update file info checker

EBIvariation · Jul 15, 2024 · f2109d5 · f2109d5
1 parent e1672ae
commit f2109d5
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Showing 2 changed files with 62 additions and 28 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java b/src/main/java/uk/ac/ebi/eva/submission/service/SubmissionService.java
@@ -98,53 +98,58 @@ public Submission initiateSubmission(SubmissionAccount submissionAccount) {
     }
 
     public void checkMetadataFileInfoMatchesWithUploadedFiles(SubmissionAccount submissionAccount, String submissionId, JsonNode metadataJson) {
+        Map<String, Long> metadataFileInfo = new HashMap<>();
+        if (metadataJson.get(METADATA_FILES_TAG) != null) {
+            metadataFileInfo = StreamSupport.stream(metadataJson.get(METADATA_FILES_TAG).spliterator(), false)
+                    .collect(Collectors.toMap(
+                            dataNode -> dataNode.get(METADATA_FILE_NAME).asText(),
+                            dataNode -> dataNode.get(METADATA_FILE_SIZE).asLong()
+                    ));
+        }
+        if (metadataFileInfo.isEmpty()) {
+            throw new MetadataFileInfoMismatchException("Metadata json file does not have any file info");
+        }
+
         String directoryToList = String.format("%s/%s", submissionAccount.getId(), submissionId);
         String uploadedFilesInfo = globusDirectoryProvisioner.listSubmittedFiles(directoryToList);
         if (uploadedFilesInfo.isEmpty()) {
             throw new MetadataFileInfoMismatchException("Failed to retrieve any file info from submission directory.");
         } else {
+            Map<String, Long> globusFileInfo = new HashMap<>();
             try {
                 ObjectMapper mapper = new ObjectMapper();
                 ObjectNode globusFileInfoJson = (ObjectNode) mapper.readTree(uploadedFilesInfo);
-                Map<String, Long> globusFileInfo = new HashMap<>();
                 if (globusFileInfoJson.get(GLOBUS_FILES_TAG) != null) {
                     globusFileInfo = StreamSupport.stream(globusFileInfoJson.get(GLOBUS_FILES_TAG).spliterator(), false)
-                            .filter(dataNode -> dataNode.get(GLOBUS_FILE_NAME).asText().endsWith(".vcf") || dataNode.get(GLOBUS_FILE_NAME).asText().endsWith(".vcf.gz"))
                             .collect(Collectors.toMap(
                                     dataNode -> dataNode.get(GLOBUS_FILE_NAME).asText(),
                                     dataNode -> dataNode.get(GLOBUS_FILE_SIZE).asLong()
                             ));
                 }
+            } catch (JsonProcessingException ex) {
+                throw new MetadataFileInfoMismatchException("Error parsing fileInfo from Submission Directory");
+            }
 
-                Map<String, Long> metadataFileInfo = StreamSupport.stream(metadataJson.get(METADATA_FILES_TAG).spliterator(), false)
-                        .collect(Collectors.toMap(
-                                dataNode -> dataNode.get(METADATA_FILE_NAME).asText(),
-                                dataNode -> dataNode.get(METADATA_FILE_SIZE).asLong()
-                        ));
-
-                List<String> missingFileList = new ArrayList<>();
-                String fileSizeMismatchInfo = "";
-
-                for (Map.Entry<String, Long> fileEntry : metadataFileInfo.entrySet()) {
-                    String fileName = fileEntry.getKey();
-                    Long metadataFileSize = fileEntry.getValue();
-                    if (globusFileInfo.containsKey(fileName)) {
-                        Long fileSizeInGlobus = globusFileInfo.get(fileName);
-                        if (!metadataFileSize.equals(fileSizeInGlobus)) {
-                            fileSizeMismatchInfo += fileName + ": metadata json file size (" + metadataFileSize + ") is not equal to uploaded file size (" + fileSizeInGlobus + ")\n";
-                        }
-                    } else {
-                        missingFileList.add(fileName);
+            List<String> missingFileList = new ArrayList<>();
+            String fileSizeMismatchInfo = "";
+
+            for (Map.Entry<String, Long> fileEntry : metadataFileInfo.entrySet()) {
+                String fileName = fileEntry.getKey();
+                Long metadataFileSize = fileEntry.getValue();
+                if (globusFileInfo.containsKey(fileName)) {
+                    Long fileSizeInGlobus = globusFileInfo.get(fileName);
+                    if (!metadataFileSize.equals(fileSizeInGlobus)) {
+                        fileSizeMismatchInfo += fileName + ": metadata json file size (" + metadataFileSize + ") is not equal to uploaded file size (" + fileSizeInGlobus + ")\n";
                     }
+                } else {
+                    missingFileList.add(fileName);
                 }
+            }
 
-                if (!missingFileList.isEmpty() || !fileSizeMismatchInfo.isEmpty()) {
-                    String missingFileMsg = missingFileList.isEmpty() ? "" : "There are some files mentioned in metadata json but not uploaded. Files : " + String.join(", ", missingFileList) + "\n";
-                    String fileSizeMismatchMsg = fileSizeMismatchInfo.isEmpty() ? "" : "There are some files mentioned in metadata json whose size does not match with the files uploaded.\n" + fileSizeMismatchInfo;
-                    throw new MetadataFileInfoMismatchException(missingFileMsg + fileSizeMismatchMsg);
-                }
-            } catch (JsonProcessingException ex) {
-                throw new MetadataFileInfoMismatchException("Error parsing fileInfo from Submission Directory");
+            if (!missingFileList.isEmpty() || !fileSizeMismatchInfo.isEmpty()) {
+                String missingFileMsg = missingFileList.isEmpty() ? "" : "There are some files mentioned in metadata json but not uploaded. Files : " + String.join(", ", missingFileList) + "\n";
+                String fileSizeMismatchMsg = fileSizeMismatchInfo.isEmpty() ? "" : "There are some files mentioned in metadata json whose size does not match with the files uploaded.\n" + fileSizeMismatchInfo;
+                throw new MetadataFileInfoMismatchException(missingFileMsg + fileSizeMismatchMsg);
             }
         }
     }

diff --git a/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java b/src/test/java/uk/ac/ebi/eva/submission/integration/SubmissionWSIntegrationTest.java
@@ -345,6 +345,35 @@ public void testUploadMetadataJsonAndMarkUploaded() throws Exception {
         assertThat(submissionDetails.getMetadataJson().get("project").get("description").asText()).isEqualTo(projectDescription);
     }
 
+    @Test
+    @Transactional
+    public void testMarkSubmissionUploadNoFileInfoInMetadatajson() throws Exception {
+        String userToken = "webinUserToken";
+        SubmissionAccount submissionAccount = getWebinUserAccount();
+        String submissionId = createNewSubmissionEntry(submissionAccount);
+
+        when(webinTokenService.getWebinUserAccountFromToken(anyString())).thenReturn(submissionAccount);
+        doNothing().when(mailSender).sendEmail(anyString(), anyString(), anyString());
+        when(globusDirectoryProvisioner.listSubmittedFiles(submissionAccount.getId() + "/" + submissionId)).thenReturn("");
+
+        // create metadata json
+        ObjectMapper mapper = new ObjectMapper();
+        ObjectNode metadataRootNode = mapper.createObjectNode();
+        ArrayNode filesArrayNode = mapper.createArrayNode();
+        metadataRootNode.put("files", filesArrayNode);
+
+
+        HttpHeaders httpHeaders = new HttpHeaders();
+        httpHeaders.setBearerAuth(userToken);
+        mvc.perform(put("/v1/submission/" + submissionId + "/uploaded")
+                        .headers(httpHeaders)
+                        .content(mapper.writeValueAsString(metadataRootNode))
+                        .contentType(MediaType.APPLICATION_JSON))
+                .andExpect(status().isBadRequest())
+                .andExpect(content().string("Metadata json file does not have any file info"));
+    }
+
+
     @Test
     @Transactional
     public void testMarkSubmissionUploadErrorGettingInfoFromGlobus() throws Exception {