Module Gnumed.business.gmClinNarrative
GNUmed clinical narrative business object.
Expand source code
"""GNUmed clinical narrative business object."""
#============================================================
__author__ = "Carlos Moro <cfmoro1976@yahoo.es>, Karsten Hilbert <Karsten.Hilbert@gmx.net>"
__license__ = 'GPL v2 or later (for details see http://gnu.org)'
import sys
import logging
if __name__ == '__main__':
sys.path.insert(0, '../../')
_ = lambda x:x
from Gnumed.pycommon import gmPG2
from Gnumed.pycommon import gmBusinessDBObject
from Gnumed.pycommon import gmTools
from Gnumed.pycommon import gmDispatcher
from Gnumed.pycommon import gmHooks
from Gnumed.business import gmCoding
from Gnumed.business import gmSoapDefs
_log = logging.getLogger('gm.emr')
#============================================================
def _on_soap_modified():
"""Always relates to the active patient."""
gmHooks.run_hook_script(hook = 'after_soap_modified')
gmDispatcher.connect(_on_soap_modified, 'clin.clin_narrative_mod_db')
#============================================================
class cNarrative(gmBusinessDBObject.cBusinessDBObject):
"""Represents one clinical free text entry."""
_cmd_fetch_payload = "SELECT * FROM clin.v_narrative WHERE pk_narrative = %s"
_cmds_store_payload = [
"""update clin.clin_narrative set
narrative = %(narrative)s,
clin_when = %(date)s,
soap_cat = lower(%(soap_cat)s),
fk_encounter = %(pk_encounter)s,
fk_episode = %(pk_episode)s
WHERE
pk = %(pk_narrative)s
AND
xmin = %(xmin_clin_narrative)s
RETURNING
xmin AS xmin_clin_narrative"""
]
_updatable_fields = [
'narrative',
'date',
'soap_cat',
'pk_episode',
'pk_encounter'
]
#--------------------------------------------------------
def format_maximum_information(self, patient=None):
return self.format(fancy = True, width = 70).split('\n')
#--------------------------------------------------------
def format(self, left_margin='', fancy=False, width=75):
if fancy:
txt = gmTools.wrap (
text = _('%s: %s by %.8s (v%s)\n%s') % (
self._payload[self._idx['date']].strftime('%x %H:%M'),
gmSoapDefs.soap_cat2l10n_str[self._payload[self._idx['soap_cat']]],
self._payload[self._idx['modified_by']],
self._payload[self._idx['row_version']],
self._payload[self._idx['narrative']]
),
width = width,
initial_indent = '',
subsequent_indent = left_margin + ' '
)
else:
txt = '%s [%s]: %s (%.8s)' % (
self._payload[self._idx['date']].strftime('%x %H:%M'),
gmSoapDefs.soap_cat2l10n[self._payload[self._idx['soap_cat']]],
self._payload[self._idx['narrative']],
self._payload[self._idx['modified_by']]
)
if len(txt) > width:
txt = txt[:width] + gmTools.u_ellipsis
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)"""
if pk_code in self._payload[self._idx['pk_generic_codes']]:
return
cmd = """
INSERT INTO clin.lnk_code2narrative
(fk_item, fk_generic_code)
SELECT
%(item)s,
%(code)s
WHERE NOT EXISTS (
SELECT 1 FROM clin.lnk_code2narrative
WHERE
fk_item = %(item)s
AND
fk_generic_code = %(code)s
)"""
args = {
'item': self._payload[self._idx['pk_narrative']],
'code': pk_code
}
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return
#--------------------------------------------------------
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_code2narrative WHERE fk_item = %(item)s AND fk_generic_code = %(code)s"
args = {
'item': self._payload[self._idx['pk_narrative']],
'code': pk_code
}
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}])
return True
#--------------------------------------------------------
# properties
#--------------------------------------------------------
def _get_generic_codes(self):
if len(self._payload[self._idx['pk_generic_codes']]) == 0:
return []
cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)'
args = {'pks': self._payload[self._idx['pk_generic_codes']]}
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_lnk_code2item'}) for r in rows ]
def _set_generic_codes(self, pk_codes):
queries = []
# remove all codes
if len(self._payload[self._idx['pk_generic_codes']]) > 0:
queries.append ({
'cmd': 'DELETE FROM clin.lnk_code2narrative WHERE fk_item = %(narr)s AND fk_generic_code = ANY(%(codes)s)',
'args': {
'narr': self._payload[self._idx['pk_narrative']],
'codes': self._payload[self._idx['pk_generic_codes']]
}
})
# add new codes
for pk_code in pk_codes:
queries.append ({
'cmd': 'INSERT INTO clin.lnk_code2narrative (fk_item, fk_generic_code) VALUES (%(narr)s, %(pk_code)s)',
'args': {
'narr': self._payload[self._idx['pk_narrative']],
'pk_code': pk_code
}
})
if len(queries) == 0:
return
# run it all in one transaction
rows, idx = gmPG2.run_rw_queries(queries = queries)
return
generic_codes = property(_get_generic_codes, _set_generic_codes)
#============================================================
def create_progress_note(soap=None, episode_id=None, encounter_id=None, link_obj=None):
"""Create clinical narrative entries.
<soap>
must be a dict, the keys being SOAP categories (including U and
None=admin) and the values being text (possibly multi-line)
Existing but empty ('' or None) categories are skipped.
"""
if soap is None:
return True
if not gmSoapDefs.are_valid_soap_cats(list(soap), allow_upper = True):
raise ValueError('invalid SOAP category in <soap> dictionary: %s', soap)
if link_obj is None:
link_obj = gmPG2.get_connection(readonly = False)
conn_commit = link_obj.commit
conn_close = link_obj.close
else:
conn_commit = lambda *x: None
conn_close = lambda *x: None
instances = {}
for cat in soap:
val = soap[cat]
if val is None:
continue
if ''.join([ v.strip() for v in val ]) == '':
continue
instance = create_narrative_item (
narrative = '\n'.join([ v.strip() for v in val ]),
soap_cat = cat,
episode_id = episode_id,
encounter_id = encounter_id,
link_obj = link_obj
)
if instance is None:
continue
instances[cat] = instance
conn_commit()
conn_close()
return instances
#============================================================
def create_narrative_item(narrative=None, soap_cat=None, episode_id=None, encounter_id=None, link_obj=None):
"""Creates a new clinical narrative entry
narrative - free text clinical narrative
soap_cat - soap category
episode_id - episodes's primary key
encounter_id - encounter's primary key
any of the args being None (except soap_cat) will fail the SQL code
"""
# silently do not insert empty narrative
narrative = narrative.strip()
if narrative == '':
return None
args = {'enc': encounter_id, 'epi': episode_id, 'soap': soap_cat, 'narr': narrative}
# insert new narrative
# but, also silently, do not insert true duplicates
# this should check for .provider = current_user but
# the view has provider mapped to their staff alias
cmd = """
INSERT INTO clin.clin_narrative
(fk_encounter, fk_episode, narrative, soap_cat)
SELECT
%(enc)s, %(epi)s, %(narr)s, lower(%(soap)s)
WHERE NOT EXISTS (
SELECT 1 FROM clin.v_narrative
WHERE
pk_encounter = %(enc)s
AND
pk_episode = %(epi)s
AND
soap_cat = lower(%(soap)s)
AND
narrative = %(narr)s
)
RETURNING pk"""
rows, idx = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False)
if len(rows) == 1:
# re-use same link_obj if given because when called from create_progress_note we won't yet see rows inside a new tx
return cNarrative(aPK_obj = rows[0]['pk'], link_obj = link_obj)
if len(rows) > 1:
raise Exception('more than one row returned from single-row INSERT')
# retrieve existing narrative
cmd = """
SELECT * FROM clin.v_narrative
WHERE
pk_encounter = %(enc)s
AND
pk_episode = %(epi)s
AND
soap_cat = lower(%(soap)s)
AND
narrative = %(narr)s
"""
rows, idx = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
if len(rows) == 1:
return cNarrative(row = {'pk_field': 'pk_narrative', 'data': rows[0], 'idx': idx})
raise Exception('retrieving known-to-exist narrative row returned 0 or >1 result: %s' % len(rows))
#------------------------------------------------------------
def delete_clin_narrative(narrative=None):
"""Deletes a clin.clin_narrative row by it's PK."""
cmd = "DELETE FROM clin.clin_narrative WHERE pk=%s"
rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': [narrative]}])
return True
#------------------------------------------------------------
def get_narrative(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, patient=None, order_by=None):
"""Get SOAP notes pertinent to this encounter.
since
- initial date for narrative items
until
- final date for narrative items
encounters
- list of encounters whose narrative are to be retrieved
episodes
- list of episodes whose narrative are to be retrieved
issues
- list of health issues whose narrative are to be retrieved
soap_cats
- list of SOAP categories of the narrative to be retrieved
"""
where_parts = ['TRUE']
args = {}
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 issues is not None:
where_parts.append('pk_health_issue = ANY(%(issues)s)')
args['issues'] = issues
if patient is not None:
where_parts.append('pk_patient = %(pat)s')
args['pat'] = patient
if soap_cats is not None:
where_parts.append('c_vn.soap_cat = ANY(%(soap_cats)s)')
args['soap_cats'] = soap_cats
if order_by is None:
order_by = 'ORDER BY date, soap_rank'
else:
order_by = 'ORDER BY %s' % order_by
cmd = """
SELECT
c_vn.*,
c_scr.rank AS soap_rank
FROM
clin.v_narrative c_vn
LEFT JOIN clin.soap_cat_ranks c_scr ON c_vn.soap_cat = c_scr.soap_cat
WHERE
%s
%s
""" % (
' AND '.join(where_parts),
order_by
)
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
filtered_narrative = [ cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ]
if since is not None:
filtered_narrative = [ narr for narr in filtered_narrative if narr['date'] >= since ]
if until is not None:
filtered_narrative = [ narr for narr in filtered_narrative if narr['date'] < until ]
if providers is not None:
filtered_narrative = [ narr for narr in filtered_narrative if narr['modified_by'] in providers ]
return filtered_narrative
# if issues is not None:
# filtered_narrative = (lambda narr: narr['pk_health_issue'] in issues, filtered_narrative)
#
# if episodes is not None:
# filtered_narrative = (lambda narr: narr['pk_episode'] in episodes, filtered_narrative)
#
# if encounters is not None:
# filtered_narrative = (lambda narr: narr['pk_encounter'] in encounters, filtered_narrative)
# if soap_cats is not None:
# soap_cats = map(lambda c: c.casefold(), soap_cats)
# filtered_narrative = (lambda narr: narr['soap_cat'] in soap_cats, filtered_narrative)
#------------------------------------------------------------
def get_as_journal(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None, patient=None, active_encounter=None):
if (patient is None) and (episodes is None) and (issues is None) and (encounters is None):
raise ValueError('at least one of <patient>, <episodes>, <issues>, <encounters> must not be None')
if order_by is None:
order_by = 'ORDER BY clin_when, pk_episode, scr, modified_when, src_table'
else:
order_by = 'ORDER BY %s' % order_by
where_parts = []
args = {}
if patient is not None:
where_parts.append('c_vej.pk_patient = %(pat)s')
args['pat'] = patient
if soap_cats is not None:
# work around bug in psycopg2 not being able to properly
# adapt None to NULL inside tuples
if None in soap_cats:
where_parts.append('((c_vej.soap_cat = ANY(%(soap_cat)s)) OR (c_vej.soap_cat IS NULL))')
soap_cats.remove(None)
else:
where_parts.append('c_vej.soap_cat = ANY(%(soap_cat)s)')
args['soap_cat'] = soap_cats
if time_range is not None:
where_parts.append("c_vej.clin_when > (now() - '%s days'::interval)" % time_range)
if episodes is not None:
where_parts.append("c_vej.pk_episode = ANY(%(epis)s)")
args['epis'] = episodes
if issues is not None:
where_parts.append("c_vej.pk_health_issue = ANY(%(issues)s)")
args['issues'] = issues
# FIXME: implement more constraints
cmd_journal = """
SELECT
to_char(c_vej.clin_when, 'YYYY-MM-DD') AS date,
c_vej.clin_when,
coalesce(c_vej.soap_cat, '') as soap_cat,
c_vej.narrative,
c_vej.src_table,
c_scr.rank AS scr,
c_vej.modified_when,
to_char(c_vej.modified_when, 'YYYY-MM-DD HH24:MI') AS date_modified,
c_vej.modified_by,
c_vej.row_version,
c_vej.pk_episode,
c_vej.pk_encounter,
c_vej.soap_cat as real_soap_cat,
c_vej.src_pk,
c_vej.pk_health_issue,
c_vej.health_issue,
c_vej.episode,
c_vej.issue_active,
c_vej.issue_clinically_relevant,
c_vej.episode_open,
c_vej.encounter_started,
c_vej.encounter_last_affirmed,
c_vej.encounter_l10n_type,
c_vej.pk_patient
FROM
clin.v_emr_journal c_vej
join clin.soap_cat_ranks c_scr on (c_scr.soap_cat IS NOT DISTINCT FROM c_vej.soap_cat)
WHERE
%s
""" % '\n\t\t\t\t\tAND\n\t\t\t\t'.join(where_parts)
if active_encounter is None:
cmd = cmd_journal + '\n ' + order_by
else:
args['pk_enc'] = active_encounter['pk_encounter']
args['enc_start'] = active_encounter['started']
args['enc_last_affirmed'] = active_encounter['last_affirmed']
args['enc_type'] = active_encounter['l10n_type']
args['enc_pat'] = active_encounter['pk_patient']
cmd_hints = """
SELECT
to_char(now(), 'YYYY-MM-DD') AS date,
now() as clin_when,
'u'::text as soap_cat,
hints.title || E'\n' || hints.hint
as narrative,
-- .src_table does not correspond with the
-- .src_pk column source because it is generated
-- from clin.get_hints_for_patient()
'ref.auto_hint'::text as src_table,
c_scr.rank AS scr,
now() as modified_when,
to_char(now(), 'YYYY-MM-DD HH24:MI') AS date_modified,
current_user as modified_by,
0::integer as row_version,
NULL::integer as pk_episode,
%(pk_enc)s as pk_encounter,
'u'::text as real_soap_cat,
hints.pk_auto_hint as src_pk,
NULL::integer as pk_health_issue,
''::text as health_issue,
''::text as episode,
False as issue_active,
False as issue_clinically_relevant,
False as episode_open,
%(enc_start)s as encounter_started,
%(enc_last_affirmed)s as encounter_last_affirmed,
%(enc_type)s as encounter_l10n_type,
%(enc_pat)s as pk_patient
FROM
clin.get_hints_for_patient(%(enc_pat)s) AS hints
JOIN clin.soap_cat_ranks c_scr ON (c_scr.soap_cat = 'u')
"""
cmd = cmd_journal + '\nUNION ALL\n' + cmd_hints + '\n' + order_by
journal_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True)
return journal_rows
#============================================================
# convenience functions
#============================================================
def search_text_across_emrs(search_term=None):
if search_term is None:
return []
if search_term.strip() == '':
return []
cmd = 'SELECT * FROM clin.v_narrative4search WHERE narrative ~* %(term)s ORDER BY pk_patient LIMIT 1000'
rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'term': search_term}}], get_col_idx = False)
return rows
#============================================================
# main
#------------------------------------------------------------
if __name__ == '__main__':
if len(sys.argv) < 2:
sys.exit()
if sys.argv[1] != 'test':
sys.exit()
del _
from Gnumed.pycommon import gmI18N
gmI18N.activate_locale()
gmI18N.install_domain(domain = 'gnumed')
gmPG2.request_login_params(setup_pool = True)
#-----------------------------------------
def test_narrative():
print("\nnarrative test")
print("--------------")
narrative = cNarrative(aPK_obj=7)
fields = narrative.get_fields()
for field in fields:
print(field, ':', narrative[field])
print("updatable:", narrative.get_updatable_fields())
print("codes:", narrative.generic_codes)
#print "adding code..."
#narrative.add_code('Test code', 'Test coding system')
#print "codes:", diagnose.get_codes()
#print "creating narrative..."
#new_narrative = create_narrative_item(narrative = 'Test narrative', soap_cat = 'a', episode_id=1, encounter_id=2)
#print new_narrative
#-----------------------------------------
def test_search_text_across_emrs():
results = search_text_across_emrs('cut')
for r in results:
print(r)
#-----------------------------------------
test_search_text_across_emrs()
#test_narrative()Functions
def create_narrative_item(narrative=None, soap_cat=None, episode_id=None, encounter_id=None, link_obj=None)-
Creates a new clinical narrative entry
narrative - free text clinical narrative soap_cat - soap category episode_id - episodes's primary key encounter_id - encounter's primary key
any of the args being None (except soap_cat) will fail the SQL code
Expand source code
def create_narrative_item(narrative=None, soap_cat=None, episode_id=None, encounter_id=None, link_obj=None): """Creates a new clinical narrative entry narrative - free text clinical narrative soap_cat - soap category episode_id - episodes's primary key encounter_id - encounter's primary key any of the args being None (except soap_cat) will fail the SQL code """ # silently do not insert empty narrative narrative = narrative.strip() if narrative == '': return None args = {'enc': encounter_id, 'epi': episode_id, 'soap': soap_cat, 'narr': narrative} # insert new narrative # but, also silently, do not insert true duplicates # this should check for .provider = current_user but # the view has provider mapped to their staff alias cmd = """ INSERT INTO clin.clin_narrative (fk_encounter, fk_episode, narrative, soap_cat) SELECT %(enc)s, %(epi)s, %(narr)s, lower(%(soap)s) WHERE NOT EXISTS ( SELECT 1 FROM clin.v_narrative WHERE pk_encounter = %(enc)s AND pk_episode = %(epi)s AND soap_cat = lower(%(soap)s) AND narrative = %(narr)s ) RETURNING pk""" rows, idx = gmPG2.run_rw_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], return_data = True, get_col_idx = False) if len(rows) == 1: # re-use same link_obj if given because when called from create_progress_note we won't yet see rows inside a new tx return cNarrative(aPK_obj = rows[0]['pk'], link_obj = link_obj) if len(rows) > 1: raise Exception('more than one row returned from single-row INSERT') # retrieve existing narrative cmd = """ SELECT * FROM clin.v_narrative WHERE pk_encounter = %(enc)s AND pk_episode = %(epi)s AND soap_cat = lower(%(soap)s) AND narrative = %(narr)s """ rows, idx = gmPG2.run_ro_queries(link_obj = link_obj, queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) if len(rows) == 1: return cNarrative(row = {'pk_field': 'pk_narrative', 'data': rows[0], 'idx': idx}) raise Exception('retrieving known-to-exist narrative row returned 0 or >1 result: %s' % len(rows)) def create_progress_note(soap=None, episode_id=None, encounter_id=None, link_obj=None)-
Create clinical narrative entries.
must be a dict, the keys being SOAP categories (including U and None=admin) and the values being text (possibly multi-line) Existing but empty ('' or None) categories are skipped.
Expand source code
def create_progress_note(soap=None, episode_id=None, encounter_id=None, link_obj=None): """Create clinical narrative entries. <soap> must be a dict, the keys being SOAP categories (including U and None=admin) and the values being text (possibly multi-line) Existing but empty ('' or None) categories are skipped. """ if soap is None: return True if not gmSoapDefs.are_valid_soap_cats(list(soap), allow_upper = True): raise ValueError('invalid SOAP category in <soap> dictionary: %s', soap) if link_obj is None: link_obj = gmPG2.get_connection(readonly = False) conn_commit = link_obj.commit conn_close = link_obj.close else: conn_commit = lambda *x: None conn_close = lambda *x: None instances = {} for cat in soap: val = soap[cat] if val is None: continue if ''.join([ v.strip() for v in val ]) == '': continue instance = create_narrative_item ( narrative = '\n'.join([ v.strip() for v in val ]), soap_cat = cat, episode_id = episode_id, encounter_id = encounter_id, link_obj = link_obj ) if instance is None: continue instances[cat] = instance conn_commit() conn_close() return instances def delete_clin_narrative(narrative=None)-
Deletes a clin.clin_narrative row by it's PK.
Expand source code
def delete_clin_narrative(narrative=None): """Deletes a clin.clin_narrative row by it's PK.""" cmd = "DELETE FROM clin.clin_narrative WHERE pk=%s" rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': [narrative]}]) return True def get_as_journal(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None, patient=None, active_encounter=None)-
Expand source code
def get_as_journal(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, order_by=None, time_range=None, patient=None, active_encounter=None): if (patient is None) and (episodes is None) and (issues is None) and (encounters is None): raise ValueError('at least one of <patient>, <episodes>, <issues>, <encounters> must not be None') if order_by is None: order_by = 'ORDER BY clin_when, pk_episode, scr, modified_when, src_table' else: order_by = 'ORDER BY %s' % order_by where_parts = [] args = {} if patient is not None: where_parts.append('c_vej.pk_patient = %(pat)s') args['pat'] = patient if soap_cats is not None: # work around bug in psycopg2 not being able to properly # adapt None to NULL inside tuples if None in soap_cats: where_parts.append('((c_vej.soap_cat = ANY(%(soap_cat)s)) OR (c_vej.soap_cat IS NULL))') soap_cats.remove(None) else: where_parts.append('c_vej.soap_cat = ANY(%(soap_cat)s)') args['soap_cat'] = soap_cats if time_range is not None: where_parts.append("c_vej.clin_when > (now() - '%s days'::interval)" % time_range) if episodes is not None: where_parts.append("c_vej.pk_episode = ANY(%(epis)s)") args['epis'] = episodes if issues is not None: where_parts.append("c_vej.pk_health_issue = ANY(%(issues)s)") args['issues'] = issues # FIXME: implement more constraints cmd_journal = """ SELECT to_char(c_vej.clin_when, 'YYYY-MM-DD') AS date, c_vej.clin_when, coalesce(c_vej.soap_cat, '') as soap_cat, c_vej.narrative, c_vej.src_table, c_scr.rank AS scr, c_vej.modified_when, to_char(c_vej.modified_when, 'YYYY-MM-DD HH24:MI') AS date_modified, c_vej.modified_by, c_vej.row_version, c_vej.pk_episode, c_vej.pk_encounter, c_vej.soap_cat as real_soap_cat, c_vej.src_pk, c_vej.pk_health_issue, c_vej.health_issue, c_vej.episode, c_vej.issue_active, c_vej.issue_clinically_relevant, c_vej.episode_open, c_vej.encounter_started, c_vej.encounter_last_affirmed, c_vej.encounter_l10n_type, c_vej.pk_patient FROM clin.v_emr_journal c_vej join clin.soap_cat_ranks c_scr on (c_scr.soap_cat IS NOT DISTINCT FROM c_vej.soap_cat) WHERE %s """ % '\n\t\t\t\t\tAND\n\t\t\t\t'.join(where_parts) if active_encounter is None: cmd = cmd_journal + '\n ' + order_by else: args['pk_enc'] = active_encounter['pk_encounter'] args['enc_start'] = active_encounter['started'] args['enc_last_affirmed'] = active_encounter['last_affirmed'] args['enc_type'] = active_encounter['l10n_type'] args['enc_pat'] = active_encounter['pk_patient'] cmd_hints = """ SELECT to_char(now(), 'YYYY-MM-DD') AS date, now() as clin_when, 'u'::text as soap_cat, hints.title || E'\n' || hints.hint as narrative, -- .src_table does not correspond with the -- .src_pk column source because it is generated -- from clin.get_hints_for_patient() 'ref.auto_hint'::text as src_table, c_scr.rank AS scr, now() as modified_when, to_char(now(), 'YYYY-MM-DD HH24:MI') AS date_modified, current_user as modified_by, 0::integer as row_version, NULL::integer as pk_episode, %(pk_enc)s as pk_encounter, 'u'::text as real_soap_cat, hints.pk_auto_hint as src_pk, NULL::integer as pk_health_issue, ''::text as health_issue, ''::text as episode, False as issue_active, False as issue_clinically_relevant, False as episode_open, %(enc_start)s as encounter_started, %(enc_last_affirmed)s as encounter_last_affirmed, %(enc_type)s as encounter_l10n_type, %(enc_pat)s as pk_patient FROM clin.get_hints_for_patient(%(enc_pat)s) AS hints JOIN clin.soap_cat_ranks c_scr ON (c_scr.soap_cat = 'u') """ cmd = cmd_journal + '\nUNION ALL\n' + cmd_hints + '\n' + order_by journal_rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return journal_rows def get_narrative(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, patient=None, order_by=None)-
Get SOAP notes pertinent to this encounter.
since - initial date for narrative items until - final date for narrative items encounters - list of encounters whose narrative are to be retrieved episodes - list of episodes whose narrative are to be retrieved issues - list of health issues whose narrative are to be retrieved soap_cats - list of SOAP categories of the narrative to be retrieved
Expand source code
def get_narrative(since=None, until=None, encounters=None, episodes=None, issues=None, soap_cats=None, providers=None, patient=None, order_by=None): """Get SOAP notes pertinent to this encounter. since - initial date for narrative items until - final date for narrative items encounters - list of encounters whose narrative are to be retrieved episodes - list of episodes whose narrative are to be retrieved issues - list of health issues whose narrative are to be retrieved soap_cats - list of SOAP categories of the narrative to be retrieved """ where_parts = ['TRUE'] args = {} 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 issues is not None: where_parts.append('pk_health_issue = ANY(%(issues)s)') args['issues'] = issues if patient is not None: where_parts.append('pk_patient = %(pat)s') args['pat'] = patient if soap_cats is not None: where_parts.append('c_vn.soap_cat = ANY(%(soap_cats)s)') args['soap_cats'] = soap_cats if order_by is None: order_by = 'ORDER BY date, soap_rank' else: order_by = 'ORDER BY %s' % order_by cmd = """ SELECT c_vn.*, c_scr.rank AS soap_rank FROM clin.v_narrative c_vn LEFT JOIN clin.soap_cat_ranks c_scr ON c_vn.soap_cat = c_scr.soap_cat WHERE %s %s """ % ( ' AND '.join(where_parts), order_by ) rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) filtered_narrative = [ cNarrative(row = {'pk_field': 'pk_narrative', 'idx': idx, 'data': row}) for row in rows ] if since is not None: filtered_narrative = [ narr for narr in filtered_narrative if narr['date'] >= since ] if until is not None: filtered_narrative = [ narr for narr in filtered_narrative if narr['date'] < until ] if providers is not None: filtered_narrative = [ narr for narr in filtered_narrative if narr['modified_by'] in providers ] return filtered_narrative def search_text_across_emrs(search_term=None)-
Expand source code
def search_text_across_emrs(search_term=None): if search_term is None: return [] if search_term.strip() == '': return [] cmd = 'SELECT * FROM clin.v_narrative4search WHERE narrative ~* %(term)s ORDER BY pk_patient LIMIT 1000' rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': {'term': search_term}}], get_col_idx = False) return rows
Classes
class cNarrative (aPK_obj: int | dict = None, row: dict = None, link_obj=None)-
Represents one clinical free text entry.
Call init from child classes like so:
super().__init__(aPK_obj = aPK_obj, row = row, link_obj = link_obj)Args
aPK_obj- retrieve data from backend
- a simple value the primary key WHERE condition must be a simple column
- a dictionary of values the primary key WHERE condition must be a subselect consuming the dict and producing the single-value primary key
row- must hold the fields
- idx: a dict mapping field names to position
- data: the field values in a list (as returned by cursor.fetchone() in the DB-API)
- pk_field: the name of the primary key field OR
- pk_obj: a dictionary suitable for passed to cursor.execute and holding the primary key values, used for composite PKs
- for example:
row = { 'data': rows[0], 'idx': idx, 'pk_field': 'pk_XXX (the PK column name)', 'pk_obj': {'pk_col1': pk_col1_val, 'pk_col2': pk_col2_val} } rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) objects = [ cChildClass(row = {'data': r, 'idx': idx, 'pk_field': 'the PK column name'}) for r in rows ]
Expand source code
class cNarrative(gmBusinessDBObject.cBusinessDBObject): """Represents one clinical free text entry.""" _cmd_fetch_payload = "SELECT * FROM clin.v_narrative WHERE pk_narrative = %s" _cmds_store_payload = [ """update clin.clin_narrative set narrative = %(narrative)s, clin_when = %(date)s, soap_cat = lower(%(soap_cat)s), fk_encounter = %(pk_encounter)s, fk_episode = %(pk_episode)s WHERE pk = %(pk_narrative)s AND xmin = %(xmin_clin_narrative)s RETURNING xmin AS xmin_clin_narrative""" ] _updatable_fields = [ 'narrative', 'date', 'soap_cat', 'pk_episode', 'pk_encounter' ] #-------------------------------------------------------- def format_maximum_information(self, patient=None): return self.format(fancy = True, width = 70).split('\n') #-------------------------------------------------------- def format(self, left_margin='', fancy=False, width=75): if fancy: txt = gmTools.wrap ( text = _('%s: %s by %.8s (v%s)\n%s') % ( self._payload[self._idx['date']].strftime('%x %H:%M'), gmSoapDefs.soap_cat2l10n_str[self._payload[self._idx['soap_cat']]], self._payload[self._idx['modified_by']], self._payload[self._idx['row_version']], self._payload[self._idx['narrative']] ), width = width, initial_indent = '', subsequent_indent = left_margin + ' ' ) else: txt = '%s [%s]: %s (%.8s)' % ( self._payload[self._idx['date']].strftime('%x %H:%M'), gmSoapDefs.soap_cat2l10n[self._payload[self._idx['soap_cat']]], self._payload[self._idx['narrative']], self._payload[self._idx['modified_by']] ) if len(txt) > width: txt = txt[:width] + gmTools.u_ellipsis 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)""" if pk_code in self._payload[self._idx['pk_generic_codes']]: return cmd = """ INSERT INTO clin.lnk_code2narrative (fk_item, fk_generic_code) SELECT %(item)s, %(code)s WHERE NOT EXISTS ( SELECT 1 FROM clin.lnk_code2narrative WHERE fk_item = %(item)s AND fk_generic_code = %(code)s )""" args = { 'item': self._payload[self._idx['pk_narrative']], 'code': pk_code } rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return #-------------------------------------------------------- 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_code2narrative WHERE fk_item = %(item)s AND fk_generic_code = %(code)s" args = { 'item': self._payload[self._idx['pk_narrative']], 'code': pk_code } rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True #-------------------------------------------------------- # properties #-------------------------------------------------------- def _get_generic_codes(self): if len(self._payload[self._idx['pk_generic_codes']]) == 0: return [] cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)' args = {'pks': self._payload[self._idx['pk_generic_codes']]} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_lnk_code2item'}) for r in rows ] def _set_generic_codes(self, pk_codes): queries = [] # remove all codes if len(self._payload[self._idx['pk_generic_codes']]) > 0: queries.append ({ 'cmd': 'DELETE FROM clin.lnk_code2narrative WHERE fk_item = %(narr)s AND fk_generic_code = ANY(%(codes)s)', 'args': { 'narr': self._payload[self._idx['pk_narrative']], 'codes': self._payload[self._idx['pk_generic_codes']] } }) # add new codes for pk_code in pk_codes: queries.append ({ 'cmd': 'INSERT INTO clin.lnk_code2narrative (fk_item, fk_generic_code) VALUES (%(narr)s, %(pk_code)s)', 'args': { 'narr': self._payload[self._idx['pk_narrative']], 'pk_code': pk_code } }) if len(queries) == 0: return # run it all in one transaction rows, idx = gmPG2.run_rw_queries(queries = queries) return generic_codes = property(_get_generic_codes, _set_generic_codes)Ancestors
Instance variables
var generic_codes-
Expand source code
def _get_generic_codes(self): if len(self._payload[self._idx['pk_generic_codes']]) == 0: return [] cmd = gmCoding._SQL_get_generic_linked_codes % 'pk_generic_code = ANY(%(pks)s)' args = {'pks': self._payload[self._idx['pk_generic_codes']]} rows, idx = gmPG2.run_ro_queries(queries = [{'cmd': cmd, 'args': args}], get_col_idx = True) return [ gmCoding.cGenericLinkedCode(row = {'data': r, 'idx': idx, 'pk_field': 'pk_lnk_code2item'}) 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)""" if pk_code in self._payload[self._idx['pk_generic_codes']]: return cmd = """ INSERT INTO clin.lnk_code2narrative (fk_item, fk_generic_code) SELECT %(item)s, %(code)s WHERE NOT EXISTS ( SELECT 1 FROM clin.lnk_code2narrative WHERE fk_item = %(item)s AND fk_generic_code = %(code)s )""" args = { 'item': self._payload[self._idx['pk_narrative']], 'code': pk_code } rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return def format_maximum_information(self, patient=None)-
Expand source code
def format_maximum_information(self, patient=None): return self.format(fancy = True, width = 70).split('\n') 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_code2narrative WHERE fk_item = %(item)s AND fk_generic_code = %(code)s" args = { 'item': self._payload[self._idx['pk_narrative']], 'code': pk_code } rows, idx = gmPG2.run_rw_queries(queries = [{'cmd': cmd, 'args': args}]) return True
Inherited members