/**
* to avoid overwriting the undo source tree on repeated processing sequence numbers are added and
* checked
*
* @param sourceDir - the original source directory
* @return the directory of the undo archive
* @throws FileNotFoundException
* @throws IOException
*/
private File initUndoArchive(File sourceDir) throws FileNotFoundException, IOException {
File parentDir = sourceDir.getAbsoluteFile().getParentFile();
if (parentDir == null) {
throw new FileNotFoundException(
"Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");
}
String sourceDirName = sourceDir.getName();
int seqNo = 1;
File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
while (undoDir.exists()) {
undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + ++seqNo); // increment
}
// create root directory
if (!undoDir.mkdir()) {
pr("ERROR creating Undo Archive directory ");
throw new IOException("ERROR creating Undo Archive directory ");
}
// Undo is suppressed to prevent undo of undo
File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
try {
fSuppressUndo.createNewFile();
} catch (IOException e) {
pr("ERROR creating Suppress Undo File " + e.toString());
throw e;
}
return undoDir;
}
private void setEPerson(Context context, String eperson) throws Exception {
if (eperson == null) {
pr("Error - an eperson to do the importing must be specified");
pr(" (run with -h flag for details)");
throw new Exception("EPerson not specified.");
}
EPerson myEPerson = null;
if (eperson.indexOf('@') != -1) {
// @ sign, must be an email
myEPerson = EPerson.findByEmail(context, eperson);
} else {
myEPerson = EPerson.find(context, Integer.parseInt(eperson));
}
if (myEPerson == null) {
pr("Error, eperson cannot be found: " + eperson);
throw new Exception("Invalid EPerson");
}
context.setCurrentUser(myEPerson);
}
/**
* Delete bitstream from item
*
* @param context
* @param ItemArchive
* @param isTest
* @param suppressUndo
* @throws IllegalArgumentException
* @throws ParseException
* @throws IOException
* @throws AuthorizeException
* @throws SQLException
*/
public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo)
throws IllegalArgumentException, IOException, SQLException, AuthorizeException,
ParseException {
File f = new File(itarch.getDirectory(), ItemUpdate.DELETE_CONTENTS_FILE);
if (!f.exists()) {
ItemUpdate.pr(
"Warning: Delete_contents file for item " + itarch.getDirectoryName() + " not found.");
} else {
List<Integer> list = MetadataUtilities.readDeleteContentsFile(f);
if (list.isEmpty()) {
ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName());
} else {
for (int id : list) {
try {
Bitstream bs = Bitstream.find(context, id);
if (bs == null) {
ItemUpdate.pr("Bitstream not found by id: " + id);
} else {
Bundle[] bundles = bs.getBundles();
for (Bundle b : bundles) {
if (isTest) {
ItemUpdate.pr("Delete bitstream with id = " + id);
} else {
b.removeBitstream(bs);
ItemUpdate.pr("Deleted bitstream with id = " + id);
}
}
if (alterProvenance) {
DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
String append =
"Bitstream " + bs.getName() + " deleted on " + DCDate.getCurrent() + "; ";
Item item = bundles[0].getItems()[0];
ItemUpdate.pr("Append provenance with: " + append);
if (!isTest) {
MetadataUtilities.appendMetadata(item, dtom, false, append);
}
}
}
} catch (SQLException e) {
ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
}
}
}
}
}
/** @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);
}
private void processArchive(
Context context,
String sourceDirPath,
String itemField,
String metadataIndexName,
boolean alterProvenance,
boolean isTest)
throws Exception {
// open and process the source directory
File sourceDir = new File(sourceDirPath);
if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory()) {
pr("Error, cannot open archive source directory " + sourceDirPath);
throw new Exception("error with archive source directory " + sourceDirPath);
}
String[] dircontents = sourceDir.list(directoryFilter); // just the names, not the path
Arrays.sort(dircontents);
// Undo is suppressed to prevent undo of undo
boolean suppressUndo = false;
File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
if (fSuppressUndo.exists()) {
suppressUndo = true;
}
File undoDir = null; // sibling directory of source archive
if (!suppressUndo && !isTest) {
undoDir = initUndoArchive(sourceDir);
}
int itemCount = 0;
int successItemCount = 0;
for (String dirname : dircontents) {
itemCount++;
pr("");
pr("processing item " + dirname);
try {
ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
for (UpdateAction action : actionMgr) {
pr("action: " + action.getClass().getName());
action.execute(context, itarch, isTest, suppressUndo);
if (!isTest && !suppressUndo) {
itarch.writeUndo(undoDir);
}
}
if (!isTest) {
Item item = itarch.getItem();
item.update(); // need to update before commit
context.commit();
item.decache();
}
ItemUpdate.pr("Item " + dirname + " completed");
successItemCount++;
} catch (Exception e) {
pr("Exception processing item " + dirname + ": " + e.toString());
}
}
if (!suppressUndo && !isTest) {
StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
sb.append(" -e ").append(this.eperson);
sb.append(" -s ").append(undoDir);
if (itemField != null) {
sb.append(" -i ").append(itemField);
}
if (!alterProvenance) {
sb.append(" -P ");
}
if (isTest) {
sb.append(" -t ");
}
for (String actionOption : undoActionList) {
sb.append(actionOption);
}
PrintWriter pw = null;
try {
File cmdFile = new File(undoDir.getParent(), undoDir.getName() + "_command.sh");
pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
pw.println(sb.toString());
} finally {
pw.close();
}
}
pr("");
pr(
"Done processing. Successful items: "
+ successItemCount
+ " of "
+ itemCount
+ " items in source archive");
pr("");
}