/**
* Authenticate the given service document request. This extracts the appropriate information from
* the request and forwards to the appropriate authentication method
*
* @param auth
* @return
* @throws DSpaceSwordException
* @throws SwordError
* @throws SwordAuthException
*/
public SwordContext authenticate(AuthCredentials auth)
throws DSpaceSwordException, SwordError, SwordAuthException {
Context context = this.constructContext();
SwordContext sc = null;
try {
sc = this.authenticate(context, auth);
} catch (DSpaceSwordException e) {
if (context != null && context.isValid()) {
context.abort();
}
throw e;
} catch (SwordError e) {
if (context != null && context.isValid()) {
context.abort();
}
throw e;
} catch (SwordAuthException e) {
if (context != null && context.isValid()) {
context.abort();
}
throw e;
} catch (RuntimeException e) {
if (context != null && context.isValid()) {
context.abort();
}
throw e;
}
return sc;
}
/**
* Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods.
*
* @param request servlet request
* @param response servlet response
* @throws ServletException if a servlet-specific error occurs
* @throws IOException if an I/O error occurs
*/
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
// we expect a path in the form /resource/<prefix>/<suffix>.
String pathInfo = request.getPathInfo();
log.debug("Pathinfo: " + pathInfo);
if (StringUtils.isEmpty(pathInfo) || StringUtils.countMatches(pathInfo, "/") < 2) {
log.debug("Path does not contain the expected number of slashes.");
response.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
// remove trailing slash of the path info and split it.
String[] path = request.getPathInfo().substring(1).split("/");
String handle = path[0] + "/" + path[1];
String dspaceURL = (new DSpace()).getConfigurationService().getProperty("dspace.url");
// Prepare content negotiation
int requestedMimeType = Negotiator.negotiate(request.getHeader(ACCEPT_HEADER_NAME));
Context context = null;
DSpaceObject dso = null;
try {
context = new Context(Context.READ_ONLY);
dso = handleService.resolveToObject(context, handle);
} catch (SQLException ex) {
log.error("SQLException: " + ex.getMessage(), ex);
context.abort();
// probably a problem with the db connection => send Service Unavailable
response.sendError(HttpServletResponse.SC_SERVICE_UNAVAILABLE);
return;
} catch (IllegalStateException ex) {
log.error(
"Cannot resolve handle " + handle + ". IllegalStateException:" + ex.getMessage(), ex);
context.abort();
response.sendError(HttpServletResponse.SC_BAD_REQUEST);
return;
}
if (dso == null) {
log.info("Cannot resolve handle '" + handle + "' to dso. => 404");
context.abort();
response.sendError(HttpServletResponse.SC_NOT_FOUND);
return;
}
// close the context and send forward.
context.abort();
Negotiator.sendRedirect(response, handle, "", requestedMimeType, true);
}
/** * Method to check current status of the service and logged in user. * * <p>okay: true | false authenticated: true | false epersonEMAIL: [email protected] epersonNAME: * John Doe * * @param headers Request header which contains the header named "rest-dspace-token" containing * the token as value. * @return status the Status object with information about REST API * @throws UnsupportedEncodingException The Character Encoding is not supported. */ @GET @Path("/status") @Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML}) public Status status(@Context HttpHeaders headers) throws UnsupportedEncodingException { org.dspace.core.Context context = null; try { context = Resource.createContext(); EPerson ePerson = context.getCurrentUser(); if (ePerson != null) { // DB EPerson needed since token won't have full info, need context EPerson dbEPerson = epersonService.findByEmail(context, ePerson.getEmail()); Status status = new Status(dbEPerson.getEmail(), dbEPerson.getFullName()); return status; } } catch (ContextException e) { Resource.processException("Status context error: " + e.getMessage(), context); } catch (SQLException e) { Resource.processException("Status eperson db lookup error: " + e.getMessage(), context); } finally { context.abort(); } // fallback status, unauth return new Status(); }
/**
* Delete the specified handle. It is assumed that the user has already confirmed this selection.
*
* @param context The current DSpace context.
* @param handleID ID of handle to be removed.
* @return A results object.
*/
public static FlowResult processDeleteHandle(Context context, int handleID)
throws SQLException, AuthorizeException, IOException {
FlowResult result = new FlowResult();
result.setContinue(true);
result.setOutcome(true);
result.setMessage(T_handle_deletion_failed);
try {
Handle handleDeleted = Handle.find(context, handleID);
HandleManager.changeHandle(context, handleDeleted.getHandle(), null, false);
handleDeleted.delete();
context.commit();
result.setContinue(true);
result.setOutcome(true);
result.setMessage(T_handle_successfully_deleted);
} catch (Exception e) {
log.error(e.getMessage());
context.abort();
}
return result;
}
@GET
@Path("/login-shibboleth")
@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
public Response shibbolethLoginEndPoint() {
org.dspace.core.Context context = null;
try {
context = Resource.createContext();
AuthenticationService authenticationService =
AuthenticateServiceFactory.getInstance().getAuthenticationService();
Iterator<AuthenticationMethod> authenticationMethodIterator =
authenticationService.authenticationMethodIterator();
while (authenticationMethodIterator.hasNext()) {
AuthenticationMethod authenticationMethod = authenticationMethodIterator.next();
if (authenticationMethod instanceof ShibAuthentication) {
// TODO: Perhaps look for a better way of handling this ?
org.dspace.services.model.Request currentRequest =
new DSpace().getRequestService().getCurrentRequest();
String loginPageURL =
authenticationMethod.loginPageURL(
context,
currentRequest.getHttpServletRequest(),
currentRequest.getHttpServletResponse());
if (StringUtils.isNotBlank(loginPageURL)) {
currentRequest.getHttpServletResponse().sendRedirect(loginPageURL);
}
}
}
context.abort();
} catch (ContextException | SQLException | IOException e) {
Resource.processException("Shibboleth endpoint error: " + e.getMessage(), context);
} finally {
if (context != null && context.isValid()) {
context.abort();
}
}
return Response.ok().build();
}
/**
* Find collection from DSpace database. It is encapsulation of method
* org.dspace.content.Collection.find with checking if item exist and if user logged into context
* has permission to do passed action.
*
* @param context Context of actual logged user.
* @param id Id of collection in DSpace.
* @param action Constant from org.dspace.core.Constants.
* @return It returns DSpace collection.
* @throws WebApplicationException Is thrown when item with passed id is not exists and if user
* has no permission to do passed action.
*/
private org.dspace.content.Collection findCollection(
org.dspace.core.Context context, int id, int action) throws WebApplicationException {
org.dspace.content.Collection collection = null;
try {
collection = org.dspace.content.Collection.find(context, id);
if (collection == null) {
context.abort();
log.warn("Collection(id=" + id + ") was not found!");
throw new WebApplicationException(Response.Status.NOT_FOUND);
} else if (!AuthorizeManager.authorizeActionBoolean(context, collection, action)) {
context.abort();
if (context.getCurrentUser() != null) {
log.error(
"User("
+ context.getCurrentUser().getEmail()
+ ") has not permission to "
+ getActionString(action)
+ " collection!");
} else {
log.error(
"User(anonymous) has not permission to " + getActionString(action) + " collection!");
}
throw new WebApplicationException(Response.Status.UNAUTHORIZED);
}
} catch (SQLException e) {
processException(
"Something get wrong while finding collection(id="
+ id
+ "). SQLException, Message: "
+ e,
context);
}
return collection;
}
public static void main(String[] args) {
// get a context from an anonymous user.
// don't switch off authorization system! We'll export the converted
// data into a triple store that provides a public sparql endpoint.
// all exported rdf data can be read by anonymous users.
// We won't change the database => read_only context will assure this.
Context context = new Context(Context.READ_ONLY);
RDFizer myself = null;
myself = new RDFizer();
myself.overrideContext(context);
myself.runCLI(args);
// we don't change anything in the database, so abort the context.
context.abort();
}
/**
* Save a registry to a filepath
*
* @param file filepath
* @param schema schema definition to save
* @throws SQLException if database error
* @throws IOException if IO error
* @throws SAXException if XML error
* @throws RegistryExportException if export error
*/
public static void saveRegistry(String file, String schema)
throws SQLException, IOException, SAXException, RegistryExportException {
// create a context
Context context = new Context();
context.setIgnoreAuthorization(true);
OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
xmlFormat.setLineWidth(120);
xmlFormat.setIndent(4);
XMLSerializer xmlSerializer =
new XMLSerializer(new BufferedWriter(new FileWriter(file)), xmlFormat);
// XMLSerializer xmlSerializer = new XMLSerializer(System.out, xmlFormat);
xmlSerializer.startDocument();
xmlSerializer.startElement("dspace-dc-types", null);
// Save the schema definition(s)
saveSchema(context, xmlSerializer, schema);
List<MetadataField> mdFields = null;
// If a single schema has been specified
if (schema != null && !"".equals(schema)) {
// Get the id of that schema
MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
if (mdSchema == null) {
throw new RegistryExportException("no schema to export");
}
// Get the metadata fields only for the specified schema
mdFields = metadataFieldService.findAllInSchema(context, mdSchema);
} else {
// Get the metadata fields for all the schemas
mdFields = metadataFieldService.findAll(context);
}
// Output the metadata fields
for (MetadataField mdField : mdFields) {
saveType(context, xmlSerializer, mdField);
}
xmlSerializer.endElement("dspace-dc-types");
xmlSerializer.endDocument();
// abort the context, as we shouldn't have changed it!!
context.abort();
}
/** Return the list of running applications. */
public static List<AbstractDSpaceWebapp> getApps() {
ArrayList<AbstractDSpaceWebapp> apps = new ArrayList<AbstractDSpaceWebapp>();
TableRowIterator tri;
Context context = null;
HttpMethod request = null;
try {
context = new Context();
tri = DatabaseManager.queryTable(context, "Webapp", "SELECT * FROM Webapp");
for (TableRow row : tri.toList()) {
DSpaceWebapp app = new DSpaceWebapp();
app.kind = row.getStringColumn("AppName");
app.url = row.getStringColumn("URL");
app.started = row.getDateColumn("Started");
app.uiQ = row.getBooleanColumn("isUI");
HttpClient client = new HttpClient();
request = new HeadMethod(app.url);
int status = client.executeMethod(request);
request.getResponseBody();
if (status != HttpStatus.SC_OK) {
DatabaseManager.delete(context, row);
context.commit();
continue;
}
apps.add(app);
}
} catch (SQLException e) {
log.error("Unable to list running applications", e);
} catch (HttpException e) {
log.error("Failure checking for a running webapp", e);
} catch (IOException e) {
log.error("Failure checking for a running webapp", e);
} finally {
if (null != request) {
request.releaseConnection();
}
if (null != context) {
context.abort();
}
}
return apps;
}
/**
* Change handle prefix. It is assumed that the user has already confirmed this selection.
*
* @param context The current DSpace context.
* @param oldPrefix The prefix to be replace.
* @param newPrefix The prefix to be used.
* @param archiveOldHandles Should the former handles be archived?
* @return A results object.
*/
public static FlowResult changeHandlePrefix(
Context context, String oldPrefix, String newPrefix, boolean archiveOldHandles)
throws SQLException, AuthorizeException, IOException {
FlowResult result = new FlowResult();
result.setContinue(false);
result.setOutcome(false);
// If we have errors, the form needs to be resubmitted to fix those problems
if (StringUtils.isEmpty(oldPrefix)) {
result.addError("old_prefix_empty");
}
if (StringUtils.isEmpty(newPrefix)) {
result.addError("new_prefix_empty");
}
if (result.getErrors() == null && oldPrefix.equals(newPrefix)) {
result.addError("old_prefix_equals_new_prefix");
}
if (result.getErrors() == null) {
try {
// change prefixes
HandleManager.changePrefix(context, oldPrefix, newPrefix, archiveOldHandles);
context.commit();
// reindex
IndexBrowse.main(new String[] {"-i"});
result.setContinue(true);
result.setOutcome(true);
result.setMessage(T_prefix_successfully_changed);
} catch (Exception e) {
result.setMessage(T_prefix_change_failed);
log.error(e.getMessage());
context.abort();
}
}
return result;
}
/** @param argv */
public static void main(String[] argv) {
// create an options object and populate it
CommandLineParser parser = new PosixParser();
Options options = new Options();
// processing basis for determining items
// item-specific changes with metadata in source directory with dublin_core.xml files
options.addOption("s", "source", true, "root directory of source dspace archive ");
// actions on items
options.addOption(
"a",
"addmetadata",
true,
"add metadata specified for each item; multiples separated by semicolon ';'");
options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
options.addOption("A", "addbitstreams", false, "add bitstreams as specified for each item");
// extra work to get optional argument
Option delBitstreamOption =
new Option("D", "deletebitstreams", true, "delete bitstreams as specified for each item");
delBitstreamOption.setOptionalArg(true);
delBitstreamOption.setArgName("BitstreamFilter");
options.addOption(delBitstreamOption);
// other params
options.addOption("e", "eperson", true, "email of eperson doing the update");
options.addOption(
"i",
"itemfield",
true,
"optional metadata field that containing item identifier; default is dc.identifier.uri");
options.addOption(
"F", "filter-properties", true, "filter class name; only for deleting bitstream");
options.addOption("v", "verbose", false, "verbose logging");
// special run states
options.addOption("t", "test", false, "test run - do not actually import items");
options.addOption(
"P", "provenance", false, "suppress altering provenance field for bitstream changes");
options.addOption("h", "help", false, "help");
int status = 0;
boolean isTest = false;
boolean alterProvenance = true;
String itemField = null;
String metadataIndexName = null;
Context context = null;
ItemUpdate iu = new ItemUpdate();
try {
CommandLine line = parser.parse(options, argv);
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("ItemUpdate", options);
pr("");
pr("Examples:");
pr(
" adding metadata: ItemUpdate -e [email protected] -s sourcedir -a dc.contributor -a dc.subject ");
pr(
" deleting metadata: ItemUpdate -e [email protected] -s sourcedir -d dc.description.other");
pr(" adding bitstreams: ItemUpdate -e [email protected] -s sourcedir -A -i dc.identifier");
pr(" deleting bitstreams: ItemUpdate -e [email protected] -s sourcedir -D ORIGINAL ");
pr("");
System.exit(0);
}
if (line.hasOption('v')) {
verbose = true;
}
if (line.hasOption('P')) {
alterProvenance = false;
pr("Suppressing changes to Provenance field option");
}
iu.eperson = line.getOptionValue('e'); // db ID or email
if (!line.hasOption('s')) // item specific changes from archive dir
{
pr("Missing source archive option");
System.exit(1);
}
String sourcedir = line.getOptionValue('s');
if (line.hasOption('t')) // test
{
isTest = true;
pr("**Test Run** - not actually updating items.");
}
if (line.hasOption('i')) {
itemField = line.getOptionValue('i');
}
if (line.hasOption('d')) {
String[] targetFields = line.getOptionValues('d');
DeleteMetadataAction delMetadataAction =
(DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
delMetadataAction.addTargetFields(targetFields);
// undo is an add
for (String field : targetFields) {
iu.undoActionList.add(" -a " + field + " ");
}
pr("Delete metadata for fields: ");
for (String s : targetFields) {
pr(" " + s);
}
}
if (line.hasOption('a')) {
String[] targetFields = line.getOptionValues('a');
AddMetadataAction addMetadataAction =
(AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class);
addMetadataAction.addTargetFields(targetFields);
// undo is a delete followed by an add of a replace record for target fields
for (String field : targetFields) {
iu.undoActionList.add(" -d " + field + " ");
}
for (String field : targetFields) {
iu.undoActionList.add(" -a " + field + " ");
}
pr("Add metadata for fields: ");
for (String s : targetFields) {
pr(" " + s);
}
}
if (line.hasOption('D')) // undo not supported
{
pr("Delete bitstreams ");
String[] filterNames = line.getOptionValues('D');
if ((filterNames != null) && (filterNames.length > 1)) {
pr("Error: Only one filter can be a used at a time.");
System.exit(1);
}
String filterName = line.getOptionValue('D');
pr("Filter argument: " + filterName);
if (filterName == null) // indicates using delete_contents files
{
DeleteBitstreamsAction delAction =
(DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class);
delAction.setAlterProvenance(alterProvenance);
} else {
// check if param is on ALIAS list
String filterClassname = filterAliases.get(filterName);
if (filterClassname == null) {
filterClassname = filterName;
}
BitstreamFilter filter = null;
try {
Class<?> cfilter = Class.forName(filterClassname);
pr("BitstreamFilter class to instantiate: " + cfilter.toString());
filter =
(BitstreamFilter) cfilter.newInstance(); // unfortunate cast, an erasure consequence
} catch (Exception e) {
pr("Error: Failure instantiating bitstream filter class: " + filterClassname);
System.exit(1);
}
String filterPropertiesName = line.getOptionValue('F');
if (filterPropertiesName != null) // not always required
{
try {
// TODO try multiple relative locations, e.g. source dir
if (!filterPropertiesName.startsWith("/")) {
filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
}
filter.initProperties(filterPropertiesName);
} catch (Exception e) {
pr(
"Error: Failure finding properties file for bitstream filter class: "
+ filterPropertiesName);
System.exit(1);
}
}
DeleteBitstreamsByFilterAction delAction =
(DeleteBitstreamsByFilterAction)
iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
delAction.setAlterProvenance(alterProvenance);
delAction.setBitstreamFilter(filter);
// undo not supported
}
}
if (line.hasOption('A')) {
pr("Add bitstreams ");
AddBitstreamsAction addAction =
(AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
addAction.setAlterProvenance(alterProvenance);
iu.undoActionList.add(" -D "); // delete_contents file will be written, no arg required
}
if (!iu.actionMgr.hasActions()) {
pr("Error - an action must be specified");
System.exit(1);
} else {
pr("Actions to be performed: ");
for (UpdateAction ua : iu.actionMgr) {
pr(" " + ua.getClass().getName());
}
}
pr("ItemUpdate - initializing run on " + (new Date()).toString());
context = new Context();
iu.setEPerson(context, iu.eperson);
context.setIgnoreAuthorization(true);
HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
HANDLE_PREFIX = "http://hdl.handle.net/";
}
iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);
context.complete(); // complete all transactions
context.setIgnoreAuthorization(false);
} catch (Exception e) {
if (context != null && context.isValid()) {
context.abort();
context.setIgnoreAuthorization(false);
}
e.printStackTrace();
pr(e.toString());
status = 1;
}
if (isTest) {
pr("***End of Test Run***");
} else {
pr("End.");
}
System.exit(status);
}
public static void main(String[] argv) throws Exception {
Options options = new Options();
options.addOption("c", "collection", true, "destination collection(s) Handle (repeatable)");
options.addOption("e", "eperson", true, "email address of eperson doing importing");
options.addOption(
"w",
"install",
false,
"disable workflow; install immediately without going through collection's workflow");
options.addOption("t", "type", true, "package type or MIMEtype");
options.addOption(
"o", "option", true, "Packager option to pass to plugin, \"name=value\" (repeatable)");
options.addOption(
"d", "disseminate", false, "Disseminate package (output); default is to submit.");
options.addOption("i", "item", true, "Handle of item to disseminate.");
options.addOption("h", "help", false, "help");
CommandLineParser parser = new PosixParser();
CommandLine line = parser.parse(options, argv);
String sourceFile = null;
String eperson = null;
String[] collections = null;
boolean useWorkflow = true;
String packageType = null;
boolean submit = true;
String itemHandle = null;
PackageParameters pkgParams = new PackageParameters();
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("Packager [options] package-file|-\n", options);
System.out.println("\nAvailable Submission Package (SIP) types:");
String pn[] = PluginManager.getAllPluginNames(PackageIngester.class);
for (int i = 0; i < pn.length; ++i) System.out.println(" " + pn[i]);
System.out.println("\nAvailable Dissemination Package (DIP) types:");
pn = PluginManager.getAllPluginNames(PackageDisseminator.class);
for (int i = 0; i < pn.length; ++i) System.out.println(" " + pn[i]);
System.exit(0);
}
if (line.hasOption('w')) useWorkflow = false;
if (line.hasOption('e')) eperson = line.getOptionValue('e');
if (line.hasOption('c')) collections = line.getOptionValues('c');
if (line.hasOption('t')) packageType = line.getOptionValue('t');
if (line.hasOption('i')) itemHandle = line.getOptionValue('i');
String files[] = line.getArgs();
if (files.length > 0) sourceFile = files[0];
if (line.hasOption('d')) submit = false;
if (line.hasOption('o')) {
String popt[] = line.getOptionValues('o');
for (int i = 0; i < popt.length; ++i) {
String pair[] = popt[i].split("\\=", 2);
if (pair.length == 2) pkgParams.addProperty(pair[0].trim(), pair[1].trim());
else if (pair.length == 1) pkgParams.addProperty(pair[0].trim(), "");
else System.err.println("Warning: Illegal package option format: \"" + popt[i] + "\"");
}
}
// Sanity checks on arg list: required args
if (sourceFile == null
|| eperson == null
|| packageType == null
|| (submit && collections == null)) {
System.err.println("Error - missing a REQUIRED argument or option.\n");
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("PackageManager [options] package-file|-\n", options);
System.exit(0);
}
// find the EPerson, assign to context
Context context = new Context();
EPerson myEPerson = null;
myEPerson = EPerson.findByEmail(context, eperson);
if (myEPerson == null) usageError("Error, eperson cannot be found: " + eperson);
context.setCurrentUser(myEPerson);
if (submit) {
// make sure we have an input file
// GWaller 11/1/10 Disable piping of input in - we need to archive the package so it is
// simpler to assume a file stream
// rather than save the System.in bytes and re-read.
if (sourceFile.equals("-")) {
usageError(
"Error, input piping not allowed. Specify a file name of a physical file to read");
}
InputStream source = new FileInputStream(sourceFile);
PackageIngester sip =
(PackageIngester) PluginManager.getNamedPlugin(PackageIngester.class, packageType);
if (sip == null) usageError("Error, Unknown package type: " + packageType);
// find collections
Collection[] mycollections = null;
System.out.println("Destination collections:");
// validate each collection arg to see if it's a real collection
mycollections = new Collection[collections.length];
for (int i = 0; i < collections.length; i++) {
// sanity check: did handle resolve, and to a collection?
DSpaceObject dso = HandleManager.resolveToObject(context, collections[i]);
if (dso == null)
throw new IllegalArgumentException(
"Bad collection list -- "
+ "Cannot resolve collection handle \""
+ collections[i]
+ "\"");
else if (dso.getType() != Constants.COLLECTION)
throw new IllegalArgumentException(
"Bad collection list -- "
+ "Object at handle \""
+ collections[i]
+ "\" is not a collection!");
mycollections[i] = (Collection) dso;
System.out.println(
(i == 0 ? " Owning " : " ") + " Collection: " + mycollections[i].getMetadata("name"));
}
try {
// GWaller 26/08/09 Support array of collections
WorkspaceItem wi = sip.ingest(context, mycollections, source, pkgParams, null);
// GWaller 11/1/10 IssueID #157 Archive the package
InputStream sourceCopy = new FileInputStream(sourceFile);
Bundle archivedBundle =
BundleUtils.getBundleByName(wi.getItem(), Constants.ARCHIVED_CONTENT_PACKAGE_BUNDLE);
Bitstream bs = archivedBundle.createBitstream(sourceCopy);
bs.setName(new File(sourceFile).getName());
bs.update();
archivedBundle.update();
if (useWorkflow) {
String handle = null;
// Check if workflow completes immediately, and
// return Handle if so.
WorkflowItem wfi = WorkflowManager.startWithoutNotify(context, wi);
if (wfi.getState() == WorkflowManager.WFSTATE_ARCHIVE) {
Item ni = wfi.getItem();
handle = HandleManager.findHandle(context, ni);
}
if (handle == null)
System.out.println("Created Workflow item, ID=" + String.valueOf(wfi.getID()));
else System.out.println("Created and installed item, handle=" + handle);
} else {
InstallItem.installItem(context, wi);
System.out.println(
"Created and installed item, handle="
+ HandleManager.findHandle(context, wi.getItem()));
}
context.complete();
System.exit(0);
} catch (Exception e) {
// abort all operations
context.abort();
e.printStackTrace();
System.out.println(e);
System.exit(1);
}
} else {
OutputStream dest =
(sourceFile.equals("-"))
? (OutputStream) System.out
: (OutputStream) (new FileOutputStream(sourceFile));
PackageDisseminator dip =
(PackageDisseminator)
PluginManager.getNamedPlugin(PackageDisseminator.class, packageType);
if (dip == null) usageError("Error, Unknown package type: " + packageType);
DSpaceObject dso = HandleManager.resolveToObject(context, itemHandle);
if (dso == null)
throw new IllegalArgumentException(
"Bad Item handle -- " + "Cannot resolve handle \"" + itemHandle);
dip.disseminate(context, dso, pkgParams, dest);
}
}
/**
* Save the handle.
*
* <p>If the handleID is -1 then a new handle is created.
*
* @param context The current dspace context
* @param handleID The handle ID, or -1 for a new handle.
* @param url The handle URL
* @param resourceTypeID The type of referenced resource
* @param resourceID ID of referenced resource
* @return A result
*/
public static FlowResult processSaveHandle(
Context context,
int handleID,
String handle,
String url,
int resourceTypeID,
int resourceID,
boolean archiveOldHandle)
throws SQLException, AuthorizeException, UIException {
FlowResult result = new FlowResult();
result.setParameter("handle_id", handleID);
result.setContinue(false);
result.setOutcome(false);
// If we have errors, the form needs to be resubmitted to fix those problems
if (StringUtils.isEmpty(handle)) {
result.addError("handle_empty");
}
if (resourceTypeID == -1 && resourceID == -1 && StringUtils.isEmpty(url)) {
result.addError("url_empty");
} else if (StringUtils.isEmpty(url)) {
if (resourceTypeID == -1) {
result.addError("resource_type_id_empty");
}
if (resourceID == -1) {
result.addError("resource_id_empty");
}
}
if (result.getErrors() == null) {
try {
Handle h = null;
if (handleID == -1) {
h = Handle.create(context, null, handle);
} else {
h = Handle.find(context, handleID);
if (h.getHandle() != handle) {
HandleManager.changeHandle(context, h.getHandle(), handle, archiveOldHandle);
}
}
h.setHandle(handle);
h.setURL(url);
h.setResourceTypeID(resourceTypeID);
h.setResourceID(resourceID);
h.update();
context.commit();
result.setContinue(true);
result.setOutcome(true);
result.setMessage(T_handle_successfully_saved);
} catch (Exception e) {
result.setMessage(T_handle_saving_failed);
log.error(e.getMessage());
context.abort();
}
}
return result;
}
/**
* Delete item in collection.
*
* @param collectionId Id of collection which will be deleted.
* @param itemId Id of item in colletion.
* @return It returns status code: OK(200). NOT_FOUND(404) if item or collection was not found,
* UNAUTHORIZED(401) if user is not allowed to delete item or permission to write into
* collection.
* @throws WebApplicationException It can be thrown by: SQLException, when was problem with
* database reading or writting. AuthorizeException, when was problem with authorization to
* item or collection. IOException, when was problem with removing item. ContextException,
* when was problem with creating context of DSpace.
*/
@DELETE
@Path("/{collection_id}/items/{item_id}")
@Consumes({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
public Response deleteCollectionItem(
@PathParam("collection_id") Integer collectionId,
@PathParam("item_id") Integer itemId,
@QueryParam("userIP") String user_ip,
@QueryParam("userAgent") String user_agent,
@QueryParam("xforwarderfor") String xforwarderfor,
@Context HttpHeaders headers,
@Context HttpServletRequest request)
throws WebApplicationException {
log.info("Delete item(id=" + itemId + ") in collection(id=" + collectionId + ").");
org.dspace.core.Context context = null;
try {
context = createContext(getUser(headers));
org.dspace.content.Collection dspaceCollection =
findCollection(context, collectionId, org.dspace.core.Constants.WRITE);
org.dspace.content.Item item = null;
org.dspace.content.ItemIterator dspaceItems = dspaceCollection.getItems();
while (dspaceItems.hasNext()) {
org.dspace.content.Item dspaceItem = dspaceItems.next();
if (dspaceItem.getID() == itemId) {
item = dspaceItem;
}
}
if (item == null) {
context.abort();
log.warn("Item(id=" + itemId + ") was not found!");
throw new WebApplicationException(Response.Status.NOT_FOUND);
} else if (!AuthorizeManager.authorizeActionBoolean(
context, item, org.dspace.core.Constants.REMOVE)) {
context.abort();
if (context.getCurrentUser() != null) {
log.error(
"User("
+ context.getCurrentUser().getEmail()
+ ") has not permission to delete item!");
} else {
log.error("User(anonymous) has not permission to delete item!");
}
throw new WebApplicationException(Response.Status.UNAUTHORIZED);
}
writeStats(
dspaceCollection,
UsageEvent.Action.UPDATE,
user_ip,
user_agent,
xforwarderfor,
headers,
request,
context);
writeStats(
item,
UsageEvent.Action.REMOVE,
user_ip,
user_agent,
xforwarderfor,
headers,
request,
context);
dspaceCollection.removeItem(item);
context.complete();
} catch (ContextException e) {
processException(
"Could not delete item(id="
+ itemId
+ ") in collection(id="
+ collectionId
+ "), ContextException. Message: "
+ e.getMessage(),
context);
} catch (SQLException e) {
processException(
"Could not delete item(id="
+ itemId
+ ") in collection(id="
+ collectionId
+ "), SQLException. Message: "
+ e,
context);
} catch (AuthorizeException e) {
processException(
"Could not delete item(id="
+ itemId
+ ") in collection(id="
+ collectionId
+ "), AuthorizeException. Message: "
+ e,
context);
} catch (IOException e) {
processException(
"Could not delete item(id="
+ itemId
+ ") in collection(id="
+ collectionId
+ "), IOException. Message: "
+ e,
context);
} finally {
processFinally(context);
}
log.info(
"Item(id=" + itemId + ") in collection(id=" + collectionId + ") was successfully deleted.");
return Response.ok().build();
}
/**
* Method for invoking subscriptions via the command line
*
* @param argv command-line arguments, none used yet
*/
public static void main(String[] argv) {
log.info("#### START DELETE: -----" + new Date() + " ----- ####");
String usage =
"it.cilea.hku.authority.ScriptRPSubscribe [-t] or nothing to send out subscriptions.";
Options options = new Options();
HelpFormatter formatter = new HelpFormatter();
CommandLine line = null;
{
Option opt = new Option("t", "test", false, "Run test session");
opt.setRequired(false);
options.addOption(opt);
}
{
Option opt = new Option("h", "help", false, "Print this help message");
opt.setRequired(false);
options.addOption(opt);
}
try {
line = new PosixParser().parse(options, argv);
} catch (Exception e) {
// automatically generate the help statement
formatter.printHelp(usage, e.getMessage(), options, "");
System.exit(1);
}
if (line.hasOption("h")) {
// automatically generate the help statement
formatter.printHelp(usage, options);
System.exit(1);
}
boolean test = line.hasOption("t");
if (test) log.setLevel(Level.DEBUG);
Context context = null;
try {
context = new Context();
Researcher researcher = new Researcher();
ApplicationService applicationService = researcher.getApplicationService();
List<CrisComponentsService> serviceComponent = researcher.getAllCrisComponents();
for (CrisComponentsService service : serviceComponent) {
for (ICRISComponent component : service.getComponents().values()) {
RelationConfiguration relationConfiguration = component.getRelationConfiguration();
if (Item.class.isAssignableFrom(relationConfiguration.getRelationClass())) {
Integer key = CrisConstants.getEntityType(component.getTarget());
String query = relationConfiguration.getQuery();
if (!mapRelationFields.containsKey(key)) {
List<String> rels = new LinkedList<String>();
rels.add(query);
mapRelationFields.put(key, rels);
} else {
mapRelationFields.get(key).add(query);
}
}
}
}
processDaily(researcher, applicationService, context, test);
} catch (Exception e) {
log.error(e.getMessage(), e);
} finally {
if (context != null && context.isValid()) {
// Nothing is actually written
context.abort();
}
}
log.info("#### END: -----" + new Date() + " ----- ####");
System.exit(0);
}
public static void main(String[] argv) throws Exception {
// set headless for non-gui workstations
System.setProperty("java.awt.headless", "true");
// create an options object and populate it
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption(
"v", "verbose", false, "print all extracted text and other details to STDOUT");
options.addOption("f", "force", false, "force all bitstreams to be processed");
options.addOption(
"n", "noindex", false, "do NOT update the search index after filtering bitstreams");
options.addOption("i", "identifier", true, "ONLY process bitstreams belonging to identifier");
options.addOption("m", "maximum", true, "process no more than maximum items");
options.addOption("h", "help", false, "help");
CommandLine line = parser.parse(options, argv);
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("MediaFilter\n", options);
System.exit(0);
}
if (line.hasOption('v')) {
isVerbose = true;
}
if (line.hasOption('n')) {
updateIndex = false;
}
if (line.hasOption('f')) {
isForce = true;
}
if (line.hasOption('i')) {
identifier = line.getOptionValue('i');
}
if (line.hasOption('m')) {
max2Process = Integer.parseInt(line.getOptionValue('m'));
if (max2Process <= 1) {
System.out.println("Invalid maximum value '" + line.getOptionValue('m') + "' - ignoring");
max2Process = Integer.MAX_VALUE;
}
}
// set up filters
filterClasses = (MediaFilter[]) PluginManager.getPluginSequence(MediaFilter.class);
for (int i = 0; i < filterClasses.length; i++) {
String filterName = filterClasses[i].getClass().getName();
String formats = ConfigurationManager.getProperty("filter." + filterName + ".inputFormats");
if (formats != null) {
filterFormats.put(filterName, Arrays.asList(formats.split(",[\\s]*")));
}
}
Context c = null;
try {
c = new Context();
// have to be super-user to do the filtering
c.setIgnoreAuthorization(true);
// now apply the filters
if (identifier == null) {
applyFiltersAllItems(c);
} else // restrict application scope to identifier
{
DSpaceObject dso = HandleManager.resolveToObject(c, identifier);
if (dso == null) {
throw new IllegalArgumentException(
"Cannot resolve " + identifier + " to a DSpace object");
}
switch (dso.getType()) {
case Constants.COMMUNITY:
applyFiltersCommunity(c, (Community) dso);
break;
case Constants.COLLECTION:
applyFiltersCollection(c, (Collection) dso);
break;
case Constants.ITEM:
applyFiltersItem(c, (Item) dso);
break;
}
}
// update search index?
if (updateIndex) {
System.out.println("Updating search index:");
DSIndexer.updateIndex(c);
}
c.complete();
c = null;
} finally {
if (c != null) {
c.abort();
}
}
}
public static void main(String[] argv) throws Exception {
DSIndexer.setBatchProcessingMode(true);
Date startTime = new Date();
int status = 0;
try {
// create an options object and populate it
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption("a", "add", false, "add items to DSpace");
options.addOption("r", "replace", false, "replace items in mapfile");
options.addOption("d", "delete", false, "delete items listed in mapfile");
options.addOption("s", "source", true, "source of items (directory)");
options.addOption("z", "zip", true, "name of zip file");
options.addOption("c", "collection", true, "destination collection(s) Handle or database ID");
options.addOption("m", "mapfile", true, "mapfile items in mapfile");
options.addOption("e", "eperson", true, "email of eperson doing importing");
options.addOption("w", "workflow", false, "send submission through collection's workflow");
options.addOption(
"n",
"notify",
false,
"if sending submissions through the workflow, send notification emails");
options.addOption("t", "test", false, "test run - do not actually import items");
options.addOption("p", "template", false, "apply template");
options.addOption("R", "resume", false, "resume a failed import (add only)");
options.addOption("q", "quiet", false, "don't display metadata");
options.addOption("h", "help", false, "help");
CommandLine line = parser.parse(options, argv);
String command = null; // add replace remove, etc
String sourcedir = null;
String mapfile = null;
String eperson = null; // db ID or email
String[] collections = null; // db ID or handles
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("ItemImport\n", options);
System.out.println(
"\nadding items: ItemImport -a -e eperson -c collection -s sourcedir -m mapfile");
System.out.println(
"\nadding items from zip file: ItemImport -a -e eperson -c collection -s sourcedir -z filename.zip -m mapfile");
System.out.println(
"replacing items: ItemImport -r -e eperson -c collection -s sourcedir -m mapfile");
System.out.println("deleting items: ItemImport -d -e eperson -m mapfile");
System.out.println(
"If multiple collections are specified, the first collection will be the one that owns the item.");
System.exit(0);
}
if (line.hasOption('a')) {
command = "add";
}
if (line.hasOption('r')) {
command = "replace";
}
if (line.hasOption('d')) {
command = "delete";
}
if (line.hasOption('w')) {
useWorkflow = true;
if (line.hasOption('n')) {
useWorkflowSendEmail = true;
}
}
if (line.hasOption('t')) {
isTest = true;
System.out.println("**Test Run** - not actually importing items.");
}
if (line.hasOption('p')) {
template = true;
}
if (line.hasOption('s')) // source
{
sourcedir = line.getOptionValue('s');
}
if (line.hasOption('m')) // mapfile
{
mapfile = line.getOptionValue('m');
}
if (line.hasOption('e')) // eperson
{
eperson = line.getOptionValue('e');
}
if (line.hasOption('c')) // collections
{
collections = line.getOptionValues('c');
}
if (line.hasOption('R')) {
isResume = true;
System.out.println("**Resume import** - attempting to import items not already imported");
}
if (line.hasOption('q')) {
isQuiet = true;
}
boolean zip = false;
String zipfilename = "";
String ziptempdir = ConfigurationManager.getProperty("org.dspace.app.itemexport.work.dir");
if (line.hasOption('z')) {
zip = true;
zipfilename = sourcedir + System.getProperty("file.separator") + line.getOptionValue('z');
}
// now validate
// must have a command set
if (command == null) {
System.out.println(
"Error - must run with either add, replace, or remove (run with -h flag for details)");
System.exit(1);
} else if ("add".equals(command) || "replace".equals(command)) {
if (sourcedir == null) {
System.out.println("Error - a source directory containing items must be set");
System.out.println(" (run with -h flag for details)");
System.exit(1);
}
if (mapfile == null) {
System.out.println("Error - a map file to hold importing results must be specified");
System.out.println(" (run with -h flag for details)");
System.exit(1);
}
if (eperson == null) {
System.out.println("Error - an eperson to do the importing must be specified");
System.out.println(" (run with -h flag for details)");
System.exit(1);
}
if (collections == null) {
System.out.println("Error - at least one destination collection must be specified");
System.out.println(" (run with -h flag for details)");
System.exit(1);
}
} else if ("delete".equals(command)) {
if (eperson == null) {
System.out.println("Error - an eperson to do the importing must be specified");
System.exit(1);
}
if (mapfile == null) {
System.out.println("Error - a map file must be specified");
System.exit(1);
}
}
// can only resume for adds
if (isResume && !"add".equals(command)) {
System.out.println("Error - resume option only works with --add command");
System.exit(1);
}
// do checks around mapfile - if mapfile exists and 'add' is selected,
// resume must be chosen
File myFile = new File(mapfile);
if (!isResume && "add".equals(command) && myFile.exists()) {
System.out.println("Error - the mapfile " + mapfile + " already exists.");
System.out.println(
"Either delete it or use --resume if attempting to resume an aborted import.");
System.exit(1);
}
// does the zip file exist and can we write to the temp directory
if (zip) {
File zipfile = new File(sourcedir);
if (!zipfile.canRead()) {
System.out.println("Zip file '" + sourcedir + "' does not exist, or is not readable.");
System.exit(1);
}
if (ziptempdir == null) {
System.out.println(
"Unable to unzip import file as the key 'org.dspace.app.itemexport.work.dir' is not set in dspace.cfg");
System.exit(1);
}
zipfile = new File(ziptempdir);
if (!zipfile.isDirectory()) {
System.out.println(
"'"
+ ConfigurationManager.getProperty("org.dspace.app.itemexport.work.dir")
+ "' as defined by the key 'org.dspace.app.itemexport.work.dir' in dspace.cfg "
+ "is not a valid directory");
System.exit(1);
}
File tempdir = new File(ziptempdir);
if (!tempdir.exists() && !tempdir.mkdirs()) {
log.error("Unable to create temporary directory");
}
sourcedir = ziptempdir + System.getProperty("file.separator") + line.getOptionValue("z");
ziptempdir =
ziptempdir
+ System.getProperty("file.separator")
+ line.getOptionValue("z")
+ System.getProperty("file.separator");
}
ItemImport myloader = new ItemImport();
// create a context
Context c = new Context();
// find the EPerson, assign to context
EPerson myEPerson = null;
if (eperson.indexOf('@') != -1) {
// @ sign, must be an email
myEPerson = EPerson.findByEmail(c, eperson);
} else {
myEPerson = EPerson.find(c, Integer.parseInt(eperson));
}
if (myEPerson == null) {
System.out.println("Error, eperson cannot be found: " + eperson);
System.exit(1);
}
c.setCurrentUser(myEPerson);
// find collections
Collection[] mycollections = null;
// don't need to validate collections set if command is "delete"
if (!"delete".equals(command)) {
System.out.println("Destination collections:");
mycollections = new Collection[collections.length];
// validate each collection arg to see if it's a real collection
for (int i = 0; i < collections.length; i++) {
// is the ID a handle?
if (collections[i].indexOf('/') != -1) {
// string has a / so it must be a handle - try and resolve
// it
mycollections[i] = (Collection) HandleManager.resolveToObject(c, collections[i]);
// resolved, now make sure it's a collection
if ((mycollections[i] == null)
|| (mycollections[i].getType() != Constants.COLLECTION)) {
mycollections[i] = null;
}
}
// not a handle, try and treat it as an integer collection
// database ID
else if (collections[i] != null) {
mycollections[i] = Collection.find(c, Integer.parseInt(collections[i]));
}
// was the collection valid?
if (mycollections[i] == null) {
throw new IllegalArgumentException(
"Cannot resolve " + collections[i] + " to collection");
}
// print progress info
String owningPrefix = "";
if (i == 0) {
owningPrefix = "Owning ";
}
System.out.println(owningPrefix + " Collection: " + mycollections[i].getMetadata("name"));
}
} // end of validating collections
try {
// If this is a zip archive, unzip it first
if (zip) {
ZipFile zf = new ZipFile(zipfilename);
ZipEntry entry;
Enumeration<? extends ZipEntry> entries = zf.entries();
while (entries.hasMoreElements()) {
entry = entries.nextElement();
if (entry.isDirectory()) {
if (!new File(ziptempdir + entry.getName()).mkdir()) {
log.error("Unable to create contents directory");
}
} else {
System.out.println("Extracting file: " + entry.getName());
int index = entry.getName().lastIndexOf('/');
if (index == -1) {
// Was it created on Windows instead?
index = entry.getName().lastIndexOf('\\');
}
if (index > 0) {
File dir = new File(ziptempdir + entry.getName().substring(0, index));
if (!dir.mkdirs()) {
log.error("Unable to create directory");
}
}
byte[] buffer = new byte[1024];
int len;
InputStream in = zf.getInputStream(entry);
BufferedOutputStream out =
new BufferedOutputStream(new FileOutputStream(ziptempdir + entry.getName()));
while ((len = in.read(buffer)) >= 0) {
out.write(buffer, 0, len);
}
in.close();
out.close();
}
}
}
c.turnOffAuthorisationSystem();
if ("add".equals(command)) {
myloader.addItems(c, mycollections, sourcedir, mapfile, template);
} else if ("replace".equals(command)) {
myloader.replaceItems(c, mycollections, sourcedir, mapfile, template);
} else if ("delete".equals(command)) {
myloader.deleteItems(c, mapfile);
}
// complete all transactions
c.complete();
} catch (Exception e) {
// abort all operations
if (mapOut != null) {
mapOut.close();
}
mapOut = null;
c.abort();
e.printStackTrace();
System.out.println(e);
status = 1;
}
// Delete the unzipped file
try {
if (zip) {
System.gc();
System.out.println("Deleting temporary zip directory: " + ziptempdir);
ItemImport.deleteDirectory(new File(ziptempdir));
}
} catch (Exception ex) {
System.out.println("Unable to delete temporary zip archive location: " + ziptempdir);
}
if (mapOut != null) {
mapOut.close();
}
if (isTest) {
System.out.println("***End of Test Run***");
}
} finally {
DSIndexer.setBatchProcessingMode(false);
Date endTime = new Date();
System.out.println("Started: " + startTime.getTime());
System.out.println("Ended: " + endTime.getTime());
System.out.println(
"Elapsed time: "
+ ((endTime.getTime() - startTime.getTime()) / 1000)
+ " secs ("
+ (endTime.getTime() - startTime.getTime())
+ " msecs)");
}
System.exit(status);
}