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Fix value_as_concept_id missing from CTE when Measurement abnormal=true #233

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Fix value_as_concept_id missing from CTE when Measurement abnormal=true #233

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13 changes: 6 additions & 7 deletions src/main/java/org/ohdsi/circe/cohortdefinition/builders/MeasurementSqlBuilder.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
package org.ohdsi.circe.cohortdefinition.builders;

import org.apache.commons.lang3.ArrayUtils;
import org.apache.commons.lang3.StringUtils;
import org.ohdsi.circe.cohortdefinition.Measurement;
import org.ohdsi.circe.helper.ResourceHelper;
Expand Down Expand Up @@ -102,10 +103,8 @@ protected List<String> resolveSelectClauses(T criteria) {
selectCols.add("m.operator_concept_id");
}

// valueAsConcept
if ((criteria.valueAsConcept != null && criteria.valueAsConcept.length > 0) ||
criteria.valueAsConceptCS != null
) {
// valueAsConcept or abnormal
if (ArrayUtils.isNotEmpty(criteria.valueAsConcept) || criteria.valueAsConceptCS != null || Boolean.TRUE.equals(criteria.abnormal)) {
selectCols.add("m.value_as_concept_id");
}

Expand Down Expand Up @@ -140,7 +139,7 @@ protected List<String> resolveJoinClauses(T criteria) {
List<String> joinClauses = new ArrayList<>();

// join to PERSON
if (criteria.age != null ||
if (criteria.age != null ||
(criteria.gender != null && criteria.gender.length > 0) ||
criteria.genderCS != null
) {
Expand Down Expand Up @@ -207,7 +206,7 @@ protected List<String> resolveWhereClauses(T criteria) {
if (criteria.valueAsConceptCS != null) {
whereClauses.add(getCodesetInExpression("C.value_as_concept_id", criteria.valueAsConceptCS));
}

// unit
if (criteria.unit != null && criteria.unit.length > 0) {
ArrayList<Long> conceptIds = getConceptIdsFromConcepts(criteria.unit);
Expand All @@ -218,7 +217,7 @@ protected List<String> resolveWhereClauses(T criteria) {
if (criteria.unitCS != null) {
whereClauses.add(getCodesetInExpression("C.unit_concept_id", criteria.unitCS));
}

// rangeLow
if (criteria.rangeLow != null) {
whereClauses.add(buildNumericRangeClause("C.range_low", criteria.rangeLow, ".4f"));
Expand Down
53 changes: 40 additions & 13 deletions src/test/java/org/ohdsi/circe/cohortdefinition/builders/CriteriaQuery_5_0_0_Test.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@
import org.dbunit.operation.DatabaseOperation;
import org.junit.BeforeClass;
import org.junit.Test;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsString;
import org.ohdsi.circe.AbstractDatabaseTest;
import org.ohdsi.circe.cohortdefinition.ConceptSetSelection;
import org.ohdsi.circe.cohortdefinition.ConditionEra;
Expand Down Expand Up @@ -64,7 +66,7 @@ public class CriteriaQuery_5_0_0_Test extends AbstractDatabaseTest {
private static final ConceptSetSelection CONCEPTSET_2 = null;
private static final ConceptSetSelection CONCEPTSET_3 = null;
private static final ConceptSetSelection CONCEPTSET_4 = null;


private String renderQuery(String query) {
String result = StringUtils.replace(query, "#Codesets", "temp.codesets");
Expand All @@ -91,7 +93,7 @@ public static void beforeClass() {
prepareSchema("cdm", CDM_DDL_PATH);
prepareSchema("temp", TEMP_DDL_PATH);
}

private ConceptSetSelection createConceptSetSelection(Integer id, boolean isExcluded) {
ConceptSetSelection css = new ConceptSetSelection();
css.codesetId = id;
Expand Down Expand Up @@ -147,7 +149,7 @@ public void testConditionEraDateOffset() throws Exception {
// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}

@Test
public void testConditionEraConceptSet() throws Exception {
final String[] testDataSetsPrep = new String[]{
Expand Down Expand Up @@ -252,7 +254,7 @@ public void testConditionOccurrenceConceptSet() throws Exception {
criteria.genderCS = createConceptSetSelection(1,false);
criteria.visitTypeCS = createConceptSetSelection(2,false);
criteria.providerSpecialtyCS = createConceptSetSelection(3,false);


ConditionOccurrenceSqlBuilder<ConditionOccurrence> builder = new ConditionOccurrenceSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));
Expand All @@ -270,7 +272,7 @@ public void testConditionOccurrenceConceptSet() throws Exception {
// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}

@Test
public void testDeathDateOffset() throws Exception {
final String[] testDataSetsPrep = new String[]{
Expand Down Expand Up @@ -315,7 +317,7 @@ public void testDeathDateOffset() throws Exception {
Assertion.assertEquals(expectedDataSet, actualDataSet);
}


@Test
public void testDeathConceptSet() throws Exception {
final String[] testDataSetsPrep = new String[]{
Expand Down Expand Up @@ -505,7 +507,7 @@ public void testDoseEraConceptSet() throws Exception {
criteria.codesetId = 1;
criteria.genderCS = createConceptSetSelection(1,false);
criteria.unitCS = createConceptSetSelection(3,false);


DoseEraSqlBuilder<DoseEra> builder = new DoseEraSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));
Expand All @@ -522,7 +524,7 @@ public void testDoseEraConceptSet() throws Exception {

// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}
}

@Test
public void testDrugEraDateOffset() throws Exception {
Expand Down Expand Up @@ -691,7 +693,7 @@ public void testDrugExposureConceptSet() throws Exception {

// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}
}

@Test
public void testMeasurementDateOffset() throws Exception {
Expand Down Expand Up @@ -763,7 +765,7 @@ public void testMeasurementConceptSet() throws Exception {
criteria.genderCS = createConceptSetSelection(1,false);
criteria.providerSpecialtyCS = createConceptSetSelection(3,false);
criteria.visitTypeCS = createConceptSetSelection(2,false);

MeasurementSqlBuilder<Measurement> builder = new MeasurementSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));

Expand Down Expand Up @@ -942,7 +944,7 @@ public void testObservationPeriodConceptSet() throws Exception {
// Test 1: simple query with no special conditions
ObservationPeriod criteria = new ObservationPeriod();
criteria.periodTypeCS = createConceptSetSelection(1,false);

ObservationPeriodSqlBuilder<ObservationPeriod> builder = new ObservationPeriodSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));

Expand Down Expand Up @@ -1082,7 +1084,7 @@ public void testProcedureOccurrenceConceptSet() throws Exception {
criteria.procedureTypeCS = createConceptSetSelection(2,false);
criteria.visitTypeCS = createConceptSetSelection(2,false);
criteria.providerSpecialtyCS = createConceptSetSelection(3,false);

ProcedureOccurrenceSqlBuilder<ProcedureOccurrence> builder = new ProcedureOccurrenceSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));

Expand Down Expand Up @@ -1124,7 +1126,7 @@ public void testSpecimenConceptSet() throws Exception {
criteria.unitCS = createConceptSetSelection(3,false);
criteria.anatomicSiteCS = createConceptSetSelection(2,false);
criteria.diseaseStatusCS = createConceptSetSelection(3,false);

SpecimenSqlBuilder<Specimen> builder = new SpecimenSqlBuilder<>();
String query = renderQuery(builder.getCriteriaSql(criteria));

Expand Down Expand Up @@ -1226,4 +1228,29 @@ public void testVisitOccurrenceConceptSet() throws Exception {
// Assert actual database table match expected table
Assertion.assertEquals(expectedDataSet, actualDataSet);
}

@Test
public void testMeasurementAbnormal() throws Exception {
final IDatabaseConnection dbUnitCon = getConnection();
DatabaseOperation.CLEAN_INSERT.execute(dbUnitCon, DataSetFactory.createDataSet(new String[]{ "/datasets/vocabulary.json", "/criteria/codesets.json", "/criteria/measurementAbnormal_PREP.json"}));

Measurement criteria = new Measurement();
criteria.codesetId = 1;
criteria.abnormal = true;

String query = renderQuery(new MeasurementSqlBuilder<>().getCriteriaSql(criteria));

assertThat(query, containsString("m.value_as_concept_id"));
assertThat(query, containsString("C.value_as_number < C.range_low"));
assertThat(query, containsString("C.value_as_number > C.range_high"));
assertThat(query, containsString("C.value_as_concept_id in (4155142, 4155143)"));

// Verify the query executes without error and returns only abnormal measurements
ITable actual = new SortedTable(
dbUnitCon.createQueryTable("measurement.abnormal", query),
new String[]{"person_id", "start_date"}
);
IDataSet expected = DataSetFactory.createDataSet(new String[]{"/criteria/measurementAbnormal_VERIFY.json"});
Assertion.assertEquals(expected, new CompositeDataSet(new ITable[]{actual}));
}
}
86 changes: 86 additions & 0 deletions src/test/resources/criteria/measurementAbnormal_PREP.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
{
"cdm.person": [
{
"person_id":1,
"gender_concept_id":0,
"year_of_birth":0,
"race_concept_id":0,
"ethnicity_concept_id":0
},
{
"person_id":2,
"gender_concept_id":0,
"year_of_birth":0,
"race_concept_id":0,
"ethnicity_concept_id":0
},
{
"person_id":3,
"gender_concept_id":0,
"year_of_birth":0,
"race_concept_id":0,
"ethnicity_concept_id":0
},
{
"person_id":4,
"gender_concept_id":0,
"year_of_birth":0,
"race_concept_id":0,
"ethnicity_concept_id":0
},
{
"person_id":5,
"gender_concept_id":0,
"year_of_birth":0,
"race_concept_id":0,
"ethnicity_concept_id":0
}
],
"cdm.measurement": [
{
"measurement_id": 1,
"person_id":1,
"measurement_concept_id":1,
"measurement_date":"2000-01-01",
"measurement_type_concept_id":0,
"value_as_number":5,
"range_low":10,
"range_high":20
},
{
"measurement_id": 2,
"person_id":2,
"measurement_concept_id":1,
"measurement_date":"2000-01-01",
"measurement_type_concept_id":0,
"value_as_concept_id":4155142
},
{
"measurement_id": 3,
"person_id":3,
"measurement_concept_id":1,
"measurement_date":"2000-01-01",
"measurement_type_concept_id":0,
"value_as_number":15,
"range_low":10,
"range_high":20
},
{
"measurement_id": 4,
"person_id":4,
"measurement_concept_id":1,
"measurement_date":"2000-01-01",
"measurement_type_concept_id":0
},
{
"measurement_id": 5,
"person_id":5,
"measurement_concept_id":1,
"measurement_date":"2000-01-01",
"measurement_type_concept_id":0,
"value_as_number":25,
"range_low":10,
"range_high":20
}
]
}
28 changes: 28 additions & 0 deletions src/test/resources/criteria/measurementAbnormal_VERIFY.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
{
"measurement.abnormal": [
{
"person_id": 1,
"event_id": 1,
"start_date": "2000-01-01",
"end_date": "2000-01-02",
"visit_occurrence_id": null,
"sort_date": "2000-01-01"
},
{
"person_id": 2,
"event_id": 2,
"start_date": "2000-01-01",
"end_date": "2000-01-02",
"visit_occurrence_id": null,
"sort_date": "2000-01-01"
},
{
"person_id": 5,
"event_id": 5,
"start_date": "2000-01-01",
"end_date": "2000-01-02",
"visit_occurrence_id": null,
"sort_date": "2000-01-01"
}
]
}