/**
* 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.rdf;
import com.hp.hpl.jena.rdf.model.Model;
import java.io.PrintWriter;
import java.sql.SQLException;
import java.util.Set;
import java.util.concurrent.CopyOnWriteArraySet;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.dspace.authorize.AuthorizeException;
import org.dspace.content.Collection;
import org.dspace.content.Community;
import org.dspace.content.DSpaceObject;
import org.dspace.content.Item;
import org.dspace.content.ItemIterator;
import org.dspace.content.Site;
import org.dspace.core.Constants;
import org.dspace.core.Context;
import org.dspace.handle.HandleManager;
import org.dspace.services.ConfigurationService;
import org.dspace.utils.DSpace;
/**
* This class manages the handling of RDF data in DSpace. It generates
* identifiers, it loads data, it manages the conversion of DSpace Objects into
* RDF data. It can be used as instantiated object as well as CLI.
*
* @author Pascal-Nicolas Becker (dspace -at- pascal -hyphen- becker -dot- de)
*/
public class RDFizer {
private static final Logger log = Logger.getLogger(RDFizer.class);
protected ConfigurationService configurationService;
protected boolean stdout;
protected boolean verbose;
protected boolean dryrun;
protected String lang;
protected Context context;
/**
* Set to remember with DSpaceObject were converted or deleted from the
* triplestore already. This set is helpful when converting or deleting
* multiple DSpaceObjects (g.e. Communities with all Subcommunities and
* Items).
*/
protected Set<String> processed;
public RDFizer() throws SQLException
{
this.configurationService = new DSpace().getConfigurationService();
this.stdout = false;
this.verbose = false;
this.dryrun = false;
this.lang = "TURTLE";
this.processed = new CopyOnWriteArraySet<String>();
this.context = new Context(Context.READ_ONLY);
}
/**
* This method allows you to override the context used for conversion and to
* determine which DSpaceObjects should be deleted from the triplestore,
* consider well if this is really necessary.
* If this method is not used the context of an anonymous user will be used.
* <p>
* Please consider: If your triplestore offers a public sparql endpoint
* all information readable with the provided context will be exposed to
* public!
* If you store your data in a private triplestore that does not provides
* public access, you might consider to use this method to convert all data
* stored in your repository.
* </p>
*
* @param context
*/
protected void overrideContext(Context context)
{
this.context = context;
}
/**
* Returns whether all converted data is printed to stdout. Turtle will be
* used as serialization.
* @return
*/
public boolean isStdout() {
return stdout;
}
/**
* Set this to true to print all generated data to stdout. The data will be
* stored as well, unless {@code dryrun} is set true. Turtle will be used
* as serialization.
* @param stdout
*/
public void setStdout(boolean stdout) {
this.stdout = stdout;
}
/**
* Returns whether verbose information is printed to System.err. Probably
* this is helpful for CLI only.
* @return
*/
public boolean isVerbose() {
return verbose;
}
/**
* Set this to true to print verbose information to System.err. Probably
* this is helpful for CLI only.
* @param verbose
*/
public void setVerbose(boolean verbose) {
this.verbose = verbose;
}
/**
* Returns whether this is a dry run. Probably this is helpful for CLI only.
* @return
*/
public boolean isDryrun() {
return dryrun;
}
/**
* Set this true to prevent any changes on the triple store. Probably this
* is helpful for CLI usage only.
* @param dryrun
*/
public void setDryrun(boolean dryrun) {
this.dryrun = dryrun;
}
/**
* Deletes all data stored in the triplestore (drops all named graphs and
* cleans the default graph).
*/
public void deleteAll()
{
report("Sending delete command to the triple store.");
if (!this.dryrun) RDFConfiguration.getRDFStorage().deleteAll();
report("Deleted all data from the triplestore.");
}
/**
* Delete the data about the DSpaceObject from the triplestore.
* All data about descendent Subcommunities, Collections and Items will be
* deleted as well.
*/
public void delete(DSpaceObject dso, boolean reset)
throws SQLException
{
if (dso.getType() != Constants.SITE
&& dso.getType() != Constants.COMMUNITY
&& dso.getType() != Constants.COLLECTION
&& dso.getType() != Constants.ITEM)
{
throw new IllegalArgumentException(dso.getTypeText()
+ " is currently not supported as independent entity.");
}
if (dso.getType() == Constants.SITE)
{
// we don't need to iterate over all objects, use a shorctut:
this.deleteAll();
}
Callback callback = new Callback() {
@Override
protected void callback(DSpaceObject dso)
throws SQLException
{
String identifier = RDFUtil.generateIdentifier(context, dso);
if (StringUtils.isEmpty(identifier))
{
System.err.println("Cannot determine RDF URI for "
+ dso.getTypeText() + " " + dso.getID() + "(handle "
+ dso.getHandle() + ")" + ", skipping. Please "
+ "delete it specifing the RDF URI.");
log.error("Cannot detgermine RDF URI for "
+ dso.getTypeText() + " " + dso.getID() + "(handle "
+ dso.getHandle() + ")" + ", skipping deletion.");
return;
}
report("Deleting Named Graph" + identifier);
if (!dryrun)
{
RDFConfiguration.getRDFStorage().delete(identifier);
}
}
};
this.dspaceDFS(dso, callback, false, reset);
}
/**
* Converts and stores all DSpaceObjects that are readable for an anonymous
* user.
*/
public void convertAll()
throws SQLException
{
report("Starting conversion of all DSpaceItems, this may take a while...");
this.convert(new Site(), true);
report("Conversion ended.");
}
protected void convert(DSpaceObject dso, boolean reset)
throws SQLException
{
if (dso.getType() != Constants.SITE
&& dso.getType() != Constants.COMMUNITY
&& dso.getType() != Constants.COLLECTION
&& dso.getType() != Constants.ITEM)
{
throw new IllegalArgumentException(dso.getTypeText()
+ " is currently not supported as independent entity.");
}
Callback callback = new Callback() {
@Override
protected void callback(DSpaceObject dso)
throws SQLException
{
Model converted = null;
try
{
if (dryrun)
{
converted = RDFUtil.convert(context, dso);
} else {
converted = RDFUtil.convertAndStore(context, dso);
}
} catch (ItemNotArchivedException ex) {
if (!(dso instanceof Item)) throw new IllegalStateException(ex.getMessage(), ex);
report("Skipping conversion 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 conversion 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 conversion of Item " + dso.getID()
+ " (handle " + dso.getHandle() + "): Item is not "
+ "discoverable.");
return;
} catch (AuthorizeException ex) {
report("Skipping conversion of " + dso.getTypeText() + " "
+ dso.getID() + " (handle " + dso.getHandle() + ")"
+ ", not authorized: " + ex.getMessage());
return;
} catch (RDFMissingIdentifierException ex) {
String errormessage = "Skipping conversion of "
+ dso.getTypeText() + " " + dso.getID()
+ " (handle " + dso.getHandle() + ").";
log.error(errormessage, ex);
System.err.println(errormessage
+ " Error while converting: " + ex.getMessage());
return;
}
if (stdout) {
if (converted == null)
{
System.err.println("Conversion of " + dso.getTypeText()
+ " " + dso.getID() + " resulted in no data.");
} else {
converted.write(System.out, lang);
}
}
if (converted != null) converted.close();
}
};
this.dspaceDFS(dso, callback, true, reset);
}
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(dso.getTypeText()
+ " is currently not supported as independent entity.");
}
if (reset)
{
this.processed.clear();
}
if (isProcessed(dso))
{
log.debug("Skipping processing of " + dso.getTypeText() + " "
+ 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 " + dso.getTypeText() + " " + dso.getID() + handle + ".");
// 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
// (g.e. 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 " + dso.getTypeText() + " "
+ dso.getID() + " (handle " + dso.getHandle() + ")"
+ ", not authorized: " + ex.getMessage());
return;
}
}
if (dso instanceof Site)
{
Community[] communities = Community.findAllTop(context);
for (Community community : communities)
{
this.dspaceDFS(community, callback, check, false);
}
}
if (dso instanceof Community)
{
Community[] subcommunities = ((Community) dso).getSubcommunities();
for (Community sub : subcommunities)
{
this.dspaceDFS(sub, callback, check, false);
}
Collection[] collections = ((Community) dso).getCollections();
for (Collection collection : collections)
{
this.dspaceDFS(collection, callback, check, false);
}
}
if (dso instanceof Collection)
{
ItemIterator items = ((Collection) dso).getAllItems();
while (items.hasNext())
{
Item item = items.next();
this.dspaceDFS(item, callback, check, false);
item.decache();
}
}
// Currently Bundles and Bitsreams arn't supported as independent entities.
// The should be converted as part of an item. So we do not need to make
// the recursive call for them.
//
// 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 " + dso.getTypeText() + " " + dso.getID()
+ " (handle " + dso.getHandle() + ").");
}
protected boolean isProcessed(DSpaceObject dso)
{
String key = Integer.toString(dso.getType()) + "/"
+ Integer.toString(dso.getID());
return this.processed.contains(key);
}
protected void markProcessed(DSpaceObject dso)
{
String key = Integer.toString(dso.getType()) + "/"
+ Integer.toString(dso.getID());
this.processed.add(key);
}
protected void report(String message)
{
if (this.verbose)
{
System.err.println(message);
}
log.debug(message);
}
protected void runCLI(String[] args)
{
// prepare CLI and parse arguments
Options options = createOptions();
CommandLineParser parser = new PosixParser();
CommandLine line = null;
try
{
line = parser.parse(options, args);
}
catch (ParseException ex)
{
usage(options);
System.err.println();
System.err.println(ex.getMessage());
log.fatal(ex);
System.exit(1);
}
String[] remainingArgs = line.getArgs();
if (remainingArgs.length > 0)
{
this.usage(options);
System.err.println();
StringBuilder builder = new StringBuilder(100);
for (String argument : remainingArgs)
{
if (builder.length() > 0) builder.append(", ");
builder.append(argument);
}
String argumentsLine = builder.toString().trim();
argumentsLine.substring(0, argumentsLine.length() - 1);
System.err.print("Cannot recognize the following argument");
if (remainingArgs.length >= 2) System.err.print("s");
System.err.println(": " + argumentsLine + ".");
System.exit(1);
}
// set member variables depending on CLI arguments.
if (line.hasOption("verbose"))
{
setVerbose(true);
}
if (line.hasOption("dry-run"))
{
setDryrun(true);
}
if (line.hasOption("stdout"))
{
setStdout(true);
}
// check mutual exclusive arguments
if (line.hasOption("delete") && line.hasOption("delete-all"))
{
usage(options);
System.err.println("\n\nYou cannot use the options --delete <handle> "
+ "and --delete-all together.");
System.exit(1);
}
if (line.hasOption("convert-all")
&& (line.hasOption("delete") || line.hasOption("delete-all")))
{
usage(options);
System.err.println("\n\nYou cannot use the option --convert-all "
+ "together with --delete or --delete-all.");
System.exit(1);
}
if (line.hasOption("identifiers")
&& (line.hasOption("delete") || line.hasOption("delete-all")))
{
usage(options);
System.err.println("\n\nYou cannot use the option --identifiers <handle> "
+ "together with --delete or --delete-all.");
System.exit(1);
}
if (line.hasOption("stdout")
&& (line.hasOption("delete") || line.hasOption("delete-all")))
{
usage(options);
System.err.println("\n\nYou cannot use the option --stdout together "
+ "with --delete or --deleta-all.");
System.exit(1);
}
// Run commands depending on CLI arguments.
// process help first to prevent further evaluation of given options.
if (line.hasOption('h'))
{
usage(options);
System.exit(0);
}
if (line.hasOption("delete"))
{
String[] identifiers = line.getOptionValues("delete");
for (String identifier : identifiers)
{
if (!StringUtils.startsWithIgnoreCase(identifier, "hdl:"))
{
if (!this.dryrun)
{
RDFConfiguration.getRDFStorage().delete(identifier);
}
if (this.verbose)
{
System.err.println("Deleted " + identifier + ".");
}
continue;
}
String handle = identifier.substring(4);
log.debug("Trying to resolve identifier " + handle + ".");
DSpaceObject dso = resolveHandle(handle);
if (dso == null) {
// resolveHandle reports problems and return null in case
// of an error or an unresolvable handle.
// Don't report it a second time, just continue...
continue;
}
log.debug("Resolved identifier " + handle + " as "
+ dso.getTypeText() + " " + dso.getID());
try
{
this.delete(dso, true);
}
catch (SQLException ex)
{
log.error(ex);
System.err.println("A problem with the database connection "
+ "occured. Canceled pending actions.");
System.err.println(ex.getMessage());
ex.printStackTrace(System.err);
System.exit(1);
}
}
System.exit(0);
}
if (line.hasOption("delete-all"))
{
this.deleteAll();
System.exit(0);
}
if (line.hasOption("identifiers"))
{
String[] identifiers = line.getOptionValues("identifiers");
report("Starting conversion of specified DSpaceObjects...");
this.processed.clear();
for (String handle : identifiers)
{
log.debug("Trying to resolve identifier " + handle + ".");
DSpaceObject dso = resolveHandle(handle);
if (dso == null) {
// resolveHandle reports problems and return null in case
// of an error or an unresolvable handle.
// Don't report it a second time, just continue...
continue;
}
try
{
this.convert(dso, false);
}
catch (SQLException ex)
{
log.error(ex);
System.err.println("A problem with the database connection "
+ "occured. Canceled pending actions.");
System.err.println(ex.getMessage());
ex.printStackTrace(System.err);
System.exit(1);
}
}
report("Conversion ended.");
System.exit(0);
}
if (line.hasOption("convert-all"))
{
try {
this.convertAll();
}
catch (SQLException ex)
{
log.error(ex);
System.err.println("A problem with the database connection "
+ "occured. Canceled pending actions.");
System.err.println(ex.getMessage());
ex.printStackTrace(System.err);
System.exit(1);
}
System.exit(0);
}
this.usage(options);
System.exit(0);
}
protected DSpaceObject resolveHandle(String handle)
{
DSpaceObject dso = null;
try
{
dso = HandleManager.resolveToObject(this.context, handle);
}
catch (SQLException ex)
{
log.error(ex);
System.err.println("A problem with the database connection "
+ "occured. Canceled pending actions.");
System.err.println(ex.getMessage());
ex.printStackTrace(System.err);
System.exit(1);
}
catch (IllegalStateException ex)
{
log.error(ex);
System.err.println("Cannot recognize identifier '"
+ handle + "', skipping.");
return null;
}
if (dso == null)
{
System.err.println("Cannot resolve identifier '" + handle
+ "', skipping.");
log.debug("Couldn't resolve identifier '" + handle
+ "', dso was null.");
return null;
}
if (dso.getType() != Constants.SITE
&& dso.getType() != Constants.COMMUNITY
&& dso.getType() != Constants.COLLECTION
&& dso.getType() != Constants.ITEM)
{
System.err.println(dso.getTypeText() + " are currently not "
+ "supported as independent entities. Bundles and Bitstreams "
+ "should be processed as part of their item.");
return null;
}
return dso;
}
protected Options createOptions() {
Options options = new Options();
options.addOption("h", "help", false, "Print usage information and exit.");
options.addOption("v", "verbose", false, "Print verbose information to "
+ "stderr while converting data.");
options.addOption("n", "dry-run", false, "Don't store the converted "
+ "data in the triple store, don't delete data from the "
+ "triplestore. Make a dry run, simulation what would happen.");
options.addOption("o", "stdout", false, "Print all converted data to " +
"stdout using turtle as serialization.");
options.addOption("n", "dry-run", false, "Don't send any data or commands " +
"to the triplestore. Usefull for debugging or in conjunction " +
"with --stdout.");
options.addOption("c", "convert-all", false, "Convert all DSpace Objects" +
" that are readable for an anonymous user. This may take a long time" +
"depending on the number of stored communties, collections and " +
"items. Existing information in the triple store will be updated.");
Option optIdentifiers = OptionBuilder.withLongOpt("identifiers")
.hasArgs()
.withArgName("handle")
.withValueSeparator(' ')
.withDescription("Only convert these DSpace Objects. If you specify "
+ "a Community or Collection all of their Items will be "
+ "converted as well. Separate multiple identifiers with a "
+ "space.")
.create('i');
options.addOption(optIdentifiers);
Option optDelete = OptionBuilder.withLongOpt("delete")
.hasArgs()
.withArgName("hdl:handle | URI")
.withValueSeparator(' ')
.withDescription("Delete previously converted data. Specify "
+ "either the handle of a DSpaceObject in the format "
+ "'hdl:<handle>' or the URI used to identify the rdf "
+ "data in the triplestore. If you specify a Community, "
+ "Collection or Item by its handle all converted "
+ "information about attached Subcommunities, "
+ "Collections, Items, Bundles and Bitstreams will be "
+ "deleted as well. Separate multiple identifiers with "
+ "a space.")
.create();
options.addOption(optDelete);
Option optDeleteAll = OptionBuilder.withLongOpt("delete-all")
.withDescription("Delete all converted data from the triplestore.")
.create();
options.addOption(optDeleteAll);
return options;
}
protected static void usage(Options options)
{
String cliSyntax = "[dspace-bin]/bin/dspace rdfizer [OPTIONS...]";
String header = "";
String footer = "\nYou cannot use the options --convert-all, --identifiers " +
"or --stdout together with --delete or --delete-all.\n" +
"Please use at least one option out of --convert-all, --delete, " +
"--delete-all or --identifiers.\n";
PrintWriter err = new PrintWriter(System.err);
HelpFormatter helpformater = new HelpFormatter();
helpformater.printHelp(err, 79, cliSyntax, header, options, 2, 2, footer);
err.flush();
// don't close PrintWriter err, as it would close System.err!
}
public static void main(String[] args)
{
// get a context from an anonymous user.
// don't switch off authorization system! We'll export the converted
// data into a triple store that provides a public sparql endpoint.
// all exported rdf data can be read by anonymous users.
// We won't change the database => read_only context will assure this.
Context context = null;
try {
context = new Context(Context.READ_ONLY);
}
catch (SQLException sqle)
{
log.info("Caught SQLException: ", sqle);
System.err.println("Can't connect to database: " + sqle.getMessage());
context.abort();
System.exit(-1);
}
RDFizer myself = null;
try {
myself = new RDFizer();
} catch (SQLException ex) {
System.err.println("A problem with the database occured: "
+ ex.getMessage());
ex.printStackTrace(System.err);
log.error(ex);
context.abort();
System.exit(1);
}
myself.overrideContext(context);
myself.runCLI(args);
// we don't change anything in the database, so abort the context.
context.abort();
}
protected abstract class Callback
{
protected abstract void callback(DSpaceObject dso)
throws SQLException;
}
}