X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Forg%2Fvamsas%2Fclient%2Fsimpleclient%2FVamsasArchive.java;h=93c775caf209dc7e64236971585013dd10119196;hb=99cfce21cfd9e358f4f5ae628498ebad75c0b932;hp=721cdf96a7c8a5e32db019fc9c4e1184f7246e99;hpb=1f066b7b070342e9a41189e039e80d2fefb57976;p=vamsas.git
diff --git a/src/org/vamsas/client/simpleclient/VamsasArchive.java b/src/org/vamsas/client/simpleclient/VamsasArchive.java
index 721cdf9..93c775c 100644
--- a/src/org/vamsas/client/simpleclient/VamsasArchive.java
+++ b/src/org/vamsas/client/simpleclient/VamsasArchive.java
@@ -11,6 +11,8 @@ import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarOutputStream;
@@ -22,10 +24,11 @@ import org.vamsas.client.SessionHandle;
import org.vamsas.client.UserHandle;
import org.vamsas.client.VorbaIdFactory;
import org.vamsas.client.VorbaXmlBinder;
-import org.vamsas.client.object;
+import org.vamsas.client.Vobject;
import org.vamsas.objects.core.ApplicationData;
import org.vamsas.objects.core.VAMSAS;
import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.objects.utils.AppDataReference;
import org.vamsas.objects.utils.DocumentStuff;
import org.vamsas.objects.utils.ProvenanceStuff;
import org.vamsas.objects.utils.document.VersionEntries;
@@ -41,13 +44,78 @@ import org.vamsas.objects.utils.document.VersionEntries;
public class VamsasArchive {
private static Log log = LogFactory.getLog(VamsasArchive.class);
/**
+ * Access original document if it exists, and get VAMSAS root objects.
+ * @return vector of vamsas roots from original document
+ * @throws IOException
+ */
+ public static Vobject[] getOriginalRoots(VamsasArchive ths) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
+ if (oReader!=null) {
+
+ if (oReader.isValid()) {
+ InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
+ VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
+ if (doc!=null)
+ return doc.getVAMSAS();
+ // TODO ensure embedded appDatas are garbage collected to save memory
+ } else {
+ InputStream vxmlis = oReader.getVamsasXmlStream();
+ if (vxmlis!=null) { // Might be an old vamsas file.
+ BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
+ InputStreamReader vxml = new InputStreamReader(ixml);
+ VAMSAS root[] = new VAMSAS[1];
+ root[0] = VAMSAS.unmarshal(vxml);
+ if (root[0]!=null)
+ return root;
+ }
+ }
+ }
+ return null;
+ }
+ /**
+ * Access the original vamsas document for a VamsasArchive class, and return it.
+ * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
+ * the current document - only use this one if you want the 'backup' version.
+ * TODO: catch OutOfMemoryError - they are likely to occur here.
+ * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
+ * @param ths
+ * @return null if no document exists.
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return VamsasArchive.getOriginalVamsasDocument(ths, null);
+ }
+ /**
+ * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
+ * @param ths
+ * @param vorba
+ * @return
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
+ if (oReader!=null) {
+ ths.setVorba(vorba);
+ return ths.vorba.getVamsasDocument(oReader);
+ }
+ // otherwise - there was no valid original document to read.
+ return null;
+ }
+ /**
* destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
*/
java.io.File archive=null;
/**
* locked IO handler for new archive file
*/
- SessionFile rchive=null;
+ SessionFile rchive=null;
/**
* original archive file to be updated (or null if virgin) where new data will finally reside
*/
@@ -56,6 +124,7 @@ public class VamsasArchive {
* original archive IO handler
*/
SessionFile odoclock = null;
+ Lock destinationLock = null;
/**
* Original archive reader class
*/
@@ -72,10 +141,35 @@ public class VamsasArchive {
* JarEntries written to archive
*/
Hashtable entries = null;
+
/**
* true if we aren't just updating an archive
*/
private boolean virginArchive=false;
+
+ /**
+ * name of backup of existing archive that has been updated/overwritten.
+ * onlu one backup will be made - and this is it.
+ */
+ File originalBackup = null;
+
+ boolean donotdeletebackup=false;
+ private final int _TRANSFER_BUFFER=4096*4;
+ protected SimpleDocument vorba = null;
+ /**
+ * Access and return current vamsas Document, if it exists, or create a new one
+ * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
+ * TODO: possibly modify internal state to lock low-level files
+ * (like the IClientDocument interface instance constructer would do)
+ * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
+ *
+ * @return
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ private VamsasDocument _doc=null;
+
/**
* Create a new vamsas archive
* File locks are made immediately to avoid contention
@@ -85,14 +179,35 @@ public class VamsasArchive {
* @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
*/
public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
+ this(archive, false, vamsasdocument, null);
+ }
+ public VamsasArchive(File archive, boolean vamsasdocument, boolean overwrite) throws IOException {
+ this(archive, overwrite, vamsasdocument, null);
+ }
+ /**
+ *
+ * @param archive file to write
+ * @param overwrite true if original contents should be deleted
+ * @param vamsasdocument true if a proper VamsasDocument archive is to be written.
+ * @param extantLock SessionFile object holding a lock for the
+ * @throws IOException
+ */
+ public VamsasArchive(File archive, boolean overwrite, boolean vamsasdocument, SessionFile extantLock) throws IOException {
super();
- if (archive==null || (archive!=null && !archive.canWrite())) {
- log.fatal("Invalid parameters for VamsasArchive constructor:"+((archive!=null)
+ if (archive==null || (archive!=null && !(archive.getParentFile().canWrite() && (!archive.exists() || archive.canWrite())))) {
+ log.fatal("Expect Badness! -- Invalid parameters for VamsasArchive constructor:"+((archive!=null)
? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
+ return;
}
+
this.vamsasdocument = vamsasdocument;
- if (archive.exists()) {
+ if (archive.exists() && !overwrite) {
this.original = archive;
+ if (extantLock!=null)
+ this.odoclock = extantLock;
+ else
+ this.odoclock = new SessionFile(archive);
+ odoclock.lockFile(); // lock the file *immediatly*
this.archive = null; // archive will be a temp file when the open method is called
virginArchive=false;
try {
@@ -103,92 +218,31 @@ public class VamsasArchive {
} else {
this.original = null;
this.archive = archive; // archive is written in place.
+ if (extantLock!=null)
+ rchive=extantLock;
+ else
+ rchive = new SessionFile(archive);
+ rchive.lockFile();
+ rchive.fileLock.rafile.setLength(0); // empty the archive.
virginArchive = true;
}
- this.openArchive();
- }
- /**
- * name of backup of existing archive that has been updated/overwritten.
- * onlu one backup will be made - and this is it.
- */
- File originalBackup = null;
-
- private void makeBackup() {
- if (!virginArchive) {
- if (originalBackup==null && original!=null && original.exists()) {
- try {
- accessOriginal();
- originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
- }
- catch (IOException e) {
- log.warn("Problem whilst making a backup of original archive.",e);
- }
- }
- }
- }
-
- /**
- * called after archive is written to put file in its final place
- * TODO: FINISH ?? original should have sessionFile, and archive should also have sessionFile
- */
- private void updateOriginal() {
- if (!virginArchive) {
- // make sure original document really is backed up and then overwrite it.
- if (odoc!=null) {
- // try to shut the odoc reader.
- odoc.close();
- odoc = null;
- }
- // Make a backup if it isn't done already
- if (originalBackup==null)
- makeBackup();
- try {
- // copy new Archive data that was writen to a temporary file
- odoclock.updateFrom(null, rchive);
- }
- catch (IOException e) {
- log.error("Problem updating archive from temporary file! - backup in '"
- +backupFile().getAbsolutePath()+"'",e);
- }
- } else {
- // don't need to do anything.
- }
+ this.openArchive(); // open archive
}
/**
- * called by app to get name of backup if it was made.
- * @return null or a valid file object
+ * open original archive file for exclusive (locked) reading.
+ * @throws IOException
*/
- public File backupFile() {
-
- if (!virginArchive) {
- makeBackup();
- return ((original!=null) ? originalBackup : null);
+ private void accessOriginal() throws IOException {
+ if (original!=null && original.exists()) {
+ if (odoclock==null)
+ odoclock = new SessionFile(original);
+ odoclock.lockFile();
+ if (odoc == null)
+ odoc = new VamsasArchiveReader(original);
}
- return null;
- }
- /**
- *
- * @return JarEntry name for the vamsas XML stream in this archive
- */
- protected String getDocumentJarEntry() {
- if (vamsasdocument)
- return VamsasArchiveReader.VAMSASDOC;
- return VamsasArchiveReader.VAMSASXML;
}
/**
- * @return true if Vamsas Document has been written to archive
- */
- protected boolean isDocumentWritten() {
- if (newarchive==null)
- log.warn("isDocumentWritten() called for unopened archive.");
- if (entries!=null) {
- if (entries.containsKey(getDocumentJarEntry()))
- return true;
- }
- return false;
- }
- /**
* Add unique entry strings to internal JarEntries list.
* @param entry
* @return true if entry was unique and was added.
@@ -214,69 +268,17 @@ public class VamsasArchive {
newarchive.putNextEntry(je);
return true;
}
-
/**
- * opens the new archive ready for writing. If the new archive is replacing an existing one,
- * then the existing archive will be locked, and the new archive written to a temporary file.
- * The new archive will be put in place once close() is called.
- * @throws IOException
+ * called by app to get name of backup if it was made.
+ * If this is called, the caller app *must* delete the backup themselves.
+ * @return null or a valid file object
*/
- private void openArchive() throws IOException {
+ public File backupFile() {
- if (newarchive!=null) {
- log.warn("openArchive() called multiple times.");
- throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
- }
- if (archive==null && (virginArchive || original==null)) {
- log.warn("openArchive called on uninitialised VamsasArchive object.");
- throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
- }
if (!virginArchive) {
- // lock the original
- accessOriginal();
- // make a temporary file to write to
- archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
- } else {
- if (archive.exists())
- log.warn("New archive file name already in use! Possible lock failure imminent?");
- }
-
- rchive = new SessionFile(archive);
- rchive.lockFile();
- newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));
- entries = new Hashtable();
- }
- /**
- * Safely initializes the VAMSAS XML document Jar Entry.
- * @return Writer to pass to the marshalling function.
- * @throws IOException if a document entry has already been written.
- */
- public PrintWriter getDocumentOutputStream() throws IOException {
- if (newarchive==null)
- openArchive();
- if (!isDocumentWritten()) {
- try {
- if (addValidEntry(getDocumentJarEntry()))
- return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
- } catch (Exception e) {
- log.warn("Problems opening XML document JarEntry stream",e);
- }
- } else {
- throw new IOException("Vamsas Document output stream is already written.");
- }
- return null;
- }
- /**
- * Opens and returns the applicationData output stream for the appdataReference string.
- * @param appdataReference
- * @return Output stream to write to
- * @throws IOException
- */
- public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
- if (newarchive==null)
- openArchive();
- if (addValidEntry(appdataReference)) {
- return new AppDataOutputStream(newarchive);
+ makeBackup();
+ donotdeletebackup=false; // external reference has been made.
+ return ((original!=null) ? originalBackup : null);
}
return null;
}
@@ -290,32 +292,22 @@ public class VamsasArchive {
try {
newarchive.close();
- } catch (Exception e) {};
+ } catch (Exception e) {
+ log.debug("Whilst closing newarchive",e);
+ };
if (!virginArchive) {
// then there is something to recover.
- if (originalBackup!=null) {
- // backup has been made.
- // revert from backup and delete it (changing backup filename)
- if (rchive==null) {
- rchive = new SessionFile(original);
- }
- SessionFile bckup = new SessionFile(originalBackup);
-
- try {
- rchive.updateFrom(null, bckup); // recover from backup file.
- bckup.unlockFile();
- bckup=null;
- originalBackup.delete();
- originalBackup=null;
- }
- catch (Exception e) {
- log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
- return false;
- }
+ try {
+ recoverBackup();
+ }
+ catch (Exception e) {
+ log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
+ return false;
}
}
+
} else {
- log.info("cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
+ log.warn("Client Error: cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
}
closeAndReset(); // tidy up and release locks.
return true;
@@ -328,7 +320,7 @@ public class VamsasArchive {
private void closeAndReset() {
if (rchive!=null) {
rchive.unlockFile();
- rchive = null;
+ rchive=null;
}
if (original!=null) {
if (odoc!=null) {
@@ -342,27 +334,259 @@ public class VamsasArchive {
odoclock = null;
}
}
+ removeBackup();
newarchive=null;
original=null;
entries=null;
}
-
- private final int _TRANSFER_BUFFER=4096*4;
/**
- * open original archive file for exclusive (locked) reading.
- * @throws IOException
+ * Tidies up and closes archive, removing any backups that were created.
+ * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
+ * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
+ * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
*/
- private void accessOriginal() throws IOException {
- if (original!=null && original.exists()) {
- if (odoclock==null)
- odoclock = new SessionFile(original);
- odoclock.lockFile();
- if (odoc == null)
- odoc = new VamsasArchiveReader(original);
- }
- }
+ public void closeArchive() throws IOException {
+ if (newarchive!=null) {
+ newarchive.closeEntry();
+ if (!isDocumentWritten())
+ log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
+ newarchive.close();
+ updateOriginal();
+ closeAndReset();
+ } else {
+ log.warn("Attempt to close archive that has not been opened for writing.");
+ }
+ }
+ /**
+ * Opens and returns the applicationData output stream for the appdataReference string.
+ * @param appdataReference
+ * @return Output stream to write to
+ * @throws IOException
+ */
+ public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
+ if (newarchive==null)
+ throw new IOException("Attempt to write to closed VamsasArchive object.");
+ if (addValidEntry(appdataReference)) {
+ return new AppDataOutputStream(newarchive);
+ }
+ return null;
+ }
+
+ /**
+ *
+ * @return JarEntry name for the vamsas XML stream in this archive
+ */
+ protected String getDocumentJarEntry() {
+ if (vamsasdocument)
+ return VamsasArchiveReader.VAMSASDOC;
+ return VamsasArchiveReader.VAMSASXML;
+ }
+ /**
+ * Safely initializes the VAMSAS XML document Jar Entry.
+ * @return Writer to pass to the marshalling function.
+ * @throws IOException if a document entry has already been written.
+ */
+ public PrintWriter getDocumentOutputStream() throws IOException {
+ if (newarchive==null)
+ openArchive();
+ if (!isDocumentWritten()) {
+ try {
+ if (addValidEntry(getDocumentJarEntry()))
+ return new PrintWriter(new java.io.OutputStreamWriter(newarchive, "UTF-8"));
+ } catch (Exception e) {
+ log.warn("Problems opening XML document JarEntry stream",e);
+ }
+ } else {
+ throw new IOException("Vamsas Document output stream is already written.");
+ }
+ return null;
+ }
/**
+ * Access original archive if it exists, pass the reader to the client
+ * Note: this is NOT thread safe and a call to closeArchive() will by necessity
+ * close and invalidate the VamsasArchiveReader object.
+ * @return null if no original archive exists.
+ */
+ public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
+ if (!virginArchive) {
+ accessOriginal();
+ return odoc;
+ }
+ return null;
+ }
+ /**
+ * returns original document's root vamsas elements.
+ * @return
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ public Vobject[] getOriginalRoots() throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return VamsasArchive.getOriginalRoots(this);
+ }
+ /**
+ * @return original document or a new empty document (with default provenance)
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ public VamsasDocument getVamsasDocument() throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return getVamsasDocument("org.vamsas.simpleclient.VamsasArchive", "Created new empty document", null);
+ }
+ /**
+ * Return the original document or a new empty document with initial provenance entry.
+ * @param provenance_user (null sets user to be the class name)
+ * @param provenance_action (null sets action to be 'created new document')
+ * @param version (null means use latest version)
+ * @return (original document or a new vamsas document with supplied provenance and version info)
+ * @throws IOException
+ * @throws org.exolab.castor.xml.MarshalException
+ * @throws org.exolab.castor.xml.ValidationException
+ */
+ public VamsasDocument getVamsasDocument(String provenance_user, String provenance_action, String version) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ if (_doc!=null)
+ return _doc;
+ _doc = getOriginalVamsasDocument(this, getVorba());
+ if (_doc!=null)
+ return _doc;
+ // validate parameters
+ if (provenance_user==null)
+ provenance_user = "org.vamsas.simpleclient.VamsasArchive";
+ if (provenance_action == null)
+ provenance_action="Created new empty document";
+ if (version==null)
+ version = VersionEntries.latestVersion();
+ // Create a new document and return it
+ _doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()},
+ ProvenanceStuff.newProvenance(provenance_user, provenance_action), version);
+ return _doc;
+ }
+ /**
+ * @return Returns the current VorbaIdFactory for the archive.
+ */
+ public VorbaIdFactory getVorba() {
+ if (vorba==null)
+ vorba = new SimpleDocument("simpleclient.VamsasArchive");
+ return vorba.getVorba();
+ }
+ /**
+ * @return true if Vamsas Document has been written to archive
+ */
+ protected boolean isDocumentWritten() {
+ if (newarchive==null)
+ log.warn("isDocumentWritten() called for unopened archive.");
+ if (entries!=null) {
+ if (entries.containsKey(getDocumentJarEntry()))
+ return true;
+ }
+ return false;
+ }
+ private void makeBackup() {
+ if (!virginArchive) {
+ if (originalBackup==null && original!=null && original.exists()) {
+ try {
+ accessOriginal();
+ originalBackup = odoclock.backupSessionFile(null, original.getName(), ".bak", original.getParentFile());
+ }
+ catch (IOException e) {
+ log.warn("Problem whilst making a backup of original archive.",e);
+ }
+ }
+ }
+ }
+ /**
+ * opens the new archive ready for writing. If the new archive is replacing an existing one,
+ * then the existing archive will be locked, and the new archive written to a temporary file.
+ * The new archive will be put in place once close() is called.
+ * @param doclock TODO
+ * @throws IOException
+ */
+ private void openArchive() throws IOException {
+
+ if (newarchive!=null) {
+ log.warn("openArchive() called multiple times.");
+ throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
+ }
+ if (archive==null && (virginArchive || original==null)) {
+ log.warn("openArchive called on uninitialised VamsasArchive object.");
+ throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
+ }
+ if (!virginArchive) {
+ // lock the original
+ accessOriginal();
+ // make a temporary file to write to
+ archive = File.createTempFile(original.getName(), ".new",original.getParentFile());
+ } else {
+ if (archive.exists())
+ log.warn("New archive file name already in use! Possible lock failure imminent?");
+ }
+
+ if (rchive==null)
+ rchive = new SessionFile(archive);
+ if (!rchive.lockFile())
+ throw new IOException("Failed to get lock on file "+archive);
+ newarchive = new JarOutputStream(new BufferedOutputStream(new java.io.FileOutputStream(archive)));
+ entries = new Hashtable();
+ }
+ public void putVamsasDocument(VamsasDocument doc) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ putVamsasDocument(doc, getVorba());
+ }
+
+ public void putVamsasDocument(VamsasDocument doc, VorbaIdFactory vorba) throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
+ }
+
+ /**
+ * recovers the original file's contents from the (temporary) backup.
+ * @throws Exception if any SessionFile or file removal operations fail.
+ */
+ private void recoverBackup() throws Exception {
+ if (originalBackup!=null) {
+ // backup has been made.
+ // revert from backup and delete it (changing backup filename)
+ if (rchive==null) {
+ rchive = new SessionFile(original);
+ }
+ SessionFile bckup = new SessionFile(originalBackup);
+
+ rchive.updateFrom(null, bckup); // recover from backup file.
+ bckup.unlockFile();
+ bckup=null;
+ removeBackup();
+ }
+ }
+
+ /**
+ * forget about any backup that was made - removing it first if it was only temporary.
+ */
+ private void removeBackup() {
+ if (originalBackup!=null) {
+ log.debug("Removing backup in "+originalBackup.getAbsolutePath());
+ if (!donotdeletebackup)
+ if (!originalBackup.delete())
+ log.info("VamsasArchive couldn't remove temporary backup "+originalBackup.getAbsolutePath());
+ originalBackup=null;
+ }
+ }
+ /**
+ * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
+ */
+ public void setVorba(VorbaIdFactory Vorba) {
+ if (Vorba!=null) {
+ if (vorba==null)
+ vorba = new SimpleDocument(Vorba);
+ else
+ vorba.setVorba(Vorba);
+ } else
+ getVorba();
+ }
+ /**
* Convenience method to copy over the referred entry from the backup to the new version.
* Warning messages are raised if no backup exists or the
* entry doesn't exist in the backed-up original.
@@ -374,6 +598,7 @@ public class VamsasArchive {
public boolean transferAppDataEntry(String AppDataReference) throws IOException {
return transferAppDataEntry(AppDataReference, AppDataReference);
}
+
/**
* Transfers an AppDataReference from old to new vamsas archive, with a name change.
* @see transferAppDataEntry(String AppDataReference)
@@ -420,208 +645,67 @@ public class VamsasArchive {
+AppDataReference+"' as '"+NewAppDataReference+"' ("+count+" bytes)");
return true;
}
+
/**
- * Tidies up and closes archive, removing any backups that were created.
- * NOTE: It is up to the caller to delete the original archive backup obtained from backupFile()
- * TODO: ensure all extant AppDataReference jar entries are transferred to new Jar
- * TODO: provide convenient mechanism for generating new unique AppDataReferences and adding them to the document
- */
- public void closeArchive() throws IOException {
- if (newarchive!=null) {
- newarchive.closeEntry();
- if (!isDocumentWritten())
- log.warn("Premature closure of archive '"+archive.getAbsolutePath()+"': No document has been written.");
- newarchive.close();
- updateOriginal();
- closeAndReset();
- } else {
- log.warn("Attempt to close archive that has not been opened for writing.");
- }
- }
- /**
- * Access original archive if it exists, pass the reader to the client
- * Note: this is NOT thread safe and a call to closeArchive() will by necessity
- * close and invalidate the VamsasArchiveReader object.
- * @return null if no original archive exists.
+ * transfers any AppDataReferences existing in the old document
+ * that haven't already been transferred to the new one
+ * TODO: LATER: do the same for transfers requiring a namechange - more document dependent.
+ * @return true if data was transferred.
*/
- public VamsasArchiveReader getOriginalArchiveReader() throws IOException {
- if (!virginArchive) {
- accessOriginal();
- return odoc;
+ public boolean transferRemainingAppDatas() throws IOException {
+ boolean transfered=false;
+ if (original==null || !original.exists()) {
+ log.warn("No backup archive exists.");
+ return false;
}
- return null;
- }
- /**
- * returns original document's root vamsas elements.
- * @return
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- */
- public object[] getOriginalRoots() throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return VamsasArchive.getOriginalRoots(this);
- }
- /**
- * Access original document if it exists, and get VAMSAS root objects.
- * @return vector of vamsas roots from original document
- * @throws IOException
- */
- public static object[] getOriginalRoots(VamsasArchive ths) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
- if (oReader!=null) {
-
- if (oReader.isValid()) {
- InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
- VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
- if (doc!=null)
- return doc.getVAMSAS();
- // TODO ensure embedded appDatas are garbage collected to save memory
- } else {
- InputStream vxmlis = oReader.getVamsasXmlStream();
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- VAMSAS root[] = new VAMSAS[1];
- root[0] = VAMSAS.unmarshal(vxml);
- if (root[0]!=null)
- return root;
+ accessOriginal();
+
+ if (getVorba()!=null) {
+ Vector originalRefs=null;
+ try {
+ originalRefs = vorba.getReferencedEntries(getVamsasDocument(), getOriginalArchiveReader());
+ } catch (Exception e) {
+ log.warn("Problems accessing original document entries!",e);
+ }
+ if (originalRefs!=null) {
+ Iterator ref = originalRefs.iterator();
+ while (ref.hasNext()) {
+ String oldentry = (String) ref.next();
+ if (oldentry!=null && !entries.containsKey(oldentry)) {
+ log.debug("Transferring remaining entry '"+oldentry+"'");
+ transfered |= transferAppDataEntry(oldentry);
+ }
}
}
- }
- return null;
- }
- protected VorbaIdFactory vorba = null;
-
- /**
- * @return Returns the current VorbaIdFactory for the archive.
- */
- public VorbaIdFactory getVorba() {
- return vorba;
+ }
+ return transfered;
}
-
/**
- * @param vorba the VorbaIdFactory to use for accessing vamsas objects.
- */
- public void setVorba(VorbaIdFactory vorba) {
- this.vorba = vorba;
- }
-
- /**
- * Access and return current vamsas Document, if it exists, or create a new one
- * (without affecting VamsasArchive object state - so is NOT THREAD SAFE)
- * TODO: possibly modify internal state to lock low-level files
- * (like the IClientDocument interface instance constructer would do)
- * @see org.vamsas.simpleclient.VamsasArchive.getOriginalVamsasDocument for additional caveats
- *
- * @return
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- */
- public VamsasDocument getVamsasDocument() throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasDocument doc = getOriginalVamsasDocument(this, getVorba());
- if (doc!=null)
- return doc;
- // Create a new document and return it
- doc = DocumentStuff.newVamsasDocument(new VAMSAS[] { new VAMSAS()},
- ProvenanceStuff.newProvenance("org.vamsas.simpleclient.VamsasArchive", "Created new empty document")
- , VersionEntries.latestVersion());
- return doc;
- }
- /**
- * Access the original vamsas document for a VamsasArchive class, and return it.
- * Users of the VamsasArchive class should use the getVamsasDocument method to retrieve
- * the current document - only use this one if you want the 'backup' version.
- * TODO: catch OutOfMemoryError - they are likely to occur here.
- * NOTE: vamsas.xml datastreams are constructed as 'ALPHA_VERSION' vamsas documents.
- * @param ths
- * @return null if no document exists.
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
+ * called after archive is written to put file in its final place
*/
- public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return VamsasArchive.getOriginalVamsasDocument(ths, null);
- }
- private VorbaIdFactory makeDefaultFactory(VorbaIdFactory vorba) {
- if (vorba==null) {
- vorba = getVorba();
- if (vorba==null) {
- vorba = IdFactory.getDummyFactory("simpleclient.VamsasArchive");
- setVorba(vorba); // save for later use
+ private void updateOriginal() {
+ if (!virginArchive) {
+ // make sure original document really is backed up and then overwrite it.
+ if (odoc!=null) {
+ // try to shut the odoc reader.
+ odoc.close();
+ odoc = null;
}
- }
- return vorba;
- }
- /**
- * Uses VorbaXmlBinder to retrieve the VamsasDocument from the original archive referred to by ths
- * @param ths
- * @param vorba
- * @return
- * @throws IOException
- * @throws org.exolab.castor.xml.MarshalException
- * @throws org.exolab.castor.xml.ValidationException
- */
- public static VamsasDocument getOriginalVamsasDocument(VamsasArchive ths, VorbaIdFactory vorba) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
- if (oReader!=null) {
- // check the factory
- vorba = ths.makeDefaultFactory(vorba);
- if (oReader.isValid()) {
- InputStreamReader vdoc = new InputStreamReader(oReader.getVamsasDocumentStream());
- Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vdoc, vorba, new VamsasDocument());
- if (unmarsh==null)
- log.fatal("Couldn't unmarshall document!");
-
- object[] vobjs = (object[]) unmarsh[0];
- if (vobjs!=null) {
- VamsasDocument doc=(VamsasDocument) vobjs[0];
- if (doc!=null)
- return doc;
- }
- log.debug("Found no VamsasDocument object in properly formatted Vamsas Archive.");
- } else {
- // deprecated data handler
- InputStream vxmlis = oReader.getVamsasXmlStream();
- if (vxmlis!=null) { // Might be an old vamsas file.
- BufferedInputStream ixml = new BufferedInputStream(oReader.getVamsasXmlStream());
- InputStreamReader vxml = new InputStreamReader(ixml);
- Object unmarsh[] = VorbaXmlBinder.getVamsasObjects(vxml, vorba, new VAMSAS());
-
- if (unmarsh==null)
- log.fatal("Couldn't unmarshall document!");
-
- VAMSAS root[]= new VAMSAS[] { null};
- root[0] = (VAMSAS) unmarsh[0];
-
- if (root[0]==null) {
- log.debug("Found no VAMSAS object in VamsasXML stream.");
- } else {
- log.debug("Making new VamsasDocument from VamsasXML stream.");
- VamsasDocument doc = DocumentStuff.newVamsasDocument(root,
- ProvenanceStuff.newProvenance(
- "org.vamsas.simpleclient.VamsasArchive", // TODO: VAMSAS: decide on 'system' operations provenance form
- "Vamsas Document constructed from vamsas.xml in "
- // TODO: VAMSAS: decide on machine readable info embedding in provenance should be done
- +ths.original+""), VersionEntries.ALPHA_VERSION);
- root[0]=null;
- root=null;
- return doc;
- }
- }
+ // Make a backup if it isn't done already
+ makeBackup();
+ try {
+ // copy new Archive data that was writen to a temporary file
+ odoclock.updateFrom(null, rchive);
}
+ catch (IOException e) {
+ // TODO: LATER: decide if leaving nastily named backup files around is necessary.
+ log.error("Problem updating archive from temporary file! - backup left in '"
+ +backupFile().getAbsolutePath()+"'",e);
+ }
+ // Tidy up if necessary.
+ removeBackup();
+ } else {
+
}
- // otherwise - there was no valid original document to read.
- return null;
- }
- public void putVamsasDocument(VamsasDocument doc) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VorbaIdFactory vorba = makeDefaultFactory(null);
- VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
}
}