Include Type Concept vocabulary in Data Sources condition by type report (fixes OHDSI/Atlas#2644)

src/main/resources/resources/cdmresults/sql/report/condition/drilldown/byType.sql

@@ -11,23 +11,27 @@ ON ar1.stratum_1 = CAST(c1.concept_id AS VARCHAR(255))
 INNER JOIN
 (
 SELECT concept_id,
+CASE WHEN lower(vocabulary_id) = 'condition type' THEN
 CASE WHEN concept_name LIKE 'Inpatient%' THEN 10
 WHEN concept_name LIKE 'Outpatient%' THEN 20
 ELSE concept_id END
 +
 CASE WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name LIKE '%primary%' OR concept_name LIKE '%1st position%') THEN 1
 WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name NOT LIKE '%primary%' AND concept_name NOT LIKE '%1st position%') THEN 2
-ELSE 0 END AS concept_group_id,
+ELSE 0 END
+ELSE concept_id END AS concept_group_id,
+CASE WHEN lower(vocabulary_id) = 'condition type' THEN
 CONCAT(
   CASE WHEN concept_name LIKE 'Inpatient%' THEN 'Claim- Inpatient: '
   WHEN concept_name LIKE 'Outpatient%' THEN 'Claim- Outpatient: '
   ELSE concept_name END,
   CASE WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name LIKE '%primary%' OR concept_name LIKE '%1st position%') THEN 'Primary diagnosis'
   WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name NOT LIKE '%primary%' AND concept_name NOT LIKE '%1st position%') THEN 'Secondary diagnosis'
   ELSE '' END
-) AS concept_group_name
+)
+ELSE concept_name END AS concept_group_name
 FROM @vocab_database_schema.concept
-WHERE lower(vocabulary_id) = 'condition type'
+WHERE lower(vocabulary_id) IN ('condition type', 'type concept')
 
 ) c2
 ON ar1.stratum_2 = CAST(c2.concept_id AS VARCHAR(255))

src/main/resources/resources/cdmresults/sql/report/condition/drilldownsummary/byType.sql

@@ -11,23 +11,27 @@ ON ar1.stratum_1 = CAST(c1.concept_id AS VARCHAR(255))
 INNER JOIN
 (
 SELECT concept_id,
+CASE WHEN lower(vocabulary_id) = 'condition type' THEN
 CASE WHEN concept_name LIKE 'Inpatient%' THEN 10
 WHEN concept_name LIKE 'Outpatient%' THEN 20
 ELSE concept_id END
 +
 CASE WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name LIKE '%primary%' OR concept_name LIKE '%1st position%') THEN 1
 WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name NOT LIKE '%primary%' AND concept_name NOT LIKE '%1st position%') THEN 2
-ELSE 0 END AS concept_group_id,
+ELSE 0 END
+ELSE concept_id END AS concept_group_id,
+CASE WHEN lower(vocabulary_id) = 'condition type' THEN
 CONCAT(
   CASE WHEN concept_name LIKE 'Inpatient%' THEN 'Claim- Inpatient: '
   WHEN concept_name LIKE 'Outpatient%' THEN 'Claim- Outpatient: '
   ELSE concept_name END,
   CASE WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name LIKE '%primary%' OR concept_name LIKE '%1st position%') THEN 'Primary diagnosis'
   WHEN (concept_name LIKE 'Inpatient%' OR concept_name LIKE 'Outpatient%' ) AND (concept_name NOT LIKE '%primary%' AND concept_name NOT LIKE '%1st position%') THEN 'Secondary diagnosis'
   ELSE '' END
-) AS concept_group_name
+)
+ELSE concept_name END AS concept_group_name
 FROM @vocab_database_schema.concept
-WHERE lower(vocabulary_id) = 'condition type'
+WHERE lower(vocabulary_id) IN ('condition type', 'type concept')
 
 ) c2
 ON ar1.stratum_2 = CAST(c2.concept_id AS VARCHAR(255))

src/test/java/org/ohdsi/webapi/report/CDMResultsConditionByTypeTest.java

@@ -0,0 +1,133 @@
+package org.ohdsi.webapi.report;
+
+import static org.junit.Assert.assertEquals;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import java.util.HashMap;
+import java.util.Map;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.ohdsi.webapi.AbstractDatabaseTest;
+import org.ohdsi.webapi.source.Source;
+import org.ohdsi.webapi.source.SourceDaimon;
+
+/**
+ * Runs the Data Sources condition drilldown queries against the embedded Postgres instance and checks
+ * the "by type" results for condition type concepts from both the deprecated 'Condition Type' vocabulary
+ * and the current 'Type Concept' vocabulary.
+ */
+public class CDMResultsConditionByTypeTest extends AbstractDatabaseTest {
+
+    private static final String RESULTS_SCHEMA = "condition_by_type_results";
+
+    private static final int CONDITION_CONCEPT_ID = 201826;
+
+    private CDMResultsAnalysisRunner runner;
+    private Source source;
+
+    @Before
+    public void setUp() {
+
+        runner = new CDMResultsAnalysisRunner();
+        runner.init("postgresql", new ObjectMapper());
+
+        source = mock(Source.class);
+        when(source.getTableQualifier(SourceDaimon.DaimonType.Results)).thenReturn(RESULTS_SCHEMA);
+        when(source.getTableQualifier(SourceDaimon.DaimonType.Vocabulary)).thenReturn(RESULTS_SCHEMA);
+        when(source.getTableQualifier(SourceDaimon.DaimonType.CDM)).thenReturn(RESULTS_SCHEMA);
+        when(source.getSourceDialect()).thenReturn("postgresql");
+
+        jdbcTemplate.execute(String.format("DROP SCHEMA IF EXISTS %1$s CASCADE; CREATE SCHEMA %1$s;", RESULTS_SCHEMA));
+        jdbcTemplate.execute(String.format("CREATE TABLE %s.achilles_results (analysis_id INT, stratum_1 VARCHAR(255), "
+                + "stratum_2 VARCHAR(255), stratum_3 VARCHAR(255), stratum_4 VARCHAR(255), stratum_5 VARCHAR(255), "
+                + "count_value BIGINT)", RESULTS_SCHEMA));
+        jdbcTemplate.execute(String.format("CREATE TABLE %s.achilles_results_dist (analysis_id INT, "
+                + "stratum_1 VARCHAR(255), stratum_2 VARCHAR(255), stratum_3 VARCHAR(255), stratum_4 VARCHAR(255), "
+                + "stratum_5 VARCHAR(255), count_value BIGINT, min_value FLOAT, max_value FLOAT, avg_value FLOAT, "
+                + "stdev_value FLOAT, median_value FLOAT, p10_value FLOAT, p25_value FLOAT, p75_value FLOAT, "
+                + "p90_value FLOAT)", RESULTS_SCHEMA));
+        jdbcTemplate.execute(String.format("CREATE TABLE %s.concept (concept_id INT, concept_name VARCHAR(255), "
+                + "domain_id VARCHAR(20), vocabulary_id VARCHAR(20), concept_class_id VARCHAR(20), "
+                + "standard_concept VARCHAR(1), concept_code VARCHAR(50))", RESULTS_SCHEMA));
+
+        insertConcept(CONDITION_CONCEPT_ID, "Type 2 diabetes mellitus", "Condition", "SNOMED", "Clinical Finding", "S");
+        // condition type concepts from the vocabulary that was deprecated in 2020
+        insertConcept(38000200, "Inpatient header - 1st position", "Type Concept", "Condition Type", "Condition Type", null);
+        insertConcept(38000201, "Inpatient header - 2nd position", "Type Concept", "Condition Type", "Condition Type", null);
+        // condition type concepts from the current 'Type Concept' vocabulary
+        insertConcept(32817, "EHR", "Type Concept", "Type Concept", "Type Concept", "S");
+        insertConcept(32810, "Claim", "Type Concept", "Type Concept", "Type Concept", "S");
+        insertConcept(32855, "Inpatient claim header", "Type Concept", "Type Concept", "Type Concept", "S");
+
+        // number of condition occurrence records by condition_concept_id and condition_type_concept_id
+        insertResult(405, CONDITION_CONCEPT_ID, 38000200, 5);
+        insertResult(405, CONDITION_CONCEPT_ID, 38000201, 3);
+        insertResult(405, CONDITION_CONCEPT_ID, 32817, 7);
+        insertResult(405, CONDITION_CONCEPT_ID, 32810, 11);
+        insertResult(405, CONDITION_CONCEPT_ID, 32855, 13);
+    }
+
+    @After
+    public void tearDown() {
+
+        jdbcTemplate.execute(String.format("DROP SCHEMA IF EXISTS %s CASCADE", RESULTS_SCHEMA));
+    }
+
+    private void insertConcept(int conceptId, String conceptName, String domainId, String vocabularyId,
+                               String conceptClassId, String standardConcept) {
+
+        jdbcTemplate.update(String.format("INSERT INTO %s.concept (concept_id, concept_name, domain_id, vocabulary_id, "
+                + "concept_class_id, standard_concept, concept_code) VALUES (?, ?, ?, ?, ?, ?, ?)", RESULTS_SCHEMA),
+                conceptId, conceptName, domainId, vocabularyId, conceptClassId, standardConcept,
+                String.valueOf(conceptId));
+    }
+
+    private void insertResult(int analysisId, int stratum1, int stratum2, long countValue) {
+
+        jdbcTemplate.update(String.format("INSERT INTO %s.achilles_results (analysis_id, stratum_1, stratum_2, "
+                + "count_value) VALUES (?, ?, ?, ?)", RESULTS_SCHEMA),
+                analysisId, String.valueOf(stratum1), String.valueOf(stratum2), countValue);
+    }
+
+    private static Map<String, Long> countsByTypeName(JsonNode byType) {
+
+        Map<String, Long> counts = new HashMap<>();
+        for (JsonNode row : byType) {
+            assertEquals(CONDITION_CONCEPT_ID, row.get("conditionConceptId").asInt());
+            counts.put(row.get("conceptName").asText(), row.get("countValue").asLong());
+        }
+        return counts;
+    }
+
+    private static Map<String, Long> expectedCounts() {
+
+        Map<String, Long> expected = new HashMap<>();
+        expected.put("Claim- Inpatient: Primary diagnosis", 5L);
+        expected.put("Claim- Inpatient: Secondary diagnosis", 3L);
+        expected.put("EHR", 7L);
+        expected.put("Claim", 11L);
+        // the inpatient/outpatient grouping only applies to the deprecated 'Condition Type' concepts
+        expected.put("Inpatient claim header", 13L);
+        return expected;
+    }
+
+    @Test
+    public void getDrilldown_byTypeIncludesTypeConceptVocabulary() {
+
+        JsonNode drilldown = runner.getDrilldown(jdbcTemplate, "condition", CONDITION_CONCEPT_ID, source);
+
+        assertEquals(expectedCounts(), countsByTypeName(drilldown.get("byType")));
+    }
+
+    @Test
+    public void getDrilldownSummary_byTypeIncludesTypeConceptVocabulary() {
+
+        JsonNode drilldown = runner.getDrilldown(jdbcTemplate, "condition", null, source);
+
+        assertEquals(expectedCounts(), countsByTypeName(drilldown.get("byType")));
+    }
+}