Stream study generate zip content

cBioPortal · Dec 14, 2024 · c12ff23 · c12ff23
1 parent 84cb1d4
commit c12ff23
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Showing 5 changed files with 17 additions and 16 deletions.
diff --git a/src/main/java/org/cbioportal/file/export/ClinicalAttributeDataWriter.java b/src/main/java/org/cbioportal/file/export/ClinicalAttributeDataWriter.java
@@ -41,6 +41,7 @@ public void write(ClinicalAttributeData clinicalAttributeData) {
     private void writeRow(Iterable<String> row) {
         try {
             writer.write(composeRow(row));
+            writer.flush();
         } catch (IOException e) {
             throw new RuntimeException(e);
         }
@@ -49,6 +50,7 @@ private void writeRow(Iterable<String> row) {
     private void writeCommentsRow(Iterable<String> row) {
         try {
             writer.write("#" + composeRow(row));
+            writer.flush();
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/src/main/java/org/cbioportal/file/export/KeyValueMetadataWriter.java b/src/main/java/org/cbioportal/file/export/KeyValueMetadataWriter.java
@@ -71,6 +71,7 @@ private void write(LinkedHashMap<String, String> metadata) {
         metadata.forEach((key, value) -> {
             try {
                 writer.write(composeKeyValueLine(key, value));
+                writer.flush();
             } catch (IOException e) {
                 throw new RuntimeException(e);
             }

diff --git a/src/main/java/org/cbioportal/file/export/MafRecordWriter.java b/src/main/java/org/cbioportal/file/export/MafRecordWriter.java
@@ -69,6 +69,7 @@ public void write(Iterator<MafRecord> maf) {
     private void writeRow(Iterable<String> row) {
         try {
             writer.write(composeRow(row));
+            writer.flush();
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/src/main/java/org/cbioportal/service/impl/ExportService.java b/src/main/java/org/cbioportal/service/impl/ExportService.java
@@ -12,6 +12,7 @@
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.io.StringWriter;
 import java.util.HashMap;
 import java.util.List;
@@ -39,7 +40,7 @@ public ExportService(StudyService studyService,
         this.mafRecordFetcher = mafRecordFetcher;
     }
 
-    public ByteArrayOutputStream exportStudyDataToZip(String studyId) throws IOException {
+    public void exportStudyDataToZip(OutputStream outputStream, String studyId) throws IOException {
         List<CancerStudy> studies = studyService.fetchStudies(List.of(studyId), "DETAILED");
         Map<String, Set<String>> studyToSampleMap = new HashMap<>();
         if (studies.isEmpty()) {
@@ -50,16 +51,14 @@ public ByteArrayOutputStream exportStudyDataToZip(String studyId) throws IOExcep
            List<Sample> samples = sampleService.getAllSamplesInStudies(List.of(studyId), "ID", null, null, null, null);
            studyToSampleMap.put(studyId, samples.stream().map(Sample::getStableId).collect(Collectors.toSet()));
         }
-        ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
-        try (ZipOutputStream zipOutputStream = new ZipOutputStream(byteArrayOutputStream)) {
+        try (ZipOutputStream zipOutputStream = new ZipOutputStream(outputStream)) {
             // 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 {

diff --git a/src/main/java/org/cbioportal/web/ExportController.java b/src/main/java/org/cbioportal/web/ExportController.java
@@ -1,5 +1,6 @@
 package org.cbioportal.web;
 
+import jakarta.servlet.http.HttpServletResponse;
 import org.cbioportal.service.impl.ExportService;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.MediaType;
@@ -11,6 +12,7 @@
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipOutputStream;
 
@@ -26,17 +28,13 @@ public ExportController(ExportService exportService) {
     //TODO make it work for virtual studies as well
     //@PreAuthorize("hasPermission(#studyId, 'CancerStudyId', T(org.cbioportal.utils.security.AccessLevel).READ)")
     @GetMapping("/export/study/{studyId}.zip")
-    public ResponseEntity<byte[]> downloadStudyData(@PathVariable String studyId) throws IOException {
-        ByteArrayOutputStream byteArrayOutputStream = exportService.exportStudyDataToZip(studyId);
-
-        // Build the response
-        byte[] zipBytes = byteArrayOutputStream.toByteArray();
-        HttpHeaders headers = new HttpHeaders();
-        headers.setContentType(new MediaType("application", "zip"));
-        headers.setContentDispositionFormData("attachment", studyId + ".zip");
-
-        return ResponseEntity.ok()
-            .headers(headers)
-            .body(zipBytes);
+    public void downloadStudyData(HttpServletResponse response, @PathVariable String studyId) throws IOException {
+
+        response.setContentType(("application/zip"));
+        response.setHeader("Content-Disposition", "attachment; filename=\""+ studyId +".zip\"");
+
+        try (OutputStream out = response.getOutputStream()) {
+            exportService.exportStudyDataToZip(out, studyId);
+        }
     }
 }