Fix Cache for StudyViewApplier

src/main/java/org/cbioportal/web/util/StudyViewFilterApplier.java

@@ -1,30 +1,79 @@
 package org.cbioportal.web.util;
 
-import java.util.*;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.collections4.map.MultiKeyMap;
-import org.cbioportal.model.*;
+import org.cbioportal.model.Binnable;
+import org.cbioportal.model.ClinicalAttribute;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.DataBin;
+import org.cbioportal.model.DiscreteCopyNumberData;
+import org.cbioportal.model.Gene;
 import org.cbioportal.model.GeneFilter;
+import org.cbioportal.model.GeneFilterQuery;
+import org.cbioportal.model.GenePanelData;
+import org.cbioportal.model.GenericAssayDataBin;
+import org.cbioportal.model.GenomicDataBin;
+import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.MolecularProfile.MolecularAlterationType;
-import org.cbioportal.service.*;
+import org.cbioportal.model.MolecularProfileCaseIdentifier;
+import org.cbioportal.model.Sample;
+import org.cbioportal.model.SampleList;
+import org.cbioportal.service.ClinicalAttributeService;
+import org.cbioportal.service.DiscreteCopyNumberService;
+import org.cbioportal.service.GenePanelService;
+import org.cbioportal.service.GeneService;
+import org.cbioportal.service.GenericAssayService;
+import org.cbioportal.service.MolecularDataService;
+import org.cbioportal.service.MolecularProfileService;
+import org.cbioportal.service.MutationService;
+import org.cbioportal.service.SampleListService;
+import org.cbioportal.service.SampleService;
+import org.cbioportal.service.StructuralVariantService;
 import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.util.MolecularProfileUtil;
-import org.cbioportal.web.parameter.*;
-import org.cbioportal.web.util.appliers.*;
+import org.cbioportal.web.parameter.ClinicalDataFilter;
+import org.cbioportal.web.parameter.ClinicalDataType;
+import org.cbioportal.web.parameter.DataBinCountFilter;
+import org.cbioportal.web.parameter.DataBinFilter;
+import org.cbioportal.web.parameter.DataBinMethod;
+import org.cbioportal.web.parameter.DataFilter;
+import org.cbioportal.web.parameter.DiscreteCopyNumberEventType;
+import org.cbioportal.web.parameter.GeneIdType;
+import org.cbioportal.web.parameter.GenericAssayDataBinCountFilter;
+import org.cbioportal.web.parameter.GenericAssayDataBinFilter;
+import org.cbioportal.web.parameter.GenericAssayDataFilter;
+import org.cbioportal.web.parameter.GenomicDataBinCountFilter;
+import org.cbioportal.web.parameter.GenomicDataBinFilter;
+import org.cbioportal.web.parameter.GenomicDataFilter;
+import org.cbioportal.web.parameter.Projection;
+import org.cbioportal.web.parameter.SampleIdentifier;
+import org.cbioportal.web.parameter.StudyViewFilter;
+import org.cbioportal.web.util.appliers.StudyViewSubFilterApplier;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.context.ApplicationContext;
 import org.springframework.stereotype.Component;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Set;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 
 @Component
 public class StudyViewFilterApplier {
     @Autowired
     private ApplicationContext applicationContext;
 
+    private StudyViewFilterApplier instance;
+
     // This gets initialized and overwritten. We do this because Spring's unit tests
     // don't know how to autowire this, even though production Spring does. If we 
     // don't give this an initial value, we get NPEs.
@@ -67,6 +116,14 @@ public class StudyViewFilterApplier {
     @Autowired
     private MolecularProfileUtil molecularProfileUtil;
 
+
+    private StudyViewFilterApplier getInstance() {
+        if (Objects.isNull(instance)) {
+            instance = applicationContext.getBean(StudyViewFilterApplier.class);
+        }
+        return instance;
+    }
+
     Function<Sample, SampleIdentifier> sampleToSampleIdentifier = new Function<Sample, SampleIdentifier>() {
 
         public SampleIdentifier apply(Sample sample) {
@@ -78,7 +135,7 @@ public SampleIdentifier apply(Sample sample) {
     };
 
     public List<SampleIdentifier> apply(StudyViewFilter studyViewFilter) {
-        return this.cachedApply(studyViewFilter);
+        return this.getInstance().cachedApply(studyViewFilter);
     }
 
     @Cacheable(

src/test/java/org/cbioportal/web/util/StudyViewFilterApplierTest.java

@@ -1,8 +1,20 @@
 package org.cbioportal.web.util;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.cbioportal.model.*;
+import org.cbioportal.model.CNA;
+import org.cbioportal.model.ClinicalAttribute;
+import org.cbioportal.model.ClinicalData;
+import org.cbioportal.model.DiscreteCopyNumberData;
+import org.cbioportal.model.Gene;
+import org.cbioportal.model.GeneFilter;
+import org.cbioportal.model.GeneFilterQuery;
+import org.cbioportal.model.GenericAssayData;
+import org.cbioportal.model.MolecularProfile;
 import org.cbioportal.model.MolecularProfile.MolecularAlterationType;
+import org.cbioportal.model.MolecularProfileCaseIdentifier;
+import org.cbioportal.model.Mutation;
+import org.cbioportal.model.Patient;
+import org.cbioportal.model.Sample;
 import org.cbioportal.model.util.Select;
 import org.cbioportal.service.ClinicalAttributeService;
 import org.cbioportal.service.ClinicalDataService;
@@ -20,6 +32,7 @@
 import org.cbioportal.service.impl.CustomDataServiceImpl;
 import org.cbioportal.service.util.MolecularProfileUtil;
 import org.cbioportal.service.util.SessionServiceRequestHandler;
+import org.cbioportal.web.config.TestConfig;
 import org.cbioportal.web.parameter.ClinicalDataFilter;
 import org.cbioportal.web.parameter.DataFilterValue;
 import org.cbioportal.web.parameter.GeneIdType;
@@ -35,21 +48,31 @@
 import org.mockito.Mock;
 import org.mockito.MockitoAnnotations;
 import org.mockito.Spy;
-import org.mockito.junit.MockitoJUnitRunner;
+import org.springframework.context.ApplicationContext;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
 import org.springframework.util.ResourceUtils;
 
 import java.io.IOException;
 import java.math.BigDecimal;
 import java.nio.file.Files;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
 
 import static com.google.common.collect.ImmutableList.of;
-import static com.google.common.collect.Lists.newArrayList;
-import static java.util.stream.Collectors.*;
-import static org.mockito.ArgumentMatchers.*;
+import static java.util.stream.Collectors.toList;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyList;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.ArgumentMatchers.isNull;
 import static org.mockito.Mockito.when;
 
-@RunWith(MockitoJUnitRunner.Silent.class)
+@RunWith(SpringJUnit4ClassRunner.class)
+@ContextConfiguration(classes = TestConfig.class)
 public class StudyViewFilterApplierTest {
 
     public static final String STUDY_ID = "study_id";
@@ -75,6 +98,9 @@ public class StudyViewFilterApplierTest {
 
     @InjectMocks
     private StudyViewFilterApplier studyViewFilterApplier;
+
+    @Mock
+    private ApplicationContext applicationContext;
 
     @Mock
     private SampleService sampleService;
@@ -138,11 +164,12 @@ public class StudyViewFilterApplierTest {
     @Before
     public void setup() {
         MockitoAnnotations.initMocks(this);
+        when(applicationContext.getBean(StudyViewFilterApplier.class)).thenReturn(studyViewFilterApplier);
     }
 
     @Test
     public void apply() throws Exception {
-
+        
         List<String> studyIds = new ArrayList<>();
         studyIds.add(STUDY_ID);
         studyIds.add(STUDY_ID);