add integration tests for cna-genes and sv-genes (#11221)

Co-authored-by: Bryan Lai <[email protected]>
cBioPortal · Nov 22, 2024 · 4d4b302 · 4d4b302
1 parent c039cad
commit 4d4b302
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Showing 4 changed files with 137 additions and 2 deletions.
diff --git a/...esources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml b/...esources/org/cbioportal/persistence/mybatisclickhouse/StudyViewAlterationFilterMapper.xml
@@ -29,8 +29,9 @@
         <choose>
             <when test="alterationFilterHelper.getCnaTypeList.hasNone()">NULL</when>
             <when test="!alterationFilterHelper.getCnaTypeList.hasAll()">
-                cna_event.ALTERATION IN
-                <foreach item="type" collection="cnaTypes" open="("
+                AND
+                genomic_event_derived.cna_alteration IN
+                <foreach item="type" collection="alterationFilterHelper.getCnaTypeList()" open="("
                          separator="," close=")">
                     #{type}
                 </foreach>

diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/CNAGenesTest.java
@@ -0,0 +1,76 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.model.AlterationFilter;
+import org.cbioportal.model.CNA;
+import org.cbioportal.persistence.helper.AlterationFilterHelper;
+import org.cbioportal.persistence.helper.StudyViewFilterHelper;
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+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.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+
+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 CNAGenesTest extends AbstractTestcontainers {
+
+    private static final String STUDY_TCGA_PUB = "study_tcga_pub";
+
+    @Autowired
+    private StudyViewMapper studyViewMapper;
+
+    @Test
+    public void getCnaGenes() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+        var alterationCountByGenes = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
+            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
+        assertEquals(3, alterationCountByGenes.size());
+
+        // Test cna count for akt1
+        var testAKT1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "AKT1"))
+            .mapToInt(c -> c.getTotalCount().intValue())
+            .sum();
+        assertEquals(3, testAKT1AlterationCount);
+    }
+
+    @Test
+    public void getCnaGenesWithAlterationFilter() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
+
+        // Create AlterationFilter
+        AlterationFilter alterationFilter = new AlterationFilter();
+        Map<CNA, Boolean> cnaEventTypeFilterMap = new HashMap<>();
+        cnaEventTypeFilterMap.put(CNA.HOMDEL, false);
+        cnaEventTypeFilterMap.put(CNA.AMP, true);
+        alterationFilter.setCopyNumberAlterationEventTypes(cnaEventTypeFilterMap);
+
+        var alterationCountByGenes = studyViewMapper.getCnaGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
+            AlterationFilterHelper.build(alterationFilter));
+        assertEquals(2, alterationCountByGenes.size());
+
+        // Test cna count for akt1 filtering for AMP
+        var testAKT1AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "AKT1"))
+            .mapToInt(c -> c.getTotalCount().intValue())
+            .sum();
+        assertEquals(2, testAKT1AlterationCount);
+    }
+}
diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StructuralVariantGenesTest.java
@@ -0,0 +1,56 @@
+package org.cbioportal.persistence.mybatisclickhouse;
+
+import org.cbioportal.persistence.helper.AlterationFilterHelper;
+import org.cbioportal.persistence.helper.StudyViewFilterHelper;
+import org.cbioportal.persistence.mybatisclickhouse.config.MyBatisConfig;
+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 java.util.Objects;
+
+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 StructuralVariantGenesTest extends AbstractTestcontainers {
+
+    private static final String STUDY_TCGA_PUB = "study_tcga_pub";
+    private static final String STUDY_ACC_TCGA = "acc_tcga";
+
+    @Autowired
+    private StudyViewMapper studyViewMapper;
+
+    @Test
+    public void getStructuralVariantGenes() {
+        StudyViewFilter studyViewFilter = new StudyViewFilter();
+        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB, STUDY_ACC_TCGA));
+        var alterationCountByGenes = studyViewMapper.getStructuralVariantGenes(StudyViewFilterHelper.build(studyViewFilter, null, null),
+            AlterationFilterHelper.build(studyViewFilter.getAlterationFilter()));
+        assertEquals(8, alterationCountByGenes.size());
+
+        // Test sv count for eml4 which is in one study
+        var testeml4AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "eml4"))
+            .mapToInt(c -> c.getTotalCount().intValue())
+            .sum();
+        assertEquals(1, testeml4AlterationCount);
+
+        // Test sv count for ncoa4 which is in both studies
+        var testncoa4AlterationCount = alterationCountByGenes.stream().filter(a -> Objects.equals(a.getHugoGeneSymbol(), "ncoa4"))
+            .mapToInt(c -> c.getTotalCount().intValue())
+            .sum();
+        assertEquals(3, testncoa4AlterationCount);
+    }
+}
diff --git a/src/test/resources/clickhouse_data.sql b/src/test/resources/clickhouse_data.sql
@@ -230,6 +230,7 @@ insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,3,1
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,4,null);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,6,2);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,6,1);
+insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (1,7,null);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,2,1);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,2,2);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (2,3,1);
@@ -275,6 +276,7 @@ insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,4,
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (13,6,null);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (14,2,null);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (14,4,null);
+insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (15,13,null);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (301,16,3);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (301,17,3);
 insert into sample_profile (sample_id,genetic_profile_id,panel_id) values (302,16,3);