IQSS/8846 - Fix HTML tags popup

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

@@ -1861,7 +1861,7 @@ The API call requires a Json body that includes the embargo's end date (dateAvai
 Remove an Embargo on Files in a Dataset
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-/api/datasets/$dataset-id/files/actions/:unset-embargo can be used to remove an embargo on one or more files in a dataset. Embargoes can be removed from files that are only in a draft dataset version (and are not in any previously published version) by anyone who can edit the dataset. The same API call can be used by a superuser to remove embargos from files that have already been released as part of a previously published dataset version.
+``/api/datasets/$dataset-id/files/actions/:unset-embargo`` can be used to remove an embargo on one or more files in a dataset. Embargoes can be removed from files that are only in a draft dataset version (and are not in any previously published version) by anyone who can edit the dataset. The same API call can be used by a superuser to remove embargos from files that have already been released as part of a previously published dataset version.
 
 The API call requires a Json body that includes the list of the fileIds that the embargo should be removed from. All files listed must be in the specified dataset. For example: 
 
@@ -1873,6 +1873,61 @@ The API call requires a Json body that includes the list of the fileIds that the
   export JSON='{"fileIds":[300,301]}'
 
   curl -H "X-Dataverse-key: $API_TOKEN" -H "Content-Type:application/json" "$SERVER_URL/api/datasets/:persistentId/files/actions/:unset-embargo?persistentId=$PERSISTENT_IDENTIFIER" -d "$JSON"
+
+
+Get the Archival Status of a Dataset By Version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Archiving is an optional feature that may be configured for a Dataverse instance. When that is enabled, this API call be used to retrieve the status. Note that this requires "superuser" credentials.
+
+``GET /api/datasets/$dataset-id/$version/archivalStatus`` returns the archival status of the specified dataset version.
+
+The response is a JSON object that will contain a "status" which may be "success", "pending", or "failure" and a "message" which is archive system specific. For "success" the message should provide an identifier or link to the archival copy. For example:
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export PERSISTENT_IDENTIFIER=doi:10.5072/FK2/7U7YBV
+  export VERSION=1.0
+
+  curl -H "X-Dataverse-key: $API_TOKEN" -H "Accept:application/json" "$SERVER_URL/api/datasets/:persistentId/$VERSION/archivalStatus?persistentId=$PERSISTENT_IDENTIFIER"
+
+Set the Archival Status of a Dataset By Version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Archiving is an optional feature that may be configured for a Dataverse instance. When that is enabled, this API call be used to set the status. Note that this is intended to be used by the archival system and requires "superuser" credentials.
+
+``PUT /api/datasets/$dataset-id/$version/archivalStatus`` sets the archival status of the specified dataset version.
+
+The body is a JSON object that must contain a "status" which may be "success", "pending", or "failure" and a "message" which is archive system specific. For "success" the message should provide an identifier or link to the archival copy. For example:
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export PERSISTENT_IDENTIFIER=doi:10.5072/FK2/7U7YBV
+  export VERSION=1.0
+  export JSON='{"status":"failure","message":"Something went wrong"}'
+
+  curl -H "X-Dataverse-key: $API_TOKEN" -H "Content-Type:application/json" -X PUT "$SERVER_URL/api/datasets/:persistentId/$VERSION/archivalStatus?persistentId=$PERSISTENT_IDENTIFIER" -d "$JSON"
+
+Delete the Archival Status of a Dataset By Version
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Archiving is an optional feature that may be configured for a Dataverse instance. When that is enabled, this API call be used to delete the status. Note that this is intended to be used by the archival system and requires "superuser" credentials.
+
+``DELETE /api/datasets/$dataset-id/$version/archivalStatus`` deletes the archival status of the specified dataset version.
+
+.. code-block:: bash
+
+  export API_TOKEN=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
+  export SERVER_URL=https://demo.dataverse.org
+  export PERSISTENT_IDENTIFIER=doi:10.5072/FK2/7U7YBV
+  export VERSION=1.0
+
+  curl -H "X-Dataverse-key: $API_TOKEN" -X DELETE "$SERVER_URL/api/datasets/:persistentId/$VERSION/archivalStatus?persistentId=$PERSISTENT_IDENTIFIER"
+
 
 Files
 -----

src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java

@@ -6,11 +6,11 @@
 import edu.harvard.iq.dataverse.branding.BrandingUtil;
 import edu.harvard.iq.dataverse.dataset.DatasetUtil;
 import edu.harvard.iq.dataverse.license.License;
-import edu.harvard.iq.dataverse.util.BundleUtil;
 import edu.harvard.iq.dataverse.util.FileUtil;
 import edu.harvard.iq.dataverse.util.StringUtil;
 import edu.harvard.iq.dataverse.util.SystemConfig;
 import edu.harvard.iq.dataverse.util.DateUtil;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
 import edu.harvard.iq.dataverse.workflows.WorkflowComment;
 import java.io.Serializable;
@@ -27,6 +27,7 @@
 import javax.json.Json;
 import javax.json.JsonArray;
 import javax.json.JsonArrayBuilder;
+import javax.json.JsonObject;
 import javax.json.JsonObjectBuilder;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -94,6 +95,14 @@ public enum VersionState {
     public static final int ARCHIVE_NOTE_MAX_LENGTH = 1000;
     public static final int VERSION_NOTE_MAX_LENGTH = 1000;
 
+    //Archival copies: Status message required components
+    public static final String ARCHIVAL_STATUS = "status";
+    public static final String ARCHIVAL_STATUS_MESSAGE = "message";
+    //Archival Copies: Allowed Statuses
+    public static final String ARCHIVAL_STATUS_PENDING = "pending";
+    public static final String ARCHIVAL_STATUS_SUCCESS = "success";
+    public static final String ARCHIVAL_STATUS_FAILURE = "failure";
+
     @Id
     @GeneratedValue(strategy = GenerationType.IDENTITY)
     private Long id;
@@ -152,6 +161,11 @@ public enum VersionState {
     // removed pending further investigation (v4.13)
     private String archiveNote;
 
+    // Originally a simple string indicating the location of the archival copy. As
+    // of v5.12, repurposed to provide a more general json archival status (failure,
+    // pending, success) and message (serialized as a string). The archival copy
+    // location is now expected as the contents of the message for the status
+    // 'success'. See the /api/datasets/{id}/{version}/archivalStatus API calls for more details
     @Column(nullable=true, columnDefinition = "TEXT")
     private String archivalCopyLocation;
 
@@ -180,6 +194,8 @@ public enum VersionState {
     @Transient
     private DatasetVersionDifference dvd;
 
+    @Transient 
+    private JsonObject archivalStatus;
 
     public Long getId() {
         return this.id;
@@ -319,9 +335,39 @@ public void setArchiveNote(String note) {
     public String getArchivalCopyLocation() {
         return archivalCopyLocation;
     }
+
+    public String getArchivalCopyLocationStatus() {
+        populateArchivalStatus(false);
+
+        if(archivalStatus!=null) {
+            return archivalStatus.getString(ARCHIVAL_STATUS);
+        } 
+        return null;
+    }
+    public String getArchivalCopyLocationMessage() {
+        populateArchivalStatus(false);
+        if(archivalStatus!=null) {
+            return archivalStatus.getString(ARCHIVAL_STATUS_MESSAGE);
+        } 
+        return null;
+    }
+
+    private void populateArchivalStatus(boolean force) {
+        if(archivalStatus ==null || force) {
+            if(archivalCopyLocation!=null) {
+                try {
+            archivalStatus = JsonUtil.getJsonObject(archivalCopyLocation);
+                } catch(Exception e) {
+                    logger.warning("DatasetVersion id: " + id + "has a non-JsonObject value, parsing error: " + e.getMessage());
+                    logger.fine(archivalCopyLocation);
+                }
+            }
+        }
+    }
 
     public void setArchivalCopyLocation(String location) {
         this.archivalCopyLocation = location;
+        populateArchivalStatus(true);
     }
 
     public String getDeaccessionLink() {

src/main/java/edu/harvard/iq/dataverse/DatasetVersionServiceBean.java

@@ -1187,4 +1187,12 @@ private DatasetVersion getPreviousVersionWithUnf(DatasetVersion datasetVersion)
         return null;
     }
 
+    /**
+     * Merges the passed datasetversion to the persistence context.
+     * @param ver the DatasetVersion whose new state we want to persist.
+     * @return The managed entity representing {@code ver}.
+     */
+    public DatasetVersion merge( DatasetVersion ver ) {
+        return em.merge(ver);
+    }
 } // end class

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

@@ -87,6 +87,7 @@
 import edu.harvard.iq.dataverse.util.json.JSONLDUtil;
 import edu.harvard.iq.dataverse.util.json.JsonLDTerm;
 import edu.harvard.iq.dataverse.util.json.JsonParseException;
+import edu.harvard.iq.dataverse.util.json.JsonUtil;
 import edu.harvard.iq.dataverse.search.IndexServiceBean;
 import static edu.harvard.iq.dataverse.util.json.JsonPrinter.*;
 import static edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder.jsonObjectBuilder;
@@ -216,6 +217,9 @@ public class Datasets extends AbstractApiBean {
     @Inject
     DataverseRoleServiceBean dataverseRoleService;
 
+    @EJB
+    DatasetVersionServiceBean datasetversionService;
+
     /**
      * Used to consolidate the way we parse and handle dataset versions.
      * @param <T> 
@@ -2259,7 +2263,7 @@ public Response completeMPUpload(String partETagBody, @QueryParam("globalid") St
 				eTagList.add(new PartETag(Integer.parseInt(partNo), object.getString(partNo)));
 			}
 			for(PartETag et: eTagList) {
-				logger.info("Part: " + et.getPartNumber() + " : " + et.getETag());
+				logger.fine("Part: " + et.getPartNumber() + " : " + et.getETag());
 			}
 		} catch (JsonException je) {
 			logger.info("Unable to parse eTags from: " + partETagBody);
@@ -2524,7 +2528,7 @@ public Command<DatasetVersion> handleLatestPublished() {
         if ( dsv == null || dsv.getId() == null ) {
             throw new WrappedResponse( notFound("Dataset version " + versionNumber + " of dataset " + ds.getId() + " not found") );
         }
-        if (dsv.isReleased()) {
+        if (dsv.isReleased()&& uriInfo!=null) {
             MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, ds);
             mdcLogService.logEntry(entry);
         }
@@ -3282,4 +3286,104 @@ public Response getCurationStates() throws WrappedResponse {
         csvSB.append("\n");
         return ok(csvSB.toString(), MediaType.valueOf(FileUtil.MIME_TYPE_CSV), "datasets.status.csv");
     }
+
+    // APIs to manage archival status
+
+    @GET
+    @Produces(MediaType.APPLICATION_JSON)
+    @Path("/{id}/{version}/archivalStatus")
+    public Response getDatasetVersionArchivalStatus(@PathParam("id") String datasetId,
+            @PathParam("version") String versionNumber, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
+
+        try {
+            AuthenticatedUser au = findAuthenticatedUserOrDie();
+            if (!au.isSuperuser()) {
+                return error(Response.Status.FORBIDDEN, "Superusers only.");
+            }
+            DataverseRequest req = createDataverseRequest(au);
+            DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo,
+                    headers);
+
+            if (dsv.getArchivalCopyLocation() == null) {
+                return error(Status.NO_CONTENT, "This dataset version has not been archived");
+            } else {
+                JsonObject status = JsonUtil.getJsonObject(dsv.getArchivalCopyLocation());
+                return ok(status);
+            }
+        } catch (WrappedResponse wr) {
+            return wr.getResponse();
+        }
+    }
+
+    @PUT
+    @Consumes(MediaType.APPLICATION_JSON)
+    @Path("/{id}/{version}/archivalStatus")
+    public Response setDatasetVersionArchivalStatus(@PathParam("id") String datasetId,
+            @PathParam("version") String versionNumber, JsonObject update, @Context UriInfo uriInfo,
+            @Context HttpHeaders headers) {
+
+        logger.fine(JsonUtil.prettyPrint(update));
+        try {
+            AuthenticatedUser au = findAuthenticatedUserOrDie();
+
+            if (!au.isSuperuser()) {
+                return error(Response.Status.FORBIDDEN, "Superusers only.");
+            }
+
+            if (update.containsKey(DatasetVersion.ARCHIVAL_STATUS) && update.containsKey(DatasetVersion.ARCHIVAL_STATUS_MESSAGE)) {
+                String status = update.getString(DatasetVersion.ARCHIVAL_STATUS);
+                if (status.equals(DatasetVersion.ARCHIVAL_STATUS_PENDING) || status.equals(DatasetVersion.ARCHIVAL_STATUS_FAILURE)
+                        || status.equals(DatasetVersion.ARCHIVAL_STATUS_SUCCESS)) {
+
+                    DataverseRequest req = createDataverseRequest(au);
+                    DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId),
+                            uriInfo, headers);
+
+                    if (dsv == null) {
+                        return error(Status.NOT_FOUND, "Dataset version not found");
+                    }
+
+                    dsv.setArchivalCopyLocation(JsonUtil.prettyPrint(update));
+                    dsv = datasetversionService.merge(dsv);
+                    logger.fine("location now: " + dsv.getArchivalCopyLocation());
+                    logger.fine("status now: " + dsv.getArchivalCopyLocationStatus());
+                    logger.fine("message now: " + dsv.getArchivalCopyLocationMessage());
+
+                    return ok("Status updated");
+                }
+            }
+        } catch (WrappedResponse wr) {
+            return wr.getResponse();
+        }
+
+        return error(Status.BAD_REQUEST, "Unacceptable status format");
+    }
+
+    @DELETE
+    @Produces(MediaType.APPLICATION_JSON)
+    @Path("/{id}/{version}/archivalStatus")
+    public Response deleteDatasetVersionArchivalStatus(@PathParam("id") String datasetId,
+            @PathParam("version") String versionNumber, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
+
+        try {
+            AuthenticatedUser au = findAuthenticatedUserOrDie();
+            if (!au.isSuperuser()) {
+                return error(Response.Status.FORBIDDEN, "Superusers only.");
+            }
+
+            DataverseRequest req = createDataverseRequest(au);
+            DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo,
+                    headers);
+            if (dsv == null) {
+                return error(Status.NOT_FOUND, "Dataset version not found");
+            }
+            dsv.setArchivalCopyLocation(null);
+            dsv = datasetversionService.merge(dsv);
+
+            return ok("Status deleted");
+
+        } catch (WrappedResponse wr) {
+            return wr.getResponse();
+        }
+    }
 }

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/DuraCloudSubmitToArchiveCommand.java

@@ -23,6 +23,9 @@
 import java.util.Map;
 import java.util.logging.Logger;
 
+import javax.json.Json;
+import javax.json.JsonObjectBuilder;
+
 import org.apache.commons.codec.binary.Hex;
 import org.duracloud.client.ContentStore;
 import org.duracloud.client.ContentStoreManager;
@@ -88,6 +91,11 @@ public WorkflowStepResult performArchiveSubmission(DatasetVersion dv, ApiToken t
                         .replace('.', '-').toLowerCase() + "_v" + dv.getFriendlyVersionNumber();
 
                 ContentStore store;
+                //Set a failure status that will be updated if we succeed
+                JsonObjectBuilder statusObject = Json.createObjectBuilder();
+                statusObject.add(DatasetVersion.ARCHIVAL_STATUS, DatasetVersion.ARCHIVAL_STATUS_FAILURE);
+                statusObject.add(DatasetVersion.ARCHIVAL_STATUS_MESSAGE, "Bag not transferred");
+
                 try {
                     /*
                      * If there is a failure in creating a space, it is likely that a prior version
@@ -194,7 +202,9 @@ public void run() {
                         sb.append("/duradmin/spaces/sm/");
                         sb.append(store.getStoreId());
                         sb.append("/" + spaceName + "/" + fileName);
-                        dv.setArchivalCopyLocation(sb.toString());
+                        statusObject.add(DatasetVersion.ARCHIVAL_STATUS, DatasetVersion.ARCHIVAL_STATUS_SUCCESS);
+                        statusObject.add(DatasetVersion.ARCHIVAL_STATUS_MESSAGE, sb.toString());
+
                         logger.fine("DuraCloud Submission step complete: " + sb.toString());
                     } catch (ContentStoreException | IOException e) {
                         // TODO Auto-generated catch block
@@ -217,6 +227,9 @@ public void run() {
                 } catch (NoSuchAlgorithmException e) {
                     logger.severe("MD5 MessageDigest not available!");
                 }
+                finally {
+                    dv.setArchivalCopyLocation(statusObject.build().toString());
+                }
             } else {
                 logger.warning(
                         "DuraCloud Submision Workflow aborted: Dataset locked for finalizePublication, or because file validation failed");