public class SessionHandle {
/**
+ * @param sessionUrn
+ */
+ public SessionHandle(String sessionUrn) {
+ super();
+ SessionUrn = sessionUrn;
+ }
+ /**
* @return Returns the sessionUrn.
*/
public String getSessionUrn() {
*/
package org.vamsas.client;
+import java.util.Hashtable;
+
/**
* A VorbaIdFactory is constructed by an IClient instance.
* It guarantees that any new VorbaId objects are unique
* @author jimp
*/
public abstract class VorbaIdFactory implements IVorbaIdFactory {
+ protected Hashtable extantids=null;
/**
* construct a new id appropriate for this client in the vamsas session.
*
* correctly.
*/
public abstract VorbaId makeVorbaId();
+
+ /**
+ * internal method to access the protected VorbaId object constructor
+ * This shennanigan is to prevent casual generation of VorbaIds
+ * (which may destroy the integrity of a Vamsas Document!)
+ * @param id
+ * @return new VorbaId object
+ */
+ protected VorbaId newId(String id) {
+ return VorbaId.newId(id);
+ }
+ /**
+ * Called by VorbaXmlBinder so the record of newly unmarshalled object Ids
+ * is accessible to the Document's VorbaIdFactory instance.
+ * @param idtable
+ */
+ protected void setNewIdHash(Hashtable idtable) {
+ extantids = idtable;
+ }
/**
* TODO: decide if these are needed.
*
package org.vamsas.client;
import java.io.IOException;
+import java.io.PrintWriter;
import java.io.Reader;
import java.io.Writer;
import java.lang.reflect.Field;
import java.util.Iterator;
import java.util.Vector;
+import org.exolab.castor.mapping.FieldHandler;
+import org.exolab.castor.mapping.GeneralizedFieldHandler;
+import org.exolab.castor.mapping.ValidityException;
import org.exolab.castor.xml.IDResolver;
import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.MarshalListener;
import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.UnmarshalListener;
import org.exolab.castor.xml.Unmarshaller;
* to avoid validation exceptions when marshalling new objects
* into the vamsas document.
*/
-public class VorbaXmlBinder implements UnmarshalListener {
+public class VorbaXmlBinder extends GeneralizedFieldHandler implements UnmarshalListener, MarshalListener {
private final IVorbaIdFactory vorbafactory;
private final Vector obj;
*/
public void initialized(Object object) {
}
-
+
/*
* Check if the object has an 'id' field - if it does, copy the value into
* the VorbaId field of object, and add the object to the VorbaId hash.
* writes the VamsasDocument to the given stream.
* TODO: ensure that (at least) default provenance entries are written for objects.
* @param outstream
+ * @param vorba valid VorbaIdFactory to construct any missing IDs
* @param doc
* @throws IOException
* @throws MarshalException
* @throws ValidationException
*/
- private static void setVamsasDocument(Writer outstream, VamsasDocument doc)
+ public static void putVamsasDocument(PrintWriter outstream, VorbaIdFactory vorba, VamsasDocument doc)
throws IOException, MarshalException, ValidationException {
+ // Ensure references
+ if (vorba==null)
+ throw new Error("Null VorbaIdVactory Parameter");
+ if (doc.__vorba==null)
+ doc.__vorba = vorba;
+ doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ?
+ final Vector refstomake = new Vector();
+ VorbaXmlBinder binder = new VorbaXmlBinder(vorba, refstomake, vorba.extantids);
Marshaller marshaller = new Marshaller(outstream);
+ marshaller.setMarshalAsDocument(true);
+ marshaller.setMarshalListener(binder);
marshaller.marshal(doc);
}
+ private static boolean ensure_references(Vector unrefed, Hashtable objrefs) {
+ boolean sync=true;
+ if (unrefed.size()>0) {
+ sync=false; // document is out of sync - ids have been created.
+ java.util.Iterator newobj = unrefed.listIterator();
+ while (newobj.hasNext()) {
+ object o = (object) newobj.next();
+ // forces registration and id field update.
+ VorbaId id = o.getVorbaId();
+ if (!objrefs.containsKey(id)) {
+ objrefs.put(id.id, o);
+ } else {
+ throw new Error("Serious! Duplicate reference made by vorbaIdFactory!");
+ }
+ }
+ }
+ return sync;
+ }
/**
* Unmarshals a vamsasDocument object from a stream, registers
* unregistered objects, records existing VorbaIds, and completes
* vamsasDocument is written back to disk to propagate the new VorbaIds.
* TODO: ensure that provenance is correct for newly registered objects
* @param instream - the XML input stream
- * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
+ * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
+ * @param root the root element's org.vamsas.objects.core object.
* @return null or {(Object) VamsasDocument object, (Object) Hashtable of object references, (Object) Boolean(sync) }
*/
- public static Object[] getVamsasDocument(Reader instream,
- IVorbaIdFactory factory) {
- Unmarshaller unmarshaller = new Unmarshaller(instream);
+ public static Object[] getVamsasObjects(Reader instream,
+ IVorbaIdFactory factory, object root) {
+ Unmarshaller unmarshaller = new Unmarshaller(root);
unmarshaller.setIDResolver(new IDResolver() {
public Object resolve(String id) {
System.err.println("Warning - id " + id
try {
while (instream.ready()) {
Object obj = unmarshaller.unmarshal(instream);
- boolean sync=true;
- if (obj instanceof VamsasDocument) {
- if (unrefed.size()>0) {
- sync=false; // document is out of sync - ids have been created.
- java.util.Iterator newobj = unrefed.listIterator();
- while (newobj.hasNext()) {
- object o = (object) newobj.next();
- // forces registration and id field update.
- VorbaId id = o.getVorbaId();
- if (!objrefs.containsKey(id)) {
- objrefs.put(id.id, o);
- } else {
- throw new Error("Serious! Duplicate reference made by vorbaIdFactory!");
- }
- }
- }
- return new Object[] { obj, objrefs, new Boolean(sync)};
+ boolean sync=ensure_references(unrefed, objrefs);
+ if (!(obj instanceof object))
+ return null;
+ return new Object[] { obj, objrefs, new Boolean(sync)};
}
- }
} catch (MarshalException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return null;
}
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.xml.MarshalListener#postMarshal(java.lang.Object)
+ */
+ public void postMarshal(Object object) {
+ // TODO Auto-generated method stub
+
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.xml.MarshalListener#preMarshal(java.lang.Object)
+ */
+ public boolean preMarshal(Object newobj) {
+ if (newobj instanceof object) {
+ object nobj = (object) newobj;
+ nobj.set__stored_in_document(true);
+ Field fd = null;
+ try {
+ if (nobj.isRegisterable()) {
+ // make sure the id field is set
+ nobj.__vorba = vorbafactory;
+ fd = nobj.getClass().getField("_id");
+ if (fd.get(nobj) != null) {
+ fd.set(nobj, nobj.getVorbaId().getId());
+ /* all thats needed perhaps
+ *
+ *if (idstring.length() > 0) {
+ if (!objrefs.containsKey(idstring)) {
+ objrefs.put(idstring, nobj);
+ nobj.setVorbaId(VorbaId.newId(idstring));
+ } else {
+ System.err.println("Serious problem : duplicate id '"+idstring+"' found! expect badness.");
+ return false; // TODO: HANDLE duplicate XML ids correctly
+ }*/
+ }
+ }
+ } catch (Exception e) {
+ return false;
+ };
+
+ }
+ return false;
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponGet(java.lang.Object)
+ */
+ public Object convertUponGet(Object value) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#convertUponSet(java.lang.Object)
+ */
+ public Object convertUponSet(Object value) {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#getFieldType()
+ */
+ public Class getFieldType() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#newInstance(java.lang.Object, java.lang.Object[])
+ */
+ public Object newInstance(Object parent, Object[] args) throws IllegalStateException {
+ // TODO Auto-generated method stub
+ return super.newInstance(parent, args);
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#newInstance(java.lang.Object)
+ */
+ public Object newInstance(Object parent) throws IllegalStateException {
+ // TODO Auto-generated method stub
+ return super.newInstance(parent);
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.GeneralizedFieldHandler#setCollectionIteration(boolean)
+ */
+ public void setCollectionIteration(boolean autoCollectionIteration) {
+ // TODO Auto-generated method stub
+ super.setCollectionIteration(autoCollectionIteration);
+ }
+
+ /* (non-Javadoc)
+ * @see org.exolab.castor.mapping.AbstractFieldHandler#hasValue(java.lang.Object)
+ */
+ public boolean hasValue(Object object) {
+ // TODO Auto-generated method stub
+ return super.hasValue(object);
+ }
}
\ No newline at end of file
*/
package org.vamsas.client;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.Iterator;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.exolab.castor.mapping.FieldDescriptor;
+import org.exolab.castor.mapping.FieldHandler;
+import org.exolab.castor.xml.util.XMLClassDescriptorImpl;
+import org.vamsas.test.simpleclient.VamsasArchive;
+
/**
* Base class for all Vamsas objects extracted from an IClientDocument. An
* object maybe registered or unregistered.
*
*/
public abstract class object {
-
+ static Log log = LogFactory.getLog(object.class);
+
/**
* unique id for all vamsas objects allows unambiguous referencing to any
* object in the vamsas document
*/
private void testInstanceForIdField() {
// look for the id field (should be an NCName string)
- // TODO: decide if 'id' is an appropriate reserved attribute name for the
- // VorbaId
+ // TODO: decide if 'id' is an appropriate reserved attribute name for the VorbaId
try {
- java.lang.reflect.Field fd = this.getClass().getField("id");
- if (fd.getType().getClass().equals("astring".getClass())) {
+ java.lang.reflect.Field fd = this.getClass().getDeclaredField("_id");
+ if (String.class.isAssignableFrom(fd.getType())) {
this.setRegisterable(true);
}
} catch (SecurityException e) {
*/
protected void setInstanceIdField() {
if (registerable) {
- if (vorbaId != null)
+ if (__vorba != null)
try {
- java.lang.reflect.Field fd = this.getClass().getField("id");
- fd.set((Object) this, (Object) new String(vorbaId.id));
- } catch (IllegalAccessException e) {
+ Method fd = this.getClass().getMethod("setId", new Class[] { String.class });
+ fd.invoke((Object) this, new Object[] {new String(this.getVorbaId().id)});
+ log.info(this.getClass().getName()+" called setInstanceIdField!");
+ } catch (InvocationTargetException e) {
+ System.err
+ .println("SourceGeneration of "
+ + this.getClass().toString()
+ + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.");
+ e.printStackTrace(System.err);
+ }
+ catch (IllegalAccessException e) {
System.err
.println("SourceGeneration of "
+ this.getClass().toString()
- + "\n has resulted in an inaccessible 'id' field!\nCannot set ID from the vorbaId object.");
+ + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId object.");
e.printStackTrace(System.err);
} catch (SecurityException e) {
e.printStackTrace(System.err);
- } catch (NoSuchFieldException e) {
+ } catch (NoSuchMethodException e) {
this.setRegisterable(false);
}
} else {
protected void setRegisterable(boolean registerable) {
this.registerable = registerable;
}
+ /**
+ * ensure's internal id field corresponds to vorbaId and
+ * cascade through all fields referring to an instance of object
+ * calling the same method on them.
+ * TODO: LATER: properly apply castors own field mechanisms to get at accessors
+ *
+ */
+ protected void __ensure_instance_ids() {
+ if (__vorba==null)
+ throw new Error("Improperly intialised org.vamsas.client.object - no VorbaFactory given.");
+ log.info(this.getClass()+".__ensure_instance_ids()");
+ if (!__stored_in_document && registerable)
+ setInstanceIdField();
+ Class descriptor = null;
+ XMLClassDescriptorImpl descimpl = null;
+ try {
+ // castor descriptor resolver magic
+ descriptor = this.getClass().getClassLoader().loadClass(this.getClass().getName()+"Descriptor");
+ descimpl = (XMLClassDescriptorImpl) descriptor.getConstructor(null).newInstance(null);
+ } catch (Exception e) {
+ log.error("Couldn't resolve descriptor for "+this.getClass().getName());
+ return;
+ }
+ FieldDescriptor fields[] = descimpl.getFields();
+ for (int i=0,j=fields.length; i<j; i++) {
+ Class type= fields[i].getFieldType();
+ if (type.isArray()) {
+ if (object[].class.isAssignableFrom(type)) {
+ try {
+ Object val = fields[i].getHandler().getValue(this);
+ if (val!=null) {
+ object vals[] = (object[]) val;
+ for (int k=0, l=vals.length; k<l; k++) {
+ if (vals[k].__vorba==null)
+ vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
+ vals[k].__ensure_instance_ids();
+ }
+ }
+ }
+ catch (Exception e) {
+ log.error("Client error - could not access array "+type.getName()+" in "+this.getClass().getName(), e);
+ }
+ }
+ } else
+ if (object.class.isAssignableFrom(type)) {
+ try {
+ FieldHandler fh = fields[i].getHandler();
+ object rf = null;
+ if (fh != null) {
+ Object fval = fh.getValue(this);
+ if (fval!=null) {
+ if (fval.getClass().isArray()) {
+ //if (object[].class.isAssignableFrom(type)) {
+ try {
+ object vals[] = (object[]) fval;
+ for (int k=0, l=vals.length; k<l; k++) {
+ if (vals[k].__vorba==null)
+ vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
+ vals[k].__ensure_instance_ids();
+ }
+ }
+ catch (Exception e) {
+ log.error("Client error - could not access (fhval)array "+type.getName()+" in "+this.getClass().getName(), e);
+ }
+ //}
+ } else {
+ rf = (object) fval;
+ log.info("Got value for "+fields[i].getFieldName());
+ }
+ }
+ } else {
+ // fuck around, fuck around, jump up jump up and get down! */
+ Object o = fields[i].getClassDescriptor();
+ if (o!=null) {
+ // XMLClassDescriptorImpl fclasdes = (XMLClassDescriptorImpl) o;
+ String methname = "get"+fields[i].getFieldName();
+ Method fgetmeth = this.getClass().getMethod(methname,null);
+ if (fgetmeth!=null) {
+ Object fval = fgetmeth.invoke(this,null);
+ if (fval!=null)
+ rf = (object) fval;
+ } else {
+ log.warn("Couldn't find "+this.getClass().getName()+"."+methname);
+ }
+ }
+ }
+ if (rf!=null) {
+ if (rf.__vorba==null)
+ rf.__vorba = __vorba; // propagate IVorbaIdFactory
+ rf.__ensure_instance_ids();
+ }
+ }
+ catch (Exception e) {
+ log.error("Client error - could not access "+type.getName()+" in "+this.getClass().getName(), e);
+ }
+ }
+ }
+
+ }
}
--- /dev/null
+/**
+ *
+ */
+package org.vamsas.client.simpleclient;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.ClientHandle;
+import org.vamsas.client.SessionHandle;
+import org.vamsas.client.UserHandle;
+import org.vamsas.client.VorbaId;
+import org.vamsas.client.VorbaIdFactory;
+import org.vamsas.objects.utils.document.VersionEntries;
+
+import java.util.Hashtable;
+import java.util.zip.CRC32;
+/**
+ * Simplest VorbaId constructor
+ * @author jimp
+ *
+ */
+public class IdFactory extends VorbaIdFactory {
+ static Log log = LogFactory.getLog(IdFactory.class);
+ private SessionHandle session=null;
+ private ClientHandle client;
+ private UserHandle user;
+ private CRC32 unique=new CRC32(); // used to attempt a unique but predictable stream for IDs
+ private String idstring;
+ int sequence=0; // incrementing value for next new ID
+ /**
+ *
+ */
+ public IdFactory() {
+ super();
+ // TODO Auto-generated constructor stub
+ }
+
+ /**
+ * @param session
+ * @param client
+ * @param user
+ */
+ protected IdFactory(SessionHandle session, ClientHandle client, UserHandle user) {
+ super();
+ this.session = session;
+ this.client = client;
+ this.user = user;
+ unique.reset();
+ unique.update(new Object[] { session, client, user}.toString().getBytes());
+ idstring = "vamsas:"+session.getSessionUrn()+":"+unique.getValue()+":"+client.getClientUrn()+"/";
+ sequence=0;
+ extantids=new Hashtable();
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#makeVorbaId()
+ */
+ public VorbaId makeVorbaId() {
+ if (session==null)
+ throw new Error("makeVorbaId called on improperly initialised IdFactory object!");
+ String newidstring;
+ do {
+ if (sequence!=0) {
+ sequence++;
+ } else {
+ idstring+="1/";
+ }
+ newidstring=idstring+Integer.toString(sequence);
+ } while (extantids.containsKey(newidstring));
+ VorbaId id = newId(newidstring);
+ return id;
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#setSession(org.vamsas.client.SessionHandle)
+ */
+ protected void setSession(SessionHandle sessionhandle) {
+ if (sessionhandle!=null)
+ session=sessionhandle;
+ else
+ log.warn("setSession(null) called.");
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#getSessionHandle()
+ */
+ public SessionHandle getSessionHandle() {
+ return session;
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#setClient(org.vamsas.client.ClientHandle)
+ */
+ protected void setClient(ClientHandle appHandle) {
+ if (appHandle!=null)
+ client = appHandle;
+ else
+ log.warn("setClient(null) called.");
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#getClientHandle()
+ */
+ public ClientHandle getClientHandle() {
+ return client;
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#setUser(org.vamsas.client.UserHandle)
+ */
+ protected void setUser(UserHandle userHandle) {
+ if (userHandle!=null)
+ user = userHandle;
+ else
+ log.warn("setUser(null) called.");
+ }
+
+ /* (non-Javadoc)
+ * @see org.vamsas.client.VorbaIdFactory#getUserHandle()
+ */
+ public UserHandle getUserHandle() {
+ return user;
+ }
+ /**
+ * Convenience method used for default behaviour in testing
+ * and any anonymous internal vamsasDocument unmarshalling
+ * @param clientname
+ * @return
+ */
+ protected static IdFactory getDummyFactory(String clientname) {
+ if (clientname==null)
+ clientname="org.vamsas.client.simpleclient.IdFactory";
+ return new IdFactory(new SessionHandle("dummy.session"),
+ new ClientHandle(clientname,VersionEntries.latestVersion()),
+ new UserHandle("arnoldUser", "none"));
+ }
+}
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;
}
}
}
-
+
/**
* 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.
}
}
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[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);
- 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(null);
+ VorbaXmlBinder.putVamsasDocument(getDocumentOutputStream(), vorba, doc);
+ }
}
if ((start-end)!=Sequence.length())
seq.setEnd(end+Sequence.length());
}
- seq.getVorbaId();
return seq;
}
public static AlignmentSequence newAlignmentSequence(String name, String alSequence, Sequence refseq, int start, int end) {
apuser.setOrganization("disOrganised");
String appdata_ref = "vamsas:org.vamsas.test.simpleclient.VamsasArchive/"+apuser.getOrganization()+"/"+apuser.getFullname();
org.vamsas.client.simpleclient.VamsasArchive va = new org.vamsas.client.simpleclient.VamsasArchive(backup, true);
+ log.info("Getting the document from the backup-original.");
+ VamsasDocument vadoc;
VamsasArchiveReader vread = va.getOriginalArchiveReader();
+
+ vadoc = va.getVamsasDocument();
+ log.info("Got document. Adding stuff.");
+
if (vread.getAppdataStream(appdata_ref)!=null) {
int i=0;
while (vread.getAppdataStream(appdata_ref+"/"+Integer.toString(++i))!=null)
apdos.writeObject(appdata_ref);
apdos.writeObject(apuser); // some random content
apdos.close(); // this should *not* close the archive!
+ log.info("Written Appdata Stream");
log.info("Preparing to write new document.");
doc.addApplicationData(appdata);
doc.addVAMSAS(Core.getDemoVamsas());
- PrintWriter vxml = varchive.getDocumentOutputStream();
- doc.marshal(vxml);
+ va.putVamsasDocument(doc); // gets stream and puts it.
// TODO: verify that the vxml stream close method overridden ?
va.closeArchive();
log.info("Dump of new vamsas document :");
va = new org.vamsas.client.simpleclient.VamsasArchive(backup, true); // TODO - refactor Reader class to have deserializing helpers
ArchiveReports.reportDocument(va.getVamsasDocument(), va.getOriginalArchiveReader(), true);
- backup.delete(); // tidy up
+ // backup.delete(); // tidy up
}
- log.info("Cancelling write to original archive "+av);
+ log.info("Now Cancelling write to original archive "+av);
varchive.cancelArchive();
} catch (Exception e) {
git://source.jalview.org / vamsas.git / commitdiff