BY clin_when_day
)
AS grouped_days
ORDER BY clin_when_day %s
""" % (
' AND '.join(where_parts),
gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC')
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
return rows
#------------------------------------------------------------------
def get_issues_or_episodes_for_results(self, tests=None):
"""Get the issues/episodes for which we have results."""
where_parts = ['pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if tests is not None:
where_parts.append('pk_test_type = ANY(%(tests)s)')
args['tests'] = tests
where = ' AND '.join(where_parts)
cmd = """
SELECT * FROM ((
-- issues, each including all it"s episodes
SELECT
health_issue AS problem,
pk_health_issue,
NULL::integer AS pk_episode,
1 AS rank
FROM clin.v_test_results
WHERE pk_health_issue IS NOT NULL AND %s
GROUP BY pk_health_issue, problem
) UNION ALL (
-- episodes w/o issue
SELECT
episode AS problem,
NULL::integer AS pk_health_issue,
pk_episode,
2 AS rank
FROM clin.v_test_results
WHERE pk_health_issue IS NULL AND %s
GROUP BY pk_episode, problem
)) AS grouped_union
ORDER BY rank, problem
""" % (where, where)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False)
return rows
#------------------------------------------------------------------
def get_test_results(self, encounters=None, episodes=None, tests=None, order_by=None):
return gmPathLab.get_test_results (
pk_patient = self.pk_patient,
encounters = encounters,
episodes = episodes,
order_by = order_by
)
#------------------------------------------------------------------
def get_test_results_by_date(self, encounter=None, episodes=None, tests=None, reverse_chronological=True):
where_parts = ['pk_patient = %(pat)s']
args = {'pat': self.pk_patient}
if tests is not None:
where_parts.append('pk_test_type = ANY(%(tests)s)')
args['tests'] = tests
if encounter is not None:
where_parts.append('pk_encounter = %(enc)s')
args['enc'] = encounter
if episodes is not None:
where_parts.append('pk_episode = ANY(%(epis)s)')
args['epis'] = episodes
cmd = """
SELECT * FROM clin.v_test_results
WHERE %s
ORDER BY clin_when %s, pk_episode, unified_name
""" % (
' AND '.join(where_parts),
gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC')
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
tests = [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ]
return tests
#------------------------------------------------------------------
def add_test_result(self, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None):
try:
epi = int(episode)
except Exception:
epi = episode['pk_episode']
try:
type = int(type)
except Exception:
type = type['pk_test_type']
tr = gmPathLab.create_test_result (
link_obj = link_obj,
encounter = self.current_encounter['pk_encounter'],
episode = epi,
type = type,
intended_reviewer = intended_reviewer,
val_num = val_num,
val_alpha = val_alpha,
unit = unit
)
return tr
#------------------------------------------------------------------
def get_labs_as_org_units(self):
where = 'pk_org_unit IN (%s)' % """
SELECT DISTINCT fk_org_unit FROM clin.test_org WHERE pk IN (
SELECT DISTINCT pk_test_org FROM clin.v_test_results where pk_patient = %(pat)s
)"""
args = {'pat': self.pk_patient}
cmd = gmOrganization._SQL_get_org_unit % where
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ]
#------------------------------------------------------------------
def _get_best_gfr_or_crea(self):
measured_gfrs = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_gfr_quantity, max_no_of_results = 1)
measured_gfr = measured_gfrs[0] if len(measured_gfrs) > 0 else None
creas = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_creatinine_quantity, max_no_of_results = 1)
crea = creas[0] if len(creas) > 0 else None
if (measured_gfr is None) and (crea is None):
return None
if (measured_gfr is not None) and (crea is None):
return measured_gfr
# from here, Crea cannot be None anymore
if measured_gfr is None:
eGFR = self.calculator.eGFR
if eGFR.numeric_value is None:
return crea
return eGFR
# from here, measured_gfr cannot be None anymore, either
two_weeks = pydt.timedelta(weeks = 2)
gfr_too_old = (crea['clin_when'] - measured_gfr['clin_when']) > two_weeks
if not gfr_too_old:
return measured_gfr
# from here, measured_gfr is considered too
# old, so attempt a more timely estimate
eGFR = self.calculator.eGFR
if eGFR.numeric_value is None:
# return crea since we cannot get a
# better estimate for some reason
return crea
return eGFR
best_gfr_or_crea = property(_get_best_gfr_or_crea)
#------------------------------------------------------------------
def _get_bmi(self):
return self.calculator.bmi
bmi = property(_get_bmi)
#------------------------------------------------------------------
def _get_dynamic_hints(self):
return gmAutoHints.get_hints_for_patient(pk_identity = self.pk_patient, pk_encounter = self.current_encounter['pk_encounter'])
dynamic_hints = property(_get_dynamic_hints)
#------------------------------------------------------------------
#------------------------------------------------------------------
#------------------------------------------------------------------
#------------------------------------------------------------------
#============================================================
# main
#------------------------------------------------------------
if __name__ == "__main__":
if len(sys.argv) == 1:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
def _do_delayed(*args, **kwargs):
print(args)
print(kwargs)
args[0](*args[1:], **kwargs)
set_delayed_executor(_do_delayed)
#-----------------------------------------
def test_allergy_state():
emr = cClinicalRecord(aPKey=1)
state = emr.allergy_state
print("allergy state is:", state)
print("setting state to 0")
emr.allergy_state = gmAllergy.ALLERGY_STATE_NONE
print("setting state to None")
emr.allergy_state = gmAllergy.ALLERGY_STATE_UNKNOWN
print("setting state to 'abc' (should fail)")
emr.allergy_state = 'abc'
#-----------------------------------------
def test_get_test_names():
emr = cClinicalRecord(aPKey = 6)
rows = emr.get_test_types_for_results(unique_meta_types = True)
print("test result names:", len(rows))
# for row in rows:
# print row
#-----------------------------------------
def test_get_dates_for_results():
emr = cClinicalRecord(aPKey=12)
rows = emr.get_dates_for_results()
print("test result dates:")
for row in rows:
print(row)
#-----------------------------------------
def test_get_measurements():
#emr = cClinicalRecord(aPKey=12)
#rows, idx = emr.get_measurements_by_date()
print("test results:")
#for row in rows:
# print(row)
#-----------------------------------------
def test_get_test_results_by_date():
emr = cClinicalRecord(aPKey=12)
tests = emr.get_test_results_by_date()
print("test results:")
for test in tests:
print(test)
#-----------------------------------------
def test_get_statistics():
emr = cClinicalRecord(aPKey=12)
for key, item in emr.get_statistics().items():
print(key, ":", item)
#-----------------------------------------
def test_get_problems():
emr = cClinicalRecord(aPKey=12)
probs = emr.get_problems()
print("normal probs (%s):" % len(probs))
for p in probs:
print('%s (%s)' % (p['problem'], p['type']))
probs = emr.get_problems(include_closed_episodes=True)
print("probs + closed episodes (%s):" % len(probs))
for p in probs:
print('%s (%s)' % (p['problem'], p['type']))
probs = emr.get_problems(include_irrelevant_issues=True)
print("probs + issues (%s):" % len(probs))
for p in probs:
print('%s (%s)' % (p['problem'], p['type']))
probs = emr.get_problems(include_closed_episodes=True, include_irrelevant_issues=True)
print("probs + issues + epis (%s):" % len(probs))
for p in probs:
print('%s (%s)' % (p['problem'], p['type']))
#-----------------------------------------
def test_add_test_result():
emr = cClinicalRecord(aPKey=12)
tr = emr.add_test_result (
episode = 1,
intended_reviewer = 1,
type = 1,
val_num = 75,
val_alpha = 'somewhat obese',
unit = 'kg'
)
print(tr)
#-----------------------------------------
def test_get_most_recent_episode():
emr = cClinicalRecord(aPKey=12)
print(emr.get_most_recent_episode(issue = 2))
#-----------------------------------------
def test_get_almost_recent_encounter():
emr = cClinicalRecord(aPKey=12)
print(emr.get_last_encounter(issue_id=2))
print(emr.get_last_but_one_encounter(issue_id=2))
#-----------------------------------------
def test_get_encounters():
emr = cClinicalRecord(aPKey = 5)
print(emr.get_first_encounter(episode_id = 1638))
print(emr.get_last_encounter(episode_id = 1638))
#-----------------------------------------
def test_get_issues():
emr = cClinicalRecord(aPKey = 12)
for issue in emr.health_issues:
print(issue['description'])
#-----------------------------------------
def test_get_dx():
emr = cClinicalRecord(aPKey = 12)
for dx in emr.candidate_diagnoses:
print(dx)
#-----------------------------------------
def test_get_meds():
emr = cClinicalRecord(aPKey = 12)
for med in emr.get_current_medications():
print('\n'.join(med.format_maximum_information()))
input()
#-----------------------------------------
def test_get_abuses():
emr = cClinicalRecord(aPKey=12)
for med in emr.abused_substances:
print(med.format(single_line = True))
#-----------------------------------------
def test_is_allergic_to():
emr = cClinicalRecord(aPKey = 12)
print(emr.is_allergic_to(atcs = sys.argv[2:], inns = sys.argv[2:], product_name = sys.argv[2]))
#-----------------------------------------
def test_get_as_journal():
emr = cClinicalRecord(aPKey = 12)
for journal_line in emr.get_as_journal():
#print(list(journal_line))
print('%(date)s %(modified_by)s %(soap_cat)s %(narrative)s' % journal_line)
print("")
#-----------------------------------------
def test_get_most_recent():
emr = cClinicalRecord(aPKey=12)
print(emr.get_most_recent_results_for_test_type())
#-----------------------------------------
def test_episodes():
emr = cClinicalRecord(aPKey=12)
print("episodes:", emr.episodes)
print("unlinked:", emr.unlinked_episodes)
#-----------------------------------------
def test_format_as_journal():
emr = cClinicalRecord(aPKey=12)
from Gnumed.business.gmPerson import cPatient
pat = cPatient(aPK_obj = 12)
print(emr.format_as_journal(left_margin = 1, patient = pat))
#-----------------------------------------
gmPG2.request_login_params(setup_pool = True)
from Gnumed.business import gmPraxis
gmPraxis.activate_first_praxis_branch()
#test_allergy_state()
#test_is_allergic_to()
#test_get_test_names()
#test_get_dates_for_results()
#test_get_measurements()
#test_get_test_results_by_date()
#test_get_statistics()
#test_get_problems()
#test_add_test_result()
#test_get_most_recent_episode()
#test_get_almost_recent_encounter()
#test_get_meds()
#test_get_as_journal()
#test_get_most_recent()
#test_episodes()
#test_format_as_journal()
test_get_abuses()
#test_get_encounters()
#test_get_issues()
#test_get_dx()
#emr = cClinicalRecord(aPKey = 12)
# # Vacc regimes
# vacc_regimes = emr.get_scheduled_vaccination_regimes(indications = ['tetanus'])
# print '\nVaccination regimes: '
# for a_regime in vacc_regimes:
# pass
# #print a_regime
# vacc_regime = emr.get_scheduled_vaccination_regimes(ID=10)
# #print vacc_regime
# # vaccination regimes and vaccinations for regimes
# scheduled_vaccs = emr.get_scheduled_vaccinations(indications = ['tetanus'])
# print 'Vaccinations for the regime:'
# for a_scheduled_vacc in scheduled_vaccs:
# pass
# #print ' %s' %(a_scheduled_vacc)
# # vaccination next shot and booster
# v1 = emr.vaccinations
# print(v1)
# v2 = gmVaccination.get_vaccinations(pk_identity = 12, return_pks = True)
# print(v2)
# for v in v1:
# if v['pk_vaccination'] not in v2:
# print('ERROR')
# for a_vacc in vaccinations:
# print '\nVaccination %s , date: %s, booster: %s, seq no: %s' %(a_vacc['batch_no'], a_vacc['date'].strftime('%Y-%m-%d'), a_vacc['is_booster'], a_vacc['seq_no'])
# # first and last encounters
# first_encounter = emr.get_first_encounter(issue_id = 1)
# print '\nFirst encounter: ' + str(first_encounter)
# last_encounter = emr.get_last_encounter(episode_id = 1)
# print '\nLast encounter: ' + str(last_encounter)
# print ''
#dump = record.get_missing_vaccinations()
#f = io.open('vaccs.lst', 'wb')
#if dump is not None:
# print "=== due ==="
# f.write(u"=== due ===\n")
# for row in dump['due']:
# print row
# f.write(repr(row))
# f.write(u'\n')
# print "=== overdue ==="
# f.write(u"=== overdue ===\n")
# for row in dump['overdue']:
# print row
# f.write(repr(row))
# f.write(u'\n')
#f.close()Functions
def format_clin_root_item(table, pk, patient=None)-
Expand source code
def format_clin_root_item(table, pk, patient=None): instance = instantiate_clin_root_item(table, pk) if instance is None: return _('cannot instantiate clinical root item <%s(%s)>' % (table, pk)) # if patient is not None: # if patient.ID != instance['pk_patient']: # raise ValueError(u'patient passed in: [%s], but instance is: [%s:%s:%s]' % (patient.ID, table, pk, instance['pk_patient'])) if hasattr(instance, 'format_maximum_information'): return '\n'.join(instance.format_maximum_information(patient = patient)) if hasattr(instance, 'format'): try: formatted = instance.format(patient = patient) except TypeError: formatted = instance.format() if type(formatted) == type([]): return '\n'.join(formatted) return formatted d = instance.fields_as_dict ( date_format = '%Y %b %d %H:%M', none_string = gmTools.u_diameter, escape_style = None, bool_strings = [_('True'), _('False')] ) return gmTools.format_dict_like(d, tabular = True, value_delimiters = None) def instantiate_clin_root_item(table, pk)-
Expand source code
def instantiate_clin_root_item(table, pk): try: item_class = _map_table2class[table] except KeyError: _log.error('unmapped clin_root_item entry [%s], cannot instantiate', table) return None return item_class(aPK_obj = pk) def set_delayed_executor(executor)-
Expand source code
def set_delayed_executor(executor): if not callable(executor): raise TypeError('executor <%s> is not callable' % executor) global _delayed_execute _delayed_execute = executor _log.debug('setting delayed executor to <%s>', executor)
Classes
class cClinicalRecord (aPKey=None)-
Fails if
- no connection to database possible
- patient referenced by aPKey does not exist
Expand source code
class cClinicalRecord(object): def __init__(self, aPKey=None):#, allow_user_interaction=True, encounter=None): """Fails if - no connection to database possible - patient referenced by aPKey does not exist """ self.pk_patient = aPKey # == identity.pk == primary key self.gender = None self.dob = None from Gnumed.business import gmPraxis global _here if _here is None: _here = gmPraxis.gmCurrentPraxisBranch() self.__encounter = None self.__setup_active_encounter() # register backend notification interests # (keep this last so we won't hang on threads when # failing this constructor for other reasons ...) if not self._register_interests(): raise gmExceptions.ConstructorError("cannot register signal interests") self.__calculator = None _log.debug('Instantiated clinical record for patient [%s].' % self.pk_patient) #-------------------------------------------------------- def cleanup(self): _log.debug('cleaning up after clinical record for patient [%s]' % self.pk_patient) if self.__encounter is not None: self.__encounter.unlock(exclusive = False) return True #-------------------------------------------------------- def log_access(self, action=None): if action is None: action = 'EMR access for pk_identity [%s]' % self.pk_patient args = {'action': action} cmd = 'SELECT gm.log_access2emr(%(action)s)' gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) #-------------------------------------------------------- def _get_calculator(self): if self.__calculator is None: from Gnumed.business.gmClinicalCalculator import cClinicalCalculator self.__calculator = cClinicalCalculator() from Gnumed.business.gmPerson import gmCurrentPatient curr_pat = gmCurrentPatient() if curr_pat.ID == self.pk_patient: self.__calculator.patient = curr_pat else: from Gnumed.business.gmPerson import cPatient self.__calculator.patient = cPatient(self.pk_patient) return self.__calculator calculator = property(_get_calculator) #-------------------------------------------------------- # messaging #-------------------------------------------------------- def _register_interests(self): gmDispatcher.connect(signal = 'gm_table_mod', receiver = self.db_modification_callback) return True #-------------------------------------------------------- def db_modification_callback(self, **kwds): if kwds['table'] != 'clin.encounter': return True if self.current_encounter is None: _log.debug('locally no encounter current, ignoring encounter modification signal') return True if int(kwds['pk_of_row']) != self.current_encounter['pk_encounter']: _log.debug('DB reported modification of encounter: #%s', kwds['pk_of_row']) _log.debug('our locally active encounter is: #%s', self.current_encounter['pk_encounter']) _log.debug('modified encounter != our encounter, ignoring') return True _log.debug('remote modification of our encounter signalled (local: #%s, remote: #%s)', self.current_encounter['pk_encounter'], kwds['pk_of_row']) # did someone delete the current encounter from under our feet ? if kwds['operation'] == 'DELETE': _log.error('local encounter has been DELETEd remotely, trying to get now-active encounter from database') if self.current_encounter.is_modified(): _log.error('local encounter instance has .is_modified()=True, losing local changes') _log.error('this hints at an error in .is_modified handling') # dirty fix: get now-active encounter self.current_encounter.unlock(exclusive = False) self.__encounter = None self.__setup_active_encounter() gmDispatcher.send('current_encounter_switched') return True # get the current encounter as an extra instance # from the database to check for changes curr_enc_in_db = gmEMRStructItems.cEncounter(aPK_obj = self.current_encounter['pk_encounter']) # the encounter just retrieved and the active encounter # have got the same transaction ID so there's no change # in the database, there could be a local change in # the active encounter but that doesn't matter because # no one else can have written to the DB so far (XMIN match) if curr_enc_in_db['xmin_encounter'] == self.current_encounter['xmin_encounter']: _log.debug('in-client and in-DB instance of encounter #%s have matching XMINs (%s), DB has NOT been written to since we last loaded the encounter, checking:', self.current_encounter['pk_encounter'], self.current_encounter['xmin_encounter']) if self.current_encounter.is_modified(): _log.error('encounter modification signalled from DB, with same XMIN as in local in-client instance of encounter, BUT local instance ALSO has .is_modified()=True') _log.error('this may hint at an error with .is_modified handling') gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB') # here we might want to ask the user for advice on how to proceed else: _log.debug('locally not flagged as modified') return True # there must have been a change to the active encounter # committed to the database from elsewhere (different XMIN), # we must deny to propagate the change, however, if # there are pending local changes, or, rather, we should ask # the user for advice if self.current_encounter.is_modified(): gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB') raise ValueError('unsaved changes in locally active encounter [%s], cannot switch to DB state of encounter [%s]' % ( self.current_encounter['pk_encounter'], curr_enc_in_db['pk_encounter'] )) # don't do this, because same_payload() does not compare _all_ # fields so we can get into a reality disconnect if we # don't announce the modification # if self.current_encounter.same_payload(another_object = curr_enc_in_db): # _log.debug('clin.encounter_mod_db received but no change to active encounter payload') # return True # there was a change in the database from elsewhere; # locally, however, we don't have any pending changes; # therefore we can propagate the remote change locally # without losing anything; # this really should be the standard case gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') _log.debug('active encounter modified remotely, no locally pending changes, reloading from DB and locally announcing the remote modification') self.current_encounter.refetch_payload() gmDispatcher.send('current_encounter_modified') return True #-------------------------------------------------------- # API: family history #-------------------------------------------------------- def get_family_history(self, episodes=None, issues=None, encounters=None): fhx = gmFamilyHistory.get_family_history ( order_by = 'l10n_relation, condition', patient = self.pk_patient ) if episodes is not None: fhx = [ f for f in fhx if f['pk_episode'] in episodes ] if issues is not None: fhx = [ f for f in fhx if f['pk_health_issue'] in issues ] if encounters is not None: fhx = [ f for f in fhx if f['pk_encounter'] in encounters ] return fhx #-------------------------------------------------------- def add_family_history(self, episode=None, condition=None, relation=None): return gmFamilyHistory.create_family_history ( encounter = self.current_encounter['pk_encounter'], episode = episode, condition = condition, relation = relation ) #-------------------------------------------------------- # API: pregnancy #-------------------------------------------------------- def _get_gender(self): if self.__gender is not None: return self.__gender cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) self.__gender = rows[0]['gender'] self.__dob = rows[0]['dob'] def _set_gender(self, gender): self.__gender = gender gender = property(_get_gender, _set_gender) #-------------------------------------------------------- def _get_dob(self): if self.__dob is not None: return self.__dob cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) self.__gender = rows[0]['gender'] self.__dob = rows[0]['dob'] def _set_dob(self, dob): self.__dob = dob dob = property(_get_dob, _set_dob) #-------------------------------------------------------- def _get_EDC(self): cmd = 'SELECT edc FROM clin.patient WHERE fk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) if len(rows) == 0: return None return rows[0]['edc'] def _set_EDC(self, edc): cmd = """ INSERT INTO clin.patient (fk_identity, edc) SELECT %(pat)s, %(edc)s WHERE NOT EXISTS ( SELECT 1 FROM clin.patient WHERE fk_identity = %(pat)s ) RETURNING pk""" args = {'pat': self.pk_patient, 'edc': edc} rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False, return_data = True) if len(rows) == 0: cmd = 'UPDATE clin.patient SET edc = %(edc)s WHERE fk_identity = %(pat)s' gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) EDC = property(_get_EDC, _set_EDC) #-------------------------------------------------------- def _EDC_is_fishy(self): edc = self.EDC if edc is None: return False if self.gender != 'f': return True now = gmDateTime.pydt_now_here() # mother too young if (self.dob + pydt.timedelta(weeks = 5 * 52)) > now: return True # mother too old if (self.dob + pydt.timedelta(weeks = 55 * 52)) < now: return True # Beulah Hunter, 375 days (http://www.reference.com/motif/health/longest-human-pregnancy-on-record) # EDC too far in the future if (edc - pydt.timedelta(days = 380)) > now: return True # even if the pregnancy would have *started* when it # was documented to *end* it would be over by now by # all accounts # EDC too far in the past if edc < (now - pydt.timedelta(days = 380)): return True EDC_is_fishy = property(_EDC_is_fishy) #-------------------------------------------------------- # API: performed procedures #-------------------------------------------------------- def get_performed_procedures(self, episodes=None, issues=None): procs = gmEMRStructItems.get_performed_procedures(patient = self.pk_patient) if episodes is not None: procs = [ p for p in procs if p['pk_episode'] in episodes ] if issues is not None: procs = [ p for p in procs if p['pk_health_issue'] in issues ] return procs performed_procedures = property(get_performed_procedures) #-------------------------------------------------------- def get_latest_performed_procedure(self): return gmEMRStructItems.get_latest_performed_procedure(patient = self.pk_patient) #-------------------------------------------------------- def add_performed_procedure(self, episode=None, location=None, hospital_stay=None, procedure=None): return gmEMRStructItems.create_performed_procedure ( encounter = self.current_encounter['pk_encounter'], episode = episode, location = location, hospital_stay = hospital_stay, procedure = procedure ) #-------------------------------------------------------- def get_procedure_locations_as_org_units(self): where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_procedures_not_at_hospital WHERE pk_patient = %(pat)s)' args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] #-------------------------------------------------------- # API: hospitalizations #-------------------------------------------------------- def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False): stays = gmEMRStructItems.get_patient_hospital_stays(patient = self.pk_patient, ongoing_only = ongoing_only) if episodes is not None: stays = [ s for s in stays if s['pk_episode'] in episodes ] if issues is not None: stays = [ s for s in stays if s['pk_health_issue'] in issues ] return stays hospital_stays = property(get_hospital_stays) #-------------------------------------------------------- def get_latest_hospital_stay(self): return gmEMRStructItems.get_latest_patient_hospital_stay(patient = self.pk_patient) #-------------------------------------------------------- def add_hospital_stay(self, episode=None, fk_org_unit=None): return gmEMRStructItems.create_hospital_stay ( encounter = self.current_encounter['pk_encounter'], episode = episode, fk_org_unit = fk_org_unit ) #-------------------------------------------------------- def get_hospital_stay_stats_by_hospital(self, cover_period=None): args = {'pat': self.pk_patient, 'range': cover_period} where_parts = ['pk_patient = %(pat)s'] if cover_period is not None: where_parts.append('discharge > (now() - %(range)s)') cmd = """ SELECT hospital, COUNT(*) AS frequency FROM clin.v_hospital_stays WHERE %s GROUP BY hospital ORDER BY frequency DESC """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows #-------------------------------------------------------- def get_attended_hospitals_as_org_units(self): where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s)' args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] #-------------------------------------------------------- # API: narrative #-------------------------------------------------------- def add_notes(self, notes=None, episode=None, encounter=None): enc = gmTools.coalesce ( encounter, self.current_encounter['pk_encounter'] ) for note in notes: gmClinNarrative.create_narrative_item ( narrative = note[1], soap_cat = note[0], episode_id = episode, encounter_id = enc ) return True #-------------------------------------------------------- def add_clin_narrative(self, note='', soap_cat='s', episode=None, link_obj=None): if note.strip() == '': _log.info('will not create empty clinical note') return None if isinstance(episode, gmEMRStructItems.cEpisode): episode = episode['pk_episode'] instance = gmClinNarrative.create_narrative_item ( link_obj = link_obj, narrative = note, soap_cat = soap_cat, episode_id = episode, encounter_id = self.current_encounter['pk_encounter'] ) return instance #-------------------------------------------------------- def get_clin_narrative(self, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None): """Get SOAP notes pertinent to this encounter. encounters - list of encounters the narrative of which are to be retrieved episodes - list of episodes the narrative of which are to be retrieved issues - list of health issues the narrative of which are to be retrieved soap_cats - list of SOAP categories of the narrative to be retrieved """ where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') if len(issues) == 0: args['issues'] = [] else: if isinstance(issues[0], gmEMRStructItems.cHealthIssue): args['issues'] = [ i['pk_health_issue'] for i in issues ] elif isinstance(issues[0], int): args['issues'] = issues else: raise ValueError('<issues> must be list of type int (=pk) or cHealthIssue, but 1st issue is: %s' % issues[0]) if episodes is not None: where_parts.append('pk_episode = ANY(%(epis)s)') if len(episodes) == 0: args['epis'] = [] else: if isinstance(episodes[0], gmEMRStructItems.cEpisode): args['epis'] = [ e['pk_episode'] for e in episodes ] elif isinstance(episodes[0], int): args['epis'] = episodes else: raise ValueError('<episodes> must be list of type int (=pk) or cEpisode, but 1st episode is: %s' % episodes[0]) if encounters is not None: where_parts.append('pk_encounter = ANY(%(encs)s)') if len(encounters) == 0: args['encs'] = [] else: if isinstance(encounters[0], gmEMRStructItems.cEncounter): args['encs'] = [ e['pk_encounter'] for e in encounters ] elif isinstance(encounters[0], int): args['encs'] = encounters else: raise ValueError('<encounters> must be list of type int (=pk) or cEncounter, but 1st encounter is: %s' % encounters[0]) if soap_cats is not None: where_parts.append('c_vn.soap_cat = ANY(%(cats)s)') args['cats'] = gmSoapDefs.soap_cats_str2list(soap_cats) if providers is not None: where_parts.append('c_vn.modified_by = ANY(%(docs)s)') args['docs'] = providers cmd = """ SELECT c_vn.*, c_scr.rank AS soap_rank FROM clin.v_narrative c_vn LEFT JOIN clin.soap_cat_ranks c_scr on c_vn.soap_cat = c_scr.soap_cat WHERE %s ORDER BY date, soap_rank """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmClinNarrative.cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ] #-------------------------------------------------------- def search_narrative_simple(self, search_term=''): search_term = search_term.strip() if search_term == '': return [] cmd = """ SELECT *, coalesce((SELECT description FROM clin.episode WHERE pk = vn4s.pk_episode), vn4s.src_table) as episode, coalesce((SELECT description FROM clin.health_issue WHERE pk = vn4s.pk_health_issue), vn4s.src_table) as health_issue, (SELECT started FROM clin.encounter WHERE pk = vn4s.pk_encounter) as encounter_started, (SELECT last_affirmed FROM clin.encounter WHERE pk = vn4s.pk_encounter) as encounter_ended, (SELECT _(description) FROM clin.encounter_type WHERE pk = (SELECT fk_type FROM clin.encounter WHERE pk = vn4s.pk_encounter)) as encounter_type FROM clin.v_narrative4search vn4s WHERE pk_patient = %(pat)s and vn4s.narrative ~ %(term)s order by encounter_started """ # case sensitive rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient, 'term': search_term}}]) return rows #-------------------------------------------------------- def get_patient_ID(self): return self.pk_patient #-------------------------------------------------------- def get_statistics(self): union_query = '\n union all\n'.join ([ """ SELECT (( -- all relevant health issues + active episodes WITH health issue SELECT COUNT(*) FROM clin.v_problem_list WHERE pk_patient = %(pat)s AND pk_health_issue is not null ) + ( -- active episodes WITHOUT health issue SELECT COUNT(*) FROM clin.v_problem_list WHERE pk_patient = %(pat)s AND pk_health_issue is null ))""", 'SELECT COUNT(*) FROM clin.encounter WHERE fk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_pat_items WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM blobs.v_doc_med WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_test_results WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_procedures WHERE pk_patient = %(pat)s', """ SELECT COUNT(*) FROM clin.v_intakes WHERE pk_patient = %(pat)s AND use_type IS NOT NULL """, 'SELECT COUNT(*) FROM clin.v_vaccinations WHERE pk_patient = %(pat)s' ]) rows, idx = gmPG2.run_ro_queries ( queries = [{'cmd': union_query, 'args': {'pat': self.pk_patient}}], get_col_idx = False ) stats = dict ( problems = rows[0][0], encounters = rows[1][0], items = rows[2][0], documents = rows[3][0], results = rows[4][0], stays = rows[5][0], procedures = rows[6][0], active_drugs = rows[7][0], vaccinations = rows[8][0] ) return stats #-------------------------------------------------------- def format_statistics(self): return _( 'Medical problems: %(problems)s\n' 'Total encounters: %(encounters)s\n' 'Total EMR entries: %(items)s\n' 'Active medications: %(active_drugs)s\n' 'Documents: %(documents)s\n' 'Test results: %(results)s\n' 'Hospitalizations: %(stays)s\n' 'Procedures: %(procedures)s\n' 'Vaccinations: %(vaccinations)s' ) % self.get_statistics() #-------------------------------------------------------- def format_summary(self) -> str: cmd = "SELECT dob FROM dem.v_all_persons WHERE pk_identity = %(pk)s" args = {'pk': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) dob = rows[0]['dob'] stats = self.get_statistics() first = self.get_first_encounter() last = self.get_last_encounter() probs = self.get_problems() txt = '' if len(probs) > 0: txt += _(' %s known problems, clinically relevant thereof:\n') % stats['problems'] else: txt += _(' %s known problems\n') % stats['problems'] for prob in probs: if not prob['clinically_relevant']: continue txt += ' \u00BB%s\u00AB (%s)\n' % ( prob['problem'], gmTools.bool2subst(prob['problem_active'], _('active'), _('inactive')) ) txt += '\n' txt += _(' %s encounters from %s to %s\n') % ( stats['encounters'], gmDateTime.pydt_strftime(first['started'], '%Y %b %d'), gmDateTime.pydt_strftime(last['started'], '%Y %b %d') ) txt += _(' %s active medications\n') % stats['active_drugs'] txt += _(' %s documents\n') % stats['documents'] txt += _(' %s test results\n') % stats['results'] txt += _(' %s hospitalizations') % stats['stays'] if stats['stays'] == 0: txt += '\n' else: txt += _(', most recently:\n%s\n') % self.get_latest_hospital_stay().format(left_margin = 3) # FIXME: perhaps only count "ongoing ones" txt += _(' %s performed procedures') % stats['procedures'] if stats['procedures'] == 0: txt += '\n' else: txt += _(', most recently:\n%s\n') % self.get_latest_performed_procedure().format(left_margin = 3) txt += '\n' txt += _('Allergies and Intolerances\n') allg_state = self.allergy_state txt += ' ' if allg_state: txt += allg_state.state_string if allg_state['last_confirmed']: txt += _(' (last confirmed %s)') % gmDateTime.pydt_strftime(allg_state['last_confirmed'], '%Y %b %d') txt += '\n' txt += gmTools.coalesce(allg_state['comment'], '', ' %s\n') else: txt += _('allergy state not acquired') txt += '\n' for allg in self.get_allergies(): txt += ' %s: %s\n' % ( allg['descriptor'], gmTools.coalesce(allg['reaction'], _('unknown reaction')) ) meds = self.get_current_medications(order_by = 'substance') if len(meds) > 0: txt += '\n' txt += _('Medications and Substances') txt += '\n' for m in meds: txt += '%s\n' % m.format_as_single_line(left_margin = 1) fhx = self.get_family_history() if len(fhx) > 0: txt += '\n' txt += _('Family History') txt += '\n' for f in fhx: txt += '%s\n' % f.format(left_margin = 1) jobs = get_occupations(pk_identity = self.pk_patient) if len(jobs) > 0: txt += '\n' txt += _('Occupations') txt += '\n' for job in jobs: txt += ' %s%s\n' % ( job['l10n_occupation'], gmTools.coalesce(job['activities'], '', ': %s') ) vaccs = self.get_latest_vaccinations() if len(vaccs) > 0: txt += '\n' txt += _('Vaccinations') txt += '\n' inds = sorted(vaccs) for ind in inds: ind_count, vacc = vaccs[ind] if dob is None: age_given = '' else: age_given = ' @ %s' % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age ( start = dob, end = vacc['date_given'] )) since = _('%s ago') % gmDateTime.format_interval_medically(vacc['interval_since_given']) txt += ' %s (%s%s): %s%s (%s %s%s%s)\n' % ( ind, gmTools.u_sum, ind_count, #gmDateTime.pydt_strftime(vacc['date_given'], '%b %Y'), since, age_given, vacc['vaccine'], gmTools.u_left_double_angle_quote, vacc['batch_no'], gmTools.u_right_double_angle_quote ) care = self.get_external_care_items(order_by = 'issue, organization, unit, provider', exclude_inactive = True) if len(care) > 0: txt += '\n' txt += _('External care') txt += '\n' for item in care: txt += ' %s: %s\n' % ( item['issue'], gmTools.coalesce ( item['provider'], '%s@%s' % (item['unit'], item['organization']), '%%s (%s@%s)' % (item['unit'], item['organization']) ) ) return txt #-------------------------------------------------------- def format_as_journal(self, left_margin=0, patient=None): txt = '' for enc in self.get_encounters(skip_empty = True): txt += gmTools.u_box_horiz_4dashes * 70 + '\n' txt += enc.format ( episodes = None, # means: each touched upon left_margin = left_margin, patient = patient, fancy_header = False, with_soap = True, with_docs = True, with_tests = True, with_vaccinations = True, with_co_encountlet_hints = False, # irrelevant with_rfe_aoe = True, with_family_history = True, by_episode = True ) return txt #-------------------------------------------------------- def get_as_journal(self, since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None): return gmClinNarrative.get_as_journal ( patient = self.pk_patient, since = since, until = until, encounters = encounters, episodes = episodes, issues = issues, soap_cats = soap_cats, providers = providers, order_by = order_by, time_range = time_range, active_encounter = self.active_encounter ) #------------------------------------------------------------------ def get_generic_emr_items(self, pk_encounters=None, pk_episodes=None, pk_health_issues=None, use_active_encounter=False, order_by=None): if use_active_encounter: active_encounter = self.active_encounter else: active_encounter = None return gmGenericEMRItem.get_generic_emr_items ( patient = self.pk_patient, encounters = pk_encounters, episodes = pk_episodes, issues = pk_health_issues, active_encounter = active_encounter, order_by = order_by ) #-------------------------------------------------------- # API: allergy #-------------------------------------------------------- def get_allergies(self, remove_sensitivities=False, since=None, until=None, encounters=None, episodes=None, issues=None, ID_list=None): """Retrieves patient allergy items. remove_sensitivities - retrieve real allergies only, without sensitivities since - initial date for allergy items until - final date for allergy items encounters - list of encounters whose allergies are to be retrieved episodes - list of episodes whose allergies are to be retrieved issues - list of health issues whose allergies are to be retrieved """ cmd = "SELECT * FROM clin.v_pat_allergies WHERE pk_patient=%s order by descriptor" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}], get_col_idx = True) filtered_allergies = [] for r in rows: filtered_allergies.append(gmAllergy.cAllergy(row = {'data': r, 'idx': idx, 'pk_field': 'pk_allergy'})) # ok, let's constrain our list if ID_list is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_allergy'] in ID_list ] if len(filtered_allergies) == 0: _log.error('no allergies of list [%s] found for patient [%s]' % (str(ID_list), self.pk_patient)) # better fail here contrary to what we do elsewhere return None else: return filtered_allergies if remove_sensitivities: filtered_allergies = [ allg for allg in filtered_allergies if allg['type'] == 'allergy' ] if since is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] >= since ] if until is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] < until ] if issues is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_health_issue'] in issues ] if episodes is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_episode'] in episodes ] if encounters is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_encounter'] in encounters ] return filtered_allergies #-------------------------------------------------------- def add_allergy(self, allergene=None, allg_type=None, encounter_id=None, episode_id=None): if encounter_id is None: encounter_id = self.current_encounter['pk_encounter'] if episode_id is None: issue = self.add_health_issue(issue_name = _('Allergies/Intolerances')) epi = self.add_episode(episode_name = _('Allergy detail: %s') % allergene, pk_health_issue = issue['pk_health_issue']) episode_id = epi['pk_episode'] new_allergy = gmAllergy.create_allergy ( allergene = allergene, allg_type = allg_type, encounter_id = encounter_id, episode_id = episode_id ) return new_allergy #-------------------------------------------------------- def delete_allergy(self, pk_allergy=None): cmd = 'delete FROM clin.allergy WHERE pk=%(pk_allg)s' args = {'pk_allg': pk_allergy} gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) #-------------------------------------------------------- def is_allergic_to(self, atcs=None, inns=None, product_name=None): """Cave: only use with one potential allergic agent otherwise you won't know which of the agents the allergy is to.""" # not state acquired if not self.allergy_state: return None # we don't know the state if self.allergy_state['has_allergy'] is None: return None # we know there's no allergies if self.allergy_state['has_allergy'] == 0: return False args = { 'atcs': atcs, 'inns': inns, 'prod_name': product_name, 'pat': self.pk_patient } allergenes = [] where_parts = [] if len(atcs) == 0: atcs = None if atcs is not None: where_parts.append('atc_code = ANY(%(atcs)s)') if len(inns) == 0: inns = None if inns is not None: where_parts.append('generics = ANY(%(inns)s)') allergenes.extend(inns) if product_name is not None: where_parts.append('substance = %(prod_name)s') allergenes.append(product_name) if len(allergenes) != 0: where_parts.append('allergene = ANY(%(allgs)s)') args['allgs'] = allergenes cmd = """ SELECT * FROM clin.v_pat_allergies WHERE pk_patient = %%(pat)s AND ( %s )""" % ' OR '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return False return gmAllergy.cAllergy(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_allergy'}) #-------------------------------------------------------- def ensure_has_allergy_state(self) -> gmAllergy.cAllergyState: return gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) #-------------------------------------------------------- def _set_allergy_state(self, state): if state not in gmAllergy.ALLERGY_STATES: raise ValueError('[%s].__set_allergy_state(): <state> must be one of %s' % (self.__class__.__name__, gmAllergy.ALLERGY_STATES)) allg_state = gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) allg_state['has_allergy'] = state allg_state.save_payload() return True def _get_allergy_state(self) -> gmAllergy.cAllergyState: return gmAllergy.get_allergy_state(pk_encounter = self.current_encounter['pk_encounter']) allergy_state = property(_get_allergy_state, _set_allergy_state) #-------------------------------------------------------- # API: external care #-------------------------------------------------------- def get_external_care_items(self, order_by=None, exclude_inactive=False): return gmExternalCare.get_external_care_items ( pk_identity = self.pk_patient, order_by = order_by, exclude_inactive = exclude_inactive ) external_care_items = property(get_external_care_items) #-------------------------------------------------------- # API: episodes #-------------------------------------------------------- def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False): """Fetches from backend patient episodes. id_list - Episodes' PKs list issues - Health issues' PKs list to filter episodes by open_status - return all (None) episodes, only open (True) or closed (False) one(s) """ if (unlinked_only is True) and (issues is not None): raise ValueError('<unlinked_only> cannot be TRUE if <issues> is not None') if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by args = { 'pat': self.pk_patient, 'open': open_status } where_parts = ['pk_patient = %(pat)s'] if open_status is not None: where_parts.append('episode_open IS %(open)s') if unlinked_only: where_parts.append('pk_health_issue is NULL') if issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') args['issues'] = issues if id_list is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = id_list cmd = "SELECT * FROM clin.v_pat_episodes WHERE %s %s" % ( ' AND '.join(where_parts), order_by ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmEMRStructItems.cEpisode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_episode'}) for r in rows ] episodes = property(get_episodes) #------------------------------------------------------------------ def get_unlinked_episodes(self, open_status=None, order_by=None): return self.get_episodes(open_status = open_status, order_by = order_by, unlinked_only = True) unlinked_episodes = property(get_unlinked_episodes) #------------------------------------------------------------------ def get_episodes_by_encounter(self, pk_encounter=None): cmd = """SELECT distinct pk_episode from clin.v_pat_items WHERE pk_encounter=%(enc)s and pk_patient=%(pat)s""" args = { 'enc': gmTools.coalesce(pk_encounter, self.current_encounter['pk_encounter']), 'pat': self.pk_patient } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return [] epis = [] for row in rows: epis.append(row[0]) return self.get_episodes(id_list=epis) #------------------------------------------------------------------ def add_episode(self, episode_name=None, pk_health_issue=None, is_open=False, allow_dupes=False, link_obj=None): """Add episode 'episode_name' for a patient's health issue. - silently returns if episode already exists """ episode = gmEMRStructItems.create_episode ( link_obj = link_obj, pk_health_issue = pk_health_issue, episode_name = episode_name, is_open = is_open, encounter = self.current_encounter['pk_encounter'], allow_dupes = allow_dupes ) return episode #-------------------------------------------------------- def get_most_recent_episode(self, issue=None): # try to find the episode with the most recently modified clinical item issue_where = gmTools.coalesce ( value2test = issue, return_instead = '', value2return = 'and pk_health_issue = %(issue)s' ) cmd = """ SELECT pk from clin.episode WHERE pk = ( SELECT distinct on(pk_episode) pk_episode from clin.v_pat_items WHERE pk_patient = %%(pat)s and modified_when = ( SELECT max(vpi.modified_when) from clin.v_pat_items vpi WHERE vpi.pk_patient = %%(pat)s ) %s -- guard against several episodes created at the same moment of time limit 1 )""" % issue_where rows, idx = gmPG2.run_ro_queries(queries = [ {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} ]) if len(rows) != 0: return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) # no clinical items recorded, so try to find # the youngest episode for this patient cmd = """ SELECT vpe0.pk_episode from clin.v_pat_episodes vpe0 WHERE vpe0.pk_patient = %%(pat)s and vpe0.episode_modified_when = ( SELECT max(vpe1.episode_modified_when) from clin.v_pat_episodes vpe1 WHERE vpe1.pk_episode = vpe0.pk_episode ) %s""" % issue_where rows, idx = gmPG2.run_ro_queries(queries = [ {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} ]) if len(rows) != 0: return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) return None #-------------------------------------------------------- def episode2problem(self, episode=None): return gmEMRStructItems.episode2problem(episode=episode) #-------------------------------------------------------- # API: problems #-------------------------------------------------------- def get_problems(self, episodes=None, issues=None, include_closed_episodes=False, include_irrelevant_issues=False): """Retrieve a patient's problems. "Problems" are the UNION of: - issues which are .clinically_relevant - episodes which are .is_open Therefore, both an issue and the open episode thereof can each be listed as a problem. include_closed_episodes/include_irrelevant_issues will include those -- which departs from the definition of the problem list being "active" items only ... episodes - episodes' PKs to filter problems by issues - health issues' PKs to filter problems by """ # FIXME: this could use a good measure of streamlining, probably args = {'pat': self.pk_patient} cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_problem_list WHERE pk_patient = %(pat)s ORDER BY problem""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) # Instantiate problem items problems = [] for row in rows: pk_args = { 'pk_patient': self.pk_patient, 'pk_health_issue': row['pk_health_issue'], 'pk_episode': row['pk_episode'] } problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = False)) # include non-problems ? other_rows = [] if include_closed_episodes: cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'episode'""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) other_rows.extend(rows) if include_irrelevant_issues: cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'health issue'""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) other_rows.extend(rows) if len(other_rows) > 0: for row in other_rows: pk_args = { 'pk_patient': self.pk_patient, 'pk_health_issue': row['pk_health_issue'], 'pk_episode': row['pk_episode'] } problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = True)) # filter if issues is not None: problems = [ p for p in problems if p['pk_health_issue'] in issues ] if episodes is not None: problems = [ p for p in problems if p['pk_episode'] in episodes ] return problems #-------------------------------------------------------- def reclass_problem(self, problem): return gmEMRStructItems.reclass_problem(problem = problem) #-------------------------------------------------------- def get_candidate_diagnoses(self): cmd = "SELECT * FROM clin.v_candidate_diagnoses WHERE pk_patient = %(pat)s" rows, idx = gmPG2.run_ro_queries ( queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = False ) return rows candidate_diagnoses = property(get_candidate_diagnoses) #-------------------------------------------------------- # API: health issues #-------------------------------------------------------- def get_health_issues(self, id_list = None): cmd = "SELECT *, xmin_health_issue FROM clin.v_health_issues WHERE pk_patient = %(pat)s ORDER BY description" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = True) issues = [ gmEMRStructItems.cHealthIssue(row = {'idx': idx, 'data': r, 'pk_field': 'pk_health_issue'}) for r in rows ] if id_list is None: return issues if len(id_list) == 0: raise ValueError('id_list to filter by is empty, most likely a programming error') filtered_issues = [] for issue in issues: if issue['pk_health_issue'] in id_list: filtered_issues.append(issue) return filtered_issues health_issues = property(get_health_issues) #------------------------------------------------------------------ def add_health_issue(self, issue_name=None): """Adds patient health issue.""" return gmEMRStructItems.create_health_issue ( description = issue_name, encounter = self.current_encounter['pk_encounter'], patient = self.pk_patient ) #-------------------------------------------------------- def health_issue2problem(self, issue=None): return gmEMRStructItems.health_issue2problem(health_issue = issue) #-------------------------------------------------------- # API: substance intake #-------------------------------------------------------- def get_current_medications(self, include_inactive=True, order_by=None, episodes=None, issues=None): return self._get_current_substance_intakes ( include_inactive = include_inactive, order_by = order_by, episodes = episodes, issues = issues, exclude_medications = False, exclude_potential_abuses = True ) #-------------------------------------------------------- def _get_abused_substances(self, order_by=None): return self._get_current_substance_intakes ( include_inactive = True, order_by = order_by, episodes = None, issues = None, exclude_medications = True, exclude_potential_abuses = False ) abused_substances = property(_get_abused_substances) #-------------------------------------------------------- def _get_current_substance_intakes(self, include_inactive=True, order_by=None, episodes=None, issues=None, exclude_potential_abuses=False, exclude_medications=False): where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if include_inactive: table = 'clin.v_intakes' else: table = 'clin.v_intakes__active' if exclude_potential_abuses: where_parts.append('use_type IS NULL') if exclude_medications: where_parts.append('use_type IS NOT NULL') if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by cmd = "SELECT * FROM %s WHERE %s %s" % ( table, '\nAND '.join(where_parts), order_by ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) intakes = [ gmMedication.cSubstanceIntakeEntry(row = {'idx': idx, 'data': r, 'pk_field': 'pk_intake'}) for r in rows ] if episodes is not None: intakes = [ i for i in intakes if i['pk_episode'] in episodes ] if issues is not None: intakes = [ i for i in intakes if i ['pk_health_issue'] in issues ] return intakes #-------------------------------------------------------- def add_substance_intake(self, pk_component=None, pk_episode=None, pk_drug_product=None, pk_health_issue=None): pk_enc = self.current_encounter['pk_encounter'] if pk_episode is None: pk_episode = gmMedication.create_default_medication_history_episode ( pk_health_issue = pk_health_issue, encounter = pk_enc ) return gmMedication.create_substance_intake ( pk_component = pk_component, pk_encounter = pk_enc, pk_episode = pk_episode, pk_drug_product = pk_drug_product ) #-------------------------------------------------------- def substance_intake_exists(self, pk_component=None, pk_substance=None, pk_drug_product=None): return gmMedication.substance_intake_exists ( pk_component = pk_component, pk_substance = pk_substance, pk_identity = self.pk_patient, pk_drug_product = pk_drug_product ) #-------------------------------------------------------- # API: vaccinations #-------------------------------------------------------- def add_vaccination(self, episode=None, vaccine=None, batch_no=None): return gmVaccination.create_vaccination ( encounter = self.current_encounter['pk_encounter'], episode = episode, vaccine = vaccine, batch_no = batch_no ) #-------------------------------------------------------- def get_latest_vaccinations(self, episodes=None, issues=None, atc_indications=None): """Returns latest given vaccination for each vaccinated indication. as a dict {'l10n_indication': cVaccination instance} Note that this will produce duplicate vaccination instances on combi-indication vaccines ! """ args = {'pat': self.pk_patient} where_parts = ['c_v_shots.pk_patient = %(pat)s'] if (episodes is not None) and (len(episodes) > 0): where_parts.append('c_v_shots.pk_episode = ANY(%(epis)s)') args['epis'] = episodes if (issues is not None) and (len(issues) > 0): where_parts.append('c_v_shots.pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(issues)s))') args['issues'] = issues if (atc_indications is not None) and (len(atc_indications) > 0): where_parts.append('c_v_plv4i.atc_indication = ANY(%(atc_inds)s)') args['atc_inds'] = atc_indications # find the shots cmd = """ SELECT c_v_shots.*, c_v_plv4i.l10n_indication, c_v_plv4i.no_of_shots FROM clin.v_vaccinations c_v_shots JOIN clin.v_pat_last_vacc4indication c_v_plv4i ON (c_v_shots.pk_vaccination = c_v_plv4i.pk_vaccination) WHERE %s """ % '\nAND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) # none found if len(rows) == 0: return {} # turn them into vaccinations # (idx is constant) vaccs = {} for shot_row in rows: vaccs[shot_row['l10n_indication']] = ( shot_row['no_of_shots'], gmVaccination.cVaccination(row = {'idx': idx, 'data': shot_row, 'pk_field': 'pk_vaccination'}) ) return vaccs #-------------------------------------------------------- def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None): return gmVaccination.get_vaccinations ( pk_identity = self.pk_patient, pk_episodes = episodes, pk_health_issues = issues, pk_encounters = encounters, order_by = order_by, return_pks = False ) vaccinations = property(get_vaccinations) #------------------------------------------------------------------ # API: encounters #------------------------------------------------------------------ def _get_current_encounter(self): return self.__encounter def _set_current_encounter(self, encounter): # first ever setting ? -> fast path if self.__encounter is None: _log.debug('first setting of active encounter in this clinical record instance') encounter.lock(exclusive = False) # lock new self.__encounter = encounter gmDispatcher.send('current_encounter_switched') return True # real switch -> slow path _log.debug('switching of active encounter') # fail if the currently active encounter has unsaved changes if self.__encounter.is_modified(): gmTools.compare_dict_likes(self.__encounter, encounter, 'modified enc in client', 'enc to switch to') _log.error('current in client: %s', self.__encounter) raise ValueError('unsaved changes in active encounter [%s], cannot switch to another one [%s]' % ( self.__encounter['pk_encounter'], encounter['pk_encounter'] )) prev_enc = self.__encounter encounter.lock(exclusive = False) # lock new self.__encounter = encounter prev_enc.unlock(exclusive = False) # unlock old gmDispatcher.send('current_encounter_switched') return True current_encounter = property(_get_current_encounter, _set_current_encounter) active_encounter = property(_get_current_encounter, _set_current_encounter) #-------------------------------------------------------- def __setup_active_encounter(self): _log.debug('setting up active encounter for identity [%s]', self.pk_patient) # log access to patient record (HIPAA, for example) _delayed_execute(self.log_access, action = 'setting up active encounter for identity [%s]' % self.pk_patient) # cleanup (not async, because we don't want recent encounters # to become the active one just because they are recent) self.remove_empty_encounters() # activate very recent encounter if available if self.__activate_very_recent_encounter(): return fairly_recent_enc = self.__get_fairly_recent_encounter() # create new encounter for the time being self.start_new_encounter() if fairly_recent_enc is None: return # but check whether user wants to continue a "fairly recent" one gmDispatcher.send ( signal = 'ask_for_encounter_continuation', new_encounter = self.__encounter, fairly_recent_encounter = fairly_recent_enc ) #------------------------------------------------------------------ def __activate_very_recent_encounter(self): """Try to attach to a "very recent" encounter if there is one. returns: False: no "very recent" encounter True: success """ min_ttl = gmCfgDB.get4user ( option = 'encounter.minimum_ttl', workplace = _here.active_workplace, default = '1 hour 30 minutes' ) cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = ( SELECT pk_encounter FROM clin.v_most_recent_encounters WHERE pk_patient = %s and last_affirmed > (now() - %s::interval) ORDER BY last_affirmed DESC LIMIT 1 )""" enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, min_ttl]}], get_col_idx = True) # none found if len(enc_rows) == 0: _log.debug('no <very recent> encounter (younger than [%s]) found' % min_ttl) return False _log.debug('"very recent" encounter [%s] found and re-activated' % enc_rows[0]['pk_encounter']) # attach to existing self.current_encounter = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) return True #------------------------------------------------------------------ def __get_fairly_recent_encounter(self): min_ttl = gmCfgDB.get4user ( option = 'encounter.minimum_ttl', workplace = _here.active_workplace, default = '1 hour 30 minutes' ) max_ttl = gmCfgDB.get4user ( option = 'encounter.maximum_ttl', workplace = _here.active_workplace, default = '6 hours' ) # do we happen to have a "fairly recent" candidate ? cmd = gmEMRStructItems.SQL_get_encounters % """pk_encounter = ( SELECT pk_encounter FROM clin.v_most_recent_encounters WHERE pk_patient=%s AND last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) ORDER BY last_affirmed DESC LIMIT 1 )""" enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True) # none found if len(enc_rows) == 0: _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) return None _log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter']) return gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) # #------------------------------------------------------------------ # def __check_for_fairly_recent_encounter(self): # # min_ttl = gmCfgDB.get4user ( # option = u'encounter.minimum_ttl', # workplace = _here.active_workplace, # default = u'1 hour 30 minutes' # ) # max_ttl = gmCfgDB.get4user ( # option = u'encounter.maximum_ttl', # workplace = _here.active_workplace, # default = u'6 hours' # ) # # # do we happen to have a "fairly recent" candidate ? # cmd = gmEMRStructItems.SQL_get_encounters % u"""pk_encounter = ( # SELECT pk_encounter # FROM clin.v_most_recent_encounters # WHERE # pk_patient=%s # AND # last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) # ORDER BY # last_affirmed DESC # LIMIT 1 # )""" # enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}], get_col_idx = True) # # # none found # if len(enc_rows) == 0: # _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) # return # # _log.debug('"fairly recent" encounter [%s] found', enc_rows[0]['pk_encounter']) # fairly_recent_enc = gmEMRStructItems.cEncounter(row = {'data': enc_rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) # gmDispatcher.send(u'ask_for_encounter_continuation', current = self.__encounter, fairly_recent_encounter = fairly_recent_enc) # #------------------------------------------------------------------ # def __activate_fairly_recent_encounter(self, allow_user_interaction=True): # """Try to attach to a "fairly recent" encounter if there is one. # # returns: # False: no "fairly recent" encounter, create new one # True: success # """ # if _func_ask_user is None: # _log.debug('cannot ask user for guidance, not looking for fairly recent encounter') # return False # # if not allow_user_interaction: # _log.exception('user interaction not desired, not looking for fairly recent encounter') # return False # # min_ttl = gmCfgDB.get4user ( # option = u'encounter.minimum_ttl', # workplace = _here.active_workplace, # default = u'1 hour 30 minutes' # ) # max_ttl = gmCfgDB.get4user ( # option = u'encounter.maximum_ttl', # workplace = _here.active_workplace, # default = u'6 hours' # ) # cmd = u""" # SELECT pk_encounter # FROM clin.v_most_recent_encounters # WHERE # pk_patient=%s # AND # last_affirmed BETWEEN (now() - %s::interval) AND (now() - %s::interval) # ORDER BY # last_affirmed DESC""" # enc_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient, max_ttl, min_ttl]}]) # # none found # if len(enc_rows) == 0: # _log.debug('no <fairly recent> encounter (between [%s] and [%s] old) found' % (min_ttl, max_ttl)) # return False # # _log.debug('"fairly recent" encounter [%s] found', enc_rows[0][0]) # # encounter = gmEMRStructItems.cEncounter(aPK_obj=enc_rows[0][0]) # # ask user whether to attach or not # cmd = u""" # SELECT title, firstnames, lastnames, gender, dob # FROM dem.v_all_persons WHERE pk_identity=%s""" # pats, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}]) # pat = pats[0] # pat_str = u'%s %s %s (%s), %s [#%s]' % ( # gmTools.coalesce(pat[0], u'')[:5], # pat[1][:15], # pat[2][:15], # pat[3], # gmDateTime.pydt_strftime(pat[4], '%Y %b %d'), # self.pk_patient # ) # msg = _( # '%s\n' # '\n' # "This patient's chart was worked on only recently:\n" # '\n' # ' %s %s - %s (%s)\n' # '\n' # ' Reason for Encounter:\n' # ' %s\n' # ' Assessment of Encounter:\n' # ' %s\n' # '\n' # 'Do you want to continue that consultation\n' # 'or do you want to start a new one ?\n' # ) % ( # pat_str, # gmDateTime.pydt_strftime(encounter['started'], '%Y %b %d'), # gmDateTime.pydt_strftime(encounter['started'], '%H:%M'), gmDateTime.pydt_strftime(encounter['last_affirmed'], '%H:%M'), # encounter['l10n_type'], # gmTools.coalesce(encounter['reason_for_encounter'], _('none given')), # gmTools.coalesce(encounter['assessment_of_encounter'], _('none given')), # ) # attach = False # try: # attach = _func_ask_user(msg = msg, caption = _('Starting patient encounter'), encounter = encounter) # except Exception: # _log.exception('cannot ask user for guidance, not attaching to existing encounter') # return False # if not attach: # return False # # # attach to existing # self.current_encounter = encounter # _log.debug('"fairly recent" encounter re-activated') # return True #------------------------------------------------------------------ def start_new_encounter(self): enc_type = gmCfgDB.get4user ( option = 'encounter.default_type', workplace = _here.active_workplace ) if enc_type is None: enc_type = gmEMRStructItems.get_most_commonly_used_encounter_type() if enc_type is None: enc_type = 'in surgery' enc = gmEMRStructItems.create_encounter(fk_patient = self.pk_patient, enc_type = enc_type) enc['pk_org_unit'] = _here['pk_org_unit'] enc.save() self.current_encounter = enc _log.debug('new encounter [%s] activated', enc['pk_encounter']) #------------------------------------------------------------------ def get_encounters(self, since=None, until=None, id_list=None, episodes=None, issues=None, skip_empty=False, order_by=None, max_encounters=None): """Retrieves patient's encounters. id_list - PKs of encounters to fetch since - initial date for encounter items, DateTime instance until - final date for encounter items, DateTime instance episodes - PKs of the episodes the encounters belong to (many-to-many relation) issues - PKs of the health issues the encounters belong to (many-to-many relation) skip_empty - do NOT return those which do not have any of documents/clinical items/RFE/AOE NOTE: if you specify *both* issues and episodes you will get the *aggregate* of all encounters even if the episodes all belong to the health issues listed. IOW, the issues broaden the episode list rather than the episode list narrowing the episodes-from-issues list. Rationale: If it was the other way round it would be redundant to specify the list of issues at all. """ # if issues are given, translate them to their episodes if (issues is not None) and (len(issues) > 0): # - find episodes corresponding to the health issues in question cmd = "SELECT distinct pk_episode FROM clin.v_pat_episodes WHERE pk_health_issue = ANY(%(issue_pks)s) AND pk_patient = %(pat)s" args = {'issue_pks': issues, 'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) epis4issues_pks = [ r['pk_episode'] for r in rows ] if episodes is None: episodes = [] episodes.extend(epis4issues_pks) if (episodes is not None) and (len(episodes) > 0): # since the episodes to filter by belong to the patient in question so will # the encounters found with them - hence we don't need a WHERE on the patient ... # but, better safe than sorry ... args = {'epi_pks': episodes, 'pat': self.pk_patient} cmd = "SELECT DISTINCT fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter = ANY(SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) encs4epis_pks = [ r['fk_encounter'] for r in rows ] if id_list is None: id_list = [] id_list.extend(encs4epis_pks) where_parts = ['c_vpe.pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if skip_empty: where_parts.append("""NOT ( gm.is_null_or_blank_string(c_vpe.reason_for_encounter) AND gm.is_null_or_blank_string(c_vpe.assessment_of_encounter) AND NOT EXISTS ( SELECT 1 FROM clin.v_pat_items c_vpi WHERE c_vpi.pk_patient = %(pat)s AND c_vpi.pk_encounter = c_vpe.pk_encounter UNION ALL SELECT 1 FROM blobs.v_doc_med b_vdm WHERE b_vdm.pk_patient = %(pat)s AND b_vdm.pk_encounter = c_vpe.pk_encounter ))""") if since is not None: where_parts.append('c_vpe.started >= %(start)s') args['start'] = since if until is not None: where_parts.append('c_vpe.last_affirmed <= %(end)s') args['end'] = since if (id_list is not None) and (len(id_list) > 0): where_parts.append('c_vpe.pk_encounter = ANY(%(enc_pks)s)') args['enc_pks'] = id_list if order_by is None: order_by = 'c_vpe.started' if max_encounters is None: limit = '' else: limit = 'LIMIT %s' % max_encounters cmd = """ SELECT * FROM clin.v_pat_encounters c_vpe WHERE %s ORDER BY %s %s """ % ( ' AND '.join(where_parts), order_by, limit ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) encounters = [ gmEMRStructItems.cEncounter(row = {'data': r, 'idx': idx, 'pk_field': 'pk_encounter'}) for r in rows ] # we've got the encounters, start filtering filtered_encounters = [] filtered_encounters.extend(encounters) if (episodes is not None) and (len(episodes) > 0): # since the episodes to filter by belong to the patient in question so will # the encounters found with them - hence we don't need a WHERE on the patient ... # but, better safe than sorry ... args = {'epi_pks': episodes, 'pat': self.pk_patient} cmd = "SELECT distinct fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) encs4epis_pks = [ r['fk_encounter'] for r in rows ] filtered_encounters = [ enc for enc in filtered_encounters if enc['pk_encounter'] in encs4epis_pks ] return filtered_encounters #-------------------------------------------------------- def get_first_encounter(self, issue_id=None, episode_id=None): """Retrieves first encounter for a particular issue and/or episode. issue_id - First encounter associated health issue episode - First encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] first_encounter = property(get_first_encounter) #-------------------------------------------------------- def get_earliest_care_date(self): args = {'pat': self.pk_patient} cmd = """ SELECT MIN(earliest) FROM ( ( SELECT MIN(episode_modified_when) AS earliest FROM clin.v_pat_episodes WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_health_issues WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.encounter WHERE fk_patient = %(pat)s ) UNION ALL ( SELECT MIN(started) AS earliest FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_items WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(last_confirmed) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) ) AS candidates""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows[0][0] earliest_care_date = property(get_earliest_care_date) #-------------------------------------------------------- def get_most_recent_care_date(self): encounters = self.get_encounters(order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0]['last_affirmed'] most_recent_care_date = property(get_most_recent_care_date) #-------------------------------------------------------- def get_last_encounter(self, issue_id=None, episode_id=None): """Retrieves last encounter for a concrete issue and/or episode issue_id - Last encounter associated health issue episode_id - Last encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] last_encounter = property(get_last_encounter) #------------------------------------------------------------------ def get_encounter_stats_by_type(self, cover_period=None): args = {'pat': self.pk_patient, 'range': cover_period} where_parts = ['pk_patient = %(pat)s'] if cover_period is not None: where_parts.append('last_affirmed > now() - %(range)s') cmd = """ SELECT l10n_type, COUNT(*) AS frequency FROM clin.v_pat_encounters WHERE %s GROUP BY l10n_type ORDER BY frequency DESC """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows #------------------------------------------------------------------ def get_last_but_one_encounter(self, issue_id=None, episode_id=None): args = {'pat': self.pk_patient} if (issue_id is None) and (episode_id is None): cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ORDER BY started DESC LIMIT 2 """ else: where_parts = [] if issue_id is not None: where_parts.append('pk_health_issue = %(issue)s') args['issue'] = issue_id if episode_id is not None: where_parts.append('pk_episode = %(epi)s') args['epi'] = episode_id cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %%(pat)s AND pk_encounter IN ( SELECT distinct pk_encounter FROM clin.v_narrative WHERE %s ) ORDER BY started DESC LIMIT 2 """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return None # just one encounter within the above limits if len(rows) == 1: # is it the current encounter ? if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: # yes return None # no return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) # more than one encounter if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: return gmEMRStructItems.cEncounter(row = {'data': rows[1], 'idx': idx, 'pk_field': 'pk_encounter'}) return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) last_but_one_encounter = property(get_last_but_one_encounter) #------------------------------------------------------------------ def remove_empty_encounters(self): _log.debug('removing empty encounters for pk_identity [%s]', self.pk_patient) ttl = gmCfgDB.get4user ( option = 'encounter.ttl_if_empty', workplace = _here.active_workplace, default = '1 week' ) # # FIXME: this should be done async cmd = "SELECT clin.remove_old_empty_encounters(%(pat)s::INTEGER, %(ttl)s::INTERVAL)" args = {'pat': self.pk_patient, 'ttl': ttl} try: rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True) except Exception: _log.exception('error deleting empty encounters') return False if not rows[0][0]: _log.debug('no encounters deleted (less than 2 exist)') return True #------------------------------------------------------------------ # API: measurements / test results #------------------------------------------------------------------ def get_most_recent_results_for_patient(self, no_of_results=1): return gmPathLab.get_most_recent_results_for_patient ( no_of_results = no_of_results, patient = self.pk_patient ) #------------------------------------------------------------------ def get_most_recent_results_in_loinc_group(self, loincs=None, max_no_of_results=1, consider_indirect_matches=False): return gmPathLab.get_most_recent_results_in_loinc_group ( loincs = loincs, max_no_of_results = max_no_of_results, patient = self.pk_patient, consider_indirect_matches = consider_indirect_matches ) #------------------------------------------------------------------ def get_most_recent_results_for_test_type(self, test_type=None, max_no_of_results=1): return gmPathLab.get_most_recent_results_for_test_type ( test_type = test_type, max_no_of_results = max_no_of_results, patient = self.pk_patient ) #------------------------------------------------------------------ def get_most_recent_result_for_test_types(self, pk_test_types=None): return gmPathLab.get_most_recent_result_for_test_types ( pk_test_types = pk_test_types, pk_patient = self.pk_patient ) #------------------------------------------------------------------ def get_result_at_timestamp(self, timestamp=None, test_type=None, loinc=None, tolerance_interval='12 hours'): return gmPathLab.get_result_at_timestamp ( timestamp = timestamp, test_type = test_type, loinc = loinc, tolerance_interval = tolerance_interval, patient = self.pk_patient ) #------------------------------------------------------------------ def get_results_for_day(self, timestamp=None, order_by=None): return gmPathLab.get_results_for_day ( timestamp = timestamp, patient = self.pk_patient, order_by = order_by ) #------------------------------------------------------------------ def get_results_for_issue(self, pk_health_issue=None, order_by=None): return gmPathLab.get_results_for_issue ( pk_health_issue = pk_health_issue, order_by = order_by ) #------------------------------------------------------------------ def get_results_for_episode(self, pk_episode=None): return gmPathLab.get_results_for_episode(pk_episode = pk_episode) #------------------------------------------------------------------ def get_unsigned_results(self, order_by=None): if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND reviewed IS FALSE %s""" % order_by args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ] #------------------------------------------------------------------ # FIXME: use psyopg2 dbapi extension of named cursors - they are *server* side ! def get_test_types_for_results(self, order_by=None, unique_meta_types=False): """Retrieve data about test types for which this patient has results.""" if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by if unique_meta_types: cmd = """ SELECT * FROM clin.v_test_types c_vtt WHERE c_vtt.pk_test_type IN ( SELECT DISTINCT ON (c_vtr1.pk_meta_test_type) c_vtr1.pk_test_type FROM clin.v_test_results c_vtr1 WHERE c_vtr1.pk_patient = %%(pat)s AND c_vtr1.pk_meta_test_type IS NOT NULL UNION ALL SELECT DISTINCT ON (c_vtr2.pk_test_type) c_vtr2.pk_test_type FROM clin.v_test_results c_vtr2 WHERE c_vtr2.pk_patient = %%(pat)s AND c_vtr2.pk_meta_test_type IS NULL ) %s""" % order_by else: cmd = """ SELECT * FROM clin.v_test_types c_vtt WHERE c_vtt.pk_test_type IN ( SELECT DISTINCT ON (c_vtr.pk_test_type) c_vtr.pk_test_type FROM clin.v_test_results c_vtr WHERE c_vtr.pk_patient = %%(pat)s ) %s""" % order_by args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmPathLab.cMeasurementType(row = {'pk_field': 'pk_test_type', 'idx': idx, 'data': r}) for r in rows ] #------------------------------------------------------------------ def get_dates_for_results(self, tests=None, reverse_chronological=True): """Get the dates for which we have results.""" where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(epi_pks)s)') args['tests'] = tests cmd = """ SELECT DISTINCT ON (clin_when_day) clin_when_day, is_reviewed FROM ( SELECT date_trunc('day', clin_when) AS clin_when_day, bool_and(reviewed) AS is_reviewed FROM ( SELECT clin_when, reviewed, pk_patient, pk_test_result FROM clin.v_test_results WHERE %s ) AS patient_tests GROUP BY clin_when_day ) AS grouped_days ORDER BY clin_when_day %s """ % ( ' AND '.join(where_parts), gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows #------------------------------------------------------------------ def get_issues_or_episodes_for_results(self, tests=None): """Get the issues/episodes for which we have results.""" where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(tests)s)') args['tests'] = tests where = ' AND '.join(where_parts) cmd = """ SELECT * FROM (( -- issues, each including all it"s episodes SELECT health_issue AS problem, pk_health_issue, NULL::integer AS pk_episode, 1 AS rank FROM clin.v_test_results WHERE pk_health_issue IS NOT NULL AND %s GROUP BY pk_health_issue, problem ) UNION ALL ( -- episodes w/o issue SELECT episode AS problem, NULL::integer AS pk_health_issue, pk_episode, 2 AS rank FROM clin.v_test_results WHERE pk_health_issue IS NULL AND %s GROUP BY pk_episode, problem )) AS grouped_union ORDER BY rank, problem """ % (where, where) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows #------------------------------------------------------------------ def get_test_results(self, encounters=None, episodes=None, tests=None, order_by=None): return gmPathLab.get_test_results ( pk_patient = self.pk_patient, encounters = encounters, episodes = episodes, order_by = order_by ) #------------------------------------------------------------------ def get_test_results_by_date(self, encounter=None, episodes=None, tests=None, reverse_chronological=True): where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(tests)s)') args['tests'] = tests if encounter is not None: where_parts.append('pk_encounter = %(enc)s') args['enc'] = encounter if episodes is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = episodes cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY clin_when %s, pk_episode, unified_name """ % ( ' AND '.join(where_parts), gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) tests = [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ] return tests #------------------------------------------------------------------ def add_test_result(self, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None): try: epi = int(episode) except Exception: epi = episode['pk_episode'] try: type = int(type) except Exception: type = type['pk_test_type'] tr = gmPathLab.create_test_result ( link_obj = link_obj, encounter = self.current_encounter['pk_encounter'], episode = epi, type = type, intended_reviewer = intended_reviewer, val_num = val_num, val_alpha = val_alpha, unit = unit ) return tr #------------------------------------------------------------------ def get_labs_as_org_units(self): where = 'pk_org_unit IN (%s)' % """ SELECT DISTINCT fk_org_unit FROM clin.test_org WHERE pk IN ( SELECT DISTINCT pk_test_org FROM clin.v_test_results where pk_patient = %(pat)s )""" args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] #------------------------------------------------------------------ def _get_best_gfr_or_crea(self): measured_gfrs = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_gfr_quantity, max_no_of_results = 1) measured_gfr = measured_gfrs[0] if len(measured_gfrs) > 0 else None creas = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_creatinine_quantity, max_no_of_results = 1) crea = creas[0] if len(creas) > 0 else None if (measured_gfr is None) and (crea is None): return None if (measured_gfr is not None) and (crea is None): return measured_gfr # from here, Crea cannot be None anymore if measured_gfr is None: eGFR = self.calculator.eGFR if eGFR.numeric_value is None: return crea return eGFR # from here, measured_gfr cannot be None anymore, either two_weeks = pydt.timedelta(weeks = 2) gfr_too_old = (crea['clin_when'] - measured_gfr['clin_when']) > two_weeks if not gfr_too_old: return measured_gfr # from here, measured_gfr is considered too # old, so attempt a more timely estimate eGFR = self.calculator.eGFR if eGFR.numeric_value is None: # return crea since we cannot get a # better estimate for some reason return crea return eGFR best_gfr_or_crea = property(_get_best_gfr_or_crea) #------------------------------------------------------------------ def _get_bmi(self): return self.calculator.bmi bmi = property(_get_bmi) #------------------------------------------------------------------ def _get_dynamic_hints(self): return gmAutoHints.get_hints_for_patient(pk_identity = self.pk_patient, pk_encounter = self.current_encounter['pk_encounter']) dynamic_hints = property(_get_dynamic_hints) #------------------------------------------------------------------ #------------------------------------------------------------------ #------------------------------------------------------------------ #------------------------------------------------------------------Instance variables
var EDC-
Expand source code
def _get_EDC(self): cmd = 'SELECT edc FROM clin.patient WHERE fk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) if len(rows) == 0: return None return rows[0]['edc'] var EDC_is_fishy-
Expand source code
def _EDC_is_fishy(self): edc = self.EDC if edc is None: return False if self.gender != 'f': return True now = gmDateTime.pydt_now_here() # mother too young if (self.dob + pydt.timedelta(weeks = 5 * 52)) > now: return True # mother too old if (self.dob + pydt.timedelta(weeks = 55 * 52)) < now: return True # Beulah Hunter, 375 days (http://www.reference.com/motif/health/longest-human-pregnancy-on-record) # EDC too far in the future if (edc - pydt.timedelta(days = 380)) > now: return True # even if the pregnancy would have *started* when it # was documented to *end* it would be over by now by # all accounts # EDC too far in the past if edc < (now - pydt.timedelta(days = 380)): return True var abused_substances-
Expand source code
def _get_abused_substances(self, order_by=None): return self._get_current_substance_intakes ( include_inactive = True, order_by = order_by, episodes = None, issues = None, exclude_medications = True, exclude_potential_abuses = False ) var active_encounter-
Expand source code
def _get_current_encounter(self): return self.__encounter var allergy_state :Â cAllergyState-
Expand source code
def _get_allergy_state(self) -> gmAllergy.cAllergyState: return gmAllergy.get_allergy_state(pk_encounter = self.current_encounter['pk_encounter']) var best_gfr_or_crea-
Expand source code
def _get_best_gfr_or_crea(self): measured_gfrs = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_gfr_quantity, max_no_of_results = 1) measured_gfr = measured_gfrs[0] if len(measured_gfrs) > 0 else None creas = self.get_most_recent_results_in_loinc_group(loincs = gmLOINC.LOINC_creatinine_quantity, max_no_of_results = 1) crea = creas[0] if len(creas) > 0 else None if (measured_gfr is None) and (crea is None): return None if (measured_gfr is not None) and (crea is None): return measured_gfr # from here, Crea cannot be None anymore if measured_gfr is None: eGFR = self.calculator.eGFR if eGFR.numeric_value is None: return crea return eGFR # from here, measured_gfr cannot be None anymore, either two_weeks = pydt.timedelta(weeks = 2) gfr_too_old = (crea['clin_when'] - measured_gfr['clin_when']) > two_weeks if not gfr_too_old: return measured_gfr # from here, measured_gfr is considered too # old, so attempt a more timely estimate eGFR = self.calculator.eGFR if eGFR.numeric_value is None: # return crea since we cannot get a # better estimate for some reason return crea return eGFR var bmi-
Expand source code
def _get_bmi(self): return self.calculator.bmi var calculator-
Expand source code
def _get_calculator(self): if self.__calculator is None: from Gnumed.business.gmClinicalCalculator import cClinicalCalculator self.__calculator = cClinicalCalculator() from Gnumed.business.gmPerson import gmCurrentPatient curr_pat = gmCurrentPatient() if curr_pat.ID == self.pk_patient: self.__calculator.patient = curr_pat else: from Gnumed.business.gmPerson import cPatient self.__calculator.patient = cPatient(self.pk_patient) return self.__calculator var candidate_diagnoses-
Expand source code
def get_candidate_diagnoses(self): cmd = "SELECT * FROM clin.v_candidate_diagnoses WHERE pk_patient = %(pat)s" rows, idx = gmPG2.run_ro_queries ( queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = False ) return rows var current_encounter-
Expand source code
def _get_current_encounter(self): return self.__encounter var dob-
Expand source code
def _get_dob(self): if self.__dob is not None: return self.__dob cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) self.__gender = rows[0]['gender'] self.__dob = rows[0]['dob'] var dynamic_hints-
Expand source code
def _get_dynamic_hints(self): return gmAutoHints.get_hints_for_patient(pk_identity = self.pk_patient, pk_encounter = self.current_encounter['pk_encounter']) var earliest_care_date-
Expand source code
def get_earliest_care_date(self): args = {'pat': self.pk_patient} cmd = """ SELECT MIN(earliest) FROM ( ( SELECT MIN(episode_modified_when) AS earliest FROM clin.v_pat_episodes WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_health_issues WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.encounter WHERE fk_patient = %(pat)s ) UNION ALL ( SELECT MIN(started) AS earliest FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_items WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(last_confirmed) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) ) AS candidates""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows[0][0] var episodes-
Fetches from backend patient episodes.
id_list - Episodes' PKs list issues - Health issues' PKs list to filter episodes by open_status - return all (None) episodes, only open (True) or closed (False) one(s)
Expand source code
def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False): """Fetches from backend patient episodes. id_list - Episodes' PKs list issues - Health issues' PKs list to filter episodes by open_status - return all (None) episodes, only open (True) or closed (False) one(s) """ if (unlinked_only is True) and (issues is not None): raise ValueError('<unlinked_only> cannot be TRUE if <issues> is not None') if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by args = { 'pat': self.pk_patient, 'open': open_status } where_parts = ['pk_patient = %(pat)s'] if open_status is not None: where_parts.append('episode_open IS %(open)s') if unlinked_only: where_parts.append('pk_health_issue is NULL') if issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') args['issues'] = issues if id_list is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = id_list cmd = "SELECT * FROM clin.v_pat_episodes WHERE %s %s" % ( ' AND '.join(where_parts), order_by ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmEMRStructItems.cEpisode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_episode'}) for r in rows ] var external_care_items-
Expand source code
def get_external_care_items(self, order_by=None, exclude_inactive=False): return gmExternalCare.get_external_care_items ( pk_identity = self.pk_patient, order_by = order_by, exclude_inactive = exclude_inactive ) var first_encounter-
Retrieves first encounter for a particular issue and/or episode.
issue_id - First encounter associated health issue episode - First encounter associated episode
Expand source code
def get_first_encounter(self, issue_id=None, episode_id=None): """Retrieves first encounter for a particular issue and/or episode. issue_id - First encounter associated health issue episode - First encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] var gender-
Expand source code
def _get_gender(self): if self.__gender is not None: return self.__gender cmd = 'SELECT gender, dob FROM dem.v_all_persons WHERE pk_identity = %(pat)s' args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) self.__gender = rows[0]['gender'] self.__dob = rows[0]['dob'] var health_issues-
Expand source code
def get_health_issues(self, id_list = None): cmd = "SELECT *, xmin_health_issue FROM clin.v_health_issues WHERE pk_patient = %(pat)s ORDER BY description" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = True) issues = [ gmEMRStructItems.cHealthIssue(row = {'idx': idx, 'data': r, 'pk_field': 'pk_health_issue'}) for r in rows ] if id_list is None: return issues if len(id_list) == 0: raise ValueError('id_list to filter by is empty, most likely a programming error') filtered_issues = [] for issue in issues: if issue['pk_health_issue'] in id_list: filtered_issues.append(issue) return filtered_issues var hospital_stays-
Expand source code
def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False): stays = gmEMRStructItems.get_patient_hospital_stays(patient = self.pk_patient, ongoing_only = ongoing_only) if episodes is not None: stays = [ s for s in stays if s['pk_episode'] in episodes ] if issues is not None: stays = [ s for s in stays if s['pk_health_issue'] in issues ] return stays var last_but_one_encounter-
Expand source code
def get_last_but_one_encounter(self, issue_id=None, episode_id=None): args = {'pat': self.pk_patient} if (issue_id is None) and (episode_id is None): cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ORDER BY started DESC LIMIT 2 """ else: where_parts = [] if issue_id is not None: where_parts.append('pk_health_issue = %(issue)s') args['issue'] = issue_id if episode_id is not None: where_parts.append('pk_episode = %(epi)s') args['epi'] = episode_id cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %%(pat)s AND pk_encounter IN ( SELECT distinct pk_encounter FROM clin.v_narrative WHERE %s ) ORDER BY started DESC LIMIT 2 """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return None # just one encounter within the above limits if len(rows) == 1: # is it the current encounter ? if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: # yes return None # no return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) # more than one encounter if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: return gmEMRStructItems.cEncounter(row = {'data': rows[1], 'idx': idx, 'pk_field': 'pk_encounter'}) return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) var last_encounter-
Retrieves last encounter for a concrete issue and/or episode
issue_id - Last encounter associated health issue episode_id - Last encounter associated episode
Expand source code
def get_last_encounter(self, issue_id=None, episode_id=None): """Retrieves last encounter for a concrete issue and/or episode issue_id - Last encounter associated health issue episode_id - Last encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] var most_recent_care_date-
Expand source code
def get_most_recent_care_date(self): encounters = self.get_encounters(order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0]['last_affirmed'] var performed_procedures-
Expand source code
def get_performed_procedures(self, episodes=None, issues=None): procs = gmEMRStructItems.get_performed_procedures(patient = self.pk_patient) if episodes is not None: procs = [ p for p in procs if p['pk_episode'] in episodes ] if issues is not None: procs = [ p for p in procs if p['pk_health_issue'] in issues ] return procs var unlinked_episodes-
Expand source code
def get_unlinked_episodes(self, open_status=None, order_by=None): return self.get_episodes(open_status = open_status, order_by = order_by, unlinked_only = True) var vaccinations-
Expand source code
def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None): return gmVaccination.get_vaccinations ( pk_identity = self.pk_patient, pk_episodes = episodes, pk_health_issues = issues, pk_encounters = encounters, order_by = order_by, return_pks = False )
Methods
def add_allergy(self, allergene=None, allg_type=None, encounter_id=None, episode_id=None)-
Expand source code
def add_allergy(self, allergene=None, allg_type=None, encounter_id=None, episode_id=None): if encounter_id is None: encounter_id = self.current_encounter['pk_encounter'] if episode_id is None: issue = self.add_health_issue(issue_name = _('Allergies/Intolerances')) epi = self.add_episode(episode_name = _('Allergy detail: %s') % allergene, pk_health_issue = issue['pk_health_issue']) episode_id = epi['pk_episode'] new_allergy = gmAllergy.create_allergy ( allergene = allergene, allg_type = allg_type, encounter_id = encounter_id, episode_id = episode_id ) return new_allergy def add_clin_narrative(self, note='', soap_cat='s', episode=None, link_obj=None)-
Expand source code
def add_clin_narrative(self, note='', soap_cat='s', episode=None, link_obj=None): if note.strip() == '': _log.info('will not create empty clinical note') return None if isinstance(episode, gmEMRStructItems.cEpisode): episode = episode['pk_episode'] instance = gmClinNarrative.create_narrative_item ( link_obj = link_obj, narrative = note, soap_cat = soap_cat, episode_id = episode, encounter_id = self.current_encounter['pk_encounter'] ) return instance def add_episode(self, episode_name=None, pk_health_issue=None, is_open=False, allow_dupes=False, link_obj=None)-
Add episode 'episode_name' for a patient's health issue.
- silently returns if episode already exists
Expand source code
def add_episode(self, episode_name=None, pk_health_issue=None, is_open=False, allow_dupes=False, link_obj=None): """Add episode 'episode_name' for a patient's health issue. - silently returns if episode already exists """ episode = gmEMRStructItems.create_episode ( link_obj = link_obj, pk_health_issue = pk_health_issue, episode_name = episode_name, is_open = is_open, encounter = self.current_encounter['pk_encounter'], allow_dupes = allow_dupes ) return episode def add_family_history(self, episode=None, condition=None, relation=None)-
Expand source code
def add_family_history(self, episode=None, condition=None, relation=None): return gmFamilyHistory.create_family_history ( encounter = self.current_encounter['pk_encounter'], episode = episode, condition = condition, relation = relation ) def add_health_issue(self, issue_name=None)-
Adds patient health issue.
Expand source code
def add_health_issue(self, issue_name=None): """Adds patient health issue.""" return gmEMRStructItems.create_health_issue ( description = issue_name, encounter = self.current_encounter['pk_encounter'], patient = self.pk_patient ) def add_hospital_stay(self, episode=None, fk_org_unit=None)-
Expand source code
def add_hospital_stay(self, episode=None, fk_org_unit=None): return gmEMRStructItems.create_hospital_stay ( encounter = self.current_encounter['pk_encounter'], episode = episode, fk_org_unit = fk_org_unit ) def add_notes(self, notes=None, episode=None, encounter=None)-
Expand source code
def add_notes(self, notes=None, episode=None, encounter=None): enc = gmTools.coalesce ( encounter, self.current_encounter['pk_encounter'] ) for note in notes: gmClinNarrative.create_narrative_item ( narrative = note[1], soap_cat = note[0], episode_id = episode, encounter_id = enc ) return True def add_performed_procedure(self, episode=None, location=None, hospital_stay=None, procedure=None)-
Expand source code
def add_performed_procedure(self, episode=None, location=None, hospital_stay=None, procedure=None): return gmEMRStructItems.create_performed_procedure ( encounter = self.current_encounter['pk_encounter'], episode = episode, location = location, hospital_stay = hospital_stay, procedure = procedure ) def add_substance_intake(self, pk_component=None, pk_episode=None, pk_drug_product=None, pk_health_issue=None)-
Expand source code
def add_substance_intake(self, pk_component=None, pk_episode=None, pk_drug_product=None, pk_health_issue=None): pk_enc = self.current_encounter['pk_encounter'] if pk_episode is None: pk_episode = gmMedication.create_default_medication_history_episode ( pk_health_issue = pk_health_issue, encounter = pk_enc ) return gmMedication.create_substance_intake ( pk_component = pk_component, pk_encounter = pk_enc, pk_episode = pk_episode, pk_drug_product = pk_drug_product ) def add_test_result(self, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None)-
Expand source code
def add_test_result(self, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None): try: epi = int(episode) except Exception: epi = episode['pk_episode'] try: type = int(type) except Exception: type = type['pk_test_type'] tr = gmPathLab.create_test_result ( link_obj = link_obj, encounter = self.current_encounter['pk_encounter'], episode = epi, type = type, intended_reviewer = intended_reviewer, val_num = val_num, val_alpha = val_alpha, unit = unit ) return tr def add_vaccination(self, episode=None, vaccine=None, batch_no=None)-
Expand source code
def add_vaccination(self, episode=None, vaccine=None, batch_no=None): return gmVaccination.create_vaccination ( encounter = self.current_encounter['pk_encounter'], episode = episode, vaccine = vaccine, batch_no = batch_no ) def cleanup(self)-
Expand source code
def cleanup(self): _log.debug('cleaning up after clinical record for patient [%s]' % self.pk_patient) if self.__encounter is not None: self.__encounter.unlock(exclusive = False) return True def db_modification_callback(self, **kwds)-
Expand source code
def db_modification_callback(self, **kwds): if kwds['table'] != 'clin.encounter': return True if self.current_encounter is None: _log.debug('locally no encounter current, ignoring encounter modification signal') return True if int(kwds['pk_of_row']) != self.current_encounter['pk_encounter']: _log.debug('DB reported modification of encounter: #%s', kwds['pk_of_row']) _log.debug('our locally active encounter is: #%s', self.current_encounter['pk_encounter']) _log.debug('modified encounter != our encounter, ignoring') return True _log.debug('remote modification of our encounter signalled (local: #%s, remote: #%s)', self.current_encounter['pk_encounter'], kwds['pk_of_row']) # did someone delete the current encounter from under our feet ? if kwds['operation'] == 'DELETE': _log.error('local encounter has been DELETEd remotely, trying to get now-active encounter from database') if self.current_encounter.is_modified(): _log.error('local encounter instance has .is_modified()=True, losing local changes') _log.error('this hints at an error in .is_modified handling') # dirty fix: get now-active encounter self.current_encounter.unlock(exclusive = False) self.__encounter = None self.__setup_active_encounter() gmDispatcher.send('current_encounter_switched') return True # get the current encounter as an extra instance # from the database to check for changes curr_enc_in_db = gmEMRStructItems.cEncounter(aPK_obj = self.current_encounter['pk_encounter']) # the encounter just retrieved and the active encounter # have got the same transaction ID so there's no change # in the database, there could be a local change in # the active encounter but that doesn't matter because # no one else can have written to the DB so far (XMIN match) if curr_enc_in_db['xmin_encounter'] == self.current_encounter['xmin_encounter']: _log.debug('in-client and in-DB instance of encounter #%s have matching XMINs (%s), DB has NOT been written to since we last loaded the encounter, checking:', self.current_encounter['pk_encounter'], self.current_encounter['xmin_encounter']) if self.current_encounter.is_modified(): _log.error('encounter modification signalled from DB, with same XMIN as in local in-client instance of encounter, BUT local instance ALSO has .is_modified()=True') _log.error('this may hint at an error with .is_modified handling') gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB') # here we might want to ask the user for advice on how to proceed else: _log.debug('locally not flagged as modified') return True # there must have been a change to the active encounter # committed to the database from elsewhere (different XMIN), # we must deny to propagate the change, however, if # there are pending local changes, or, rather, we should ask # the user for advice if self.current_encounter.is_modified(): gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'signalled enc loaded from DB') raise ValueError('unsaved changes in locally active encounter [%s], cannot switch to DB state of encounter [%s]' % ( self.current_encounter['pk_encounter'], curr_enc_in_db['pk_encounter'] )) # don't do this, because same_payload() does not compare _all_ # fields so we can get into a reality disconnect if we # don't announce the modification # if self.current_encounter.same_payload(another_object = curr_enc_in_db): # _log.debug('clin.encounter_mod_db received but no change to active encounter payload') # return True # there was a change in the database from elsewhere; # locally, however, we don't have any pending changes; # therefore we can propagate the remote change locally # without losing anything; # this really should be the standard case gmTools.compare_dict_likes(self.current_encounter.fields_as_dict(), curr_enc_in_db.fields_as_dict(), 'modified enc in client', 'enc loaded from DB') _log.debug('active encounter modified remotely, no locally pending changes, reloading from DB and locally announcing the remote modification') self.current_encounter.refetch_payload() gmDispatcher.send('current_encounter_modified') return True def delete_allergy(self, pk_allergy=None)-
Expand source code
def delete_allergy(self, pk_allergy=None): cmd = 'delete FROM clin.allergy WHERE pk=%(pk_allg)s' args = {'pk_allg': pk_allergy} gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) def ensure_has_allergy_state(self) ‑> cAllergyState-
Expand source code
def ensure_has_allergy_state(self) -> gmAllergy.cAllergyState: return gmAllergy.ensure_has_allergy_state(encounter = self.current_encounter['pk_encounter']) def episode2problem(self, episode=None)-
Expand source code
def episode2problem(self, episode=None): return gmEMRStructItems.episode2problem(episode=episode) def format_as_journal(self, left_margin=0, patient=None)-
Expand source code
def format_as_journal(self, left_margin=0, patient=None): txt = '' for enc in self.get_encounters(skip_empty = True): txt += gmTools.u_box_horiz_4dashes * 70 + '\n' txt += enc.format ( episodes = None, # means: each touched upon left_margin = left_margin, patient = patient, fancy_header = False, with_soap = True, with_docs = True, with_tests = True, with_vaccinations = True, with_co_encountlet_hints = False, # irrelevant with_rfe_aoe = True, with_family_history = True, by_episode = True ) return txt def format_statistics(self)-
Expand source code
def format_statistics(self): return _( 'Medical problems: %(problems)s\n' 'Total encounters: %(encounters)s\n' 'Total EMR entries: %(items)s\n' 'Active medications: %(active_drugs)s\n' 'Documents: %(documents)s\n' 'Test results: %(results)s\n' 'Hospitalizations: %(stays)s\n' 'Procedures: %(procedures)s\n' 'Vaccinations: %(vaccinations)s' ) % self.get_statistics() def format_summary(self) ‑> str-
Expand source code
def format_summary(self) -> str: cmd = "SELECT dob FROM dem.v_all_persons WHERE pk_identity = %(pk)s" args = {'pk': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) dob = rows[0]['dob'] stats = self.get_statistics() first = self.get_first_encounter() last = self.get_last_encounter() probs = self.get_problems() txt = '' if len(probs) > 0: txt += _(' %s known problems, clinically relevant thereof:\n') % stats['problems'] else: txt += _(' %s known problems\n') % stats['problems'] for prob in probs: if not prob['clinically_relevant']: continue txt += ' \u00BB%s\u00AB (%s)\n' % ( prob['problem'], gmTools.bool2subst(prob['problem_active'], _('active'), _('inactive')) ) txt += '\n' txt += _(' %s encounters from %s to %s\n') % ( stats['encounters'], gmDateTime.pydt_strftime(first['started'], '%Y %b %d'), gmDateTime.pydt_strftime(last['started'], '%Y %b %d') ) txt += _(' %s active medications\n') % stats['active_drugs'] txt += _(' %s documents\n') % stats['documents'] txt += _(' %s test results\n') % stats['results'] txt += _(' %s hospitalizations') % stats['stays'] if stats['stays'] == 0: txt += '\n' else: txt += _(', most recently:\n%s\n') % self.get_latest_hospital_stay().format(left_margin = 3) # FIXME: perhaps only count "ongoing ones" txt += _(' %s performed procedures') % stats['procedures'] if stats['procedures'] == 0: txt += '\n' else: txt += _(', most recently:\n%s\n') % self.get_latest_performed_procedure().format(left_margin = 3) txt += '\n' txt += _('Allergies and Intolerances\n') allg_state = self.allergy_state txt += ' ' if allg_state: txt += allg_state.state_string if allg_state['last_confirmed']: txt += _(' (last confirmed %s)') % gmDateTime.pydt_strftime(allg_state['last_confirmed'], '%Y %b %d') txt += '\n' txt += gmTools.coalesce(allg_state['comment'], '', ' %s\n') else: txt += _('allergy state not acquired') txt += '\n' for allg in self.get_allergies(): txt += ' %s: %s\n' % ( allg['descriptor'], gmTools.coalesce(allg['reaction'], _('unknown reaction')) ) meds = self.get_current_medications(order_by = 'substance') if len(meds) > 0: txt += '\n' txt += _('Medications and Substances') txt += '\n' for m in meds: txt += '%s\n' % m.format_as_single_line(left_margin = 1) fhx = self.get_family_history() if len(fhx) > 0: txt += '\n' txt += _('Family History') txt += '\n' for f in fhx: txt += '%s\n' % f.format(left_margin = 1) jobs = get_occupations(pk_identity = self.pk_patient) if len(jobs) > 0: txt += '\n' txt += _('Occupations') txt += '\n' for job in jobs: txt += ' %s%s\n' % ( job['l10n_occupation'], gmTools.coalesce(job['activities'], '', ': %s') ) vaccs = self.get_latest_vaccinations() if len(vaccs) > 0: txt += '\n' txt += _('Vaccinations') txt += '\n' inds = sorted(vaccs) for ind in inds: ind_count, vacc = vaccs[ind] if dob is None: age_given = '' else: age_given = ' @ %s' % gmDateTime.format_apparent_age_medically(gmDateTime.calculate_apparent_age ( start = dob, end = vacc['date_given'] )) since = _('%s ago') % gmDateTime.format_interval_medically(vacc['interval_since_given']) txt += ' %s (%s%s): %s%s (%s %s%s%s)\n' % ( ind, gmTools.u_sum, ind_count, #gmDateTime.pydt_strftime(vacc['date_given'], '%b %Y'), since, age_given, vacc['vaccine'], gmTools.u_left_double_angle_quote, vacc['batch_no'], gmTools.u_right_double_angle_quote ) care = self.get_external_care_items(order_by = 'issue, organization, unit, provider', exclude_inactive = True) if len(care) > 0: txt += '\n' txt += _('External care') txt += '\n' for item in care: txt += ' %s: %s\n' % ( item['issue'], gmTools.coalesce ( item['provider'], '%s@%s' % (item['unit'], item['organization']), '%%s (%s@%s)' % (item['unit'], item['organization']) ) ) return txt def get_allergies(self, remove_sensitivities=False, since=None, until=None, encounters=None, episodes=None, issues=None, ID_list=None)-
Retrieves patient allergy items.
remove_sensitivities - retrieve real allergies only, without sensitivities since - initial date for allergy items until - final date for allergy items encounters - list of encounters whose allergies are to be retrieved episodes - list of episodes whose allergies are to be retrieved issues - list of health issues whose allergies are to be retrieved
Expand source code
def get_allergies(self, remove_sensitivities=False, since=None, until=None, encounters=None, episodes=None, issues=None, ID_list=None): """Retrieves patient allergy items. remove_sensitivities - retrieve real allergies only, without sensitivities since - initial date for allergy items until - final date for allergy items encounters - list of encounters whose allergies are to be retrieved episodes - list of episodes whose allergies are to be retrieved issues - list of health issues whose allergies are to be retrieved """ cmd = "SELECT * FROM clin.v_pat_allergies WHERE pk_patient=%s order by descriptor" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': [self.pk_patient]}], get_col_idx = True) filtered_allergies = [] for r in rows: filtered_allergies.append(gmAllergy.cAllergy(row = {'data': r, 'idx': idx, 'pk_field': 'pk_allergy'})) # ok, let's constrain our list if ID_list is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_allergy'] in ID_list ] if len(filtered_allergies) == 0: _log.error('no allergies of list [%s] found for patient [%s]' % (str(ID_list), self.pk_patient)) # better fail here contrary to what we do elsewhere return None else: return filtered_allergies if remove_sensitivities: filtered_allergies = [ allg for allg in filtered_allergies if allg['type'] == 'allergy' ] if since is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] >= since ] if until is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['date'] < until ] if issues is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_health_issue'] in issues ] if episodes is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_episode'] in episodes ] if encounters is not None: filtered_allergies = [ allg for allg in filtered_allergies if allg['pk_encounter'] in encounters ] return filtered_allergies def get_as_journal(self, since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None)-
Expand source code
def get_as_journal(self, since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None): return gmClinNarrative.get_as_journal ( patient = self.pk_patient, since = since, until = until, encounters = encounters, episodes = episodes, issues = issues, soap_cats = soap_cats, providers = providers, order_by = order_by, time_range = time_range, active_encounter = self.active_encounter ) def get_attended_hospitals_as_org_units(self)-
Expand source code
def get_attended_hospitals_as_org_units(self): where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s)' args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] def get_candidate_diagnoses(self)-
Expand source code
def get_candidate_diagnoses(self): cmd = "SELECT * FROM clin.v_candidate_diagnoses WHERE pk_patient = %(pat)s" rows, idx = gmPG2.run_ro_queries ( queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = False ) return rows def get_clin_narrative(self, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None)-
Get SOAP notes pertinent to this encounter.
encounters - list of encounters the narrative of which are to be retrieved episodes - list of episodes the narrative of which are to be retrieved issues - list of health issues the narrative of which are to be retrieved soap_cats - list of SOAP categories of the narrative to be retrieved
Expand source code
def get_clin_narrative(self, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None): """Get SOAP notes pertinent to this encounter. encounters - list of encounters the narrative of which are to be retrieved episodes - list of episodes the narrative of which are to be retrieved issues - list of health issues the narrative of which are to be retrieved soap_cats - list of SOAP categories of the narrative to be retrieved """ where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') if len(issues) == 0: args['issues'] = [] else: if isinstance(issues[0], gmEMRStructItems.cHealthIssue): args['issues'] = [ i['pk_health_issue'] for i in issues ] elif isinstance(issues[0], int): args['issues'] = issues else: raise ValueError('<issues> must be list of type int (=pk) or cHealthIssue, but 1st issue is: %s' % issues[0]) if episodes is not None: where_parts.append('pk_episode = ANY(%(epis)s)') if len(episodes) == 0: args['epis'] = [] else: if isinstance(episodes[0], gmEMRStructItems.cEpisode): args['epis'] = [ e['pk_episode'] for e in episodes ] elif isinstance(episodes[0], int): args['epis'] = episodes else: raise ValueError('<episodes> must be list of type int (=pk) or cEpisode, but 1st episode is: %s' % episodes[0]) if encounters is not None: where_parts.append('pk_encounter = ANY(%(encs)s)') if len(encounters) == 0: args['encs'] = [] else: if isinstance(encounters[0], gmEMRStructItems.cEncounter): args['encs'] = [ e['pk_encounter'] for e in encounters ] elif isinstance(encounters[0], int): args['encs'] = encounters else: raise ValueError('<encounters> must be list of type int (=pk) or cEncounter, but 1st encounter is: %s' % encounters[0]) if soap_cats is not None: where_parts.append('c_vn.soap_cat = ANY(%(cats)s)') args['cats'] = gmSoapDefs.soap_cats_str2list(soap_cats) if providers is not None: where_parts.append('c_vn.modified_by = ANY(%(docs)s)') args['docs'] = providers cmd = """ SELECT c_vn.*, c_scr.rank AS soap_rank FROM clin.v_narrative c_vn LEFT JOIN clin.soap_cat_ranks c_scr on c_vn.soap_cat = c_scr.soap_cat WHERE %s ORDER BY date, soap_rank """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmClinNarrative.cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ] def get_current_medications(self, include_inactive=True, order_by=None, episodes=None, issues=None)-
Expand source code
def get_current_medications(self, include_inactive=True, order_by=None, episodes=None, issues=None): return self._get_current_substance_intakes ( include_inactive = include_inactive, order_by = order_by, episodes = episodes, issues = issues, exclude_medications = False, exclude_potential_abuses = True ) def get_dates_for_results(self, tests=None, reverse_chronological=True)-
Get the dates for which we have results.
Expand source code
def get_dates_for_results(self, tests=None, reverse_chronological=True): """Get the dates for which we have results.""" where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(epi_pks)s)') args['tests'] = tests cmd = """ SELECT DISTINCT ON (clin_when_day) clin_when_day, is_reviewed FROM ( SELECT date_trunc('day', clin_when) AS clin_when_day, bool_and(reviewed) AS is_reviewed FROM ( SELECT clin_when, reviewed, pk_patient, pk_test_result FROM clin.v_test_results WHERE %s ) AS patient_tests GROUP BY clin_when_day ) AS grouped_days ORDER BY clin_when_day %s """ % ( ' AND '.join(where_parts), gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows def get_earliest_care_date(self)-
Expand source code
def get_earliest_care_date(self): args = {'pat': self.pk_patient} cmd = """ SELECT MIN(earliest) FROM ( ( SELECT MIN(episode_modified_when) AS earliest FROM clin.v_pat_episodes WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_health_issues WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.encounter WHERE fk_patient = %(pat)s ) UNION ALL ( SELECT MIN(started) AS earliest FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_items WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(modified_when) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) UNION ALL ( SELECT MIN(last_confirmed) AS earliest FROM clin.v_pat_allergy_state WHERE pk_patient = %(pat)s ) ) AS candidates""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows[0][0] def get_encounter_stats_by_type(self, cover_period=None)-
Expand source code
def get_encounter_stats_by_type(self, cover_period=None): args = {'pat': self.pk_patient, 'range': cover_period} where_parts = ['pk_patient = %(pat)s'] if cover_period is not None: where_parts.append('last_affirmed > now() - %(range)s') cmd = """ SELECT l10n_type, COUNT(*) AS frequency FROM clin.v_pat_encounters WHERE %s GROUP BY l10n_type ORDER BY frequency DESC """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows def get_encounters(self, since=None, until=None, id_list=None, episodes=None, issues=None, skip_empty=False, order_by=None, max_encounters=None)-
Retrieves patient's encounters.
id_list - PKs of encounters to fetch since - initial date for encounter items, DateTime instance until - final date for encounter items, DateTime instance episodes - PKs of the episodes the encounters belong to (many-to-many relation) issues - PKs of the health issues the encounters belong to (many-to-many relation) skip_empty - do NOT return those which do not have any of documents/clinical items/RFE/AOE
NOTE: if you specify both issues and episodes you will get the aggregate of all encounters even if the episodes all belong to the health issues listed. IOW, the issues broaden the episode list rather than the episode list narrowing the episodes-from-issues list. Rationale: If it was the other way round it would be redundant to specify the list of issues at all.
Expand source code
def get_encounters(self, since=None, until=None, id_list=None, episodes=None, issues=None, skip_empty=False, order_by=None, max_encounters=None): """Retrieves patient's encounters. id_list - PKs of encounters to fetch since - initial date for encounter items, DateTime instance until - final date for encounter items, DateTime instance episodes - PKs of the episodes the encounters belong to (many-to-many relation) issues - PKs of the health issues the encounters belong to (many-to-many relation) skip_empty - do NOT return those which do not have any of documents/clinical items/RFE/AOE NOTE: if you specify *both* issues and episodes you will get the *aggregate* of all encounters even if the episodes all belong to the health issues listed. IOW, the issues broaden the episode list rather than the episode list narrowing the episodes-from-issues list. Rationale: If it was the other way round it would be redundant to specify the list of issues at all. """ # if issues are given, translate them to their episodes if (issues is not None) and (len(issues) > 0): # - find episodes corresponding to the health issues in question cmd = "SELECT distinct pk_episode FROM clin.v_pat_episodes WHERE pk_health_issue = ANY(%(issue_pks)s) AND pk_patient = %(pat)s" args = {'issue_pks': issues, 'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) epis4issues_pks = [ r['pk_episode'] for r in rows ] if episodes is None: episodes = [] episodes.extend(epis4issues_pks) if (episodes is not None) and (len(episodes) > 0): # since the episodes to filter by belong to the patient in question so will # the encounters found with them - hence we don't need a WHERE on the patient ... # but, better safe than sorry ... args = {'epi_pks': episodes, 'pat': self.pk_patient} cmd = "SELECT DISTINCT fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter = ANY(SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) encs4epis_pks = [ r['fk_encounter'] for r in rows ] if id_list is None: id_list = [] id_list.extend(encs4epis_pks) where_parts = ['c_vpe.pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if skip_empty: where_parts.append("""NOT ( gm.is_null_or_blank_string(c_vpe.reason_for_encounter) AND gm.is_null_or_blank_string(c_vpe.assessment_of_encounter) AND NOT EXISTS ( SELECT 1 FROM clin.v_pat_items c_vpi WHERE c_vpi.pk_patient = %(pat)s AND c_vpi.pk_encounter = c_vpe.pk_encounter UNION ALL SELECT 1 FROM blobs.v_doc_med b_vdm WHERE b_vdm.pk_patient = %(pat)s AND b_vdm.pk_encounter = c_vpe.pk_encounter ))""") if since is not None: where_parts.append('c_vpe.started >= %(start)s') args['start'] = since if until is not None: where_parts.append('c_vpe.last_affirmed <= %(end)s') args['end'] = since if (id_list is not None) and (len(id_list) > 0): where_parts.append('c_vpe.pk_encounter = ANY(%(enc_pks)s)') args['enc_pks'] = id_list if order_by is None: order_by = 'c_vpe.started' if max_encounters is None: limit = '' else: limit = 'LIMIT %s' % max_encounters cmd = """ SELECT * FROM clin.v_pat_encounters c_vpe WHERE %s ORDER BY %s %s """ % ( ' AND '.join(where_parts), order_by, limit ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) encounters = [ gmEMRStructItems.cEncounter(row = {'data': r, 'idx': idx, 'pk_field': 'pk_encounter'}) for r in rows ] # we've got the encounters, start filtering filtered_encounters = [] filtered_encounters.extend(encounters) if (episodes is not None) and (len(episodes) > 0): # since the episodes to filter by belong to the patient in question so will # the encounters found with them - hence we don't need a WHERE on the patient ... # but, better safe than sorry ... args = {'epi_pks': episodes, 'pat': self.pk_patient} cmd = "SELECT distinct fk_encounter FROM clin.clin_root_item WHERE fk_episode = ANY(%(epi_pks)s) AND fk_encounter IN (SELECT pk FROM clin.encounter WHERE fk_patient = %(pat)s)" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) encs4epis_pks = [ r['fk_encounter'] for r in rows ] filtered_encounters = [ enc for enc in filtered_encounters if enc['pk_encounter'] in encs4epis_pks ] return filtered_encounters def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False)-
Fetches from backend patient episodes.
id_list - Episodes' PKs list issues - Health issues' PKs list to filter episodes by open_status - return all (None) episodes, only open (True) or closed (False) one(s)
Expand source code
def get_episodes(self, id_list=None, issues=None, open_status=None, order_by=None, unlinked_only=False): """Fetches from backend patient episodes. id_list - Episodes' PKs list issues - Health issues' PKs list to filter episodes by open_status - return all (None) episodes, only open (True) or closed (False) one(s) """ if (unlinked_only is True) and (issues is not None): raise ValueError('<unlinked_only> cannot be TRUE if <issues> is not None') if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by args = { 'pat': self.pk_patient, 'open': open_status } where_parts = ['pk_patient = %(pat)s'] if open_status is not None: where_parts.append('episode_open IS %(open)s') if unlinked_only: where_parts.append('pk_health_issue is NULL') if issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') args['issues'] = issues if id_list is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = id_list cmd = "SELECT * FROM clin.v_pat_episodes WHERE %s %s" % ( ' AND '.join(where_parts), order_by ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmEMRStructItems.cEpisode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_episode'}) for r in rows ] def get_episodes_by_encounter(self, pk_encounter=None)-
Expand source code
def get_episodes_by_encounter(self, pk_encounter=None): cmd = """SELECT distinct pk_episode from clin.v_pat_items WHERE pk_encounter=%(enc)s and pk_patient=%(pat)s""" args = { 'enc': gmTools.coalesce(pk_encounter, self.current_encounter['pk_encounter']), 'pat': self.pk_patient } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return [] epis = [] for row in rows: epis.append(row[0]) return self.get_episodes(id_list=epis) def get_external_care_items(self, order_by=None, exclude_inactive=False)-
Expand source code
def get_external_care_items(self, order_by=None, exclude_inactive=False): return gmExternalCare.get_external_care_items ( pk_identity = self.pk_patient, order_by = order_by, exclude_inactive = exclude_inactive ) def get_family_history(self, episodes=None, issues=None, encounters=None)-
Expand source code
def get_family_history(self, episodes=None, issues=None, encounters=None): fhx = gmFamilyHistory.get_family_history ( order_by = 'l10n_relation, condition', patient = self.pk_patient ) if episodes is not None: fhx = [ f for f in fhx if f['pk_episode'] in episodes ] if issues is not None: fhx = [ f for f in fhx if f['pk_health_issue'] in issues ] if encounters is not None: fhx = [ f for f in fhx if f['pk_encounter'] in encounters ] return fhx def get_first_encounter(self, issue_id=None, episode_id=None)-
Retrieves first encounter for a particular issue and/or episode.
issue_id - First encounter associated health issue episode - First encounter associated episode
Expand source code
def get_first_encounter(self, issue_id=None, episode_id=None): """Retrieves first encounter for a particular issue and/or episode. issue_id - First encounter associated health issue episode - First encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] def get_generic_emr_items(self, pk_encounters=None, pk_episodes=None, pk_health_issues=None, use_active_encounter=False, order_by=None)-
Expand source code
def get_generic_emr_items(self, pk_encounters=None, pk_episodes=None, pk_health_issues=None, use_active_encounter=False, order_by=None): if use_active_encounter: active_encounter = self.active_encounter else: active_encounter = None return gmGenericEMRItem.get_generic_emr_items ( patient = self.pk_patient, encounters = pk_encounters, episodes = pk_episodes, issues = pk_health_issues, active_encounter = active_encounter, order_by = order_by ) def get_health_issues(self, id_list=None)-
Expand source code
def get_health_issues(self, id_list = None): cmd = "SELECT *, xmin_health_issue FROM clin.v_health_issues WHERE pk_patient = %(pat)s ORDER BY description" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient}}], get_col_idx = True) issues = [ gmEMRStructItems.cHealthIssue(row = {'idx': idx, 'data': r, 'pk_field': 'pk_health_issue'}) for r in rows ] if id_list is None: return issues if len(id_list) == 0: raise ValueError('id_list to filter by is empty, most likely a programming error') filtered_issues = [] for issue in issues: if issue['pk_health_issue'] in id_list: filtered_issues.append(issue) return filtered_issues def get_hospital_stay_stats_by_hospital(self, cover_period=None)-
Expand source code
def get_hospital_stay_stats_by_hospital(self, cover_period=None): args = {'pat': self.pk_patient, 'range': cover_period} where_parts = ['pk_patient = %(pat)s'] if cover_period is not None: where_parts.append('discharge > (now() - %(range)s)') cmd = """ SELECT hospital, COUNT(*) AS frequency FROM clin.v_hospital_stays WHERE %s GROUP BY hospital ORDER BY frequency DESC """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return rows def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False)-
Expand source code
def get_hospital_stays(self, episodes=None, issues=None, ongoing_only=False): stays = gmEMRStructItems.get_patient_hospital_stays(patient = self.pk_patient, ongoing_only = ongoing_only) if episodes is not None: stays = [ s for s in stays if s['pk_episode'] in episodes ] if issues is not None: stays = [ s for s in stays if s['pk_health_issue'] in issues ] return stays def get_issues_or_episodes_for_results(self, tests=None)-
Get the issues/episodes for which we have results.
Expand source code
def get_issues_or_episodes_for_results(self, tests=None): """Get the issues/episodes for which we have results.""" where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(tests)s)') args['tests'] = tests where = ' AND '.join(where_parts) cmd = """ SELECT * FROM (( -- issues, each including all it"s episodes SELECT health_issue AS problem, pk_health_issue, NULL::integer AS pk_episode, 1 AS rank FROM clin.v_test_results WHERE pk_health_issue IS NOT NULL AND %s GROUP BY pk_health_issue, problem ) UNION ALL ( -- episodes w/o issue SELECT episode AS problem, NULL::integer AS pk_health_issue, pk_episode, 2 AS rank FROM clin.v_test_results WHERE pk_health_issue IS NULL AND %s GROUP BY pk_episode, problem )) AS grouped_union ORDER BY rank, problem """ % (where, where) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) return rows def get_labs_as_org_units(self)-
Expand source code
def get_labs_as_org_units(self): where = 'pk_org_unit IN (%s)' % """ SELECT DISTINCT fk_org_unit FROM clin.test_org WHERE pk IN ( SELECT DISTINCT pk_test_org FROM clin.v_test_results where pk_patient = %(pat)s )""" args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] def get_last_but_one_encounter(self, issue_id=None, episode_id=None)-
Expand source code
def get_last_but_one_encounter(self, issue_id=None, episode_id=None): args = {'pat': self.pk_patient} if (issue_id is None) and (episode_id is None): cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %(pat)s ORDER BY started DESC LIMIT 2 """ else: where_parts = [] if issue_id is not None: where_parts.append('pk_health_issue = %(issue)s') args['issue'] = issue_id if episode_id is not None: where_parts.append('pk_episode = %(epi)s') args['epi'] = episode_id cmd = """ SELECT * FROM clin.v_pat_encounters WHERE pk_patient = %%(pat)s AND pk_encounter IN ( SELECT distinct pk_encounter FROM clin.v_narrative WHERE %s ) ORDER BY started DESC LIMIT 2 """ % ' AND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return None # just one encounter within the above limits if len(rows) == 1: # is it the current encounter ? if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: # yes return None # no return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) # more than one encounter if rows[0]['pk_encounter'] == self.current_encounter['pk_encounter']: return gmEMRStructItems.cEncounter(row = {'data': rows[1], 'idx': idx, 'pk_field': 'pk_encounter'}) return gmEMRStructItems.cEncounter(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_encounter'}) def get_last_encounter(self, issue_id=None, episode_id=None)-
Retrieves last encounter for a concrete issue and/or episode
issue_id - Last encounter associated health issue episode_id - Last encounter associated episode
Expand source code
def get_last_encounter(self, issue_id=None, episode_id=None): """Retrieves last encounter for a concrete issue and/or episode issue_id - Last encounter associated health issue episode_id - Last encounter associated episode """ if issue_id is None: issues = None else: issues = [issue_id] if episode_id is None: episodes = None else: episodes = [episode_id] encounters = self.get_encounters(issues = issues, episodes = episodes, order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0] def get_latest_hospital_stay(self)-
Expand source code
def get_latest_hospital_stay(self): return gmEMRStructItems.get_latest_patient_hospital_stay(patient = self.pk_patient) def get_latest_performed_procedure(self)-
Expand source code
def get_latest_performed_procedure(self): return gmEMRStructItems.get_latest_performed_procedure(patient = self.pk_patient) def get_latest_vaccinations(self, episodes=None, issues=None, atc_indications=None)-
Returns latest given vaccination for each vaccinated indication.
as a dict {'l10n_indication': cVaccination instance}
Note that this will produce duplicate vaccination instances on combi-indication vaccines !
Expand source code
def get_latest_vaccinations(self, episodes=None, issues=None, atc_indications=None): """Returns latest given vaccination for each vaccinated indication. as a dict {'l10n_indication': cVaccination instance} Note that this will produce duplicate vaccination instances on combi-indication vaccines ! """ args = {'pat': self.pk_patient} where_parts = ['c_v_shots.pk_patient = %(pat)s'] if (episodes is not None) and (len(episodes) > 0): where_parts.append('c_v_shots.pk_episode = ANY(%(epis)s)') args['epis'] = episodes if (issues is not None) and (len(issues) > 0): where_parts.append('c_v_shots.pk_episode = ANY(SELECT pk FROM clin.episode WHERE fk_health_issue = ANY(%(issues)s))') args['issues'] = issues if (atc_indications is not None) and (len(atc_indications) > 0): where_parts.append('c_v_plv4i.atc_indication = ANY(%(atc_inds)s)') args['atc_inds'] = atc_indications # find the shots cmd = """ SELECT c_v_shots.*, c_v_plv4i.l10n_indication, c_v_plv4i.no_of_shots FROM clin.v_vaccinations c_v_shots JOIN clin.v_pat_last_vacc4indication c_v_plv4i ON (c_v_shots.pk_vaccination = c_v_plv4i.pk_vaccination) WHERE %s """ % '\nAND '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) # none found if len(rows) == 0: return {} # turn them into vaccinations # (idx is constant) vaccs = {} for shot_row in rows: vaccs[shot_row['l10n_indication']] = ( shot_row['no_of_shots'], gmVaccination.cVaccination(row = {'idx': idx, 'data': shot_row, 'pk_field': 'pk_vaccination'}) ) return vaccs def get_most_recent_care_date(self)-
Expand source code
def get_most_recent_care_date(self): encounters = self.get_encounters(order_by = 'started DESC', max_encounters = 1) if len(encounters) == 0: return None return encounters[0]['last_affirmed'] def get_most_recent_episode(self, issue=None)-
Expand source code
def get_most_recent_episode(self, issue=None): # try to find the episode with the most recently modified clinical item issue_where = gmTools.coalesce ( value2test = issue, return_instead = '', value2return = 'and pk_health_issue = %(issue)s' ) cmd = """ SELECT pk from clin.episode WHERE pk = ( SELECT distinct on(pk_episode) pk_episode from clin.v_pat_items WHERE pk_patient = %%(pat)s and modified_when = ( SELECT max(vpi.modified_when) from clin.v_pat_items vpi WHERE vpi.pk_patient = %%(pat)s ) %s -- guard against several episodes created at the same moment of time limit 1 )""" % issue_where rows, idx = gmPG2.run_ro_queries(queries = [ {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} ]) if len(rows) != 0: return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) # no clinical items recorded, so try to find # the youngest episode for this patient cmd = """ SELECT vpe0.pk_episode from clin.v_pat_episodes vpe0 WHERE vpe0.pk_patient = %%(pat)s and vpe0.episode_modified_when = ( SELECT max(vpe1.episode_modified_when) from clin.v_pat_episodes vpe1 WHERE vpe1.pk_episode = vpe0.pk_episode ) %s""" % issue_where rows, idx = gmPG2.run_ro_queries(queries = [ {'cmd': cmd, 'args': {'pat': self.pk_patient, 'issue': issue}} ]) if len(rows) != 0: return gmEMRStructItems.cEpisode(aPK_obj=rows[0][0]) return None def get_most_recent_result_for_test_types(self, pk_test_types=None)-
Expand source code
def get_most_recent_result_for_test_types(self, pk_test_types=None): return gmPathLab.get_most_recent_result_for_test_types ( pk_test_types = pk_test_types, pk_patient = self.pk_patient ) def get_most_recent_results_for_patient(self, no_of_results=1)-
Expand source code
def get_most_recent_results_for_patient(self, no_of_results=1): return gmPathLab.get_most_recent_results_for_patient ( no_of_results = no_of_results, patient = self.pk_patient ) def get_most_recent_results_for_test_type(self, test_type=None, max_no_of_results=1)-
Expand source code
def get_most_recent_results_for_test_type(self, test_type=None, max_no_of_results=1): return gmPathLab.get_most_recent_results_for_test_type ( test_type = test_type, max_no_of_results = max_no_of_results, patient = self.pk_patient ) def get_most_recent_results_in_loinc_group(self, loincs=None, max_no_of_results=1, consider_indirect_matches=False)-
Expand source code
def get_most_recent_results_in_loinc_group(self, loincs=None, max_no_of_results=1, consider_indirect_matches=False): return gmPathLab.get_most_recent_results_in_loinc_group ( loincs = loincs, max_no_of_results = max_no_of_results, patient = self.pk_patient, consider_indirect_matches = consider_indirect_matches ) def get_patient_ID(self)-
Expand source code
def get_patient_ID(self): return self.pk_patient def get_performed_procedures(self, episodes=None, issues=None)-
Expand source code
def get_performed_procedures(self, episodes=None, issues=None): procs = gmEMRStructItems.get_performed_procedures(patient = self.pk_patient) if episodes is not None: procs = [ p for p in procs if p['pk_episode'] in episodes ] if issues is not None: procs = [ p for p in procs if p['pk_health_issue'] in issues ] return procs def get_problems(self, episodes=None, issues=None, include_closed_episodes=False, include_irrelevant_issues=False)-
Retrieve a patient's problems.
"Problems" are the UNION of:
- issues which are .clinically_relevant - episodes which are .is_openTherefore, both an issue and the open episode thereof can each be listed as a problem.
include_closed_episodes/include_irrelevant_issues will include those – which departs from the definition of the problem list being "active" items only …
episodes - episodes' PKs to filter problems by issues - health issues' PKs to filter problems by
Expand source code
def get_problems(self, episodes=None, issues=None, include_closed_episodes=False, include_irrelevant_issues=False): """Retrieve a patient's problems. "Problems" are the UNION of: - issues which are .clinically_relevant - episodes which are .is_open Therefore, both an issue and the open episode thereof can each be listed as a problem. include_closed_episodes/include_irrelevant_issues will include those -- which departs from the definition of the problem list being "active" items only ... episodes - episodes' PKs to filter problems by issues - health issues' PKs to filter problems by """ # FIXME: this could use a good measure of streamlining, probably args = {'pat': self.pk_patient} cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_problem_list WHERE pk_patient = %(pat)s ORDER BY problem""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) # Instantiate problem items problems = [] for row in rows: pk_args = { 'pk_patient': self.pk_patient, 'pk_health_issue': row['pk_health_issue'], 'pk_episode': row['pk_episode'] } problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = False)) # include non-problems ? other_rows = [] if include_closed_episodes: cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'episode'""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) other_rows.extend(rows) if include_irrelevant_issues: cmd = """SELECT pk_health_issue, pk_episode FROM clin.v_potential_problem_list WHERE pk_patient = %(pat)s and type = 'health issue'""" rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = False) other_rows.extend(rows) if len(other_rows) > 0: for row in other_rows: pk_args = { 'pk_patient': self.pk_patient, 'pk_health_issue': row['pk_health_issue'], 'pk_episode': row['pk_episode'] } problems.append(gmEMRStructItems.cProblem(aPK_obj = pk_args, try_potential_problems = True)) # filter if issues is not None: problems = [ p for p in problems if p['pk_health_issue'] in issues ] if episodes is not None: problems = [ p for p in problems if p['pk_episode'] in episodes ] return problems def get_procedure_locations_as_org_units(self)-
Expand source code
def get_procedure_locations_as_org_units(self): where = 'pk_org_unit IN (SELECT DISTINCT pk_org_unit FROM clin.v_procedures_not_at_hospital WHERE pk_patient = %(pat)s)' args = {'pat': self.pk_patient} cmd = gmOrganization._SQL_get_org_unit % where rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmOrganization.cOrgUnit(row = {'pk_field': 'pk_org_unit', 'data': r, 'idx': idx}) for r in rows ] def get_result_at_timestamp(self, timestamp=None, test_type=None, loinc=None, tolerance_interval='12 hours')-
Expand source code
def get_result_at_timestamp(self, timestamp=None, test_type=None, loinc=None, tolerance_interval='12 hours'): return gmPathLab.get_result_at_timestamp ( timestamp = timestamp, test_type = test_type, loinc = loinc, tolerance_interval = tolerance_interval, patient = self.pk_patient ) def get_results_for_day(self, timestamp=None, order_by=None)-
Expand source code
def get_results_for_day(self, timestamp=None, order_by=None): return gmPathLab.get_results_for_day ( timestamp = timestamp, patient = self.pk_patient, order_by = order_by ) def get_results_for_episode(self, pk_episode=None)-
Expand source code
def get_results_for_episode(self, pk_episode=None): return gmPathLab.get_results_for_episode(pk_episode = pk_episode) def get_results_for_issue(self, pk_health_issue=None, order_by=None)-
Expand source code
def get_results_for_issue(self, pk_health_issue=None, order_by=None): return gmPathLab.get_results_for_issue ( pk_health_issue = pk_health_issue, order_by = order_by ) def get_statistics(self)-
Expand source code
def get_statistics(self): union_query = '\n union all\n'.join ([ """ SELECT (( -- all relevant health issues + active episodes WITH health issue SELECT COUNT(*) FROM clin.v_problem_list WHERE pk_patient = %(pat)s AND pk_health_issue is not null ) + ( -- active episodes WITHOUT health issue SELECT COUNT(*) FROM clin.v_problem_list WHERE pk_patient = %(pat)s AND pk_health_issue is null ))""", 'SELECT COUNT(*) FROM clin.encounter WHERE fk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_pat_items WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM blobs.v_doc_med WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_test_results WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_hospital_stays WHERE pk_patient = %(pat)s', 'SELECT COUNT(*) FROM clin.v_procedures WHERE pk_patient = %(pat)s', """ SELECT COUNT(*) FROM clin.v_intakes WHERE pk_patient = %(pat)s AND use_type IS NOT NULL """, 'SELECT COUNT(*) FROM clin.v_vaccinations WHERE pk_patient = %(pat)s' ]) rows, idx = gmPG2.run_ro_queries ( queries = [{'cmd': union_query, 'args': {'pat': self.pk_patient}}], get_col_idx = False ) stats = dict ( problems = rows[0][0], encounters = rows[1][0], items = rows[2][0], documents = rows[3][0], results = rows[4][0], stays = rows[5][0], procedures = rows[6][0], active_drugs = rows[7][0], vaccinations = rows[8][0] ) return stats def get_test_results(self, encounters=None, episodes=None, tests=None, order_by=None)-
Expand source code
def get_test_results(self, encounters=None, episodes=None, tests=None, order_by=None): return gmPathLab.get_test_results ( pk_patient = self.pk_patient, encounters = encounters, episodes = episodes, order_by = order_by ) def get_test_results_by_date(self, encounter=None, episodes=None, tests=None, reverse_chronological=True)-
Expand source code
def get_test_results_by_date(self, encounter=None, episodes=None, tests=None, reverse_chronological=True): where_parts = ['pk_patient = %(pat)s'] args = {'pat': self.pk_patient} if tests is not None: where_parts.append('pk_test_type = ANY(%(tests)s)') args['tests'] = tests if encounter is not None: where_parts.append('pk_encounter = %(enc)s') args['enc'] = encounter if episodes is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = episodes cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY clin_when %s, pk_episode, unified_name """ % ( ' AND '.join(where_parts), gmTools.bool2subst(reverse_chronological, 'DESC', 'ASC', 'DESC') ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) tests = [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ] return tests def get_test_types_for_results(self, order_by=None, unique_meta_types=False)-
Retrieve data about test types for which this patient has results.
Expand source code
def get_test_types_for_results(self, order_by=None, unique_meta_types=False): """Retrieve data about test types for which this patient has results.""" if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by if unique_meta_types: cmd = """ SELECT * FROM clin.v_test_types c_vtt WHERE c_vtt.pk_test_type IN ( SELECT DISTINCT ON (c_vtr1.pk_meta_test_type) c_vtr1.pk_test_type FROM clin.v_test_results c_vtr1 WHERE c_vtr1.pk_patient = %%(pat)s AND c_vtr1.pk_meta_test_type IS NOT NULL UNION ALL SELECT DISTINCT ON (c_vtr2.pk_test_type) c_vtr2.pk_test_type FROM clin.v_test_results c_vtr2 WHERE c_vtr2.pk_patient = %%(pat)s AND c_vtr2.pk_meta_test_type IS NULL ) %s""" % order_by else: cmd = """ SELECT * FROM clin.v_test_types c_vtt WHERE c_vtt.pk_test_type IN ( SELECT DISTINCT ON (c_vtr.pk_test_type) c_vtr.pk_test_type FROM clin.v_test_results c_vtr WHERE c_vtr.pk_patient = %%(pat)s ) %s""" % order_by args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmPathLab.cMeasurementType(row = {'pk_field': 'pk_test_type', 'idx': idx, 'data': r}) for r in rows ] def get_unlinked_episodes(self, open_status=None, order_by=None)-
Expand source code
def get_unlinked_episodes(self, open_status=None, order_by=None): return self.get_episodes(open_status = open_status, order_by = order_by, unlinked_only = True) def get_unsigned_results(self, order_by=None)-
Expand source code
def get_unsigned_results(self, order_by=None): if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND reviewed IS FALSE %s""" % order_by args = {'pat': self.pk_patient} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmPathLab.cTestResult(row = {'pk_field': 'pk_test_result', 'idx': idx, 'data': r}) for r in rows ] def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None)-
Expand source code
def get_vaccinations(self, order_by=None, episodes=None, issues=None, encounters=None): return gmVaccination.get_vaccinations ( pk_identity = self.pk_patient, pk_episodes = episodes, pk_health_issues = issues, pk_encounters = encounters, order_by = order_by, return_pks = False ) def health_issue2problem(self, issue=None)-
Expand source code
def health_issue2problem(self, issue=None): return gmEMRStructItems.health_issue2problem(health_issue = issue) def is_allergic_to(self, atcs=None, inns=None, product_name=None)-
Cave: only use with one potential allergic agent otherwise you won't know which of the agents the allergy is to.
Expand source code
def is_allergic_to(self, atcs=None, inns=None, product_name=None): """Cave: only use with one potential allergic agent otherwise you won't know which of the agents the allergy is to.""" # not state acquired if not self.allergy_state: return None # we don't know the state if self.allergy_state['has_allergy'] is None: return None # we know there's no allergies if self.allergy_state['has_allergy'] == 0: return False args = { 'atcs': atcs, 'inns': inns, 'prod_name': product_name, 'pat': self.pk_patient } allergenes = [] where_parts = [] if len(atcs) == 0: atcs = None if atcs is not None: where_parts.append('atc_code = ANY(%(atcs)s)') if len(inns) == 0: inns = None if inns is not None: where_parts.append('generics = ANY(%(inns)s)') allergenes.extend(inns) if product_name is not None: where_parts.append('substance = %(prod_name)s') allergenes.append(product_name) if len(allergenes) != 0: where_parts.append('allergene = ANY(%(allgs)s)') args['allgs'] = allergenes cmd = """ SELECT * FROM clin.v_pat_allergies WHERE pk_patient = %%(pat)s AND ( %s )""" % ' OR '.join(where_parts) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 0: return False return gmAllergy.cAllergy(row = {'data': rows[0], 'idx': idx, 'pk_field': 'pk_allergy'}) def log_access(self, action=None)-
Expand source code
def log_access(self, action=None): if action is None: action = 'EMR access for pk_identity [%s]' % self.pk_patient args = {'action': action} cmd = 'SELECT gm.log_access2emr(%(action)s)' gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) def reclass_problem(self, problem)-
Expand source code
def reclass_problem(self, problem): return gmEMRStructItems.reclass_problem(problem = problem) def remove_empty_encounters(self)-
Expand source code
def remove_empty_encounters(self): _log.debug('removing empty encounters for pk_identity [%s]', self.pk_patient) ttl = gmCfgDB.get4user ( option = 'encounter.ttl_if_empty', workplace = _here.active_workplace, default = '1 week' ) # # FIXME: this should be done async cmd = "SELECT clin.remove_old_empty_encounters(%(pat)s::INTEGER, %(ttl)s::INTERVAL)" args = {'pat': self.pk_patient, 'ttl': ttl} try: rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True) except Exception: _log.exception('error deleting empty encounters') return False if not rows[0][0]: _log.debug('no encounters deleted (less than 2 exist)') return True def search_narrative_simple(self, search_term='')-
Expand source code
def search_narrative_simple(self, search_term=''): search_term = search_term.strip() if search_term == '': return [] cmd = """ SELECT *, coalesce((SELECT description FROM clin.episode WHERE pk = vn4s.pk_episode), vn4s.src_table) as episode, coalesce((SELECT description FROM clin.health_issue WHERE pk = vn4s.pk_health_issue), vn4s.src_table) as health_issue, (SELECT started FROM clin.encounter WHERE pk = vn4s.pk_encounter) as encounter_started, (SELECT last_affirmed FROM clin.encounter WHERE pk = vn4s.pk_encounter) as encounter_ended, (SELECT _(description) FROM clin.encounter_type WHERE pk = (SELECT fk_type FROM clin.encounter WHERE pk = vn4s.pk_encounter)) as encounter_type FROM clin.v_narrative4search vn4s WHERE pk_patient = %(pat)s and vn4s.narrative ~ %(term)s order by encounter_started """ # case sensitive rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'pat': self.pk_patient, 'term': search_term}}]) return rows def start_new_encounter(self)-
Expand source code
def start_new_encounter(self): enc_type = gmCfgDB.get4user ( option = 'encounter.default_type', workplace = _here.active_workplace ) if enc_type is None: enc_type = gmEMRStructItems.get_most_commonly_used_encounter_type() if enc_type is None: enc_type = 'in surgery' enc = gmEMRStructItems.create_encounter(fk_patient = self.pk_patient, enc_type = enc_type) enc['pk_org_unit'] = _here['pk_org_unit'] enc.save() self.current_encounter = enc _log.debug('new encounter [%s] activated', enc['pk_encounter']) def substance_intake_exists(self, pk_component=None, pk_substance=None, pk_drug_product=None)-
Expand source code
def substance_intake_exists(self, pk_component=None, pk_substance=None, pk_drug_product=None): return gmMedication.substance_intake_exists ( pk_component = pk_component, pk_substance = pk_substance, pk_identity = self.pk_patient, pk_drug_product = pk_drug_product )