/**
* The contents of this file are subject to the license and copyright
* detailed in the LICENSE and NOTICE files at the root of the source
* tree and available online at
*
* http://www.dspace.org/license/
*/
package org.dspace.app.itemimport;
import gr.ekt.bte.core.DataLoader;
import gr.ekt.bte.core.TransformationEngine;
import gr.ekt.bte.core.TransformationResult;
import gr.ekt.bte.core.TransformationSpec;
import gr.ekt.bte.dataloader.FileDataLoader;
import gr.ekt.bteio.generators.DSpaceOutputGenerator;
import gr.ekt.bteio.loaders.OAIPMHDataLoader;
import java.io.*;
import java.net.URL;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.zip.ZipFile;
import java.util.zip.ZipEntry;
import javax.mail.MessagingException;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import javax.xml.transform.TransformerException;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.collections.ComparatorUtils;
import org.apache.commons.io.FileDeleteStrategy;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.RandomStringUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.apache.xpath.XPathAPI;
import org.dspace.authorize.AuthorizeException;
import org.dspace.authorize.AuthorizeManager;
import org.dspace.authorize.ResourcePolicy;
import org.dspace.content.*;
import org.dspace.content.Collection;
import org.dspace.core.ConfigurationManager;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.core.Email;
import org.dspace.core.I18nUtil;
import org.dspace.core.LogManager;
import org.dspace.eperson.EPerson;
import org.dspace.eperson.Group;
import org.dspace.handle.HandleManager;
import org.dspace.search.DSIndexer;
import org.dspace.utils.DSpace;
import org.dspace.workflow.WorkflowManager;
import org.dspace.xmlworkflow.XmlWorkflowManager;
import org.w3c.dom.Document;
import org.w3c.dom.NamedNodeMap;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.SAXException;
/**
* Import items into DSpace. The conventional use is upload files by copying
* them. DSpace writes the item's bitstreams into its assetstore. Metadata is
* also loaded to the DSpace database.
* <P>
* A second use assumes the bitstream files already exist in a storage
* resource accessible to DSpace. In this case the bitstreams are 'registered'.
* That is, the metadata is loaded to the DSpace database and DSpace is given
* the location of the file which is subsumed into DSpace.
* <P>
* The distinction is controlled by the format of lines in the 'contents' file.
* See comments in processContentsFile() below.
* <P>
* Modified by David Little, UCSD Libraries 12/21/04 to
* allow the registration of files (bitstreams) into DSpace.
*/
public class ItemImport
{
private static final Logger log = Logger.getLogger(ItemImport.class);
private static boolean useWorkflow = false;
private static boolean useWorkflowSendEmail = false;
private static boolean isTest = false;
private static boolean isResume = false;
private static boolean isQuiet = false;
private static boolean template = false;
private static PrintWriter mapOut = null;
private static final String tempWorkDir = ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir");
static {
//Ensure tempWorkDir exists
File tempWorkDirFile = new File(tempWorkDir);
if (!tempWorkDirFile.exists()){
boolean success = tempWorkDirFile.mkdir();
if (success) {
log.info("Created org.dspace.app.batchitemimport.work.dir of: " + tempWorkDir);
} else {
log.error("Cannot create batch import directory! " + tempWorkDir);
}
}
}
// File listing filter to look for metadata files
private static FilenameFilter metadataFileFilter = new FilenameFilter()
{
public boolean accept(File dir, String n)
{
return n.startsWith("metadata_");
}
};
// File listing filter to check for folders
private static FilenameFilter directoryFilter = new FilenameFilter()
{
public boolean accept(File dir, String n)
{
File item = new File(dir.getAbsolutePath() + File.separatorChar + n);
return item.isDirectory();
}
};
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("b", "add-bte", false, "add items to DSpace via Biblio-Transformation-Engine (BTE)");
options.addOption("r", "replace", false, "replace items in mapfile");
options.addOption("d", "delete", false,
"delete items listed in mapfile");
options.addOption("i", "inputtype", true, "input type in case of BTE import");
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 bteInputType = null; //ris, endnote, tsv, csv, bibtex
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('b'))
{
command = "add-bte";
}
if (line.hasOption('i'))
{
bteInputType = line.getOptionValue('i');
}
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 = "";
if (line.hasOption('z'))
{
zip = true;
zipfilename = sourcedir + System.getProperty("file.separator") + line.getOptionValue('z');
}
//By default assume collections will be given on the command line
boolean commandLineCollections = true;
// 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("No collections given. Assuming 'collections' file inside item directory");
commandLineCollections = false;
}
}
else if ("add-bte".equals(command))
{
//Source dir can be null, the user can specify the parameters for his loader in the Spring XML configuration file
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("No collections given. Assuming 'collections' file inside item directory");
commandLineCollections = false;
}
if (bteInputType == null)
{
System.out
.println("Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have specified in BTE Spring XML configuration file) 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) && !"add-bte".equals(command))
{
System.out
.println("Error - resume option only works with the --add or the --add-bte commands");
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);
}
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"
// also if no collections are given in the command line
if (!"delete".equals(command) && commandLineCollections)
{
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) {
sourcedir = unzip(sourcedir, zipfilename);
}
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);
}
else if ("add-bte".equals(command))
{
myloader.addBTEItems(c, mycollections, sourcedir, mapfile, template, bteInputType, null);
}
// complete all transactions
c.complete();
}
catch (Exception e)
{
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: " + tempWorkDir);
ItemImport.deleteDirectory(new File(tempWorkDir));
}
}
catch (Exception ex)
{
System.out.println("Unable to delete temporary zip archive location: " + tempWorkDir);
}
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);
}
/**
* In this method, the BTE is instantiated. THe workflow generates the DSpace files
* necessary for the upload, and the default item import method is called
* @param c The contect
* @param mycollections The collections the items are inserted to
* @param sourceDir The filepath to the file to read data from
* @param mapFile The filepath to mapfile to be generated
* @param template
* @param inputType The type of the input data (bibtex, csv, etc.)
* @param workingDir The path to create temporary files (for command line or UI based)
* @throws Exception
*/
private void addBTEItems(Context c, Collection[] mycollections,
String sourceDir, String mapFile, boolean template, String inputType, String workingDir) throws Exception
{
//Determine the folder where BTE will output the results
String outputFolder = null;
if (workingDir == null){ //This indicates a command line import, create a random path
File importDir = new File(ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir"));
if (!importDir.exists()){
boolean success = importDir.mkdir();
if (!success) {
log.info("Cannot create batch import directory!");
throw new Exception("Cannot create batch import directory!");
}
}
//Get a random folder in case two admins batch import data at the same time
outputFolder = importDir + File.separator + generateRandomFilename(true);
}
else { //This indicates a UI import, working dir is preconfigured
outputFolder = workingDir;
}
BTEBatchImportService dls = new DSpace().getSingletonService(BTEBatchImportService.class);
DataLoader dataLoader = dls.getDataLoaders().get(inputType);
Map<String, String> outputMap = dls.getOutputMap();
TransformationEngine te = dls.getTransformationEngine();
if (dataLoader==null){
System.out.println("ERROR: The key used in -i parameter must match a valid DataLoader in the BTE Spring XML configuration file!");
return;
}
if (outputMap==null){
System.out.println("ERROR: The key used in -i parameter must match a valid outputMapping in the BTE Spring XML configuration file!");
return;
}
if (dataLoader instanceof FileDataLoader){
FileDataLoader fdl = (FileDataLoader) dataLoader;
if (!StringUtils.isBlank(sourceDir)) {
System.out.println("INFO: Dataloader will load data from the file specified in the command prompt (and not from the Spring XML configuration file)");
fdl.setFilename(sourceDir);
}
}
else if (dataLoader instanceof OAIPMHDataLoader){
OAIPMHDataLoader fdl = (OAIPMHDataLoader) dataLoader;
System.out.println(sourceDir);
if (!StringUtils.isBlank(sourceDir)){
System.out.println("INFO: Dataloader will load data from the address specified in the command prompt (and not from the Spring XML configuration file)");
fdl.setServerAddress(sourceDir);
}
}
if (dataLoader!=null){
System.out.println("INFO: Dataloader " + dataLoader.toString()+" will be used for the import!");
te.setDataLoader(dataLoader);
DSpaceOutputGenerator outputGenerator = new DSpaceOutputGenerator(outputMap);
outputGenerator.setOutputDirectory(outputFolder);
te.setOutputGenerator(outputGenerator);
try {
TransformationResult res = te.transform(new TransformationSpec());
List<String> output = res.getOutput();
outputGenerator.writeOutput(output);
} catch (Exception e) {
System.err.println("Exception");
e.printStackTrace();
throw e;
}
ItemImport myloader = new ItemImport();
myloader.addItems(c, mycollections, outputFolder, mapFile, template);
}
}
public void addItemsAtomic(Context c, Collection[] mycollections, String sourceDir, String mapFile, boolean template) throws Exception {
try {
addItems(c, mycollections, sourceDir, mapFile, template);
} catch (Exception addException) {
log.error("AddItems encountered an error, will try to revert. Error: " + addException.getMessage());
deleteItems(c, mapFile);
c.commit();
log.info("Attempted to delete partial (errored) import");
throw addException;
}
}
public void addItems(Context c, Collection[] mycollections,
String sourceDir, String mapFile, boolean template) throws Exception
{
// create the mapfile
File outFile = null;
try {
Map<String, String> skipItems = new HashMap<String, String>(); // set of items to skip if in 'resume'
// mode
System.out.println("Adding items from directory: " + sourceDir);
System.out.println("Generating mapfile: " + mapFile);
boolean directoryFileCollections = false;
if (mycollections == null)
{
directoryFileCollections = true;
}
if (!isTest)
{
// get the directory names of items to skip (will be in keys of
// hash)
if (isResume)
{
skipItems = readMapFile(mapFile);
}
// sneaky isResume == true means open file in append mode
outFile = new File(mapFile);
mapOut = new PrintWriter(new FileWriter(outFile, isResume));
if (mapOut == null)
{
throw new Exception("can't open mapfile: " + mapFile);
}
}
// open and process the source directory
File d = new java.io.File(sourceDir);
if (d == null || !d.isDirectory())
{
throw new Exception("Error, cannot open source directory " + sourceDir);
}
String[] dircontents = d.list(directoryFilter);
Arrays.sort(dircontents, ComparatorUtils.naturalComparator());
for (int i = 0; i < dircontents.length; i++)
{
if (skipItems.containsKey(dircontents[i]))
{
System.out.println("Skipping import of " + dircontents[i]);
}
else
{
Collection [] clist;
if (directoryFileCollections) {
String path = sourceDir + File.separatorChar + dircontents[i];
try {
Collection[] cols = processCollectionFile(c, path, "collections");
if (cols == null) {
System.out.println("No collections specified for item " + dircontents[i] + ". Skipping.");
continue;
}
clist = cols;
}
catch (IllegalArgumentException e)
{
System.out.println(e.getMessage() + " Skipping." );
continue;
}
}
else
{
clist = mycollections;
}
addItem(c, mycollections, sourceDir, dircontents[i], mapOut, template);
System.out.println(i + " " + dircontents[i]);
c.clearCache();
}
}
} finally {
if(mapOut!=null) {
mapOut.flush();
mapOut.close();
}
}
}
private void replaceItems(Context c, Collection[] mycollections,
String sourceDir, String mapFile, boolean template) throws Exception
{
// verify the source directory
File d = new java.io.File(sourceDir);
if (d == null || !d.isDirectory())
{
throw new Exception("Error, cannot open source directory "
+ sourceDir);
}
// read in HashMap first, to get list of handles & source dirs
Map<String, String> myHash = readMapFile(mapFile);
// for each handle, re-import the item, discard the new handle
// and re-assign the old handle
for (Map.Entry<String, String> mapEntry : myHash.entrySet())
{
// get the old handle
String newItemName = mapEntry.getKey();
String oldHandle = mapEntry.getValue();
Item oldItem = null;
if (oldHandle.indexOf('/') != -1)
{
System.out.println("\tReplacing: " + oldHandle);
// add new item, locate old one
oldItem = (Item) HandleManager.resolveToObject(c, oldHandle);
}
else
{
oldItem = Item.find(c, Integer.parseInt(oldHandle));
}
/* Rather than exposing public item methods to change handles --
* two handles can't exist at the same time due to key constraints
* so would require temp handle being stored, old being copied to new and
* new being copied to old, all a bit messy -- a handle file is written to
* the import directory containing the old handle, the existing item is
* deleted and then the import runs as though it were loading an item which
* had already been assigned a handle (so a new handle is not even assigned).
* As a commit does not occur until after a successful add, it is safe to
* do a delete as any error results in an aborted transaction without harming
* the original item */
File handleFile = new File(sourceDir + File.separatorChar + newItemName + File.separatorChar + "handle");
PrintWriter handleOut = new PrintWriter(new FileWriter(handleFile, true));
if (handleOut == null)
{
throw new Exception("can't open handle file: " + handleFile.getCanonicalPath());
}
handleOut.println(oldHandle);
handleOut.close();
deleteItem(c, oldItem);
addItem(c, mycollections, sourceDir, newItemName, null, template);
c.clearCache();
}
}
private void deleteItems(Context c, String mapFile) throws Exception
{
System.out.println("Deleting items listed in mapfile: " + mapFile);
// read in the mapfile
Map<String, String> myhash = readMapFile(mapFile);
// now delete everything that appeared in the mapFile
Iterator<String> i = myhash.keySet().iterator();
while (i.hasNext())
{
String itemID = myhash.get(i.next());
if (itemID.indexOf('/') != -1)
{
String myhandle = itemID;
System.out.println("Deleting item " + myhandle);
deleteItem(c, myhandle);
}
else
{
// it's an ID
Item myitem = Item.find(c, Integer.parseInt(itemID));
System.out.println("Deleting item " + itemID);
deleteItem(c, myitem);
}
c.clearCache();
}
}
/**
* item? try and add it to the archive.
* @param mycollections - add item to these Collections.
* @param path - directory containing the item directories.
* @param itemname handle - non-null means we have a pre-defined handle already
* @param mapOut - mapfile we're writing
*/
private Item addItem(Context c, Collection[] mycollections, String path,
String itemname, PrintWriter mapOut, boolean template) throws Exception
{
String mapOutputString = null;
System.out.println("Adding item from directory " + itemname);
// create workspace item
Item myitem = null;
WorkspaceItem wi = null;
if (!isTest)
{
wi = WorkspaceItem.create(c, mycollections[0], template);
myitem = wi.getItem();
}
// now fill out dublin core for item
loadMetadata(c, myitem, path + File.separatorChar + itemname
+ File.separatorChar);
// and the bitstreams from the contents file
// process contents file, add bistreams and bundles, return any
// non-standard permissions
List<String> options = processContentsFile(c, myitem, path
+ File.separatorChar + itemname, "contents");
if (useWorkflow)
{
// don't process handle file
// start up a workflow
if (!isTest)
{
// Should we send a workflow alert email or not?
if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow")) {
if (useWorkflowSendEmail) {
XmlWorkflowManager.start(c, wi);
} else {
XmlWorkflowManager.startWithoutNotify(c, wi);
}
} else {
if (useWorkflowSendEmail) {
WorkflowManager.start(c, wi);
}
else
{
WorkflowManager.startWithoutNotify(c, wi);
}
}
// send ID to the mapfile
mapOutputString = itemname + " " + myitem.getID();
}
}
else
{
// only process handle file if not using workflow system
String myhandle = processHandleFile(c, myitem, path
+ File.separatorChar + itemname, "handle");
// put item in system
if (!isTest)
{
try {
InstallItem.installItem(c, wi, myhandle);
} catch (Exception e) {
wi.deleteAll();
log.error("Exception after install item, try to revert...", e);
throw e;
}
// find the handle, and output to map file
myhandle = HandleManager.findHandle(c, myitem);
mapOutputString = itemname + " " + myhandle;
}
// set permissions if specified in contents file
if (options.size() > 0)
{
System.out.println("Processing options");
processOptions(c, myitem, options);
}
}
// now add to multiple collections if requested
if (mycollections.length > 1)
{
for (int i = 1; i < mycollections.length; i++)
{
if (!isTest)
{
mycollections[i].addItem(myitem);
}
}
}
// made it this far, everything is fine, commit transaction
if (mapOut != null)
{
mapOut.println(mapOutputString);
}
c.commit();
return myitem;
}
// remove, given the actual item
private void deleteItem(Context c, Item myitem) throws Exception
{
if (!isTest)
{
Collection[] collections = myitem.getCollections();
// Remove item from all the collections it's in
for (int i = 0; i < collections.length; i++)
{
collections[i].removeItem(myitem);
}
}
}
// remove, given a handle
private void deleteItem(Context c, String myhandle) throws Exception
{
// bit of a hack - to remove an item, you must remove it
// from all collections it's a part of, then it will be removed
Item myitem = (Item) HandleManager.resolveToObject(c, myhandle);
if (myitem == null)
{
System.out.println("Error - cannot locate item - already deleted?");
}
else
{
deleteItem(c, myitem);
}
}
////////////////////////////////////
// utility methods
////////////////////////////////////
// read in the map file and generate a hashmap of (file,handle) pairs
private Map<String, String> readMapFile(String filename) throws Exception
{
Map<String, String> myHash = new HashMap<String, String>();
BufferedReader is = null;
try
{
is = new BufferedReader(new FileReader(filename));
String line;
while ((line = is.readLine()) != null)
{
String myFile;
String myHandle;
// a line should be archive filename<whitespace>handle
StringTokenizer st = new StringTokenizer(line);
if (st.hasMoreTokens())
{
myFile = st.nextToken();
}
else
{
throw new Exception("Bad mapfile line:\n" + line);
}
if (st.hasMoreTokens())
{
myHandle = st.nextToken();
}
else
{
throw new Exception("Bad mapfile line:\n" + line);
}
myHash.put(myFile, myHandle);
}
}
finally
{
if (is != null)
{
is.close();
}
}
return myHash;
}
// Load all metadata schemas into the item.
private void loadMetadata(Context c, Item myitem, String path)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException
{
// Load the dublin core metadata
loadDublinCore(c, myitem, path + "dublin_core.xml");
// Load any additional metadata schemas
File folder = new File(path);
File file[] = folder.listFiles(metadataFileFilter);
for (int i = 0; i < file.length; i++)
{
loadDublinCore(c, myitem, file[i].getAbsolutePath());
}
}
private void loadDublinCore(Context c, Item myitem, String filename)
throws SQLException, IOException, ParserConfigurationException,
SAXException, TransformerException, AuthorizeException
{
Document document = loadXML(filename);
// Get the schema, for backward compatibility we will default to the
// dublin core schema if the schema name is not available in the import
// file
String schema;
NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");
Node schemaAttr = metadata.item(0).getAttributes().getNamedItem(
"schema");
if (schemaAttr == null)
{
schema = MetadataSchema.DC_SCHEMA;
}
else
{
schema = schemaAttr.getNodeValue();
}
// Get the nodes corresponding to formats
NodeList dcNodes = XPathAPI.selectNodeList(document,
"/dublin_core/dcvalue");
if (!isQuiet)
{
System.out.println("\tLoading dublin core from " + filename);
}
// Add each one as a new format to the registry
for (int i = 0; i < dcNodes.getLength(); i++)
{
Node n = dcNodes.item(i);
addDCValue(c, myitem, schema, n);
}
}
private void addDCValue(Context c, Item i, String schema, Node n) throws TransformerException, SQLException, AuthorizeException
{
String value = getStringValue(n); //n.getNodeValue();
// compensate for empty value getting read as "null", which won't display
if (value == null)
{
value = "";
}
// //getElementData(n, "element");
String element = getAttributeValue(n, "element");
String qualifier = getAttributeValue(n, "qualifier"); //NodeValue();
// //getElementData(n,
// "qualifier");
String language = getAttributeValue(n, "language");
if (language != null)
{
language = language.trim();
}
if (!isQuiet)
{
System.out.println("\tSchema: " + schema + " Element: " + element + " Qualifier: " + qualifier
+ " Value: " + value);
}
if ("none".equals(qualifier) || "".equals(qualifier))
{
qualifier = null;
}
// if language isn't set, use the system's default value
if (StringUtils.isEmpty(language))
{
language = ConfigurationManager.getProperty("default.language");
}
// a goofy default, but there it is
if (language == null)
{
language = "en";
}
if (!isTest)
{
i.addMetadata(schema, element, qualifier, language, value);
}
else
{
// If we're just test the import, let's check that the actual metadata field exists.
MetadataSchema foundSchema = MetadataSchema.find(c,schema);
if (foundSchema == null)
{
System.out.println("ERROR: schema '"+schema+"' was not found in the registry.");
return;
}
int schemaID = foundSchema.getSchemaID();
MetadataField foundField = MetadataField.findByElement(c, schemaID, element, qualifier);
if (foundField == null)
{
System.out.println("ERROR: Metadata field: '"+schema+"."+element+"."+qualifier+"' was not found in the registry.");
return;
}
}
}
/**
* Read the collections file inside the item directory. If there
* is one and it is not empty return a list of collections in
* which the item should be inserted. If it does not exist or it
* is empty return null.
*
* @param c The context
* @param path The path to the data directory for this item
* @param filename The collections file filename. Should be "collections"
* @return A list of collections in which to insert the item or null
*/
private Collection[] processCollectionFile(Context c, String path, String filename) throws IOException, SQLException
{
File file = new File(path + File.separatorChar + filename);
ArrayList<Collection> collections = new ArrayList<Collection>();
Collection[] result = null;
System.out.println("Processing collections file: " + filename);
if(file.exists())
{
BufferedReader br = null;
try
{
br = new BufferedReader(new FileReader(file));
String line = null;
while ((line = br.readLine()) != null)
{
DSpaceObject obj = null;
if (line.indexOf('/') != -1)
{
obj = HandleManager.resolveToObject(c, line);
if (obj == null || obj.getType() != Constants.COLLECTION)
{
obj = null;
}
}
else
{
obj = Collection.find(c, Integer.parseInt(line));
}
if (obj == null) {
throw new IllegalArgumentException("Cannot resolve " + line + " to a collection.");
}
collections.add((Collection)obj);
}
result = new Collection[collections.size()];
for (int i = 0; i < result.length; i++) {
result[i] = collections.get(i);
}
}
catch (FileNotFoundException e)
{
System.out.println("No collections file found.");
}
finally
{
if (br != null)
{
try {
br.close();
} catch (IOException e) {
System.out.println("Non-critical problem releasing resources.");
}
}
}
}
return result;
}
/**
* Read in the handle file or return null if empty or doesn't exist
*/
private String processHandleFile(Context c, Item i, String path, String filename)
{
File file = new File(path + File.separatorChar + filename);
String result = null;
System.out.println("Processing handle file: " + filename);
if (file.exists())
{
BufferedReader is = null;
try
{
is = new BufferedReader(new FileReader(file));
// result gets contents of file, or null
result = is.readLine();
System.out.println("read handle: '" + result + "'");
}
catch (FileNotFoundException e)
{
// probably no handle file, just return null
System.out.println("It appears there is no handle file -- generating one");
}
catch (IOException e)
{
// probably no handle file, just return null
System.out.println("It appears there is no handle file -- generating one");
}
finally
{
if (is != null)
{
try
{
is.close();
}
catch (IOException e1)
{
System.err.println("Non-critical problem releasing resources.");
}
}
}
}
else
{
// probably no handle file, just return null
System.out.println("It appears there is no handle file -- generating one");
}
return result;
}
/**
* Given a contents file and an item, stuffing it with bitstreams from the
* contents file Returns a List of Strings with lines from the contents
* file that request non-default bitstream permission
*/
private List<String> processContentsFile(Context c, Item i, String path,
String filename) throws SQLException, IOException,
AuthorizeException
{
File contentsFile = new File(path + File.separatorChar + filename);
String line = "";
List<String> options = new ArrayList<String>();
System.out.println("\tProcessing contents file: " + contentsFile);
if (contentsFile.exists())
{
BufferedReader is = null;
try
{
is = new BufferedReader(new FileReader(contentsFile));
while ((line = is.readLine()) != null)
{
if ("".equals(line.trim()))
{
continue;
}
// 1) registered into dspace (leading -r)
// 2) imported conventionally into dspace (no -r)
if (line.trim().startsWith("-r "))
{
// line should be one of these two:
// -r -s n -f filepath
// -r -s n -f filepath\tbundle:bundlename
// where
// n is the assetstore number
// filepath is the path of the file to be registered
// bundlename is an optional bundle name
String sRegistrationLine = line.trim();
int iAssetstore = -1;
String sFilePath = null;
String sBundle = null;
StringTokenizer tokenizer = new StringTokenizer(sRegistrationLine);
while (tokenizer.hasMoreTokens())
{
String sToken = tokenizer.nextToken();
if ("-r".equals(sToken))
{
continue;
}
else if ("-s".equals(sToken) && tokenizer.hasMoreTokens())
{
try
{
iAssetstore =
Integer.parseInt(tokenizer.nextToken());
}
catch (NumberFormatException e)
{
// ignore - iAssetstore remains -1
}
}
else if ("-f".equals(sToken) && tokenizer.hasMoreTokens())
{
sFilePath = tokenizer.nextToken();
}
else if (sToken.startsWith("bundle:"))
{
sBundle = sToken.substring(7);
}
else
{
// unrecognized token - should be no problem
}
} // while
if (iAssetstore == -1 || sFilePath == null)
{
System.out.println("\tERROR: invalid contents file line");
System.out.println("\t\tSkipping line: "
+ sRegistrationLine);
continue;
}
// look for descriptions
boolean descriptionExists = false;
String descriptionMarker = "\tdescription:";
int dMarkerIndex = line.indexOf(descriptionMarker);
int dEndIndex = 0;
if (dMarkerIndex > 0)
{
dEndIndex = line.indexOf("\t", dMarkerIndex + 1);
if (dEndIndex == -1)
{
dEndIndex = line.length();
}
descriptionExists = true;
}
String sDescription = "";
if (descriptionExists)
{
sDescription = line.substring(dMarkerIndex, dEndIndex);
sDescription = sDescription.replaceFirst("description:", "");
}
registerBitstream(c, i, iAssetstore, sFilePath, sBundle, sDescription);
System.out.println("\tRegistering Bitstream: " + sFilePath
+ "\tAssetstore: " + iAssetstore
+ "\tBundle: " + sBundle
+ "\tDescription: " + sDescription);
continue; // process next line in contents file
}
int bitstreamEndIndex = line.indexOf('\t');
if (bitstreamEndIndex == -1)
{
// no extra info
processContentFileEntry(c, i, path, line, null, false);
System.out.println("\tBitstream: " + line);
}
else
{
String bitstreamName = line.substring(0, bitstreamEndIndex);
boolean bundleExists = false;
boolean permissionsExist = false;
boolean descriptionExists = false;
// look for a bundle name
String bundleMarker = "\tbundle:";
int bMarkerIndex = line.indexOf(bundleMarker);
int bEndIndex = 0;
if (bMarkerIndex > 0)
{
bEndIndex = line.indexOf("\t", bMarkerIndex + 1);
if (bEndIndex == -1)
{
bEndIndex = line.length();
}
bundleExists = true;
}
// look for permissions
String permissionsMarker = "\tpermissions:";
int pMarkerIndex = line.indexOf(permissionsMarker);
int pEndIndex = 0;
if (pMarkerIndex > 0)
{
pEndIndex = line.indexOf("\t", pMarkerIndex + 1);
if (pEndIndex == -1)
{
pEndIndex = line.length();
}
permissionsExist = true;
}
// look for descriptions
String descriptionMarker = "\tdescription:";
int dMarkerIndex = line.indexOf(descriptionMarker);
int dEndIndex = 0;
if (dMarkerIndex > 0)
{
dEndIndex = line.indexOf("\t", dMarkerIndex + 1);
if (dEndIndex == -1)
{
dEndIndex = line.length();
}
descriptionExists = true;
}
// is this the primary bitstream?
String primaryBitstreamMarker = "\tprimary:true";
boolean primary = false;
String primaryStr = "";
if (line.contains(primaryBitstreamMarker))
{
primary = true;
primaryStr = "\t **Setting as primary bitstream**";
}
if (bundleExists)
{
String bundleName = line.substring(bMarkerIndex
+ bundleMarker.length(), bEndIndex).trim();
processContentFileEntry(c, i, path, bitstreamName, bundleName, primary);
System.out.println("\tBitstream: " + bitstreamName +
"\tBundle: " + bundleName +
primaryStr);
}
else
{
processContentFileEntry(c, i, path, bitstreamName, null, primary);
System.out.println("\tBitstream: " + bitstreamName + primaryStr);
}
if (permissionsExist || descriptionExists)
{
String extraInfo = bitstreamName;
if (permissionsExist)
{
extraInfo = extraInfo
+ line.substring(pMarkerIndex, pEndIndex);
}
if (descriptionExists)
{
extraInfo = extraInfo
+ line.substring(dMarkerIndex, dEndIndex);
}
options.add(extraInfo);
}
}
}
}
finally
{
if (is != null)
{
is.close();
}
}
}
else
{
String[] dirListing = new File(path).list();
for (String fileName : dirListing)
{
if (!"dublin_core.xml".equals(fileName) && !fileName.equals("handle") && !fileName.startsWith("metadata_"))
{
throw new FileNotFoundException("No contents file found");
}
}
System.out.println("No contents file found - but only metadata files found. Assuming metadata only.");
}
return options;
}
/**
* each entry represents a bitstream....
* @param c
* @param i
* @param path
* @param fileName
* @param bundleName
* @throws SQLException
* @throws IOException
* @throws AuthorizeException
*/
private void processContentFileEntry(Context c, Item i, String path,
String fileName, String bundleName, boolean primary) throws SQLException,
IOException, AuthorizeException
{
String fullpath = path + File.separatorChar + fileName;
// get an input stream
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(
fullpath));
Bitstream bs = null;
String newBundleName = bundleName;
if (bundleName == null)
{
// is it license.txt?
if ("license.txt".equals(fileName))
{
newBundleName = "LICENSE";
}
else
{
// call it ORIGINAL
newBundleName = "ORIGINAL";
}
}
if (!isTest)
{
// find the bundle
Bundle[] bundles = i.getBundles(newBundleName);
Bundle targetBundle = null;
if (bundles.length < 1)
{
// not found, create a new one
targetBundle = i.createBundle(newBundleName);
}
else
{
// put bitstreams into first bundle
targetBundle = bundles[0];
}
// now add the bitstream
bs = targetBundle.createBitstream(bis);
bs.setName(fileName);
// Identify the format
// FIXME - guessing format guesses license.txt incorrectly as a text
// file format!
BitstreamFormat bf = FormatIdentifier.guessFormat(c, bs);
bs.setFormat(bf);
// Is this a the primary bitstream?
if (primary)
{
targetBundle.setPrimaryBitstreamID(bs.getID());
targetBundle.update();
}
bs.update();
}
bis.close();
}
/**
* Register the bitstream file into DSpace
*
* @param c
* @param i
* @param assetstore
* @param bitstreamPath the full filepath expressed in the contents file
* @param bundleName
* @throws SQLException
* @throws IOException
* @throws AuthorizeException
*/
private void registerBitstream(Context c, Item i, int assetstore,
String bitstreamPath, String bundleName, String description )
throws SQLException, IOException, AuthorizeException
{
// TODO validate assetstore number
// TODO make sure the bitstream is there
Bitstream bs = null;
String newBundleName = bundleName;
if (bundleName == null)
{
// is it license.txt?
if (bitstreamPath.endsWith("license.txt"))
{
newBundleName = "LICENSE";
}
else
{
// call it ORIGINAL
newBundleName = "ORIGINAL";
}
}
if(!isTest)
{
// find the bundle
Bundle[] bundles = i.getBundles(newBundleName);
Bundle targetBundle = null;
if( bundles.length < 1 )
{
// not found, create a new one
targetBundle = i.createBundle(newBundleName);
}
else
{
// put bitstreams into first bundle
targetBundle = bundles[0];
}
// now add the bitstream
bs = targetBundle.registerBitstream(assetstore, bitstreamPath);
// set the name to just the filename
int iLastSlash = bitstreamPath.lastIndexOf('/');
bs.setName(bitstreamPath.substring(iLastSlash + 1));
// Identify the format
// FIXME - guessing format guesses license.txt incorrectly as a text file format!
BitstreamFormat bf = FormatIdentifier.guessFormat(c, bs);
bs.setFormat(bf);
bs.setDescription(description);
bs.update();
}
}
/**
*
* Process the Options to apply to the Item. The options are tab delimited
*
* Options:
* 48217870-MIT.pdf permissions: -r 'MIT Users' description: Full printable version (MIT only)
* permissions:[r|w]-['group name']
* description: 'the description of the file'
*
* where:
* [r|w] (meaning: read|write)
* ['MIT Users'] (the group name)
*
* @param c
* @param myItem
* @param options
* @throws SQLException
* @throws AuthorizeException
*/
private void processOptions(Context c, Item myItem, List<String> options)
throws SQLException, AuthorizeException
{
for (String line : options)
{
System.out.println("\tprocessing " + line);
boolean permissionsExist = false;
boolean descriptionExists = false;
String permissionsMarker = "\tpermissions:";
int pMarkerIndex = line.indexOf(permissionsMarker);
int pEndIndex = 0;
if (pMarkerIndex > 0)
{
pEndIndex = line.indexOf("\t", pMarkerIndex + 1);
if (pEndIndex == -1)
{
pEndIndex = line.length();
}
permissionsExist = true;
}
String descriptionMarker = "\tdescription:";
int dMarkerIndex = line.indexOf(descriptionMarker);
int dEndIndex = 0;
if (dMarkerIndex > 0)
{
dEndIndex = line.indexOf("\t", dMarkerIndex + 1);
if (dEndIndex == -1)
{
dEndIndex = line.length();
}
descriptionExists = true;
}
int bsEndIndex = line.indexOf("\t");
String bitstreamName = line.substring(0, bsEndIndex);
int actionID = -1;
String groupName = "";
Group myGroup = null;
if (permissionsExist)
{
String thisPermission = line.substring(pMarkerIndex
+ permissionsMarker.length(), pEndIndex);
// get permission type ("read" or "write")
int pTypeIndex = thisPermission.indexOf('-');
// get permission group (should be in single quotes)
int groupIndex = thisPermission.indexOf('\'', pTypeIndex);
int groupEndIndex = thisPermission.indexOf('\'', groupIndex + 1);
// if not in single quotes, assume everything after type flag is
// group name
if (groupIndex == -1)
{
groupIndex = thisPermission.indexOf(' ', pTypeIndex);
groupEndIndex = thisPermission.length();
}
groupName = thisPermission.substring(groupIndex + 1,
groupEndIndex);
if (thisPermission.toLowerCase().charAt(pTypeIndex + 1) == 'r')
{
actionID = Constants.READ;
}
else if (thisPermission.toLowerCase().charAt(pTypeIndex + 1) == 'w')
{
actionID = Constants.WRITE;
}
try
{
myGroup = Group.findByName(c, groupName);
}
catch (SQLException sqle)
{
System.out.println("SQL Exception finding group name: "
+ groupName);
// do nothing, will check for null group later
}
}
String thisDescription = "";
if (descriptionExists)
{
thisDescription = line.substring(
dMarkerIndex + descriptionMarker.length(), dEndIndex)
.trim();
}
Bitstream bs = null;
boolean notfound = true;
if (!isTest)
{
// find bitstream
Bitstream[] bitstreams = myItem.getNonInternalBitstreams();
for (int j = 0; j < bitstreams.length && notfound; j++)
{
if (bitstreams[j].getName().equals(bitstreamName))
{
bs = bitstreams[j];
notfound = false;
}
}
}
if (notfound && !isTest)
{
// this should never happen
System.out.println("\tdefault permissions set for "
+ bitstreamName);
}
else if (!isTest)
{
if (permissionsExist)
{
if (myGroup == null)
{
System.out.println("\t" + groupName
+ " not found, permissions set to default");
}
else if (actionID == -1)
{
System.out
.println("\tinvalid permissions flag, permissions set to default");
}
else
{
System.out.println("\tSetting special permissions for "
+ bitstreamName);
setPermission(c, myGroup, actionID, bs);
}
}
if (descriptionExists)
{
System.out.println("\tSetting description for "
+ bitstreamName);
bs.setDescription(thisDescription);
bs.update();
}
}
}
}
/**
* Set the Permission on a Bitstream.
*
* @param c
* @param g
* @param actionID
* @param bs
* @throws SQLException
* @throws AuthorizeException
*/
private void setPermission(Context c, Group g, int actionID, Bitstream bs)
throws SQLException, AuthorizeException
{
if (!isTest)
{
// remove the default policy
AuthorizeManager.removeAllPolicies(c, bs);
// add the policy
ResourcePolicy rp = ResourcePolicy.create(c);
rp.setResource(bs);
rp.setAction(actionID);
rp.setGroup(g);
rp.update();
}
else
{
if (actionID == Constants.READ)
{
System.out.println("\t\tpermissions: READ for " + g.getName());
}
else if (actionID == Constants.WRITE)
{
System.out.println("\t\tpermissions: WRITE for " + g.getName());
}
}
}
// XML utility methods
/**
* Lookup an attribute from a DOM node.
* @param n
* @param name
* @return
*/
private String getAttributeValue(Node n, String name)
{
NamedNodeMap nm = n.getAttributes();
for (int i = 0; i < nm.getLength(); i++)
{
Node node = nm.item(i);
if (name.equals(node.getNodeName()))
{
return node.getNodeValue();
}
}
return "";
}
/**
* Return the String value of a Node.
* @param node
* @return
*/
private String getStringValue(Node node)
{
String value = node.getNodeValue();
if (node.hasChildNodes())
{
Node first = node.getFirstChild();
if (first.getNodeType() == Node.TEXT_NODE)
{
return first.getNodeValue();
}
}
return value;
}
/**
* Load in the XML from file.
*
* @param filename
* the filename to load from
*
* @return the DOM representation of the XML file
*/
private static Document loadXML(String filename) throws IOException,
ParserConfigurationException, SAXException
{
DocumentBuilder builder = DocumentBuilderFactory.newInstance()
.newDocumentBuilder();
return builder.parse(new File(filename));
}
/**
* Delete a directory and its child files and directories
* @param path The directory to delete
* @return Whether the deletion was successful or not
*/
private static boolean deleteDirectory(File path)
{
if (path.exists())
{
File[] files = path.listFiles();
for (int i = 0; i < files.length; i++)
{
if (files[i].isDirectory())
{
deleteDirectory(files[i]);
}
else
{
if (!files[i].delete())
{
log.error("Unable to delete file: " + files[i].getName());
}
}
}
}
boolean pathDeleted = path.delete();
return (pathDeleted);
}
public static String unzip(File zipfile) throws IOException {
return unzip(zipfile, null);
}
public static String unzip(File zipfile, String destDir) throws IOException {
// 2
// does the zip file exist and can we write to the temp directory
if (!zipfile.canRead())
{
log.error("Zip file '" + zipfile.getAbsolutePath() + "' does not exist, or is not readable.");
}
String destinationDir = destDir;
if (destinationDir == null){
destinationDir = tempWorkDir;
}
File tempdir = new File(destinationDir);
if (!tempdir.isDirectory())
{
log.error("'" + 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");
}
if (!tempdir.exists() && !tempdir.mkdirs())
{
log.error("Unable to create temporary directory: " + tempdir.getAbsolutePath());
}
String sourcedir = destinationDir + System.getProperty("file.separator") + zipfile.getName();
String zipDir = destinationDir + System.getProperty("file.separator") + zipfile.getName() + System.getProperty("file.separator");
// 3
String sourceDirForZip = sourcedir;
ZipFile zf = new ZipFile(zipfile);
ZipEntry entry;
Enumeration<? extends ZipEntry> entries = zf.entries();
while (entries.hasMoreElements())
{
entry = entries.nextElement();
if (entry.isDirectory())
{
if (!new File(zipDir + entry.getName()).mkdir())
{
log.error("Unable to create contents directory: " + zipDir + entry.getName());
}
}
else
{
System.out.println("Extracting file: " + entry.getName());
log.info("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(zipDir + entry.getName().substring(0, index));
if (!dir.exists() && !dir.mkdirs())
{
log.error("Unable to create directory: " + dir.getAbsolutePath());
}
//Entries could have too many directories, and we need to adjust the sourcedir
// file1.zip (SimpleArchiveFormat / item1 / contents|dublin_core|...
// SimpleArchiveFormat / item2 / contents|dublin_core|...
// or
// file2.zip (item1 / contents|dublin_core|...
// item2 / contents|dublin_core|...
//regex supports either windows or *nix file paths
String[] entryChunks = entry.getName().split("/|\\\\");
if(entryChunks.length > 2) {
if(sourceDirForZip == sourcedir) {
sourceDirForZip = sourcedir + "/" + entryChunks[0];
}
}
}
byte[] buffer = new byte[1024];
int len;
InputStream in = zf.getInputStream(entry);
BufferedOutputStream out = new BufferedOutputStream(
new FileOutputStream(zipDir + entry.getName()));
while((len = in.read(buffer)) >= 0)
{
out.write(buffer, 0, len);
}
in.close();
out.close();
}
}
//Close zip file
zf.close();
if(sourceDirForZip != sourcedir) {
sourcedir = sourceDirForZip;
System.out.println("Set sourceDir using path inside of Zip: " + sourcedir);
log.info("Set sourceDir using path inside of Zip: " + sourcedir);
}
return sourcedir;
}
public static String unzip(String sourcedir, String zipfilename) throws IOException {
File zipfile = new File(sourcedir + File.separator + zipfilename);
return unzip(zipfile);
}
/**
* Generate a random filename based on current time
* @param hidden: add . as a prefix to make the file hidden
* @return the filename
*/
private static String generateRandomFilename(boolean hidden)
{
String filename = String.format("%s", RandomStringUtils.randomAlphanumeric(8));
SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd_HHmm");
String datePart = sdf.format(new Date());
filename = datePart+"_"+filename;
return filename;
}
/**
*
* Given a local file or public URL to a zip file that has the Simple Archive Format, this method imports the contents to DSpace
* @param filepath The filepath to local file or the public URL of the zip file
* @param owningCollection The owning collection the items will belong to
* @param otherCollections The collections the created items will be inserted to, apart from the owning one
* @param resumeDir In case of a resume request, the directory that containsthe old mapfile and data
* @param inputType The input type of the data (bibtex, csv, etc.), in case of local file
* @param context The context
* @throws Exception
*/
public static void processUIImport(String filepath, Collection owningCollection, String[] otherCollections, String resumeDir, String inputType, Context context) throws Exception
{
final EPerson eperson = context.getCurrentUser();
final String[] theOtherCollections = otherCollections;
final Collection theOwningCollection = owningCollection;
final String theFilePath = filepath;
final String theInputType = inputType;
final String theResumeDir = resumeDir;
Thread go = new Thread()
{
public void run()
{
Context context = null;
try {
// create a new dspace context
context = new Context();
context.setCurrentUser(eperson);
context.setIgnoreAuthorization(true);
String importDir = null;
boolean isResume = theResumeDir!=null;
List<Collection> collectionList = new ArrayList<Collection>();
if (theOtherCollections != null){
for (String colID : theOtherCollections){
int colId = Integer.parseInt(colID);
if (colId != theOwningCollection.getID()){
Collection col = Collection.find(context, colId);
if (col != null){
collectionList.add(col);
}
}
}
}
Collection[] otherCollections = collectionList.toArray(new Collection[collectionList.size()]);
importDir = ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir") + File.separator + "batchuploads" + File.separator + context.getCurrentUser().getID() + File.separator + (isResume?theResumeDir:(new GregorianCalendar()).getTimeInMillis());
File importDirFile = new File(importDir);
if (!importDirFile.exists()){
boolean success = importDirFile.mkdirs();
if (!success) {
log.info("Cannot create batch import directory!");
throw new Exception("Cannot create batch import directory!");
}
}
String dataPath = null;
String dataDir = null;
if (theInputType.equals("saf")){ //In case of Simple Archive Format import
dataPath = importDirFile + File.separator + "data.zip";
dataDir = importDirFile + File.separator + "data_unzipped2" + File.separator;
}
else { // For all other imports
dataPath = importDirFile + File.separator + (new File(theFilePath)).getName();
dataDir = importDirFile + File.separator + "data" + File.separator;
}
//Clear these files, if a resume
if (isResume){
(new File(dataPath)).delete();
FileDeleteStrategy.FORCE.delete(new File(dataDir));
}
//In case of Simple Archive Format import we need an extra effort to download the zip file and unzip it
String sourcePath = null;
if (theInputType.equals("saf")){
OutputStream os = new FileOutputStream(dataPath);
byte[] b = new byte[2048];
int length;
InputStream is = new URL(theFilePath).openStream();
while ((length = is.read(b)) != -1) {
os.write(b, 0, length);
}
is.close();
os.close();
sourcePath = unzip(new File(dataPath), dataDir);
//Move files to the required folder
FileUtils.moveDirectory(new File(sourcePath), new File(importDirFile + File.separator + "data_unzipped" + File.separator));
FileDeleteStrategy.FORCE.delete(new File(dataDir));
dataDir = importDirFile + File.separator + "data_unzipped" + File.separator;
}
//Create mapfile path
String mapFilePath = importDirFile + File.separator + "mapfile";
Collection[] finalCollections = null;
if (theOwningCollection != null){
finalCollections = new Collection[otherCollections.length + 1];
finalCollections[0] = theOwningCollection;
for (int i=0; i<otherCollections.length; i++){
finalCollections[i+1] = otherCollections[i];
}
}
ItemImport myloader = new ItemImport();
myloader.isResume = isResume;
if (theInputType.equals("saf")){ //In case of Simple Archive Format import
myloader.addItems(context, finalCollections, dataDir, mapFilePath, template);
}
else { // For all other imports (via BTE)
myloader.addBTEItems(context, finalCollections, theFilePath, mapFilePath, template, theInputType, dataDir);
}
// email message letting user know the file is ready for
// download
emailSuccessMessage(context, eperson, mapFilePath);
context.complete();
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
// abort all operations
if (mapOut != null)
{
mapOut.close();
}
mapOut = null;
try
{
emailErrorMessage(eperson, e.getMessage());
throw new Exception(e.getMessage());
}
catch (Exception e2)
{
// wont throw here
}
}
finally
{
// close the mapfile writer
if (mapOut != null)
{
mapOut.close();
}
// Make sure the database connection gets closed in all conditions.
try {
context.complete();
} catch (SQLException sqle) {
context.abort();
}
}
}
};
go.isDaemon();
go.start();
}
/**
* Since the BTE batch import is done in a new thread we are unable to communicate
* with calling method about success or failure. We accomplish this
* communication with email instead. Send a success email once the batch
* import is complete
*
* @param context
* - the current Context
* @param eperson
* - eperson to send the email to
* @param fileName
* - the filepath to the mapfile created by the batch import
* @throws MessagingException
*/
public static void emailSuccessMessage(Context context, EPerson eperson,
String fileName) throws MessagingException
{
try
{
Locale supportedLocale = I18nUtil.getEPersonLocale(eperson);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "bte_batch_import_success"));
email.addRecipient(eperson.getEmail());
email.addArgument(fileName);
email.send();
}
catch (Exception e)
{
log.warn(LogManager.getHeader(context, "emailSuccessMessage", "cannot notify user of export"), e);
}
}
/**
* Since the BTE batch import is done in a new thread we are unable to communicate
* with calling method about success or failure. We accomplis this
* communication with email instead. Send an error email if the batch
* import fails
*
* @param eperson
* - EPerson to send the error message to
* @param error
* - the error message
* @throws MessagingException
*/
public static void emailErrorMessage(EPerson eperson, String error)
throws MessagingException
{
log.warn("An error occured during item export, the user will be notified. " + error);
try
{
Locale supportedLocale = I18nUtil.getEPersonLocale(eperson);
Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "bte_batch_import_error"));
email.addRecipient(eperson.getEmail());
email.addArgument(error);
email.addArgument(ConfigurationManager.getProperty("dspace.url") + "/feedback");
email.send();
}
catch (Exception e)
{
log.warn("error during item export error notification", e);
}
}
public static List<BatchUpload> getImportsAvailable(EPerson eperson)
throws Exception
{
File uploadDir = new File(getImportUploadableDirectory(eperson.getID()));
if (!uploadDir.exists() || !uploadDir.isDirectory())
{
return null;
}
List<BatchUpload> fileNames = new ArrayList<BatchUpload>();
for (String fileName : uploadDir.list())
{
File file = new File(uploadDir + File.separator + fileName);
if (file.isDirectory()){
BatchUpload upload = new BatchUpload(file);
fileNames.add(upload);
}
}
if (fileNames.size() > 0)
{
return fileNames;
}
return null;
}
public static String getImportUploadableDirectory(int ePersonID)
throws Exception
{
String uploadDir = ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir");
if (uploadDir == null)
{
throw new Exception(
"A dspace.cfg entry for 'org.dspace.app.batchitemimport.work.dir' does not exist.");
}
return uploadDir + File.separator + "batchuploads" + File.separator + ePersonID;
}
public void deleteBatchUpload(Context c, String uploadId) throws Exception
{
String uploadDir = null;
String mapFilePath = null;
uploadDir = ItemImport.getImportUploadableDirectory(c.getCurrentUser().getID()) + File.separator + uploadId;
mapFilePath = uploadDir + File.separator + "mapfile";
this.deleteItems(c, mapFilePath);
// complete all transactions
c.commit();
FileDeleteStrategy.FORCE.delete(new File(uploadDir));
}
public static String getTempWorkDir() {
return tempWorkDir;
}
public static File getTempWorkDirFile() {
File tempDirFile = new File(getTempWorkDir());
if(!tempDirFile.exists()) {
tempDirFile.mkdirs();
}
return tempDirFile;
}
public static void cleanupZipTemp() {
System.out.println("Deleting temporary zip directory: " + tempWorkDir);
ItemImport.deleteDirectory(new File(tempWorkDir));
}
}