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core: add some missing Encounter.class codes #334

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Jan 7, 2025
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core: add some missing Encounter.class codes #334

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2 changes: 1 addition & 1 deletion cumulus_library/studies/core/core_templates/encounter.sql.jinja
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Expand Up @@ -135,6 +135,6 @@ SELECT DISTINCT
concat('Encounter/', e.id) AS encounter_ref
FROM temp_encounter AS e
LEFT JOIN core__fhir_mapping_expected_act_encounter_code_v3 AS eac
ON e.class_code = eac.found
ON e.class_code = eac.found AND e.class_system = eac.found_system
LEFT JOIN core__fhir_act_encounter_code_v3 AS ac ON eac.expected = ac.code
INNER JOIN core__patient AS p ON e.subject_ref = p.subject_ref;
38 changes: 23 additions & 15 deletions cumulus_library/studies/core/fhir_mapping_tables.sql
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Expand Up @@ -118,23 +118,31 @@ SELECT * FROM

-- ############################################################
-- FHIR mapping of as found Encounter codes to the expected encounter code from
-- http://hl7.org/fhir/STU3/v3/ActEncounterCode/vs.html
-- http://hl7.org/fhir/R4/v3/ActEncounterCode/vs.html

CREATE TABLE core__fhir_mapping_expected_act_encounter_code_v3 AS
SELECT * FROM
(
VALUES
('AMB', 'AMB'),
('AMB', 'R'),
('AMB', 'O'),
('EMER', 'EMER'),
('EMER', 'E'),
('FLD', 'FLD'),
('HH', 'HH'),
('IMP', 'IMP'),
('ACUTE', 'ACUTE'),
('NONAC', 'NONAC'),
('PRENC', 'PRENC'),
('SS', 'SS'),
('VR', 'VR')
) AS t (expected, found);
-- http://hl7.org/fhir/R4/v3/ActEncounterCode/vs.html
-- This is the modern, expected class system.
('AMB', 'AMB', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('EMER', 'EMER', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('FLD', 'FLD', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('HH', 'HH', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('IMP', 'IMP', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('ACUTE', 'ACUTE', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('NONAC', 'NONAC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('OBSENC', 'OBSENC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('PRENC', 'PRENC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('SS', 'SS', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('VR', 'VR', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
-- http://terminology.hl7.org/CodeSystem/v2-0004
-- This is an older class system, still in active use apparently (at BCH Cerner).
-- Unmapped codes: B (obstetrics), C (commercial), N (not applicable), U (unknown)
('EMER', 'E', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('IMP', 'I', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('AMB', 'O', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('PRENC', 'P', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('AMB', 'R', 'http://terminology.hl7.org/CodeSystem/v2-0004') -- recurring patient
Comment on lines +129 to +147
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have we checked this against a recent-ish epic? just to make sure these codes are actually present in the form we'd expect as opposed to the proprietary format?

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In the export I have from the Epic sandbox, it's always urn:oid:1.2.840.114350.1.72.1.7.7.10.696784.13260 and codes like 13 or 17

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And this field is just a raw coding - so only room for one code & system pair 😦

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Can we use multiple entries in this table? like core/fhir_mapping_tables.sql?

) AS t (expected, found, found_system);
4 changes: 3 additions & 1 deletion cumulus_library/studies/core/reference_sql/builder_encounter.sql
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Expand Up @@ -582,6 +582,7 @@ temp_encounter_completion AS (
SELECT
ece.encounter_id,
(
-- Every time you add a resource here, update core-study-details.md
BOOL_OR(ec.table_name = 'allergyintolerance')
AND BOOL_OR(ec.table_name = 'condition')
AND BOOL_OR(ec.table_name = 'diagnosticreport')
Expand Down Expand Up @@ -705,7 +706,7 @@ SELECT DISTINCT
concat('Encounter/', e.id) AS encounter_ref
FROM temp_encounter AS e
LEFT JOIN core__fhir_mapping_expected_act_encounter_code_v3 AS eac
ON e.class_code = eac.found
ON e.class_code = eac.found AND e.class_system = eac.found_system
LEFT JOIN core__fhir_act_encounter_code_v3 AS ac ON eac.expected = ac.code
INNER JOIN core__patient AS p ON e.subject_ref = p.subject_ref;

Expand Down Expand Up @@ -735,6 +736,7 @@ temp_encounter_completion AS (
SELECT
ece.encounter_id,
(
-- Every time you add a resource here, update core-study-details.md
BOOL_OR(ec.table_name = 'allergyintolerance')
AND BOOL_OR(ec.table_name = 'condition')
AND BOOL_OR(ec.table_name = 'diagnosticreport')
Expand Down
38 changes: 23 additions & 15 deletions cumulus_library/studies/core/reference_sql/builder_prereq_tables.sql
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Expand Up @@ -258,23 +258,31 @@ SELECT * FROM

-- ############################################################
-- FHIR mapping of as found Encounter codes to the expected encounter code from
-- http://hl7.org/fhir/STU3/v3/ActEncounterCode/vs.html
-- http://hl7.org/fhir/R4/v3/ActEncounterCode/vs.html

CREATE TABLE core__fhir_mapping_expected_act_encounter_code_v3 AS
SELECT * FROM
(
VALUES
('AMB', 'AMB'),
('AMB', 'R'),
('AMB', 'O'),
('EMER', 'EMER'),
('EMER', 'E'),
('FLD', 'FLD'),
('HH', 'HH'),
('IMP', 'IMP'),
('ACUTE', 'ACUTE'),
('NONAC', 'NONAC'),
('PRENC', 'PRENC'),
('SS', 'SS'),
('VR', 'VR')
) AS t (expected, found);
-- http://hl7.org/fhir/R4/v3/ActEncounterCode/vs.html
-- This is the modern, expected class system.
('AMB', 'AMB', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('EMER', 'EMER', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('FLD', 'FLD', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('HH', 'HH', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('IMP', 'IMP', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('ACUTE', 'ACUTE', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('NONAC', 'NONAC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('OBSENC', 'OBSENC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('PRENC', 'PRENC', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('SS', 'SS', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
('VR', 'VR', 'http://terminology.hl7.org/CodeSystem/v3-ActCode'),
-- http://terminology.hl7.org/CodeSystem/v2-0004
-- This is an older class system, still in active use apparently (at BCH Cerner).
-- Unmapped codes: B (obstetrics), C (commercial), N (not applicable), U (unknown)
('EMER', 'E', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('IMP', 'I', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('AMB', 'O', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('PRENC', 'P', 'http://terminology.hl7.org/CodeSystem/v2-0004'),
('AMB', 'R', 'http://terminology.hl7.org/CodeSystem/v2-0004') -- recurring patient
) AS t (expected, found, found_system);
25 changes: 25 additions & 0 deletions tests/core/test_core_encounters.py
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@@ -0,0 +1,25 @@
"""Tests for core__encounter"""

import json

from tests import testbed_utils


def test_core_enc_class(tmp_path):
"""Verify that we handle multiply rows as needed when multiple options appear"""
v2_sys = "http://terminology.hl7.org/CodeSystem/v2-0004"
v3_sys = "http://terminology.hl7.org/CodeSystem/v3-ActCode"

testbed = testbed_utils.LocalTestbed(tmp_path)
testbed.add_encounter("o", **{"class": {"code": "O", "system": v2_sys}})
testbed.add_encounter("obsenc", **{"class": {"code": "OBSENC", "system": v3_sys}})
testbed.add_encounter("unsupported", **{"class": {"code": "?", "system": v3_sys}})

con = testbed.build()
df = con.sql("SELECT id, class_code, class_display FROM core__encounter ORDER BY id").df()
rows = json.loads(df.to_json(orient="records"))
assert rows == [
{"id": "o", "class_code": "AMB", "class_display": "ambulatory"},
{"id": "obsenc", "class_code": "OBSENC", "class_display": "observation encounter"},
{"id": "unsupported", "class_code": None, "class_display": None},
]
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