@Override
public int perform(DSpaceObject dso) throws IOException {
status = Curator.CURATE_SKIP;
logDebugMessage("The target dso is " + dso.getName());
if (dso instanceof Item) {
status = Curator.CURATE_SUCCESS;
Item item = (Item) dso;
try {
openSession();
} catch (IOException ioE) {
// no point going further - set result and error out
closeSession();
setResult(CONNECT_FAIL_MESSAGE);
return Curator.CURATE_ERROR;
}
try {
Bundle bundle = item.getBundles("ORIGINAL")[0];
results = new ArrayList<String>();
for (Bitstream bitstream : bundle.getBitstreams()) {
InputStream inputstream = bitstream.retrieve();
logDebugMessage("Scanning " + bitstream.getName() + " . . . ");
int bstatus = scan(bitstream, inputstream, getItemHandle(item));
inputstream.close();
if (bstatus == Curator.CURATE_ERROR) {
// no point going further - set result and error out
setResult(SCAN_FAIL_MESSAGE);
status = bstatus;
break;
}
if (failfast && bstatus == Curator.CURATE_FAIL) {
status = bstatus;
break;
} else if (bstatus == Curator.CURATE_FAIL && status == Curator.CURATE_SUCCESS) {
status = bstatus;
}
}
} catch (AuthorizeException authE) {
throw new IOException(authE.getMessage(), authE);
} catch (SQLException sqlE) {
throw new IOException(sqlE.getMessage(), sqlE);
} finally {
closeSession();
}
if (status != Curator.CURATE_ERROR) {
formatResults(item);
}
}
return status;
}
@GET
@Path("/{bitstream_id}/retrieve")
public javax.ws.rs.core.Response getFile(
@PathParam("bitstream_id") final Integer bitstream_id,
@QueryParam("userIP") String user_ip,
@QueryParam("userAgent") String user_agent,
@QueryParam("xforwarderfor") String xforwarderfor,
@Context HttpHeaders headers,
@Context HttpServletRequest request) {
org.dspace.core.Context context = null;
try {
context = new org.dspace.core.Context();
org.dspace.content.Bitstream bitstream =
org.dspace.content.Bitstream.find(context, bitstream_id);
if (AuthorizeManager.authorizeActionBoolean(
context, bitstream, org.dspace.core.Constants.READ)) {
if (writeStatistics) {
writeStats(context, bitstream_id, user_ip, user_agent, xforwarderfor, headers, request);
}
return Response.ok(bitstream.retrieve()).type(bitstream.getFormat().getMIMEType()).build();
} else {
throw new WebApplicationException(Response.Status.UNAUTHORIZED);
}
} catch (IOException e) {
log.error(e.getMessage());
throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
} catch (SQLException e) {
log.error(e.getMessage());
throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
} catch (AuthorizeException e) {
log.error(e.getMessage());
throw new WebApplicationException(Response.Status.UNAUTHORIZED);
} finally {
if (context != null) {
try {
context.complete();
} catch (SQLException e) {
log.error(e.getMessage() + " occurred while trying to close");
}
}
}
}
/** Write out a METS manifest. Mostly lifted from Rob Tansley's METS exporter. */
private void writeManifest(Context context, Item item, PackageParameters params, OutputStream out)
throws PackageValidationException, CrosswalkException, AuthorizeException, SQLException,
IOException {
try {
// Create the METS file
Mets mets = new Mets();
// Top-level stuff
mets.setID(gensym("mets"));
mets.setOBJID("hdl:" + item.getHandle());
mets.setLABEL("DSpace Item");
mets.setPROFILE(getProfile());
// MetsHdr
MetsHdr metsHdr = new MetsHdr();
metsHdr.setCREATEDATE(new Date()); // FIXME: CREATEDATE is now:
// maybe should be item create
// date?
// Agent
Agent agent = new Agent();
agent.setROLE(Role.CUSTODIAN);
agent.setTYPE(Type.ORGANIZATION);
Name name = new Name();
name.getContent().add(new PCData(ConfigurationManager.getProperty("dspace.name")));
agent.getContent().add(name);
metsHdr.getContent().add(agent);
mets.getContent().add(metsHdr);
// add DMD sections
// Each type element MAY be either just a MODS-and-crosswalk name, OR
// a combination "MODS-name:crosswalk-name" (e.g. "DC:qDC").
String dmdTypes[] = getDmdTypes(params);
// record of ID of each dmdsec to make DMDID in structmap.
String dmdGroup = gensym("dmd_group");
String dmdId[] = new String[dmdTypes.length];
for (int i = 0; i < dmdTypes.length; ++i) {
dmdId[i] = gensym("dmd");
XmlData xmlData = new XmlData();
String xwalkName, metsName;
String parts[] = dmdTypes[i].split(":", 2);
if (parts.length > 1) {
metsName = parts[0];
xwalkName = parts[1];
} else xwalkName = metsName = dmdTypes[i];
DisseminationCrosswalk xwalk =
(DisseminationCrosswalk)
PluginManager.getNamedPlugin(DisseminationCrosswalk.class, xwalkName);
if (xwalk == null)
throw new PackageValidationException("Cannot find " + dmdTypes[i] + " crosswalk plugin!");
else crosswalkToMets(xwalk, item, xmlData);
DmdSec dmdSec = new DmdSec();
dmdSec.setID(dmdId[i]);
dmdSec.setGROUPID(dmdGroup);
MdWrap mdWrap = new MdWrap();
setMdType(mdWrap, metsName);
mdWrap.getContent().add(xmlData);
dmdSec.getContent().add(mdWrap);
mets.getContent().add(dmdSec);
}
// Only add license AMD section if there are any licenses.
// Catch authorization failures accessing license bitstreams
// only if we are skipping unauthorized bitstreams.
String licenseID = null;
try {
AmdSec amdSec = new AmdSec();
addRightsMd(context, item, amdSec);
if (amdSec.getContent().size() > 0) {
licenseID = gensym("license");
amdSec.setID(licenseID);
mets.getContent().add(amdSec);
}
} catch (AuthorizeException e) {
String unauth = (params == null) ? null : params.getProperty("unauthorized");
if (!(unauth != null && unauth.equalsIgnoreCase("skip"))) throw e;
else log.warn("Skipping license metadata because of access failure: " + e.toString());
}
// FIXME: History data???? Nooooo!!!!
// fileSec - all non-metadata bundles go into fileGrp,
// and each bitstream therein into a file.
// Create the bitstream-level techMd and div's for structmap
// at the same time so we can connec the IDREFs to IDs.
FileSec fileSec = new FileSec();
String techMdType = getTechMdType(params);
String parts[] = techMdType.split(":", 2);
String xwalkName, metsName;
if (parts.length > 1) {
metsName = parts[0];
xwalkName = parts[1];
} else xwalkName = metsName = techMdType;
DisseminationCrosswalk xwalk =
(DisseminationCrosswalk)
PluginManager.getNamedPlugin(DisseminationCrosswalk.class, xwalkName);
if (xwalk == null)
throw new PackageValidationException("Cannot find " + xwalkName + " crosswalk plugin!");
// log the primary bitstream for structmap
String primaryBitstreamFileID = null;
// accumulate content DIV items to put in structMap later.
List contentDivs = new ArrayList();
// how to handle unauthorized bundle/bitstream:
String unauth = (params == null) ? null : params.getProperty("unauthorized");
Bundle[] bundles = item.getBundles();
for (int i = 0; i < bundles.length; i++) {
if (PackageUtils.isMetaInfoBundle(bundles[i])) continue;
// unauthorized bundle?
// NOTE: This must match the logic in disseminate()
if (!AuthorizeManager.authorizeActionBoolean(context, bundles[i], Constants.READ)) {
if (unauth != null && (unauth.equalsIgnoreCase("skip"))) continue;
else
throw new AuthorizeException(
"Not authorized to read Bundle named \"" + bundles[i].getName() + "\"");
}
Bitstream[] bitstreams = bundles[i].getBitstreams();
// Create a fileGrp
FileGrp fileGrp = new FileGrp();
// Bundle name for USE attribute
String bName = bundles[i].getName();
if ((bName != null) && !bName.equals("")) fileGrp.setUSE(bundleToFileGrp(bName));
// watch for primary bitstream
int primaryBitstreamID = -1;
boolean isContentBundle = false;
if ((bName != null) && bName.equals("ORIGINAL")) {
isContentBundle = true;
primaryBitstreamID = bundles[i].getPrimaryBitstreamID();
}
for (int bits = 0; bits < bitstreams.length; bits++) {
// Check for authorization. Handle unauthorized
// bitstreams to match the logic in disseminate(),
// i.e. "unauth=zero" means include a 0-length bitstream,
// "unauth=skip" means to ignore it (and exclude from
// manifest).
boolean auth =
AuthorizeManager.authorizeActionBoolean(context, bitstreams[bits], Constants.READ);
if (!auth) {
if (unauth != null && unauth.equalsIgnoreCase("skip")) continue;
else if (!(unauth != null && unauth.equalsIgnoreCase("zero")))
throw new AuthorizeException(
"Not authorized to read Bitstream, SID="
+ String.valueOf(bitstreams[bits].getSequenceID()));
}
String sid = String.valueOf(bitstreams[bits].getSequenceID());
edu.harvard.hul.ois.mets.File file = new edu.harvard.hul.ois.mets.File();
String xmlIDstart = "bitstream_";
String fileID = xmlIDstart + sid;
file.setID(fileID);
// log primary bitstream for later (structMap)
if (bitstreams[bits].getID() == primaryBitstreamID) primaryBitstreamFileID = fileID;
// if this is content, add to structmap too:
if (isContentBundle) {
Div div = new Div();
div.setID(gensym("div"));
div.setTYPE("DSpace Content Bitstream");
Fptr fptr = new Fptr();
fptr.setFILEID(fileID);
div.getContent().add(fptr);
contentDivs.add(div);
}
file.setSEQ(bitstreams[bits].getSequenceID());
String groupID = "GROUP_" + xmlIDstart + sid;
/*
* If we're in THUMBNAIL or TEXT bundles, the bitstream is
* extracted text or a thumbnail, so we use the name to work
* out which bitstream to be in the same group as
*/
if ((bundles[i].getName() != null)
&& (bundles[i].getName().equals("THUMBNAIL")
|| bundles[i].getName().startsWith("TEXT"))) {
// Try and find the original bitstream, and chuck the
// derived bitstream in the same group
Bitstream original = findOriginalBitstream(item, bitstreams[bits]);
if (original != null) {
groupID = "GROUP_" + xmlIDstart + original.getSequenceID();
}
}
file.setGROUPID(groupID);
file.setMIMETYPE(bitstreams[bits].getFormat().getMIMEType());
// FIXME: CREATED: no date
file.setSIZE(auth ? bitstreams[bits].getSize() : 0);
// translate checksum and type to METS, if available.
String csType = bitstreams[bits].getChecksumAlgorithm();
String cs = bitstreams[bits].getChecksum();
if (auth && cs != null && csType != null) {
try {
file.setCHECKSUMTYPE(Checksumtype.parse(csType));
file.setCHECKSUM(cs);
} catch (MetsException e) {
log.warn("Cannot set bitstream checksum type=" + csType + " in METS.");
}
}
// FLocat: filename is MD5 checksum
FLocat flocat = new FLocat();
flocat.setLOCTYPE(Loctype.URL);
flocat.setXlinkHref(makeBitstreamName(bitstreams[bits]));
// Make bitstream techMD metadata, add to file.
String techID = "techMd_for_bitstream_" + bitstreams[bits].getSequenceID();
AmdSec fAmdSec = new AmdSec();
fAmdSec.setID(techID);
TechMD techMd = new TechMD();
techMd.setID(gensym("tech"));
MdWrap mdWrap = new MdWrap();
setMdType(mdWrap, metsName);
XmlData xmlData = new XmlData();
mdWrap.getContent().add(xmlData);
techMd.getContent().add(mdWrap);
fAmdSec.getContent().add(techMd);
mets.getContent().add(fAmdSec);
crosswalkToMets(xwalk, bitstreams[bits], xmlData);
file.setADMID(techID);
// Add FLocat to File, and File to FileGrp
file.getContent().add(flocat);
fileGrp.getContent().add(file);
}
// Add fileGrp to fileSec
fileSec.getContent().add(fileGrp);
}
// Add fileSec to document
mets.getContent().add(fileSec);
// Create simple structMap: initial div represents the Item,
// and user-visible content bitstreams are in its child divs.
StringBuffer dmdIds = new StringBuffer();
for (int i = 0; i < dmdId.length; ++i) dmdIds.append(" " + dmdId[i]);
StructMap structMap = new StructMap();
structMap.setID(gensym("struct"));
structMap.setTYPE("LOGICAL");
structMap.setLABEL("DSpace");
Div div0 = new Div();
div0.setID(gensym("div"));
div0.setTYPE("DSpace Item");
div0.setDMDID(dmdIds.substring(1));
if (licenseID != null) div0.setADMID(licenseID);
// if there is a primary bitstream, add FPTR to it.
if (primaryBitstreamFileID != null) {
Fptr fptr = new Fptr();
fptr.setFILEID(primaryBitstreamFileID);
div0.getContent().add(fptr);
}
// add DIV for each content bitstream
div0.getContent().addAll(contentDivs);
structMap.getContent().add(div0);
// Does subclass have something to add to structMap?
addStructMap(context, item, params, mets);
mets.getContent().add(structMap);
mets.validate(new MetsValidator());
mets.write(new MetsWriter(out));
} catch (MetsException e) {
// We don't pass up a MetsException, so callers don't need to
// know the details of the METS toolkit
// e.printStackTrace();
throw new PackageValidationException(e);
}
}
public static void main(String[] argv) throws Exception {
// create an options object and populate it
CommandLineParser parser = new PosixParser();
Options options = new Options();
options.addOption("s", "set", false, "set a parent/child relationship");
options.addOption("r", "remove", false, "remove a parent/child relationship");
options.addOption("p", "parent", true, "parent community (handle or database ID)");
options.addOption("c", "child", true, "child community (handle or databaseID)");
options.addOption("h", "help", false, "help");
CommandLine line = parser.parse(options, argv);
String command = null; // set or remove
String parentID = null;
String childID = null;
if (line.hasOption('h')) {
HelpFormatter myhelp = new HelpFormatter();
myhelp.printHelp("CommunityFiliator\n", options);
System.out.println("\nestablish a relationship: CommunityFiliator -s -p parentID -c childID");
System.out.println("remove a relationship: CommunityFiliator -r -p parentID -c childID");
System.exit(0);
}
if (line.hasOption('s')) {
command = "set";
}
if (line.hasOption('r')) {
command = "remove";
}
if (line.hasOption('p')) // parent
{
parentID = line.getOptionValue('p');
}
if (line.hasOption('c')) // child
{
childID = line.getOptionValue('c');
}
// now validate
// must have a command set
if (command == null) {
System.out.println(
"Error - must run with either set or remove (run with -h flag for details)");
System.exit(1);
}
if (command.equals("set") || command.equals("remove")) {
if (parentID == null) {
System.out.println("Error - a parentID must be specified (run with -h flag for details)");
System.exit(1);
}
if (childID == null) {
System.out.println("Error - a childID must be specified (run with -h flag for details)");
System.exit(1);
}
}
CommunityFiliator filiator = new CommunityFiliator();
Context c = new Context();
// ve are superuser!
c.setIgnoreAuthorization(true);
try {
// validate and resolve the parent and child IDs into commmunities
Community parent = filiator.resolveCommunity(c, parentID);
Community child = filiator.resolveCommunity(c, childID);
if (parent == null) {
System.out.println("Error, parent community cannot be found: " + parentID);
System.exit(1);
}
if (child == null) {
System.out.println("Error, child community cannot be found: " + childID);
System.exit(1);
}
if (command.equals("set")) {
filiator.filiate(c, parent, child);
} else {
filiator.defiliate(c, parent, child);
}
} catch (SQLException sqlE) {
System.out.println("Error - SQL exception: " + sqlE.toString());
} catch (AuthorizeException authE) {
System.out.println("Error - Authorize exception: " + authE.toString());
} catch (IOException ioE) {
System.out.println("Error - IO exception: " + ioE.toString());
}
}
/**
* Return instance of collection with passed id. You can add more properties through expand
* parameter.
*
* @param expand String in which is what you want to add to returned instance of collection.
* Options are: "all", "parentCommunityList", "parentCommunity", "items", "license" and
* "logo". If you want to use multiple options, it must be separated by commas.
* @param limit Limit value for items in list in collection. Default value is 100.
* @param offset Offset of start index in list of items of collection. Default value is 0.
* @param filters Comma separated list of Item Filters to use to evaluate against the items in a
* collection
* @param query_field List of metadata fields to evaluate in a metadata query. Each list value is
* used in conjunction with a query_op and query_field.
* @param query_op List of metadata operators to use in a metadata query. Each list value is used
* in conjunction with a query_field and query_field.
* @param query_val List of metadata values to evaluate in a metadata query. Each list value is
* used in conjunction with a query_value and query_op.
* @param collSel List of collections to query.
* @param headers If you want to access to collection under logged user into context. In headers
* must be set header "rest-dspace-token" with passed token from login method.
* @return Return instance of collection. It can also return status code NOT_FOUND(404) if id of
* collection is incorrect or status code UNATHORIZED(401) if user has no permission to read
* collection.
* @throws WebApplicationException It is thrown when was problem with database reading
* (SQLException) or problem with creating context(ContextException). It is thrown by
* NOT_FOUND and UNATHORIZED status codes, too.
*/
@GET
@Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
public org.dspace.rest.common.ItemFilter getItemQuery(
@QueryParam("expand") String expand,
@QueryParam("limit") @DefaultValue("100") Integer limit,
@QueryParam("offset") @DefaultValue("0") Integer offset,
@QueryParam("userIP") String user_ip,
@QueryParam("userAgent") String user_agent,
@QueryParam("xforwarderfor") String xforwarderfor,
@QueryParam("filters") @DefaultValue("is_item,all_filters") String filters,
@QueryParam("query_field[]") @DefaultValue("dc.title") List<String> query_field,
@QueryParam("query_op[]") @DefaultValue("exists") List<String> query_op,
@QueryParam("query_val[]") @DefaultValue("") List<String> query_val,
@QueryParam("collSel[]") @DefaultValue("") List<String> collSel,
@Context HttpHeaders headers,
@Context HttpServletRequest request) {
org.dspace.core.Context context = null;
ItemFilterSet itemFilterSet = new ItemFilterSet(filters, true);
ItemFilter result = itemFilterSet.getAllFiltersFilter();
try {
context = createContext(getUser(headers));
if (!configurationService.getBooleanProperty("rest.reporting-authenticate", true)) {
context.turnOffAuthorisationSystem();
}
int index = Math.min(query_field.size(), Math.min(query_op.size(), query_val.size()));
List<ItemFilterQuery> itemFilterQueries = new ArrayList<ItemFilterQuery>();
for (int i = 0; i < index; i++) {
itemFilterQueries.add(
new ItemFilterQuery(query_field.get(i), query_op.get(i), query_val.get(i)));
}
String regexClause = configurationService.getProperty("rest.regex-clause");
if (regexClause == null) {
regexClause = "";
}
List<UUID> uuids = getUuidsFromStrings(collSel);
List<List<MetadataField>> listFieldList = getMetadataFieldsList(context, query_field);
Iterator<org.dspace.content.Item> childItems =
itemService.findByMetadataQuery(
context, listFieldList, query_op, query_val, uuids, regexClause, offset, limit);
int count = itemFilterSet.processSaveItems(context, childItems, true, expand);
writeStats(
siteService.findSite(context),
UsageEvent.Action.VIEW,
user_ip,
user_agent,
xforwarderfor,
headers,
request,
context);
result.annotateQuery(query_field, query_op, query_val);
result.setUnfilteredItemCount(count);
context.complete();
} catch (IOException e) {
processException(e.getMessage(), context);
} catch (SQLException e) {
processException(e.getMessage(), context);
} catch (AuthorizeException e) {
processException(e.getMessage(), context);
} catch (ContextException e) {
processException("Unauthorized filtered item query. " + e.getMessage(), context);
} finally {
processFinally(context);
}
return result;
}
protected void dspaceDFS(DSpaceObject dso, Callback callback, boolean check, boolean reset)
throws SQLException {
if (dso.getType() != Constants.SITE
&& dso.getType() != Constants.COMMUNITY
&& dso.getType() != Constants.COLLECTION
&& dso.getType() != Constants.ITEM) {
throw new IllegalArgumentException(
contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
+ " is currently not supported as independent entity.");
}
if (reset) {
this.processed.clear();
}
if (isProcessed(dso)) {
log.debug(
"Skipping processing of "
+ contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
+ " "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ "), already processed.");
return;
}
markProcessed(dso);
// this is useful to debug depth first search, but it is really noisy.
// log.debug("Procesing " + contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso) +
// " " + dso.getID() + ":" + dso.getHandle() + ".");
// if this method is used for conversion we should check if we have the
// permissions to read a DSO before converting all of it decendents
// (e.g. check read permission on a community before converting all of
// its subcommunties and collections).
// just skip items with missing permissions and report them.
if (check) {
try {
RDFUtil.isPublic(context, dso);
} catch (ItemNotArchivedException ex) {
if (!(dso instanceof Item)) throw new IllegalStateException(ex.getMessage(), ex);
report(
"Skipping processing of Item "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ "): Item is not "
+ "archived.");
return;
} catch (ItemWithdrawnException ex) {
if (!(dso instanceof Item)) throw new IllegalStateException(ex.getMessage(), ex);
report(
"Skipping processing of Item "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ "): Item is "
+ "withdrawn.");
return;
} catch (ItemNotDiscoverableException ex) {
if (!(dso instanceof Item)) throw new IllegalStateException(ex.getMessage(), ex);
report(
"Skipping processing of Item "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ "): Item is not "
+ "discoverable.");
return;
} catch (AuthorizeException ex) {
report(
"Skipping processing of "
+ contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
+ " "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ ")"
+ ", not authorized: "
+ ex.getMessage());
return;
}
}
if (dso instanceof Site) {
List<Community> communities = communityService.findAllTop(context);
for (Community community : communities) {
this.dspaceDFS(community, callback, check, false);
}
}
if (dso instanceof Community) {
List<Community> subcommunities = ((Community) dso).getSubcommunities();
for (Community sub : subcommunities) {
this.dspaceDFS(sub, callback, check, false);
}
List<Collection> collections = ((Community) dso).getCollections();
for (Collection collection : collections) {
this.dspaceDFS(collection, callback, check, false);
}
}
if (dso instanceof Collection) {
Iterator<Item> items = itemService.findAllByCollection(context, (Collection) dso);
while (items.hasNext()) {
Item item = items.next();
this.dspaceDFS(item, callback, check, false);
}
}
// Currently Bundles and Bitsreams aren't supported as independent entities.
// They should be converted as part of an item. So we do not need to make
// the recursive call for them. An item itself will be converted as part
// of the callback call below.
// The following code is left here for the day, we decide to also convert
// bundles and/or bitstreams.
//
// if (dso instanceof Item)
// {
// Bundle[] bundles = ((Item) dso).getBundles();
// for (Bundle bundle : bundles)
// {
// this.dspaceDFS(bundle, callback, check, false);
// }
// }
//
// if (dso instanceof Bundle)
// {
// Bitstream[] bistreams = ((Bundle) dso).getBitstreams();
// for (Bitstream bitstream : bistreams)
// {
// this.dspaceDFS(bitstream, callback, check, false);
// }
// }
callback.callback(dso);
report(
"Processed "
+ contentServiceFactory.getDSpaceObjectService(dso).getTypeText(dso)
+ " "
+ dso.getID()
+ " (handle "
+ dso.getHandle()
+ ").");
}