Simple entry point. Fetch MAF records and write them to zip file

src/main/java/org/cbioportal/file/export/MafRecordFetcher.java

@@ -0,0 +1,78 @@
+package org.cbioportal.file.export;
+
+import org.cbioportal.file.model.MafRecord;
+import org.cbioportal.model.MolecularProfile;
+import org.cbioportal.model.Mutation;
+import org.cbioportal.service.MolecularProfileService;
+import org.cbioportal.service.MutationService;
+import org.springframework.stereotype.Component;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+@Component
+public class MafRecordFetcher {
+
+    private final MolecularProfileService molecularProfileService;
+    private final MutationService mutationService;
+
+    public MafRecordFetcher(MolecularProfileService molecularProfileService, MutationService mutationService) {
+        this.molecularProfileService = molecularProfileService;
+        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());
+        List<Integer> entrezGeneIds = List.of();
+        List<Mutation> mutationList = mutationService.getMutationsInMultipleMolecularProfiles(
+            molecularProfileStableIds, sampleIds, entrezGeneIds, "EXPORT", null, null, null, null);
+        return mutationList.stream()
+            .filter(mutation -> sampleIdsByStudyId.get(mutation.getStudyId()).contains(mutation.getSampleId()))
+            .map(mutation -> new MafRecord(
+                mutation.getGene().getHugoGeneSymbol(),
+                mutation.getGene().getEntrezGeneId().toString(),
+                mutation.getCenter(),
+                mutation.getNcbiBuild(),
+                mutation.getChr(),
+                mutation.getStartPosition(),
+                mutation.getEndPosition(),
+                "+",
+                mutation.getMutationType(),
+                mutation.getVariantType(),
+                mutation.getReferenceAllele(),
+                mutation.getTumorSeqAllele(),
+                //TODO check if this is correct
+                mutation.getTumorSeqAllele(),
+                mutation.getDbSnpRs(),
+                mutation.getDbSnpValStatus(),
+                mutation.getSampleId(),
+                mutation.getMatchedNormSampleBarcode(),
+                mutation.getMatchNormSeqAllele1(),
+                mutation.getMatchNormSeqAllele2(),
+                mutation.getTumorValidationAllele1(),
+                mutation.getTumorValidationAllele2(),
+                mutation.getMatchNormValidationAllele1(),
+                mutation.getMatchNormValidationAllele2(),
+                mutation.getVerificationStatus(),
+                mutation.getValidationStatus(),
+                mutation.getMutationStatus(),
+                mutation.getSequencingPhase(),
+                mutation.getSequenceSource(),
+                mutation.getValidationMethod(),
+                mutation.getScore() == null ? null : mutation.getScore().toString(),
+                mutation.getBamFile(),
+                mutation.getSequencer(),
+                //TODO how to calculate HgvpShort?
+                "",
+                mutation.getTumorAltCount(),
+                mutation.getTumorRefCount(),
+                mutation.getNormalAltCount(),
+                mutation.getNormalRefCount()
+            )).iterator();
+    }
+}

src/main/java/org/cbioportal/file/model/MafRecord.java

@@ -32,12 +32,12 @@ public record MafRecord(
     /**
      * Start position of event.
      */
-    Integer startPosition,
+    Long startPosition,
 
     /**
      * End position of event.
      */
-    Integer endPosition,
+    Long endPosition,
 
     /**
      * We assume that the mutation is reported for the + strand.
@@ -150,12 +150,12 @@ public record MafRecord(
     String validationMethod,
 
     /**
-     * Not used.
+     * Score
      */
     String score,
 
     /**
-     * Not used.
+     * The BAM file used to call the variant.
      */
     String bamFile,
 

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

@@ -33,6 +33,22 @@ public class Mutation extends Alteration implements Serializable {
     @JsonRawValue
     @Schema(type = "java.util.Map")
     private Object annotationJSON;
+    private String dbSnpRs;
+    private String dbSnpValStatus;
+    private String matchedNormSampleBarcode;
+    private String matchNormSeqAllele1;
+    private String matchNormSeqAllele2;
+    private String tumorValidationAllele1;
+    private String tumorValidationAllele2;
+    private String matchNormValidationAllele1;
+    private String matchNormValidationAllele2;
+    private String verificationStatus;
+    private String sequencingPhase;
+    private String sequenceSource;
+    private String validationMethod;
+    private BigDecimal score;
+    private String bamFile;
+    private String sequencer;
 
     public String getCenter() {
         return center;
@@ -213,4 +229,131 @@ public void setAnnotationJSON(String annotationJSON) {
         this.annotationJSON = annotationJSON;
     }
 
+    public String getDbSnpRs() {
+        return dbSnpRs;
+    }
+
+    public void setDbSnpRs(String dbSnpRs) {
+        this.dbSnpRs = dbSnpRs;
+    }
+
+    public String getDbSnpValStatus() {
+        return dbSnpValStatus;
+    }
+
+    public void setDbSnpValStatus(String dbSnpValStatus) {
+        this.dbSnpValStatus = dbSnpValStatus;
+    }
+
+    public String getMatchedNormSampleBarcode() {
+        return matchedNormSampleBarcode;
+    }
+
+    public void setMatchedNormSampleBarcode(String matchedNormSampleBarcode) {
+        this.matchedNormSampleBarcode = matchedNormSampleBarcode;
+    }
+
+    public String getMatchNormSeqAllele1() {
+        return matchNormSeqAllele1;
+    }
+
+    public void setMatchNormSeqAllele1(String matchNormSeqAllele1) {
+        this.matchNormSeqAllele1 = matchNormSeqAllele1;
+    }
+
+    public String getMatchNormSeqAllele2() {
+        return matchNormSeqAllele2;
+    }
+
+    public void setMatchNormSeqAllele2(String matchNormSeqAllele2) {
+        this.matchNormSeqAllele2 = matchNormSeqAllele2;
+    }
+
+    public String getTumorValidationAllele1() {
+        return tumorValidationAllele1;
+    }
+
+    public void setTumorValidationAllele1(String tumorValidationAllele1) {
+        this.tumorValidationAllele1 = tumorValidationAllele1;
+    }
+
+    public String getTumorValidationAllele2() {
+        return tumorValidationAllele2;
+    }
+
+    public void setTumorValidationAllele2(String tumorValidationAllele2) {
+        this.tumorValidationAllele2 = tumorValidationAllele2;
+    }
+
+    public String getMatchNormValidationAllele1() {
+        return matchNormValidationAllele1;
+    }
+
+    public void setMatchNormValidationAllele1(String matchNormValidationAllele1) {
+        this.matchNormValidationAllele1 = matchNormValidationAllele1;
+    }
+
+    public String getMatchNormValidationAllele2() {
+        return matchNormValidationAllele2;
+    }
+
+    public void setMatchNormValidationAllele2(String matchNormValidationAllele2) {
+        this.matchNormValidationAllele2 = matchNormValidationAllele2;
+    }
+
+    public String getVerificationStatus() {
+        return verificationStatus;
+    }
+
+    public void setVerificationStatus(String verificationStatus) {
+        this.verificationStatus = verificationStatus;
+    }
+
+    public String getSequencingPhase() {
+        return sequencingPhase;
+    }
+
+    public void setSequencingPhase(String sequencingPhase) {
+        this.sequencingPhase = sequencingPhase;
+    }
+
+    public String getSequenceSource() {
+        return sequenceSource;
+    }
+
+    public void setSequenceSource(String sequenceSource) {
+        this.sequenceSource = sequenceSource;
+    }
+
+    public String getValidationMethod() {
+        return validationMethod;
+    }
+
+    public void setValidationMethod(String validationMethod) {
+        this.validationMethod = validationMethod;
+    }
+
+    public BigDecimal getScore() {
+        return score;
+    }
+
+    public void setScore(BigDecimal score) {
+        this.score = score;
+    }
+
+    public String getBamFile() {
+        return bamFile;
+    }
+
+    public void setBamFile(String bamFile) {
+        this.bamFile = bamFile;
+    }
+
+    public String getSequencer() {
+        return sequencer;
+    }
+
+    public void setSequencer(String sequencer) {
+        this.sequencer = sequencer;
+    }
 }

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

@@ -1,76 +1,74 @@
 package org.cbioportal.service.impl;
 
-import org.apache.commons.lang3.tuple.Pair;
-import org.cbioportal.model.*;
+import org.cbioportal.file.export.MafRecordFetcher;
+import org.cbioportal.file.export.MafRecordWriter;
+import org.cbioportal.model.CancerStudy;
+import org.cbioportal.model.Sample;
 import org.cbioportal.service.*;
-import org.cbioportal.service.exception.MolecularProfileNotFoundException;
-import org.cbioportal.service.exception.PatientNotFoundException;
-import org.cbioportal.service.exception.SampleNotFoundException;
-import org.cbioportal.service.exception.StudyNotFoundException;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.cbioportal.service.util.SessionServiceRequestHandler;
+import org.cbioportal.web.parameter.VirtualStudy;
+import org.cbioportal.web.parameter.VirtualStudySamples;
 import org.springframework.stereotype.Service;
 
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.StringWriter;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 @Service
 public class ExportService {
 
-    @Autowired
-    PatientService patientService;
-
-    @Autowired
-    SampleService sampleService;
-
-    @Autowired
-    ClinicalDataService clinicalDataService;
-
-    @Autowired
-    MutationService mutationService;
-
-    @Autowired
-    MolecularProfileService molecularProfileService; 
+    private final StudyService studyService;
+    private final SessionServiceRequestHandler sessionServiceRequestHandler;
+    private final SampleService sampleService;
+    private final MafRecordFetcher mafRecordFetcher;
+
+    public ExportService(StudyService studyService,
+                         SessionServiceRequestHandler sessionServiceRequestHandler,
+                         SampleService sampleService,
+                         MafRecordFetcher mafRecordFetcher) {
+        this.studyService = studyService;
+        this.sessionServiceRequestHandler = sessionServiceRequestHandler;
+        this.sampleService = sampleService;
+        this.mafRecordFetcher = mafRecordFetcher;
+    }
 
-    public void exportData(Map<String, List<String>> samples) throws SampleNotFoundException, StudyNotFoundException, PatientNotFoundException, MolecularProfileNotFoundException {
-        if (samples.size() > 1) {
-            //virtual study
+    public ByteArrayOutputStream exportStudyDataToZip(String studyId) throws IOException {
+        List<CancerStudy> studies = studyService.fetchStudies(List.of(studyId), "DETAILED");
+        Map<String, Set<String>> studyToSampleMap = new HashMap<>();
+        if (studies.isEmpty()) {
+           VirtualStudy virtualStudy = sessionServiceRequestHandler.getVirtualStudyById(studyId);
+           studyToSampleMap.putAll(
+               virtualStudy.getData().getStudies().stream().collect(Collectors.toMap(VirtualStudySamples::getId, VirtualStudySamples::getSamples)));
+        } else {
+           List<Sample> samples = sampleService.getAllSamplesInStudies(List.of(studyId), "ID", null, null, null, null);
+           studyToSampleMap.put(studyId, samples.stream().map(Sample::getStableId).collect(Collectors.toSet()));
         }
-        for (Map.Entry<String, List<String>> studySamples: samples.entrySet()) {
-            String studyId = studySamples.getKey();
-            for (String sampleId: studySamples.getValue()) {
-                Sample sample = sampleService.getSampleInStudy(studyId, sampleId);
-                String patientStableId = sample.getPatientStableId();
-                String sampleStableId = sample.getStableId();
-                List<ClinicalData> sampleClinicalData = clinicalDataService.getAllClinicalDataOfSampleInStudy(studyId, sampleStableId, null, null, null, null, null, null);
-                for (ClinicalData sampleClinicalDatum : sampleClinicalData) {
-                   ClinicalAttribute clinicalAttribute = sampleClinicalDatum.getClinicalAttribute();
-                   sampleClinicalDatum.getAttrId();
-                   sampleClinicalDatum.getAttrValue();
-                }
-                Patient patient = patientService.getPatientInStudy(studyId, patientStableId);
-                List<ClinicalData> patientClinicalData = clinicalDataService.getAllClinicalDataOfPatientInStudy(studyId, patientStableId, null, null, null, null, null, null);
-                for (ClinicalData patientClinicalDataItem : patientClinicalData) {
-                    ClinicalAttribute clinicalAttribute = patientClinicalDataItem.getClinicalAttribute();
-                    patientClinicalDataItem.getAttrId();
-                    patientClinicalDataItem.getAttrValue();
-                }
-            }
-            List<MolecularProfileCaseIdentifier> molecularProfileCaseIdentifiers = molecularProfileService.getMolecularProfileCaseIdentifiers(List.of(studyId), studySamples.getValue());
-            for (MolecularProfileCaseIdentifier molecularProfileCaseIdentifier : molecularProfileCaseIdentifiers) {
-               MolecularProfile molecularProfile = molecularProfileService.getMolecularProfile(molecularProfileCaseIdentifier.getMolecularProfileId());
-               MolecularProfile.MolecularAlterationType molecularAlterationType = molecularProfile.getMolecularAlterationType();
-               molecularProfile.getDatatype();
-               molecularProfile.getName();
-               switch (molecularAlterationType) {
-                   case MUTATION_EXTENDED -> {
-                       List<Mutation> mutationList = mutationService.getMutationsInMultipleMolecularProfilesByGeneQueries(List.of(molecularProfileCaseIdentifier.getMolecularProfileId()), studySamples.getValue(), List.of(), "DETAILED", 10000, 1, null, null);
-                       for (Mutation mutation : mutationList) {
-                           mutation.getChr();
-                       }
-                   }
-               }
-            }
+        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+        try (ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream)) {
+            // Add files to the ZIP
+            StringWriter mafRecordsStringWriter = new StringWriter();
+            MafRecordWriter mafRecordWriter = new MafRecordWriter(mafRecordsStringWriter);
+            //TODO do not produce the file if no data has been retrieved
+            mafRecordWriter.write(mafRecordFetcher.fetch(studyToSampleMap));
+            addFileToZip(zipOutputStream, "data_mutation.txt", mafRecordsStringWriter.toString().getBytes());
         }
+        return byteArrayOutputStream;
+    }
+
+    private void addFileToZip(ZipOutputStream zipOutputStream, String fileName, byte[] fileContent) throws IOException {
+        // Create a new ZIP entry for the file
+        ZipEntry zipEntry = new ZipEntry(fileName);
+        zipOutputStream.putNextEntry(zipEntry);
+
+        // Write file content
+        zipOutputStream.write(fileContent);
+        zipOutputStream.closeEntry();
     }
 }