1 package org.vamsas.client.simpleclient;
3 import java.io.BufferedInputStream;
4 import java.io.BufferedOutputStream;
5 import java.io.DataOutputStream;
7 import java.io.IOException;
8 import java.io.InputStream;
9 import java.io.InputStreamReader;
10 import java.io.OutputStream;
11 import java.io.OutputStreamWriter;
12 import java.io.PrintWriter;
13 import java.util.Hashtable;
14 import java.util.Iterator;
15 import java.util.Vector;
16 import java.util.jar.JarEntry;
17 import java.util.jar.JarOutputStream;
18 import java.util.jar.Manifest;
20 import org.apache.commons.logging.Log;
21 import org.apache.commons.logging.LogFactory;
22 import org.vamsas.client.ClientHandle;
23 import org.vamsas.client.IVorbaIdFactory;
24 import org.vamsas.client.SessionHandle;
25 import org.vamsas.client.UserHandle;
26 import org.vamsas.client.VorbaIdFactory;
27 import org.vamsas.client.VorbaXmlBinder;
28 import org.vamsas.client.Vobject;
29 import org.vamsas.objects.core.ApplicationData;
30 import org.vamsas.objects.core.VAMSAS;
31 import org.vamsas.objects.core.VamsasDocument;
32 import org.vamsas.objects.utils.AppDataReference;
33 import org.vamsas.objects.utils.DocumentStuff;
34 import org.vamsas.objects.utils.ProvenanceStuff;
35 import org.vamsas.objects.utils.document.VersionEntries;
38 * Class for high-level io and Jar manipulation involved in creating
39 * or updating a vamsas archive (with backups).
40 * Writes to a temporary file and then swaps new file for backup.
41 * uses the sessionFile locking mechanism for safe I/O
45 public class VamsasArchive {
46 private static Log log = LogFactory.getLog(VamsasArchive.class);
48 * Access original document if it exists, and get VAMSAS root objects.
49 * @return vector of vamsas roots from original document
52 public static Vobject[] getOriginalRoots(VamsasArchive ths) throws IOException,
53 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
54 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
57 if (oReader.isValid()) {
58 InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
59 VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
61 return doc.getVAMSAS();
62 // TODO ensure embedded appDatas are garbage collected to save memory
64 InputStream vxmlis = oReader.getVamsasXmlStream();
65 if (vxmlis!=null) { // Might be an old vamsas file.
66 BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
67 InputStreamReader vxml = new InputStreamReader(ixml);
68 VAMSAS root[] = new VAMSAS[1];
69 root[0] = VAMSAS.unmarshal(vxml);
78 * Access the original vamsas document for a VamsasArchive class, and return it.
79 * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
80 * the current document - only use this one if you want the 'backup' version.
81 * TODO: catch OutOfMemoryError - they are likely to occur here.
82 * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
84 * @return null if no document exists.
86 * @throws org.exolab.castor.xml.MarshalException
87 * @throws org.exolab.castor.xml.ValidationException
89 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
90 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
91 return VamsasArchive.getOriginalVamsasDocument(ths, null);
94 * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
99 * @throws org.exolab.castor.xml.MarshalException
100 * @throws org.exolab.castor.xml.ValidationException
102 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
103 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
104 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
107 return ths.vorba.getVamsasDocument(oReader);
109 // otherwise - there was no valid original document to read.
113 * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
115 java.io.File archive=null;
117 * locked IO handler for new archive file
119 SessionFile rchive=null;
121 * original archive file to be updated (or null if virgin) where new data will finally reside
123 java.io.File original=null;
125 * original archive IO handler
127 SessionFile odoclock = null;
128 Lock destinationLock = null;
130 * Original archive reader class
132 VamsasArchiveReader odoc = null;
134 * true if a real vamsas document is being written.
136 boolean vamsasdocument=true;
138 * Output stream for archived data
140 JarOutputStream newarchive=null;
142 * JarEntries written to archive
144 Hashtable entries = null;
147 * true if we aren't just updating an archive
149 private boolean virginArchive=false;
152 * name of backup of existing archive that has been updated/overwritten.
153 * only one backup will be made - and this is it.
155 File originalBackup = null;
157 boolean donotdeletebackup=false;
158 private final int _TRANSFER_BUFFER=4096*4;
159 protected SimpleDocument vorba = null;
161 * LATER: ? CUT'n'Paste error ?
162 * Access and return current vamsas Document, if it exists, or create a new one
163 * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
164 * _TODO: possibly modify internal state to lock low-level files
165 * (like the IClientDocument interface instance constructer would do)
166 * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
169 * @throws IOException
170 * @throws org.exolab.castor.xml.MarshalException
171 * @throws org.exolab.castor.xml.ValidationException
172 * ????? where does this live JBPNote ?
174 private VamsasDocument _doc=null;
177 * Create a new vamsas archive
178 * File locks are made immediately to avoid contention
180 * @param archive - file spec for new vamsas archive
181 * @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
182 * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
184 public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
185 this(archive, false, vamsasdocument, null);
187 public VamsasArchive(File archive, boolean vamsasdocument, boolean overwrite) throws IOException {
188 this(archive, overwrite, vamsasdocument, null);
191 * Constructor for accessing Files under file-lock management (ie a session file)
193 * @param vamsasdocument
195 * @throws IOException
197 public VamsasArchive(VamsasFile archive, boolean vamsasdocument, boolean overwrite) throws IOException {
198 this(archive.sessionFile, overwrite, vamsasdocument, archive);
199 log.debug("using non-functional lock-IO stream jar access constructor");
203 * @param archive file to write
204 * @param overwrite true if original contents should be deleted
205 * @param vamsasdocument true if a proper VamsasDocument archive is to be written.
206 * @param extantLock SessionFile object holding a lock for the <object>archive</object>
207 * @throws IOException
209 public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException {
211 if (archive==null || (archive!=null && !(archive.getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
212 log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null)
213 ? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
217 this.vamsasdocument = vamsasdocument;
218 if (archive.exists() && !overwrite) {
219 this.original = archive;
220 if (extantLock!=null) {
221 this.odoclock = extantLock;
222 if (odoclock.fileLock==null || !odoclock.fileLock.isLocked())
225 this.odoclock = new SessionFile(archive);
227 odoclock.lockFile(); // lock the file *immediatly*
228 this.archive = null; // archive will be a temp file when the open method is called
231 this.accessOriginal();
232 } catch (IOException e) {
233 throw new IOException("Lock failed for existing archive"+archive);
236 this.original = null;
237 this.archive = archive; // archive is written in place.
238 if (extantLock!=null)
241 rchive = new SessionFile(archive);
243 if (rchive.fileLock==null || rchive.fileLock.rafile==null || !rchive.fileLock.isLocked())
244 throw new IOException("Lock failed for new archive"+archive);
245 rchive.fileLock.rafile.setLength(0); // empty the archive.
246 virginArchive = true;
248 this.openArchive(); // open archive
251 * open original archive file for exclusive (locked) reading.
252 * @throws IOException
254 private void accessOriginal() throws IOException {
255 if (original!=null && original.exists()) {
257 odoclock = new SessionFile(original);
260 odoc = new VamsasArchiveReader(original);
261 // this constructor is not implemented yet odoc = new VamsasArchiveReader(odoclock.fileLock);
266 * Add unique entry strings to internal JarEntries list.
268 * @return true if entry was unique and was added.
270 private boolean addEntry(String entry) {
272 entries=new Hashtable();
273 if (entries.containsKey(entry))
275 entries.put(entry, new Integer(entries.size()));
279 * adds named entry to newarchive or returns false.
281 * @return true if entry was unique and could be added
282 * @throws IOException if entry name was invalid or a new entry could not be made on newarchive
284 private boolean addValidEntry(String entry) throws IOException {
285 JarEntry je = new JarEntry(entry);
286 if (!addEntry(entry))
289 newarchive.putNextEntry(je);
293 * called by app to get name of backup if it was made.
294 * If this is called, the caller app *must* delete the backup themselves.
295 * @return null or a valid file object
297 public File backupFile() {
299 if (!virginArchive) {
301 donotdeletebackup=false; // external reference has been made.
302 return ((original!=null) ? originalBackup : null);
308 * Stops any current write to archive, and reverts to the backup if it exists.
309 * All existing locks on the original will be released. All backup files are removed.
311 public boolean cancelArchive() {
312 if (newarchive!=null) {
314 newarchive.closeEntry();
315 newarchive.putNextEntry(new JarEntry("deleted"));
316 newarchive.closeEntry();
319 } catch (Exception e) {
320 log.debug("Whilst closing newarchive",e);
322 if (!virginArchive) {
323 // then there is something to recover.
327 catch (Exception e) {
328 log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
334 log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
336 closeAndReset(); // tidy up and release locks.
341 * only do this if you want to destroy the current file output stream
344 private void closeAndReset() {
349 if (original!=null) {
356 if (odoclock!=null) {
357 odoclock.unlockFile();
367 * Tidies up and closes archive, removing any backups that were created.
368 * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
369 * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
370 * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
372 public void closeArchive() throws IOException {
373 if (newarchive!=null) {
375 newarchive.closeEntry();
376 if (!isDocumentWritten())
377 log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
378 newarchive.close(); // use newarchive.finish(); for a stream IO
382 log.warn("Attempt to close archive that has not been opened for writing.");
386 * Opens and returns the applicationData output stream for the appdataReference string.
387 * @param appdataReference
388 * @return Output stream to write to
389 * @throws IOException
391 public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
392 if (newarchive==null)
393 throw new IOException("Attempt to write to closed VamsasArchive object.");
394 if (addValidEntry(appdataReference)) {
395 return new AppDataOutputStream(newarchive);
402 * @return JarEntry name for the vamsas XML stream in this archive
404 protected String getDocumentJarEntry() {
406 return VamsasArchiveReader.VAMSASDOC;
407 return VamsasArchiveReader.VAMSASXML;
410 * Safely initializes the VAMSAS XML document Jar Entry.
411 * @return Writer to pass to the marshalling function.
412 * @throws IOException if a document entry has already been written.
414 public PrintWriter getDocumentOutputStream() throws IOException {
415 if (newarchive==null)
417 if (!isDocumentWritten()) {
419 if (addValidEntry(getDocumentJarEntry()))
420 return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
421 } catch (Exception e) {
422 log.warn("Problems opening XML document JarEntry stream",e);
425 throw new IOException("Vamsas Document output stream is already written.");
431 * Access original archive if it exists, pass the reader to the client
432 * Note: this is NOT thread safe and a call to closeArchive() will by necessity
433 * close and invalidate the VamsasArchiveReader object.
434 * @return null if no original archive exists.
436 public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
437 if (!virginArchive) {
444 * returns original document's root vamsas elements.
446 * @throws IOException
447 * @throws org.exolab.castor.xml.MarshalException
448 * @throws org.exolab.castor.xml.ValidationException
450 public Vobject[] getOriginalRoots() throws IOException,
451 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
452 return VamsasArchive.getOriginalRoots(this);
455 * @return original document or a new empty document (with default provenance)
456 * @throws IOException
457 * @throws org.exolab.castor.xml.MarshalException
458 * @throws org.exolab.castor.xml.ValidationException
460 public VamsasDocument getVamsasDocument() throws IOException,
461 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
462 return getVamsasDocument("org.vamsas.simpleclient.VamsasArchive", "Created new empty document", null);
465 * Return the original document or a new empty document with initial provenance entry.
466 * @param provenance_user (null sets user to be the class name)
467 * @param provenance_action (null sets action to be 'created new document')
468 * @param version (null means use latest version)
469 * @return (original document or a new vamsas document with supplied provenance and version info)
470 * @throws IOException
471 * @throws org.exolab.castor.xml.MarshalException
472 * @throws org.exolab.castor.xml.ValidationException
474 public VamsasDocument getVamsasDocument(String provenance_user, String provenance_action, String version) throws IOException,
475 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
478 _doc = getOriginalVamsasDocument(this, getVorba());
481 // validate parameters
482 if (provenance_user==null)
483 provenance_user = "org.vamsas.simpleclient.VamsasArchive";
484 if (provenance_action == null)
485 provenance_action="Created new empty document";
487 version = VersionEntries.latestVersion();
488 // Create a new document and return it
489 _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()},
490 ProvenanceStuff.newProvenance(provenance_user, provenance_action), version);
494 * @return Returns the current VorbaIdFactory for the archive.
496 public VorbaIdFactory getVorba() {
498 vorba = new SimpleDocument("simpleclient.VamsasArchive");
499 return vorba.getVorba();
502 * @return true if Vamsas Document has been written to archive
504 protected boolean isDocumentWritten() {
505 if (newarchive==null)
506 log.warn("isDocumentWritten() called for unopened archive.");
508 if (entries.containsKey(getDocumentJarEntry()))
513 private void makeBackup() {
514 if (!virginArchive) {
515 if (originalBackup==null && original!=null && original.exists()) {
518 originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
520 catch (IOException e) {
521 log.warn("Problem whilst making a backup of original archive.",e);
527 * opens the new archive ready for writing. If the new archive is replacing an existing one,
528 * then the existing archive will be locked, and the new archive written to a temporary file.
529 * The new archive will be put in place once close() is called.
530 * @param doclock LATER - pass existing lock on document, if it exists.... no need yet?
531 * @throws IOException
533 private void openArchive() throws IOException {
535 if (newarchive!=null) {
536 log.warn("openArchive() called multiple times.");
537 throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
539 if (archive==null && (virginArchive || original==null)) {
540 log.warn("openArchive called on uninitialised VamsasArchive object.");
541 throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
543 if (!virginArchive) {
546 // make a temporary file to write to
547 archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
549 if (archive.exists())
550 log.warn("New archive file name already in use! Possible lock failure imminent?");
554 rchive = new SessionFile(archive);
555 if (!rchive.lockFile())
556 throw new IOException("Failed to get lock on file "+archive);
557 // LATER: locked IO stream based access.
558 //Manifest newmanifest = new Manifest();
559 //newarchive = new JarOutputStream(rchive.fileLock.getBufferedOutputStream(true), newmanifest);
560 newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));
561 entries = new Hashtable();
563 public void putVamsasDocument(VamsasDocument doc) throws IOException,
564 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
565 putVamsasDocument(doc, getVorba());
568 public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException,
569 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
571 doc.setVersion(VersionEntries.latestVersion()); // LATER: ensure this does the correct thing.
572 VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
576 * recovers the original file's contents from the (temporary) backup.
577 * @throws Exception if any SessionFile or file removal operations fail.
579 private void recoverBackup() throws Exception {
580 if (originalBackup!=null) {
581 // backup has been made.
582 // revert from backup and delete it (changing backup filename)
584 rchive = new SessionFile(original);
586 SessionFile bckup = new SessionFile(originalBackup);
588 rchive.updateFrom(null, bckup); // recover from backup file.
596 * forget about any backup that was made - removing it first if it was only temporary.
598 private void removeBackup() {
599 if (originalBackup!=null) {
600 log.debug("Removing backup in "+originalBackup.getAbsolutePath());
601 if (!donotdeletebackup)
602 if (!originalBackup.delete())
603 log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath());
608 * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
610 public void setVorba(VorbaIdFactory Vorba) {
613 vorba = new SimpleDocument(Vorba);
615 vorba.setVorba(Vorba);
620 * Convenience method to copy over the referred entry from the backup to the new version.
621 * Warning messages are raised if no backup exists or the
622 * entry doesn't exist in the backed-up original.
623 * Duplicate writes return true - but a warning message will also be raised.
624 * @param AppDataReference
625 * @return true if AppDataReference now exists in the new document
626 * @throws IOException
628 public boolean transferAppDataEntry(String AppDataReference) throws IOException {
629 return transferAppDataEntry(AppDataReference, AppDataReference);
632 * Validates the AppDataReference: not null and not already written to archive.
633 * @param AppDataReference
634 * @return true if valid. false if not
635 * @throws IOException for really broken references!
637 protected boolean _validNewAppDataReference(String newAppDataReference) throws IOException {
638 // LATER: Specify valid AppDataReference form in all VamsasArchive handlers
639 if (newAppDataReference==null)
640 throw new IOException("null newAppDataReference!");
641 if (entries.containsKey(newAppDataReference)) {
642 log.warn("Attempt to write '"+newAppDataReference+"' twice! - IGNORED");
643 // LATER: fix me? warning message should raise an exception here.
649 * Transfers an AppDataReference from old to new vamsas archive, with a name change.
650 * @see transferAppDataEntry(String AppDataReference)
651 * @param AppDataReference
652 * @param NewAppDataReference - AppDataReference in new Archive
654 * @throws IOException
656 public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException {
657 if (original==null || !original.exists()) {
658 log.warn("No backup archive exists.");
661 if (AppDataReference==null)
662 throw new IOException("null AppDataReference!");
664 if (!_validNewAppDataReference(NewAppDataReference))
669 java.io.InputStream adstream = odoc.getAppdataStream(AppDataReference);
671 if (adstream==null) {
672 log.warn("AppDataReference '"+AppDataReference+"' doesn't exist in backup archive.");
676 java.io.OutputStream adout = getAppDataStream(NewAppDataReference);
677 // copy over the bytes
680 byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
682 if ((written = adstream.read(buffer))>-1) {
683 adout.write(buffer, 0, written);
684 log.debug("Transferring "+written+".");
687 } while (written>-1);
688 log.debug("Sucessfully transferred AppData for '"
689 +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
693 * write data from a stream into an appData reference.
694 * @param AppDataReference - New AppDataReference not already written to archive
695 * @param adstream Source of data for appData reference - read until .read(buffer) returns -1
696 * @return true on success.
697 * @throws IOException for file IO or invalid AppDataReference string
699 public boolean writeAppdataFromStream(String AppDataReference, java.io.InputStream adstream) throws IOException {
700 if (!_validNewAppDataReference(AppDataReference)) {
701 log.warn("Invalid AppDataReference passed to writeAppdataFromStream");
702 throw new IOException("Invalid AppDataReference! (null, or maybe non-unique)!");
705 if (AppDataReference==null) {
706 log.warn("null appdata passed.");
707 throw new IOException("Null AppDataReference");
710 java.io.OutputStream adout = getAppDataStream(AppDataReference);
711 // copy over the bytes
714 byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
716 if ((written = adstream.read(buffer))>-1) {
717 adout.write(buffer, 0, written);
718 log.debug("Transferring "+written+".");
721 } while (written>-1);
725 * transfers any AppDataReferences existing in the old document
726 * that haven't already been transferred to the new one
727 * LATER: do the same for transfers requiring a namechange - more document dependent.
728 * @return true if data was transferred.
730 public boolean transferRemainingAppDatas() throws IOException {
731 boolean transfered=false;
732 if (original==null || !original.exists()) {
733 log.warn("No backup archive exists.");
738 if (getVorba()!=null) {
739 Vector originalRefs=null;
741 originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader());
742 } catch (Exception e) {
743 log.warn("Problems accessing original document entries!",e);
745 if (originalRefs!=null) {
746 Iterator ref = originalRefs.iterator();
747 while (ref.hasNext()) {
748 String oldentry = (String) ref.next();
749 if (oldentry!=null && !entries.containsKey(oldentry)) {
750 log.debug("Transferring remaining entry '"+oldentry+"'");
751 transfered |= transferAppDataEntry(oldentry);
759 * called after archive is written to put file in its final place
761 private void updateOriginal() {
762 if (!virginArchive) {
763 // make sure original document really is backed up and then overwrite it.
765 // try to shut the odoc reader.
769 // Make a backup if it isn't done already
772 // copy new Archive data that was writen to a temporary file
773 odoclock.updateFrom(null, rchive);
775 catch (IOException e) {
776 // LATER: decide if leaving nastily named backup files around is necessary.
777 log.error("Problem updating archive from temporary file! - backup left in '"
778 +backupFile().getAbsolutePath()+"'",e);
780 // Tidy up if necessary.