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Keep Procedure concepts without a vocabulary row in the concept hierarchy (fixes OHDSI/Atlas#2926) #2581

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Merged
chrisknoll merged 1 commit into from
Nov 6, 2026
Merged

Keep Procedure concepts without a vocabulary row in the concept hierarchy (fixes OHDSI/Atlas#2926) #2581

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4 changes: 2 additions & 2 deletions src/main/resources/ddl/results/init_concept_hierarchy.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -276,9 +276,9 @@ FROM
(
SELECT
c1.concept_id,
CONCAT(v1.vocabulary_name, ' ', c1.concept_code, ': ', c1.concept_name) AS proc_concept_name
CONCAT(COALESCE(v1.vocabulary_name, c1.vocabulary_id), ' ', c1.concept_code, ': ', c1.concept_name) AS proc_concept_name
FROM @vocab_schema.concept c1
INNER JOIN @vocab_schema.vocabulary v1 ON c1.vocabulary_id = v1.vocabulary_id
LEFT JOIN @vocab_schema.vocabulary v1 ON c1.vocabulary_id = v1.vocabulary_id
WHERE c1.domain_id = 'Procedure'
) procs
LEFT JOIN (
Expand Down
48 changes: 44 additions & 4 deletions src/test/java/org/ohdsi/webapi/service/DDLServiceTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@ public class DDLServiceTest extends AbstractDatabaseTest {
private static final int ATC_4TH = 21604303;
private static final int ATC_2ND = 21604253;
private static final int ATC_1ST = 21604180;
private static final int APPENDECTOMY = 4336464;
private static final int CUSTOM_PROCEDURE = 2000000001;

@Before
public void setUp() {
Expand Down Expand Up @@ -69,9 +71,21 @@ public void tearDown() {

private void insertConcept(int conceptId, String name, String vocabularyId, String conceptClassId, String standard) {

insertConcept(conceptId, name, "Drug", vocabularyId, conceptClassId, standard, null);
}

private void insertConcept(int conceptId, String name, String domainId, String vocabularyId, String conceptClassId,
String standard, String conceptCode) {

jdbcTemplate.update(String.format("INSERT INTO %s.concept (concept_id, concept_name, domain_id, vocabulary_id, "
+ "concept_class_id, standard_concept) VALUES (?, ?, 'Drug', ?, ?, ?)", VOCAB_SCHEMA),
conceptId, name, vocabularyId, conceptClassId, standard);
+ "concept_class_id, standard_concept, concept_code) VALUES (?, ?, ?, ?, ?, ?, ?)", VOCAB_SCHEMA),
conceptId, name, domainId, vocabularyId, conceptClassId, standard, conceptCode);
}

private void insertVocabulary(String vocabularyId, String vocabularyName) {

jdbcTemplate.update(String.format("INSERT INTO %s.vocabulary (vocabulary_id, vocabulary_name) VALUES (?, ?)",
VOCAB_SCHEMA), vocabularyId, vocabularyName);
}

private void insertAncestor(int ancestorId, int descendantId, int levels) {
Expand All @@ -81,15 +95,20 @@ private void insertAncestor(int ancestorId, int descendantId, int levels) {
ancestorId, descendantId, levels, levels);
}

@Test
public void initConceptHierarchy_drugHierarchyUsesStandardIngredientsOnly() {
private void runInitConceptHierarchy() {

for (String path : DDLService.INIT_CONCEPT_HIERARCHY_FILE_PATHS) {
String sql = SqlRender.renderSql(ResourceHelper.GetResourceAsString(path),
new String[]{DDLService.VOCAB_SCHEMA, DDLService.RESULTS_SCHEMA},
new String[]{VOCAB_SCHEMA, RESULTS_SCHEMA});
jdbcTemplate.execute(SqlTranslate.translateSql(sql, "postgresql"));
}
}

@Test
public void initConceptHierarchy_drugHierarchyUsesStandardIngredientsOnly() {

runInitConceptHierarchy();

List<Map<String, Object>> rows = jdbcTemplate.queryForList(String.format("SELECT concept_id, "
+ "level1_concept_name, level2_concept_name, level3_concept_name, level4_concept_name "
Expand All @@ -105,4 +124,25 @@ public void initConceptHierarchy_drugHierarchyUsesStandardIngredientsOnly() {
assertEquals(ACETAMINOPHEN, rows.get(0).get("concept_id"));
assertEquals(ACETAMINOPHEN_TABLET, rows.get(1).get("concept_id"));
}

@Test
public void initConceptHierarchy_procedureHierarchyKeepsConceptsWithoutVocabularyRow() {

insertVocabulary("SNOMED", "Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)");
insertConcept(APPENDECTOMY, "Appendectomy", "Procedure", "SNOMED", "Procedure", "S", "80146002");
// site-specific concept whose vocabulary_id has no row in the vocabulary table
insertConcept(CUSTOM_PROCEDURE, "Local procedure", "Procedure", "Local", "Procedure", null, "LP-1");

runInitConceptHierarchy();

List<Map<String, Object>> rows = jdbcTemplate.queryForList(String.format("SELECT concept_id, concept_name "
+ "FROM %s.concept_hierarchy WHERE treemap = 'Procedure' ORDER BY concept_id", RESULTS_SCHEMA));

assertEquals(2, rows.size());
assertEquals(APPENDECTOMY, rows.get(0).get("concept_id"));
assertEquals("Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO) 80146002: Appendectomy",
rows.get(0).get("concept_name"));
assertEquals(CUSTOM_PROCEDURE, rows.get(1).get("concept_id"));
assertEquals("Local LP-1: Local procedure", rows.get(1).get("concept_name"));
}
}
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