Merge branch 'master' into fix-10313

docs/About-Us.md

@@ -42,6 +42,7 @@ The cBioPortal for Cancer Genomics was originally developed at [Memorial Sloan K
 ## Caris Life Sciences
 * Jianjiong Gao
 * Priti Kumari
+* Karthik Kalletla
 
 ## The Hyve
 * Oleguer Plantalech
@@ -82,7 +83,6 @@ The cBioPortal for Cancer Genomics was originally developed at [Memorial Sloan K
 * Zachary Heins
 * Michael Heuer
 * Anders Jacobsen
-* Karthik Kalletla
 * Peter Kok
 * Erik Larsson
 * Dong Li

docs/deployment/customization/portal.properties-Reference.md

@@ -153,6 +153,13 @@ Different samples of a patient may have been analyzed with different gene panels
 skin.patientview.filter_genes_profiled_all_samples=
 ```
 
+### Control default settings of the VAF line chart in the genomic evolution tab of patient view
+If you want to enable log scale and sequential mode by default, set this property to `true`:
+```
+vaf.log_scale.default=true|false
+vaf.sequential_mode.default=true|false
+```
+
 ### Control unauthorized studies to be displayed on the home page
 
 By default, on an authenticated portal the home page will only show studies for which the current user is authorized. By setting the _skin.home\_page.show\_unauthorized\_studies_ property to _true_ the home page will also show unauthorized studies. The unauthorized studies will appear greyed out and cannot be selected for downstream analysis in Results View or Study View.
@@ -436,6 +443,11 @@ oncoprint.oncokb.default=true|false
 oncoprint.hotspots.default=true|false
 ```
 
+If you want to enable oncoprint heatmap clustering by default, set this property to `true`:
+```
+oncoprint.clustered.default=true|false
+```
+
 **Automatic hiding of variants of unknown significance (VUS)**
 
 By default, the selection box to hide VUS mutations is unchecked. If you want to automatically hide VUS, set this property to `true`. Default is `false`.

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

@@ -0,0 +1,35 @@
+package org.cbioportal.model;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class GenomicDataCountItem implements Serializable {
+
+    private String hugoGeneSymbol;
+    private String profileType;
+    private List<GenomicDataCount> counts;
+
+    public String getHugoGeneSymbol() {
+        return hugoGeneSymbol;
+    }
+
+    public void setHugoGeneSymbol(String hugoGeneSymbol) {
+        this.hugoGeneSymbol = hugoGeneSymbol;
+    }
+
+    public String getProfileType() {
+        return profileType;
+    }
+
+    public void setProfileType(String profileType) {
+        this.profileType = profileType;
+    }
+
+    public List<GenomicDataCount> getCounts() {
+        return counts;
+    }
+
+    public void setCounts(List<GenomicDataCount> counts) {
+        this.counts = counts;
+    }
+}

pom.xml

@@ -276,7 +276,7 @@
   </profiles>
 
   <properties>
-    <frontend.version>v5.3.16</frontend.version>
+    <frontend.version>v5.3.17</frontend.version>
     <frontend.groupId>com.github.cbioportal</frontend.groupId>
     <spring.version>5.2.20.RELEASE</spring.version>
     <spring.integration.version>5.3.0.RELEASE</spring.integration.version>

portal/src/main/webapp/config_service.jsp

@@ -37,6 +37,7 @@
             "oncoprint.custom_driver_annotation.binary.default",
             "oncoprint.oncokb.default",
             "oncoprint.hotspots.default",
+            "oncoprint.clustered.default",
             "genomenexus.url",
             "genomenexus.url.grch38",
             "google_analytics_profile_id",
@@ -146,7 +147,9 @@
             "skin.patient_view.structural_variant_table.columns.show_on_init",
             "comparison.categorical_na_values",
             "study_download_url",
-            "skin.home_page.show_reference_genome"
+            "skin.home_page.show_reference_genome",
+            "vaf.sequential_mode.default",
+            "vaf.log_scale.default"
         };
 
 

service/src/main/java/org/cbioportal/service/StudyViewService.java

@@ -1,6 +1,8 @@
 package org.cbioportal.service;
 
+import org.apache.commons.math3.util.Pair;
 import org.cbioportal.model.*;
+import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.exception.StudyNotFoundException;
 
 import java.util.List;
@@ -19,6 +21,8 @@ List<AlterationCountByGene> getStructuralVariantAlterationCountByGenes(List<Stri
     List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> studyIds, List<String> sampleIds, AlterationFilter annotationFilter)
         throws StudyNotFoundException;
 
+    List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<String> studyIds, List<String> sampleIds, List<Pair<String, String>> genomicDataFilters);
+
     List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String> sampleIds, List<String> studyIds, List<String> stableIds, List<String> profileTypes);
 
 }

service/src/main/java/org/cbioportal/service/impl/StudyViewServiceImpl.java

@@ -2,6 +2,7 @@
 
 import org.apache.commons.collections4.map.MultiKeyMap;
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.math3.util.Pair;
 import org.cbioportal.model.*;
 import org.cbioportal.model.util.Select;
 import org.cbioportal.persistence.AlterationRepository;
@@ -15,6 +16,7 @@
 import java.util.*;
 import java.util.function.Function;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 @Service
 public class StudyViewServiceImpl implements StudyViewService {
@@ -37,6 +39,12 @@ public class StudyViewServiceImpl implements StudyViewService {
     @Autowired
     private AlterationRepository alterationRepository;
 
+    @Autowired
+    private GeneService geneService;
+
+    @Autowired 
+    private MolecularDataService molecularDataService;
+
     @Override
     public List<GenomicDataCount> getGenomicDataCounts(List<String> studyIds, List<String> sampleIds) {
         List<MolecularProfileCaseIdentifier> molecularProfileSampleIdentifiers =
@@ -154,7 +162,7 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
         throws StudyNotFoundException {
         List<MolecularProfileCaseIdentifier> caseIdentifiers =
             molecularProfileService.getFirstDiscreteCNAProfileCaseIdentifiers(studyIds, sampleIds);
-        Select<CNA> cnaTypes = Select.byValues(CNA_TYPES_AMP_AND_HOMDEL);
+
         List<CopyNumberCountByGene> copyNumberCountByGenes = alterationCountService.getSampleCnaGeneCounts(
             caseIdentifiers,
             Select.all(),
@@ -186,6 +194,96 @@ public List<CopyNumberCountByGene> getCNAAlterationCountByGenes(List<String> stu
         return copyNumberCountByGenes;
     }
 
+    @Override
+    public List<GenomicDataCountItem> getCNAAlterationCountsByGeneSpecific(List<String> studyIds, 
+                                                                           List<String> sampleIds,
+                                                                           List<Pair<String, String>> genomicDataFilters) {
+
+        List<MolecularProfile> molecularProfiles = molecularProfileService.getMolecularProfilesInStudies(studyIds,
+            "SUMMARY");
+
+        Map<String, List<MolecularProfile>> molecularProfileMap = molecularProfileUtil
+            .categorizeMolecularProfilesByStableIdSuffixes(molecularProfiles);
+
+        Set<String> hugoGeneSymbols = genomicDataFilters.stream().map(Pair::getKey)
+            .collect(Collectors.toSet());
+
+        Map<String, Integer> geneSymbolIdMap = geneService
+            .fetchGenes(new ArrayList<>(hugoGeneSymbols), "HUGO_GENE_SYMBOL",
+                "SUMMARY")
+            .stream().collect(Collectors.toMap(Gene::getHugoGeneSymbol, Gene::getEntrezGeneId));
+
+        return genomicDataFilters
+            .stream()
+            .flatMap(gdFilter -> {
+                GenomicDataCountItem genomicDataCountItem = new GenomicDataCountItem();
+                String hugoGeneSymbol = gdFilter.getKey();
+                String profileType = gdFilter.getValue();
+                genomicDataCountItem.setHugoGeneSymbol(hugoGeneSymbol);
+                genomicDataCountItem.setProfileType(profileType);
+
+                List<String> stableIds = Arrays.asList(geneSymbolIdMap.get(hugoGeneSymbol).toString());
+
+                Map<String, String> studyIdToMolecularProfileIdMap = molecularProfileMap
+                    .getOrDefault(profileType, new ArrayList<MolecularProfile>()).stream()
+                    .collect(Collectors.toMap(MolecularProfile::getCancerStudyIdentifier,
+                        MolecularProfile::getStableId));
+
+                List<String> mappedSampleIds = new ArrayList<>();
+                List<String> mappedProfileIds = new ArrayList<>();
+
+                for (int i = 0; i < sampleIds.size(); i++) {
+                    String studyId = studyIds.get(i);
+                    if (studyIdToMolecularProfileIdMap.containsKey(studyId)) {
+                        mappedSampleIds.add(sampleIds.get(i));
+                        mappedProfileIds.add(studyIdToMolecularProfileIdMap.get(studyId));
+                    }
+                }
+
+                if (mappedSampleIds.isEmpty()) {
+                    return Stream.of();
+                }
+
+                List<GeneMolecularData> geneMolecularDataList = molecularDataService.getMolecularDataInMultipleMolecularProfiles(mappedProfileIds, mappedSampleIds,
+                        stableIds.stream().map(Integer::parseInt).collect(Collectors.toList()), "SUMMARY");
+
+                List<GenomicDataCount> genomicDataCounts = geneMolecularDataList
+                    .stream()
+                    .filter(g -> StringUtils.isNotEmpty(g.getValue()) && !g.getValue().equals("NA"))
+                    .collect(Collectors.groupingBy(GeneMolecularData::getValue))
+                    .entrySet()
+                    .stream()
+                    .map(entry -> {
+                        Integer alteration = Integer.valueOf(entry.getKey());
+                        List<GeneMolecularData> geneMolecularData = entry.getValue();
+                        int count = geneMolecularData.size();
+
+                        String label = CNA.getByCode(alteration.shortValue()).getDescription();
+
+                        GenomicDataCount genomicDataCount = new GenomicDataCount();
+                        genomicDataCount.setLabel(label);
+                        genomicDataCount.setValue(String.valueOf(alteration));
+                        genomicDataCount.setCount(count);
+
+                        return genomicDataCount;
+                    }).collect(Collectors.toList());
+
+                int totalCount = genomicDataCounts.stream().mapToInt(GenomicDataCount::getCount).sum();
+                int naCount = sampleIds.size() - totalCount;
+
+                if (naCount > 0) {
+                    GenomicDataCount genomicDataCount = new GenomicDataCount();
+                    genomicDataCount.setLabel("NA");
+                    genomicDataCount.setValue("NA");
+                    genomicDataCount.setCount(naCount);
+                    genomicDataCounts.add(genomicDataCount);
+                }
+
+                genomicDataCountItem.setCounts(genomicDataCounts);
+                return Stream.of(genomicDataCountItem);
+            }).collect(Collectors.toList());
+    };
+
     @Override
     public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String> sampleIds, List<String> studyIds,
                                                                List<String> stableIds, List<String> profileTypes) {
@@ -261,5 +359,4 @@ public List<GenericAssayDataCountItem> fetchGenericAssayDataCounts(List<String>
             })
             .collect(Collectors.toList());
     }
-
 }

service/src/test/java/org/cbioportal/service/impl/BaseServiceImplTest.java

@@ -59,5 +59,7 @@ public class BaseServiceImplTest {
     public static final String CATEGORY_VALUE_1 = "category_value1";
     public static final String CATEGORY_VALUE_2 = "category_value2";
     public static final String EMPTY_VALUE_1 = "";
-    public static final String EMPTY_VALUE_2 = "NA";    
+    public static final String EMPTY_VALUE_2 = "NA";
+    public static final String PROFILE_TYPE_1 = "profile_type1";
+    public static final String PROFILE_TYPE_2 = "profile_type2";
 }

service/src/test/java/org/cbioportal/service/impl/StudyViewServiceImplTest.java

@@ -14,10 +14,7 @@
 import org.mockito.Spy;
 import org.mockito.junit.MockitoJUnitRunner;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
 
 import static org.mockito.ArgumentMatchers.*;
 
@@ -41,6 +38,10 @@ public class StudyViewServiceImplTest extends BaseServiceImplTest {
     private SignificantCopyNumberRegionService significantCopyNumberRegionService;
     @Mock
     private GenericAssayService genericAssayService;
+    @Mock
+    private MolecularDataService molecularDataService;
+    @Mock
+    private GeneService geneService;
     private AlterationFilter alterationFilter = new AlterationFilter();
 
     @Test
@@ -255,6 +256,79 @@ public void getCNAAlterationCountByGenes() throws Exception {
         Assert.assertEquals(1, result.size());
     }
 
+    @Test
+    public void getCNAAlterationCountByGeneSpecific() throws Exception {
+
+        List<String> sampleIds = Arrays.asList(BaseServiceImplTest.SAMPLE_ID1, BaseServiceImplTest.SAMPLE_ID2, BaseServiceImplTest.SAMPLE_ID3);
+        List<String> studyIds = Collections.nCopies(3, BaseServiceImplTest.STUDY_ID);
+        List<Pair<String, String>> genomicDataFilters = new ArrayList<>();
+        Pair<String, String> genomicDataFilter1 = new Pair<>(BaseServiceImplTest.HUGO_GENE_SYMBOL_1, BaseServiceImplTest.PROFILE_TYPE_1);
+        Pair<String, String> genomicDataFilter2 = new Pair<>(BaseServiceImplTest.HUGO_GENE_SYMBOL_2, BaseServiceImplTest.PROFILE_TYPE_2);
+        genomicDataFilters.add(genomicDataFilter1);
+        genomicDataFilters.add(genomicDataFilter2);
+
+        List<MolecularProfile> molecularProfiles = new ArrayList<>();
+        MolecularProfile molecularProfile = new MolecularProfile();
+        molecularProfile.setCancerStudyIdentifier(BaseServiceImplTest.STUDY_ID);
+        molecularProfile.setStableId(BaseServiceImplTest.STUDY_ID + "_" + BaseServiceImplTest.MOLECULAR_PROFILE_ID_A);
+        molecularProfiles.add(molecularProfile);
+
+        Mockito.when(molecularProfileService.getMolecularProfilesInStudies(studyIds, "SUMMARY"))
+            .thenReturn(molecularProfiles);
+
+        Map<String, List<MolecularProfile>> molecularProfileMap = new HashMap<>();
+        molecularProfileMap.put(BaseServiceImplTest.PROFILE_TYPE_1, molecularProfiles);
+        molecularProfileMap.put(BaseServiceImplTest.PROFILE_TYPE_2, molecularProfiles);
+
+        Mockito.when(molecularProfileUtil.categorizeMolecularProfilesByStableIdSuffixes(molecularProfiles))
+            .thenReturn(molecularProfileMap);
+
+        List<Gene> genes = new ArrayList<>();
+        Gene gene1 = new Gene();
+        gene1.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_1);
+        gene1.setHugoGeneSymbol(BaseServiceImplTest.HUGO_GENE_SYMBOL_1);
+        Gene gene2 = new Gene();
+        gene2.setEntrezGeneId(BaseServiceImplTest.ENTREZ_GENE_ID_2);
+        gene2.setHugoGeneSymbol(BaseServiceImplTest.HUGO_GENE_SYMBOL_2);
+        genes.add(gene1);
+        genes.add(gene2);
+
+        Mockito.when(geneService.fetchGenes(anyList(), anyString(), anyString()))
+                .thenReturn(genes);
+
+        List<GeneMolecularData> geneMolecularData = new ArrayList<>();
+        GeneMolecularData geneMolecularData1 = new GeneMolecularData();
+        geneMolecularData1.setValue("-2");
+        GeneMolecularData geneMolecularData2 = new GeneMolecularData();
+        geneMolecularData2.setValue("-2");
+        GeneMolecularData geneMolecularData3 = new GeneMolecularData();
+        geneMolecularData3.setValue("2");
+        GeneMolecularData geneMolecularData4 = new GeneMolecularData();
+        geneMolecularData4.setValue("2");
+        geneMolecularData.add(geneMolecularData1);
+        geneMolecularData.add(geneMolecularData2);
+        geneMolecularData.add(geneMolecularData3);
+        geneMolecularData.add(geneMolecularData4);
+
+        Mockito.when(molecularDataService.getMolecularDataInMultipleMolecularProfiles(
+            anyList(),
+            anyList(),
+            anyList(),
+            anyString()))
+            .thenReturn(geneMolecularData);
+
+        List<GenomicDataCountItem> result = studyViewService.getCNAAlterationCountsByGeneSpecific(studyIds, sampleIds, genomicDataFilters);
+        Assert.assertEquals(2, result.size());
+        Assert.assertEquals(BaseServiceImplTest.HUGO_GENE_SYMBOL_1, result.get(0).getHugoGeneSymbol());
+        Assert.assertEquals(BaseServiceImplTest.PROFILE_TYPE_1, result.get(0).getProfileType());
+        Assert.assertEquals(2, result.get(0).getCounts().get(0).getCount().intValue());
+        Assert.assertEquals(2, result.get(0).getCounts().get(1).getCount().intValue());
+        Assert.assertEquals(BaseServiceImplTest.HUGO_GENE_SYMBOL_2, result.get(1).getHugoGeneSymbol());
+        Assert.assertEquals(BaseServiceImplTest.PROFILE_TYPE_2, result.get(1).getProfileType());
+        Assert.assertEquals(2, result.get(1).getCounts().get(0).getCount().intValue());
+        Assert.assertEquals(2, result.get(1).getCounts().get(1).getCount().intValue());
+    }
+
     @Test
     public void fetchGenericAssayDataCounts() throws Exception {
 

src/main/resources/portal.properties.EXAMPLE

@@ -317,6 +317,7 @@ oncoprint.oncokb.default=true
 oncoprint.hotspots.default=true
 # oncoprint.hide_vus.default=true
 # oncoprint.clinical_tracks.config_json=classpath:/oncoprint-default-tracks.json
+# oncoprint.clustered.default=true
 
 # Custom gene sets
 # querypage.setsofgenes.location=file:/<path>
@@ -436,4 +437,7 @@ persistence.cache_type=no-cache
 # Allows download links within DataSets Tab (See Portal.Properties documentation for more info)
 # study_download_url=
 
-# download_group=
+# download_group=
+
+# vaf.sequential_mode.default=false
+# vaf.log_scale.default=false