import org.vamsas.objects.core.ApplicationData;
import org.vamsas.objects.core.VAMSAS;
import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.objects.utils.DocumentStuff;
+import org.vamsas.objects.utils.ProvenanceStuff;
+import org.vamsas.objects.utils.document.VersionEntries;
/**
- * Class for creating a vamsas archive
- * (with backups)
+ * Class for high-level io and Jar manipulation involved in creating
+ * or updating a vamsas archive (with backups).
* Writes to a temporary file and then swaps new file for backup.
* uses the sessionFile locking mechanism for safe I/O
* @author jimp
public class VamsasArchive {
private static Log log = LogFactory.getLog(VamsasArchive.class);
/**
- * destination of new archive data
+ * destination of new archive data (tempfile if virginarchive=true, original archive location otherwise)
*/
java.io.File archive=null;
/**
*/
SessionFile rchive=null;
/**
- * original archive file that is to be updated
+ * original archive file to be updated (or null if virgin) where new data will finally reside
*/
java.io.File original=null;
/**
private boolean virginArchive=false;
/**
* Create a new vamsas archive
- * nb. No file locks are made until open() is called.
+ * File locks are made immediately to avoid contention
+ *
* @param archive - file spec for new vamsas archive
* @param vamsasdocument true if archive is to be a fully fledged vamsas document archive
+ * @throws IOException if call to accessOriginal failed for updates, or openArchive failed.
*/
- public VamsasArchive(File archive, boolean vamsasdocument) {
+ public VamsasArchive(File archive, boolean vamsasdocument) throws IOException {
super();
- if (archive==null || (archive!=null && archive.canWrite())) {
+ if (archive==null || (archive!=null && !archive.canWrite())) {
log.fatal("Invalid parameters for VamsasArchive constructor:"+((archive!=null)
? "File cannot be overwritten." : "Null Object not valid constructor parameter"));
}
this.original = archive;
this.archive = null; // archive will be a temp file when the open method is called
virginArchive=false;
+ try {
+ this.accessOriginal();
+ } catch (IOException e) {
+ throw new IOException("Lock failed for existing archive"+archive);
+ }
} else {
this.original = null;
this.archive = archive; // archive is written in place.
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;
}
}
}
+
/**
* called after archive is written to put file in its final place
- * TODO: FINISH original should have sessionFile, and archive should also have sessionFile
+ * TODO: FINISH ?? original should have sessionFile, and archive should also have sessionFile
*/
private void updateOriginal() {
- if (original!=null) {
- if (!virginArchive) {
+ 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;
+ odoc = null;
}
- if (!archive.getAbsolutePath().equals(original)) {
- if (originalBackup==null)
- makeBackup();
- try {
- odoclock.updateFrom(null, rchive);
- }
- catch (IOException e) {
- log.error("Problem updating archive from temporary file!",e);
- }
- } else {
- log.warn("archive and original are the same file! ("+archive.getAbsolutePath()+")");
+ // 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);
}
- } // else virginArchive are put in correct place from the beginning
-
+ catch (IOException e) {
+ log.error("Problem updating archive from temporary file! - backup in '"
+ +backupFile().getAbsolutePath()+"'",e);
+ }
+ } else {
+ // don't need to do anything.
}
}
/**
if (!virginArchive) {
makeBackup();
- return ((original==null) ? originalBackup : null);
-
+ return ((original!=null) ? originalBackup : null);
+
}
return null;
}
-
+ /**
+ *
+ * @return JarEntry name for the vamsas XML stream in this archive
+ */
protected String getDocumentJarEntry() {
if (vamsasdocument)
return VamsasArchiveReader.VAMSASDOC;
log.warn("isDocumentWritten called for unopened archive.");
if (entries!=null) {
if (entries.containsKey(getDocumentJarEntry()))
- return true;
+ return true;
}
return false;
}
log.warn("openArchive() called multiple times.");
throw new IOException("Vamsas Archive '"+archive.getAbsolutePath()+"' is already open.");
}
-
- if (archive==null) {
- if (original==null) {
- log.warn("openArchive called on uninitialised VamsasArchive object.");
- throw new IOException("Badly initialised VamsasArchive object - no archive file specified.");
- }
+ 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());
+ 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);
if (newarchive!=null) {
try {
newarchive.close();
+
} catch (Exception e) {};
if (!virginArchive) {
// then there is something to recover.
}
SessionFile bckup = new SessionFile(originalBackup);
- try {
- rchive.updateFrom(null,bckup); // recover from backup file.
- bckup.unlockFile();
- bckup=null;
- originalBackup.delete();
- }
- catch (Exception e) {
- log.warn("Problems when trying to cancel Archive "+archive.getAbsolutePath(), e);
- return false;
- }
+ 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;
+ }
}
// original is untouched
// just delete temp files
- }
+
+ }
} else {
log.info("cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
}
*
*/
private void closeAndReset() {
- rchive.unlockFile();
- rchive = null;
+ if (rchive!=null) {
+ rchive.unlockFile();
+ rchive = null;
+ }
if (original!=null) {
if (odoc!=null) {
odoc.close();
odoc=null;
}
- archive.delete();
+ if (archive!=null)
+ archive.delete();
if (odoclock!=null) {
odoclock.unlockFile();
odoclock = null;
original=null;
entries=null;
}
-
+
private final int _TRANSFER_BUFFER=4096*4;
/**
- * open backup for exclusive (locked) reading.
+ * open original archive file for exclusive (locked) reading.
* @throws IOException
*/
private void accessOriginal() throws IOException {
odoc = new VamsasArchiveReader(original);
}
}
-
+
/**
* 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
* @throws IOException
*/
public static object[] getOriginalRoots(VamsasArchive ths) throws IOException,
- org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
VamsasArchiveReader oReader = ths.getOriginalArchiveReader();
if (oReader!=null) {
VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
if (doc!=null)
return doc.getVAMSAS();
- // TODO ensure embedded appDatas are garbage collected
+ // TODO ensure embedded appDatas are garbage collected to save memory
} else {
InputStream vxmlis = oReader.getVamsasXmlStream();
if (vxmlis!=null) { // Might be an old vamsas file.
}
return 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
+ */
+ public VamsasDocument getVamsasDocument() throws IOException,
+ org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ VamsasDocument doc = getOriginalVamsasDocument(this);
+ 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
+ */
+ public static VamsasDocument getOriginalVamsasDocument(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;
+ } 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);
+ VAMSAS root[] = new VAMSAS[1];
+ root[0] = VAMSAS.unmarshal(vxml);
+ if (root[0]!=null) {
+ log.debug("Reading old format vamsas.xml into a dummy document.");
+ 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 <file>"
+ // TODO: VAMSAS: decide on machine readable info embedding in provenance should be done
+ +ths.original+"</file>"), VersionEntries.ALPHA_VERSION);
+ root[0]=null;
+ root=null;
+ return doc;
+ }
+ }
+ }
+ } // otherwise - there was no valid original document to read.
+ return null;
+ }
}
git://source.jalview.org / vamsas.git / commitdiff