add unit tests for clinical data counts sql

src/test/java/org/cbioportal/persistence/mybatisclickhouse/ClinicalDataCountTest.java

@@ -0,0 +1,243 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.model.ClinicalDataCount;
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+import org.cbioportal.web.parameter.CategorizedClinicalDataCountFilter;
+import org.cbioportal.web.parameter.ClinicalDataFilter;
+import org.cbioportal.web.parameter.DataFilterValue;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
+import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.context.annotation.Import;
+import org.springframework.test.annotation.DirtiesContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringRunner;
+
+import java.math.BigDecimal;
+import java.util.Collections;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+
+@RunWith(SpringRunner.class)
+@Import(MyBatisConfig.class)
+@DataJpaTest
+@DirtiesContext
+@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
+@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
+public class ClinicalDataCountTest extends AbstractTestcontainers {
+    private static final String STUDY_ACC_TCGA = "acc_tcga";
+    private static final String STUDY_GENIE_PUB = "study_genie_pub";
+
+    @Autowired
+    private StudyViewMapper studyViewMapper;
+
+    @Test
+    public void getMutationCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        var mutationsCounts = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(),
+            false,
+            List.of("mutation_count"),
+            Collections.emptyList()
+        );
+
+        assertEquals(6, mutationsCounts.size());
+        assertEquals(1, findClinicaDataCount(mutationsCounts, "11"));
+        assertEquals(1, findClinicaDataCount(mutationsCounts, "6"));
+        assertEquals(2, findClinicaDataCount(mutationsCounts, "4"));
+        assertEquals(4, findClinicaDataCount(mutationsCounts, "2"));
+        assertEquals(2, findClinicaDataCount(mutationsCounts, "1"));
+        // 1 empty string + 1 'NAN' + 11 samples with no data
+        assertEquals(13, findClinicaDataCount(mutationsCounts, "NA"));
+    }
+
+    @Test
+    public void getCenterCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        var categoricalClinicalDataCounts = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(),
+            false,
+            List.of("center"),
+            Collections.emptyList()
+        );
+
+        assertEquals(7, categoricalClinicalDataCounts.size());
+        assertEquals(3, findClinicaDataCount(categoricalClinicalDataCounts, "msk"));
+        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "dfci"));
+        assertEquals(2, findClinicaDataCount(categoricalClinicalDataCounts, "chop"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "mda"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ohsu"));
+        assertEquals(1, findClinicaDataCount(categoricalClinicalDataCounts, "ucsf"));
+        // 1 empty string + 1 'NA' + 11 samples with no data
+        assertEquals(13, findClinicaDataCount(categoricalClinicalDataCounts, "NA"));
+    }
+
+    @Test
+    public void getMutationAndCenterCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        var combinedClinicalDataCounts = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(),
+            false,
+            List.of("mutation_count", "center"),
+            Collections.emptyList()
+        );
+
+        assertEquals(13, combinedClinicalDataCounts.size());
+    }
+
+    @Test
+    public void getAgeCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        var ageCounts = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(),
+            false,
+            List.of("age"),
+            Collections.emptyList()
+        );
+
+        assertAgeCounts(ageCounts);
+
+        // 1 empty string + 1 'NAN' + 1 'N/A' + 1 patient without data
+        assertEquals(4, findClinicaDataCount(ageCounts, "NA"));
+    }
+
+    @Test
+    public void getAgeCountsForMultipleStudies() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB, STUDY_ACC_TCGA));
+
+        var ageCounts = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter.getBuilder().build(),
+            false,
+            List.of("age"),
+            Collections.emptyList()
+        );
+
+        // everything should be exactly the same as single study (STUDY_GENIE_PUB) filter
+        // except NA counts
+        assertAgeCounts(ageCounts);
+
+        // TODO this fails because of a known issue 
+        //  (https://github.com/cBioPortal/rfc80-team/issues/39)
+        // 1 empty string + 1 'NAN' + 1 'N/A' + 1 GENIE_PUB patient without data + 4 ACC_TCGA data without data
+        // assertEquals(8, findClinicaDataCount(ageCounts, "NA"));
+    }
+
+    private void assertAgeCounts(List<ClinicalDataCount> ageCounts) {
+        assertEquals(14, ageCounts.size());
+
+        assertEquals(3, findClinicaDataCount(ageCounts, "<18"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "18"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "22"));
+        assertEquals(2, findClinicaDataCount(ageCounts, "42"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "66"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "66"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "68"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "77"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "78"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "79"));
+        assertEquals(2, findClinicaDataCount(ageCounts, "80"));
+        assertEquals(2, findClinicaDataCount(ageCounts, "82"));
+        assertEquals(1, findClinicaDataCount(ageCounts, "89"));
+        assertEquals(2, findClinicaDataCount(ageCounts, ">89"));
+    }
+
+    @Test
+    public void getMutationCountsFilteredByAge() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        // filter patients with age between 20 and 70
+        // (there are 5 patients within this range, which are 307..311)
+        ClinicalDataFilter filter = buildClinicalDataFilter("age", 20, 70);
+        studyViewFilter.setClinicalDataFilters(List.of(filter));
+
+        var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter
+                .getBuilder()
+                .setPatientNumericalClinicalDataFilters(List.of(filter))
+                .build(),
+            true,
+            List.of("mutation_count"),
+            Collections.emptyList()
+        );
+
+        assertEquals(3, mutationCountsFiltered.size());
+        assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "2"));
+        assertEquals(2, findClinicaDataCount(mutationCountsFiltered, "1"));
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "NA"));
+    }
+
+    @Test
+    public void getMutationCountsFilteredByAgeWithSpecialValues() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        // filter patients with age less than 20
+        // (there are 4 patients within this range, which are 301,302,303, and 306)
+        ClinicalDataFilter filter = buildClinicalDataFilter("age", null, 20);
+        studyViewFilter.setClinicalDataFilters(List.of(filter));
+
+        var mutationCountsFiltered = studyViewMapper.getClinicalDataCounts(
+            studyViewFilter,
+            CategorizedClinicalDataCountFilter
+                .getBuilder()
+                .setPatientNumericalClinicalDataFilters(List.of(filter))
+                .build(),
+            true,
+            List.of("mutation_count"),
+            Collections.emptyList()
+        );
+
+        // TODO commented out tests below are failing due to a known issue 
+        //  (https://github.com/cBioPortal/rfc80-team/issues/32)
+        // assertEquals(4, mutationCountsFiltered.size());
+        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "11")); // patient 301
+        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "6")); // patient 302
+        // assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "4")); // patient 303
+        assertEquals(1, findClinicaDataCount(mutationCountsFiltered, "2")); // patient 306
+
+        // no patients/samples with NA
+        assertEquals(0, findClinicaDataCount(mutationCountsFiltered, "NA")); 
+    }
+
+    private ClinicalDataFilter buildClinicalDataFilter(String attributeId, Integer start, Integer end) {
+        DataFilterValue value = new DataFilterValue();
+        if (start != null) {
+            value.setStart(BigDecimal.valueOf(start));
+        }
+        if (end != null) {
+            value.setEnd(BigDecimal.valueOf(end));
+        }
+
+        ClinicalDataFilter filter = new ClinicalDataFilter();
+        filter.setAttributeId(attributeId);
+        filter.setValues(List.of(value));
+
+        return filter;
+    }
+
+    private int findClinicaDataCount(List<ClinicalDataCount> counts, String attrValue) {
+        var count = counts.stream().filter(c -> c.getValue().equals(attrValue)).findAny().orElse(null);
+
+        return count == null ? 0 : count.getCount();
+    }
+}

src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java

@@ -25,7 +25,6 @@
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.junit4.SpringRunner;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -236,5 +235,4 @@ public void getSampleTreatmentCounts() {
         assertEquals(0, sampleTreatmentCounts.size());
 
     }
-
 }