Merge branch 'develop' into 11188-version-difference-summary

doc/release-notes/11230-deleteFiles api call.md

@@ -0,0 +1 @@
+A new /api/datasets/{id}/deleteFiles call has beed added to the API, allowing delete of multiple file from the latest version of a dataset in one operation.

doc/sphinx-guides/source/api/native-api.rst

@@ -3574,6 +3574,39 @@ To update the blocks that are linked, send an array with those blocks.
 
 To remove all links to blocks, send an empty array.
 
+Delete Files from a Dataset
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Delete files from a dataset. This API call allows you to delete multiple files from a dataset in a single operation.
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export PERSISTENT_IDENTIFIER=doi:10.5072/FK2ABCDEF
+
+  curl -H "X-Dataverse-key:$API_TOKEN" -X PUT "$SERVER_URL/api/datasets/:persistentId/deleteFiles?persistentId=$PERSISTENT_IDENTIFIER" \
+  -H "Content-Type: application/json" \
+  -d '{"fileIds": [1, 2, 3]}'
+
+The fully expanded example above (without environment variables) looks like this:
+
+.. code-block:: bash
+
+  curl -H "X-Dataverse-key:xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx" -X PUT "https://demo.dataverse.org/api/datasets/:persistentId/deleteFiles?persistentId=doi:10.5072/FK2ABCDEF" \
+  -H "Content-Type: application/json" \
+  -d '{"fileIds": [1, 2, 3]}'
+
+The ``fileIds`` in the JSON payload should be an array of file IDs that you want to delete from the dataset.
+
+You must have the appropriate permissions to delete files from the dataset.
+
+Upon success, the API will return a JSON response with a success message and the number of files deleted.
+
+The API call will report a 400 (BAD REQUEST) error if any of the files specified do not exist or are not in the latest version of the specified dataset.
+The ``fileIds`` in the JSON payload should be an array of file IDs that you want to delete from the dataset.
+
+
 Files
 -----
 

src/main/java/edu/harvard/iq/dataverse/api/Datasets.java

@@ -100,12 +100,14 @@
 
 import static edu.harvard.iq.dataverse.api.ApiConstants.*;
 import edu.harvard.iq.dataverse.engine.command.exception.IllegalCommandException;
+import edu.harvard.iq.dataverse.engine.command.exception.PermissionException;
 import edu.harvard.iq.dataverse.dataset.DatasetType;
 import edu.harvard.iq.dataverse.dataset.DatasetTypeServiceBean;
 import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
 import static jakarta.ws.rs.core.Response.Status.BAD_REQUEST;
 import static jakarta.ws.rs.core.Response.Status.NOT_FOUND;
+import static jakarta.ws.rs.core.Response.Status.FORBIDDEN;
 
 @Path("datasets")
 public class Datasets extends AbstractApiBean {
@@ -5425,4 +5427,67 @@ public Response updateDatasetTypeLinksWithMetadataBlocks(@Context ContainerReque
         }
     }
 
+    @PUT
+    @AuthRequired
+    @Path("{id}/deleteFiles")
+    @Consumes(MediaType.APPLICATION_JSON)
+    public Response deleteDatasetFiles(@Context ContainerRequestContext crc, @PathParam("id") String id,
+            JsonArray fileIds) {
+        try {
+            getRequestAuthenticatedUserOrDie(crc);
+        } catch (WrappedResponse ex) {
+            return ex.getResponse();
+        }
+        return response(req -> {
+            Dataset dataset = findDatasetOrDie(id);
+            // Convert JsonArray to List<Long>
+            List<Long> fileIdList = new ArrayList<>();
+            for (JsonValue value : fileIds) {
+                fileIdList.add(((JsonNumber) value).longValue());
+            }
+            // Find the files to be deleted
+            List<FileMetadata> filesToDelete = dataset.getOrCreateEditVersion().getFileMetadatas().stream()
+                    .filter(fileMetadata -> fileIdList.contains(fileMetadata.getDataFile().getId()))
+                    .collect(Collectors.toList());
+
+            if (filesToDelete.isEmpty()) {
+                return badRequest("No files found with the provided IDs.");
+            }
+
+            if (filesToDelete.size() != fileIds.size()) {
+                return badRequest(
+                        "Some files listed are not present in the latest dataset version and cannot be deleted.");
+            }
+            try {
+
+                UpdateDatasetVersionCommand update_cmd = new UpdateDatasetVersionCommand(dataset, req, filesToDelete);
+
+                commandEngine.submit(update_cmd);
+                for (FileMetadata fm : filesToDelete) {
+                    DataFile dataFile = fm.getDataFile();
+                    boolean deletePhysicalFile = !dataFile.isReleased();
+                    if (deletePhysicalFile) {
+                        try {
+                            fileService.finalizeFileDelete(dataFile.getId(),
+                                    fileService.getPhysicalFileToDelete(dataFile));
+                        } catch (IOException ioex) {
+                            logger.warning("Failed to delete the physical file associated with the deleted datafile id="
+                                    + dataFile.getId() + ", storage location: "
+                                    + fileService.getPhysicalFileToDelete(dataFile));
+                        }
+                    }
+                }
+            } catch (PermissionException ex) {
+                return error(FORBIDDEN, "You do not have permission to delete files ont this dataset.");
+            } catch (CommandException ex) {
+                return error(BAD_REQUEST,
+                        "File deletes failed for dataset ID " + id + " (CommandException): " + ex.getMessage());
+            } catch (EJBException ex) {
+                return error(jakarta.ws.rs.core.Response.Status.INTERNAL_SERVER_ERROR,
+                        "File deletes failed for dataset ID " + id + "(EJBException): " + ex.getMessage());
+            }
+            return ok(fileIds.size() + " files deleted successfully");
+
+        }, getRequestUser(crc));
+    }
 }

src/test/java/edu/harvard/iq/dataverse/api/DatasetsIT.java

@@ -63,6 +63,7 @@
 import static java.lang.Thread.sleep;
 import static org.hamcrest.CoreMatchers.*;
 import static org.hamcrest.Matchers.contains;
+import static org.hamcrest.Matchers.hasEntry;
 import static org.junit.jupiter.api.Assertions.*;
 
 public class DatasetsIT {
@@ -5722,4 +5723,140 @@ public void testRequireFilesToPublishDatasets() {
         publishDatasetResponse.prettyPrint();
         publishDatasetResponse.then().assertThat().statusCode(OK.getStatusCode());
     }
+
+    @Test
+    public void testDeleteFiles() {
+        Response createUser = UtilIT.createRandomUser();
+        String username = UtilIT.getUsernameFromResponse(createUser);
+        String apiToken = UtilIT.getApiTokenFromResponse(createUser);
+
+        Response createDataverseResponse = UtilIT.createRandomDataverse(apiToken);
+        String dataverseAlias = UtilIT.getAliasFromResponse(createDataverseResponse);
+
+        Response createDatasetResponse = UtilIT.createRandomDatasetViaNativeApi(dataverseAlias, apiToken);
+        Integer datasetId = UtilIT.getDatasetIdFromResponse(createDatasetResponse);
+
+        // Add files to the dataset
+        String pathToFile1 = "scripts/api/data/licenses/licenseCC0-1.0.json";
+        String pathToFile2 = "scripts/api/data/licenses/licenseCC-BY-4.0.json";
+        String pathToFile3 = "scripts/api/data/licenses/licenseCC-BY-NC-4.0.json";
+        String pathToFile4 = "scripts/api/data/licenses/licenseCC-BY-NC-ND-4.0.json";
+        String pathToFile5 = "scripts/api/data/licenses/licenseCC-BY-ND-4.0.json";
+
+        JsonObjectBuilder json = Json.createObjectBuilder();
+        json.add("description", "File 1");
+        Response addFile1Response = UtilIT.uploadFileViaNative(datasetId.toString(), pathToFile1, json.build(), apiToken);
+        Long file1Id = JsonPath.from(addFile1Response.body().asString()).getLong("data.files[0].dataFile.id");
+
+        json.add("description", "File 2");
+        Response addFile2Response = UtilIT.uploadFileViaNative(datasetId.toString(), pathToFile2, json.build(), apiToken);
+        Long file2Id = JsonPath.from(addFile2Response.body().asString()).getLong("data.files[0].dataFile.id");
+
+        json.add("description", "File 3");
+        Response addFile3Response = UtilIT.uploadFileViaNative(datasetId.toString(), pathToFile3, json.build(), apiToken);
+        Long file3Id = JsonPath.from(addFile3Response.body().asString()).getLong("data.files[0].dataFile.id");
+
+        json.add("description", "File 4");
+        Response addFile4Response = UtilIT.uploadFileViaNative(datasetId.toString(), pathToFile4, json.build(), apiToken);
+        Long file4Id = JsonPath.from(addFile4Response.body().asString()).getLong("data.files[0].dataFile.id");
+
+        json.add("description", "File 5");
+        Response addFile5Response = UtilIT.uploadFileViaNative(datasetId.toString(), pathToFile5, json.build(), apiToken);
+        Long file5Id = JsonPath.from(addFile5Response.body().asString()).getLong("data.files[0].dataFile.id");
+
+        // Delete files 1 and 2
+        JsonArrayBuilder fileIdsToDelete = Json.createArrayBuilder();
+        fileIdsToDelete.add(file1Id);
+        fileIdsToDelete.add(file2Id);
+
+        Response deleteFilesResponse = UtilIT.deleteDatasetFiles(datasetId.toString(), fileIdsToDelete.build(), apiToken);
+        deleteFilesResponse.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.message", startsWith("2"));
+
+        // Verify files were deleted
+        Response getDatasetResponse = UtilIT.nativeGet(datasetId, apiToken);
+        getDatasetResponse.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file1Id + " }.size()", equalTo(0))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file2Id + " }.size()", equalTo(0))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file3Id + " }.size()", equalTo(1))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file4Id + " }.size()", equalTo(1))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file5Id + " }.size()", equalTo(1));
+
+
+        // Test deleting after dataset publication
+        Response publishDataverseResponse = UtilIT.publishDataverseViaNativeApi(dataverseAlias, apiToken);
+        publishDataverseResponse.then().assertThat().statusCode(OK.getStatusCode());
+
+        // Publish the dataset
+        Response publishDatasetResponse = UtilIT.publishDatasetViaNativeApi(datasetId, "major", apiToken);
+        publishDatasetResponse.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Delete files 3 and 4 from the published dataset
+        fileIdsToDelete = Json.createArrayBuilder();
+        fileIdsToDelete.add(file3Id);
+        fileIdsToDelete.add(file4Id);
+
+        deleteFilesResponse = UtilIT.deleteDatasetFiles(datasetId.toString(), fileIdsToDelete.build(), apiToken);
+        deleteFilesResponse.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.message", startsWith("2"));
+
+        // Verify files were deleted
+        getDatasetResponse = UtilIT.nativeGet(datasetId, apiToken);
+        getDatasetResponse.then().assertThat()
+                .statusCode(OK.getStatusCode())
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file3Id + " }.size()", equalTo(0))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file4Id + " }.size()", equalTo(0))
+                .body("data.latestVersion.files.findAll { it.dataFile.id == " + file5Id + " }.size()", equalTo(1));
+
+        // Test error conditions
+
+        // Try to delete a non-existent file
+        fileIdsToDelete = Json.createArrayBuilder();
+        fileIdsToDelete.add(999999L);
+
+        deleteFilesResponse = UtilIT.deleteDatasetFiles(datasetId.toString(), fileIdsToDelete.build(), apiToken);
+        deleteFilesResponse.then().assertThat()
+                .statusCode(BAD_REQUEST.getStatusCode())
+                .body("message", containsString("No files"));
+
+        // Try to delete files from a non-existent dataset
+        deleteFilesResponse = UtilIT.deleteDatasetFiles("999999", fileIdsToDelete.build(), apiToken);
+        deleteFilesResponse.then().assertThat()
+                .statusCode(NOT_FOUND.getStatusCode());
+
+        // Try to delete files without proper permissions
+        // Create a second user
+        Response createSecondUser = UtilIT.createRandomUser();
+        String unauthorizedUsername = UtilIT.getUsernameFromResponse(createSecondUser);
+        String unauthorizedUserApiToken = UtilIT.getApiTokenFromResponse(createSecondUser);
+
+        //Reset to a valid file id
+        fileIdsToDelete = Json.createArrayBuilder();
+        fileIdsToDelete.add(file5Id);
+        deleteFilesResponse = UtilIT.deleteDatasetFiles(datasetId.toString(), fileIdsToDelete.build(), unauthorizedUserApiToken);
+        deleteFilesResponse.then().assertThat()
+                .statusCode(FORBIDDEN.getStatusCode());
+
+        // Make the user a superuser to destroy dataset
+        Response makeSuperUserResponse = UtilIT.setSuperuserStatus(username, true);
+        makeSuperUserResponse.then().assertThat()
+                .statusCode(OK.getStatusCode());
+
+        // Clean up
+        Response destroyDatasetResponse = UtilIT.destroyDataset(datasetId, apiToken);
+        assertEquals(200, destroyDatasetResponse.getStatusCode());
+
+        Response deleteDataverseResponse = UtilIT.deleteDataverse(dataverseAlias, apiToken);
+        assertEquals(200, deleteDataverseResponse.getStatusCode());
+
+        Response deleteUnauthorizedUserResponse = UtilIT.deleteUser(unauthorizedUsername);
+        assertEquals(200, deleteUnauthorizedUserResponse.getStatusCode());
+
+        Response deleteUserResponse = UtilIT.deleteUser(username);
+        assertEquals(200, deleteUserResponse.getStatusCode());
+    }
 }

src/test/java/edu/harvard/iq/dataverse/api/UtilIT.java

@@ -11,6 +11,7 @@
 import java.util.*;
 import java.util.logging.Logger;
 import jakarta.json.Json;
+import jakarta.json.JsonArray;
 import jakarta.json.JsonObjectBuilder;
 import jakarta.json.JsonArrayBuilder;
 import jakarta.json.JsonObject;
@@ -4577,4 +4578,13 @@ static Response deleteDataverseFeaturedItems(String dataverseAlias, String apiTo
                 .header(API_TOKEN_HTTP_HEADER, apiToken)
                 .delete("/api/dataverses/" + dataverseAlias + "/featuredItems");
     }
+
+    public static Response deleteDatasetFiles(String datasetId, JsonArray fileIds, String apiToken) {
+        String path = String.format("/api/datasets/%s/deleteFiles", datasetId);
+        return given()
+                .header(API_TOKEN_HTTP_HEADER, apiToken)
+                .contentType(ContentType.JSON)
+                .body(fileIds.toString())
+                .put(path);
+    }
 }