Add tests for categorical

src/main/java/org/cbioportal/model/GenericAssayDataCount.java

@@ -7,6 +7,13 @@ public class GenericAssayDataCount implements Serializable {
     private String value;
     private Integer count;
 
+    public GenericAssayDataCount() {}
+
+    public GenericAssayDataCount(String value, Integer count) {
+        this.value = value;
+        this.count = count;
+    }
+
     public String getValue() {
         return value;
     }

src/main/java/org/cbioportal/model/GenericAssayDataCountItem.java

@@ -7,6 +7,13 @@ public class GenericAssayDataCountItem implements Serializable {
     private String stableId;
     private List<GenericAssayDataCount> counts;
 
+    public GenericAssayDataCountItem() {}
+
+    public GenericAssayDataCountItem(String stableId, List<GenericAssayDataCount> counts) {
+        this.stableId = stableId;
+        this.counts = counts;
+    }
+
     public String getStableId() {
         return stableId;
     }

src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java

@@ -63,6 +63,7 @@ private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilte
 
         CategorizedGenericAssayDataCountFilter.Builder builder = CategorizedGenericAssayDataCountFilter.getBuilder();
 
+        // No BINARY in the database yet
         List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
             .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE"))
             .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))

src/main/java/org/cbioportal/web/parameter/GenericAssayDataFilter.java

@@ -6,6 +6,13 @@ public class GenericAssayDataFilter extends DataFilter implements Serializable {
     private String stableId;
     private String profileType;
 
+    public GenericAssayDataFilter() {}
+
+    public GenericAssayDataFilter(String stableId, String profileType) {
+        this.stableId = stableId;
+        this.profileType = profileType;
+    }
+
     public String getStableId() {
         return stableId;
     }

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

@@ -132,8 +132,8 @@ public void getSamplesFilteredByClinicalData() {
             )
         );
         var filteredSamples5 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
-        // 4 acc_tcga + 4 study_genie_pub samples with "NA" AGE data or no AGE data 
-        assertEquals(8, filteredSamples5.size());
+        // 4 acc_tcga + 7 study_genie_pub samples with "NA" AGE data or no AGE data 
+        assertEquals(11, filteredSamples5.size());
 
         // NA + UNKNOWN
         studyViewFilter.setClinicalDataFilters(
@@ -147,8 +147,8 @@ public void getSamplesFilteredByClinicalData() {
             )
         );
         var filteredSamples6 = studyViewMapper.getFilteredSamples(StudyViewFilterHelper.build(studyViewFilter, null, new ArrayList<>()));
-        // 8 NA + 1 UNKNOWN
-        assertEquals(9, filteredSamples6.size());
+        // 11 NA + 1 UNKNOWN
+        assertEquals(12, filteredSamples6.size());
     }
 
     private DataFilterValue newDataFilterValue(Double start, Double end, String value) {

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

@@ -0,0 +1,87 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.model.GenericAssayDataCount;
+import org.cbioportal.model.GenericAssayDataCountItem;
+import org.cbioportal.persistence.helper.StudyViewFilterHelper;
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
+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.util.List;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+@RunWith(SpringRunner.class)
+@Import(MyBatisConfig.class)
+@DataJpaTest
+@DirtiesContext
+@AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
+@ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
+public class GenericAssayDataCountsTest extends AbstractTestcontainers {
+
+    private static final String ACC_TCGA = "acc_tcga";
+    private static final String STUDY_GENIE_PUB = "study_genie_pub";
+
+    @Autowired
+    private StudyViewMapper studyViewMapper;
+
+    @Test
+    public void getSampleCategoricalGenericAssayDataCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(ACC_TCGA));
+
+        GenericAssayDataFilter genericAssayDataFilter = new GenericAssayDataFilter("1p_status", "armlevel_cna");
+        List<GenericAssayDataCountItem> actualCounts = studyViewMapper.getGenericAssayDataCounts(
+            StudyViewFilterHelper.build(studyViewFilter, null, null),
+            List.of(genericAssayDataFilter)
+        );
+
+        List<GenericAssayDataCountItem> expectedCounts = List.of(
+            new GenericAssayDataCountItem("1p_status", List.of(
+                new GenericAssayDataCount("Loss", 1),
+                new GenericAssayDataCount("Gain", 1),
+                new GenericAssayDataCount("Unchanged", 1),
+                new GenericAssayDataCount("NA", 1)
+            ))
+        );
+
+        assertThat(actualCounts)
+            .usingRecursiveComparison()
+            .ignoringCollectionOrder()
+            .isEqualTo(expectedCounts);
+    }
+
+    @Test
+    public void getPatientCategoricalGenericAssayDataCounts() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_GENIE_PUB));
+
+        GenericAssayDataFilter genericAssayDataFilter = new GenericAssayDataFilter("DMETS_DX_ADRENAL", "distant_mets");
+        List<GenericAssayDataCountItem> actualCounts = studyViewMapper.getGenericAssayDataCounts(
+            StudyViewFilterHelper.build(studyViewFilter, null, null),
+            List.of(genericAssayDataFilter)
+        );
+
+        List<GenericAssayDataCountItem> expectedCounts = List.of(
+            new GenericAssayDataCountItem("DMETS_DX_ADRENAL", List.of(
+                new GenericAssayDataCount("No", 9),
+                new GenericAssayDataCount("Yes", 1),
+                new GenericAssayDataCount("NA", 14)
+            ))
+        );
+
+        assertThat(actualCounts)
+            .usingRecursiveComparison()
+            .ignoringCollectionOrder()
+            .isEqualTo(expectedCounts);
+    }
+}

src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationCountsTest.java → src/test/java/org/cbioportal/persistence/mybatisclickhouse/MutationDataCountsTest.java

@@ -28,7 +28,7 @@
 @DirtiesContext
 @AutoConfigureTestDatabase(replace= AutoConfigureTestDatabase.Replace.NONE)
 @ContextConfiguration(initializers = AbstractTestcontainers.Initializer.class)
-public class MutationCountsTest extends AbstractTestcontainers {
+public class MutationDataCountsTest extends AbstractTestcontainers {
 
     private static final String STUDY_TCGA_PUB = "study_tcga_pub";
 

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

@@ -59,8 +59,8 @@ public void getMutationCounts() {
         assertEquals(2, findClinicaDataCount(mutationsCounts, "4"));
         assertEquals(4, findClinicaDataCount(mutationsCounts, "2"));
         assertEquals(2, findClinicaDataCount(mutationsCounts, "1"));
-        // 1 empty string + 1 'NAN' + 12 samples with no data
-        assertEquals(14, findClinicaDataCount(mutationsCounts, "NA"));
+        // 1 empty string + 1 'NAN' + 15 samples with no data
+        assertEquals(17, findClinicaDataCount(mutationsCounts, "NA"));
     }
 
     @Test