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;
19 import org.apache.commons.logging.Log;
20 import org.apache.commons.logging.LogFactory;
21 import org.vamsas.client.ClientHandle;
22 import org.vamsas.client.IVorbaIdFactory;
23 import org.vamsas.client.SessionHandle;
24 import org.vamsas.client.UserHandle;
25 import org.vamsas.client.VorbaIdFactory;
26 import org.vamsas.client.VorbaXmlBinder;
27 import org.vamsas.client.object;
28 import org.vamsas.objects.core.ApplicationData;
29 import org.vamsas.objects.core.VAMSAS;
30 import org.vamsas.objects.core.VamsasDocument;
31 import org.vamsas.objects.utils.AppDataReference;
32 import org.vamsas.objects.utils.DocumentStuff;
33 import org.vamsas.objects.utils.ProvenanceStuff;
34 import org.vamsas.objects.utils.document.VersionEntries;
37 * Class for high-level io and Jar manipulation involved in creating
38 * or updating a vamsas archive (with backups).
39 * Writes to a temporary file and then swaps new file for backup.
40 * uses the sessionFile locking mechanism for safe I/O
44 public class VamsasArchive {
45 private static Log log = LogFactory.getLog(VamsasArchive.class);
47 * Access original document if it exists, and get VAMSAS root objects.
48 * @return vector of vamsas roots from original document
51 public static object[] getOriginalRoots(VamsasArchive ths) throws IOException,
52 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
53 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
56 if (oReader.isValid()) {
57 InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
58 VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
60 return doc.getVAMSAS();
61 // TODO ensure embedded appDatas are garbage collected to save memory
63 InputStream vxmlis = oReader.getVamsasXmlStream();
64 if (vxmlis!=null) { // Might be an old vamsas file.
65 BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
66 InputStreamReader vxml = new InputStreamReader(ixml);
67 VAMSAS root[] = new VAMSAS[1];
68 root[0] = VAMSAS.unmarshal(vxml);
77 * Access the original vamsas document for a VamsasArchive class, and return it.
78 * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
79 * the current document - only use this one if you want the 'backup' version.
80 * TODO: catch OutOfMemoryError - they are likely to occur here.
81 * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
83 * @return null if no document exists.
85 * @throws org.exolab.castor.xml.MarshalException
86 * @throws org.exolab.castor.xml.ValidationException
88 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
89 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
90 return VamsasArchive.getOriginalVamsasDocument(ths, null);
93 * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
98 * @throws org.exolab.castor.xml.MarshalException
99 * @throws org.exolab.castor.xml.ValidationException
101 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
102 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
103 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
106 return ths.vorba.getVamsasDocument(oReader);
108 // otherwise - there was no valid original document to read.
112 * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
114 java.io.File archive=null;
116 * locked IO handler for new archive file
118 SessionFile rchive=null;
120 * original archive file to be updated (or null if virgin) where new data will finally reside
122 java.io.File original=null;
124 * original archive IO handler
126 SessionFile odoclock = null;
127 Lock destinationLock = null;
129 * Original archive reader class
131 VamsasArchiveReader odoc = null;
133 * true if a real vamsas document is being written.
135 boolean vamsasdocument=true;
137 * Output stream for archived data
139 JarOutputStream newarchive=null;
141 * JarEntries written to archive
143 Hashtable entries = null;
146 * true if we aren't just updating an archive
148 private boolean virginArchive=false;
151 * name of backup of existing archive that has been updated/overwritten.
152 * onlu one backup will be made - and this is it.
154 File originalBackup = null;
156 boolean donotdeletebackup=false;
157 private final int _TRANSFER_BUFFER=4096*4;
158 protected SimpleDocument vorba = null;
160 * Access and return current vamsas Document, if it exists, or create a new one
161 * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
162 * TODO: possibly modify internal state to lock low-level files
163 * (like the IClientDocument interface instance constructer would do)
164 * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
167 * @throws IOException
168 * @throws org.exolab.castor.xml.MarshalException
169 * @throws org.exolab.castor.xml.ValidationException
171 private VamsasDocument _doc=null;
174 * Create a new vamsas archive
175 * File locks are made immediately to avoid contention
177 * @param archive - file spec for new vamsas archive
178 * @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
179 * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
181 public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
182 this(archive, false, vamsasdocument, null);
184 public VamsasArchive(File archive, boolean vamsasdocument, boolean overwrite) throws IOException {
185 this(archive, overwrite, vamsasdocument, null);
189 * @param archive file to write
190 * @param overwrite true if original contents should be deleted
191 * @param vamsasdocument true if a proper VamsasDocument archive is to be written.
192 * @param extantLock SessionFile object holding a lock for the <object>archive</object>
193 * @throws IOException
195 public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException {
197 if (archive==null || (archive!=null && !(archive.getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
198 log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null)
199 ? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
203 this.vamsasdocument = vamsasdocument;
204 if (archive.exists() && !overwrite) {
205 this.original = archive;
206 if (extantLock!=null)
207 this.odoclock = extantLock;
209 this.odoclock = new SessionFile(archive);
210 odoclock.lockFile(); // lock the file *immediatly*
211 this.archive = null; // archive will be a temp file when the open method is called
214 this.accessOriginal();
215 } catch (IOException e) {
216 throw new IOException("Lock failed for existing archive"+archive);
219 this.original = null;
220 this.archive = archive; // archive is written in place.
221 if (extantLock!=null)
224 rchive = new SessionFile(archive);
226 rchive.fileLock.rafile.setLength(0); // empty the archive.
227 virginArchive = true;
229 this.openArchive(); // open archive
232 * open original archive file for exclusive (locked) reading.
233 * @throws IOException
235 private void accessOriginal() throws IOException {
236 if (original!=null && original.exists()) {
238 odoclock = new SessionFile(original);
241 odoc = new VamsasArchiveReader(original);
246 * Add unique entry strings to internal JarEntries list.
248 * @return true if entry was unique and was added.
250 private boolean addEntry(String entry) {
252 entries=new Hashtable();
253 if (entries.containsKey(entry))
255 entries.put(entry, new Integer(entries.size()));
259 * adds named entry to newarchive or returns false.
261 * @return true if entry was unique and could be added
262 * @throws IOException if entry name was invalid or a new entry could not be made on newarchive
264 private boolean addValidEntry(String entry) throws IOException {
265 JarEntry je = new JarEntry(entry);
266 if (!addEntry(entry))
268 newarchive.putNextEntry(je);
272 * called by app to get name of backup if it was made.
273 * If this is called, the caller app *must* delete the backup themselves.
274 * @return null or a valid file object
276 public File backupFile() {
278 if (!virginArchive) {
280 donotdeletebackup=false; // external reference has been made.
281 return ((original!=null) ? originalBackup : null);
287 * Stops any current write to archive, and reverts to the backup if it exists.
288 * All existing locks on the original will be released. All backup files are removed.
290 public boolean cancelArchive() {
291 if (newarchive!=null) {
295 } catch (Exception e) {
296 log.debug("Whilst closing newarchive",e);
298 if (!virginArchive) {
299 // then there is something to recover.
303 catch (Exception e) {
304 log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
310 log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
312 closeAndReset(); // tidy up and release locks.
317 * only do this if you want to destroy the current file output stream
320 private void closeAndReset() {
325 if (original!=null) {
332 if (odoclock!=null) {
333 odoclock.unlockFile();
343 * Tidies up and closes archive, removing any backups that were created.
344 * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
345 * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
346 * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
348 public void closeArchive() throws IOException {
349 if (newarchive!=null) {
350 newarchive.closeEntry();
351 if (!isDocumentWritten())
352 log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
357 log.warn("Attempt to close archive that has not been opened for writing.");
361 * Opens and returns the applicationData output stream for the appdataReference string.
362 * @param appdataReference
363 * @return Output stream to write to
364 * @throws IOException
366 public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
367 if (newarchive==null)
368 throw new IOException("Attempt to write to closed VamsasArchive object.");
369 if (addValidEntry(appdataReference)) {
370 return new AppDataOutputStream(newarchive);
377 * @return JarEntry name for the vamsas XML stream in this archive
379 protected String getDocumentJarEntry() {
381 return VamsasArchiveReader.VAMSASDOC;
382 return VamsasArchiveReader.VAMSASXML;
385 * Safely initializes the VAMSAS XML document Jar Entry.
386 * @return Writer to pass to the marshalling function.
387 * @throws IOException if a document entry has already been written.
389 public PrintWriter getDocumentOutputStream() throws IOException {
390 if (newarchive==null)
392 if (!isDocumentWritten()) {
394 if (addValidEntry(getDocumentJarEntry()))
395 return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
396 } catch (Exception e) {
397 log.warn("Problems opening XML document JarEntry stream",e);
400 throw new IOException("Vamsas Document output stream is already written.");
406 * Access original archive if it exists, pass the reader to the client
407 * Note: this is NOT thread safe and a call to closeArchive() will by necessity
408 * close and invalidate the VamsasArchiveReader object.
409 * @return null if no original archive exists.
411 public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
412 if (!virginArchive) {
419 * returns original document's root vamsas elements.
421 * @throws IOException
422 * @throws org.exolab.castor.xml.MarshalException
423 * @throws org.exolab.castor.xml.ValidationException
425 public object[] getOriginalRoots() throws IOException,
426 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
427 return VamsasArchive.getOriginalRoots(this);
430 * @return original document or a new empty document (with default provenance)
431 * @throws IOException
432 * @throws org.exolab.castor.xml.MarshalException
433 * @throws org.exolab.castor.xml.ValidationException
435 public VamsasDocument getVamsasDocument() throws IOException,
436 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
437 return getVamsasDocument("org.vamsas.simpleclient.VamsasArchive", "Created new empty document", null);
440 * Return the original document or a new empty document with initial provenance entry.
441 * @param provenance_user (null sets user to be the class name)
442 * @param provenance_action (null sets action to be 'created new document')
443 * @param version (null means use latest version)
444 * @return (original document or a new vamsas document with supplied provenance and version info)
445 * @throws IOException
446 * @throws org.exolab.castor.xml.MarshalException
447 * @throws org.exolab.castor.xml.ValidationException
449 public VamsasDocument getVamsasDocument(String provenance_user, String provenance_action, String version) throws IOException,
450 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
453 _doc = getOriginalVamsasDocument(this, getVorba());
456 // validate parameters
457 if (provenance_user==null)
458 provenance_user = "org.vamsas.simpleclient.VamsasArchive";
459 if (provenance_action == null)
460 provenance_action="Created new empty document";
462 version = VersionEntries.latestVersion();
463 // Create a new document and return it
464 _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()},
465 ProvenanceStuff.newProvenance(provenance_user, provenance_action), version);
469 * @return Returns the current VorbaIdFactory for the archive.
471 public VorbaIdFactory getVorba() {
473 vorba = new SimpleDocument("simpleclient.VamsasArchive");
474 return vorba.getVorba();
477 * @return true if Vamsas Document has been written to archive
479 protected boolean isDocumentWritten() {
480 if (newarchive==null)
481 log.warn("isDocumentWritten() called for unopened archive.");
483 if (entries.containsKey(getDocumentJarEntry()))
488 private void makeBackup() {
489 if (!virginArchive) {
490 if (originalBackup==null && original!=null && original.exists()) {
493 originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
495 catch (IOException e) {
496 log.warn("Problem whilst making a backup of original archive.",e);
502 * opens the new archive ready for writing. If the new archive is replacing an existing one,
503 * then the existing archive will be locked, and the new archive written to a temporary file.
504 * The new archive will be put in place once close() is called.
505 * @param doclock TODO
506 * @throws IOException
508 private void openArchive() throws IOException {
510 if (newarchive!=null) {
511 log.warn("openArchive() called multiple times.");
512 throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
514 if (archive==null && (virginArchive || original==null)) {
515 log.warn("openArchive called on uninitialised VamsasArchive object.");
516 throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
518 if (!virginArchive) {
521 // make a temporary file to write to
522 archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
524 if (archive.exists())
525 log.warn("New archive file name already in use! Possible lock failure imminent?");
529 rchive = new SessionFile(archive);
530 if (!rchive.lockFile())
531 throw new IOException("Failed to get lock on file "+archive);
532 newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));
533 entries = new Hashtable();
535 public void putVamsasDocument(VamsasDocument doc) throws IOException,
536 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
537 putVamsasDocument(doc, getVorba());
540 public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException,
541 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
542 VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
546 * recovers the original file's contents from the (temporary) backup.
547 * @throws Exception if any SessionFile or file removal operations fail.
549 private void recoverBackup() throws Exception {
550 if (originalBackup!=null) {
551 // backup has been made.
552 // revert from backup and delete it (changing backup filename)
554 rchive = new SessionFile(original);
556 SessionFile bckup = new SessionFile(originalBackup);
558 rchive.updateFrom(null, bckup); // recover from backup file.
566 * forget about any backup that was made - removing it first if it was only temporary.
568 private void removeBackup() {
569 if (originalBackup!=null) {
570 log.debug("Removing backup in "+originalBackup.getAbsolutePath());
571 if (!donotdeletebackup)
572 if (!originalBackup.delete())
573 log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath());
578 * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
580 public void setVorba(VorbaIdFactory Vorba) {
583 vorba = new SimpleDocument(Vorba);
585 vorba.setVorba(Vorba);
590 * Convenience method to copy over the referred entry from the backup to the new version.
591 * Warning messages are raised if no backup exists or the
592 * entry doesn't exist in the backed-up original.
593 * Duplicate writes return true - but a warning message will also be raised.
594 * @param AppDataReference
595 * @return true if AppDataReference now exists in the new document
596 * @throws IOException
598 public boolean transferAppDataEntry(String AppDataReference) throws IOException {
599 return transferAppDataEntry(AppDataReference, AppDataReference);
603 * Transfers an AppDataReference from old to new vamsas archive, with a name change.
604 * @see transferAppDataEntry(String AppDataReference)
605 * @param AppDataReference
606 * @param NewAppDataReference - AppDataReference in new Archive
608 * @throws IOException
610 public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException {
611 // TODO: Specify valid AppDataReference form in all VamsasArchive handlers
612 if (AppDataReference==null)
613 throw new IOException("null AppDataReference!");
614 if (original==null || !original.exists()) {
615 log.warn("No backup archive exists.");
618 if (entries.containsKey(NewAppDataReference)) {
619 log.warn("Attempt to write '"+NewAppDataReference+"' twice! - IGNORED");
625 java.io.InputStream adstream = odoc.getAppdataStream(AppDataReference);
627 if (adstream==null) {
628 log.warn("AppDataReference '"+AppDataReference+"' doesn't exist in backup archive.");
632 java.io.OutputStream adout = getAppDataStream(NewAppDataReference);
633 // copy over the bytes
636 byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
638 if ((written = adstream.read(buffer))>-1) {
639 adout.write(buffer, 0, written);
640 log.debug("Transferring "+written+".");
643 } while (written>-1);
644 log.debug("Sucessfully transferred AppData for '"
645 +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
650 * transfers any AppDataReferences existing in the old document
651 * that haven't already been transferred to the new one
652 * TODO: LATER: do the same for transfers requiring a namechange - more document dependent.
653 * @return true if data was transferred.
655 public boolean transferRemainingAppDatas() throws IOException {
656 boolean transfered=false;
657 if (original==null || !original.exists()) {
658 log.warn("No backup archive exists.");
663 if (getVorba()!=null) {
664 Vector originalRefs=null;
666 originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader());
667 } catch (Exception e) {
668 log.warn("Problems accessing original document entries!",e);
670 if (originalRefs!=null) {
671 Iterator ref = originalRefs.iterator();
672 while (ref.hasNext()) {
673 String oldentry = (String) ref.next();
674 if (oldentry!=null && !entries.containsKey(oldentry)) {
675 log.debug("Transferring remaining entry '"+oldentry+"'");
676 transfered |= transferAppDataEntry(oldentry);
684 * called after archive is written to put file in its final place
686 private void updateOriginal() {
687 if (!virginArchive) {
688 // make sure original document really is backed up and then overwrite it.
690 // try to shut the odoc reader.
694 // Make a backup if it isn't done already
697 // copy new Archive data that was writen to a temporary file
698 odoclock.updateFrom(null, rchive);
700 catch (IOException e) {
701 // TODO: LATER: decide if leaving nastily named backup files around is necessary.
702 log.error("Problem updating archive from temporary file! - backup left in '"
703 +backupFile().getAbsolutePath()+"'",e);
705 // Tidy up if necessary.