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Datasets.java
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Datasets.java
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package edu.harvard.iq.dataverse.api;
import edu.harvard.iq.dataverse.ControlledVocabularyValue;
import edu.harvard.iq.dataverse.DataFile;
import edu.harvard.iq.dataverse.DataFileServiceBean;
import edu.harvard.iq.dataverse.Dataset;
import edu.harvard.iq.dataverse.DatasetField;
import edu.harvard.iq.dataverse.DatasetFieldCompoundValue;
import edu.harvard.iq.dataverse.DatasetFieldServiceBean;
import edu.harvard.iq.dataverse.DatasetFieldType;
import edu.harvard.iq.dataverse.DatasetFieldValue;
import edu.harvard.iq.dataverse.DatasetLock;
import edu.harvard.iq.dataverse.DatasetServiceBean;
import edu.harvard.iq.dataverse.DatasetVersion;
import edu.harvard.iq.dataverse.Dataverse;
import edu.harvard.iq.dataverse.DataverseRequestServiceBean;
import edu.harvard.iq.dataverse.DataverseServiceBean;
import edu.harvard.iq.dataverse.DataverseSession;
import edu.harvard.iq.dataverse.DvObject;
import edu.harvard.iq.dataverse.EjbDataverseEngine;
import edu.harvard.iq.dataverse.MetadataBlock;
import edu.harvard.iq.dataverse.MetadataBlockServiceBean;
import edu.harvard.iq.dataverse.PermissionServiceBean;
import edu.harvard.iq.dataverse.RoleAssignment;
import edu.harvard.iq.dataverse.UserNotification;
import edu.harvard.iq.dataverse.UserNotificationServiceBean;
import edu.harvard.iq.dataverse.authorization.AuthenticationServiceBean;
import edu.harvard.iq.dataverse.authorization.DataverseRole;
import edu.harvard.iq.dataverse.authorization.Permission;
import edu.harvard.iq.dataverse.authorization.RoleAssignee;
import edu.harvard.iq.dataverse.authorization.users.AuthenticatedUser;
import edu.harvard.iq.dataverse.authorization.users.User;
import edu.harvard.iq.dataverse.batch.jobs.importer.ImportMode;
import edu.harvard.iq.dataverse.datacapturemodule.DataCaptureModuleUtil;
import edu.harvard.iq.dataverse.datacapturemodule.ScriptRequestResponse;
import edu.harvard.iq.dataverse.dataset.DatasetThumbnail;
import edu.harvard.iq.dataverse.dataset.DatasetUtil;
import edu.harvard.iq.dataverse.datasetutility.AddReplaceFileHelper;
import edu.harvard.iq.dataverse.datasetutility.DataFileTagException;
import edu.harvard.iq.dataverse.datasetutility.NoFilesException;
import edu.harvard.iq.dataverse.datasetutility.OptionalFileParams;
import edu.harvard.iq.dataverse.engine.command.Command;
import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
import edu.harvard.iq.dataverse.engine.command.impl.AbstractSubmitToArchiveCommand;
import edu.harvard.iq.dataverse.engine.command.impl.AddLockCommand;
import edu.harvard.iq.dataverse.engine.command.impl.AssignRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreateDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CreatePrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.CuratePublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeleteDatasetLinkingDataverseCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DeletePrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.DestroyDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetSpecificPublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetDraftDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetLatestAccessibleDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetLatestPublishedDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.GetPrivateUrlCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ImportFromFileSystemCommand;
import edu.harvard.iq.dataverse.engine.command.impl.LinkDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ListRoleAssignments;
import edu.harvard.iq.dataverse.engine.command.impl.ListVersionsCommand;
import edu.harvard.iq.dataverse.engine.command.impl.MoveDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetCommand;
import edu.harvard.iq.dataverse.engine.command.impl.PublishDatasetResult;
import edu.harvard.iq.dataverse.engine.command.impl.RemoveLockCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RequestRsyncScriptCommand;
import edu.harvard.iq.dataverse.engine.command.impl.ReturnDatasetToAuthorCommand;
import edu.harvard.iq.dataverse.engine.command.impl.SetDatasetCitationDateCommand;
import edu.harvard.iq.dataverse.engine.command.impl.SubmitDatasetForReviewCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetVersionCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetTargetURLCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDatasetThumbnailCommand;
import edu.harvard.iq.dataverse.export.DDIExportServiceBean;
import edu.harvard.iq.dataverse.export.ExportService;
import edu.harvard.iq.dataverse.ingest.IngestServiceBean;
import edu.harvard.iq.dataverse.privateurl.PrivateUrl;
import edu.harvard.iq.dataverse.S3PackageImporter;
import static edu.harvard.iq.dataverse.api.AbstractApiBean.error;
import edu.harvard.iq.dataverse.api.dto.RoleAssignmentDTO;
import edu.harvard.iq.dataverse.batch.util.LoggingUtil;
import edu.harvard.iq.dataverse.dataaccess.DataAccess;
import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
import edu.harvard.iq.dataverse.dataaccess.S3AccessIO;
import edu.harvard.iq.dataverse.engine.command.exception.CommandException;
import edu.harvard.iq.dataverse.engine.command.exception.UnforcedCommandException;
import edu.harvard.iq.dataverse.engine.command.impl.GetDatasetStorageSizeCommand;
import edu.harvard.iq.dataverse.engine.command.impl.RevokeRoleCommand;
import edu.harvard.iq.dataverse.engine.command.impl.UpdateDvObjectPIDMetadataCommand;
import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitations;
import edu.harvard.iq.dataverse.makedatacount.DatasetExternalCitationsServiceBean;
import edu.harvard.iq.dataverse.makedatacount.DatasetMetrics;
import edu.harvard.iq.dataverse.makedatacount.DatasetMetricsServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountLoggingServiceBean.MakeDataCountEntry;
import edu.harvard.iq.dataverse.makedatacount.MakeDataCountUtil;
import edu.harvard.iq.dataverse.settings.SettingsServiceBean;
import edu.harvard.iq.dataverse.util.ArchiverUtil;
import edu.harvard.iq.dataverse.util.BundleUtil;
import edu.harvard.iq.dataverse.util.EjbUtil;
import edu.harvard.iq.dataverse.util.FileUtil;
import edu.harvard.iq.dataverse.util.SystemConfig;
import edu.harvard.iq.dataverse.util.json.JsonParseException;
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;
import edu.harvard.iq.dataverse.util.json.NullSafeJsonBuilder;
import java.io.IOException;
import java.io.InputStream;
import java.io.StringReader;
import java.sql.Timestamp;
import java.text.MessageFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.ejb.EJB;
import javax.ejb.EJBException;
import javax.inject.Inject;
import javax.json.Json;
import javax.json.JsonArray;
import javax.json.JsonArrayBuilder;
import javax.json.JsonObject;
import javax.json.JsonObjectBuilder;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.GET;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
import javax.ws.rs.PathParam;
import javax.ws.rs.Produces;
import javax.ws.rs.QueryParam;
import javax.ws.rs.core.Context;
import javax.ws.rs.core.HttpHeaders;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.Response.Status;
import static javax.ws.rs.core.Response.Status.BAD_REQUEST;
import javax.ws.rs.core.UriInfo;
import org.apache.solr.client.solrj.SolrServerException;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.glassfish.jersey.media.multipart.FormDataContentDisposition;
import org.glassfish.jersey.media.multipart.FormDataParam;
@Path("datasets")
public class Datasets extends AbstractApiBean {
private static final Logger logger = Logger.getLogger(Datasets.class.getCanonicalName());
@Inject DataverseSession session;
@EJB
DatasetServiceBean datasetService;
@EJB
DataverseServiceBean dataverseService;
@EJB
UserNotificationServiceBean userNotificationService;
@EJB
PermissionServiceBean permissionService;
@EJB
AuthenticationServiceBean authenticationServiceBean;
@EJB
DDIExportServiceBean ddiExportService;
@EJB
DatasetFieldServiceBean datasetfieldService;
@EJB
MetadataBlockServiceBean metadataBlockService;
@EJB
DataFileServiceBean fileService;
@EJB
IngestServiceBean ingestService;
@EJB
EjbDataverseEngine commandEngine;
@EJB
IndexServiceBean indexService;
@EJB
S3PackageImporter s3PackageImporter;
@EJB
SettingsServiceBean settingsService;
// TODO: Move to AbstractApiBean
@EJB
DatasetMetricsServiceBean datasetMetricsSvc;
@EJB
DatasetExternalCitationsServiceBean datasetExternalCitationsService;
@Inject
MakeDataCountLoggingServiceBean mdcLogService;
@Inject
DataverseRequestServiceBean dvRequestService;
/**
* Used to consolidate the way we parse and handle dataset versions.
* @param <T>
*/
public interface DsVersionHandler<T> {
T handleLatest();
T handleDraft();
T handleSpecific( long major, long minor );
T handleLatestPublished();
}
@GET
@Path("{id}")
public Response getDataset(@PathParam("id") String id, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) {
return response( req -> {
final Dataset retrieved = execCommand(new GetDatasetCommand(req, findDatasetOrDie(id)));
final DatasetVersion latest = execCommand(new GetLatestAccessibleDatasetVersionCommand(req, retrieved));
final JsonObjectBuilder jsonbuilder = json(retrieved);
//Report MDC if this is a released version (could be draft if user has access, or user may not have access at all and is not getting metadata beyond the minimum)
if((latest != null) && latest.isReleased()) {
MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, retrieved);
mdcLogService.logEntry(entry);
}
return ok(jsonbuilder.add("latestVersion", (latest != null) ? json(latest) : null));
});
}
// TODO:
// This API call should, ideally, call findUserOrDie() and the GetDatasetCommand
// to obtain the dataset that we are trying to export - which would handle
// Auth in the process... For now, Auth isn't necessary - since export ONLY
// WORKS on published datasets, which are open to the world. -- L.A. 4.5
@GET
@Path("/export")
@Produces({"application/xml", "application/json", "application/html" })
public Response exportDataset(@QueryParam("persistentId") String persistentId, @QueryParam("exporter") String exporter, @Context UriInfo uriInfo, @Context HttpHeaders headers, @Context HttpServletResponse response) {
try {
Dataset dataset = datasetService.findByGlobalId(persistentId);
if (dataset == null) {
return error(Response.Status.NOT_FOUND, "A dataset with the persistentId " + persistentId + " could not be found.");
}
ExportService instance = ExportService.getInstance(settingsSvc);
InputStream is = instance.getExport(dataset, exporter);
String mediaType = instance.getMediaType(exporter);
//Export is only possible for released (non-draft) dataset versions so we can log without checking to see if this is a request for a draft
MakeDataCountLoggingServiceBean.MakeDataCountEntry entry = new MakeDataCountEntry(uriInfo, headers, dvRequestService, dataset);
mdcLogService.logEntry(entry);
return Response.ok()
.entity(is)
.type(mediaType).
build();
} catch (Exception wr) {
return error(Response.Status.FORBIDDEN, "Export Failed");
}
}
@DELETE
@Path("{id}")
public Response deleteDataset( @PathParam("id") String id) {
// Internally, "DeleteDatasetCommand" simply redirects to "DeleteDatasetVersionCommand"
// (and there's a comment that says "TODO: remove this command")
// do we need an exposed API call for it?
// And DeleteDatasetVersionCommand further redirects to DestroyDatasetCommand,
// if the dataset only has 1 version... In other words, the functionality
// currently provided by this API is covered between the "deleteDraftVersion" and
// "destroyDataset" API calls.
// (The logic below follows the current implementation of the underlying
// commands!)
return response( req -> {
Dataset doomed = findDatasetOrDie(id);
DatasetVersion doomedVersion = doomed.getLatestVersion();
User u = findUserOrDie();
boolean destroy = false;
if (doomed.getVersions().size() == 1) {
if (doomed.isReleased() && (!(u instanceof AuthenticatedUser) || !u.isSuperuser())) {
throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Only superusers can delete published datasets"));
}
destroy = true;
} else {
if (!doomedVersion.isDraft()) {
throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is a published dataset with multiple versions. This API can only delete the latest version if it is a DRAFT"));
}
}
// Gather the locations of the physical files that will need to be
// deleted once the destroy command execution has been finalized:
Map<Long, String> deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomedVersion, destroy);
execCommand( new DeleteDatasetCommand(req, findDatasetOrDie(id)));
// If we have gotten this far, the destroy command has succeeded,
// so we can finalize it by permanently deleting the physical files:
// (DataFileService will double-check that the datafiles no
// longer exist in the database, before attempting to delete
// the physical files)
if (!deleteStorageLocations.isEmpty()) {
fileService.finalizeFileDeletes(deleteStorageLocations);
}
return ok("Dataset " + id + " deleted");
});
}
@DELETE
@Path("{id}/destroy")
public Response destroyDataset(@PathParam("id") String id) {
return response(req -> {
// first check if dataset is released, and if so, if user is a superuser
Dataset doomed = findDatasetOrDie(id);
User u = findUserOrDie();
if (doomed.isReleased() && (!(u instanceof AuthenticatedUser) || !u.isSuperuser())) {
throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "Destroy can only be called by superusers."));
}
// Gather the locations of the physical files that will need to be
// deleted once the destroy command execution has been finalized:
Map<Long, String> deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed);
execCommand(new DestroyDatasetCommand(doomed, req));
// If we have gotten this far, the destroy command has succeeded,
// so we can finalize permanently deleting the physical files:
// (DataFileService will double-check that the datafiles no
// longer exist in the database, before attempting to delete
// the physical files)
if (!deleteStorageLocations.isEmpty()) {
fileService.finalizeFileDeletes(deleteStorageLocations);
}
return ok("Dataset " + id + " destroyed");
});
}
@DELETE
@Path("{id}/versions/{versionId}")
public Response deleteDraftVersion( @PathParam("id") String id, @PathParam("versionId") String versionId ){
if ( ! ":draft".equals(versionId) ) {
return badRequest("Only the :draft version can be deleted");
}
return response( req -> {
Dataset dataset = findDatasetOrDie(id);
DatasetVersion doomed = dataset.getLatestVersion();
if (!doomed.isDraft()) {
throw new WrappedResponse(error(Response.Status.UNAUTHORIZED, "This is NOT a DRAFT version"));
}
// Gather the locations of the physical files that will need to be
// deleted once the destroy command execution has been finalized:
Map<Long, String> deleteStorageLocations = fileService.getPhysicalFilesToDelete(doomed);
execCommand( new DeleteDatasetVersionCommand(req, dataset));
// If we have gotten this far, the delete command has succeeded -
// by either deleting the Draft version of a published dataset,
// or destroying an unpublished one.
// This means we can finalize permanently deleting the physical files:
// (DataFileService will double-check that the datafiles no
// longer exist in the database, before attempting to delete
// the physical files)
if (!deleteStorageLocations.isEmpty()) {
fileService.finalizeFileDeletes(deleteStorageLocations);
}
return ok("Draft version of dataset " + id + " deleted");
});
}
@DELETE
@Path("{datasetId}/deleteLink/{linkedDataverseId}")
public Response deleteDatasetLinkingDataverse( @PathParam("datasetId") String datasetId, @PathParam("linkedDataverseId") String linkedDataverseId) {
boolean index = true;
return response(req -> {
execCommand(new DeleteDatasetLinkingDataverseCommand(req, findDatasetOrDie(datasetId), findDatasetLinkingDataverseOrDie(datasetId, linkedDataverseId), index));
return ok("Link from Dataset " + datasetId + " to linked Dataverse " + linkedDataverseId + " deleted");
});
}
@PUT
@Path("{id}/citationdate")
public Response setCitationDate( @PathParam("id") String id, String dsfTypeName) {
return response( req -> {
if ( dsfTypeName.trim().isEmpty() ){
return badRequest("Please provide a dataset field type in the requst body.");
}
DatasetFieldType dsfType = null;
if (!":publicationDate".equals(dsfTypeName)) {
dsfType = datasetFieldSvc.findByName(dsfTypeName);
if (dsfType == null) {
return badRequest("Dataset Field Type Name " + dsfTypeName + " not found.");
}
}
execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), dsfType));
return ok("Citation Date for dataset " + id + " set to: " + (dsfType != null ? dsfType.getDisplayName() : "default"));
});
}
@DELETE
@Path("{id}/citationdate")
public Response useDefaultCitationDate( @PathParam("id") String id) {
return response( req -> {
execCommand(new SetDatasetCitationDateCommand(req, findDatasetOrDie(id), null));
return ok("Citation Date for dataset " + id + " set to default");
});
}
@GET
@Path("{id}/versions")
public Response listVersions( @PathParam("id") String id ) {
return response( req ->
ok( execCommand( new ListVersionsCommand(req, findDatasetOrDie(id)) )
.stream()
.map( d -> json(d) )
.collect(toJsonArray())));
}
@GET
@Path("{id}/versions/{versionId}")
public Response getVersion( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
return response( req -> {
DatasetVersion dsv = getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers);
return (dsv == null || dsv.getId() == null) ? notFound("Dataset version not found")
: ok(json(dsv));
});
}
@GET
@Path("{id}/versions/{versionId}/files")
public Response getVersionFiles( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
return response( req -> ok( jsonFileMetadatas(
getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers).getFileMetadatas())));
}
@GET
@Path("{id}/versions/{versionId}/metadata")
public Response getVersionMetadata( @PathParam("id") String datasetId, @PathParam("versionId") String versionId, @Context UriInfo uriInfo, @Context HttpHeaders headers) {
return response( req -> ok(
jsonByBlocks(
getDatasetVersionOrDie(req, versionId, findDatasetOrDie(datasetId), uriInfo, headers )
.getDatasetFields())));
}
@GET
@Path("{id}/versions/{versionNumber}/metadata/{block}")
public Response getVersionMetadataBlock( @PathParam("id") String datasetId,
@PathParam("versionNumber") String versionNumber,
@PathParam("block") String blockName,
@Context UriInfo uriInfo,
@Context HttpHeaders headers ) {
return response( req -> {
DatasetVersion dsv = getDatasetVersionOrDie(req, versionNumber, findDatasetOrDie(datasetId), uriInfo, headers );
Map<MetadataBlock, List<DatasetField>> fieldsByBlock = DatasetField.groupByBlock(dsv.getDatasetFields());
for ( Map.Entry<MetadataBlock, List<DatasetField>> p : fieldsByBlock.entrySet() ) {
if ( p.getKey().getName().equals(blockName) ) {
return ok(json(p.getKey(), p.getValue()));
}
}
return notFound("metadata block named " + blockName + " not found");
});
}
@GET
@Path("{id}/modifyRegistration")
public Response updateDatasetTargetURL(@PathParam("id") String id ) {
return response( req -> {
execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(id), req));
return ok("Dataset " + id + " target url updated");
});
}
@POST
@Path("/modifyRegistrationAll")
public Response updateDatasetTargetURLAll() {
return response( req -> {
datasetService.findAll().forEach( ds -> {
try {
execCommand(new UpdateDatasetTargetURLCommand(findDatasetOrDie(ds.getId().toString()), req));
} catch (WrappedResponse ex) {
Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex);
}
});
return ok("Update All Dataset target url completed");
});
}
@POST
@Path("{id}/modifyRegistrationMetadata")
public Response updateDatasetPIDMetadata(@PathParam("id") String id) {
try {
Dataset dataset = findDatasetOrDie(id);
if (!dataset.isReleased()) {
return error(Response.Status.BAD_REQUEST, BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.failure.dataset.must.be.released"));
}
} catch (WrappedResponse ex) {
Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex);
}
return response(req -> {
execCommand(new UpdateDvObjectPIDMetadataCommand(findDatasetOrDie(id), req));
List<String> args = Arrays.asList(id);
return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.single.dataset", args));
});
}
@GET
@Path("/modifyRegistrationPIDMetadataAll")
public Response updateDatasetPIDMetadataAll() {
return response( req -> {
datasetService.findAll().forEach( ds -> {
try {
execCommand(new UpdateDvObjectPIDMetadataCommand(findDatasetOrDie(ds.getId().toString()), req));
} catch (WrappedResponse ex) {
Logger.getLogger(Datasets.class.getName()).log(Level.SEVERE, null, ex);
}
});
return ok(BundleUtil.getStringFromBundle("datasets.api.updatePIDMetadata.success.for.update.all"));
});
}
@PUT
@Path("{id}/versions/{versionId}")
public Response updateDraftVersion( String jsonBody, @PathParam("id") String id, @PathParam("versionId") String versionId ){
if ( ! ":draft".equals(versionId) ) {
return error( Response.Status.BAD_REQUEST, "Only the :draft version can be updated");
}
try ( StringReader rdr = new StringReader(jsonBody) ) {
DataverseRequest req = createDataverseRequest(findUserOrDie());
Dataset ds = findDatasetOrDie(id);
JsonObject json = Json.createReader(rdr).readObject();
DatasetVersion incomingVersion = jsonParser().parseDatasetVersion(json);
// clear possibly stale fields from the incoming dataset version.
// creation and modification dates are updated by the commands.
incomingVersion.setId(null);
incomingVersion.setVersionNumber(null);
incomingVersion.setMinorVersionNumber(null);
incomingVersion.setVersionState(DatasetVersion.VersionState.DRAFT);
incomingVersion.setDataset(ds);
incomingVersion.setCreateTime(null);
incomingVersion.setLastUpdateTime(null);
if (!incomingVersion.getFileMetadatas().isEmpty()){
return error( Response.Status.BAD_REQUEST, "You may not add files via this api.");
}
boolean updateDraft = ds.getLatestVersion().isDraft();
DatasetVersion managedVersion;
if ( updateDraft ) {
final DatasetVersion editVersion = ds.getEditVersion();
editVersion.setDatasetFields(incomingVersion.getDatasetFields());
editVersion.setTermsOfUseAndAccess( incomingVersion.getTermsOfUseAndAccess() );
Dataset managedDataset = execCommand(new UpdateDatasetVersionCommand(ds, req));
managedVersion = managedDataset.getEditVersion();
} else {
managedVersion = execCommand(new CreateDatasetVersionCommand(req, ds, incomingVersion));
}
// DatasetVersion managedVersion = execCommand( updateDraft
// ? new UpdateDatasetVersionCommand(req, incomingVersion)
// : new CreateDatasetVersionCommand(req, ds, incomingVersion));
return ok( json(managedVersion) );
} catch (JsonParseException ex) {
logger.log(Level.SEVERE, "Semantic error parsing dataset version Json: " + ex.getMessage(), ex);
return error( Response.Status.BAD_REQUEST, "Error parsing dataset version: " + ex.getMessage() );
} catch (WrappedResponse ex) {
return ex.getResponse();
}
}
@PUT
@Path("{id}/deleteMetadata")
public Response deleteVersionMetadata(String jsonBody, @PathParam("id") String id) throws WrappedResponse {
DataverseRequest req = createDataverseRequest(findUserOrDie());
return processDatasetFieldDataDelete(jsonBody, id, req);
}
private Response processDatasetFieldDataDelete(String jsonBody, String id, DataverseRequest req) {
try (StringReader rdr = new StringReader(jsonBody)) {
Dataset ds = findDatasetOrDie(id);
JsonObject json = Json.createReader(rdr).readObject();
DatasetVersion dsv = ds.getEditVersion();
List<DatasetField> fields = new LinkedList<>();
DatasetField singleField = null;
JsonArray fieldsJson = json.getJsonArray("fields");
if (fieldsJson == null) {
singleField = jsonParser().parseField(json, Boolean.FALSE);
fields.add(singleField);
} else {
fields = jsonParser().parseMultipleFields(json);
}
dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
List<ControlledVocabularyValue> controlledVocabularyItemsToRemove = new ArrayList<ControlledVocabularyValue>();
List<DatasetFieldValue> datasetFieldValueItemsToRemove = new ArrayList<DatasetFieldValue>();
List<DatasetFieldCompoundValue> datasetFieldCompoundValueItemsToRemove = new ArrayList<DatasetFieldCompoundValue>();
for (DatasetField updateField : fields) {
boolean found = false;
for (DatasetField dsf : dsv.getDatasetFields()) {
if (dsf.getDatasetFieldType().equals(updateField.getDatasetFieldType())) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
if (updateField.getDatasetFieldType().isControlledVocabulary()) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
for (ControlledVocabularyValue cvv : updateField.getControlledVocabularyValues()) {
for (ControlledVocabularyValue existing : dsf.getControlledVocabularyValues()) {
if (existing.getStrValue().equals(cvv.getStrValue())) {
found = true;
controlledVocabularyItemsToRemove.add(existing);
}
}
if (!found) {
logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + cvv.getStrValue() + " not found.");
return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + cvv.getStrValue() + " not found.");
}
}
for (ControlledVocabularyValue remove : controlledVocabularyItemsToRemove) {
dsf.getControlledVocabularyValues().remove(remove);
}
} else {
if (dsf.getSingleControlledVocabularyValue().getStrValue().equals(updateField.getSingleControlledVocabularyValue().getStrValue())) {
found = true;
dsf.setSingleControlledVocabularyValue(null);
}
}
} else {
if (!updateField.getDatasetFieldType().isCompound()) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
for (DatasetFieldValue dfv : updateField.getDatasetFieldValues()) {
for (DatasetFieldValue edsfv : dsf.getDatasetFieldValues()) {
if (edsfv.getDisplayValue().equals(dfv.getDisplayValue())) {
found = true;
datasetFieldValueItemsToRemove.add(dfv);
}
}
if (!found) {
logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + dfv.getDisplayValue() + " not found.");
return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + dfv.getDisplayValue() + " not found.");
}
}
datasetFieldValueItemsToRemove.forEach((remove) -> {
dsf.getDatasetFieldValues().remove(remove);
});
} else {
if (dsf.getSingleValue().getDisplayValue().equals(updateField.getSingleValue().getDisplayValue())) {
found = true;
dsf.setSingleValue(null);
}
}
} else {
for (DatasetFieldCompoundValue dfcv : updateField.getDatasetFieldCompoundValues()) {
String deleteVal = getCompoundDisplayValue(dfcv);
for (DatasetFieldCompoundValue existing : dsf.getDatasetFieldCompoundValues()) {
String existingString = getCompoundDisplayValue(existing);
if (existingString.equals(deleteVal)) {
found = true;
datasetFieldCompoundValueItemsToRemove.add(existing);
}
}
datasetFieldCompoundValueItemsToRemove.forEach((remove) -> {
dsf.getDatasetFieldCompoundValues().remove(remove);
});
if (!found) {
logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found.");
return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + deleteVal + " not found.");
}
}
}
}
} else {
found = true;
dsf.setSingleValue(null);
dsf.setSingleControlledVocabularyValue(null);
}
break;
}
}
if (!found){
String displayValue = !updateField.getDisplayValue().isEmpty() ? updateField.getDisplayValue() : updateField.getCompoundDisplayValue();
logger.log(Level.SEVERE, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." );
return error(Response.Status.BAD_REQUEST, "Delete metadata failed: " + updateField.getDatasetFieldType().getDisplayName() + ": " + displayValue + " not found." );
}
}
boolean updateDraft = ds.getLatestVersion().isDraft();
DatasetVersion managedVersion = updateDraft
? execCommand(new UpdateDatasetVersionCommand(ds, req)).getEditVersion()
: execCommand(new CreateDatasetVersionCommand(req, ds, dsv));
return ok(json(managedVersion));
} catch (JsonParseException ex) {
logger.log(Level.SEVERE, "Semantic error parsing dataset update Json: " + ex.getMessage(), ex);
return error(Response.Status.BAD_REQUEST, "Error processing metadata delete: " + ex.getMessage());
} catch (WrappedResponse ex) {
logger.log(Level.SEVERE, "Delete metadata error: " + ex.getMessage(), ex);
return ex.getResponse();
}
}
private String getCompoundDisplayValue (DatasetFieldCompoundValue dscv){
String returnString = "";
for (DatasetField dsf : dscv.getChildDatasetFields()) {
for (String value : dsf.getValues()) {
if (!(value == null)) {
returnString += (returnString.isEmpty() ? "" : "; ") + value.trim();
}
}
}
return returnString;
}
@PUT
@Path("{id}/editMetadata")
public Response editVersionMetadata(String jsonBody, @PathParam("id") String id, @QueryParam("replace") Boolean replace) throws WrappedResponse{
Boolean replaceData = replace != null;
DataverseRequest req = createDataverseRequest(findUserOrDie());
return processDatasetUpdate(jsonBody, id, req, replaceData);
}
private Response processDatasetUpdate(String jsonBody, String id, DataverseRequest req, Boolean replaceData){
try (StringReader rdr = new StringReader(jsonBody)) {
Dataset ds = findDatasetOrDie(id);
JsonObject json = Json.createReader(rdr).readObject();
DatasetVersion dsv = ds.getEditVersion();
List<DatasetField> fields = new LinkedList<>();
DatasetField singleField = null;
JsonArray fieldsJson = json.getJsonArray("fields");
if( fieldsJson == null ){
singleField = jsonParser().parseField(json, Boolean.FALSE);
fields.add(singleField);
} else{
fields = jsonParser().parseMultipleFields(json);
}
String valdationErrors = validateDatasetFieldValues(fields);
if (!valdationErrors.isEmpty()) {
logger.log(Level.SEVERE, "Semantic error parsing dataset update Json: " + valdationErrors, valdationErrors);
return error(Response.Status.BAD_REQUEST, "Error parsing dataset update: " + valdationErrors);
}
dsv.setVersionState(DatasetVersion.VersionState.DRAFT);
//loop through the update fields
// and compare to the version fields
//if exist add/replace values
//if not add entire dsf
for (DatasetField updateField : fields) {
boolean found = false;
for (DatasetField dsf : dsv.getDatasetFields()) {
if (dsf.getDatasetFieldType().equals(updateField.getDatasetFieldType())) {
found = true;
if (dsf.isEmpty() || dsf.getDatasetFieldType().isAllowMultiples() || replaceData) {
List priorCVV = new ArrayList<>();
String cvvDisplay = "";
if (updateField.getDatasetFieldType().isControlledVocabulary()) {
cvvDisplay = dsf.getDisplayValue();
for (ControlledVocabularyValue cvvOld : dsf.getControlledVocabularyValues()) {
priorCVV.add(cvvOld);
}
}
if (replaceData) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
dsf.setDatasetFieldCompoundValues(new ArrayList<>());
dsf.setDatasetFieldValues(new ArrayList<>());
dsf.setControlledVocabularyValues(new ArrayList<>());
priorCVV.clear();
dsf.getControlledVocabularyValues().clear();
} else {
dsf.setSingleValue("");
dsf.setSingleControlledVocabularyValue(null);
}
}
if (updateField.getDatasetFieldType().isControlledVocabulary()) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
for (ControlledVocabularyValue cvv : updateField.getControlledVocabularyValues()) {
if (!cvvDisplay.contains(cvv.getStrValue())) {
priorCVV.add(cvv);
}
}
dsf.setControlledVocabularyValues(priorCVV);
} else {
dsf.setSingleControlledVocabularyValue(updateField.getSingleControlledVocabularyValue());
}
} else {
if (!updateField.getDatasetFieldType().isCompound()) {
if (dsf.getDatasetFieldType().isAllowMultiples()) {
for (DatasetFieldValue dfv : updateField.getDatasetFieldValues()) {
if (!dsf.getDisplayValue().contains(dfv.getDisplayValue())) {
dfv.setDatasetField(dsf);
dsf.getDatasetFieldValues().add(dfv);
}
}
} else {
dsf.setSingleValue(updateField.getValue());
}
} else {
for (DatasetFieldCompoundValue dfcv : updateField.getDatasetFieldCompoundValues()) {
if (!dsf.getCompoundDisplayValue().contains(updateField.getCompoundDisplayValue())) {
dfcv.setParentDatasetField(dsf);
dsf.setDatasetVersion(dsv);
dsf.getDatasetFieldCompoundValues().add(dfcv);
}
}
}
}
} else {
if (!dsf.isEmpty() && !dsf.getDatasetFieldType().isAllowMultiples() || !replaceData) {
return error(Response.Status.BAD_REQUEST, "You may not add data to a field that already has data and does not allow multiples. Use replace=true to replace existing data (" + dsf.getDatasetFieldType().getDisplayName() + ")");
}
}
break;
}
}
if (!found) {
updateField.setDatasetVersion(dsv);
dsv.getDatasetFields().add(updateField);
}
}
boolean updateDraft = ds.getLatestVersion().isDraft();
DatasetVersion managedVersion;
if (updateDraft) {
managedVersion = execCommand(new UpdateDatasetVersionCommand(ds, req)).getEditVersion();
} else {
managedVersion = execCommand(new CreateDatasetVersionCommand(req, ds, dsv));
}
return ok(json(managedVersion));
} catch (JsonParseException ex) {
logger.log(Level.SEVERE, "Semantic error parsing dataset update Json: " + ex.getMessage(), ex);
return error(Response.Status.BAD_REQUEST, "Error parsing dataset update: " + ex.getMessage());
} catch (WrappedResponse ex) {
logger.log(Level.SEVERE, "Update metdata error: " + ex.getMessage(), ex);
return ex.getResponse();
}
}
private String validateDatasetFieldValues(List<DatasetField> fields) {
StringBuilder error = new StringBuilder();
for (DatasetField dsf : fields) {
if (dsf.getDatasetFieldType().isAllowMultiples() && dsf.getControlledVocabularyValues().isEmpty()
&& dsf.getDatasetFieldCompoundValues().isEmpty() && dsf.getDatasetFieldValues().isEmpty()) {
error.append("Empty multiple value for field: ").append(dsf.getDatasetFieldType().getDisplayName()).append(" ");
} else if (!dsf.getDatasetFieldType().isAllowMultiples() && dsf.getSingleValue().getValue().isEmpty()) {
error.append("Empty value for field: ").append(dsf.getDatasetFieldType().getDisplayName()).append(" ");
}
}
if (!error.toString().isEmpty()) {
return (error.toString());
}
return "";
}
/**
* @deprecated This was shipped as a GET but should have been a POST, see https://github.com/IQSS/dataverse/issues/2431
*/
@GET
@Path("{id}/actions/:publish")
@Deprecated
public Response publishDataseUsingGetDeprecated( @PathParam("id") String id, @QueryParam("type") String type ) {
logger.info("publishDataseUsingGetDeprecated called on id " + id + ". Encourage use of POST rather than GET, which is deprecated.");
return publishDataset(id, type);
}
@POST
@Path("{id}/actions/:publish")
public Response publishDataset(@PathParam("id") String id, @QueryParam("type") String type) {
try {
if (type == null) {
return error(Response.Status.BAD_REQUEST, "Missing 'type' parameter (either 'major','minor', or 'updatecurrent').");
}
boolean updateCurrent=false;
AuthenticatedUser user = findAuthenticatedUserOrDie();
type = type.toLowerCase();
boolean isMinor=false;
switch (type) {
case "minor":
isMinor = true;
break;
case "major":
isMinor = false;
break;
case "updatecurrent":
if(user.isSuperuser()) {
updateCurrent=true;
} else {
return error(Response.Status.FORBIDDEN, "Only superusers can update the current version");
}
break;
default:
return error(Response.Status.BAD_REQUEST, "Illegal 'type' parameter value '" + type + "'. It needs to be either 'major', 'minor', or 'updatecurrent'.");
}
Dataset ds = findDatasetOrDie(id);
if (updateCurrent) {
/*
* Note: The code here mirrors that in the
* edu.harvard.iq.dataverse.DatasetPage:updateCurrentVersion method. Any changes
* to the core logic (i.e. beyond updating the messaging about results) should
* be applied to the code there as well.
*/
String errorMsg = null;
String successMsg = null;
try {
CuratePublishedDatasetVersionCommand cmd = new CuratePublishedDatasetVersionCommand(ds, createDataverseRequest(user));
ds = commandEngine.submit(cmd);
successMsg = BundleUtil.getStringFromBundle("datasetversion.update.success");
// If configured, update archive copy as well
String className = settingsService.get(SettingsServiceBean.Key.ArchiverClassName.toString());
DatasetVersion updateVersion = ds.getLatestVersion();
AbstractSubmitToArchiveCommand archiveCommand = ArchiverUtil.createSubmitToArchiveCommand(className, createDataverseRequest(user), updateVersion);
if (archiveCommand != null) {
// Delete the record of any existing copy since it is now out of date/incorrect
updateVersion.setArchivalCopyLocation(null);
/*
* Then try to generate and submit an archival copy. Note that running this
* command within the CuratePublishedDatasetVersionCommand was causing an error:
* "The attribute [id] of class
* [edu.harvard.iq.dataverse.DatasetFieldCompoundValue] is mapped to a primary
* key column in the database. Updates are not allowed." To avoid that, and to
* simplify reporting back to the GUI whether this optional step succeeded, I've
* pulled this out as a separate submit().
*/
try {
updateVersion = commandEngine.submit(archiveCommand);
if (updateVersion.getArchivalCopyLocation() != null) {
successMsg = BundleUtil.getStringFromBundle("datasetversion.update.archive.success");
} else {
successMsg = BundleUtil.getStringFromBundle("datasetversion.update.archive.failure");
}
} catch (CommandException ex) {