package org.vamsas.test.simpleclient;
+import java.util.Hashtable;
import java.util.Vector;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.IClientAppdata;
+import org.vamsas.client.Vobject;
import org.vamsas.client.VorbaId;
import org.vamsas.client.simpleclient.ClientDocument;
import org.vamsas.client.simpleclient.VamsasArchive;
import org.vamsas.objects.utils.ProvenanceStuff;
// simple holder to pass to client.
-public class ClientDoc {
+public class ClientDoc extends org.vamsas.client.ClientDocument {
+ /* (non-Javadoc)
+ * @see org.vamsas.client.IClientDocument#getClientAppdata()
+ */
+ public IClientAppdata getClientAppdata() {
+ throw new Error("Appdata access is not implemented in the test.simpleclient.ClientDoc instance."); // TODO Auto-generated method stub
+ }
protected boolean isModified=false;
private Log log = LogFactory.getLog(ClientDoc.class);
protected VamsasDocument doc;
protected VamsasArchive iohandler=null;
protected VamsasArchiveReader reader=null;
private String user=null;
+ private String app=null;
/**
* @param doc
* @param iohandler
* @param reader
+ * @param app
* @param user
*/
- public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String user) {
- super();
+ public ClientDoc(VamsasDocument doc, VamsasArchive iohandler, VamsasArchiveReader reader, String app, String user, Hashtable objrefs) {
+ super(objrefs, (iohandler!=null) ? iohandler.getVorba() : null);
this.doc = doc;
this.iohandler = iohandler;
this.reader = reader;
+ this.app = app;
this.user = user;
+ this.objrefs = objrefs;
_VamsasRoots = doc.getVAMSAS();
}
// AppDataOutputStream appd;
*/
protected Entry getProvenanceEntry(String action) {
// VAMSAS: modify schema to allow referencing of user field (plus other issues, ClientUrn field, machine readable action, input parameters, additional data generated notes
- Entry prov = ProvenanceStuff.newProvenanceEntry(user, action);
+ Entry prov = ProvenanceStuff.newProvenanceEntry(app, user, action);
return prov;
}
public VAMSAS[] getVamsasRoots() {
public VamsasArchiveReader getReader() {
return reader;
}
+ private void _finalize() {
+ log.debug("finalizing clientDoc");
+ if (doc!=null) {
+ doc = null;
+ }
+ if (_VamsasRoots!=null) {
+ for (int i=0; i<_VamsasRoots.length; i++)
+ _VamsasRoots[i]=null;
+ _VamsasRoots=null;
+
+ }
+
+ if (reader!=null) {
+ log.debug("Closing and removing reader reference");
+ reader.close();
+ reader=null;
+ }
+ if (iohandler!=null) {
+ log.debug("Removing ioHandler reference.");
+ iohandler.cancelArchive();
+ iohandler=null;
+ }
+ }
protected void finalize() throws Throwable {
+ _finalize();
super.finalize();
- //if (reader!=null)
- // reader.close();
- //reader=null;
-// if (iohandler!=null) {
-// iohandler.cancelArchive(); // otherwise the original may be overwritten.
-// }
+ }
+ private java.util.Hashtable objrefs=null;
+
+ public VorbaId[] registerObjects(Vobject[] unregistered) {
+ if (doc==null) {
+ log.warn("registerObjects[] called on null document.");
+ return null;
+ }
+ if (objrefs==null) {
+ log.warn("registerObjects[] called for null objrefs hasharray.");
+ return null;
+ }
+ if (unregistered!=null) {
+ VorbaId ids[] = new VorbaId[unregistered.length];
+ for (int i=0,k=unregistered.length; i<k; i++)
+ if (unregistered[i]!=null) {
+ log.warn("Null Vobject passed to registerObject[] at position "+i);
+ return null;
+ } else {
+ ids[i]=registerObject(unregistered[i]);
+ }
+ log.debug("Registered "+unregistered.length+" objects - total of "+objrefs.size()+" ids.");
+ return ids;
+ }
+ return null;
+ }
+ /* (non-Javadoc)
+ * @see org.vamsas.client.IClientDocument#registerObject(org.vamsas.client.Vobject)
+ */
+ public VorbaId registerObject(Vobject unregistered) {
+ if (doc==null) {
+ log.warn("registerObjects called on null document.");
+ return null;
+ }
+ if (objrefs==null) {
+ log.warn("registerObjects called for null objrefs hasharray.");
+ return null;
+ }
+ if (iohandler==null) {
+ log.warn("registerObjects called for read only document.");
+ return null;
+ }
+
+ if (unregistered!=null) {
+ VorbaId id = this._registerObject(unregistered);
+ log.debug("Registered object - total of "+objrefs.size()+" ids.");
+ return id;
+ }
+ log.warn("Null Vobject passed to registerObject.");
+ return null;
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
+ */
+ public Vobject getObject(VorbaId id) {
+ if (objrefs==null) {
+ log.debug("getObject called on null objrefs list.");
+ return null;
+ }
+ if (objrefs.containsKey(id.getId()))
+ return (Vobject) objrefs.get(id.getId());
+ log.debug("Returning null Vobject reference for id "+id.getId());
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see org.vamsas.client.IClientDocument#getObjects(org.vamsas.client.VorbaId[])
+ */
+ public Vobject[] getObjects(VorbaId[] ids) {
+ if (objrefs==null) {
+ log.debug("getObject[] called on null objrefs list.");
+ return null;
+ }
+ Vobject[] vo = new Vobject[ids.length];
+ for (int i=0,j=ids.length; i<j;i++)
+ if (objrefs.containsKey(ids[i]))
+ vo[i] = (Vobject) objrefs.get(ids[i]);
+ else
+ log.debug("Returning null Vobject reference for id "+ids[i].getId());
+ return vo;
+ }
+ protected void updateDocumentRoots() {
+ if (doc==null) {
+ log.error("updateDocumentRoots called on null document. Probably an implementation error.");
+ return;
+ }
+ if (isModified) {
+ if (_VamsasRoots!=null) {
+ doc.setVAMSAS(_VamsasRoots);
+ _VamsasRoots=null;
+ }
+ }
+ }
+ /**
+ * tell vamsas client to close the document and reset the object. Once closed, nothing can be done with the object.
+ *
+ */
+ public void closeDoc() {
+ if (doc!=null) {
+ log.debug("Closing open document.");
+ _finalize();
+ } else {
+ log.warn("Ignoring closeDoc on invalid document.");
+ }
}
}
\ No newline at end of file
git://source.jalview.org / vamsas.git / blobdiff