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 * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
49 java.io.File archive=null;
51 * locked IO handler for new archive file
53 SessionFile rchive=null;
55 * original archive file to be updated (or null if virgin) where new data will finally reside
57 java.io.File original=null;
59 * original archive IO handler
61 SessionFile odoclock = null;
63 * Original archive reader class
65 VamsasArchiveReader odoc = null;
67 * true if a real vamsas document is being written.
69 boolean vamsasdocument=true;
71 * Output stream for archived data
73 JarOutputStream newarchive=null;
75 * JarEntries written to archive
77 Hashtable entries = null;
79 * true if we aren't just updating an archive
81 private boolean virginArchive=false;
83 * Create a new vamsas archive
84 * File locks are made immediately to avoid contention
86 * @param archive - file spec for new vamsas archive
87 * @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
88 * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
90 public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
92 if (archive==null || (archive!=null && !(archive.getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
93 log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null)
94 ? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
97 this.vamsasdocument = vamsasdocument;
98 if (archive.exists()) {
99 this.original = archive;
100 this.archive = null; // archive will be a temp file when the open method is called
103 this.accessOriginal();
104 } catch (IOException e) {
105 throw new IOException("Lock failed for existing archive"+archive);
108 this.original = null;
109 this.archive = archive; // archive is written in place.
110 virginArchive = true;
112 this.openArchive(); // open archive
115 * name of backup of existing archive that has been updated/overwritten.
116 * onlu one backup will be made - and this is it.
118 File originalBackup = null;
120 private void makeBackup() {
121 if (!virginArchive) {
122 if (originalBackup==null && original!=null && original.exists()) {
125 originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
127 catch (IOException e) {
128 log.warn("Problem whilst making a backup of original archive.",e);
135 * called after archive is written to put file in its final place
137 private void updateOriginal() {
138 if (!virginArchive) {
139 // make sure original document really is backed up and then overwrite it.
141 // try to shut the odoc reader.
145 // Make a backup if it isn't done already
148 // copy new Archive data that was writen to a temporary file
149 odoclock.updateFrom(null, rchive);
151 catch (IOException e) {
152 // TODO: LATER: decide if leaving nastily named backup files around is necessary.
153 log.error("Problem updating archive from temporary file! - backup left in '"
154 +backupFile().getAbsolutePath()+"'",e);
156 // Tidy up if necessary.
162 boolean donotdeletebackup=false;
164 * called by app to get name of backup if it was made.
165 * If this is called, the caller app *must* delete the backup themselves.
166 * @return null or a valid file object
168 public File backupFile() {
170 if (!virginArchive) {
172 donotdeletebackup=false; // external reference has been made.
173 return ((original!=null) ? originalBackup : null);
179 * @return JarEntry name for the vamsas XML stream in this archive
181 protected String getDocumentJarEntry() {
183 return VamsasArchiveReader.VAMSASDOC;
184 return VamsasArchiveReader.VAMSASXML;
188 * @return true if Vamsas Document has been written to archive
190 protected boolean isDocumentWritten() {
191 if (newarchive==null)
192 log.warn("isDocumentWritten() called for unopened archive.");
194 if (entries.containsKey(getDocumentJarEntry()))
200 * Add unique entry strings to internal JarEntries list.
202 * @return true if entry was unique and was added.
204 private boolean addEntry(String entry) {
206 entries=new Hashtable();
207 if (entries.containsKey(entry))
209 entries.put(entry, new Integer(entries.size()));
213 * adds named entry to newarchive or returns false.
215 * @return true if entry was unique and could be added
216 * @throws IOException if entry name was invalid or a new entry could not be made on newarchive
218 private boolean addValidEntry(String entry) throws IOException {
219 JarEntry je = new JarEntry(entry);
220 if (!addEntry(entry))
222 newarchive.putNextEntry(je);
227 * opens the new archive ready for writing. If the new archive is replacing an existing one,
228 * then the existing archive will be locked, and the new archive written to a temporary file.
229 * The new archive will be put in place once close() is called.
230 * @throws IOException
232 private void openArchive() throws IOException {
234 if (newarchive!=null) {
235 log.warn("openArchive() called multiple times.");
236 throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
238 if (archive==null && (virginArchive || original==null)) {
239 log.warn("openArchive called on uninitialised VamsasArchive object.");
240 throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
242 if (!virginArchive) {
245 // make a temporary file to write to
246 archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
248 if (archive.exists())
249 log.warn("New archive file name already in use! Possible lock failure imminent?");
252 rchive = new SessionFile(archive);
254 newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));
255 entries = new Hashtable();
258 * Safely initializes the VAMSAS XML document Jar Entry.
259 * @return Writer to pass to the marshalling function.
260 * @throws IOException if a document entry has already been written.
262 public PrintWriter getDocumentOutputStream() throws IOException {
263 if (newarchive==null)
265 if (!isDocumentWritten()) {
267 if (addValidEntry(getDocumentJarEntry()))
268 return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
269 } catch (Exception e) {
270 log.warn("Problems opening XML document JarEntry stream",e);
273 throw new IOException("Vamsas Document output stream is already written.");
278 * Opens and returns the applicationData output stream for the appdataReference string.
279 * @param appdataReference
280 * @return Output stream to write to
281 * @throws IOException
283 public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
284 if (newarchive==null)
286 if (addValidEntry(appdataReference)) {
287 return new AppDataOutputStream(newarchive);
293 * Stops any current write to archive, and reverts to the backup if it exists.
294 * All existing locks on the original will be released. All backup files are removed.
296 public boolean cancelArchive() {
297 if (newarchive!=null) {
301 } catch (Exception e) {
302 log.debug("Whilst closing newarchive",e);
304 if (!virginArchive) {
305 // then there is something to recover.
309 catch (Exception e) {
310 log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
316 log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
318 closeAndReset(); // tidy up and release locks.
323 * recovers the original file's contents from the (temporary) backup.
324 * @throws Exception if any SessionFile or file removal operations fail.
326 private void recoverBackup() throws Exception {
327 if (originalBackup!=null) {
328 // backup has been made.
329 // revert from backup and delete it (changing backup filename)
331 rchive = new SessionFile(original);
333 SessionFile bckup = new SessionFile(originalBackup);
335 rchive.updateFrom(null, bckup); // recover from backup file.
342 * forget about any backup that was made - removing it first if it was only temporary.
344 private void removeBackup() {
345 if (originalBackup!=null) {
346 log.debug("Removing backup in "+originalBackup.getAbsolutePath());
347 if (!donotdeletebackup)
348 if (!originalBackup.delete())
349 log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath());
354 * only do this if you want to destroy the current file output stream
357 private void closeAndReset() {
362 if (original!=null) {
369 if (odoclock!=null) {
370 odoclock.unlockFile();
380 private final int _TRANSFER_BUFFER=4096*4;
382 * open original archive file for exclusive (locked) reading.
383 * @throws IOException
385 private void accessOriginal() throws IOException {
386 if (original!=null && original.exists()) {
388 odoclock = new SessionFile(original);
391 odoc = new VamsasArchiveReader(original);
396 * Convenience method to copy over the referred entry from the backup to the new version.
397 * Warning messages are raised if no backup exists or the
398 * entry doesn't exist in the backed-up original.
399 * Duplicate writes return true - but a warning message will also be raised.
400 * @param AppDataReference
401 * @return true if AppDataReference now exists in the new document
402 * @throws IOException
404 public boolean transferAppDataEntry(String AppDataReference) throws IOException {
405 return transferAppDataEntry(AppDataReference, AppDataReference);
408 * Transfers an AppDataReference from old to new vamsas archive, with a name change.
409 * @see transferAppDataEntry(String AppDataReference)
410 * @param AppDataReference
411 * @param NewAppDataReference - AppDataReference in new Archive
413 * @throws IOException
415 public boolean transferAppDataEntry(String AppDataReference, String NewAppDataReference) throws IOException {
416 // TODO: Specify valid AppDataReference form in all VamsasArchive handlers
417 if (AppDataReference==null)
418 throw new IOException("null AppDataReference!");
419 if (original==null || !original.exists()) {
420 log.warn("No backup archive exists.");
423 if (entries.containsKey(NewAppDataReference)) {
424 log.warn("Attempt to write '"+NewAppDataReference+"' twice! - IGNORED");
430 java.io.InputStream adstream = odoc.getAppdataStream(AppDataReference);
432 if (adstream==null) {
433 log.warn("AppDataReference '"+AppDataReference+"' doesn't exist in backup archive.");
437 java.io.OutputStream adout = getAppDataStream(NewAppDataReference);
438 // copy over the bytes
441 byte[] buffer = new byte[_TRANSFER_BUFFER]; // conservative estimate of a sensible buffer
443 if ((written = adstream.read(buffer))>-1) {
444 adout.write(buffer, 0, written);
445 log.debug("Transferring "+written+".");
448 } while (written>-1);
449 log.debug("Sucessfully transferred AppData for '"
450 +AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
454 * transfers any AppDataReferences existing in the old document
455 * that haven't already been transferred to the new one
456 * TODO: LATER: do the same for transfers requiring a namechange - more document dependent.
457 * @return true if data was transferred.
459 public boolean transferRemainingAppDatas() throws IOException {
460 boolean transfered=false;
461 if (original==null || !original.exists()) {
462 log.warn("No backup archive exists.");
467 if (getVorba()!=null) {
468 Vector originalRefs=null;
470 originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader());
471 } catch (Exception e) {
472 log.warn("Problems accessing original document entries!",e);
474 if (originalRefs!=null) {
475 Iterator ref = originalRefs.iterator();
476 while (ref.hasNext()) {
477 String oldentry = (String) ref.next();
478 if (oldentry!=null && !entries.containsKey(oldentry)) {
479 log.debug("Transferring remaining entry '"+oldentry+"'");
480 transfered |= transferAppDataEntry(oldentry);
488 * Tidies up and closes archive, removing any backups that were created.
489 * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
490 * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
491 * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
493 public void closeArchive() throws IOException {
494 if (newarchive!=null) {
495 newarchive.closeEntry();
496 if (!isDocumentWritten())
497 log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
502 log.warn("Attempt to close archive that has not been opened for writing.");
506 * Access original archive if it exists, pass the reader to the client
507 * Note: this is NOT thread safe and a call to closeArchive() will by necessity
508 * close and invalidate the VamsasArchiveReader object.
509 * @return null if no original archive exists.
511 public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
512 if (!virginArchive) {
519 * returns original document's root vamsas elements.
521 * @throws IOException
522 * @throws org.exolab.castor.xml.MarshalException
523 * @throws org.exolab.castor.xml.ValidationException
525 public object[] getOriginalRoots() throws IOException,
526 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
527 return VamsasArchive.getOriginalRoots(this);
530 * Access original document if it exists, and get VAMSAS root objects.
531 * @return vector of vamsas roots from original document
532 * @throws IOException
534 public static object[] getOriginalRoots(VamsasArchive ths) throws IOException,
535 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
536 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
539 if (oReader.isValid()) {
540 InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
541 VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
543 return doc.getVAMSAS();
544 // TODO ensure embedded appDatas are garbage collected to save memory
546 InputStream vxmlis = oReader.getVamsasXmlStream();
547 if (vxmlis!=null) { // Might be an old vamsas file.
548 BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
549 InputStreamReader vxml = new InputStreamReader(ixml);
550 VAMSAS root[] = new VAMSAS[1];
551 root[0] = VAMSAS.unmarshal(vxml);
559 protected SimpleDocument vorba = null;
562 * @return Returns the current VorbaIdFactory for the archive.
564 public VorbaIdFactory getVorba() {
566 vorba = new SimpleDocument("simpleclient.VamsasArchive");
567 return vorba.getVorba();
571 * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
573 public void setVorba(VorbaIdFactory Vorba) {
576 vorba = new SimpleDocument(Vorba);
578 vorba.setVorba(Vorba);
584 * Access and return current vamsas Document, if it exists, or create a new one
585 * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
586 * TODO: possibly modify internal state to lock low-level files
587 * (like the IClientDocument interface instance constructer would do)
588 * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
591 * @throws IOException
592 * @throws org.exolab.castor.xml.MarshalException
593 * @throws org.exolab.castor.xml.ValidationException
595 private VamsasDocument _doc=null;
596 public VamsasDocument getVamsasDocument() throws IOException,
597 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
600 _doc = getOriginalVamsasDocument(this, getVorba());
603 // Create a new document and return it
604 _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()},
605 ProvenanceStuff.newProvenance("org.vamsas.simpleclient.VamsasArchive", "Created new empty document")
606 , VersionEntries.latestVersion());
610 * Access the original vamsas document for a VamsasArchive class, and return it.
611 * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
612 * the current document - only use this one if you want the 'backup' version.
613 * TODO: catch OutOfMemoryError - they are likely to occur here.
614 * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
616 * @return null if no document exists.
617 * @throws IOException
618 * @throws org.exolab.castor.xml.MarshalException
619 * @throws org.exolab.castor.xml.ValidationException
621 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
622 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
623 return VamsasArchive.getOriginalVamsasDocument(ths, null);
627 * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
631 * @throws IOException
632 * @throws org.exolab.castor.xml.MarshalException
633 * @throws org.exolab.castor.xml.ValidationException
635 public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
636 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
637 VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
640 return ths.vorba.getVamsasDocument(oReader);
642 // otherwise - there was no valid original document to read.
646 public void putVamsasDocument(VamsasDocument doc) throws IOException,
647 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
648 putVamsasDocument(doc, getVorba());
650 public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException,
651 org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
652 VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);