[BI-3032] - Prevent .vcf file name duplication

src/main/java/org/breedinginsight/services/geno/impl/GigwaGenotypeServiceImpl.java

@@ -224,6 +224,21 @@ public ImportResponse submitGenotypeData(UUID userId, UUID programId, UUID submi
         progress.setId(upload.getImporterProgressId());
         upload.setProgress(progress);
 
+        //Query all filenames to avoid duplicate file uploads
+        String fileName = uploadedFile.getFilename();
+        List<GenotypeImportDetails> existingImports = getGenotypeImports(programId);
+        for (GenotypeImportDetails existingImport : existingImports) {
+            if (existingImport.getGenotypingFileName().equals(fileName)){
+                ImportResponse response = new ImportResponse();
+                upload.getProgress().setStatuscode((short)HttpStatus.BAD_REQUEST.getCode());
+                upload.getProgress().setMessage(String.format("Import cannot proceed. File name '%s' already exists in the database.", fileName));
+                importDAO.updateProgress(upload.getProgress());
+                response.setImportId(upload.getId());
+                response.setProgress(progress);
+                return response;
+            }
+        }
+
         String gigwaAuthToken;
         try {
             gigwaAuthToken = getAuthToken();

src/test/java/org/breedinginsight/services/geno/impl/GigwaGenotypeServiceImplIntegrationTest.java

@@ -561,6 +561,39 @@ public void testSubmitInvalidHeader() throws ApiException {
         assertEquals("Header row is not valid VCF format", response.getProgress().getMessage());
     }
 
+@Test
+    public void testSubmitSameFileName() throws ApiException, IOException {
+        UUID programId = UUID.fromString("29162e85-e739-4f19-9fd0-0c377ed59956");
+        String programKey = "TESTSUBMITDUPNAME";
+        UUID submissionId = UUID.randomUUID();
+        setupMocksForSubmitGenoData(programId, submissionId, buildSamplesFromValidVcf());
+
+        // First upload should be accepted for asynchronous processing.
+        AtomicReference<ImportResponse> importResponse = new AtomicReference<>();
+        assertTimeout(Duration.of(2, ChronoUnit.MINUTES), () -> importResponse.set(submitGenoData(programId, programKey, submissionId, "sample.vcf")), "Upload did not complete within the time period");
+
+        ImportResponse response = importResponse.get();
+        assertNotNull(response);
+        assertNotNull(response.getProgress());
+        assertEquals((short) HttpStatus.ACCEPTED.getCode(),
+                response.getProgress().getStatuscode(),
+                "Error importing geno file: " + response.getProgress().getMessage());
+
+        // The DAO is mocked: explicitly simulate the completed import before resubmitting.
+        doReturn(List.of(GenotypeImportDetails.builder()
+                .genotypingFileName("sample.vcf")
+                .build()))
+                .when(genotypeImportDAO).getGenotypeImportsByProgramId(programId);
+        AtomicReference<ImportResponse> importResponseTwo = new AtomicReference<>();
+        assertTimeout(Duration.of(2, ChronoUnit.MINUTES), () -> importResponseTwo.set(submitGenoData(programId, programKey, submissionId, "sample.vcf")), "Upload did not complete within the time period");
+
+        ImportResponse responseTwo = importResponseTwo.get();
+        assertNotNull(responseTwo);
+        assertNotNull(responseTwo.getProgress());
+        assertEquals((short) HttpStatus.BAD_REQUEST.getCode(), responseTwo.getProgress().getStatuscode());
+        assertEquals("Import cannot proceed. File name 'sample.vcf' already exists in the database.", responseTwo.getProgress().getMessage());
+    }
+
     @Test
     public void testSubmitMissingSubmissionSamples() throws ApiException {
         UUID programId = UUID.fromString("29162e85-e739-4f19-9fd0-0c377ed59956");