Module Gnumed.business.gmPathLab
GNUmed measurements related business objects.
Expand source code
"""GNUmed measurements related business objects."""
# FIXME: use UCUM from Regenstrief Institute
#============================================================
__author__ = "K.Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = "GPL"
import sys
import logging
import decimal
import re as regex
import os.path
if __name__ == '__main__':
sys.path.insert(0, '../../')
_ = lambda x:x
else:
try:
_
except NameError:
from Gnumed.pycommon import gmI18N
gmI18N.activate_locale()
gmI18N.install_domain()
from Gnumed.pycommon import gmDateTime
from Gnumed.pycommon import gmExceptions
from Gnumed.pycommon import gmBusinessDBObject
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmDispatcher
from Gnumed.pycommon import gmHooks
from Gnumed.pycommon import gmCfgINI
from Gnumed.business import gmOrganization
from Gnumed.business import gmCoding
_log = logging.getLogger('gm.lab')
_cfg = gmCfgINI.gmCfgData()
#============================================================
HL7_RESULT_STATI = {
None: _('unknown'),
'': _('empty status'),
'C': _('C (HL7: Correction, replaces previous final)'),
'D': _('D (HL7: Deletion)'),
'F': _('F (HL7: Final)'),
'I': _('I (HL7: pending, specimen In lab)'),
'P': _('P (HL7: Preliminary)'),
'R': _('R (HL7: result entered, not yet verified)'),
'S': _('S (HL7: partial)'),
'X': _('X (HL7: cannot obtain results for this observation)'),
'U': _('U (HL7: mark as final (I/P/R/S -> F, value Unchanged)'),
'W': _('W (HL7: original Wrong (say, wrong patient))')
}
URL_test_result_information = 'http://www.laborlexikon.de'
URL_test_result_information_search = "https://www.google.de/search?as_oq=%(search_term)s&num=10&as_sitesearch=laborlexikon.de"
#============================================================
def _on_test_result_modified():
"""Always relates to the active patient."""
gmHooks.run_hook_script(hook = 'after_test_result_modified')
gmDispatcher.connect(_on_test_result_modified, 'clin.test_result_mod_db')
#============================================================
_SQL_get_test_orgs = "SELECT * FROM clin.v_test_orgs WHERE %s"
class cTestOrg(gmBusinessDBObject.cBusinessDBObject):
"""Represents one test org/lab."""
_cmd_fetch_payload = _SQL_get_test_orgs % 'pk_test_org = %s'
_cmds_store_payload = [
"""UPDATE clin.test_org SET
fk_org_unit = %(pk_org_unit)s,
contact = gm.nullify_empty_string(%(test_org_contact)s),
comment = gm.nullify_empty_string(%(comment)s)
WHERE
pk = %(pk_test_org)s
AND
xmin = %(xmin_test_org)s
RETURNING
xmin AS xmin_test_org
"""
]
_updatable_fields = [
'pk_org_unit',
'test_org_contact',
'comment'
]
#------------------------------------------------------------
def create_test_org(name=None, comment=None, pk_org_unit=None, link_obj=None):
_log.debug('creating test org [%s:%s:%s]', name, comment, pk_org_unit)
if name is None:
name = 'unassigned lab'
# get org unit
if pk_org_unit is None:
org = gmOrganization.create_org (
link_obj = link_obj,
organization = name,
category = 'Laboratory'
)
org_unit = gmOrganization.create_org_unit (
link_obj = link_obj,
pk_organization = org['pk_org'],
unit = name
)
pk_org_unit = org_unit['pk_org_unit']
# test org exists ?
args = {'pk_unit': pk_org_unit}
cmd = 'SELECT pk_test_org FROM clin.v_test_orgs WHERE pk_org_unit = %(pk_unit)s'
rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
cmd = 'INSERT INTO clin.test_org (fk_org_unit) VALUES (%(pk_unit)s) RETURNING pk'
rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True)
test_org = cTestOrg(link_obj = link_obj, aPK_obj = rows[0][0])
if comment is not None:
comment = comment.strip()
test_org['comment'] = comment
test_org.save(conn = link_obj)
return test_org
#------------------------------------------------------------
def delete_test_org(test_org=None):
args = {'pk': test_org}
cmd = """
DELETE FROM clin.test_org
WHERE
pk = %(pk)s
AND
NOT EXISTS (SELECT 1 FROM clin.lab_request WHERE fk_test_org = %(pk)s LIMIT 1)
AND
NOT EXISTS (SELECT 1 FROM clin.test_type WHERE fk_test_org = %(pk)s LIMIT 1)
"""
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#------------------------------------------------------------
def get_test_orgs(order_by='unit', return_pks=False):
cmd = 'SELECT * FROM clin.v_test_orgs ORDER BY %s' % order_by
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
if return_pks:
return [ r['pk_test_org'] for r in rows ]
return [ cTestOrg(row = {'pk_field': 'pk_test_org', 'data': r}) for r in rows ]
#============================================================
# test panels / profiles
#------------------------------------------------------------
_SQL_get_test_panels = "SELECT * FROM clin.v_test_panels WHERE %s"
class cTestPanel(gmBusinessDBObject.cBusinessDBObject):
"""Represents a grouping/listing of tests into a panel."""
_cmd_fetch_payload = _SQL_get_test_panels % "pk_test_panel = %s"
_cmds_store_payload = [
"""
UPDATE clin.test_panel SET
description = gm.nullify_empty_string(%(description)s),
comment = gm.nullify_empty_string(%(comment)s)
WHERE
pk = %(pk_test_panel)s
AND
xmin = %(xmin_test_panel)s
RETURNING
xmin AS xmin_test_panel
"""
]
_updatable_fields = [
'description',
'comment'
]
#--------------------------------------------------------
def format(self):
txt = _('Test panel "%s" [#%s]\n') % (
self._payload['description'],
self._payload['pk_test_panel']
)
if self._payload['comment'] is not None:
txt += '\n'
txt += gmTools.wrap (
text = self._payload['comment'],
width = 50,
initial_indent = ' ',
subsequent_indent = ' '
)
txt += '\n'
txt += '\n'
txt += _('Includes:\n')
if len(self.included_loincs) == 0:
txt += _('no tests')
else:
tts_by_loinc = {}
for loinc in self._payload['loincs']:
tts_by_loinc[loinc] = []
for ttype in self.test_types:
tts_by_loinc[ttype['loinc']].append(ttype)
for loinc, ttypes in tts_by_loinc.items():
# maybe resolve LOINC, too
txt += _(' %s: %s\n') % (
loinc,
'; '.join([ '%(abbrev)s@%(name_org)s [#%(pk_test_type)s]' % tt for tt in ttypes ])
)
codes = self.generic_codes
if len(codes) > 0:
txt += '\n'
for c in codes:
txt += ' %s: %s (%s - %s)\n' % (
c['code'],
c['term'],
c['name_short'],
c['version']
)
return txt
#--------------------------------------------------------
def add_code(self, pk_code=None):
"""<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
cmd = "INSERT INTO clin.lnk_code2tst_pnl (fk_item, fk_generic_code) values (%(tp)s, %(code)s)"
args = {
'tp': self._payload['pk_test_panel'],
'code': pk_code
}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#--------------------------------------------------------
def remove_code(self, pk_code=None):
"""<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)"""
cmd = "DELETE FROM clin.lnk_code2tst_pnl WHERE fk_item = %(tp)s AND fk_generic_code = %(code)s"
args = {
'tp': self._payload['pk_test_panel'],
'code': pk_code
}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#--------------------------------------------------------
def get_test_types_for_results(self, pk_patient, order_by=None, unique_meta_types=False):
"""Retrieve data about test types on this panel (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_test_type IN %%(pks)s
AND
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_test_type IN %%(pks)s
AND
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_test_type = ANY(%%(pks)s)
AND
c_vtr.pk_patient = %%(pat)s
)
%s""" % order_by
args = {
'pat': pk_patient,
'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ]
}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ]
#--------------------------------------------------------
def add_loinc(self, loinc):
if self._payload['loincs'] is not None:
if loinc in self._payload['loincs']:
return
gmPG2.run_rw_queries(queries = [{
'cmd': 'INSERT INTO clin.lnk_loinc2test_panel (fk_test_panel, loinc) VALUES (%(pk_pnl)s, %(loinc)s)',
'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']}
}])
return
#--------------------------------------------------------
def remove_loinc(self, loinc):
if self._payload['loincs'] is None:
return
if loinc not in self._payload['loincs']:
return
gmPG2.run_rw_queries(queries = [{
'cmd': 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc = %(loinc)s',
'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']}
}])
return
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def _get_included_loincs(self):
return self._payload['loincs']
def _set_included_loincs(self, loincs):
queries = []
# remove those which don't belong
if len(loincs) == 0:
cmd = 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s'
else:
cmd = 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc <> ALL(%(loincs)s)'
queries.append({'cmd': cmd, 'args': {'loincs': loincs, 'pk_pnl': self._payload['pk_test_panel']}})
# add those not there yet
if len(loincs) > 0:
for loinc in loincs:
cmd = """INSERT INTO clin.lnk_loinc2test_panel (fk_test_panel, loinc)
SELECT %(pk_pnl)s, %(loinc)s WHERE NOT EXISTS (
SELECT 1 FROM clin.lnk_loinc2test_panel WHERE
fk_test_panel = %(pk_pnl)s
AND
loinc = %(loinc)s
)"""
queries.append({'cmd': cmd, 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']}})
return gmPG2.run_rw_queries(queries = queries)
included_loincs = property(_get_included_loincs, _set_included_loincs)
#--------------------------------------------------------
def _get_test_types(self):
if len(self._payload['test_types']) == 0:
return []
rows = gmPG2.run_ro_queries (
queries = [{
'cmd': _SQL_get_test_types % 'pk_test_type = ANY(%(pks)s) ORDER BY unified_abbrev',
'args': {'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ]}
}]
)
return [ cMeasurementType(row = {'data': r, 'pk_field': 'pk_test_type'}) for r in rows ]
test_types = property(_get_test_types)
#--------------------------------------------------------
def _get_generic_codes(self):
if len(self._payload['pk_generic_codes']) == 0:
return []
cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)'
args = {'pks': self._payload['pk_generic_codes']}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ]
def _set_generic_codes(self, pk_codes):
queries = []
# remove all codes
if len(self._payload['pk_generic_codes']) > 0:
queries.append ({
'cmd': 'DELETE FROM clin.lnk_code2tst_pnl WHERE fk_item = %(tp)s AND fk_generic_code = ANY(%(codes)s)',
'args': {
'tp': self._payload['pk_test_panel'],
'codes': self._payload['pk_generic_codes']
}
})
# add new codes
for pk_code in pk_codes:
queries.append ({
'cmd': 'INSERT INTO clin.lnk_code2test_panel (fk_item, fk_generic_code) VALUES (%(tp)s, %(pk_code)s)',
'args': {
'tp': self._payload['pk_test_panel'],
'pk_code': pk_code
}
})
if len(queries) == 0:
return
# run it all in one transaction
gmPG2.run_rw_queries(queries = queries)
return
generic_codes = property(_get_generic_codes, _set_generic_codes)
#--------------------------------------------------------
def get_most_recent_results(self, pk_patient=None, order_by=None, group_by_meta_type=False, include_missing=False):
if len(self._payload['test_types']) == 0:
return []
pnl_results = get_most_recent_results_for_panel (
pk_patient = pk_patient,
pk_panel = self._payload['pk_test_panel'],
order_by = order_by,
group_by_meta_type = group_by_meta_type
)
if not include_missing:
return pnl_results
loincs_found = [ r['loinc_tt'] for r in pnl_results ]
loincs_found.extend([ r['loinc_meta'] for r in pnl_results if r['loinc_meta'] not in loincs_found ])
loincs2consider = set([ tt['loinc'] for tt in self._payload['test_types'] ])
loincs_missing = loincs2consider - set(loincs_found)
pnl_results.extend(loincs_missing)
return pnl_results
#------------------------------------------------------------
def get_test_panels(order_by=None, loincs=None, return_pks=False):
where_args = {}
if loincs is None:
where_parts = ['true']
else:
where_parts = ['loincs @> %(loincs)s']
where_args['loincs'] = list(loincs)
if order_by is None:
order_by = u''
else:
order_by = ' ORDER BY %s' % order_by
cmd = (_SQL_get_test_panels % ' AND '.join(where_parts)) + order_by
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': where_args}])
if return_pks:
return [ r['pk_test_panel'] for r in rows ]
return [ cTestPanel(row = {'data': r, 'pk_field': 'pk_test_panel'}) for r in rows ]
#------------------------------------------------------------
def create_test_panel(description=None):
args = {'desc': description.strip()}
cmd = """
INSERT INTO clin.test_panel (description)
VALUES (gm.nullify_empty_string(%(desc)s))
RETURNING pk
"""
rows = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
return cTestPanel(aPK_obj = rows[0]['pk'])
#------------------------------------------------------------
def delete_test_panel(pk=None):
args = {'pk': pk}
cmd = "DELETE FROM clin.test_panel WHERE pk = %(pk)s"
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#============================================================
class cMetaTestType(gmBusinessDBObject.cBusinessDBObject):
"""Represents one meta test type under which actual test types can be aggregated."""
_cmd_fetch_payload = "SELECT *, xmin FROM clin.meta_test_type WHERE pk = %s"
_cmds_store_payload = ["""
UPDATE clin.meta_test_type SET
abbrev = %(abbrev)s,
name = %(name)s,
loinc = gm.nullify_empty_string(%(loinc)s),
comment = gm.nullify_empty_string(%(comment)s)
WHERE
pk = %(pk)s
AND
xmin = %(xmin)s
RETURNING
xmin
"""]
_updatable_fields = [
'abbrev',
'name',
'loinc',
'comment'
]
#--------------------------------------------------------
def format(self, with_tests=False, patient=None):
txt = _('Meta (%s=aggregate) test type [#%s]\n\n') % (gmTools.u_sum, self._payload['pk'])
txt += _(' Name: %s (%s)\n') % (
self._payload['abbrev'],
self._payload['name']
)
if self._payload['loinc'] is not None:
txt += ' LOINC: %s\n' % self._payload['loinc']
if self._payload['comment'] is not None:
txt += _(' Comment: %s\n') % self._payload['comment']
if with_tests:
ttypes = self.included_test_types
if len(ttypes) > 0:
txt += _(' Aggregates the following test types:\n')
for ttype in ttypes:
txt += ' - %s (%s)%s%s%s [#%s]\n' % (
ttype['name'],
ttype['abbrev'],
gmTools.coalesce(ttype['reference_unit'], '', ', %s'),
gmTools.coalesce(ttype['name_org'], '', ' (%s)'),
gmTools.coalesce(ttype['loinc'], '', ', LOINC: %s'),
ttype['pk_test_type']
)
if patient is not None:
txt += '\n'
most_recent = self.get_most_recent_result(patient = patient)
if most_recent is not None:
txt += _(' Most recent (%s): %s%s%s') % (
gmDateTime.pydt_strftime(most_recent['clin_when'], '%Y %b %d'),
most_recent['unified_val'],
gmTools.coalesce(most_recent['val_unit'], '', ' %s'),
gmTools.coalesce(most_recent['abnormality_indicator'], '', ' (%s)')
)
oldest = self.get_oldest_result(patient = patient)
if oldest is not None:
txt += '\n'
txt += _(' Oldest (%s): %s%s%s') % (
gmDateTime.pydt_strftime(oldest['clin_when'], '%Y %b %d'),
oldest['unified_val'],
gmTools.coalesce(oldest['val_unit'], '', ' %s'),
gmTools.coalesce(oldest['abnormality_indicator'], '', ' (%s)')
)
return txt
#--------------------------------------------------------
def get_most_recent_result(self, patient=None):
args = {
'pat': patient,
'mttyp': self._payload['pk']
}
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %(pat)s
AND
pk_meta_test_type = %(mttyp)s
ORDER BY clin_when DESC
LIMIT 1"""
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
#--------------------------------------------------------
def get_oldest_result(self, patient=None):
args = {
'pat': patient,
'mttyp': self._payload['pk']
}
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %(pat)s
AND
pk_meta_test_type = %(mttyp)s
ORDER BY clin_when
LIMIT 1"""
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
#--------------------------------------------------------
def get_temporally_closest_result(self, date, pk_patient):
args = {
'pat': pk_patient,
'mtyp': self._payload['pk'],
'mloinc': self._payload['loinc'],
'when': date
}
SQL = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %%(pat)s
AND
clin_when %s %%(when)s
AND
((pk_meta_test_type = %%(mtyp)s) OR (loinc_meta = %%(mloinc)s))
ORDER BY clin_when
LIMIT 1"""
# get earlier results by meta type
earlier_result = None
cmd = SQL % '<'
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
earlier_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
# get later results by meta type ?
later_result = None
cmd = SQL % '>'
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
later_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
if earlier_result is None:
return later_result
if later_result is None:
return earlier_result
earlier_ago = date - earlier_result['clin_when']
later_ago = later_result['clin_when'] - date
if earlier_ago < later_ago:
return earlier_result
return later_result
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def _get_included_test_types(self):
cmd = _SQL_get_test_types % 'pk_meta_test_type = %(pk_meta)s'
args = {'pk_meta': self._payload['pk']}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ]
included_test_types = property(_get_included_test_types)
#------------------------------------------------------------
def create_meta_type(name=None, abbreviation=None, return_existing=False):
cmd = """
INSERT INTO clin.meta_test_type (name, abbrev)
SELECT
%(name)s,
%(abbr)s
WHERE NOT EXISTS (
SELECT 1 FROM clin.meta_test_type
WHERE
name = %(name)s
AND
abbrev = %(abbr)s
)
RETURNING *, xmin
"""
args = {
'name': name.strip(),
'abbr': abbreviation.strip()
}
rows = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True)
if len(rows) == 0:
if not return_existing:
return None
cmd = "SELECT *, xmin FROM clin.meta_test_type WHERE name = %(name)s and %(abbr)s"
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return cMetaTestType(row = {'pk_field': 'pk', 'data': rows[0]})
#------------------------------------------------------------
def delete_meta_type(meta_type=None):
cmd = """
DELETE FROM clin.meta_test_type
WHERE
pk = %(pk)s
AND
NOT EXISTS (
SELECT 1 FROM clin.test_type
WHERE fk_meta_test_type = %(pk)s
)"""
args = {'pk': meta_type}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#------------------------------------------------------------
def get_meta_test_types(return_pks=False):
cmd = 'SELECT *, xmin FROM clin.meta_test_type'
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
if return_pks:
return [ r['pk'] for r in rows ]
return [ cMetaTestType(row = {'pk_field': 'pk', 'data': r}) for r in rows ]
#============================================================
_SQL_get_test_types = "SELECT * FROM clin.v_test_types WHERE %s"
class cMeasurementType(gmBusinessDBObject.cBusinessDBObject):
"""Represents one test result type."""
_cmd_fetch_payload = _SQL_get_test_types % "pk_test_type = %s"
_cmds_store_payload = [
"""UPDATE clin.test_type SET
abbrev = gm.nullify_empty_string(%(abbrev)s),
name = gm.nullify_empty_string(%(name)s),
loinc = gm.nullify_empty_string(%(loinc)s),
comment = gm.nullify_empty_string(%(comment_type)s),
reference_unit = gm.nullify_empty_string(%(reference_unit)s),
fk_test_org = %(pk_test_org)s,
fk_meta_test_type = %(pk_meta_test_type)s
WHERE
pk = %(pk_test_type)s
AND
xmin = %(xmin_test_type)s
RETURNING
xmin AS xmin_test_type"""
]
_updatable_fields = [
'abbrev',
'name',
'loinc',
'comment_type',
'reference_unit',
'pk_test_org',
'pk_meta_test_type'
]
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def _get_in_use(self):
cmd = 'SELECT EXISTS(SELECT 1 FROM clin.test_result WHERE fk_type = %(pk_type)s)'
args = {'pk_type': self._payload['pk_test_type']}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return rows[0][0]
in_use = property(_get_in_use)
#--------------------------------------------------------
def get_most_recent_results(self, patient=None, max_no_of_results=1):
results = get_most_recent_results_for_test_type (
test_type = self._payload['pk_test_type'],
max_no_of_results = max_no_of_results,
patient = patient
)
if len(results) > 0:
return results
if self._payload['loinc'] is None:
return []
return get_most_recent_results_in_loinc_group (
loincs = list(self._payload['loinc']),
max_no_of_results = max_no_of_results,
patient = patient
# ?
)
#--------------------------------------------------------
def get_oldest_result(self, patient=None):
result = get_oldest_result (
test_type = self._payload['pk_test_type'],
loinc = None,
patient = patient
)
if result is None:
if self._payload['loinc'] is not None:
result = get_oldest_result (
test_type = None,
loinc = self._payload['loinc'],
patient = patient
)
return result
#--------------------------------------------------------
def _get_test_panels(self):
if self._payload['pk_test_panels'] is None:
return None
return [ cTestPanel(aPK_obj = pk) for pk in self._payload['pk_test_panels'] ]
test_panels = property(_get_test_panels)
#--------------------------------------------------------
def get_meta_test_type(self, real_one_only=True):
if real_one_only is False:
return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type'])
if self._payload['is_fake_meta_type']:
return None
return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type'])
meta_test_type = property(get_meta_test_type)
#--------------------------------------------------------
def get_temporally_closest_normal_range(self, unit, timestamp=None):
"""Returns the closest test result which does have normal range information.
- needs <unit>
- if <timestamp> is None it will assume now() and thus return the most recent
"""
if timestamp is None:
timestamp = gmDateTime.pydt_now_here()
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_test_type = %(pk_type)s
AND
val_unit = %(unit)s
AND
(
(val_normal_min IS NOT NULL)
OR
(val_normal_max IS NOT NULL)
OR
(val_normal_range IS NOT NULL)
)
ORDER BY
CASE
WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s
ELSE %(clin_when)s - clin_when
END
LIMIT 1"""
args = {
'pk_type': self._payload['pk_test_type'],
'unit': unit,
'clin_when': timestamp
}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
r = rows[0]
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r})
#--------------------------------------------------------
def get_temporally_closest_target_range(self, unit, patient, timestamp=None):
"""Returns the closest test result which does have target range information.
- needs <unit>
- needs <patient> (as target will be per-patient)
- if <timestamp> is None it will assume now() and thus return the most recent
"""
if timestamp is None:
timestamp = gmDateTime.pydt_now_here()
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_test_type = %(pk_type)s
AND
val_unit = %(unit)s
AND
pk_patient = %(pat)s
AND
(
(val_target_min IS NOT NULL)
OR
(val_target_max IS NOT NULL)
OR
(val_target_range IS NOT NULL)
)
ORDER BY
CASE
WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s
ELSE %(clin_when)s - clin_when
END
LIMIT 1"""
args = {
'pk_type': self._payload['pk_test_type'],
'unit': unit,
'pat': patient,
'clin_when': timestamp
}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
r = rows[0]
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r})
#--------------------------------------------------------
def get_temporally_closest_unit(self, timestamp=None):
"""Returns the unit of the closest test result.
- if <timestamp> is None it will assume now() and thus return the most recent
"""
if timestamp is None:
timestamp = gmDateTime.pydt_now_here()
cmd = """
SELECT val_unit FROM clin.v_test_results
WHERE
pk_test_type = %(pk_type)s
AND
val_unit IS NOT NULL
ORDER BY
CASE
WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s
ELSE %(clin_when)s - clin_when
END
LIMIT 1"""
args = {
'pk_type': self._payload['pk_test_type'],
'clin_when': timestamp
}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return rows[0]['val_unit']
temporally_closest_unit = property(get_temporally_closest_unit)
#--------------------------------------------------------
def format(self, patient=None):
tt = ''
tt += _('Test type "%s" (%s) [#%s]\n') % (
self._payload['name'],
self._payload['abbrev'],
self._payload['pk_test_type']
)
tt += '\n'
tt += gmTools.coalesce(self._payload['loinc'], '', ' LOINC: %s\n')
tt += gmTools.coalesce(self._payload['reference_unit'], '', _(' Reference unit: %s\n'))
tt += gmTools.coalesce(self._payload['comment_type'], '', _(' Comment: %s\n'))
tt += '\n'
tt += _('Lab details:\n')
tt += _(' Name: %s\n') % gmTools.coalesce(self._payload['name_org'], '')
tt += gmTools.coalesce(self._payload['contact_org'], '', _(' Contact: %s\n'))
tt += gmTools.coalesce(self._payload['comment_org'], '', _(' Comment: %s\n'))
if self._payload['is_fake_meta_type'] is False:
tt += '\n'
tt += _('Aggregated under meta type:\n')
tt += _(' Name: %s - %s [#%s]\n') % (
self._payload['abbrev_meta'],
self._payload['name_meta'],
self._payload['pk_meta_test_type']
)
tt += gmTools.coalesce(self._payload['loinc_meta'], '', ' LOINC: %s\n')
tt += gmTools.coalesce(self._payload['comment_meta'], '', _(' Comment: %s\n'))
panels = self.test_panels
if panels is not None:
tt += '\n'
tt += _('Listed in test panels:\n')
for panel in panels:
tt += _(' Panel "%s" [#%s]\n') % (
panel['description'],
panel['pk_test_panel']
)
if patient is not None:
tt += '\n'
results = self.get_most_recent_results(patient = patient, max_no_of_results = 1)
if len(results) > 0:
result = results[0]
tt += _(' Most recent (%s): %s%s%s') % (
gmDateTime.pydt_strftime(result['clin_when'], '%Y %b %d'),
result['unified_val'],
gmTools.coalesce(result['val_unit'], '', ' %s'),
gmTools.coalesce(result['abnormality_indicator'], '', ' (%s)')
)
result = self.get_oldest_result(patient = patient)
if result is not None:
tt += '\n'
tt += _(' Oldest (%s): %s%s%s') % (
gmDateTime.pydt_strftime(result['clin_when'], '%Y %b %d'),
result['unified_val'],
gmTools.coalesce(result['val_unit'], '', ' %s'),
gmTools.coalesce(result['abnormality_indicator'], '', ' (%s)')
)
return tt
#------------------------------------------------------------
def get_measurement_types(order_by=None, loincs=None, return_pks=False):
args = {}
where_parts = []
if loincs is not None:
if len(loincs) > 0:
where_parts.append('loinc = ANY(%(loincs)s)')
args['loincs'] = loincs
if len(where_parts) == 0:
where_parts.append('TRUE')
WHERE_clause = ' AND '.join(where_parts)
cmd = (_SQL_get_test_types % WHERE_clause) + gmTools.coalesce(order_by, '', ' ORDER BY %s')
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if return_pks:
return [ r['pk_test_type'] for r in rows ]
return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ]
#------------------------------------------------------------
def find_measurement_type(lab=None, abbrev=None, name=None, link_obj=None):
if (abbrev is None) and (name is None):
raise ValueError('must have <abbrev> and/or <name> set')
where_snippets = []
if lab is None:
where_snippets.append('pk_test_org IS NULL')
else:
try:
int(lab)
where_snippets.append('pk_test_org = %(lab)s')
except (TypeError, ValueError):
where_snippets.append('pk_test_org = (SELECT pk_test_org FROM clin.v_test_orgs WHERE unit = %(lab)s)')
if abbrev is not None:
where_snippets.append('abbrev = %(abbrev)s')
if name is not None:
where_snippets.append('name = %(name)s')
where_clause = ' and '.join(where_snippets)
cmd = "select * from clin.v_test_types where %s" % where_clause
args = {'lab': lab, 'abbrev': abbrev, 'name': name}
rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
tt = cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': rows[0]})
return tt
#------------------------------------------------------------
def delete_measurement_type(measurement_type=None):
cmd = 'delete from clin.test_type where pk = %(pk)s'
args = {'pk': measurement_type}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#------------------------------------------------------------
def create_measurement_type(lab=None, abbrev=None, unit=None, name=None, link_obj=None):
"""Create or get test type."""
ttype = find_measurement_type(lab = lab, abbrev = abbrev, name = name, link_obj = link_obj)
# found ?
if ttype is not None:
return ttype
_log.debug('creating test type [%s:%s:%s:%s]', lab, abbrev, name, unit)
# not found, so create it
# if unit is None:
# _log.error('need <unit> to create test type: %s:%s:%s:%s' % (lab, abbrev, name, unit))
# raise ValueError('need <unit> to create test type')
# make query
cols = []
val_snippets = []
vals = {}
# lab
if lab is None:
lab = create_test_org(link_obj = link_obj)['pk_test_org']
cols.append('fk_test_org')
try:
vals['lab'] = int(lab)
val_snippets.append('%(lab)s')
except Exception:
vals['lab'] = lab
val_snippets.append('(SELECT pk_test_org FROM clin.v_test_orgs WHERE unit = %(lab)s)')
# code
cols.append('abbrev')
val_snippets.append('%(abbrev)s')
vals['abbrev'] = abbrev
# unit
if unit is not None:
cols.append('reference_unit')
val_snippets.append('%(unit)s')
vals['unit'] = unit
# name
if name is not None:
cols.append('name')
val_snippets.append('%(name)s')
vals['name'] = name
col_clause = ', '.join(cols)
val_clause = ', '.join(val_snippets)
queries = [
{'cmd': 'insert into clin.test_type (%s) values (%s)' % (col_clause, val_clause), 'args': vals},
{'cmd': "select * from clin.v_test_types where pk_test_type = currval(pg_get_serial_sequence('clin.test_type', 'pk'))"}
]
rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = queries, return_data = True)
ttype = cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': rows[0]})
return ttype
#============================================================
class cTestResult(gmBusinessDBObject.cBusinessDBObject):
"""Represents one test result."""
_cmd_fetch_payload = "select * from clin.v_test_results where pk_test_result = %s"
_cmds_store_payload = [
"""UPDATE clin.test_result SET
clin_when = %(clin_when)s,
narrative = nullif(trim(%(comment)s), ''),
val_num = %(val_num)s,
val_alpha = nullif(trim(%(val_alpha)s), ''),
val_unit = nullif(trim(%(val_unit)s), ''),
val_normal_min = %(val_normal_min)s,
val_normal_max = %(val_normal_max)s,
val_normal_range = nullif(trim(%(val_normal_range)s), ''),
val_target_min = %(val_target_min)s,
val_target_max = %(val_target_max)s,
val_target_range = nullif(trim(%(val_target_range)s), ''),
abnormality_indicator = nullif(trim(%(abnormality_indicator)s), ''),
norm_ref_group = nullif(trim(%(norm_ref_group)s), ''),
note_test_org = nullif(trim(%(note_test_org)s), ''),
material = nullif(trim(%(material)s), ''),
material_detail = nullif(trim(%(material_detail)s), ''),
status = gm.nullify_empty_string(%(status)s),
val_grouping = gm.nullify_empty_string(%(val_grouping)s),
source_data = gm.nullify_empty_string(%(source_data)s),
fk_intended_reviewer = %(pk_intended_reviewer)s,
fk_encounter = %(pk_encounter)s,
fk_episode = %(pk_episode)s,
fk_type = %(pk_test_type)s,
fk_request = %(pk_request)s
WHERE
pk = %(pk_test_result)s AND
xmin = %(xmin_test_result)s
RETURNING
xmin AS xmin_test_result
"""
# , u"""select xmin_test_result from clin.v_test_results where pk_test_result = %(pk_test_result)s"""
]
_updatable_fields = [
'clin_when',
'comment',
'val_num',
'val_alpha',
'val_unit',
'val_normal_min',
'val_normal_max',
'val_normal_range',
'val_target_min',
'val_target_max',
'val_target_range',
'abnormality_indicator',
'norm_ref_group',
'note_test_org',
'material',
'material_detail',
'status',
'val_grouping',
'source_data',
'pk_intended_reviewer',
'pk_encounter',
'pk_episode',
'pk_test_type',
'pk_request'
]
#--------------------------------------------------------
def format_concisely(self, date_format='%Y %b %d', with_notes=True):
range_info = gmTools.coalesce (
self.formatted_clinical_range,
self.formatted_normal_range
)
review = gmTools.bool2subst (
self._payload['reviewed'],
'',
' ' + gmTools.u_writing_hand,
' ' + gmTools.u_writing_hand
)
txt = '%s %s: %s%s%s%s%s%s' % (
gmDateTime.pydt_strftime (
self._payload['clin_when'],
date_format
),
self._payload['name_tt'],
self._payload['unified_val'],
gmTools.coalesce(self._payload['val_unit'], '', ' %s'),
gmTools.coalesce(self._payload['abnormality_indicator'], '', ' %s'),
gmTools.coalesce(range_info, '', ' (%s)'),
gmTools.coalesce(self._payload['status'], '', ' [%s]')[:2],
review
)
if with_notes:
txt += '\n'
if self._payload['note_test_org'] is not None:
txt += ' ' + _('Lab comment: %s\n') % _('\n Lab comment: ').join(self._payload['note_test_org'].split('\n'))
if self._payload['comment'] is not None:
txt += ' ' + _('Praxis comment: %s\n') % _('\n Praxis comment: ').join(self._payload['comment'].split('\n'))
return txt.strip('\n')
#--------------------------------------------------------
def format(self, with_review=True, with_evaluation=True, with_ranges=True, with_episode=True, with_type_details=True, with_source_data=False, date_format='%Y %b %d %H:%M'):
# FIXME: add battery, request details
# header
tt = _('Result from %s \n') % gmDateTime.pydt_strftime (
self._payload['clin_when'],
date_format
)
# basics
tt += ' ' + _('Type: "%(name)s" (%(abbr)s) [#%(pk_type)s]\n') % ({
'name': self._payload['name_tt'],
'abbr': self._payload['abbrev_tt'],
'pk_type': self._payload['pk_test_type']
})
if self.is_long_text:
sso = gmTools.u_superscript_one
else:
sso = ''
tt += ' ' + _('%(sso)sResult: %(val)s%(unit)s%(ind)s [#%(pk_result)s]\n') % ({
'sso': sso,
'val': self._payload['unified_val'],
'unit': gmTools.coalesce(self._payload['val_unit'], '', ' %s'),
'ind': gmTools.coalesce(self._payload['abnormality_indicator'], '', ' (%s)'),
'pk_result': self._payload['pk_test_result']
})
if self._payload['status'] is not None:
try:
stat = HL7_RESULT_STATI[self._payload['status']]
except KeyError:
stat = self._payload['status']
tt += ' ' + _('Status: %s\n') % stat
if self._payload['val_grouping'] is not None:
tt += ' ' + _('Grouping: %s\n') % self._payload['val_grouping']
if with_evaluation:
norm_eval = None
if self._payload['val_num'] is not None:
# 1) normal range
# lowered ?
if (self._payload['val_normal_min'] is not None) and (self._payload['val_num'] < self._payload['val_normal_min']):
try:
percent = (self._payload['val_num'] * 100) / self._payload['val_normal_min']
except ZeroDivisionError:
percent = None
if percent is not None:
if percent < 6:
norm_eval = _('%.1f %% of the normal lower limit') % percent
else:
norm_eval = _('%.0f %% of the normal lower limit') % percent
# raised ?
if (self._payload['val_normal_max'] is not None) and (self._payload['val_num'] > self._payload['val_normal_max']):
try:
x_times = self._payload['val_num'] / self._payload['val_normal_max']
except ZeroDivisionError:
x_times = None
if x_times is not None:
if x_times < 10:
norm_eval = _('%.1f times the normal upper limit') % x_times
else:
norm_eval = _('%.0f times the normal upper limit') % x_times
if norm_eval is not None:
tt += ' = %s\n' % norm_eval
# #-------------------------------------
# # this idea was shot down on the list
# #-------------------------------------
# # bandwidth of deviation
# if None not in [self._payload['val_normal_min'], self._payload['val_normal_max']]:
# normal_width = self._payload['val_normal_max'] - self._payload['val_normal_min']
# deviation_from_normal_range = None
# # below ?
# if self._payload['val_num'] < self._payload['val_normal_min']:
# deviation_from_normal_range = self._payload['val_normal_min'] - self._payload['val_num']
# # above ?
# elif self._payload['val_num'] > self._payload['val_normal_max']:
# deviation_from_normal_range = self._payload['val_num'] - self._payload['val_normal_max']
# if deviation_from_normal_range is None:
# try:
# times_deviation = deviation_from_normal_range / normal_width
# except ZeroDivisionError:
# times_deviation = None
# if times_deviation is not None:
# if times_deviation < 10:
# tt += u' (%s)\n' % _(u'deviates by %.1f times of the normal range') % times_deviation
# else:
# tt += u' (%s)\n' % _(u'deviates by %.0f times of the normal range') % times_deviation
# #-------------------------------------
# 2) clinical target range
norm_eval = None
# lowered ?
if (self._payload['val_target_min'] is not None) and (self._payload['val_num'] < self._payload['val_target_min']):
try:
percent = (self._payload['val_num'] * 100) / self._payload['val_target_min']
except ZeroDivisionError:
percent = None
if percent is not None:
if percent < 6:
norm_eval = _('%.1f %% of the target lower limit') % percent
else:
norm_eval = _('%.0f %% of the target lower limit') % percent
# raised ?
if (self._payload['val_target_max'] is not None) and (self._payload['val_num'] > self._payload['val_target_max']):
try:
x_times = self._payload['val_num'] / self._payload['val_target_max']
except ZeroDivisionError:
x_times = None
if x_times is not None:
if x_times < 10:
norm_eval = _('%.1f times the target upper limit') % x_times
else:
norm_eval = _('%.0f times the target upper limit') % x_times
if norm_eval is not None:
tt += ' = %s\n' % norm_eval
# #-------------------------------------
# # this idea was shot down on the list
# #-------------------------------------
# # bandwidth of deviation
# if None not in [self._payload['val_target_min'], self._payload['val_target_max']]:
# normal_width = self._payload['val_target_max'] - self._payload['val_target_min']
# deviation_from_target_range = None
# # below ?
# if self._payload['val_num'] < self._payload['val_target_min']:
# deviation_from_target_range = self._payload['val_target_min'] - self._payload['val_num']
# # above ?
# elif self._payload['val_num'] > self._payload['val_target_max']:
# deviation_from_target_range = self._payload['val_num'] - self._payload['val_target_max']
# if deviation_from_target_range is None:
# try:
# times_deviation = deviation_from_target_range / normal_width
# except ZeroDivisionError:
# times_deviation = None
# if times_deviation is not None:
# if times_deviation < 10:
# tt += u' (%s)\n' % _(u'deviates by %.1f times of the target range') % times_deviation
# else:
# tt += u' (%s)\n' % _(u'deviates by %.0f times of the target range') % times_deviation
# #-------------------------------------
tmp = ('%s%s' % (
gmTools.coalesce(self._payload['name_test_org'], ''),
gmTools.coalesce(self._payload['contact_test_org'], '', ' (%s)'),
)).strip()
if tmp != '':
tt += ' ' + _('Source: %s\n') % tmp
tt += '\n'
if self._payload['note_test_org'] is not None:
tt += ' ' + gmTools.u_superscript_one + _('Lab comment: %s\n') % _('\n Lab comment: ').join(self._payload['note_test_org'].split('\n'))
if self._payload['comment'] is not None:
tt += ' ' + gmTools.u_superscript_one + _('Praxis comment: %s\n') % _('\n Praxis comment: ').join(self._payload['comment'].split('\n'))
if with_ranges:
tt += gmTools.coalesce(self.formatted_normal_range, '', ' ' + _('Standard normal range: %s\n'))
tt += gmTools.coalesce(self.formatted_clinical_range, '', ' ' + _('Clinical target range: %s\n'))
tt += gmTools.coalesce(self._payload['norm_ref_group'], '', ' ' + _('Reference group: %s\n'))
# metadata
if with_episode:
tt += ' ' + _('Episode: %s\n') % self._payload['episode']
if self._payload['health_issue'] is not None:
tt += ' ' + _('Issue: %s\n') % self._payload['health_issue']
if self._payload['material'] is not None:
tt += ' ' + _('Material: %s\n') % self._payload['material']
if self._payload['material_detail'] is not None:
tt += ' ' + _('Details: %s\n') % self._payload['material_detail']
tt += '\n'
if with_review:
if self._payload['reviewed']:
review = gmDateTime.pydt_strftime (
self._payload['last_reviewed'],
date_format
)
else:
review = _('not yet')
tt += _('Signed (%(sig_hand)s): %(reviewed)s\n') % ({
'sig_hand': gmTools.u_writing_hand,
'reviewed': review
})
tt += ' ' + _('Responsible clinician: %s\n') % gmTools.bool2subst (
self._payload['you_are_responsible'],
_('you'),
self._payload['responsible_reviewer']
)
if self._payload['reviewed']:
tt += ' ' + _('Last reviewer: %(reviewer)s\n') % ({
'reviewer': gmTools.bool2subst (
self._payload['review_by_you'],
_('you'),
gmTools.coalesce(self._payload['last_reviewer'], '?')
)
})
tt += ' ' + _(' Technically abnormal: %(abnormal)s\n') % ({
'abnormal': gmTools.bool2subst (
self._payload['is_technically_abnormal'],
_('yes'),
_('no'),
'?'
)
})
tt += ' ' + _(' Clinically relevant: %(relevant)s\n') % ({
'relevant': gmTools.bool2subst (
self._payload['is_clinically_relevant'],
_('yes'),
_('no'),
'?'
)
})
if self._payload['review_comment'] is not None:
tt += ' ' + _(' Comment: %s\n') % self._payload['review_comment'].strip()
tt += '\n'
# type
if with_type_details:
has_details = None not in [self._payload['comment_tt'], self._payload['pk_meta_test_type'], self._payload['comment_meta']]
if has_details:
tt += _('Test type details:\n')
if self._payload['comment_tt'] is not None:
tt += ' ' + _('Type comment: %s\n') % _('\n Type comment:').join(self._payload['comment_tt'].split('\n'))
if self._payload['pk_meta_test_type'] is not None:
tt += ' ' + _('Aggregated (%s) under: %s (%s) [#%s]\n') % (
gmTools.u_sum,
self._payload['name_meta'],
self._payload['abbrev_meta'],
self._payload['pk_meta_test_type']
)
if self._payload['comment_meta'] is not None:
tt += ' ' + _('Group comment: %s\n') % _('\n Group comment: ').join(self._payload['comment_meta'].split('\n'))
if has_details:
tt += '\n'
if with_source_data:
if self._payload['source_data'] is not None:
tt += _('Source data:\n')
tt += ' ' + self._payload['source_data']
tt += '\n\n'
if with_review:
tt += _('Revisions: %(row_ver)s, last %(mod_when)s by %(mod_by)s.') % ({
'row_ver': self._payload['row_version'],
'mod_when': gmDateTime.pydt_strftime(self._payload['modified_when'],date_format),
'mod_by': self._payload['modified_by']
})
return tt
#--------------------------------------------------------
def _get_has_normal_min_or_max(self):
return (
self._payload['val_normal_min'] is not None
) or (
self._payload['val_normal_max'] is not None
)
has_normal_min_or_max = property(_get_has_normal_min_or_max)
#--------------------------------------------------------
def _get_normal_min_max(self):
has_range_info = (
self._payload['val_normal_min'] is not None
) or (
self._payload['val_normal_max'] is not None
)
if has_range_info is False:
return None
return '%s - %s' % (
gmTools.coalesce(self._payload['val_normal_min'], '?'),
gmTools.coalesce(self._payload['val_normal_max'], '?')
)
normal_min_max = property(_get_normal_min_max)
#--------------------------------------------------------
def _get_formatted_normal_range(self):
has_numerical_range = (
self._payload['val_normal_min'] is not None
) or (
self._payload['val_normal_max'] is not None
)
if has_numerical_range:
numerical_range = '%s - %s' % (
gmTools.coalesce(self._payload['val_normal_min'], '?'),
gmTools.coalesce(self._payload['val_normal_max'], '?')
)
else:
numerical_range = ''
textual_range = gmTools.coalesce (
self._payload['val_normal_range'],
'',
gmTools.bool2subst (
has_numerical_range,
' / %s',
'%s'
)
)
range_info = '%s%s' % (numerical_range, textual_range)
if range_info == '':
return None
return range_info
formatted_normal_range = property(_get_formatted_normal_range)
#--------------------------------------------------------
def _get_has_clinical_min_or_max(self):
return (
self._payload['val_target_min'] is not None
) or (
self._payload['val_target_max'] is not None
)
has_clinical_min_or_max = property(_get_has_clinical_min_or_max)
#--------------------------------------------------------
def _get_clinical_min_max(self):
has_range_info = (
self._payload['val_target_min'] is not None
) or (
self._payload['val_target_max'] is not None
)
if has_range_info is False:
return None
return '%s - %s' % (
gmTools.coalesce(self._payload['val_target_min'], '?'),
gmTools.coalesce(self._payload['val_target_max'], '?')
)
clinical_min_max = property(_get_clinical_min_max)
#--------------------------------------------------------
def _get_formatted_clinical_range(self):
has_numerical_range = (
self._payload['val_target_min'] is not None
) or (
self._payload['val_target_max'] is not None
)
if has_numerical_range:
numerical_range = '%s - %s' % (
gmTools.coalesce(self._payload['val_target_min'], '?'),
gmTools.coalesce(self._payload['val_target_max'], '?')
)
else:
numerical_range = ''
textual_range = gmTools.coalesce (
self._payload['val_target_range'],
'',
gmTools.bool2subst (
has_numerical_range,
' / %s',
'%s'
)
)
range_info = '%s%s' % (numerical_range, textual_range)
if range_info == '':
return None
return range_info
formatted_clinical_range = property(_get_formatted_clinical_range)
#--------------------------------------------------------
def _get_temporally_closest_normal_range(self):
"""Returns the closest test result which does have normal range information."""
if self._payload['val_normal_min'] is not None:
return self
if self._payload['val_normal_max'] is not None:
return self
if self._payload['val_normal_range'] is not None:
return self
cmd = """
SELECT * from clin.v_test_results
WHERE
pk_type = %(pk_type)s
AND
val_unit = %(unit)s
AND
(
(val_normal_min IS NOT NULL)
OR
(val_normal_max IS NOT NULL)
OR
(val_normal_range IS NOT NULL)
)
ORDER BY
CASE
WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s
ELSE %(clin_when)s - clin_when
END
LIMIT 1"""
args = {
'pk_type': self._payload['pk_test_type'],
'unit': self._payload['val_unit'],
'clin_when': self._payload['clin_when']
}
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
temporally_closest_normal_range = property(_get_temporally_closest_normal_range)
#--------------------------------------------------------
def _get_formatted_range(self):
has_normal_min_or_max = (
self._payload['val_normal_min'] is not None
) or (
self._payload['val_normal_max'] is not None
)
if has_normal_min_or_max:
normal_min_max = '%s - %s' % (
gmTools.coalesce(self._payload['val_normal_min'], '?'),
gmTools.coalesce(self._payload['val_normal_max'], '?')
)
has_clinical_min_or_max = (
self._payload['val_target_min'] is not None
) or (
self._payload['val_target_max'] is not None
)
if has_clinical_min_or_max:
clinical_min_max = '%s - %s' % (
gmTools.coalesce(self._payload['val_target_min'], '?'),
gmTools.coalesce(self._payload['val_target_max'], '?')
)
if has_clinical_min_or_max:
return _('Target: %(clin_min_max)s%(clin_range)s') % ({
'clin_min_max': clinical_min_max,
'clin_range': gmTools.coalesce (
self._payload['val_target_range'],
'',
gmTools.bool2subst (
has_clinical_min_or_max,
' / %s',
'%s'
)
)
})
if has_normal_min_or_max:
return _('Norm: %(norm_min_max)s%(norm_range)s') % ({
'norm_min_max': normal_min_max,
'norm_range': gmTools.coalesce (
self._payload['val_normal_range'],
'',
gmTools.bool2subst (
has_normal_min_or_max,
' / %s',
'%s'
)
)
})
if self._payload['val_target_range'] is not None:
return _('Target: %s') % self._payload['val_target_range'],
if self._payload['val_normal_range'] is not None:
return _('Norm: %s') % self._payload['val_normal_range']
return None
formatted_range = property(_get_formatted_range)
#--------------------------------------------------------
def _get_test_type(self):
return cMeasurementType(aPK_obj = self._payload['pk_test_type'])
test_type = property(_get_test_type)
#--------------------------------------------------------
def _get_is_considered_elevated(self):
# 1) the user is right (review)
if self._payload['is_technically_abnormal'] is False:
return False
# 2) the lab is right (result.abnormality_indicator)
indicator = self._payload['abnormality_indicator']
if indicator is not None:
indicator = indicator.strip()
if indicator != '':
if indicator.strip('+') == '':
return True
if indicator.strip('-') == '':
return False
# 3) non-numerical value ?
if self._payload['val_num'] is None:
return None
# 4) the target range is right
target_max = self._payload['val_target_max']
if target_max is not None:
if target_max < self._payload['val_num']:
return True
# 4) the normal range is right
normal_max = self._payload['val_normal_max']
if normal_max is not None:
if normal_max < self._payload['val_num']:
return True
return None
is_considered_elevated = property(_get_is_considered_elevated)
#--------------------------------------------------------
def _get_is_considered_lowered(self):
# 1) the user is right (review)
if self._payload['is_technically_abnormal'] is False:
return False
# 2) the lab is right (result.abnormality_indicator)
indicator = self._payload['abnormality_indicator']
if indicator is not None:
indicator = indicator.strip()
if indicator != '':
if indicator.strip('+') == '':
return False
if indicator.strip('-') == '':
return True
# 3) non-numerical value ?
if self._payload['val_num'] is None:
return None
# 4) the target range is right
target_min = self._payload['val_target_min']
if target_min is not None:
if target_min > self._payload['val_num']:
return True
# 4) the normal range is right
normal_min = self._payload['val_normal_min']
if normal_min is not None:
if normal_min > self._payload['val_num']:
return True
return None
is_considered_lowered = property(_get_is_considered_lowered)
#--------------------------------------------------------
def _get_is_considered_abnormal(self):
if self.is_considered_lowered is True:
return True
if self.is_considered_elevated is True:
return True
if (self.is_considered_lowered is False) and (self.is_considered_elevated is False):
return False
return self._payload['is_technically_abnormal']
is_considered_abnormal = property(_get_is_considered_abnormal)
#--------------------------------------------------------
def _set_reference_range(self, ref_range):
"""Parse reference range from string.
Note: does NOT save the result.
"""
ref_range = ref_range.strip().replace(' ', '')
is_range = regex.match(r'-{0,1}\d+[.,]{0,1}\d*--{0,1}\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE)
if is_range is not None:
min_val = regex.match(r'-{0,1}\d+[.,]{0,1}\d*-', ref_range, regex.UNICODE).group(0).rstrip('-')
success, min_val = gmTools.input2decimal(min_val)
max_val = (regex.search(r'--{0,1}\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE).group(0))[1:]
success, max_val = gmTools.input2decimal(max_val)
self['val_normal_min'] = min_val
self['val_normal_max'] = max_val
return
if ref_range.startswith('<'):
is_range = regex.match(r'<\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE)
if is_range is not None:
max_val = ref_range[1:]
success, max_val = gmTools.input2decimal(max_val)
self['val_normal_min'] = 0
self['val_normal_max'] = max_val
return
if ref_range.startswith('<-'):
is_range = regex.match(r'<-\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE)
if is_range is not None:
max_val = ref_range[1:]
success, max_val = gmTools.input2decimal(max_val)
self['val_normal_min'] = None
self['val_normal_max'] = max_val
return
if ref_range.startswith('>'):
is_range = regex.match(r'>\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE)
if is_range is not None:
min_val = ref_range[1:]
success, min_val = gmTools.input2decimal(min_val)
self['val_normal_min'] = min_val
self['val_normal_max'] = None
return
if ref_range.startswith('>-'):
is_range = regex.match(r'>-\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE)
if is_range is not None:
min_val = ref_range[1:]
success, min_val = gmTools.input2decimal(min_val)
self['val_normal_min'] = min_val
self['val_normal_max'] = 0
return
self['val_normal_range'] = ref_range
return
reference_range = property(lambda x:x, _set_reference_range)
#--------------------------------------------------------
def _get_formatted_abnormality_indicator(self):
# 1) the user is right
if self._payload['is_technically_abnormal'] is False:
return ''
# 2) the lab is right (result.abnormality_indicator)
indicator = self._payload['abnormality_indicator']
if indicator is not None:
indicator = indicator.strip()
if indicator != '':
return indicator
# 3) non-numerical value ? then we can't know more
if self._payload['val_num'] is None:
return None
# 4) the target range is right
target_min = self._payload['val_target_min']
if target_min is not None:
if target_min > self._payload['val_num']:
return '-'
target_max = self._payload['val_target_max']
if target_max is not None:
if target_max < self._payload['val_num']:
return '+'
# 4) the normal range is right
normal_min = self._payload['val_normal_min']
if normal_min is not None:
if normal_min > self._payload['val_num']:
return '-'
normal_max = self._payload['val_normal_max']
if normal_max is not None:
if normal_max < self._payload['val_num']:
return '+'
# reviewed, abnormal, but no indicator available
if self._payload['is_technically_abnormal'] is True:
return gmTools.u_plus_minus
return None
formatted_abnormality_indicator = property(_get_formatted_abnormality_indicator)
#--------------------------------------------------------
def _get_is_long_text(self):
if self._payload['val_alpha'] is None:
return False
lines = gmTools.strip_empty_lines(text = self._payload['val_alpha'], eol = '\n', return_list = True)
if len(lines) > 4:
return True
return False
is_long_text = property(_get_is_long_text)
#--------------------------------------------------------
def _get_estimate_numeric_value_from_alpha(self):
if self._payload['val_alpha'] is None:
return None
val = self._payload['val_alpha'].lstrip()
if val[0] == '<':
factor = decimal.Decimal(0.5)
val = val[1:]
elif val[0] == '>':
factor = 2
val = val[1:]
else:
return None
success, val = gmTools.input2decimal(initial = val)
if not success:
return None
return val * factor
estimate_numeric_value_from_alpha = property(_get_estimate_numeric_value_from_alpha)
#--------------------------------------------------------
def set_review(self, technically_abnormal=None, clinically_relevant=None, comment=None, make_me_responsible=False):
# FIXME: this is not concurrency safe
if self._payload['reviewed']:
self.__change_existing_review (
technically_abnormal = technically_abnormal,
clinically_relevant = clinically_relevant,
comment = comment
)
else:
# do not sign off unreviewed results if
# NOTHING AT ALL is known about them
if technically_abnormal is None:
if clinically_relevant is None:
comment = gmTools.none_if(comment, '', strip_string = True)
if comment is None:
if make_me_responsible is False:
return True
self.__set_new_review (
technically_abnormal = technically_abnormal,
clinically_relevant = clinically_relevant,
comment = comment
)
if make_me_responsible is True:
cmd = "SELECT pk FROM dem.staff WHERE db_user = current_user"
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}])
self['pk_intended_reviewer'] = rows[0][0]
self.save_payload()
return
self.refetch_payload()
#--------------------------------------------------------
def get_adjacent_results(self, desired_earlier_results=1, desired_later_results=1, max_offset=None):
if desired_earlier_results < 1:
raise ValueError('<desired_earlier_results> must be > 0')
if desired_later_results < 1:
raise ValueError('<desired_later_results> must be > 0')
args = {
'pat': self._payload['pk_patient'],
'ttyp': self._payload['pk_test_type'],
'tloinc': self._payload['loinc_tt'],
'mtyp': self._payload['pk_meta_test_type'],
'mloinc': self._payload['loinc_meta'],
'when': self._payload['clin_when'],
'offset': max_offset
}
WHERE = '((pk_test_type = %(ttyp)s) OR (loinc_tt = %(tloinc)s))'
WHERE_meta = '((pk_meta_test_type = %(mtyp)s) OR (loinc_meta = %(mloinc)s))'
if max_offset is not None:
WHERE = WHERE + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))'
WHERE_meta = WHERE_meta + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))'
SQL = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %%(pat)s
AND
clin_when %s %%(when)s
AND
%s
ORDER BY clin_when
LIMIT %s"""
# get earlier results
earlier_results = []
# by type
cmd = SQL % ('<', WHERE, desired_earlier_results)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ])
# by meta type ?
missing_results = desired_earlier_results - len(earlier_results)
if missing_results > 0:
cmd = SQL % ('<', WHERE_meta, missing_results)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ])
# get later results
later_results = []
# by type
cmd = SQL % ('>', WHERE, desired_later_results)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ])
# by meta type ?
missing_results = desired_later_results - len(later_results)
if missing_results > 0:
cmd = SQL % ('>', WHERE_meta, missing_results)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ])
return earlier_results, later_results
#--------------------------------------------------------
# internal API
#--------------------------------------------------------
def __set_new_review(self, technically_abnormal=None, clinically_relevant=None, comment=None):
"""Add a review to a row.
- if technically abnormal is not provided/None it will be set
to True if the lab's indicator has a meaningful value
- if clinically relevant is not provided/None it is set to
whatever technically abnormal is
"""
if technically_abnormal is None:
technically_abnormal = False
if self._payload['abnormality_indicator'] is not None:
if self._payload['abnormality_indicator'].strip() != '':
technically_abnormal = True
if clinically_relevant is None:
clinically_relevant = technically_abnormal
cmd = """
INSERT INTO clin.reviewed_test_results (
fk_reviewed_row,
is_technically_abnormal,
clinically_relevant,
comment
) VALUES (
%(pk)s,
%(abnormal)s,
%(relevant)s,
gm.nullify_empty_string(%(cmt)s)
)"""
args = {
'pk': self._payload['pk_test_result'],
'abnormal': technically_abnormal,
'relevant': clinically_relevant,
'cmt': comment
}
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#--------------------------------------------------------
def __change_existing_review(self, technically_abnormal=None, clinically_relevant=None, comment=None):
"""Change a review on a row.
- if technically abnormal/clinically relevant are
None they are not set
"""
args = {
'pk_result': self._payload['pk_test_result'],
'abnormal': technically_abnormal,
'relevant': clinically_relevant,
'cmt': comment
}
set_parts = [
'fk_reviewer = (SELECT pk FROM dem.staff WHERE db_user = current_user)',
'comment = gm.nullify_empty_string(%(cmt)s)'
]
if technically_abnormal is not None:
set_parts.append('is_technically_abnormal = %(abnormal)s')
if clinically_relevant is not None:
set_parts.append('clinically_relevant = %(relevant)s')
cmd = """
UPDATE clin.reviewed_test_results SET
%s
WHERE
fk_reviewed_row = %%(pk_result)s
""" % ',\n '.join(set_parts)
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
#------------------------------------------------------------
def get_test_results(pk_patient=None, encounters=None, episodes=None, order_by=None, return_pks=False):
where_parts = []
if pk_patient is not None:
where_parts.append('pk_patient = %(pat)s')
args = {'pat': pk_patient}
# if tests is not None:
# where_parts.append(u'pk_test_type = ANY(%(tests)s)')
# args['tests'] = tests
if encounters is not None:
where_parts.append('pk_encounter = ANY(%(encs)s)')
args['encs'] = encounters
if episodes is not None:
where_parts.append('pk_episode = ANY(%(epis)s)')
args['epis'] = episodes
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
cmd = """
SELECT * FROM clin.v_test_results
WHERE %s
%s
""" % (
' AND '.join(where_parts),
order_by
)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if return_pks:
return [ r['pk_test_result'] for r in rows ]
tests = [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
return tests
#------------------------------------------------------------
def get_most_recent_results_for_panel(pk_patient=None, pk_panel=None, order_by=None, group_by_meta_type=False):
if order_by is None:
order_by = ''
else:
order_by = 'ORDER BY %s' % order_by
args = {
'pat': pk_patient,
'pk_pnl': pk_panel
}
if group_by_meta_type:
# return most recent results in panel grouped by
# meta test type if any, non-grouped results are
# returned ungrouped :-)
cmd = """
SELECT c_vtr.*
FROM (
-- max(clin_when) per test_type-in-panel for patient
SELECT
pk_meta_test_type,
MAX(clin_when) AS max_clin_when
FROM clin.v_test_results
WHERE
pk_patient = %(pat)s
AND
pk_meta_test_type IS DISTINCT FROM NULL
AND
pk_test_type IN (
(SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s)
)
GROUP BY pk_meta_test_type
) AS latest_results
INNER JOIN clin.v_test_results c_vtr ON
c_vtr.pk_meta_test_type = latest_results.pk_meta_test_type
AND
c_vtr.clin_when = latest_results.max_clin_when
UNION ALL
SELECT c_vtr.*
FROM (
-- max(clin_when) per test_type-in-panel for patient
SELECT
pk_test_type,
MAX(clin_when) AS max_clin_when
FROM clin.v_test_results
WHERE
pk_patient = %(pat)s
AND
pk_meta_test_type IS NULL
AND
pk_test_type IN (
(SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s)
)
GROUP BY pk_test_type
) AS latest_results
INNER JOIN clin.v_test_results c_vtr ON
c_vtr.pk_test_type = latest_results.pk_test_type
AND
c_vtr.clin_when = latest_results.max_clin_when
"""
else:
# return most recent results in panel regardless of whether
# distinct test types in this panel are grouped under the
# same meta test type
cmd = """
SELECT c_vtr.*
FROM (
-- max(clin_when) per test_type-in-panel for patient
SELECT
pk_test_type,
MAX(clin_when) AS max_clin_when
FROM clin.v_test_results
WHERE
pk_patient = %(pat)s
AND
pk_test_type IN (
(SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s)
)
GROUP BY pk_test_type
) AS latest_results
-- this INNER join makes certain we do not expand
-- the row selection beyond the patient's rows
-- which we constrained to inside the SELECT
-- producing "latest_results"
INNER JOIN clin.v_test_results c_vtr ON
c_vtr.pk_test_type = latest_results.pk_test_type
AND
c_vtr.clin_when = latest_results.max_clin_when
"""
cmd += order_by
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_result_at_timestamp(timestamp=None, test_type=None, loinc=None, tolerance_interval=None, patient=None):
if None not in [test_type, loinc]:
raise ValueError('either <test_type> or <loinc> must be None')
args = {
'pat': patient,
'ttyp': test_type,
'loinc': loinc,
'ts': timestamp,
'intv': tolerance_interval
}
where_parts = ['pk_patient = %(pat)s']
if test_type is not None:
where_parts.append('pk_test_type = %(ttyp)s') # consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type']
elif loinc is not None:
where_parts.append('((loinc_tt = ANY(%(loinc)s)) OR (loinc_meta = ANY(%(loinc)s)))')
args['loinc'] = loinc
if tolerance_interval is None:
where_parts.append('clin_when = %(ts)s')
else:
where_parts.append('clin_when between (%(ts)s - %(intv)s::interval) AND (%(ts)s + %(intv)s::interval)')
cmd = """
SELECT * FROM clin.v_test_results
WHERE
%s
ORDER BY
abs(extract(epoch from age(clin_when, %%(ts)s)))
LIMIT 1""" % ' AND '.join(where_parts)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
#------------------------------------------------------------
def get_results_for_day(timestamp=None, patient=None, order_by=None):
args = {
'pat': patient,
'ts': timestamp
}
where_parts = [
'pk_patient = %(pat)s',
"date_trunc('day'::text, clin_when) = date_trunc('day'::text, %(ts)s)"
]
cmd = """
SELECT * FROM clin.v_test_results
WHERE
%s
ORDER BY
val_grouping,
abbrev_tt,
clin_when DESC
""" % ' AND '.join(where_parts)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_results_for_issue(pk_health_issue=None, order_by=None):
args = {'pk_issue': pk_health_issue}
where_parts = ['pk_health_issue = %(pk_issue)s']
cmd = """
SELECT * FROM clin.v_test_results
WHERE %s
ORDER BY
val_grouping,
abbrev_tt,
clin_when DESC
""" % ' AND '.join(where_parts)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_results_for_episode(pk_episode=None):
args = {'pk_epi': pk_episode}
where_parts = ['pk_episode = %(pk_epi)s']
cmd = """
SELECT * FROM clin.v_test_results
WHERE %s
ORDER BY
val_grouping,
abbrev_tt,
clin_when DESC
""" % ' AND '.join(where_parts)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_most_recent_results_in_loinc_group(loincs=None, max_no_of_results=1, patient=None, max_age=None, consider_indirect_matches=False):
"""Get N most recent results *among* a list of tests selected by LOINC.
1) get test types with LOINC (or meta type LOINC) in the group of <loincs>
2) from these get the test results for <patient> within the given <max_age>
3) from these return "the N=<max_no_of_results> most recent ones" or "None"
<loinc> must be a list or tuple or set, NOT a single string
<max_age> must be a string holding a PG interval or else a pydt interval
"""
assert (max_no_of_results > 0), '<max_no_of_results> must be >0'
args = {'pat': patient, 'loincs': loincs}
if max_age is None:
max_age_cond = ''
else:
max_age_cond = 'AND clin_when > (now() - %(max_age)s::interval)'
args['max_age'] = max_age
cmd = """
SELECT * FROM (
SELECT DISTINCT ON (pk_test_result) *
FROM clin.v_test_results
WHERE
pk_patient = %%(pat)s
AND
unified_loinc = ANY(%%(loincs)s)
%s
) AS distinct_results
ORDER BY
clin_when DESC
LIMIT %s""" % (
max_age_cond,
max_no_of_results
)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) > 0:
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
if not consider_indirect_matches:
return []
cmd = """
-- get the test results
SELECT * FROM clin.v_test_results c_vtr
WHERE
-- for this <patient>
pk_patient = %%(pat)s
AND
-- not having *any* LOINC (if the result did have a LOINC and had not been caught by the by-LOINC search it does not apply)
unified_loinc IS NULL
AND
-- with these meta test types (= results for the explicit equivalance group)
c_vtr.pk_meta_test_type IN (
-- get the meta test types for those types
SELECT pk_meta_test_type
FROM clin.v_test_types
WHERE
pk_meta_test_type IS NOT NULL
AND
(-- retrieve test types which have .LOINC in <loincs>
(loinc IN %%(loincs)s)
OR
(loinc_meta IN %%(loincs)s)
)
AND
-- but no result for <patient>
pk_test_type NOT IN (
select pk_test_type from clin.v_test_results WHERE pk_patient = %%(pat)s
) %s
)
-- return the N most resent result
ORDER BY clin_when DESC
LIMIT %s
""" % (
max_age_cond,
max_no_of_results
)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_most_recent_results_for_test_type(test_type=None, max_no_of_results=1, patient=None):
"""Get N most recent results for *one* defined test type."""
assert (test_type is not None), '<test_type> must not be None'
assert (max_no_of_results > 0), '<max_no_of_results> must be > 0'
args = {'pat': patient, 'ttyp': test_type}
where_parts = ['pk_patient = %(pat)s']
where_parts.append('pk_test_type = %(ttyp)s') # ?consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type']
cmd = """
SELECT * FROM clin.v_test_results
WHERE
%s
ORDER BY clin_when DESC
LIMIT %s""" % (
' AND '.join(where_parts),
max_no_of_results
)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
_SQL_most_recent_result_for_test_types = """
-- return the one most recent result for each of a list of test types
-- without regard to whether they belong to a meta test type
SELECT * FROM (
SELECT
*,
MAX(clin_when) OVER relevant_tests AS max_clin_when
FROM
clin.v_test_results
WHERE
%s
WINDOW relevant_tests AS (PARTITION BY pk_patient, pk_test_type)
) AS windowed_tests
WHERE
clin_when = max_clin_when
%s
"""
_SQL_most_recent_result_for_test_types_without_meta_type = """
-- return the one most recent result for each of a list of test types
-- none of which may belong to a meta test type
SELECT * FROM (
SELECT
*,
MAX(clin_when) OVER relevant_tests AS max_clin_when
FROM
clin.v_test_results
WHERE
pk_meta_test_type IS NULL
AND
%s
WINDOW relevant_tests AS (PARTITION BY pk_patient, pk_test_type)
) AS windowed_tests
WHERE
clin_when = max_clin_when
"""
_SQL_most_recent_result_for_test_types_by_meta_type = """
-- return the one most recent result for each of a list of meta test types
-- derived from a list of test types
SELECT * FROM (
SELECT
*,
MAX(clin_when) OVER relevant_tests AS max_clin_when
FROM
clin.v_test_results
WHERE
pk_meta_test_type IS NOT NULL
AND
%s
WINDOW relevant_tests AS (PARTITION BY pk_patient, pk_meta_test_type)
) AS windowed_tests
WHERE
clin_when = max_clin_when
"""
def get_most_recent_result_for_test_types(pk_test_types=None, pk_patient=None, return_pks=False, consider_meta_type=False, order_by=None):
"""Return the one most recent result for *each* of a list of test types.
If <pk_test_types> is not given, most recent results for *each*
test type the patient has any results for is returned.
"""
where_parts = ['pk_patient = %(pat)s']
args = {'pat': pk_patient}
if pk_test_types is not None:
where_parts.append('pk_test_type = ANY(%(ttyps)s)')
args['ttyps'] = pk_test_types
order_by = 'ORDER BY clin_when DESC' if order_by is None else 'ORDER BY %s' % order_by
if consider_meta_type:
cmd = 'SELECT * FROM ((%s) UNION ALL (%s)) AS result_union %s' % (
_SQL_most_recent_result_for_test_types_without_meta_type % ' AND '.join(where_parts),
_SQL_most_recent_result_for_test_types_by_meta_type % ' AND '.join(where_parts),
order_by
)
else:
cmd = _SQL_most_recent_result_for_test_types % (
' AND '.join(where_parts),
order_by
)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if return_pks:
return [ r['pk_test_result'] for r in rows ]
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_most_recent_results_for_patient(no_of_results=1, patient=None):
"""Get N most recent results for a given patient."""
if no_of_results < 1:
raise ValueError('<no_of_results> must be > 0')
args = {'pat': patient}
cmd = """
SELECT * FROM clin.v_test_results
WHERE
pk_patient = %%(pat)s
ORDER BY clin_when DESC
LIMIT %s""" % no_of_results
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]
#------------------------------------------------------------
def get_oldest_result(test_type=None, loinc=None, patient=None):
if None not in [test_type, loinc]:
raise ValueError('either <test_type> or <loinc> must be None')
args = {
'pat': patient,
'ttyp': test_type,
'loinc': loinc
}
where_parts = ['pk_patient = %(pat)s']
if test_type is not None:
where_parts.append('pk_test_type = %(ttyp)s') # consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type']
elif loinc is not None:
where_parts.append('((loinc_tt = ANY(%(loinc)s)) OR (loinc_meta = ANY(%(loinc)s)))')
args['loinc'] = loinc
cmd = """
SELECT * FROM clin.v_test_results
WHERE
%s
ORDER BY clin_when
LIMIT 1""" % ' AND '.join(where_parts)
rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}])
if len(rows) == 0:
return None
return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]})
#------------------------------------------------------------
def delete_test_result(result=None):
try:
pk = int(result)
except (TypeError, AttributeError):
pk = result['pk_test_result']
cmd = 'DELETE FROM clin.test_result WHERE pk = %(pk)s'
gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': {'pk': pk}}])
#------------------------------------------------------------
def create_test_result(encounter=None, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None):
cmd1 = """
INSERT INTO clin.test_result (
fk_encounter,
fk_episode,
fk_type,
fk_intended_reviewer,
val_num,
val_alpha,
val_unit
) VALUES (
%(enc)s,
%(epi)s,
%(type)s,
%(rev)s,
%(v_num)s,
%(v_alpha)s,
%(unit)s
)
"""
cmd2 = "SELECT * from clin.v_test_results WHERE pk_test_result = currval(pg_get_serial_sequence('clin.test_result', 'pk'))"
args = {
'enc': encounter,
'epi': episode,
'type': type,
'rev': intended_reviewer,
'v_num': val_num,
'v_alpha': val_alpha,
'unit': unit
}
rows = gmPG2.run_rw_queries (
link_obj = link_obj,
queries = [
{'cmd': cmd1, 'args': args},
{'cmd': cmd2}
],
return_data = True
)
tr = cTestResult(row = {
'pk_field': 'pk_test_result',
'data': rows[0]
})
return tr
#------------------------------------------------------------
def generate_failsafe_test_results_entries(pk_patient:int=None, test_results:list[cTestResult]=None, max_width:int=80) -> list[str]:
if not test_results:
if pk_patient:
test_results = get_test_results(pk_patient = 12, order_by = 'unified_abbrev, clin_when DESC')
if not test_results:
return []
prev_abbrev = None
lines = []
for tr in test_results:
abbrev = tr['unified_abbrev']
if abbrev != prev_abbrev:
lines.append('')
lines.append('%s - %s' % (abbrev, tr['unified_name']))
prev_abbrev = abbrev
line = ' %s: %s %s%s%s' % (
tr['clin_when'].strftime('%Y %b %d %H:%m'),
tr['unified_val'],
tr['val_unit'],
gmTools.bool2subst(tr.is_considered_abnormal, ' !', '', ''),
gmTools.coalesce(tr.formatted_range, '', ' (%s)')
)
lines.append(gmTools.shorten_text(line, max_width))
if tr['note_test_org']:
cmt = _(' Lab: %s') % tr['note_test_org'].replace('\n', ' // ')
lines.append(gmTools.shorten_text(cmt, max_width))
if tr['comment']:
cmt = _(' Praxis: %s') % tr['comment'].replace('\n', ' // ')
lines.append(gmTools.shorten_text(cmt, max_width))
return lines
#------------------------------------------------------------
def format_test_results(results=None, output_format='latex'):
_log.debug('formatting test results into [%s]', output_format)
if output_format == 'latex':
return __format_test_results_latex(results = results)
msg = _('unknown test results output format [%s]') % output_format
_log.error(msg)
return msg
#------------------------------------------------------------
def __tests2latex_minipage(results=None, width='1.5cm', show_time=False, show_range=True):
if len(results) == 0:
return '\\begin{minipage}{%s} \\end{minipage}' % width
lines = []
for t in results:
tmp = ''
if show_time:
tmp += '{\\tiny (%s)} ' % t['clin_when'].strftime('%H:%M')
tmp += '%.8s' % t['unified_val']
lines.append(tmp)
tmp = ''
if show_range:
has_range = (
t['unified_target_range'] is not None
or
t['unified_target_min'] is not None
or
t['unified_target_max'] is not None
)
if has_range:
if t['unified_target_range'] is not None:
tmp += '{\\tiny %s}' % t['unified_target_range']
else:
tmp += '{\\tiny %s%s}' % (
gmTools.coalesce(t['unified_target_min'], '- ', '%s - '),
gmTools.coalesce(t['unified_target_max'], '', '%s')
)
lines.append(tmp)
return '\\begin{minipage}{%s} \\begin{flushright} %s \\end{flushright} \\end{minipage}' % (width, ' \\\\ '.join(lines))
#------------------------------------------------------------
def __tests2latex_cell(results=None, show_time=False, show_range=True):
if len(results) == 0:
return ''
lines = []
for t in results:
tmp = ''
if show_time:
tmp += '\\tiny %s ' % t['clin_when'].strftime('%H:%M')
tmp += '\\normalsize %.8s' % t['unified_val']
lines.append(tmp)
tmp = '\\tiny %s' % gmTools.coalesce(t['val_unit'], '', '%s ')
if not show_range:
lines.append(tmp)
continue
has_range = (
t['unified_target_range'] is not None
or
t['unified_target_min'] is not None
or
t['unified_target_max'] is not None
)
if not has_range:
lines.append(tmp)
continue
if t['unified_target_range'] is not None:
tmp += '[%s]' % t['unified_target_range']
else:
tmp += '[%s%s]' % (
gmTools.coalesce(t['unified_target_min'], '--', '%s--'),
gmTools.coalesce(t['unified_target_max'], '', '%s')
)
lines.append(tmp)
return ' \\\\ '.join(lines)
#------------------------------------------------------------
def __format_test_results_latex(results=None):
if len(results) == 0:
return '\\noindent %s' % _('No test results to format.')
# discover the columns and rows
dates = {}
tests = {}
grid = {}
for result in results:
# row_label = u'%s \\ \\tiny (%s)}' % (result['unified_abbrev'], result['unified_name'])
row_label = result['unified_abbrev']
tests[row_label] = None
col_label = '{\\scriptsize %s}' % result['clin_when'].strftime('%Y-%m-%d')
dates[col_label] = None
try:
grid[row_label]
except KeyError:
grid[row_label] = {}
try:
grid[row_label][col_label].append(result)
except KeyError:
grid[row_label][col_label] = [result]
col_labels = sorted(dates, reverse = True)
del dates
row_labels = sorted(tests)
del tests
col_def = len(col_labels) * '>{\\raggedleft}p{1.7cm}|'
# format them
tex = """\\noindent %s
\\noindent \\begin{tabular}{|l|%s}
\\hline
& %s \\tabularnewline
\\hline
%%s \\tabularnewline
\\hline
\\end{tabular}""" % (
_('Test results'),
col_def,
' & '.join(col_labels)
)
rows = []
# loop over rows
for rl in row_labels:
cells = [rl]
# loop over cols per row
for cl in col_labels:
try:
# get tests for this (row/col) position
tests = grid[rl][cl]
except KeyError:
# none there, so insert empty cell
cells.append(' ')
continue
cells.append (
__tests2latex_cell (
results = tests,
show_time = (len(tests) > 1),
show_range = True
)
)
rows.append(' & '.join(cells))
return tex % ' \\tabularnewline\n \\hline\n'.join(rows)
#============================================================
GPLOT_DATAFILE_HEADER = """#
# -------------------------------------------------------------
# GNUmed test results export for Gnuplot plotting
# -------------------------------------------------------------
#
# There is one (gnuplot) index per test type. Two blank
# lines will separate indices.
#
# The first line of each index contains test type abbreviation
# and test type name which can be used as title for plots:
# set key ... autotitle columnheader)
#
# Each index contains one test result per line.
#
# Columns in each line:
# 1 - clin_when at full precision:
# set timefmt "%%Y-%%m-%%d_%%H:%%M"
# timecolumn(1, "%%Y-%%m-%%d_%%H:%%M")
# 2 - value
# 3 - unit
# 4 - unified (target or normal) range: lower bound
# 5 - unified (target or normal) range: upper bound
# 6 - normal range: lower bound
# 7 - normal range: upper bound
# 8 - target range: lower bound
# 9 - target range: upper bound
# 10 - clin_when formatted into string (say, as x-axis tic label)
#
# If the timestamp of consecutive test results is on one and the
# same day one blank line is inserted such that a discontinuous
# line can be plotted if desired.
#
# -------------------------------------------------------------
#
# the file
#
# <%s.conf>
#
# will contain various gnuplot settings specific to this plot,
# such as <ylabel>, <y2label>, <title>,
# there will also be settings suitable for stacked multiplots
# -------------------------------------------------------------
"""
def export_results_for_gnuplot(results=None, filename=None, show_year=True, patient=None):
sandbox_dir = os.path.join(gmTools.gmPaths().tmp_dir, 'gplot')
if not gmTools.mkdir(sandbox_dir):
sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'gm2gpl-')
_log.debug('sandbox directory: [%s]', sandbox_dir)
if filename is None:
filename = gmTools.get_unique_filename(prefix = 'gm2gpl-', suffix = '.dat', tmp_dir = sandbox_dir)
# sort results into groups by test type
results_grouped_by_test_type = {}
for r in results:
try:
results_grouped_by_test_type[r['unified_name']].append(r)
except KeyError:
results_grouped_by_test_type[r['unified_name']] = [r]
conf_name = '%s.conf' % filename
gplot_conf = open(conf_name, mode = 'wt', encoding = 'utf8')
gplot_conf.write('# settings for stacked multiplot layouts:\n')
sub_title = _('plotted %s (GNUmed v%s)') % (
gmDateTime.pydt_now_here().strftime('%Y %b %d %H:%M'),
_cfg.get(option = 'client_version')
)
if patient is None:
plot_title = sub_title
else:
plot_title = '%s - %s\\n{/*0.8 %s}' % (
patient.get_description_gender(with_nickname = False).strip(),
patient.get_formatted_dob(format = '%Y %b %d', none_string = _('unknown DOB'), honor_estimation = True),
sub_title
)
gplot_conf.write('multiplot_title = "%s"\n' % plot_title)
gplot_conf.write('multiplot_no_of_tests = %s # number of index blocks (resp. test types)\n' % len(results_grouped_by_test_type))
gplot_conf.write('array multiplot_y_labels[multiplot_no_of_tests] # list for ylabels suitable for stacked multiplots\n')
gplot_conf.write('\n')
gplot_conf.write('# settings for individual plots, stacked or not:\n')
gplot_data = open(filename, mode = 'wt', encoding = 'utf8')
gplot_data.write(GPLOT_DATAFILE_HEADER % filename)
test_type_groups = list(results_grouped_by_test_type)
for test_type_idx in range(len(test_type_groups)):
test_type = test_type_groups[test_type_idx]
if len(results_grouped_by_test_type[test_type]) == 0:
continue
first_result = results_grouped_by_test_type[test_type][0]
if test_type_idx == 0:
gplot_conf.write('set title "%s" enhanced\n' % plot_title)
gplot_conf.write('\n')
gplot_conf.write('set ylabel "%s"\n' % first_result['unified_name'])
elif test_type_idx == 1:
gplot_conf.write('set y2label "%s"\n' % first_result['unified_name'])
gplot_conf.write('multiplot_y_labels[%s] = "%s (%s)"\n' % (test_type_idx + 1, first_result['unified_name'], first_result['unified_abbrev']))
title = '%s (%s)' % (
first_result['unified_abbrev'],
first_result['unified_name']
)
gplot_data.write('\n\n"%s" "%s"\n' % (title, title))
prev_date = None
prev_year = None
for result in sorted(results_grouped_by_test_type[test_type], key=lambda result:result['clin_when']):
curr_date = gmDateTime.pydt_strftime(result['clin_when'], '%Y-%m-%d', 'utf8', gmDateTime.acc_days)
if curr_date == prev_date:
gplot_data.write('# %s\n\n' % _('blank line inserted to allow for discontinued-line style drawing of same-day values:'))
if show_year:
if result['clin_when'].year == prev_year:
when_template = '%b %d %H:%M'
else:
when_template = '%b %d %H:%M (%Y)'
prev_year = result['clin_when'].year
else:
when_template = '%b %d'
val = result['val_num']
if val is None:
val = result.estimate_numeric_value_from_alpha
if val is None:
continue # skip distinctly non-numericable values
gplot_data.write ('%s %s "%s" %s %s %s %s %s %s "%s"\n' % (
gmDateTime.pydt_strftime(result['clin_when'], '%Y-%m-%d_%H:%M', 'utf8', gmDateTime.acc_minutes),
val,
gmTools.coalesce(result['val_unit'], '"<?>"'),
gmTools.coalesce(result['unified_target_min'], '"<?>"'),
gmTools.coalesce(result['unified_target_max'], '"<?>"'),
gmTools.coalesce(result['val_normal_min'], '"<?>"'),
gmTools.coalesce(result['val_normal_max'], '"<?>"'),
gmTools.coalesce(result['val_target_min'], '"<?>"'),
gmTools.coalesce(result['val_target_max'], '"<?>"'),
gmDateTime.pydt_strftime (
result['clin_when'],
format = when_template,
accuracy = gmDateTime.acc_minutes
)
))
prev_date = curr_date
gplot_data.close()
gplot_conf.close()
return filename
#============================================================
class cLabRequest(gmBusinessDBObject.cBusinessDBObject):
"""Represents one lab request."""
_cmd_fetch_payload = """
select *, xmin_lab_request from v_lab_requests
where pk_request=%s"""
_cmds_lock_rows_for_update = [
"""select 1 from lab_request where pk=%(pk_request)s and xmin=%(xmin_lab_request)s for update"""
]
_cmds_store_payload = [
"""update lab_request set
request_id=%(request_id)s,
lab_request_id=%(lab_request_id)s,
clin_when=%(sampled_when)s,
lab_rxd_when=%(lab_rxd_when)s,
results_reported_when=%(results_reported_when)s,
request_status=%(request_status)s,
is_pending=%(is_pending)s::bool,
narrative=%(progress_note)s
where pk=%(pk_request)s""",
"""select xmin_lab_request from v_lab_requests where pk_request=%(pk_request)s"""
]
_updatable_fields = [
'request_id',
'lab_request_id',
'sampled_when',
'lab_rxd_when',
'results_reported_when',
'request_status',
'is_pending',
'progress_note'
]
#--------------------------------------------------------
def __init__(self, aPK_obj=None, row=None):
"""Instantiate lab request.
The aPK_obj can be either a dict with the keys "req_id"
and "lab" or a simple primary key.
"""
# instantiate from row data ?
if aPK_obj is None:
gmBusinessDBObject.cBusinessDBObject.__init__(self, row=row)
return
pk = aPK_obj
# instantiate from "req_id" and "lab" ?
if type(aPK_obj) == dict:
# sanity check
try:
aPK_obj['req_id']
aPK_obj['lab']
except Exception:
_log.exception('[%s:??]: faulty <aPK_obj> structure: [%s]' % (self.__class__.__name__, aPK_obj), sys.exc_info())
raise gmExceptions.ConstructorError('[%s:??]: cannot derive PK from [%s]' % (self.__class__.__name__, aPK_obj))
# generate query
where_snippets = []
where_snippets.append('request_id=%(req_id)s')
if type(aPK_obj['lab']) == int:
where_snippets.append('pk_test_org=%(lab)s')
else:
where_snippets.append('lab_name=%(lab)s')
# where_clause = ' and '.join(where_snippets)
# cmd = "select pk_request from v_lab_requests where %s" % where_clause
# # get pk
# data = gmPG2.run_ro_query('historica', cmd, None, aPK_obj)
# if data is None:
# raise gmExceptions.ConstructorError('[%s:??]: error getting lab request for [%s]' % (self.__class__.__name__, aPK_obj))
# if len(data) == 0:
# raise gmExceptions.NoSuchClinItemError('[%s:??]: no lab request for [%s]' % (self.__class__.__name__, aPK_obj))
# pk = data[0][0]
# instantiate class
gmBusinessDBObject.cBusinessDBObject.__init__(self, aPK_obj=pk)
# #--------------------------------------------------------
# def get_patient(self):
# cmd = """
# select vpi.pk_patient, vbp.title, vbp.firstnames, vbp.lastnames, vbp.dob
# from v_pat_items vpi, v_active_persons vbp
# where
# vpi.pk_item=%s
# and
# vbp.pk_identity=vpi.pk_patient"""
# pat = gmPG2.run_ro_query('historica', cmd, None, self._payload['pk_item'])
# if pat is None:
# _log.error('cannot get patient for lab request [%s]' % self._payload['pk_item'])
# return None
# if len(pat) == 0:
# _log.error('no patient associated with lab request [%s]' % self._payload['pk_item'])
# return None
# return pat[0]
#============================================================
# convenience functions
#------------------------------------------------------------
def create_lab_request(lab=None, req_id=None, pat_id=None, encounter_id=None, episode_id=None):
"""Create or get lab request.
returns tuple (status, value):
(True, lab request instance)
(False, error message)
(None, housekeeping_todo primary key)
"""
pass
# req = None
# aPK_obj = {
# 'lab': lab,
# 'req_id': req_id
# }
# try:
# req = cLabRequest (aPK_obj)
# except gmExceptions.NoSuchClinItemError as msg:
# _log.info('%s: will try to create lab request' % str(msg))
# except gmExceptions.ConstructorError as msg:
# _log.exception(str(msg), sys.exc_info(), verbose=0)
# return (False, msg)
# found
# if req is not None:
# db_pat = req.get_patient()
# db_pat = None
# if db_pat is None:
# _log.error('cannot cross-check patient on lab request')
# return (None, '')
# # yes but ambiguous
# if pat_id != db_pat[0]:
# _log.error('lab request found for [%s:%s] but patient mismatch: expected [%s], in DB [%s]' % (lab, req_id, pat_id, db_pat))
# me = '$RCSfile: gmPathLab.py,v $ $Revision: 1.81 $'
# to = 'user'
# prob = _('The lab request already exists but belongs to a different patient.')
# sol = _('Verify which patient this lab request really belongs to.')
# ctxt = _('lab [%s], request ID [%s], expected link with patient [%s], currently linked to patient [%s]') % (lab, req_id, pat_id, db_pat)
# cat = 'lab'
# status, data = gmPG2.add_housekeeping_todo(me, to, prob, sol, ctxt, cat)
# return (None, None)
# return (True, req)
# # not found
# queries = []
# if type(lab) is int:
# cmd = "insert into lab_request (fk_encounter, fk_episode, fk_test_org, request_id) values (%s, %s, %s, %s)"
# else:
# cmd = "insert into lab_request (fk_encounter, fk_episode, fk_test_org, request_id) values (%s, %s, (select pk from test_org where internal_OBSOLETE_name=%s), %s)"
# queries.append((cmd, [encounter_id, episode_id, str(lab), req_id]))
# cmd = "select currval('lab_request_pk_seq')"
# queries.append((cmd, []))
# # insert new
# result, err = (None, 'error')
# #result, err = gmPG2.run_commit('historica', queries, True)
# if result is None:
# return (False, err)
# try:
# req = cLabRequest(aPK_obj=result[0][0])
# except gmExceptions.ConstructorError as msg:
# _log.exception(str(msg), sys.exc_info(), verbose=0)
# return (False, msg)
# return (True, req)
#------------------------------------------------------------
def get_pending_requests(limit=250):
lim = limit + 1
cmd = "select pk from lab_request where is_pending is true limit %s" % lim
rows = gmPG2.run_ro_queries(queries = cmd)
if rows is None:
_log.error('error retrieving pending lab requests')
return (None, None)
if len(rows) == 0:
return (False, [])
# more than LIMIT rows ?
if len(rows) == lim:
too_many = True
# but deliver only LIMIT rows so that our assumption holds true...
rows = rows[:limit]
else:
too_many = False
requests = []
for row in rows:
try:
requests.append(cLabRequest(aPK_obj=row[0]))
except gmExceptions.ConstructorError:
_log.exception('skipping pending lab request [%s]' % row[0], sys.exc_info(), verbose=0)
return (too_many, requests)
#------------------------------------------------------------
def get_next_request_ID(lab=None, incrementor_func=None):
"""Get logically next request ID for given lab.
- incrementor_func:
- if not supplied the next ID is guessed
- if supplied it is applied to the most recently used ID
"""
if type(lab) == int:
lab_snippet = 'vlr.fk_test_org=%s'
else:
lab_snippet = 'vlr.lab_name=%s'
lab = str(lab)
cmd = """
select request_id
from lab_request lr0
where lr0.clin_when = (
select max(vlr.sampled_when)
from v_lab_requests vlr
where %s
)""" % lab_snippet
rows = gmPG2.run_ro_queries(cmd, None, lab)
if rows is None:
_log.warning('error getting most recently used request ID for lab [%s]' % lab)
return ''
if len(rows) == 0:
return ''
most_recent = rows[0][0]
# apply supplied incrementor
if incrementor_func is not None:
try:
next = incrementor_func(most_recent)
except TypeError:
_log.error('cannot call incrementor function [%s]' % str(incrementor_func))
return most_recent
return next
# try to be smart ourselves
for pos in range(len(most_recent)):
header = most_recent[:pos]
trailer = most_recent[pos:]
try:
return '%s%s' % (header, str(int(trailer) + 1))
except ValueError:
header = most_recent[:-1]
trailer = most_recent[-1:]
return '%s%s' % (header, chr(ord(trailer) + 1))
#============================================================
def calculate_bmi(mass=None, height=None, age=None):
"""Calculate BMI.
mass: kg
height: cm
age: not yet used
returns:
(True/False, data)
True: data = (bmi, lower_normal, upper_normal)
False: data = error message
"""
converted, mass = gmTools.input2decimal(mass)
if not converted:
return False, 'mass: cannot convert <%s> to Decimal' % mass
converted, height = gmTools.input2decimal(height)
if not converted:
return False, 'height: cannot convert <%s> to Decimal' % height
approx_surface = (height / decimal.Decimal(100))**2
bmi = mass / approx_surface
print(mass, height, '->', approx_surface, '->', bmi)
lower_normal_mass = 20.0 * approx_surface
upper_normal_mass = 25.0 * approx_surface
return True, (bmi, lower_normal_mass, upper_normal_mass)
#============================================================
# main - unit testing
#------------------------------------------------------------
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
import time
del _
from Gnumed.pycommon import gmI18N
gmI18N.activate_locale()
gmI18N.install_domain('gnumed')
#------------------------------------------
def test_create_test_result():
tr = create_test_result (
encounter = 1,
episode = 1,
type = 1,
intended_reviewer = 1,
val_num = '12',
val_alpha=None,
unit = 'mg/dl'
)
print(tr)
return tr
#------------------------------------------
def test_delete_test_result():
tr = test_create_test_result()
delete_test_result(tr)
#------------------------------------------
def test_result():
r = cTestResult(aPK_obj=6)
#print r
#print r.reference_ranges
#print r.formatted_range
#print r.temporally_closest_normal_range
print(r.estimate_numeric_value_from_alpha)
#------------------------------------------
def test_request():
print("test_request()")
try:
# lab_req = cLabRequest(aPK_obj=1)
# lab_req = cLabRequest(req_id='EML#SC937-0176-CEC#11', lab=2)
data = {
'req_id': 'EML#SC937-0176-CEC#11',
'lab': 'Enterprise Main Lab'
}
lab_req = cLabRequest(aPK_obj=data)
except gmExceptions.ConstructorError as msg:
print("no such lab request:", msg)
return
print(lab_req)
fields = lab_req.get_fields()
for field in fields:
print(field, ':', lab_req[field])
print("updatable:", lab_req.get_updatable_fields())
print(time.time())
print(lab_req.get_patient())
print(time.time())
#--------------------------------------------------------
def test_unreviewed():
#data = get_unreviewed_results()
data = []
for result in data:
print(result)
#--------------------------------------------------------
def test_pending():
data = get_pending_requests()
for result in data:
print(result)
#--------------------------------------------------------
def test_create_measurement_type():
print(create_measurement_type (
lab = None,
abbrev = 'tBZ2',
unit = 'mg%',
name = 'BZ (test 2)'
))
#--------------------------------------------------------
def test_meta_test_type():
mtt = cMetaTestType(aPK_obj = 1)
print(mtt)
print(get_meta_test_types())
#--------------------------------------------------------
def test_test_type():
tt = cMeasurementType(aPK_obj = 1)
print(tt)
print(get_measurement_types())
#--------------------------------------------------------
def test_format_test_results():
results = [
cTestResult(aPK_obj=1),
cTestResult(aPK_obj=2),
cTestResult(aPK_obj=3)
# cTestResult(aPK_obj=4)
]
print(format_test_results(results = results))
#--------------------------------------------------------
def test_calculate_bmi():
done, data = calculate_bmi(mass = sys.argv[2], height = sys.argv[3])
bmi, low, high = data
print("BMI:", bmi)
print("low:", low, "kg")
print("hi :", high, "kg")
#--------------------------------------------------------
def test_test_panel():
tp = cTestPanel(aPK_obj = 2)
print(tp)
print(tp.test_types)
print(tp.format())
#--------------------------------------------------------
def test_get_most_recent_results_for_panel():
tp = cTestPanel(aPK_obj = 1)
#print tp.included_loincs
#tp = cTestPanel(aPK_obj = 3)
print(tp.format())
#most_recent = tp.get_most_recent_results(pk_patient = 12, group_by_meta_type = False)
#most_recent = tp.get_most_recent_results(pk_patient = 138, group_by_meta_type = False)
#print len(most_recent)
most_recent = tp.get_most_recent_results(pk_patient = 12, group_by_meta_type = True, include_missing = True)
#most_recent = tp.get_most_recent_results(pk_patient = 138, group_by_meta_type = True)
print('found:', len(most_recent))
for t in most_recent:
print('--------------')
if t['pk_meta_test_type'] is None:
print("standalone")
else:
print("meta")
print(t.format())
#--------------------------------------------------------
def test_get_most_recent_results_in_loinc_group():
most_recent = get_most_recent_results_in_loinc_group (
#loincs = [u'pseudo LOINC [C-reactive protein (EML)::9] (v21->v22 test panel conversion)'],
#loincs = ['8867-4'],
loincs = ['2160-0', '14682-9', '40264-4', '40248-7'],
max_no_of_results = 6,
patient = 201,
consider_indirect_matches = False
)
for t in most_recent:
print(t['loinc_tt'], t['loinc_meta'], t['unified_loinc'])
if t['pk_meta_test_type'] is None:
print("---- standalone ----")
else:
print("---- meta ----")
print(t.format())
input('next')
return
most_recent = get_most_recent_results_in_loinc_group (
#loincs = [u'pseudo LOINC [C-reactive protein (EML)::9] (v21->v22 test panel conversion)'],
#loincs = ['8867-4'],
loincs = ['2160-0', '14682-9', '40264-4', '40248-7'],
max_no_of_results = 2,
patient = 201,
consider_indirect_matches = False
#consider_indirect_matches = True
)
for t in most_recent:
if t['pk_meta_test_type'] is None:
print("---- standalone ----")
else:
print("---- meta ----")
print(t.format())
#--------------------------------------------------------
def test_export_result_for_gnuplot():
results = get_test_results(pk_patient = 12)
print(results)
export_results_for_gnuplot(results=results, filename='test.gpl', show_year=True, patient=None)
#--------------------------------------------------------
def test_get_test_results():
results = get_test_results(pk_patient = 12, order_by = 'unified_abbrev, clin_when DESC')
print(results)
#--------------------------------------------------------
def test_format_test_results_failsafe():
results = get_test_results(pk_patient = 12, order_by = 'unified_abbrev, clin_when DESC')
lines = generate_failsafe_test_results_entries(results)
for line in lines:
print(line)
#--------------------------------------------------------
#print(GPLOT_DATAFILE_HEADER % 'test')
gmPG2.request_login_params(setup_pool = True)
#test_result()
#test_create_test_result()
#test_delete_test_result()
#test_create_measurement_type()
#test_lab_result()
#test_request()
#test_create_result()
#test_unreviewed()
#test_pending()
#test_meta_test_type()
#test_test_type()
#test_format_test_results()
#test_calculate_bmi()
#test_test_panel()
#test_get_test_results()
#test_get_most_recent_results_for_panel()
#test_get_most_recent_results_in_loinc_group()
#test_export_result_for_gnuplot()
test_format_test_results_failsafe()
#============================================================Functions
def calculate_bmi(mass=None, height=None, age=None)-
Calculate BMI.
mass: kg height: cm age: not yet used
returns: (True/False, data) True: data = (bmi, lower_normal, upper_normal) False: data = error message
Expand source code
def calculate_bmi(mass=None, height=None, age=None): """Calculate BMI. mass: kg height: cm age: not yet used returns: (True/False, data) True: data = (bmi, lower_normal, upper_normal) False: data = error message """ converted, mass = gmTools.input2decimal(mass) if not converted: return False, 'mass: cannot convert <%s> to Decimal' % mass converted, height = gmTools.input2decimal(height) if not converted: return False, 'height: cannot convert <%s> to Decimal' % height approx_surface = (height / decimal.Decimal(100))**2 bmi = mass / approx_surface print(mass, height, '->', approx_surface, '->', bmi) lower_normal_mass = 20.0 * approx_surface upper_normal_mass = 25.0 * approx_surface return True, (bmi, lower_normal_mass, upper_normal_mass) def create_lab_request(lab=None, req_id=None, pat_id=None, encounter_id=None, episode_id=None)-
Create or get lab request.
returns tuple (status, value): (True, lab request instance) (False, error message) (None, housekeeping_todo primary key)
Expand source code
def create_lab_request(lab=None, req_id=None, pat_id=None, encounter_id=None, episode_id=None): """Create or get lab request. returns tuple (status, value): (True, lab request instance) (False, error message) (None, housekeeping_todo primary key) """ pass # req = None # aPK_obj = { # 'lab': lab, # 'req_id': req_id # } # try: # req = cLabRequest (aPK_obj) # except gmExceptions.NoSuchClinItemError as msg: # _log.info('%s: will try to create lab request' % str(msg)) # except gmExceptions.ConstructorError as msg: # _log.exception(str(msg), sys.exc_info(), verbose=0) # return (False, msg) # found def create_measurement_type(lab=None, abbrev=None, unit=None, name=None, link_obj=None)-
Create or get test type.
Expand source code
def create_measurement_type(lab=None, abbrev=None, unit=None, name=None, link_obj=None): """Create or get test type.""" ttype = find_measurement_type(lab = lab, abbrev = abbrev, name = name, link_obj = link_obj) # found ? if ttype is not None: return ttype _log.debug('creating test type [%s:%s:%s:%s]', lab, abbrev, name, unit) # not found, so create it # if unit is None: # _log.error('need <unit> to create test type: %s:%s:%s:%s' % (lab, abbrev, name, unit)) # raise ValueError('need <unit> to create test type') # make query cols = [] val_snippets = [] vals = {} # lab if lab is None: lab = create_test_org(link_obj = link_obj)['pk_test_org'] cols.append('fk_test_org') try: vals['lab'] = int(lab) val_snippets.append('%(lab)s') except Exception: vals['lab'] = lab val_snippets.append('(SELECT pk_test_org FROM clin.v_test_orgs WHERE unit = %(lab)s)') # code cols.append('abbrev') val_snippets.append('%(abbrev)s') vals['abbrev'] = abbrev # unit if unit is not None: cols.append('reference_unit') val_snippets.append('%(unit)s') vals['unit'] = unit # name if name is not None: cols.append('name') val_snippets.append('%(name)s') vals['name'] = name col_clause = ', '.join(cols) val_clause = ', '.join(val_snippets) queries = [ {'cmd': 'insert into clin.test_type (%s) values (%s)' % (col_clause, val_clause), 'args': vals}, {'cmd': "select * from clin.v_test_types where pk_test_type = currval(pg_get_serial_sequence('clin.test_type', 'pk'))"} ] rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = queries, return_data = True) ttype = cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': rows[0]}) return ttype def create_meta_type(name=None, abbreviation=None, return_existing=False)-
Expand source code
def create_meta_type(name=None, abbreviation=None, return_existing=False): cmd = """ INSERT INTO clin.meta_test_type (name, abbrev) SELECT %(name)s, %(abbr)s WHERE NOT EXISTS ( SELECT 1 FROM clin.meta_test_type WHERE name = %(name)s AND abbrev = %(abbr)s ) RETURNING *, xmin """ args = { 'name': name.strip(), 'abbr': abbreviation.strip() } rows = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True) if len(rows) == 0: if not return_existing: return None cmd = "SELECT *, xmin FROM clin.meta_test_type WHERE name = %(name)s and %(abbr)s" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return cMetaTestType(row = {'pk_field': 'pk', 'data': rows[0]}) def create_test_org(name=None, comment=None, pk_org_unit=None, link_obj=None)-
Expand source code
def create_test_org(name=None, comment=None, pk_org_unit=None, link_obj=None): _log.debug('creating test org [%s:%s:%s]', name, comment, pk_org_unit) if name is None: name = 'unassigned lab' # get org unit if pk_org_unit is None: org = gmOrganization.create_org ( link_obj = link_obj, organization = name, category = 'Laboratory' ) org_unit = gmOrganization.create_org_unit ( link_obj = link_obj, pk_organization = org['pk_org'], unit = name ) pk_org_unit = org_unit['pk_org_unit'] # test org exists ? args = {'pk_unit': pk_org_unit} cmd = 'SELECT pk_test_org FROM clin.v_test_orgs WHERE pk_org_unit = %(pk_unit)s' rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: cmd = 'INSERT INTO clin.test_org (fk_org_unit) VALUES (%(pk_unit)s) RETURNING pk' rows = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True) test_org = cTestOrg(link_obj = link_obj, aPK_obj = rows[0][0]) if comment is not None: comment = comment.strip() test_org['comment'] = comment test_org.save(conn = link_obj) return test_org def create_test_panel(description=None)-
Expand source code
def create_test_panel(description=None): args = {'desc': description.strip()} cmd = """ INSERT INTO clin.test_panel (description) VALUES (gm.nullify_empty_string(%(desc)s)) RETURNING pk """ rows = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}], return_data = True) return cTestPanel(aPK_obj = rows[0]['pk']) def create_test_result(encounter=None, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None)-
Expand source code
def create_test_result(encounter=None, episode=None, type=None, intended_reviewer=None, val_num=None, val_alpha=None, unit=None, link_obj=None): cmd1 = """ INSERT INTO clin.test_result ( fk_encounter, fk_episode, fk_type, fk_intended_reviewer, val_num, val_alpha, val_unit ) VALUES ( %(enc)s, %(epi)s, %(type)s, %(rev)s, %(v_num)s, %(v_alpha)s, %(unit)s ) """ cmd2 = "SELECT * from clin.v_test_results WHERE pk_test_result = currval(pg_get_serial_sequence('clin.test_result', 'pk'))" args = { 'enc': encounter, 'epi': episode, 'type': type, 'rev': intended_reviewer, 'v_num': val_num, 'v_alpha': val_alpha, 'unit': unit } rows = gmPG2.run_rw_queries ( link_obj = link_obj, queries = [ {'cmd': cmd1, 'args': args}, {'cmd': cmd2} ], return_data = True ) tr = cTestResult(row = { 'pk_field': 'pk_test_result', 'data': rows[0] }) return tr def delete_measurement_type(measurement_type=None)-
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def delete_measurement_type(measurement_type=None): cmd = 'delete from clin.test_type where pk = %(pk)s' args = {'pk': measurement_type} gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) def delete_meta_type(meta_type=None)-
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def delete_meta_type(meta_type=None): cmd = """ DELETE FROM clin.meta_test_type WHERE pk = %(pk)s AND NOT EXISTS ( SELECT 1 FROM clin.test_type WHERE fk_meta_test_type = %(pk)s )""" args = {'pk': meta_type} gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) def delete_test_org(test_org=None)-
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def delete_test_org(test_org=None): args = {'pk': test_org} cmd = """ DELETE FROM clin.test_org WHERE pk = %(pk)s AND NOT EXISTS (SELECT 1 FROM clin.lab_request WHERE fk_test_org = %(pk)s LIMIT 1) AND NOT EXISTS (SELECT 1 FROM clin.test_type WHERE fk_test_org = %(pk)s LIMIT 1) """ gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) def delete_test_panel(pk=None)-
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def delete_test_panel(pk=None): args = {'pk': pk} cmd = "DELETE FROM clin.test_panel WHERE pk = %(pk)s" gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True def delete_test_result(result=None)-
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def delete_test_result(result=None): try: pk = int(result) except (TypeError, AttributeError): pk = result['pk_test_result'] cmd = 'DELETE FROM clin.test_result WHERE pk = %(pk)s' gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': {'pk': pk}}]) def export_results_for_gnuplot(results=None, filename=None, show_year=True, patient=None)-
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def export_results_for_gnuplot(results=None, filename=None, show_year=True, patient=None): sandbox_dir = os.path.join(gmTools.gmPaths().tmp_dir, 'gplot') if not gmTools.mkdir(sandbox_dir): sandbox_dir = gmTools.mk_sandbox_dir(prefix = 'gm2gpl-') _log.debug('sandbox directory: [%s]', sandbox_dir) if filename is None: filename = gmTools.get_unique_filename(prefix = 'gm2gpl-', suffix = '.dat', tmp_dir = sandbox_dir) # sort results into groups by test type results_grouped_by_test_type = {} for r in results: try: results_grouped_by_test_type[r['unified_name']].append(r) except KeyError: results_grouped_by_test_type[r['unified_name']] = [r] conf_name = '%s.conf' % filename gplot_conf = open(conf_name, mode = 'wt', encoding = 'utf8') gplot_conf.write('# settings for stacked multiplot layouts:\n') sub_title = _('plotted %s (GNUmed v%s)') % ( gmDateTime.pydt_now_here().strftime('%Y %b %d %H:%M'), _cfg.get(option = 'client_version') ) if patient is None: plot_title = sub_title else: plot_title = '%s - %s\\n{/*0.8 %s}' % ( patient.get_description_gender(with_nickname = False).strip(), patient.get_formatted_dob(format = '%Y %b %d', none_string = _('unknown DOB'), honor_estimation = True), sub_title ) gplot_conf.write('multiplot_title = "%s"\n' % plot_title) gplot_conf.write('multiplot_no_of_tests = %s # number of index blocks (resp. test types)\n' % len(results_grouped_by_test_type)) gplot_conf.write('array multiplot_y_labels[multiplot_no_of_tests] # list for ylabels suitable for stacked multiplots\n') gplot_conf.write('\n') gplot_conf.write('# settings for individual plots, stacked or not:\n') gplot_data = open(filename, mode = 'wt', encoding = 'utf8') gplot_data.write(GPLOT_DATAFILE_HEADER % filename) test_type_groups = list(results_grouped_by_test_type) for test_type_idx in range(len(test_type_groups)): test_type = test_type_groups[test_type_idx] if len(results_grouped_by_test_type[test_type]) == 0: continue first_result = results_grouped_by_test_type[test_type][0] if test_type_idx == 0: gplot_conf.write('set title "%s" enhanced\n' % plot_title) gplot_conf.write('\n') gplot_conf.write('set ylabel "%s"\n' % first_result['unified_name']) elif test_type_idx == 1: gplot_conf.write('set y2label "%s"\n' % first_result['unified_name']) gplot_conf.write('multiplot_y_labels[%s] = "%s (%s)"\n' % (test_type_idx + 1, first_result['unified_name'], first_result['unified_abbrev'])) title = '%s (%s)' % ( first_result['unified_abbrev'], first_result['unified_name'] ) gplot_data.write('\n\n"%s" "%s"\n' % (title, title)) prev_date = None prev_year = None for result in sorted(results_grouped_by_test_type[test_type], key=lambda result:result['clin_when']): curr_date = gmDateTime.pydt_strftime(result['clin_when'], '%Y-%m-%d', 'utf8', gmDateTime.acc_days) if curr_date == prev_date: gplot_data.write('# %s\n\n' % _('blank line inserted to allow for discontinued-line style drawing of same-day values:')) if show_year: if result['clin_when'].year == prev_year: when_template = '%b %d %H:%M' else: when_template = '%b %d %H:%M (%Y)' prev_year = result['clin_when'].year else: when_template = '%b %d' val = result['val_num'] if val is None: val = result.estimate_numeric_value_from_alpha if val is None: continue # skip distinctly non-numericable values gplot_data.write ('%s %s "%s" %s %s %s %s %s %s "%s"\n' % ( gmDateTime.pydt_strftime(result['clin_when'], '%Y-%m-%d_%H:%M', 'utf8', gmDateTime.acc_minutes), val, gmTools.coalesce(result['val_unit'], '"<?>"'), gmTools.coalesce(result['unified_target_min'], '"<?>"'), gmTools.coalesce(result['unified_target_max'], '"<?>"'), gmTools.coalesce(result['val_normal_min'], '"<?>"'), gmTools.coalesce(result['val_normal_max'], '"<?>"'), gmTools.coalesce(result['val_target_min'], '"<?>"'), gmTools.coalesce(result['val_target_max'], '"<?>"'), gmDateTime.pydt_strftime ( result['clin_when'], format = when_template, accuracy = gmDateTime.acc_minutes ) )) prev_date = curr_date gplot_data.close() gplot_conf.close() return filename def find_measurement_type(lab=None, abbrev=None, name=None, link_obj=None)-
Expand source code
def find_measurement_type(lab=None, abbrev=None, name=None, link_obj=None): if (abbrev is None) and (name is None): raise ValueError('must have <abbrev> and/or <name> set') where_snippets = [] if lab is None: where_snippets.append('pk_test_org IS NULL') else: try: int(lab) where_snippets.append('pk_test_org = %(lab)s') except (TypeError, ValueError): where_snippets.append('pk_test_org = (SELECT pk_test_org FROM clin.v_test_orgs WHERE unit = %(lab)s)') if abbrev is not None: where_snippets.append('abbrev = %(abbrev)s') if name is not None: where_snippets.append('name = %(name)s') where_clause = ' and '.join(where_snippets) cmd = "select * from clin.v_test_types where %s" % where_clause args = {'lab': lab, 'abbrev': abbrev, 'name': name} rows = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None tt = cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': rows[0]}) return tt def format_test_results(results=None, output_format='latex')-
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def format_test_results(results=None, output_format='latex'): _log.debug('formatting test results into [%s]', output_format) if output_format == 'latex': return __format_test_results_latex(results = results) msg = _('unknown test results output format [%s]') % output_format _log.error(msg) return msg def generate_failsafe_test_results_entries(pk_patient: int = None, test_results: list[cTestResult] = None, max_width: int = 80) ‑> list[str]-
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def generate_failsafe_test_results_entries(pk_patient:int=None, test_results:list[cTestResult]=None, max_width:int=80) -> list[str]: if not test_results: if pk_patient: test_results = get_test_results(pk_patient = 12, order_by = 'unified_abbrev, clin_when DESC') if not test_results: return [] prev_abbrev = None lines = [] for tr in test_results: abbrev = tr['unified_abbrev'] if abbrev != prev_abbrev: lines.append('') lines.append('%s - %s' % (abbrev, tr['unified_name'])) prev_abbrev = abbrev line = ' %s: %s %s%s%s' % ( tr['clin_when'].strftime('%Y %b %d %H:%m'), tr['unified_val'], tr['val_unit'], gmTools.bool2subst(tr.is_considered_abnormal, ' !', '', ''), gmTools.coalesce(tr.formatted_range, '', ' (%s)') ) lines.append(gmTools.shorten_text(line, max_width)) if tr['note_test_org']: cmt = _(' Lab: %s') % tr['note_test_org'].replace('\n', ' // ') lines.append(gmTools.shorten_text(cmt, max_width)) if tr['comment']: cmt = _(' Praxis: %s') % tr['comment'].replace('\n', ' // ') lines.append(gmTools.shorten_text(cmt, max_width)) return lines def get_measurement_types(order_by=None, loincs=None, return_pks=False)-
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def get_measurement_types(order_by=None, loincs=None, return_pks=False): args = {} where_parts = [] if loincs is not None: if len(loincs) > 0: where_parts.append('loinc = ANY(%(loincs)s)') args['loincs'] = loincs if len(where_parts) == 0: where_parts.append('TRUE') WHERE_clause = ' AND '.join(where_parts) cmd = (_SQL_get_test_types % WHERE_clause) + gmTools.coalesce(order_by, '', ' ORDER BY %s') rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if return_pks: return [ r['pk_test_type'] for r in rows ] return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ] def get_meta_test_types(return_pks=False)-
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def get_meta_test_types(return_pks=False): cmd = 'SELECT *, xmin FROM clin.meta_test_type' rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}]) if return_pks: return [ r['pk'] for r in rows ] return [ cMetaTestType(row = {'pk_field': 'pk', 'data': r}) for r in rows ] def get_most_recent_result_for_test_types(pk_test_types=None, pk_patient=None, return_pks=False, consider_meta_type=False, order_by=None)-
Return the one most recent result for each of a list of test types.
If
is not given, most recent results for each test type the patient has any results for is returned. Expand source code
def get_most_recent_result_for_test_types(pk_test_types=None, pk_patient=None, return_pks=False, consider_meta_type=False, order_by=None): """Return the one most recent result for *each* of a list of test types. If <pk_test_types> is not given, most recent results for *each* test type the patient has any results for is returned. """ where_parts = ['pk_patient = %(pat)s'] args = {'pat': pk_patient} if pk_test_types is not None: where_parts.append('pk_test_type = ANY(%(ttyps)s)') args['ttyps'] = pk_test_types order_by = 'ORDER BY clin_when DESC' if order_by is None else 'ORDER BY %s' % order_by if consider_meta_type: cmd = 'SELECT * FROM ((%s) UNION ALL (%s)) AS result_union %s' % ( _SQL_most_recent_result_for_test_types_without_meta_type % ' AND '.join(where_parts), _SQL_most_recent_result_for_test_types_by_meta_type % ' AND '.join(where_parts), order_by ) else: cmd = _SQL_most_recent_result_for_test_types % ( ' AND '.join(where_parts), order_by ) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if return_pks: return [ r['pk_test_result'] for r in rows ] return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_most_recent_results_for_panel(pk_patient=None, pk_panel=None, order_by=None, group_by_meta_type=False)-
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def get_most_recent_results_for_panel(pk_patient=None, pk_panel=None, order_by=None, group_by_meta_type=False): if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by args = { 'pat': pk_patient, 'pk_pnl': pk_panel } if group_by_meta_type: # return most recent results in panel grouped by # meta test type if any, non-grouped results are # returned ungrouped :-) cmd = """ SELECT c_vtr.* FROM ( -- max(clin_when) per test_type-in-panel for patient SELECT pk_meta_test_type, MAX(clin_when) AS max_clin_when FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type IS DISTINCT FROM NULL AND pk_test_type IN ( (SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s) ) GROUP BY pk_meta_test_type ) AS latest_results INNER JOIN clin.v_test_results c_vtr ON c_vtr.pk_meta_test_type = latest_results.pk_meta_test_type AND c_vtr.clin_when = latest_results.max_clin_when UNION ALL SELECT c_vtr.* FROM ( -- max(clin_when) per test_type-in-panel for patient SELECT pk_test_type, MAX(clin_when) AS max_clin_when FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type IS NULL AND pk_test_type IN ( (SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s) ) GROUP BY pk_test_type ) AS latest_results INNER JOIN clin.v_test_results c_vtr ON c_vtr.pk_test_type = latest_results.pk_test_type AND c_vtr.clin_when = latest_results.max_clin_when """ else: # return most recent results in panel regardless of whether # distinct test types in this panel are grouped under the # same meta test type cmd = """ SELECT c_vtr.* FROM ( -- max(clin_when) per test_type-in-panel for patient SELECT pk_test_type, MAX(clin_when) AS max_clin_when FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_test_type IN ( (SELECT c_vtt4tp.pk_test_type FROM clin.v_test_types4test_panel c_vtt4tp WHERE c_vtt4tp.pk_test_panel = %(pk_pnl)s) ) GROUP BY pk_test_type ) AS latest_results -- this INNER join makes certain we do not expand -- the row selection beyond the patient's rows -- which we constrained to inside the SELECT -- producing "latest_results" INNER JOIN clin.v_test_results c_vtr ON c_vtr.pk_test_type = latest_results.pk_test_type AND c_vtr.clin_when = latest_results.max_clin_when """ cmd += order_by rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_most_recent_results_for_patient(no_of_results=1, patient=None)-
Get N most recent results for a given patient.
Expand source code
def get_most_recent_results_for_patient(no_of_results=1, patient=None): """Get N most recent results for a given patient.""" if no_of_results < 1: raise ValueError('<no_of_results> must be > 0') args = {'pat': patient} cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s ORDER BY clin_when DESC LIMIT %s""" % no_of_results rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_most_recent_results_for_test_type(test_type=None, max_no_of_results=1, patient=None)-
Get N most recent results for one defined test type.
Expand source code
def get_most_recent_results_for_test_type(test_type=None, max_no_of_results=1, patient=None): """Get N most recent results for *one* defined test type.""" assert (test_type is not None), '<test_type> must not be None' assert (max_no_of_results > 0), '<max_no_of_results> must be > 0' args = {'pat': patient, 'ttyp': test_type} where_parts = ['pk_patient = %(pat)s'] where_parts.append('pk_test_type = %(ttyp)s') # ?consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type'] cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY clin_when DESC LIMIT %s""" % ( ' AND '.join(where_parts), max_no_of_results ) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_most_recent_results_in_loinc_group(loincs=None, max_no_of_results=1, patient=None, max_age=None, consider_indirect_matches=False)-
Get N most recent results among a list of tests selected by LOINC.
1) get test types with LOINC (or meta type LOINC) in the group of
2) from these get the test results for within the given 3) from these return "the N= most recent ones" or "None" must be a list or tuple or set, NOT a single string must be a string holding a PG interval or else a pydt interval Expand source code
def get_most_recent_results_in_loinc_group(loincs=None, max_no_of_results=1, patient=None, max_age=None, consider_indirect_matches=False): """Get N most recent results *among* a list of tests selected by LOINC. 1) get test types with LOINC (or meta type LOINC) in the group of <loincs> 2) from these get the test results for <patient> within the given <max_age> 3) from these return "the N=<max_no_of_results> most recent ones" or "None" <loinc> must be a list or tuple or set, NOT a single string <max_age> must be a string holding a PG interval or else a pydt interval """ assert (max_no_of_results > 0), '<max_no_of_results> must be >0' args = {'pat': patient, 'loincs': loincs} if max_age is None: max_age_cond = '' else: max_age_cond = 'AND clin_when > (now() - %(max_age)s::interval)' args['max_age'] = max_age cmd = """ SELECT * FROM ( SELECT DISTINCT ON (pk_test_result) * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND unified_loinc = ANY(%%(loincs)s) %s ) AS distinct_results ORDER BY clin_when DESC LIMIT %s""" % ( max_age_cond, max_no_of_results ) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] if not consider_indirect_matches: return [] cmd = """ -- get the test results SELECT * FROM clin.v_test_results c_vtr WHERE -- for this <patient> pk_patient = %%(pat)s AND -- not having *any* LOINC (if the result did have a LOINC and had not been caught by the by-LOINC search it does not apply) unified_loinc IS NULL AND -- with these meta test types (= results for the explicit equivalance group) c_vtr.pk_meta_test_type IN ( -- get the meta test types for those types SELECT pk_meta_test_type FROM clin.v_test_types WHERE pk_meta_test_type IS NOT NULL AND (-- retrieve test types which have .LOINC in <loincs> (loinc IN %%(loincs)s) OR (loinc_meta IN %%(loincs)s) ) AND -- but no result for <patient> pk_test_type NOT IN ( select pk_test_type from clin.v_test_results WHERE pk_patient = %%(pat)s ) %s ) -- return the N most resent result ORDER BY clin_when DESC LIMIT %s """ % ( max_age_cond, max_no_of_results ) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_next_request_ID(lab=None, incrementor_func=None)-
Get logically next request ID for given lab.
- incrementor_func:
- if not supplied the next ID is guessed
- if supplied it is applied to the most recently used ID
Expand source code
def get_next_request_ID(lab=None, incrementor_func=None): """Get logically next request ID for given lab. - incrementor_func: - if not supplied the next ID is guessed - if supplied it is applied to the most recently used ID """ if type(lab) == int: lab_snippet = 'vlr.fk_test_org=%s' else: lab_snippet = 'vlr.lab_name=%s' lab = str(lab) cmd = """ select request_id from lab_request lr0 where lr0.clin_when = ( select max(vlr.sampled_when) from v_lab_requests vlr where %s )""" % lab_snippet rows = gmPG2.run_ro_queries(cmd, None, lab) if rows is None: _log.warning('error getting most recently used request ID for lab [%s]' % lab) return '' if len(rows) == 0: return '' most_recent = rows[0][0] # apply supplied incrementor if incrementor_func is not None: try: next = incrementor_func(most_recent) except TypeError: _log.error('cannot call incrementor function [%s]' % str(incrementor_func)) return most_recent return next # try to be smart ourselves for pos in range(len(most_recent)): header = most_recent[:pos] trailer = most_recent[pos:] try: return '%s%s' % (header, str(int(trailer) + 1)) except ValueError: header = most_recent[:-1] trailer = most_recent[-1:] return '%s%s' % (header, chr(ord(trailer) + 1)) def get_oldest_result(test_type=None, loinc=None, patient=None)-
Expand source code
def get_oldest_result(test_type=None, loinc=None, patient=None): if None not in [test_type, loinc]: raise ValueError('either <test_type> or <loinc> must be None') args = { 'pat': patient, 'ttyp': test_type, 'loinc': loinc } where_parts = ['pk_patient = %(pat)s'] if test_type is not None: where_parts.append('pk_test_type = %(ttyp)s') # consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type'] elif loinc is not None: where_parts.append('((loinc_tt = ANY(%(loinc)s)) OR (loinc_meta = ANY(%(loinc)s)))') args['loinc'] = loinc cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY clin_when LIMIT 1""" % ' AND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) def get_pending_requests(limit=250)-
Expand source code
def get_pending_requests(limit=250): lim = limit + 1 cmd = "select pk from lab_request where is_pending is true limit %s" % lim rows = gmPG2.run_ro_queries(queries = cmd) if rows is None: _log.error('error retrieving pending lab requests') return (None, None) if len(rows) == 0: return (False, []) # more than LIMIT rows ? if len(rows) == lim: too_many = True # but deliver only LIMIT rows so that our assumption holds true... rows = rows[:limit] else: too_many = False requests = [] for row in rows: try: requests.append(cLabRequest(aPK_obj=row[0])) except gmExceptions.ConstructorError: _log.exception('skipping pending lab request [%s]' % row[0], sys.exc_info(), verbose=0) return (too_many, requests) def get_result_at_timestamp(timestamp=None, test_type=None, loinc=None, tolerance_interval=None, patient=None)-
Expand source code
def get_result_at_timestamp(timestamp=None, test_type=None, loinc=None, tolerance_interval=None, patient=None): if None not in [test_type, loinc]: raise ValueError('either <test_type> or <loinc> must be None') args = { 'pat': patient, 'ttyp': test_type, 'loinc': loinc, 'ts': timestamp, 'intv': tolerance_interval } where_parts = ['pk_patient = %(pat)s'] if test_type is not None: where_parts.append('pk_test_type = %(ttyp)s') # consider: pk_meta_test_type = %(pkmtt)s / self._payload['pk_meta_test_type'] elif loinc is not None: where_parts.append('((loinc_tt = ANY(%(loinc)s)) OR (loinc_meta = ANY(%(loinc)s)))') args['loinc'] = loinc if tolerance_interval is None: where_parts.append('clin_when = %(ts)s') else: where_parts.append('clin_when between (%(ts)s - %(intv)s::interval) AND (%(ts)s + %(intv)s::interval)') cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY abs(extract(epoch from age(clin_when, %%(ts)s))) LIMIT 1""" % ' AND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) def get_results_for_day(timestamp=None, patient=None, order_by=None)-
Expand source code
def get_results_for_day(timestamp=None, patient=None, order_by=None): args = { 'pat': patient, 'ts': timestamp } where_parts = [ 'pk_patient = %(pat)s', "date_trunc('day'::text, clin_when) = date_trunc('day'::text, %(ts)s)" ] cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY val_grouping, abbrev_tt, clin_when DESC """ % ' AND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_results_for_episode(pk_episode=None)-
Expand source code
def get_results_for_episode(pk_episode=None): args = {'pk_epi': pk_episode} where_parts = ['pk_episode = %(pk_epi)s'] cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY val_grouping, abbrev_tt, clin_when DESC """ % ' AND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_results_for_issue(pk_health_issue=None, order_by=None)-
Expand source code
def get_results_for_issue(pk_health_issue=None, order_by=None): args = {'pk_issue': pk_health_issue} where_parts = ['pk_health_issue = %(pk_issue)s'] cmd = """ SELECT * FROM clin.v_test_results WHERE %s ORDER BY val_grouping, abbrev_tt, clin_when DESC """ % ' AND '.join(where_parts) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] def get_test_orgs(order_by='unit', return_pks=False)-
Expand source code
def get_test_orgs(order_by='unit', return_pks=False): cmd = 'SELECT * FROM clin.v_test_orgs ORDER BY %s' % order_by rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}]) if return_pks: return [ r['pk_test_org'] for r in rows ] return [ cTestOrg(row = {'pk_field': 'pk_test_org', 'data': r}) for r in rows ] def get_test_panels(order_by=None, loincs=None, return_pks=False)-
Expand source code
def get_test_panels(order_by=None, loincs=None, return_pks=False): where_args = {} if loincs is None: where_parts = ['true'] else: where_parts = ['loincs @> %(loincs)s'] where_args['loincs'] = list(loincs) if order_by is None: order_by = u'' else: order_by = ' ORDER BY %s' % order_by cmd = (_SQL_get_test_panels % ' AND '.join(where_parts)) + order_by rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': where_args}]) if return_pks: return [ r['pk_test_panel'] for r in rows ] return [ cTestPanel(row = {'data': r, 'pk_field': 'pk_test_panel'}) for r in rows ] def get_test_results(pk_patient=None, encounters=None, episodes=None, order_by=None, return_pks=False)-
Expand source code
def get_test_results(pk_patient=None, encounters=None, episodes=None, order_by=None, return_pks=False): where_parts = [] if pk_patient is not None: where_parts.append('pk_patient = %(pat)s') args = {'pat': pk_patient} # if tests is not None: # where_parts.append(u'pk_test_type = ANY(%(tests)s)') # args['tests'] = tests if encounters is not None: where_parts.append('pk_encounter = ANY(%(encs)s)') args['encs'] = encounters if episodes is not None: where_parts.append('pk_episode = ANY(%(epis)s)') args['epis'] = episodes if order_by is None: order_by = '' else: order_by = 'ORDER BY %s' % order_by cmd = """ SELECT * FROM clin.v_test_results WHERE %s %s """ % ( ' AND '.join(where_parts), order_by ) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if return_pks: return [ r['pk_test_result'] for r in rows ] tests = [ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ] return tests
Classes
class cLabRequest (aPK_obj=None, row=None)-
Represents one lab request.
Instantiate lab request.
The aPK_obj can be either a dict with the keys "req_id" and "lab" or a simple primary key.
Expand source code
class cLabRequest(gmBusinessDBObject.cBusinessDBObject): """Represents one lab request.""" _cmd_fetch_payload = """ select *, xmin_lab_request from v_lab_requests where pk_request=%s""" _cmds_lock_rows_for_update = [ """select 1 from lab_request where pk=%(pk_request)s and xmin=%(xmin_lab_request)s for update""" ] _cmds_store_payload = [ """update lab_request set request_id=%(request_id)s, lab_request_id=%(lab_request_id)s, clin_when=%(sampled_when)s, lab_rxd_when=%(lab_rxd_when)s, results_reported_when=%(results_reported_when)s, request_status=%(request_status)s, is_pending=%(is_pending)s::bool, narrative=%(progress_note)s where pk=%(pk_request)s""", """select xmin_lab_request from v_lab_requests where pk_request=%(pk_request)s""" ] _updatable_fields = [ 'request_id', 'lab_request_id', 'sampled_when', 'lab_rxd_when', 'results_reported_when', 'request_status', 'is_pending', 'progress_note' ] #-------------------------------------------------------- def __init__(self, aPK_obj=None, row=None): """Instantiate lab request. The aPK_obj can be either a dict with the keys "req_id" and "lab" or a simple primary key. """ # instantiate from row data ? if aPK_obj is None: gmBusinessDBObject.cBusinessDBObject.__init__(self, row=row) return pk = aPK_obj # instantiate from "req_id" and "lab" ? if type(aPK_obj) == dict: # sanity check try: aPK_obj['req_id'] aPK_obj['lab'] except Exception: _log.exception('[%s:??]: faulty <aPK_obj> structure: [%s]' % (self.__class__.__name__, aPK_obj), sys.exc_info()) raise gmExceptions.ConstructorError('[%s:??]: cannot derive PK from [%s]' % (self.__class__.__name__, aPK_obj)) # generate query where_snippets = [] where_snippets.append('request_id=%(req_id)s') if type(aPK_obj['lab']) == int: where_snippets.append('pk_test_org=%(lab)s') else: where_snippets.append('lab_name=%(lab)s') # where_clause = ' and '.join(where_snippets) # cmd = "select pk_request from v_lab_requests where %s" % where_clause # # get pk # data = gmPG2.run_ro_query('historica', cmd, None, aPK_obj) # if data is None: # raise gmExceptions.ConstructorError('[%s:??]: error getting lab request for [%s]' % (self.__class__.__name__, aPK_obj)) # if len(data) == 0: # raise gmExceptions.NoSuchClinItemError('[%s:??]: no lab request for [%s]' % (self.__class__.__name__, aPK_obj)) # pk = data[0][0] # instantiate class gmBusinessDBObject.cBusinessDBObject.__init__(self, aPK_obj=pk)Ancestors
Inherited members
class cMeasurementType (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents one test result type.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cMeasurementType(gmBusinessDBObject.cBusinessDBObject): """Represents one test result type.""" _cmd_fetch_payload = _SQL_get_test_types % "pk_test_type = %s" _cmds_store_payload = [ """UPDATE clin.test_type SET abbrev = gm.nullify_empty_string(%(abbrev)s), name = gm.nullify_empty_string(%(name)s), loinc = gm.nullify_empty_string(%(loinc)s), comment = gm.nullify_empty_string(%(comment_type)s), reference_unit = gm.nullify_empty_string(%(reference_unit)s), fk_test_org = %(pk_test_org)s, fk_meta_test_type = %(pk_meta_test_type)s WHERE pk = %(pk_test_type)s AND xmin = %(xmin_test_type)s RETURNING xmin AS xmin_test_type""" ] _updatable_fields = [ 'abbrev', 'name', 'loinc', 'comment_type', 'reference_unit', 'pk_test_org', 'pk_meta_test_type' ] #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_in_use(self): cmd = 'SELECT EXISTS(SELECT 1 FROM clin.test_result WHERE fk_type = %(pk_type)s)' args = {'pk_type': self._payload['pk_test_type']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return rows[0][0] in_use = property(_get_in_use) #-------------------------------------------------------- def get_most_recent_results(self, patient=None, max_no_of_results=1): results = get_most_recent_results_for_test_type ( test_type = self._payload['pk_test_type'], max_no_of_results = max_no_of_results, patient = patient ) if len(results) > 0: return results if self._payload['loinc'] is None: return [] return get_most_recent_results_in_loinc_group ( loincs = list(self._payload['loinc']), max_no_of_results = max_no_of_results, patient = patient # ? ) #-------------------------------------------------------- def get_oldest_result(self, patient=None): result = get_oldest_result ( test_type = self._payload['pk_test_type'], loinc = None, patient = patient ) if result is None: if self._payload['loinc'] is not None: result = get_oldest_result ( test_type = None, loinc = self._payload['loinc'], patient = patient ) return result #-------------------------------------------------------- def _get_test_panels(self): if self._payload['pk_test_panels'] is None: return None return [ cTestPanel(aPK_obj = pk) for pk in self._payload['pk_test_panels'] ] test_panels = property(_get_test_panels) #-------------------------------------------------------- def get_meta_test_type(self, real_one_only=True): if real_one_only is False: return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) if self._payload['is_fake_meta_type']: return None return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) meta_test_type = property(get_meta_test_type) #-------------------------------------------------------- def get_temporally_closest_normal_range(self, unit, timestamp=None): """Returns the closest test result which does have normal range information. - needs <unit> - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT * FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit = %(unit)s AND ( (val_normal_min IS NOT NULL) OR (val_normal_max IS NOT NULL) OR (val_normal_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': unit, 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None r = rows[0] return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) #-------------------------------------------------------- def get_temporally_closest_target_range(self, unit, patient, timestamp=None): """Returns the closest test result which does have target range information. - needs <unit> - needs <patient> (as target will be per-patient) - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT * FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit = %(unit)s AND pk_patient = %(pat)s AND ( (val_target_min IS NOT NULL) OR (val_target_max IS NOT NULL) OR (val_target_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': unit, 'pat': patient, 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None r = rows[0] return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) #-------------------------------------------------------- def get_temporally_closest_unit(self, timestamp=None): """Returns the unit of the closest test result. - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT val_unit FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit IS NOT NULL ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return rows[0]['val_unit'] temporally_closest_unit = property(get_temporally_closest_unit) #-------------------------------------------------------- def format(self, patient=None): tt = '' tt += _('Test type "%s" (%s) [#%s]\n') % ( self._payload['name'], self._payload['abbrev'], self._payload['pk_test_type'] ) tt += '\n' tt += gmTools.coalesce(self._payload['loinc'], '', ' LOINC: %s\n') tt += gmTools.coalesce(self._payload['reference_unit'], '', _(' Reference unit: %s\n')) tt += gmTools.coalesce(self._payload['comment_type'], '', _(' Comment: %s\n')) tt += '\n' tt += _('Lab details:\n') tt += _(' Name: %s\n') % gmTools.coalesce(self._payload['name_org'], '') tt += gmTools.coalesce(self._payload['contact_org'], '', _(' Contact: %s\n')) tt += gmTools.coalesce(self._payload['comment_org'], '', _(' Comment: %s\n')) if self._payload['is_fake_meta_type'] is False: tt += '\n' tt += _('Aggregated under meta type:\n') tt += _(' Name: %s - %s [#%s]\n') % ( self._payload['abbrev_meta'], self._payload['name_meta'], self._payload['pk_meta_test_type'] ) tt += gmTools.coalesce(self._payload['loinc_meta'], '', ' LOINC: %s\n') tt += gmTools.coalesce(self._payload['comment_meta'], '', _(' Comment: %s\n')) panels = self.test_panels if panels is not None: tt += '\n' tt += _('Listed in test panels:\n') for panel in panels: tt += _(' Panel "%s" [#%s]\n') % ( panel['description'], panel['pk_test_panel'] ) if patient is not None: tt += '\n' results = self.get_most_recent_results(patient = patient, max_no_of_results = 1) if len(results) > 0: result = results[0] tt += _(' Most recent (%s): %s%s%s') % ( gmDateTime.pydt_strftime(result['clin_when'], '%Y %b %d'), result['unified_val'], gmTools.coalesce(result['val_unit'], '', ' %s'), gmTools.coalesce(result['abnormality_indicator'], '', ' (%s)') ) result = self.get_oldest_result(patient = patient) if result is not None: tt += '\n' tt += _(' Oldest (%s): %s%s%s') % ( gmDateTime.pydt_strftime(result['clin_when'], '%Y %b %d'), result['unified_val'], gmTools.coalesce(result['val_unit'], '', ' %s'), gmTools.coalesce(result['abnormality_indicator'], '', ' (%s)') ) return ttAncestors
Instance variables
var in_use-
Expand source code
def _get_in_use(self): cmd = 'SELECT EXISTS(SELECT 1 FROM clin.test_result WHERE fk_type = %(pk_type)s)' args = {'pk_type': self._payload['pk_test_type']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return rows[0][0] var meta_test_type-
Expand source code
def get_meta_test_type(self, real_one_only=True): if real_one_only is False: return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) if self._payload['is_fake_meta_type']: return None return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) var temporally_closest_unit-
Returns the unit of the closest test result.
- if
is None it will assume now() and thus return the most recent
Expand source code
def get_temporally_closest_unit(self, timestamp=None): """Returns the unit of the closest test result. - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT val_unit FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit IS NOT NULL ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return rows[0]['val_unit'] - if
var test_panels-
Expand source code
def _get_test_panels(self): if self._payload['pk_test_panels'] is None: return None return [ cTestPanel(aPK_obj = pk) for pk in self._payload['pk_test_panels'] ]
Methods
def get_meta_test_type(self, real_one_only=True)-
Expand source code
def get_meta_test_type(self, real_one_only=True): if real_one_only is False: return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) if self._payload['is_fake_meta_type']: return None return cMetaTestType(aPK_obj = self._payload['pk_meta_test_type']) def get_most_recent_results(self, patient=None, max_no_of_results=1)-
Expand source code
def get_most_recent_results(self, patient=None, max_no_of_results=1): results = get_most_recent_results_for_test_type ( test_type = self._payload['pk_test_type'], max_no_of_results = max_no_of_results, patient = patient ) if len(results) > 0: return results if self._payload['loinc'] is None: return [] return get_most_recent_results_in_loinc_group ( loincs = list(self._payload['loinc']), max_no_of_results = max_no_of_results, patient = patient # ? ) def get_oldest_result(self, patient=None)-
Expand source code
def get_oldest_result(self, patient=None): result = get_oldest_result ( test_type = self._payload['pk_test_type'], loinc = None, patient = patient ) if result is None: if self._payload['loinc'] is not None: result = get_oldest_result ( test_type = None, loinc = self._payload['loinc'], patient = patient ) return result def get_temporally_closest_normal_range(self, unit, timestamp=None)-
Returns the closest test result which does have normal range information.
- needs
- if
is None it will assume now() and thus return the most recent
Expand source code
def get_temporally_closest_normal_range(self, unit, timestamp=None): """Returns the closest test result which does have normal range information. - needs <unit> - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT * FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit = %(unit)s AND ( (val_normal_min IS NOT NULL) OR (val_normal_max IS NOT NULL) OR (val_normal_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': unit, 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None r = rows[0] return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) - needs
def get_temporally_closest_target_range(self, unit, patient, timestamp=None)-
Returns the closest test result which does have target range information.
- needs
- needs
(as target will be per-patient) - if
is None it will assume now() and thus return the most recent
Expand source code
def get_temporally_closest_target_range(self, unit, patient, timestamp=None): """Returns the closest test result which does have target range information. - needs <unit> - needs <patient> (as target will be per-patient) - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT * FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit = %(unit)s AND pk_patient = %(pat)s AND ( (val_target_min IS NOT NULL) OR (val_target_max IS NOT NULL) OR (val_target_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': unit, 'pat': patient, 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None r = rows[0] return cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) - needs
def get_temporally_closest_unit(self, timestamp=None)-
Returns the unit of the closest test result.
- if
is None it will assume now() and thus return the most recent
Expand source code
def get_temporally_closest_unit(self, timestamp=None): """Returns the unit of the closest test result. - if <timestamp> is None it will assume now() and thus return the most recent """ if timestamp is None: timestamp = gmDateTime.pydt_now_here() cmd = """ SELECT val_unit FROM clin.v_test_results WHERE pk_test_type = %(pk_type)s AND val_unit IS NOT NULL ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'clin_when': timestamp } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return rows[0]['val_unit'] - if
Inherited members
class cMetaTestType (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents one meta test type under which actual test types can be aggregated.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cMetaTestType(gmBusinessDBObject.cBusinessDBObject): """Represents one meta test type under which actual test types can be aggregated.""" _cmd_fetch_payload = "SELECT *, xmin FROM clin.meta_test_type WHERE pk = %s" _cmds_store_payload = [""" UPDATE clin.meta_test_type SET abbrev = %(abbrev)s, name = %(name)s, loinc = gm.nullify_empty_string(%(loinc)s), comment = gm.nullify_empty_string(%(comment)s) WHERE pk = %(pk)s AND xmin = %(xmin)s RETURNING xmin """] _updatable_fields = [ 'abbrev', 'name', 'loinc', 'comment' ] #-------------------------------------------------------- def format(self, with_tests=False, patient=None): txt = _('Meta (%s=aggregate) test type [#%s]\n\n') % (gmTools.u_sum, self._payload['pk']) txt += _(' Name: %s (%s)\n') % ( self._payload['abbrev'], self._payload['name'] ) if self._payload['loinc'] is not None: txt += ' LOINC: %s\n' % self._payload['loinc'] if self._payload['comment'] is not None: txt += _(' Comment: %s\n') % self._payload['comment'] if with_tests: ttypes = self.included_test_types if len(ttypes) > 0: txt += _(' Aggregates the following test types:\n') for ttype in ttypes: txt += ' - %s (%s)%s%s%s [#%s]\n' % ( ttype['name'], ttype['abbrev'], gmTools.coalesce(ttype['reference_unit'], '', ', %s'), gmTools.coalesce(ttype['name_org'], '', ' (%s)'), gmTools.coalesce(ttype['loinc'], '', ', LOINC: %s'), ttype['pk_test_type'] ) if patient is not None: txt += '\n' most_recent = self.get_most_recent_result(patient = patient) if most_recent is not None: txt += _(' Most recent (%s): %s%s%s') % ( gmDateTime.pydt_strftime(most_recent['clin_when'], '%Y %b %d'), most_recent['unified_val'], gmTools.coalesce(most_recent['val_unit'], '', ' %s'), gmTools.coalesce(most_recent['abnormality_indicator'], '', ' (%s)') ) oldest = self.get_oldest_result(patient = patient) if oldest is not None: txt += '\n' txt += _(' Oldest (%s): %s%s%s') % ( gmDateTime.pydt_strftime(oldest['clin_when'], '%Y %b %d'), oldest['unified_val'], gmTools.coalesce(oldest['val_unit'], '', ' %s'), gmTools.coalesce(oldest['abnormality_indicator'], '', ' (%s)') ) return txt #-------------------------------------------------------- def get_most_recent_result(self, patient=None): args = { 'pat': patient, 'mttyp': self._payload['pk'] } cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type = %(mttyp)s ORDER BY clin_when DESC LIMIT 1""" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) #-------------------------------------------------------- def get_oldest_result(self, patient=None): args = { 'pat': patient, 'mttyp': self._payload['pk'] } cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type = %(mttyp)s ORDER BY clin_when LIMIT 1""" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) #-------------------------------------------------------- def get_temporally_closest_result(self, date, pk_patient): args = { 'pat': pk_patient, 'mtyp': self._payload['pk'], 'mloinc': self._payload['loinc'], 'when': date } SQL = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND clin_when %s %%(when)s AND ((pk_meta_test_type = %%(mtyp)s) OR (loinc_meta = %%(mloinc)s)) ORDER BY clin_when LIMIT 1""" # get earlier results by meta type earlier_result = None cmd = SQL % '<' rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) # get later results by meta type ? later_result = None cmd = SQL % '>' rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) if earlier_result is None: return later_result if later_result is None: return earlier_result earlier_ago = date - earlier_result['clin_when'] later_ago = later_result['clin_when'] - date if earlier_ago < later_ago: return earlier_result return later_result #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_included_test_types(self): cmd = _SQL_get_test_types % 'pk_meta_test_type = %(pk_meta)s' args = {'pk_meta': self._payload['pk']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ] included_test_types = property(_get_included_test_types)Ancestors
Instance variables
var included_test_types-
Expand source code
def _get_included_test_types(self): cmd = _SQL_get_test_types % 'pk_meta_test_type = %(pk_meta)s' args = {'pk_meta': self._payload['pk']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ]
Methods
def get_most_recent_result(self, patient=None)-
Expand source code
def get_most_recent_result(self, patient=None): args = { 'pat': patient, 'mttyp': self._payload['pk'] } cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type = %(mttyp)s ORDER BY clin_when DESC LIMIT 1""" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) def get_oldest_result(self, patient=None)-
Expand source code
def get_oldest_result(self, patient=None): args = { 'pat': patient, 'mttyp': self._payload['pk'] } cmd = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %(pat)s AND pk_meta_test_type = %(mttyp)s ORDER BY clin_when LIMIT 1""" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) def get_temporally_closest_result(self, date, pk_patient)-
Expand source code
def get_temporally_closest_result(self, date, pk_patient): args = { 'pat': pk_patient, 'mtyp': self._payload['pk'], 'mloinc': self._payload['loinc'], 'when': date } SQL = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND clin_when %s %%(when)s AND ((pk_meta_test_type = %%(mtyp)s) OR (loinc_meta = %%(mloinc)s)) ORDER BY clin_when LIMIT 1""" # get earlier results by meta type earlier_result = None cmd = SQL % '<' rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) # get later results by meta type ? later_result = None cmd = SQL % '>' rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_result = cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) if earlier_result is None: return later_result if later_result is None: return earlier_result earlier_ago = date - earlier_result['clin_when'] later_ago = later_result['clin_when'] - date if earlier_ago < later_ago: return earlier_result return later_result
Inherited members
class cTestOrg (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents one test org/lab.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cTestOrg(gmBusinessDBObject.cBusinessDBObject): """Represents one test org/lab.""" _cmd_fetch_payload = _SQL_get_test_orgs % 'pk_test_org = %s' _cmds_store_payload = [ """UPDATE clin.test_org SET fk_org_unit = %(pk_org_unit)s, contact = gm.nullify_empty_string(%(test_org_contact)s), comment = gm.nullify_empty_string(%(comment)s) WHERE pk = %(pk_test_org)s AND xmin = %(xmin_test_org)s RETURNING xmin AS xmin_test_org """ ] _updatable_fields = [ 'pk_org_unit', 'test_org_contact', 'comment' ]Ancestors
Inherited members
class cTestPanel (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents a grouping/listing of tests into a panel.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cTestPanel(gmBusinessDBObject.cBusinessDBObject): """Represents a grouping/listing of tests into a panel.""" _cmd_fetch_payload = _SQL_get_test_panels % "pk_test_panel = %s" _cmds_store_payload = [ """ UPDATE clin.test_panel SET description = gm.nullify_empty_string(%(description)s), comment = gm.nullify_empty_string(%(comment)s) WHERE pk = %(pk_test_panel)s AND xmin = %(xmin_test_panel)s RETURNING xmin AS xmin_test_panel """ ] _updatable_fields = [ 'description', 'comment' ] #-------------------------------------------------------- def format(self): txt = _('Test panel "%s" [#%s]\n') % ( self._payload['description'], self._payload['pk_test_panel'] ) if self._payload['comment'] is not None: txt += '\n' txt += gmTools.wrap ( text = self._payload['comment'], width = 50, initial_indent = ' ', subsequent_indent = ' ' ) txt += '\n' txt += '\n' txt += _('Includes:\n') if len(self.included_loincs) == 0: txt += _('no tests') else: tts_by_loinc = {} for loinc in self._payload['loincs']: tts_by_loinc[loinc] = [] for ttype in self.test_types: tts_by_loinc[ttype['loinc']].append(ttype) for loinc, ttypes in tts_by_loinc.items(): # maybe resolve LOINC, too txt += _(' %s: %s\n') % ( loinc, '; '.join([ '%(abbrev)s@%(name_org)s [#%(pk_test_type)s]' % tt for tt in ttypes ]) ) codes = self.generic_codes if len(codes) > 0: txt += '\n' for c in codes: txt += ' %s: %s (%s - %s)\n' % ( c['code'], c['term'], c['name_short'], c['version'] ) return txt #-------------------------------------------------------- def add_code(self, pk_code=None): """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)""" cmd = "INSERT INTO clin.lnk_code2tst_pnl (fk_item, fk_generic_code) values (%(tp)s, %(code)s)" args = { 'tp': self._payload['pk_test_panel'], 'code': pk_code } gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True #-------------------------------------------------------- def remove_code(self, pk_code=None): """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)""" cmd = "DELETE FROM clin.lnk_code2tst_pnl WHERE fk_item = %(tp)s AND fk_generic_code = %(code)s" args = { 'tp': self._payload['pk_test_panel'], 'code': pk_code } gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True #-------------------------------------------------------- def get_test_types_for_results(self, pk_patient, order_by=None, unique_meta_types=False): """Retrieve data about test types on this panel (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_test_type IN %%(pks)s AND 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_test_type IN %%(pks)s AND 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_test_type = ANY(%%(pks)s) AND c_vtr.pk_patient = %%(pat)s ) %s""" % order_by args = { 'pat': pk_patient, 'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ] } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ] #-------------------------------------------------------- def add_loinc(self, loinc): if self._payload['loincs'] is not None: if loinc in self._payload['loincs']: return gmPG2.run_rw_queries(queries = [{ 'cmd': 'INSERT INTO clin.lnk_loinc2test_panel (fk_test_panel, loinc) VALUES (%(pk_pnl)s, %(loinc)s)', 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']} }]) return #-------------------------------------------------------- def remove_loinc(self, loinc): if self._payload['loincs'] is None: return if loinc not in self._payload['loincs']: return gmPG2.run_rw_queries(queries = [{ 'cmd': 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc = %(loinc)s', 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']} }]) return #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_included_loincs(self): return self._payload['loincs'] def _set_included_loincs(self, loincs): queries = [] # remove those which don't belong if len(loincs) == 0: cmd = 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s' else: cmd = 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc <> ALL(%(loincs)s)' queries.append({'cmd': cmd, 'args': {'loincs': loincs, 'pk_pnl': self._payload['pk_test_panel']}}) # add those not there yet if len(loincs) > 0: for loinc in loincs: cmd = """INSERT INTO clin.lnk_loinc2test_panel (fk_test_panel, loinc) SELECT %(pk_pnl)s, %(loinc)s WHERE NOT EXISTS ( SELECT 1 FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc = %(loinc)s )""" queries.append({'cmd': cmd, 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']}}) return gmPG2.run_rw_queries(queries = queries) included_loincs = property(_get_included_loincs, _set_included_loincs) #-------------------------------------------------------- def _get_test_types(self): if len(self._payload['test_types']) == 0: return [] rows = gmPG2.run_ro_queries ( queries = [{ 'cmd': _SQL_get_test_types % 'pk_test_type = ANY(%(pks)s) ORDER BY unified_abbrev', 'args': {'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ]} }] ) return [ cMeasurementType(row = {'data': r, 'pk_field': 'pk_test_type'}) for r in rows ] test_types = property(_get_test_types) #-------------------------------------------------------- def _get_generic_codes(self): if len(self._payload['pk_generic_codes']) == 0: return [] cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)' args = {'pks': self._payload['pk_generic_codes']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ] def _set_generic_codes(self, pk_codes): queries = [] # remove all codes if len(self._payload['pk_generic_codes']) > 0: queries.append ({ 'cmd': 'DELETE FROM clin.lnk_code2tst_pnl WHERE fk_item = %(tp)s AND fk_generic_code = ANY(%(codes)s)', 'args': { 'tp': self._payload['pk_test_panel'], 'codes': self._payload['pk_generic_codes'] } }) # add new codes for pk_code in pk_codes: queries.append ({ 'cmd': 'INSERT INTO clin.lnk_code2test_panel (fk_item, fk_generic_code) VALUES (%(tp)s, %(pk_code)s)', 'args': { 'tp': self._payload['pk_test_panel'], 'pk_code': pk_code } }) if len(queries) == 0: return # run it all in one transaction gmPG2.run_rw_queries(queries = queries) return generic_codes = property(_get_generic_codes, _set_generic_codes) #-------------------------------------------------------- def get_most_recent_results(self, pk_patient=None, order_by=None, group_by_meta_type=False, include_missing=False): if len(self._payload['test_types']) == 0: return [] pnl_results = get_most_recent_results_for_panel ( pk_patient = pk_patient, pk_panel = self._payload['pk_test_panel'], order_by = order_by, group_by_meta_type = group_by_meta_type ) if not include_missing: return pnl_results loincs_found = [ r['loinc_tt'] for r in pnl_results ] loincs_found.extend([ r['loinc_meta'] for r in pnl_results if r['loinc_meta'] not in loincs_found ]) loincs2consider = set([ tt['loinc'] for tt in self._payload['test_types'] ]) loincs_missing = loincs2consider - set(loincs_found) pnl_results.extend(loincs_missing) return pnl_resultsAncestors
Instance variables
var generic_codes-
Expand source code
def _get_generic_codes(self): if len(self._payload['pk_generic_codes']) == 0: return [] cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)' args = {'pks': self._payload['pk_generic_codes']} rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'pk_field': 'pk_lnk_code2item'}) for r in rows ] var included_loincs-
Expand source code
def _get_included_loincs(self): return self._payload['loincs'] var test_types-
Expand source code
def _get_test_types(self): if len(self._payload['test_types']) == 0: return [] rows = gmPG2.run_ro_queries ( queries = [{ 'cmd': _SQL_get_test_types % 'pk_test_type = ANY(%(pks)s) ORDER BY unified_abbrev', 'args': {'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ]} }] ) return [ cMeasurementType(row = {'data': r, 'pk_field': 'pk_test_type'}) for r in rows ]
Methods
def add_code(self, pk_code=None)-
must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code) Expand source code
def add_code(self, pk_code=None): """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)""" cmd = "INSERT INTO clin.lnk_code2tst_pnl (fk_item, fk_generic_code) values (%(tp)s, %(code)s)" args = { 'tp': self._payload['pk_test_panel'], 'code': pk_code } gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True def add_loinc(self, loinc)-
Expand source code
def add_loinc(self, loinc): if self._payload['loincs'] is not None: if loinc in self._payload['loincs']: return gmPG2.run_rw_queries(queries = [{ 'cmd': 'INSERT INTO clin.lnk_loinc2test_panel (fk_test_panel, loinc) VALUES (%(pk_pnl)s, %(loinc)s)', 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']} }]) return def get_most_recent_results(self, pk_patient=None, order_by=None, group_by_meta_type=False, include_missing=False)-
Expand source code
def get_most_recent_results(self, pk_patient=None, order_by=None, group_by_meta_type=False, include_missing=False): if len(self._payload['test_types']) == 0: return [] pnl_results = get_most_recent_results_for_panel ( pk_patient = pk_patient, pk_panel = self._payload['pk_test_panel'], order_by = order_by, group_by_meta_type = group_by_meta_type ) if not include_missing: return pnl_results loincs_found = [ r['loinc_tt'] for r in pnl_results ] loincs_found.extend([ r['loinc_meta'] for r in pnl_results if r['loinc_meta'] not in loincs_found ]) loincs2consider = set([ tt['loinc'] for tt in self._payload['test_types'] ]) loincs_missing = loincs2consider - set(loincs_found) pnl_results.extend(loincs_missing) return pnl_results def get_test_types_for_results(self, pk_patient, order_by=None, unique_meta_types=False)-
Retrieve data about test types on this panel (for which this patient has results).
Expand source code
def get_test_types_for_results(self, pk_patient, order_by=None, unique_meta_types=False): """Retrieve data about test types on this panel (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_test_type IN %%(pks)s AND 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_test_type IN %%(pks)s AND 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_test_type = ANY(%%(pks)s) AND c_vtr.pk_patient = %%(pat)s ) %s""" % order_by args = { 'pat': pk_patient, 'pks': [ tt['pk_test_type'] for tt in self._payload['test_types'] ] } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) return [ cMeasurementType(row = {'pk_field': 'pk_test_type', 'data': r}) for r in rows ] def remove_code(self, pk_code=None)-
must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code) Expand source code
def remove_code(self, pk_code=None): """<pk_code> must be a value from ref.coding_system_root.pk_coding_system (clin.lnk_code2item_root.fk_generic_code)""" cmd = "DELETE FROM clin.lnk_code2tst_pnl WHERE fk_item = %(tp)s AND fk_generic_code = %(code)s" args = { 'tp': self._payload['pk_test_panel'], 'code': pk_code } gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True def remove_loinc(self, loinc)-
Expand source code
def remove_loinc(self, loinc): if self._payload['loincs'] is None: return if loinc not in self._payload['loincs']: return gmPG2.run_rw_queries(queries = [{ 'cmd': 'DELETE FROM clin.lnk_loinc2test_panel WHERE fk_test_panel = %(pk_pnl)s AND loinc = %(loinc)s', 'args': {'loinc': loinc, 'pk_pnl': self._payload['pk_test_panel']} }]) return
Inherited members
class cTestResult (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents one test result.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- an scalar value the ._cmd_fetch_payload WHERE condition must be a simple column: "… WHERE pk_col = %s"
- a dictionary of values the ._cmd_fetch_payload WHERE condition must consume the dictionary and produce a unique row
row- must hold the fields
- data: list of column values for the row selected by ._cmd_fetch_payload (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key column OR
- pk_obj: a dictionary suitable for being passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) objects = [ cChildClass(row = {'data': r, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cTestResult(gmBusinessDBObject.cBusinessDBObject): """Represents one test result.""" _cmd_fetch_payload = "select * from clin.v_test_results where pk_test_result = %s" _cmds_store_payload = [ """UPDATE clin.test_result SET clin_when = %(clin_when)s, narrative = nullif(trim(%(comment)s), ''), val_num = %(val_num)s, val_alpha = nullif(trim(%(val_alpha)s), ''), val_unit = nullif(trim(%(val_unit)s), ''), val_normal_min = %(val_normal_min)s, val_normal_max = %(val_normal_max)s, val_normal_range = nullif(trim(%(val_normal_range)s), ''), val_target_min = %(val_target_min)s, val_target_max = %(val_target_max)s, val_target_range = nullif(trim(%(val_target_range)s), ''), abnormality_indicator = nullif(trim(%(abnormality_indicator)s), ''), norm_ref_group = nullif(trim(%(norm_ref_group)s), ''), note_test_org = nullif(trim(%(note_test_org)s), ''), material = nullif(trim(%(material)s), ''), material_detail = nullif(trim(%(material_detail)s), ''), status = gm.nullify_empty_string(%(status)s), val_grouping = gm.nullify_empty_string(%(val_grouping)s), source_data = gm.nullify_empty_string(%(source_data)s), fk_intended_reviewer = %(pk_intended_reviewer)s, fk_encounter = %(pk_encounter)s, fk_episode = %(pk_episode)s, fk_type = %(pk_test_type)s, fk_request = %(pk_request)s WHERE pk = %(pk_test_result)s AND xmin = %(xmin_test_result)s RETURNING xmin AS xmin_test_result """ # , u"""select xmin_test_result from clin.v_test_results where pk_test_result = %(pk_test_result)s""" ] _updatable_fields = [ 'clin_when', 'comment', 'val_num', 'val_alpha', 'val_unit', 'val_normal_min', 'val_normal_max', 'val_normal_range', 'val_target_min', 'val_target_max', 'val_target_range', 'abnormality_indicator', 'norm_ref_group', 'note_test_org', 'material', 'material_detail', 'status', 'val_grouping', 'source_data', 'pk_intended_reviewer', 'pk_encounter', 'pk_episode', 'pk_test_type', 'pk_request' ] #-------------------------------------------------------- def format_concisely(self, date_format='%Y %b %d', with_notes=True): range_info = gmTools.coalesce ( self.formatted_clinical_range, self.formatted_normal_range ) review = gmTools.bool2subst ( self._payload['reviewed'], '', ' ' + gmTools.u_writing_hand, ' ' + gmTools.u_writing_hand ) txt = '%s %s: %s%s%s%s%s%s' % ( gmDateTime.pydt_strftime ( self._payload['clin_when'], date_format ), self._payload['name_tt'], self._payload['unified_val'], gmTools.coalesce(self._payload['val_unit'], '', ' %s'), gmTools.coalesce(self._payload['abnormality_indicator'], '', ' %s'), gmTools.coalesce(range_info, '', ' (%s)'), gmTools.coalesce(self._payload['status'], '', ' [%s]')[:2], review ) if with_notes: txt += '\n' if self._payload['note_test_org'] is not None: txt += ' ' + _('Lab comment: %s\n') % _('\n Lab comment: ').join(self._payload['note_test_org'].split('\n')) if self._payload['comment'] is not None: txt += ' ' + _('Praxis comment: %s\n') % _('\n Praxis comment: ').join(self._payload['comment'].split('\n')) return txt.strip('\n') #-------------------------------------------------------- def format(self, with_review=True, with_evaluation=True, with_ranges=True, with_episode=True, with_type_details=True, with_source_data=False, date_format='%Y %b %d %H:%M'): # FIXME: add battery, request details # header tt = _('Result from %s \n') % gmDateTime.pydt_strftime ( self._payload['clin_when'], date_format ) # basics tt += ' ' + _('Type: "%(name)s" (%(abbr)s) [#%(pk_type)s]\n') % ({ 'name': self._payload['name_tt'], 'abbr': self._payload['abbrev_tt'], 'pk_type': self._payload['pk_test_type'] }) if self.is_long_text: sso = gmTools.u_superscript_one else: sso = '' tt += ' ' + _('%(sso)sResult: %(val)s%(unit)s%(ind)s [#%(pk_result)s]\n') % ({ 'sso': sso, 'val': self._payload['unified_val'], 'unit': gmTools.coalesce(self._payload['val_unit'], '', ' %s'), 'ind': gmTools.coalesce(self._payload['abnormality_indicator'], '', ' (%s)'), 'pk_result': self._payload['pk_test_result'] }) if self._payload['status'] is not None: try: stat = HL7_RESULT_STATI[self._payload['status']] except KeyError: stat = self._payload['status'] tt += ' ' + _('Status: %s\n') % stat if self._payload['val_grouping'] is not None: tt += ' ' + _('Grouping: %s\n') % self._payload['val_grouping'] if with_evaluation: norm_eval = None if self._payload['val_num'] is not None: # 1) normal range # lowered ? if (self._payload['val_normal_min'] is not None) and (self._payload['val_num'] < self._payload['val_normal_min']): try: percent = (self._payload['val_num'] * 100) / self._payload['val_normal_min'] except ZeroDivisionError: percent = None if percent is not None: if percent < 6: norm_eval = _('%.1f %% of the normal lower limit') % percent else: norm_eval = _('%.0f %% of the normal lower limit') % percent # raised ? if (self._payload['val_normal_max'] is not None) and (self._payload['val_num'] > self._payload['val_normal_max']): try: x_times = self._payload['val_num'] / self._payload['val_normal_max'] except ZeroDivisionError: x_times = None if x_times is not None: if x_times < 10: norm_eval = _('%.1f times the normal upper limit') % x_times else: norm_eval = _('%.0f times the normal upper limit') % x_times if norm_eval is not None: tt += ' = %s\n' % norm_eval # #------------------------------------- # # this idea was shot down on the list # #------------------------------------- # # bandwidth of deviation # if None not in [self._payload['val_normal_min'], self._payload['val_normal_max']]: # normal_width = self._payload['val_normal_max'] - self._payload['val_normal_min'] # deviation_from_normal_range = None # # below ? # if self._payload['val_num'] < self._payload['val_normal_min']: # deviation_from_normal_range = self._payload['val_normal_min'] - self._payload['val_num'] # # above ? # elif self._payload['val_num'] > self._payload['val_normal_max']: # deviation_from_normal_range = self._payload['val_num'] - self._payload['val_normal_max'] # if deviation_from_normal_range is None: # try: # times_deviation = deviation_from_normal_range / normal_width # except ZeroDivisionError: # times_deviation = None # if times_deviation is not None: # if times_deviation < 10: # tt += u' (%s)\n' % _(u'deviates by %.1f times of the normal range') % times_deviation # else: # tt += u' (%s)\n' % _(u'deviates by %.0f times of the normal range') % times_deviation # #------------------------------------- # 2) clinical target range norm_eval = None # lowered ? if (self._payload['val_target_min'] is not None) and (self._payload['val_num'] < self._payload['val_target_min']): try: percent = (self._payload['val_num'] * 100) / self._payload['val_target_min'] except ZeroDivisionError: percent = None if percent is not None: if percent < 6: norm_eval = _('%.1f %% of the target lower limit') % percent else: norm_eval = _('%.0f %% of the target lower limit') % percent # raised ? if (self._payload['val_target_max'] is not None) and (self._payload['val_num'] > self._payload['val_target_max']): try: x_times = self._payload['val_num'] / self._payload['val_target_max'] except ZeroDivisionError: x_times = None if x_times is not None: if x_times < 10: norm_eval = _('%.1f times the target upper limit') % x_times else: norm_eval = _('%.0f times the target upper limit') % x_times if norm_eval is not None: tt += ' = %s\n' % norm_eval # #------------------------------------- # # this idea was shot down on the list # #------------------------------------- # # bandwidth of deviation # if None not in [self._payload['val_target_min'], self._payload['val_target_max']]: # normal_width = self._payload['val_target_max'] - self._payload['val_target_min'] # deviation_from_target_range = None # # below ? # if self._payload['val_num'] < self._payload['val_target_min']: # deviation_from_target_range = self._payload['val_target_min'] - self._payload['val_num'] # # above ? # elif self._payload['val_num'] > self._payload['val_target_max']: # deviation_from_target_range = self._payload['val_num'] - self._payload['val_target_max'] # if deviation_from_target_range is None: # try: # times_deviation = deviation_from_target_range / normal_width # except ZeroDivisionError: # times_deviation = None # if times_deviation is not None: # if times_deviation < 10: # tt += u' (%s)\n' % _(u'deviates by %.1f times of the target range') % times_deviation # else: # tt += u' (%s)\n' % _(u'deviates by %.0f times of the target range') % times_deviation # #------------------------------------- tmp = ('%s%s' % ( gmTools.coalesce(self._payload['name_test_org'], ''), gmTools.coalesce(self._payload['contact_test_org'], '', ' (%s)'), )).strip() if tmp != '': tt += ' ' + _('Source: %s\n') % tmp tt += '\n' if self._payload['note_test_org'] is not None: tt += ' ' + gmTools.u_superscript_one + _('Lab comment: %s\n') % _('\n Lab comment: ').join(self._payload['note_test_org'].split('\n')) if self._payload['comment'] is not None: tt += ' ' + gmTools.u_superscript_one + _('Praxis comment: %s\n') % _('\n Praxis comment: ').join(self._payload['comment'].split('\n')) if with_ranges: tt += gmTools.coalesce(self.formatted_normal_range, '', ' ' + _('Standard normal range: %s\n')) tt += gmTools.coalesce(self.formatted_clinical_range, '', ' ' + _('Clinical target range: %s\n')) tt += gmTools.coalesce(self._payload['norm_ref_group'], '', ' ' + _('Reference group: %s\n')) # metadata if with_episode: tt += ' ' + _('Episode: %s\n') % self._payload['episode'] if self._payload['health_issue'] is not None: tt += ' ' + _('Issue: %s\n') % self._payload['health_issue'] if self._payload['material'] is not None: tt += ' ' + _('Material: %s\n') % self._payload['material'] if self._payload['material_detail'] is not None: tt += ' ' + _('Details: %s\n') % self._payload['material_detail'] tt += '\n' if with_review: if self._payload['reviewed']: review = gmDateTime.pydt_strftime ( self._payload['last_reviewed'], date_format ) else: review = _('not yet') tt += _('Signed (%(sig_hand)s): %(reviewed)s\n') % ({ 'sig_hand': gmTools.u_writing_hand, 'reviewed': review }) tt += ' ' + _('Responsible clinician: %s\n') % gmTools.bool2subst ( self._payload['you_are_responsible'], _('you'), self._payload['responsible_reviewer'] ) if self._payload['reviewed']: tt += ' ' + _('Last reviewer: %(reviewer)s\n') % ({ 'reviewer': gmTools.bool2subst ( self._payload['review_by_you'], _('you'), gmTools.coalesce(self._payload['last_reviewer'], '?') ) }) tt += ' ' + _(' Technically abnormal: %(abnormal)s\n') % ({ 'abnormal': gmTools.bool2subst ( self._payload['is_technically_abnormal'], _('yes'), _('no'), '?' ) }) tt += ' ' + _(' Clinically relevant: %(relevant)s\n') % ({ 'relevant': gmTools.bool2subst ( self._payload['is_clinically_relevant'], _('yes'), _('no'), '?' ) }) if self._payload['review_comment'] is not None: tt += ' ' + _(' Comment: %s\n') % self._payload['review_comment'].strip() tt += '\n' # type if with_type_details: has_details = None not in [self._payload['comment_tt'], self._payload['pk_meta_test_type'], self._payload['comment_meta']] if has_details: tt += _('Test type details:\n') if self._payload['comment_tt'] is not None: tt += ' ' + _('Type comment: %s\n') % _('\n Type comment:').join(self._payload['comment_tt'].split('\n')) if self._payload['pk_meta_test_type'] is not None: tt += ' ' + _('Aggregated (%s) under: %s (%s) [#%s]\n') % ( gmTools.u_sum, self._payload['name_meta'], self._payload['abbrev_meta'], self._payload['pk_meta_test_type'] ) if self._payload['comment_meta'] is not None: tt += ' ' + _('Group comment: %s\n') % _('\n Group comment: ').join(self._payload['comment_meta'].split('\n')) if has_details: tt += '\n' if with_source_data: if self._payload['source_data'] is not None: tt += _('Source data:\n') tt += ' ' + self._payload['source_data'] tt += '\n\n' if with_review: tt += _('Revisions: %(row_ver)s, last %(mod_when)s by %(mod_by)s.') % ({ 'row_ver': self._payload['row_version'], 'mod_when': gmDateTime.pydt_strftime(self._payload['modified_when'],date_format), 'mod_by': self._payload['modified_by'] }) return tt #-------------------------------------------------------- def _get_has_normal_min_or_max(self): return ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) has_normal_min_or_max = property(_get_has_normal_min_or_max) #-------------------------------------------------------- def _get_normal_min_max(self): has_range_info = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_range_info is False: return None return '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) normal_min_max = property(_get_normal_min_max) #-------------------------------------------------------- def _get_formatted_normal_range(self): has_numerical_range = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_numerical_range: numerical_range = '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) else: numerical_range = '' textual_range = gmTools.coalesce ( self._payload['val_normal_range'], '', gmTools.bool2subst ( has_numerical_range, ' / %s', '%s' ) ) range_info = '%s%s' % (numerical_range, textual_range) if range_info == '': return None return range_info formatted_normal_range = property(_get_formatted_normal_range) #-------------------------------------------------------- def _get_has_clinical_min_or_max(self): return ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) has_clinical_min_or_max = property(_get_has_clinical_min_or_max) #-------------------------------------------------------- def _get_clinical_min_max(self): has_range_info = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_range_info is False: return None return '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) clinical_min_max = property(_get_clinical_min_max) #-------------------------------------------------------- def _get_formatted_clinical_range(self): has_numerical_range = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_numerical_range: numerical_range = '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) else: numerical_range = '' textual_range = gmTools.coalesce ( self._payload['val_target_range'], '', gmTools.bool2subst ( has_numerical_range, ' / %s', '%s' ) ) range_info = '%s%s' % (numerical_range, textual_range) if range_info == '': return None return range_info formatted_clinical_range = property(_get_formatted_clinical_range) #-------------------------------------------------------- def _get_temporally_closest_normal_range(self): """Returns the closest test result which does have normal range information.""" if self._payload['val_normal_min'] is not None: return self if self._payload['val_normal_max'] is not None: return self if self._payload['val_normal_range'] is not None: return self cmd = """ SELECT * from clin.v_test_results WHERE pk_type = %(pk_type)s AND val_unit = %(unit)s AND ( (val_normal_min IS NOT NULL) OR (val_normal_max IS NOT NULL) OR (val_normal_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': self._payload['val_unit'], 'clin_when': self._payload['clin_when'] } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) temporally_closest_normal_range = property(_get_temporally_closest_normal_range) #-------------------------------------------------------- def _get_formatted_range(self): has_normal_min_or_max = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_normal_min_or_max: normal_min_max = '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) has_clinical_min_or_max = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_clinical_min_or_max: clinical_min_max = '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) if has_clinical_min_or_max: return _('Target: %(clin_min_max)s%(clin_range)s') % ({ 'clin_min_max': clinical_min_max, 'clin_range': gmTools.coalesce ( self._payload['val_target_range'], '', gmTools.bool2subst ( has_clinical_min_or_max, ' / %s', '%s' ) ) }) if has_normal_min_or_max: return _('Norm: %(norm_min_max)s%(norm_range)s') % ({ 'norm_min_max': normal_min_max, 'norm_range': gmTools.coalesce ( self._payload['val_normal_range'], '', gmTools.bool2subst ( has_normal_min_or_max, ' / %s', '%s' ) ) }) if self._payload['val_target_range'] is not None: return _('Target: %s') % self._payload['val_target_range'], if self._payload['val_normal_range'] is not None: return _('Norm: %s') % self._payload['val_normal_range'] return None formatted_range = property(_get_formatted_range) #-------------------------------------------------------- def _get_test_type(self): return cMeasurementType(aPK_obj = self._payload['pk_test_type']) test_type = property(_get_test_type) #-------------------------------------------------------- def _get_is_considered_elevated(self): # 1) the user is right (review) if self._payload['is_technically_abnormal'] is False: return False # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': if indicator.strip('+') == '': return True if indicator.strip('-') == '': return False # 3) non-numerical value ? if self._payload['val_num'] is None: return None # 4) the target range is right target_max = self._payload['val_target_max'] if target_max is not None: if target_max < self._payload['val_num']: return True # 4) the normal range is right normal_max = self._payload['val_normal_max'] if normal_max is not None: if normal_max < self._payload['val_num']: return True return None is_considered_elevated = property(_get_is_considered_elevated) #-------------------------------------------------------- def _get_is_considered_lowered(self): # 1) the user is right (review) if self._payload['is_technically_abnormal'] is False: return False # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': if indicator.strip('+') == '': return False if indicator.strip('-') == '': return True # 3) non-numerical value ? if self._payload['val_num'] is None: return None # 4) the target range is right target_min = self._payload['val_target_min'] if target_min is not None: if target_min > self._payload['val_num']: return True # 4) the normal range is right normal_min = self._payload['val_normal_min'] if normal_min is not None: if normal_min > self._payload['val_num']: return True return None is_considered_lowered = property(_get_is_considered_lowered) #-------------------------------------------------------- def _get_is_considered_abnormal(self): if self.is_considered_lowered is True: return True if self.is_considered_elevated is True: return True if (self.is_considered_lowered is False) and (self.is_considered_elevated is False): return False return self._payload['is_technically_abnormal'] is_considered_abnormal = property(_get_is_considered_abnormal) #-------------------------------------------------------- def _set_reference_range(self, ref_range): """Parse reference range from string. Note: does NOT save the result. """ ref_range = ref_range.strip().replace(' ', '') is_range = regex.match(r'-{0,1}\d+[.,]{0,1}\d*--{0,1}\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE) if is_range is not None: min_val = regex.match(r'-{0,1}\d+[.,]{0,1}\d*-', ref_range, regex.UNICODE).group(0).rstrip('-') success, min_val = gmTools.input2decimal(min_val) max_val = (regex.search(r'--{0,1}\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE).group(0))[1:] success, max_val = gmTools.input2decimal(max_val) self['val_normal_min'] = min_val self['val_normal_max'] = max_val return if ref_range.startswith('<'): is_range = regex.match(r'<\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE) if is_range is not None: max_val = ref_range[1:] success, max_val = gmTools.input2decimal(max_val) self['val_normal_min'] = 0 self['val_normal_max'] = max_val return if ref_range.startswith('<-'): is_range = regex.match(r'<-\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE) if is_range is not None: max_val = ref_range[1:] success, max_val = gmTools.input2decimal(max_val) self['val_normal_min'] = None self['val_normal_max'] = max_val return if ref_range.startswith('>'): is_range = regex.match(r'>\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE) if is_range is not None: min_val = ref_range[1:] success, min_val = gmTools.input2decimal(min_val) self['val_normal_min'] = min_val self['val_normal_max'] = None return if ref_range.startswith('>-'): is_range = regex.match(r'>-\d+[.,]{0,1}\d*$', ref_range, regex.UNICODE) if is_range is not None: min_val = ref_range[1:] success, min_val = gmTools.input2decimal(min_val) self['val_normal_min'] = min_val self['val_normal_max'] = 0 return self['val_normal_range'] = ref_range return reference_range = property(lambda x:x, _set_reference_range) #-------------------------------------------------------- def _get_formatted_abnormality_indicator(self): # 1) the user is right if self._payload['is_technically_abnormal'] is False: return '' # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': return indicator # 3) non-numerical value ? then we can't know more if self._payload['val_num'] is None: return None # 4) the target range is right target_min = self._payload['val_target_min'] if target_min is not None: if target_min > self._payload['val_num']: return '-' target_max = self._payload['val_target_max'] if target_max is not None: if target_max < self._payload['val_num']: return '+' # 4) the normal range is right normal_min = self._payload['val_normal_min'] if normal_min is not None: if normal_min > self._payload['val_num']: return '-' normal_max = self._payload['val_normal_max'] if normal_max is not None: if normal_max < self._payload['val_num']: return '+' # reviewed, abnormal, but no indicator available if self._payload['is_technically_abnormal'] is True: return gmTools.u_plus_minus return None formatted_abnormality_indicator = property(_get_formatted_abnormality_indicator) #-------------------------------------------------------- def _get_is_long_text(self): if self._payload['val_alpha'] is None: return False lines = gmTools.strip_empty_lines(text = self._payload['val_alpha'], eol = '\n', return_list = True) if len(lines) > 4: return True return False is_long_text = property(_get_is_long_text) #-------------------------------------------------------- def _get_estimate_numeric_value_from_alpha(self): if self._payload['val_alpha'] is None: return None val = self._payload['val_alpha'].lstrip() if val[0] == '<': factor = decimal.Decimal(0.5) val = val[1:] elif val[0] == '>': factor = 2 val = val[1:] else: return None success, val = gmTools.input2decimal(initial = val) if not success: return None return val * factor estimate_numeric_value_from_alpha = property(_get_estimate_numeric_value_from_alpha) #-------------------------------------------------------- def set_review(self, technically_abnormal=None, clinically_relevant=None, comment=None, make_me_responsible=False): # FIXME: this is not concurrency safe if self._payload['reviewed']: self.__change_existing_review ( technically_abnormal = technically_abnormal, clinically_relevant = clinically_relevant, comment = comment ) else: # do not sign off unreviewed results if # NOTHING AT ALL is known about them if technically_abnormal is None: if clinically_relevant is None: comment = gmTools.none_if(comment, '', strip_string = True) if comment is None: if make_me_responsible is False: return True self.__set_new_review ( technically_abnormal = technically_abnormal, clinically_relevant = clinically_relevant, comment = comment ) if make_me_responsible is True: cmd = "SELECT pk FROM dem.staff WHERE db_user = current_user" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}]) self['pk_intended_reviewer'] = rows[0][0] self.save_payload() return self.refetch_payload() #-------------------------------------------------------- def get_adjacent_results(self, desired_earlier_results=1, desired_later_results=1, max_offset=None): if desired_earlier_results < 1: raise ValueError('<desired_earlier_results> must be > 0') if desired_later_results < 1: raise ValueError('<desired_later_results> must be > 0') args = { 'pat': self._payload['pk_patient'], 'ttyp': self._payload['pk_test_type'], 'tloinc': self._payload['loinc_tt'], 'mtyp': self._payload['pk_meta_test_type'], 'mloinc': self._payload['loinc_meta'], 'when': self._payload['clin_when'], 'offset': max_offset } WHERE = '((pk_test_type = %(ttyp)s) OR (loinc_tt = %(tloinc)s))' WHERE_meta = '((pk_meta_test_type = %(mtyp)s) OR (loinc_meta = %(mloinc)s))' if max_offset is not None: WHERE = WHERE + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))' WHERE_meta = WHERE_meta + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))' SQL = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND clin_when %s %%(when)s AND %s ORDER BY clin_when LIMIT %s""" # get earlier results earlier_results = [] # by type cmd = SQL % ('<', WHERE, desired_earlier_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # by meta type ? missing_results = desired_earlier_results - len(earlier_results) if missing_results > 0: cmd = SQL % ('<', WHERE_meta, missing_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # get later results later_results = [] # by type cmd = SQL % ('>', WHERE, desired_later_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # by meta type ? missing_results = desired_later_results - len(later_results) if missing_results > 0: cmd = SQL % ('>', WHERE_meta, missing_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) return earlier_results, later_results #-------------------------------------------------------- # internal API #-------------------------------------------------------- def __set_new_review(self, technically_abnormal=None, clinically_relevant=None, comment=None): """Add a review to a row. - if technically abnormal is not provided/None it will be set to True if the lab's indicator has a meaningful value - if clinically relevant is not provided/None it is set to whatever technically abnormal is """ if technically_abnormal is None: technically_abnormal = False if self._payload['abnormality_indicator'] is not None: if self._payload['abnormality_indicator'].strip() != '': technically_abnormal = True if clinically_relevant is None: clinically_relevant = technically_abnormal cmd = """ INSERT INTO clin.reviewed_test_results ( fk_reviewed_row, is_technically_abnormal, clinically_relevant, comment ) VALUES ( %(pk)s, %(abnormal)s, %(relevant)s, gm.nullify_empty_string(%(cmt)s) )""" args = { 'pk': self._payload['pk_test_result'], 'abnormal': technically_abnormal, 'relevant': clinically_relevant, 'cmt': comment } gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) #-------------------------------------------------------- def __change_existing_review(self, technically_abnormal=None, clinically_relevant=None, comment=None): """Change a review on a row. - if technically abnormal/clinically relevant are None they are not set """ args = { 'pk_result': self._payload['pk_test_result'], 'abnormal': technically_abnormal, 'relevant': clinically_relevant, 'cmt': comment } set_parts = [ 'fk_reviewer = (SELECT pk FROM dem.staff WHERE db_user = current_user)', 'comment = gm.nullify_empty_string(%(cmt)s)' ] if technically_abnormal is not None: set_parts.append('is_technically_abnormal = %(abnormal)s') if clinically_relevant is not None: set_parts.append('clinically_relevant = %(relevant)s') cmd = """ UPDATE clin.reviewed_test_results SET %s WHERE fk_reviewed_row = %%(pk_result)s """ % ',\n '.join(set_parts) gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])Ancestors
Instance variables
var clinical_min_max-
Expand source code
def _get_clinical_min_max(self): has_range_info = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_range_info is False: return None return '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) var estimate_numeric_value_from_alpha-
Expand source code
def _get_estimate_numeric_value_from_alpha(self): if self._payload['val_alpha'] is None: return None val = self._payload['val_alpha'].lstrip() if val[0] == '<': factor = decimal.Decimal(0.5) val = val[1:] elif val[0] == '>': factor = 2 val = val[1:] else: return None success, val = gmTools.input2decimal(initial = val) if not success: return None return val * factor var formatted_abnormality_indicator-
Expand source code
def _get_formatted_abnormality_indicator(self): # 1) the user is right if self._payload['is_technically_abnormal'] is False: return '' # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': return indicator # 3) non-numerical value ? then we can't know more if self._payload['val_num'] is None: return None # 4) the target range is right target_min = self._payload['val_target_min'] if target_min is not None: if target_min > self._payload['val_num']: return '-' target_max = self._payload['val_target_max'] if target_max is not None: if target_max < self._payload['val_num']: return '+' # 4) the normal range is right normal_min = self._payload['val_normal_min'] if normal_min is not None: if normal_min > self._payload['val_num']: return '-' normal_max = self._payload['val_normal_max'] if normal_max is not None: if normal_max < self._payload['val_num']: return '+' # reviewed, abnormal, but no indicator available if self._payload['is_technically_abnormal'] is True: return gmTools.u_plus_minus return None var formatted_clinical_range-
Expand source code
def _get_formatted_clinical_range(self): has_numerical_range = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_numerical_range: numerical_range = '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) else: numerical_range = '' textual_range = gmTools.coalesce ( self._payload['val_target_range'], '', gmTools.bool2subst ( has_numerical_range, ' / %s', '%s' ) ) range_info = '%s%s' % (numerical_range, textual_range) if range_info == '': return None return range_info var formatted_normal_range-
Expand source code
def _get_formatted_normal_range(self): has_numerical_range = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_numerical_range: numerical_range = '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) else: numerical_range = '' textual_range = gmTools.coalesce ( self._payload['val_normal_range'], '', gmTools.bool2subst ( has_numerical_range, ' / %s', '%s' ) ) range_info = '%s%s' % (numerical_range, textual_range) if range_info == '': return None return range_info var formatted_range-
Expand source code
def _get_formatted_range(self): has_normal_min_or_max = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_normal_min_or_max: normal_min_max = '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) has_clinical_min_or_max = ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) if has_clinical_min_or_max: clinical_min_max = '%s - %s' % ( gmTools.coalesce(self._payload['val_target_min'], '?'), gmTools.coalesce(self._payload['val_target_max'], '?') ) if has_clinical_min_or_max: return _('Target: %(clin_min_max)s%(clin_range)s') % ({ 'clin_min_max': clinical_min_max, 'clin_range': gmTools.coalesce ( self._payload['val_target_range'], '', gmTools.bool2subst ( has_clinical_min_or_max, ' / %s', '%s' ) ) }) if has_normal_min_or_max: return _('Norm: %(norm_min_max)s%(norm_range)s') % ({ 'norm_min_max': normal_min_max, 'norm_range': gmTools.coalesce ( self._payload['val_normal_range'], '', gmTools.bool2subst ( has_normal_min_or_max, ' / %s', '%s' ) ) }) if self._payload['val_target_range'] is not None: return _('Target: %s') % self._payload['val_target_range'], if self._payload['val_normal_range'] is not None: return _('Norm: %s') % self._payload['val_normal_range'] return None var has_clinical_min_or_max-
Expand source code
def _get_has_clinical_min_or_max(self): return ( self._payload['val_target_min'] is not None ) or ( self._payload['val_target_max'] is not None ) var has_normal_min_or_max-
Expand source code
def _get_has_normal_min_or_max(self): return ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) var is_considered_abnormal-
Expand source code
def _get_is_considered_abnormal(self): if self.is_considered_lowered is True: return True if self.is_considered_elevated is True: return True if (self.is_considered_lowered is False) and (self.is_considered_elevated is False): return False return self._payload['is_technically_abnormal'] var is_considered_elevated-
Expand source code
def _get_is_considered_elevated(self): # 1) the user is right (review) if self._payload['is_technically_abnormal'] is False: return False # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': if indicator.strip('+') == '': return True if indicator.strip('-') == '': return False # 3) non-numerical value ? if self._payload['val_num'] is None: return None # 4) the target range is right target_max = self._payload['val_target_max'] if target_max is not None: if target_max < self._payload['val_num']: return True # 4) the normal range is right normal_max = self._payload['val_normal_max'] if normal_max is not None: if normal_max < self._payload['val_num']: return True return None var is_considered_lowered-
Expand source code
def _get_is_considered_lowered(self): # 1) the user is right (review) if self._payload['is_technically_abnormal'] is False: return False # 2) the lab is right (result.abnormality_indicator) indicator = self._payload['abnormality_indicator'] if indicator is not None: indicator = indicator.strip() if indicator != '': if indicator.strip('+') == '': return False if indicator.strip('-') == '': return True # 3) non-numerical value ? if self._payload['val_num'] is None: return None # 4) the target range is right target_min = self._payload['val_target_min'] if target_min is not None: if target_min > self._payload['val_num']: return True # 4) the normal range is right normal_min = self._payload['val_normal_min'] if normal_min is not None: if normal_min > self._payload['val_num']: return True return None var is_long_text-
Expand source code
def _get_is_long_text(self): if self._payload['val_alpha'] is None: return False lines = gmTools.strip_empty_lines(text = self._payload['val_alpha'], eol = '\n', return_list = True) if len(lines) > 4: return True return False var normal_min_max-
Expand source code
def _get_normal_min_max(self): has_range_info = ( self._payload['val_normal_min'] is not None ) or ( self._payload['val_normal_max'] is not None ) if has_range_info is False: return None return '%s - %s' % ( gmTools.coalesce(self._payload['val_normal_min'], '?'), gmTools.coalesce(self._payload['val_normal_max'], '?') ) var reference_range-
Expand source code
reference_range = property(lambda x:x, _set_reference_range) var temporally_closest_normal_range-
Returns the closest test result which does have normal range information.
Expand source code
def _get_temporally_closest_normal_range(self): """Returns the closest test result which does have normal range information.""" if self._payload['val_normal_min'] is not None: return self if self._payload['val_normal_max'] is not None: return self if self._payload['val_normal_range'] is not None: return self cmd = """ SELECT * from clin.v_test_results WHERE pk_type = %(pk_type)s AND val_unit = %(unit)s AND ( (val_normal_min IS NOT NULL) OR (val_normal_max IS NOT NULL) OR (val_normal_range IS NOT NULL) ) ORDER BY CASE WHEN clin_when > %(clin_when)s THEN clin_when - %(clin_when)s ELSE %(clin_when)s - clin_when END LIMIT 1""" args = { 'pk_type': self._payload['pk_test_type'], 'unit': self._payload['val_unit'], 'clin_when': self._payload['clin_when'] } rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) == 0: return None return cTestResult(row = {'pk_field': 'pk_test_result', 'data': rows[0]}) var test_type-
Expand source code
def _get_test_type(self): return cMeasurementType(aPK_obj = self._payload['pk_test_type'])
Methods
def format_concisely(self, date_format='%Y %b %d', with_notes=True)-
Expand source code
def format_concisely(self, date_format='%Y %b %d', with_notes=True): range_info = gmTools.coalesce ( self.formatted_clinical_range, self.formatted_normal_range ) review = gmTools.bool2subst ( self._payload['reviewed'], '', ' ' + gmTools.u_writing_hand, ' ' + gmTools.u_writing_hand ) txt = '%s %s: %s%s%s%s%s%s' % ( gmDateTime.pydt_strftime ( self._payload['clin_when'], date_format ), self._payload['name_tt'], self._payload['unified_val'], gmTools.coalesce(self._payload['val_unit'], '', ' %s'), gmTools.coalesce(self._payload['abnormality_indicator'], '', ' %s'), gmTools.coalesce(range_info, '', ' (%s)'), gmTools.coalesce(self._payload['status'], '', ' [%s]')[:2], review ) if with_notes: txt += '\n' if self._payload['note_test_org'] is not None: txt += ' ' + _('Lab comment: %s\n') % _('\n Lab comment: ').join(self._payload['note_test_org'].split('\n')) if self._payload['comment'] is not None: txt += ' ' + _('Praxis comment: %s\n') % _('\n Praxis comment: ').join(self._payload['comment'].split('\n')) return txt.strip('\n') def get_adjacent_results(self, desired_earlier_results=1, desired_later_results=1, max_offset=None)-
Expand source code
def get_adjacent_results(self, desired_earlier_results=1, desired_later_results=1, max_offset=None): if desired_earlier_results < 1: raise ValueError('<desired_earlier_results> must be > 0') if desired_later_results < 1: raise ValueError('<desired_later_results> must be > 0') args = { 'pat': self._payload['pk_patient'], 'ttyp': self._payload['pk_test_type'], 'tloinc': self._payload['loinc_tt'], 'mtyp': self._payload['pk_meta_test_type'], 'mloinc': self._payload['loinc_meta'], 'when': self._payload['clin_when'], 'offset': max_offset } WHERE = '((pk_test_type = %(ttyp)s) OR (loinc_tt = %(tloinc)s))' WHERE_meta = '((pk_meta_test_type = %(mtyp)s) OR (loinc_meta = %(mloinc)s))' if max_offset is not None: WHERE = WHERE + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))' WHERE_meta = WHERE_meta + ' AND (clin_when BETWEEN (%(when)s - %(offset)s) AND (%(when)s + %(offset)s))' SQL = """ SELECT * FROM clin.v_test_results WHERE pk_patient = %%(pat)s AND clin_when %s %%(when)s AND %s ORDER BY clin_when LIMIT %s""" # get earlier results earlier_results = [] # by type cmd = SQL % ('<', WHERE, desired_earlier_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # by meta type ? missing_results = desired_earlier_results - len(earlier_results) if missing_results > 0: cmd = SQL % ('<', WHERE_meta, missing_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: earlier_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # get later results later_results = [] # by type cmd = SQL % ('>', WHERE, desired_later_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) # by meta type ? missing_results = desired_later_results - len(later_results) if missing_results > 0: cmd = SQL % ('>', WHERE_meta, missing_results) rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}]) if len(rows) > 0: later_results.extend([ cTestResult(row = {'pk_field': 'pk_test_result', 'data': r}) for r in rows ]) return earlier_results, later_results def set_review(self, technically_abnormal=None, clinically_relevant=None, comment=None, make_me_responsible=False)-
Expand source code
def set_review(self, technically_abnormal=None, clinically_relevant=None, comment=None, make_me_responsible=False): # FIXME: this is not concurrency safe if self._payload['reviewed']: self.__change_existing_review ( technically_abnormal = technically_abnormal, clinically_relevant = clinically_relevant, comment = comment ) else: # do not sign off unreviewed results if # NOTHING AT ALL is known about them if technically_abnormal is None: if clinically_relevant is None: comment = gmTools.none_if(comment, '', strip_string = True) if comment is None: if make_me_responsible is False: return True self.__set_new_review ( technically_abnormal = technically_abnormal, clinically_relevant = clinically_relevant, comment = comment ) if make_me_responsible is True: cmd = "SELECT pk FROM dem.staff WHERE db_user = current_user" rows = gmPG2.run_ro_queries(queries = [{'cmd': cmd}]) self['pk_intended_reviewer'] = rows[0][0] self.save_payload() return self.refetch_payload()
Inherited members