Merge molecular data with the same stable id only

cBioPortal · Dec 17, 2024 · b45d066 · b45d066
1 parent 2acbb73
commit b45d066
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Showing 5 changed files with 69 additions and 81 deletions.
diff --git a/src/main/java/org/cbioportal/file/export/MafRecordFetcher.java b/src/main/java/org/cbioportal/file/export/MafRecordFetcher.java
@@ -11,6 +11,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 @Component
 public class MafRecordFetcher {
@@ -23,16 +24,19 @@ public MafRecordFetcher(MolecularProfileService molecularProfileService, Mutatio
         this.mutationService = mutationService;
     }
 
-    public Iterator<MafRecord> fetch(Map<String, Set<String>> sampleIdsByStudyId) {
-        List<String> studyIds = List.copyOf(sampleIdsByStudyId.keySet());
-        List<String> molecularProfileStableIds = this.molecularProfileService.getMolecularProfilesInStudies(studyIds, "ID").stream()
-            .map(MolecularProfile::getStableId).toList();
-        List<String> sampleIds = List.copyOf(sampleIdsByStudyId.values().stream().flatMap(Set::stream).toList());
+    public Iterator<MafRecord> fetch(Map<MolecularProfile, Set<String>> molecularProfileToSamplesMap) {
+        List<String> molecularProfileStableIds = List.copyOf(molecularProfileToSamplesMap.keySet().stream().map(MolecularProfile::getStableId).toList());
+        if (molecularProfileStableIds.size() > 1) {
+            throw new IllegalArgumentException("Merging multiple molecular profiles with different stable Id is not supported");
+        }
+        List<String> sampleIds = List.copyOf(molecularProfileToSamplesMap.values().stream().flatMap(Set::stream).toList());
         List<Integer> entrezGeneIds = List.of();
         List<Mutation> mutationList = mutationService.getMutationsInMultipleMolecularProfiles(
             molecularProfileStableIds, sampleIds, entrezGeneIds, "EXPORT", null, null, null, null);
+        Map<String, Set<String>> studyIdToSamplesMap = molecularProfileToSamplesMap.entrySet().stream()
+            .collect(Collectors.toMap(molecularProfile -> molecularProfile.getKey().getCancerStudyIdentifier(), Map.Entry::getValue));
         return mutationList.stream()
-            .filter(mutation -> sampleIdsByStudyId.get(mutation.getStudyId()).contains(mutation.getSampleId()))
+            .filter(mutation -> studyIdToSamplesMap.get(mutation.getStudyId()).contains(mutation.getSampleId()))
             .map(mutation -> new MafRecord(
                 mutation.getGene().getHugoGeneSymbol(),
                 mutation.getGene().getEntrezGeneId().toString(),

diff --git a/src/main/java/org/cbioportal/file/model/GenericProfileDatatypeMetadata.java b/src/main/java/org/cbioportal/file/model/GenericProfileDatatypeMetadata.java
@@ -2,10 +2,16 @@
 
 import java.util.Optional;
 
-public interface GenericProfileDatatypeMetadata extends GenericDatatypeMetadata {
-    String stableId();
-    Boolean showProfileInAnalysisTab();
-    String profileName();
-    String profileDescription();
-    Optional<String> genePanel();
+public record GenericProfileDatatypeMetadata(
+    String stableId,
+    String geneticAlterationType,
+    String datatype,
+    String cancerStudyIdentifier,
+    String dataFilename,
+    String profileName,
+    String profileDescription,
+    Optional<String> genePanel,
+    Boolean showProfileInAnalysisTab
+) implements GenericDatatypeMetadata {
+
 }
diff --git a/src/main/java/org/cbioportal/file/model/MutationMetadata.java b/src/main/java/org/cbioportal/file/model/MutationMetadata.java
diff --git a/src/main/java/org/cbioportal/service/impl/ExportService.java b/src/main/java/org/cbioportal/service/impl/ExportService.java
@@ -5,13 +5,11 @@
 import org.cbioportal.file.model.ClinicalAttributeData;
 import org.cbioportal.file.model.ClinicalSampleAttributesMetadata;
 import org.cbioportal.file.model.MafRecord;
-import org.cbioportal.file.model.MutationMetadata;
+import org.cbioportal.file.model.GenericProfileDatatypeMetadata;
 import org.cbioportal.model.CancerStudy;
 import org.cbioportal.model.MolecularProfile;
-import org.cbioportal.model.MolecularProfileCaseIdentifier;
 import org.cbioportal.model.Sample;
 import org.cbioportal.service.*;
-import org.cbioportal.service.exception.MolecularProfileNotFoundException;
 import org.cbioportal.service.util.SessionServiceRequestHandler;
 import org.cbioportal.web.parameter.VirtualStudy;
 import org.cbioportal.web.parameter.VirtualStudyData;
@@ -21,6 +19,7 @@
 import java.io.*;
 import java.nio.charset.StandardCharsets;
 import java.util.*;
+import java.util.AbstractMap.SimpleEntry;
 import java.util.stream.Collectors;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
@@ -79,44 +78,47 @@ public void exportStudyDataToZip(OutputStream outputStream, String studyId) thro
                 zipOutputStream.closeEntry();
             }
 
-            //TODO what happens here with virtual studies? Do we merge the data from all studies?
-            List<MolecularProfileCaseIdentifier> molecularProfileCaseIdentifiers = cancerStudyInfo.studyToSampleMap.entrySet().stream().flatMap(entry -> {
-                List<String> studyIds = List.of(entry.getKey());
-                List<String> sampleIds = List.copyOf(entry.getValue());
-                //FIXME it does not do exactly what I though it should do
-                return molecularProfileService.getMolecularProfileCaseIdentifiers(studyIds, sampleIds).stream();
-            }).toList();
-            for (MolecularProfileCaseIdentifier molecularProfileCaseIdentifier : molecularProfileCaseIdentifiers) {
-                MolecularProfile molecularProfile = null;
-                try {
-                    molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileCaseIdentifier.getMolecularProfileId());
-                    MolecularProfile.MolecularAlterationType molecularAlterationType = molecularProfile.getMolecularAlterationType();
-                    switch (molecularAlterationType) {
-                        case MUTATION_EXTENDED -> {
-                            Iterator<MafRecord> mafRecordIterator = mafRecordFetcher.fetch(cancerStudyInfo.studyToSampleMap);
-                            if (mafRecordIterator.hasNext()) {
-                                zipOutputStream.putNextEntry(new ZipEntry("meta_mutations.txt"));
-                                MutationMetadata mutationMetadata = new MutationMetadata(
-                                    studyId,
-                                    "data_mutations.txt",
-                                    molecularProfile.getName(),
-                                    molecularProfile.getDescription(),
-                                    //TODO where to get gene panel from?
-                                    Optional.empty()
-                                );
-                                new KeyValueMetadataWriter(writer).write(mutationMetadata);
-                                zipOutputStream.closeEntry();
+            Map<String, List<MolecularProfile>> molecularProfilesByStableId = this.molecularProfileService.getMolecularProfilesInStudies(cancerStudyInfo.studyToSampleMap.keySet().stream().toList(), "SUMMARY").stream().collect(Collectors.groupingBy(MolecularProfile::getStableId));
+            for (Map.Entry<String, List<MolecularProfile>> molecularProfiles: molecularProfilesByStableId.entrySet()) {
+                String stableId = molecularProfiles.getKey();
+                List<MolecularProfile> molecularProfileList = molecularProfiles.getValue();
+                Map<MolecularProfile.MolecularAlterationType, String> molecularAlterationTypeToDatatype = molecularProfileList.stream()
+                    .collect(Collectors.toMap(MolecularProfile::getMolecularAlterationType, MolecularProfile::getDatatype));
+                if (molecularAlterationTypeToDatatype.size() > 1) {
+                    throw new IllegalStateException("Molecular profiles with the same stable Id ("
+                        + stableId + ") have different molecular alteration types and datatypes:" + molecularAlterationTypeToDatatype);
+                }
+                //TODO compose Map<MolecularProfile, Set<String> sampleIds> (all molecular profiles has to have the same stable Id)
+                Map<MolecularProfile, Set<String>> molecularProfileToSampleMap = molecularProfileList.stream().collect(Collectors.toMap(molecularProfile -> molecularProfile,
+                    molecularProfile -> cancerStudyInfo.studyToSampleMap.get(molecularProfile.getCancerStudyIdentifier())));
+
+                    if ("MAF".equals(molecularAlterationTypeToDatatype.get(MolecularProfile.MolecularAlterationType.MUTATION_EXTENDED))) {
+                        Iterator<MafRecord> mafRecordIterator = mafRecordFetcher.fetch(molecularProfileToSampleMap);
+                        if (mafRecordIterator.hasNext()) {
+                            zipOutputStream.putNextEntry(new ZipEntry("meta_mutations.txt"));
+                            GenericProfileDatatypeMetadata genericProfileDatatypeMetadata = new GenericProfileDatatypeMetadata(
+                                stableId,
+                                //TODO Use mol. alteration type and datatype from the map above instead
+                                MolecularProfile.MolecularAlterationType.MUTATION_EXTENDED.toString(),
+                                "MAF",
+                                studyId,
+                                "data_mutations.txt",
+                                molecularProfileList.getFirst().getName(),
+                                molecularProfileList.getFirst().getDescription(),
+                                //TODO where to get gene panel from?
+                                Optional.empty(),
+                                //Is it true for all data types?
+                                true
+                            );
+                            new KeyValueMetadataWriter(writer).write(genericProfileDatatypeMetadata);
+                            zipOutputStream.closeEntry();
 
-                                zipOutputStream.putNextEntry(new ZipEntry("data_mutations.txt"));
-                                MafRecordWriter mafRecordWriter = new MafRecordWriter(writer);
-                                mafRecordWriter.write(mafRecordIterator);
-                                zipOutputStream.closeEntry();
-                            }
+                            zipOutputStream.putNextEntry(new ZipEntry("data_mutations.txt"));
+                            MafRecordWriter mafRecordWriter = new MafRecordWriter(writer);
+                            mafRecordWriter.write(mafRecordIterator);
+                            zipOutputStream.closeEntry();
                         }
                     }
-                } catch (MolecularProfileNotFoundException e) {
-                    throw new RuntimeException(e);
-                }
             }
         }
     }

diff --git a/src/test/java/org/cbioportal/file/export/MetadataWriterTest.java b/src/test/java/org/cbioportal/file/export/MetadataWriterTest.java
@@ -2,7 +2,7 @@
 
 import org.cbioportal.file.model.CancerStudyMetadata;
 import org.cbioportal.file.model.ClinicalSampleAttributesMetadata;
-import org.cbioportal.file.model.MutationMetadata;
+import org.cbioportal.file.model.GenericProfileDatatypeMetadata;
 import org.junit.Test;
 
 import java.io.StringWriter;
@@ -61,12 +61,16 @@ public void testClinicalSampleAttributesMetadataWriter() {
 
     @Test
     public void testMutationMetadataWriter() {
-        writer.write(new MutationMetadata(
+        writer.write(new GenericProfileDatatypeMetadata(
+            "mutations",
+            "MUTATION_EXTENDED",
+            "MAF",
             "study_id1",
             "data_file.txt",
             "profile name",
             "profile description",
-            Optional.of("gene_panel")
+            Optional.of("gene_panel"),
+            true
         ));
 
         assertEquals("""