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heathduttonalisman
heathdutton
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alisman
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Fix 500 error when genomicDataFilters is empty (#11206)
When genomicDataFilters is null or empty, return an empty list instead of throwing IndexOutOfBoundsException.
1 parent 6c28892 commit 54774f4

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‎src/main/java/org/cbioportal/application/rest/vcolumnstore/ColumnarStoreStudyViewController.java‎

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@@ -12,6 +12,7 @@
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import jakarta.validation.Valid;
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import java.math.BigDecimal;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
@@ -424,6 +425,13 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchGenomicDataCounts(
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throws StudyNotFoundException {
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List<GenomicDataFilter> genomicDataFilters = genomicDataCountFilter.getGenomicDataFilters();
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StudyViewFilter studyViewFilter = genomicDataCountFilter.getStudyViewFilter();
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// If genomicDataFilters is null or empty, return an empty result list
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// This prevents IndexOutOfBoundsException in the MyBatis mapper
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if (genomicDataFilters == null || genomicDataFilters.isEmpty()) {
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return ResponseEntity.ok(Collections.emptyList());
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}
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// when there is only one filter, it means study view is doing a single chart filter operation
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// remove filter from studyViewFilter to return all data counts
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// the reason we do this is to make sure after chart get filtered, user can still see unselected
@@ -499,6 +507,13 @@ public ResponseEntity<List<GenomicDataCountItem>> fetchMutationDataCounts(
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GenomicDataCountFilter genomicDataCountFilter) {
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List<GenomicDataFilter> genomicDataFilters = genomicDataCountFilter.getGenomicDataFilters();
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StudyViewFilter studyViewFilter = genomicDataCountFilter.getStudyViewFilter();
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// If genomicDataFilters is null or empty, return an empty result list
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// This prevents IndexOutOfBoundsException in the MyBatis mapper
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if (genomicDataFilters == null || genomicDataFilters.isEmpty()) {
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return ResponseEntity.ok(Collections.emptyList());
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}
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// when there is only one filter, it means study view is doing a single chart filter operation
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// remove filter from studyViewFilter to return all data counts
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// the reason we do this is to make sure after chart get filtered, user can still see unselected

‎src/test/java/org/cbioportal/application/rest/vcolumnstore/ColumnarStoreStudyViewControllerTest.java‎

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package org.cbioportal.application.rest.vcolumnstore;
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import static org.mockito.Mockito.never;
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import static org.mockito.Mockito.verify;
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import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf;
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import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
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import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.content;
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import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.util.Arrays;
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import java.util.Collections;
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import org.cbioportal.domain.studyview.StudyViewService;
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import org.cbioportal.legacy.web.parameter.GenomicDataCountFilter;
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import org.cbioportal.legacy.web.parameter.StudyViewFilter;
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import org.junit.Test;
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import org.junit.runner.RunWith;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
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import org.springframework.boot.test.context.SpringBootTest;
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import org.springframework.boot.test.mock.mockito.MockBean;
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import org.springframework.http.MediaType;
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import org.springframework.security.test.context.support.WithMockUser;
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import org.springframework.test.context.junit4.SpringRunner;
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import org.springframework.test.web.servlet.MockMvc;
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/**
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* Unit tests for ColumnarStoreStudyViewController.
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*
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* When genomicDataFilters is empty or null, the endpoints should return
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* an empty list instead of throwing an IndexOutOfBoundsException.
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*/
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@RunWith(SpringRunner.class)
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@SpringBootTest
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@AutoConfigureMockMvc
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public class ColumnarStoreStudyViewControllerTest {
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@Autowired
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private MockMvc mockMvc;
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@Autowired
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private ObjectMapper objectMapper;
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@MockBean
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private StudyViewService studyViewService;
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private static final String TEST_STUDY_ID = "test_study";
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@Test
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@WithMockUser
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public void fetchGenomicDataCountsWithEmptyFiltersReturnsEmptyList() throws Exception {
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GenomicDataCountFilter filter = new GenomicDataCountFilter();
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filter.setGenomicDataFilters(Collections.emptyList());
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StudyViewFilter studyViewFilter = new StudyViewFilter();
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studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));
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filter.setStudyViewFilter(studyViewFilter);
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mockMvc.perform(post("/api/column-store/genomic-data-counts/fetch")
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.with(csrf())
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.contentType(MediaType.APPLICATION_JSON)
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.content(objectMapper.writeValueAsString(filter)))
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.andExpect(status().isOk())
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.andExpect(content().json("[]"));
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// Verify that the service was never called (early return due to empty filters)
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verify(studyViewService, never()).getCNACountsByGeneSpecific(
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org.mockito.ArgumentMatchers.any(),
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org.mockito.ArgumentMatchers.anyList()
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);
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}
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@Test
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@WithMockUser
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public void fetchGenomicDataCountsWithNullFiltersReturnsEmptyList() throws Exception {
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GenomicDataCountFilter filter = new GenomicDataCountFilter();
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filter.setGenomicDataFilters(null);
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StudyViewFilter studyViewFilter = new StudyViewFilter();
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studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));
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filter.setStudyViewFilter(studyViewFilter);
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mockMvc.perform(post("/api/column-store/genomic-data-counts/fetch")
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.with(csrf())
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.contentType(MediaType.APPLICATION_JSON)
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.content(objectMapper.writeValueAsString(filter)))
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.andExpect(status().isOk())
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.andExpect(content().json("[]"));
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// Verify that the service was never called (early return due to null filters)
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verify(studyViewService, never()).getCNACountsByGeneSpecific(
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org.mockito.ArgumentMatchers.any(),
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org.mockito.ArgumentMatchers.anyList()
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);
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}
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@Test
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@WithMockUser
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public void fetchMutationDataCountsWithEmptyFiltersReturnsEmptyList() throws Exception {
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GenomicDataCountFilter filter = new GenomicDataCountFilter();
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filter.setGenomicDataFilters(Collections.emptyList());
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StudyViewFilter studyViewFilter = new StudyViewFilter();
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studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));
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filter.setStudyViewFilter(studyViewFilter);
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mockMvc.perform(post("/api/column-store/mutation-data-counts/fetch")
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.with(csrf())
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.contentType(MediaType.APPLICATION_JSON)
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.content(objectMapper.writeValueAsString(filter)))
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.andExpect(status().isOk())
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.andExpect(content().json("[]"));
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// Verify that the service was never called (early return due to empty filters)
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verify(studyViewService, never()).getMutationCountsByGeneSpecific(
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org.mockito.ArgumentMatchers.any(),
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org.mockito.ArgumentMatchers.anyList()
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);
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}
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@Test
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@WithMockUser
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public void fetchMutationDataCountsWithNullFiltersReturnsEmptyList() throws Exception {
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GenomicDataCountFilter filter = new GenomicDataCountFilter();
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filter.setGenomicDataFilters(null);
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StudyViewFilter studyViewFilter = new StudyViewFilter();
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studyViewFilter.setStudyIds(Arrays.asList(TEST_STUDY_ID));
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filter.setStudyViewFilter(studyViewFilter);
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mockMvc.perform(post("/api/column-store/mutation-data-counts/fetch")
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.with(csrf())
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.contentType(MediaType.APPLICATION_JSON)
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.content(objectMapper.writeValueAsString(filter)))
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.andExpect(status().isOk())
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.andExpect(content().json("[]"));
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// Verify that the service was never called (early return due to null filters)
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verify(studyViewService, never()).getMutationCountsByGeneSpecific(
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org.mockito.ArgumentMatchers.any(),
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org.mockito.ArgumentMatchers.anyList()
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);
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}
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}

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