import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.util.Hashtable;
import java.util.jar.JarEntry;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.ClientHandle;
+import org.vamsas.client.IVorbaIdFactory;
+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.objects.core.ApplicationData;
import org.vamsas.objects.core.VAMSAS;
this.archive = archive; // archive is written in place.
virginArchive = true;
}
- this.openArchive();
+ this.openArchive(); // open archive
}
/**
* name of backup of existing archive that has been updated/overwritten.
}
}
}
-
+
/**
* 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);
- }
+ 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.
}
if (!virginArchive) {
makeBackup();
return ((original!=null) ? originalBackup : null);
-
}
return null;
}
*/
protected boolean isDocumentWritten() {
if (newarchive==null)
- log.warn("isDocumentWritten called for unopened archive.");
+ log.warn("isDocumentWritten() called for unopened archive.");
if (entries!=null) {
if (entries.containsKey(getDocumentJarEntry()))
return true;
* @throws IOException
*/
public AppDataOutputStream getAppDataStream(String appdataReference) throws IOException {
- if (newarchive!=null)
+ if (newarchive==null)
openArchive();
if (addValidEntry(appdataReference)) {
return new AppDataOutputStream(newarchive);
/**
* Stops any current write to archive, and reverts to the backup if it exists.
- * All existing locks on the original will be released.
+ * All existing locks on the original will be released. All backup files are removed.
*/
public boolean cancelArchive() {
if (newarchive!=null) {
return false;
}
}
- // original is untouched
- // just delete temp files
-
-
}
} else {
log.info("cancelArchive called before archive("+original.getAbsolutePath()+") has been opened!");
}
- closeAndReset();
+ closeAndReset(); // tidy up and release locks.
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) {
}
return null;
}
+ protected VorbaIdFactory vorba = null;
+
+ /**
+ * @return Returns the current VorbaIdFactory for the archive.
+ */
+ public VorbaIdFactory getVorba() {
+ return vorba;
+ }
+
+ /**
+ * @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)
*/
public VamsasDocument getVamsasDocument() throws IOException,
org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- VamsasDocument doc = getOriginalVamsasDocument(this);
+ VamsasDocument doc = getOriginalVamsasDocument(this, getVorba());
if (doc!=null)
return doc;
// Create a new document and return it
*/
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
+ }
+ }
+ 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());
- VamsasDocument doc = VamsasDocument.unmarshal(vdoc);
- if (doc!=null)
- return doc;
- } else {
+ 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;
+ 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);
- 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.");
+ 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
}
}
}
- } // otherwise - there was no valid original document to read.
+ }
+ // 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(getVorba());
+ VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff