+++ /dev/null
-/*
- *
- */
-package org.vamsas.client;
-
-import java.util.Hashtable;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.vamsas.objects.core.VAMSAS;
-
-/**
- * skeleton abstract class to allow client implementations
- * access to vamsas.client.Vobject registry mechanism.
- */
-public abstract class ClientDocument implements IClientDocument {
- static Log log = LogFactory.getLog(ClientDocument.class);
-
- /**
- * collection of org.vamsas.client.Vobject references
- */
- protected Hashtable vamsasObjects;
- protected IVorbaIdFactory vorbafactory;
-
- protected ClientDocument(Hashtable objects, IVorbaIdFactory factory) {
- vamsasObjects = objects;
- vorbafactory = factory;
- }
-
- /**
- * @see IClientHandle.registerObject(Vobject unregistered)
- */
- protected VorbaId _registerObject(Vobject unregistered) {
- // be ultra safe here because the user may be trying to mix different factories
- if (unregistered.__vorba==null)
- unregistered.__vorba = vorbafactory;
- else
- if (unregistered.__vorba!=vorbafactory) {
- // LATER: decide if this is allowed - it isn't for the moment.
- log.error("Attempt to overwrite info in a registered vorba Vobject (under a different IVorbaIdFactory) ! - Implementation fix needed.");
- return null;
- } else {
- // probably didn't need to call registerObject.
- log.debug("Redundant call to registerObject");
- }
- // TODO: add default provenance.
- // TODO: decide if we need to do call __ensure_instance_ids here
- // TODO: check if __ensure_instance_ids works correctly with new 'visit flag' mechanism
- unregistered.__ensure_instance_ids(); // call cascade method here :
- return unregistered.getVorbaId();
- }
-}
+++ /dev/null
-/*
- */
-package org.vamsas.client;
-
-import java.io.Serializable;
-
-/**
- * Uniquely describes a vamsas client application.
- * @author jimp
- */
-public class ClientHandle implements Serializable {
- static final long serialVersionUID = 0;
- /**
- * @param clientName
- * @param version
- */
- public ClientHandle(String clientName, String version) {
- super();
- this.clientName = clientName;
- this.version = version;
- this.setClientUrn("vamsas://"+clientName+":"+version+"/"); // TODO: decide on application handle ornthing (used to prefix new ids made by a particular application)
- }
- /**
- * (non-unique) human readable vamsas client name
- */
- String clientName;
-
- /**
- * the unambiguous client identifier
- * This may be rewritten by the Vorba object if
- * other clients with the same name, version
- * and user are involved in a session.
- *
- */
- String clientUrn;
-
- /**
- * version modifier to tag application space
- */
- String version;
-
- /**
- * @return Returns the clientUrn.
- */
- public String getClientUrn() {
- return clientUrn;
- }
-
- /**
- * May become protected - should only be set by a Vorba object.
- * @param clientUrn
- * The clientUrn to set.
- */
- public void setClientUrn(String clientUrn) {
- this.clientUrn = clientUrn;
- }
-
- /**
- * @return Returns the version.
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * @param version
- * The version to set.
- */
- public void setVersion(String version) {
- this.version = version;
- }
-
-
- /**
- * @return Returns the clientName.
- */
- public String getClientName() {
- return clientName;
- }
-
- /**
- * @param clientName
- * The clientName to set.
- */
- public void setClientName(String clientName) {
- this.clientName = clientName;
- }
-
- public boolean equals(Object that) {
- if (that instanceof ClientHandle)
- return this.equals((ClientHandle) that);
- return false;
- }
- public boolean equals(ClientHandle that) {
- return (clientName.equals(that.clientName) && version.equals(that.version) && clientUrn.equals(that.clientUrn));
- }
-}
+++ /dev/null
-package org.vamsas.client;
-
-/**
- * Enumerates the event types generated during the lifecycle of a Vamsas
- * session.
- * See the excel spreadsheet in VamsasClient/docs/VamsasSessionEventAnalysis.xls for
- * some more information about when these are generated and how they should be
- * handled.
- *
- */
-
-public class Events {
- /**
- * Generated when a client has finished updating the document.
- * Client which has completed an update should
- * not receive the event.
- * NewValue: org.vamsas.client.IClient for session.
- */
- public static final String DOCUMENT_UPDATE = "org.vamsas.client.events.documentUpdateEvent";
-
- /**
- * Generated when a new vamsas document is created (perhaps from some existing
- * Vamsas data) so an application may do its own data space initialization.
- * Raised for a new application connecting to a vamsas document
- * NewValue: org.vamsas.client.IClient for session.
- * LATER: DOCUMENT_CREATE event may be redundant
- */
- public static final String DOCUMENT_CREATE = "org.vamsas.client.events.documentCreateEvent";
-
- /**
- * Generated when a new vamsas client is attached to a session (Handle is
- * passed) Note: the newly created client does not receive the event.
- */
- public static final String CLIENT_CREATION = "org.vamsas.client.events.clientCreateEvent";
-
- /**
- * Generated when a vamsas client leaves a session (Handle is passed to all
- * others).
- */
- public static final String CLIENT_FINALIZATION = "org.vamsas.client.events.clientFinalizationEvent";
-
- /**
- * Generated prior to session Shutdown, after the last participating vamsas
- * client has finalized.
- * Probably only useful to IClientFactory implementations.
- * NewValue: <Vamsas-session URN>
- */
- public static final String SESSION_SHUTDOWN = "org.vamsas.client.events.SessionShutdownEvent";
-
- /**
- * Generated for all clients when any client calls IClient.storeDocument() to
- * allow them to store any updates before an offline copy of the session is
- * created.
- * Any client that handles this should call the
- * IClient.getDocument(), update and then IClient.updateDocument in the same
- * handler thread (the lock on the document is held until the handler exits).
- * EventName: <Vamsas-session URN>
- * NewValue: org.vamsas.client.IClient for session.
- */
- public static final String DOCUMENT_FINALIZEAPPDATA = "org.vamsas.client.events.DocumentFinalizeAppData";
-
- /**
- * Generated by Vorba stub for the sole remaining client instance in a session,
- * when it makes a call to finalizeClient().
- * It is only raised if the session has been modified since the
- * last call to storeDocument() by any application.
- * LATER: copies of a document should be on a per-user basis for multi-user sessions.
- * Sequence is as follows : 1. All other vamsas clients have
- * called finalizeClient() 2. Final living client monitors closures, and
- * realises that it is last. 3. Final client generates event to prompt
- * associated application to inquire if the user wishes to save the document
- * for future reference.
- * * Any call to finalizeClient in a thread other than the registered
- * EventListener will block until the RequestToClose handler has exited.
- * NewValue: org.vamsas.client.IClient for session.
- */
- public static final String DOCUMENT_REQUESTTOCLOSE = "org.vamas.client.DocumentRequestToCloseEvent";
-
- public static java.util.Vector EventList = initList();
-
- private static java.util.Vector initList() {
- java.util.Vector vec = new java.util.Vector();
- vec.add((Object) DOCUMENT_UPDATE);
- vec.add((Object) DOCUMENT_CREATE);
- vec.add((Object) CLIENT_CREATION);
- vec.add((Object) CLIENT_FINALIZATION);
- vec.add((Object) SESSION_SHUTDOWN);
- vec.add((Object) DOCUMENT_REQUESTTOCLOSE);
- vec.add((Object) DOCUMENT_FINALIZEAPPDATA);
- return vec;
- }
-}
+++ /dev/null
-/**
- * org.vamsas.client.IClient
- *
- */
-package org.vamsas.client;
-
-import java.beans.PropertyChangeListener;
-import java.io.IOException;
-
-/**
- * Defines the methods availabable to a vamsas
- * application for interacting with its Vorba agent
- * created by an IClientFactory instance for a particular session,
- * user, and application handle.
- * (it's VORBA, not CORBA!)
- * LATER: add exceptions for timeouts raised when there are problems accessing session data (because another application is hogging it).
- * LATER: think about situations when two applications both want a ClientDocument at the same time - can one have read-only access (and be told that another is about to update)
- */
-
-public interface IClient {
-
- /**
- * Self-documenting/describing info for the application to present
- * to the user.
- * LATER: formalise this for describing VAMSAS system, a particular
- * Vorba client agent, and a particular session.
- * @return string like VamsasClient v.1.1.1 (GPL) and whatever
- */
- public String getAbout();
-
- /**
- * convenience method to get the SessionUrn as a string (for passing directly to a text box...).
- * @return current SessionUrn
- */
- public String getSessionUrn();
- /**
- * Returns a valid URN for other applications to connect to
- * the vamsas session.
- * @return session handle for this session.
- */
- public SessionHandle getSessionHandle();
- /**
- * Included for applications with several ClientHandle
- * identities.
- * @return ClientHandle used to interact with
- * other Vamsas applications.
- */
- public ClientHandle getClientHandle();
- /**
- *
- * @return UserHandle used when interacting
- * with other Vamsas applications.
- */
- public UserHandle getUserHandle();
- /**
- * Method called by client application on exit.
- * Vorba will inform other clients if they exist.
- * If this is the last application in the session
- * then the session will be closed.
- * Note: The application should be ready to handle
- * 'RequestToCloseDocument' events from the Vorba
- * agent in the latter case and so prompt the user
- * to save the session locally.
- * LATER: pick a better name ?
- */
- public void finalizeClient();
- /**
- * register handler for updates for the current session
- */
- public void addDocumentUpdateHandler(PropertyChangeListener evt);
- /**
- * get vamsas document with
- * user and app specific data
- * IClientDocuments are not thread-safe.
- * TODO: New exception for failed document lock.
- * @throws IOException if lock is not obtainable for the document in the session
- */
- public IClientDocument getClientDocument() throws IOException;
- /**
- * Queue new Vorba objects for storage and propagation
- * to other clients (via Event.DOCUMENT_UPDATE based
- * notification of document change)
- * New objects without provenance information will be
- * given a default entry using the IClient's application,
- * user (and session) handles
- * Validity of IClientDocument object instances after this call is implementation dependent
- * TODO: consider refactoring to remove the redundant IClientDocument parameter for this method
- */
- public void updateDocument(IClientDocument newdoc);
- /**
- * Any application may call storeDocument to
- * save a local copy of the current vamsas document
- * including all application specific entries.
- *
- * @param location to write zip file
- */
- public void storeDocument(java.io.File location);
- /**
- * Any application may call importDocument to merge a stored
- * vamsasDocument into the current session.
- * Note: use a IClientFactory's implementation to make sessions out of vamsas documnts
- * LATER: VAMSAS: The IClient implementation will handle all ID 'relocations'
- * @param location
- */
- public void importDocument(java.io.File location);
- /**
- * Add a listener to a particular event chain.
- * See org.vamsas.client.Events for allowed
- * values for EventChain.
- * The EventChain value is passed as the
- * propertyName in the java.bean.PropertyChangeEvent
- * LATER: extend class to form own vamsas Event/Listener model.
- * @param EventChain Name of event. Blank/null registers handler for all events.
- * @param evt - event handler function.
- */
- public void addVorbaEventHandler(String EventChain, PropertyChangeListener evt);
- /**
- * Sets the update handler that will be called when any updates occur to objects of type rootObject.
- * @param rootObject
- * @param handler
- */
- public void setUpdateHandler(IObjectUpdate handler);
- public IObjectUpdate getUpdateHandler(Class rootObject);
- public void removeUpdateHandler(Class rootObject);
- public IObjectUpdate[] getUpdateHandlers();
- /**
- * client application calls this to force the
- * Vorba client to check for updates immediately.
- *
- */
- public void pollUpdate();
-
- /**
- * Client application calls this after any pre-session initialization
- * (registering of Handlers, etc)
- * Exceptions are raised for any failures. Any stateful calls to the session prior to
- * this will result in an implicit call to joinSession - if that results in an exception
- * then the VamsasClient should raise an Error.
- * LATER: create VAMSAS exception hierarchy (in a language agnostic manner)
- */
- public void joinSession() throws Exception;
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-
-/**
- * Object for accessing Client and User specific data
- * in an IClientDocument instance.
- *
- */
-public interface IClientAppdata {
- /**
- * @return true if Client's non-user specific application data is non-zero length.
- */
- boolean hasClientAppdata();
- /**
- * @return true if User's Client Application data is non-zero length
- */
- boolean hasUserAppdata();
- /**
- *
- * @return byte array containing the Client's non-user specific application data
- */
- byte[] getClientAppdata();
- /**
- *
- * @return byte array containing the Client's user specific application data
- */
- byte[] getUserAppdata();
- /**
- * set the non-User-specific application data
- * @param data - the new non-user-specific data
- */
- void setClientAppdata(byte[] data);
- /**
- * set the User-specific application data
- * @param data - the new user-specific data
- */
- void setUserAppdata(byte[] data);
- /**
- * @return non-user specific data output stream
- */
- DataOutput getClientOutputStream();
- /**
- * @return non-user specific data input stream
- */
- DataInput getClientInputStream();
- /**
- *
- * @return user specific data output stream
- */
- DataOutput getUserOutputStream();
- /**
- *
- * @return user specific data input stream
- */
- DataInput getUserInputStream();
-}
+++ /dev/null
-/*
- * Created on 13-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-import org.vamsas.objects.core.VAMSAS;
-
-
-/**
- * Defines the API for the Vamsas XML Document
- * as accessed by a Vamsas SimpleClient Application.
- * An instance of this interface is valid for a
- * particular set of user, session and application
- * handles.
- *
- * It initially represents a snapshot of the
- * XML document at a particular time - queriable by
- * reference or by retrieval of root objects.
- * It provides methods to make new Vobject references,
- * These are guaranteed to be unique amongst existing
- * objects in the document, all other references created
- * by this Vobject's instance and all other references
- * constructed by any other vamsas agents in the session.
- * TODO: LATER: finegrained access control for public/private user access
- * Finegrained access control: Since a clientDocument is created for a particular
- * UserHandle, there is scope for fine grain data access
- * control based on user identity.
- * A user may also want to make private notes, not
- * available to other people using the same application
- * in the same session.
- * TODO: LATER: implement a more sophisticated query interface for quickly identifying new data in a vamsas document and manipulating existing objects
- * @author jimp
- */
-public interface IClientDocument {
-
- /**
- * Get a single Vobject.
- * @param id
- * @return Vobject referred to by id or null if it doesn't exist.
- */
- Vobject getObject(VorbaId id);
- /**
- * Get a list of objects.
- * @param ids
- * @return array of objects using a vector of VorbaId ids.
- */
- Vobject[] getObjects(VorbaId[] ids);
- /**
- * Returns all root objects in document. All objects inherit
- * from org.vamsas.client.Vobject and have valid VorbaIds and provenance entries.
- * @return array of root Vamsas element objects.
- */
- VAMSAS[] getVamsasRoots();
- /**
- * set the VAMSAS roots in the document
- * TODO: decide if objects are verified for provenance and VorbaIds by this call or when document is stored
- * TODO: decide if this call should throw InvalidVamsasObject exceptions.
- * TODO: decide how this call deals with applications that 'forget' to include all VAMSAS roots (this is where reference counting/garbage collection happens)
- * @param roots
- */
- void setVamsasRoots(VAMSAS[] roots);
- /**
- * Adds a new VAMSAS root entry
- * TODO: decide on same InvalidVamsasObject exceptions.
- * TODO: decide if a 'removeVamsasRoot' method is really needed.
- * @param newroot
- */
- void addVamsasRoot(VAMSAS newroot);
- /**
- * Returns an Vobject with a valid VorbaId, and provenance element.
- * The VorbaId is so the application may refer to it in
- * its own dataspace.
- *
- * Note: An Vobject with valid VorbaId will not be reregistered.
- * Advice: Calling this method for a high-level Vobject
- * (such as org.vamsas.objects.core.VAMSAS) will
- * register all its component objects too.
- *
- * @param unregistered unregistered vamsas Vobject
- * @return VorbaId registered for vamsas Vobject
- */
- VorbaId registerObject(Vobject unregistered);
- /**
- * Returns an array of objects, each with a valid VorbaId
- * (and completed provenance entry).
- * Note: An Vobject with valid VorbaId will not be reregistered.
- * @param unregistered array of unregistered objects.
- * @return array of VorbaIds for the registered objects
- */
- VorbaId[] registerObjects(Vobject[] unregistered);
- /**
- * Get instance of Client and User specific vamsas document data access interface.
- * @return Interface to Client and user specific application data
- */
- IClientAppdata getClientAppdata();
-}
\ No newline at end of file
+++ /dev/null
-/*
- * Created on 13-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-/**
- * Defines methods for instantiating Vorba client application agents
- * @author jimp
- *
- * (it's VORBA, not CORBA!)
- */
-
-public interface IClientFactory {
-
- /**
- * Create a new Vorba Session
- * @param applicationHandle is the application's VAMSAS handle string
- * @throws NoDefaultSessionException if more than one session exists that the client may connect to
- */
- IClient getIClient(ClientHandle applicationHandle) throws NoDefaultSessionException;
- /**
- * returns new Vorba for a given session.
- * @param applicationHandle
- * @param sessionUrn session to connect to (or null to create a new session)
- * @return
- */
- IClient getIClient(ClientHandle applicationHandle, String sessionUrn);
- /**
- * returns new vorba for a given session acting as a particular identity
- * @param applicationHandle
- * @param userId
- * @param sessionUrn session to connect to (or null to create a new session)
- * @return
- */
- IClient getIClient(ClientHandle applicationHandle, UserHandle userId, String sessionUrn);
- /**
- * New session for application and specific user
- * @param applicationHandle
- * @param userId
- * @return
- * @throws NoDefaultSessionException if more than one session exists that the client may connect to
- */
- IClient getIClient(ClientHandle applicationHandle, UserHandle userId) throws NoDefaultSessionException;
-
- /**
- * enumerate the active sessions this IClientFactory instance knows about.
- * Can be used by caller to pick a session on catching a NoDefaultSessionException.
- * LATER: Define interface for discovering more information about a session (so it can be presented to a user in a meaningful way)
- * @return possibly empty array of sessionUrn strings
- */
- public String[] getCurrentSessions();
-
-}
+++ /dev/null
-package org.vamsas.client;\r
-\r
-/**\r
- * Methods implemented by a Vamsas Application's Object Update handler\r
- * @author vamsas\r
- * Introduced November 2006 Vamsas Meeting\r
- * TODO: verify this is sufficient for the per-object update event mechanism\r
- */\r
-public interface IObjectUpdate {\r
- /**\r
- * Called by the library to find out which vamsas document object this update handler is interested in\r
- * @return class that extends org.vamsas.Vobject\r
- */\r
- Class getRootVobject();\r
- /**\r
- * Called to test if this handler is to be called for updates to any Vobjects below the Root Vobject in the vamsas document.\r
- * @return false means IObjectUpdate.update(updated, cdoc) will only be called with instances of type getRootVobject(). \r
- */\r
- boolean handlesSubtreeUpdates();\r
- /**\r
- * Method called by Vamsas Client Library for all updated objects that the handler is registered for.\r
- * @param updated\r
- * @param cdoc\r
- */\r
- void update(org.vamsas.client.Vobject updated, org.vamsas.client.IClientDocument cdoc);\r
-}\r
+++ /dev/null
-/*
- * Created on 14-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-/**
- * @author jimp
- * middleware interface for generating new VorbaId objects
- * for a particular vamsas client based on the current
- * session, user and client handle. Generally implemented
- * by instances of the vamsas library api only.
- */
-public interface IVorbaIdFactory {
- /**
- * construct a new id appropriate for this client in the vamsas session.
- * @param vobject TODO
- *
- * @return valid VorbaId for session, or null if VorbaIdFactory not configured
- * correctly.
- */
- public abstract VorbaId makeVorbaId(Vobject vobject);
-
- public abstract SessionHandle getSessionHandle();
-
- public abstract ClientHandle getClientHandle();
-
- public abstract UserHandle getUserHandle();
- /**
- * called when an object is touched by the vamsas library prior to writing
- * to record last hash for the object's VorbaId
- * @param vobject
- */
- public abstract void updateHashValue(Vobject vobject);
-}
\ No newline at end of file
+++ /dev/null
-/**
- * org.vamsas.client.Iapp
- */
-package org.vamsas.client;
-public interface Iapp {
- /**
- * Define core callback functionality that a fully
- * fledged vamsas application Vobject must implement
- * TODO: define some Application Callbacks and create use cases for them
- */
-
-};
+++ /dev/null
-package org.vamsas.client;
-
-public class InvalidSessionUrnException extends Exception {
-
- /**
- *
- */
- public InvalidSessionUrnException() {
- super("Invalid Vamsas Session URN.");
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param message
- * @param cause
- */
- public InvalidSessionUrnException(String message, Throwable cause) {
- super(message, cause);
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param message
- */
- public InvalidSessionUrnException(String message) {
- super("Invalid Vamsas Session URN: "+message);
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param cause
- */
- public InvalidSessionUrnException(Throwable cause) {
- super(cause);
- // TODO Auto-generated constructor stub
- }
-
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client;
-
-/**
- * @author jimp
- * Raised if an IClient instance is requested without
- * specifying a particular vamsas session handle
- * when more than one candidate session exists.
- */
-public class NoDefaultSessionException extends Exception {
-
- /**
- *
- */
- public NoDefaultSessionException() {
- super("No Default Session Defined");
- }
-
- /**
- * @param message
- */
- public NoDefaultSessionException(String message) {
- super(message);
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param cause
- */
- public NoDefaultSessionException(Throwable cause) {
- super(cause);
- // TODO Auto-generated constructor stub
- }
-
- /**
- * @param message
- * @param cause
- */
- public NoDefaultSessionException(String message, Throwable cause) {
- super(message, cause);
- // TODO Auto-generated constructor stub
- }
-
-}
+++ /dev/null
-/*
- * Created on 12-Sep-2005
- *
- */
-package org.vamsas.client;
-
-/**
- * Uniquely locates a particular VAMSAS session.
- * @author jimp
- *
- */
-public class SessionHandle {
-
- /**
- * @param sessionUrn
- */
- public SessionHandle(String sessionUrn) {
- super();
- SessionUrn = sessionUrn;
- }
- /**
- * @return Returns the sessionUrn.
- */
- public String getSessionUrn() {
- return SessionUrn;
- }
- /**
- * @param sessionUrn The sessionUrn to set.
- */
- public void setSessionUrn(String sessionUrn) {
- SessionUrn = sessionUrn;
- }
- /**
- * The path to the vamsas session file.
- */
- String SessionUrn;
-
-}
+++ /dev/null
-/**
- *
- */
-package org.vamsas.client;
-
-import java.net.URI;
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * @author jimp
- * base class for vamsas session/document types
- * uses java.net.URI internally for construction of URN
- */
-public abstract class SessionUrn {
- protected URI urn;
- /**
- * The types of URI protocols we understand
- */
- protected static final Hashtable TYPES=new Hashtable();
-
- /**
- * construct urn for a locally stored session file
- * @param type
- * @param url
- */
- protected SessionUrn(String type, java.net.URL url) {
- if (!TYPES.containsKey(type.toLowerCase()))
- throw new Error("Unknown "+this.getClass().getName()+" type '"+type+"' for URL '"+url+"'");
- try {
- urn = URI.create(type+"://"+url.getPath());
- } catch (Exception e) {
- // TODO: something better than throwing an error should be done here.
- throw new Error(e);
- }
- }
- public String getSessionUrn() {
- return urn.toString();
- }
-}
+++ /dev/null
-/*
- * Created on 12-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-/**
- * Unique user identifier for a vamsas session.
- * Used to write user provenance information, and
- * track view/access control in multiuser sessions.
- * @author jimp
- */
-public class UserHandle {
- /**
- * @param fullName
- * @param organization
- */
- public UserHandle(String fullName, String organization) {
- this.fullName = fullName;
- Organization = organization;
- }
- String fullName;
- String Organization;
- /**
- * @return Returns the fullName.
- */
- public String getFullName() {
- return fullName;
- }
- /**
- * @param fullName The fullName to set.
- */
- public void setFullName(String fullname) {
- fullName = fullname;
- }
- /**
- * @return Returns the organization.
- */
- public String getOrganization() {
- return Organization;
- }
- /**
- * @param organization The organization to set.
- */
- public void setOrganization(String organization) {
- Organization = organization;
- }
-}
+++ /dev/null
-/**
- *
- */
-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
- * Vobject maybe registered or unregistered.
- *
- * @author jimp
- *
- */
-public abstract class Vobject {
- static Log log = LogFactory.getLog(Vobject.class);
-
- /**
- * true if Vobject was stored in a vamsas Document or has been retrieved from it
- */
- protected boolean __stored_in_document = false;
- /**
- * true if Vobject was updated since the vamsas library last read a Vobj with the same VorbaId from a document.
- */
- protected boolean __updated_since_last_read = false;
- /**
- * memory of the last doHash() value computed for the Vobject
- * @see doHash()
- */
- protected int __last_hash = 0;
- /**
- * set by testInstanceForIdField() if Vobject should have a VorbaId
- */
- protected boolean registerable = false;
- protected boolean __visited = false;
- /**
- * reference to containing object for this Vobject.
- */
- protected Vobject V_parent=null;
- /**
- * unique id for all vamsas objects allows unambiguous referencing to any
- * Vobject in the vamsas document
- */
- protected VorbaId vorbaId = null;
-
- /**
- * the source of unique VorbaIds.
- */
- protected IVorbaIdFactory __vorba = null;
-
- /* (non-Javadoc)
- * @see java.lang.Object#finalize()
- */
- protected void finalize() throws Throwable {
- V_parent=null;
- __vorba=null;
- vorbaId=null;
- super.finalize();
- }
-
- /**
- *
- */
- protected Vobject() {
- super();
- testInstanceForIdField();
- }
- java.lang.reflect.Field ___id_field=null; // set to ease pain of reflection
- /**
- * set the isRegisterable flag based on the presence of a 'private String _id' field in
- * the reflected class instance.
- */
- private void testInstanceForIdField() {
- // TODO: decide if 'id' is an appropriate reserved attribute name for the VorbaId
- // look for the id field in all castor classes (should be an NCName string)
-
- Class thisclass=this.getClass();
- setRegisterable(false);
- while (!thisclass.equals(Vobject.class)) {
- try {
- java.lang.reflect.Field fd = thisclass.getDeclaredField("_id");
- if (String.class.isAssignableFrom(fd.getType())) {
- ___id_field=fd;
- this.setRegisterable(true);
- break;
- }
- } catch (SecurityException e) {
- log.error("Unexpected Security Exception whilst finding id fields to set!",e);
- } catch (NoSuchFieldException e) {
- thisclass=thisclass.getSuperclass();
- }
- }
- }
- // boolean __testedInstance=false;
- /**
- * update the Vobject instance's _id field, based on the contents of the
- * VorbaId. Only call this if you mean to do it!
- */
- protected void setInstanceIdField() {
- /*if (!registerable && !__testedInstance) {
- testInstanceForIdField();
- __testedInstance=true;
- }*/
- if (registerable) {
- if (__vorba != null)
- try {
- Method fd = this.getClass().getMethod("setId", new Class[] { String.class });
- fd.invoke((Object) this, new Object[] {new String(this.getVorbaId().id)});
- log.debug(this.getClass().getName()+" called setInstanceIdField!");
- } catch (InvocationTargetException e) {
- log.error("SourceGeneration of "
- + this.getClass().toString()
- + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId Vobject.", e);
- }
- catch (IllegalAccessException e) {
- log.error("SourceGeneration of "
- + this.getClass().toString()
- + "\n has resulted in an inaccessible 'setId' method!\nCannot set ID from the vorbaId Vobject.", e);
- } catch (SecurityException e) {
- log.error("Security access violation for "+this.getClass().toString(),e);
- } catch (NoSuchMethodException e) {
- log.warn(this.getClass().toString()+" was erroneously marked as a Vorba Vobject class (Implementation error?)");
- this.setRegisterable(false);
- }
- } else {
- System.err.println("Client error. Trying to setInstanceIdField on a "
- + this.getClass().toString() + " (which cannot be given a vorbaId)");
- }
- }
-
- protected String __getInstanceIdField() {
- /*if (!registerable && !__testedInstance) {
- testInstanceForIdField();
- __testedInstance=true;
- }*/
- if (registerable) {
- if (__vorba != null)
- try {
- Method fd = this.getClass().getMethod("getId", (Class[]) null);
- Object idstring = fd.invoke((Object) this, (Object[]) null);
- log.debug(this.getClass().getName()+" called getInstanceIdField!");
- if (idstring!=null && idstring instanceof String) {
- if (((String) idstring).length()>0)
- return (String) idstring;
- }
- } catch (InvocationTargetException e) {
- log.error("SourceGeneration of "
- + this.getClass().toString()
- + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", e);
- }
- catch (IllegalAccessException e) {
- log.error("SourceGeneration of "
- + this.getClass().toString()
- + "\n has resulted in an inaccessible 'getId' method!\nCannot set ID from the vorbaId Vobject.", e);
- } catch (SecurityException e) {
- log.error("Security access violation for "+this.getClass().toString(),e);
- } catch (NoSuchMethodException e) {
- log.warn(this.getClass().toString()+" was erroneously marked as a Vorba Vobject class (Implementation error?)");
- this.setRegisterable(false);
- }
- } else {
- System.err.println("Client error. Trying to getInstanceIdField on a "
- + this.getClass().toString() + " (which cannot be given a vorbaId)");
- }
- return null;
- }
-
- /**
- * calculate a hash for the Vobject with all housekeeping fields at standard
- * values. (isRegisterable is an immutable attribute property)
- * TODO: decide if __stored_in_document should be included in the hash or not.
- * @return true if new hash different to last hash
- */
- synchronized protected boolean doHash() {
- long __old_hash = __last_hash;
- __last_hash = 0;
- Vobject _V_parent=V_parent;
- V_parent=null;
- VorbaId thisid = vorbaId;
- IVorbaIdFactory factory = __vorba;
- boolean stored = __stored_in_document;
- boolean updated = __updated_since_last_read;
- boolean visited = __visited;
- java.lang.reflect.Field idfield = ___id_field;
- ___id_field=null;
- __updated_since_last_read=false;
- vorbaId = null;
- __vorba = null;
- __visited=false;
- // compute hash
- __last_hash = this.hashCode();
- // reset houseskeeping variables
- ___id_field=idfield;
- vorbaId = thisid;
- __vorba = factory;
- __stored_in_document = stored;
- __updated_since_last_read=updated;
- V_parent=_V_parent;
- __visited=visited;
- return (__old_hash==0) || (__old_hash == __last_hash);
- }
-
- /**
- * TODO: combine two versions of the same collection Vobject to resolve
- * asynchronous updates to the same vamsas Vobject Merges two vamsas objects,
- * one of which is a later version of the earlier (ie they have the same
- * vorbaId but one is a later version recently read from the vamsasDocument
- * collection.
- *
- * @return
- */
- protected boolean merge(Vobject laterCopy) {
- log.warn(this.getClass().getName()+".merge() not implemented.");
- return true;
- }
-
- /**
- *
- * @return true if Vobject is registered
- */
- public boolean isRegistered() {
- return (registerable) ? (vorbaId != null) : false;
- }
-
- /**
- * Method to get fixed reference for the Vobject in the vamsas document.
- *
- * @returns null if Vobject is neither registered or not associated with a
- * properly instantiated VorbaIdFactory.
- */
- public VorbaId getVorbaId() {
- if (registerable && vorbaId == null) {
- if (this.__stored_in_document) {
- if (__vorba!=null)
- vorbaId=org.vamsas.client.VorbaId.newId(this.__getInstanceIdField());
- }
- // Try to use the associated factory.
- if (__vorba != null)
- if ((vorbaId = __vorba.makeVorbaId(this)) == null)
- return null; // Factory not valid.
- else {
- this.setInstanceIdField();
- return vorbaId;
- }
- }
- return vorbaId;
- }
-
- /**
- * used by the IClient implementation to generate unique Id based on client
- * applications current namespace.
- */
- protected void setVorbaId(VorbaId newid) {
- vorbaId = newid;
- }
-
- /**
- * @return true if Vobject is present in Vamsas Document.
- */
- public boolean is__stored_in_document() {
- return __stored_in_document;
- }
-
- /**
- * @return true if this object has been updated in the currently stored document since the last time a Vobject with the same ID was read from a Vamsas Document
- */
- public boolean is__updated_since_last_read() {
- return __updated_since_last_read;
- }
-
- /**
- * Set internal flag to indicate this object was updated since the last document read
- * @param __updated_since_last_read the __updated_since_last_read to set
- */
- protected void set__updated_since_last_read(boolean __updated_since_last_read) {
- this.__updated_since_last_read = __updated_since_last_read;
- }
-
- /**
- * for use by Vorba agent to reflect state of vamsas Vobject to client
- * application.
- * Setting stored_in_document on a registerable Vobject without a
- * vorbaId will mean is will *never* get a vorbaId and
- * horrible things will happen.
- * @param __stored_in_document true if Vobject has been marshalled into current document.
- */
- protected void set__stored_in_document(boolean __stored_in_document) {
- this.__stored_in_document = __stored_in_document;
- }
-
- /**
- * __last_hash is the hash value computed when the Vobject was last checked
- * against a IClientDocument generated by the Vobject's parent IClient
- * instance.
- *
- * @return Returns the __last_hash.
- */
- public int get__last_hash() {
- return __last_hash;
- }
-
- /**
- * @return true if Vobject can have a vorbaId
- */
- public boolean isRegisterable() {
- return registerable;
- }
-
- /**
- * Called by __testInstanceForidField and the post-unmarshalling handler
- * to indicate if Vobject will have a vorbaId.
- * @param registerable
- */
- 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 Vobject
- * calling the same method on them.
- * TODO: LATER: properly apply castors own field mechanisms to get at accessors
- * TODO: FIX CYCLIC __ensure+instance_ids
- * Implementation note for the todo:
- * this works like a depth-first search over all vamsas objects in an vamsasDocument.
- * __visited is the visited flag, any Vobj who's flag is of a different parity
- * to the visited argument will be recursed on.
- * note - the doHash() function used to be used as the 'visited' flag -
- * this *is not* a valid heuristic, although it will work "most of the time".
- * TODO: LATER? Add another method for setDefaultProvenanceField (in the spirit of setInstanceIdField) using the info from the __vorba.getClient/User/Session methods
- */
- protected void __ensure_instance_ids() {
- __ensure_instance_ids(!__visited);
- }
- protected void __ensure_instance_ids(boolean visited) {
- if (__vorba==null)
- throw new Error("Improperly intialised org.vamsas.client.Vobject - no VorbaFactory given.");
- log.debug("doing "+this.getClass()+".__ensure_instance_ids()");
- if (!__stored_in_document && registerable)
- setInstanceIdField();
- if (__visited==visited)
- return;
- __visited=visited;
- __vorba.updateHashValue(this);
-
- Class descriptor = null;
- XMLClassDescriptorImpl descimpl = null;
- try {
- // castor descriptor resolver magic
- descriptor = this.getClass().getClassLoader().loadClass(this.getClass().getName()+"Descriptor");
- descimpl = (XMLClassDescriptorImpl) descriptor.getConstructor((Class[])null).newInstance((Object[])null);
- } catch (Exception e) {
- log.fatal("Source Generation Error!: Couldn't resolve descriptor for "
- +this.getClass().getName()
- +" was 'generate descriptors' set for castorbuilder.properties?");
- return;
- }
- FieldDescriptor fields[] = descimpl.getFields();
- for (int i=0,j=fields.length; i<j; i++) {
- Class type= fields[i].getFieldType();
- if (type.isArray()) {
- if (Vobject[].class.isAssignableFrom(type)) {
- try {
- Object val = fields[i].getHandler().getValue(this);
- if (val!=null) {
- Vobject vals[] = (Vobject[]) val;
- for (int k=0, l=vals.length; k<l; k++) {
- if (vals[k].__vorba==null)
- vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
- if (vals[k].V_parent==null)
- vals[k].V_parent=this; // propagate parent reference to this element.
- vals[k].__ensure_instance_ids(visited);
- }
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access array "+type.getName()+" in "+this.getClass().getName(), e);
- }
- }
- } else
- if (Vobject.class.isAssignableFrom(type)) {
- try {
- FieldHandler fh = fields[i].getHandler();
- Vobject rf = null;
- if (fh != null) {
- Object fval = fh.getValue(this);
- if (fval!=null) {
- if (fval.getClass().isArray()) {
- //if (Vobject[].class.isAssignableFrom(type)) {
- try {
- Vobject vals[] = (Vobject[]) fval;
- for (int k=0, l=vals.length; k<l; k++) {
- if (vals[k].__vorba==null)
- vals[k].__vorba = __vorba; // propagate IVorbaIdFactory
- if (vals[k].V_parent==null)
- vals[k].V_parent=this; // propagate parent reference to this field object
- vals[k].__ensure_instance_ids(visited);
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access (fhval)array "+type.getName()+" in "+this.getClass().getName(), e);
- }
- //}
- } else {
- rf = (Vobject) fval;
- log.debug("Got value for "+fields[i].getFieldName());
- }
- }
- } else {
- // castor's mechanism doesn't work for this object... so...*/
- // 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,(Class[])null);
- if (fgetmeth!=null) {
- Object fval = fgetmeth.invoke(this,(Object[])null);
- if (fval!=null)
- rf = (Vobject) fval;
- } else {
- log.warn("Couldn't find "+this.getClass().getName()+"."+methname);
- }
- }
- }
- if (rf!=null) {
- if (rf.__vorba==null)
- rf.__vorba = __vorba; // propagate IVorbaIdFactory
- if (rf.V_parent==null)
- rf.V_parent=this; // propagate parent reference
- rf.__ensure_instance_ids(visited);
- }
- }
- catch (Exception e) {
- log.error("Client error - could not access "+type.getName()+" in "+this.getClass().getName(), e);
- }
- }
- }
-
- }
-
- /**
- * @return the __parent
- */
- public Vobject getV_parent() {
- return V_parent;
- }
-
- /**
- * @param __parent the __parent to set
- */
- protected void setV_parent(Vobject V_parent) {
- this.V_parent = V_parent;
- }
-}
+++ /dev/null
-package org.vamsas.client;\r
-\r
-/**\r
- * Holds information about Vobj instances that is held over between different writes to the document.\r
- * @author JimP\r
- *\r
- */\r
-public class Vobjhash {\r
- int hashvalue;\r
- /**\r
- * creates a record of the hash value for a vamsas document object\r
- * @param tobemarshalled\r
- */\r
- public Vobjhash(Vobject tobemarshalled) {\r
- hashvalue = tobemarshalled.get__last_hash();\r
- }\r
- /**\r
- * compares the old hash value with the unmarshalled object's most recently computed hash value.\r
- * @param unmarshalled\r
- * @return true if the hash values differ\r
- */\r
- public boolean isUpdated(Vobject unmarshalled) {\r
- return hashvalue==unmarshalled.get__last_hash();\r
- }\r
-}\r
+++ /dev/null
-/*
- * Created on 12-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-/**
- * The unique reference id for a Vamsas document Vobject,
- * used by applications to refer to the vamsas Vobject
- * within their own data space in the vamsas document.
- * TODO: decide if VorbaId should contain a reference
- * to either the IVorbaIdFactory that made it or the
- * IClient that defines the session (it might be
- * convenient).
- * @author jimp
- */
-public class VorbaId {
- protected String id;
- protected VorbaId() {
- super();
- }
- private VorbaId(String Id) {
- super();
- id = Id;
- }
- /**
- *
- * @param vorbaObject the source of vorba Ids
- * @param vobject the Vobject to be registered with a new vorba id
- * @return
- */
- protected static VorbaId newId(IVorbaIdFactory vorbaObject, Vobject vobject) {
- // Make unique id from appSpace info in vorbaObject
- synchronized (vorbaObject) {
- vobject.vorbaId=vorbaObject.makeVorbaId(vobject);
- return vobject.vorbaId;
- }
- }
- protected static VorbaId newId(String id) {
- return new VorbaId(id);
- }
- /**
- * @return Returns the id.
- */
- public String getId() {
- return id;
- }
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- if (obj instanceof String)
- return id.equals(obj);
- else if (obj instanceof VorbaId)
- return id.equals(((VorbaId)obj).id);
- return false;
- }
- /* (non-Javadoc)
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return id.hashCode();
- }
- /* (non-Javadoc)
- * @see java.lang.Object#toString()
- */
- public String toString() {
- return id;
- }
-
-}
+++ /dev/null
-/*
- * Created on 12-Sep-2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package org.vamsas.client;
-
-import java.util.Hashtable;
-import java.util.Vector;
-
-/**
- * A VorbaIdFactory is constructed by an IClient instance.
- * It guarantees that any new VorbaId objects are unique
- * within the VAMSAS session.
- *
- * @author jimp
- */
-public abstract class VorbaIdFactory implements IVorbaIdFactory {
- /**
- * hash of VorbaIds to Vobject.
- */
- protected Hashtable extantids=null;
- /**
- * hash of VorbaIds to persisted hash values
- */
- protected Hashtable extanthashv=null;
- /**
- * list of Vobjects added since last Document read.
- */
- protected Vector newobj=null;
-
- /**
- * construct a new id appropriate for this client in the vamsas session.
- *
- * @return valid VorbaId for session, or null if VorbaIdFactory not configured
- * correctly.
- */
- public abstract VorbaId makeVorbaId(Vobject vobject);
-
- /**
- * 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 Vobject Ids
- * is accessible to the Document's VorbaIdFactory instance.
- * @param idtable
- */
- protected void setNewIdHash(Hashtable idtable) {
- extantids = idtable;
- }
-
- /* (non-Javadoc)
- * @see org.vamsas.client.IVorbaIdFactory#updateHashValue(org.vamsas.client.Vobject)
- */
- public void updateHashValue(Vobject vobject) {
- if (vobject.isRegisterable())
- extanthashv.put(vobject.getVorbaId(), new Vobjhash(vobject));
- }
-
- /**
- * TODO: decide if these are needed.
- *
- * @param sessionHandle
- */
- protected abstract void setSession(SessionHandle sessionhandle);
-
- public abstract SessionHandle getSessionHandle();
-
- protected abstract void setClient(ClientHandle appHandle);
-
- public abstract ClientHandle getClientHandle();
-
- protected abstract void setUser(UserHandle userHandle);
-
- public abstract UserHandle getUserHandle();
-}
+++ /dev/null
-/**
- *
- */
-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.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-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;
-import org.exolab.castor.xml.ValidationException;
-import org.vamsas.objects.core.VamsasDocument;
-/**
- * Implements the Vamsas Vobject ID machinery for translating
- * between non-volatile XML IDs and Vobject references. Use the
- * marshalling and unmarshalling methods in this class in order
- * to add automatically computed values for required fields in objects,
- * so as to avoid validation exceptions when marshalling new objects
- * into the vamsas document.
- */
-public class VorbaXmlBinder implements UnmarshalListener {
- private static Log log = LogFactory.getLog(VorbaXmlBinder.class);
- private final IVorbaIdFactory vorbafactory;
-
- private final Vector obj;
- private final Hashtable oldobjhashes;
- private final Hashtable objrefs;
- private final Vector updatedobjs;
-
- public VorbaXmlBinder(IVorbaIdFactory vorbafactory, Vector obj, Hashtable objrefs, Hashtable oldobjhashes, Vector updatedobjs) {
- this.vorbafactory = vorbafactory;
- this.obj = obj;
- this.objrefs = objrefs;
- this.oldobjhashes = oldobjhashes;
- this.updatedobjs = updatedobjs;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#attributesProcessed(java.lang.Object)
- */
- public void attributesProcessed(Object object) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#fieldAdded(java.lang.String,
- * java.lang.Object, java.lang.Object)
- */
- public void fieldAdded(String fieldName, Object parent, Object child) {
- if (parent instanceof Vobject && child instanceof Vobject) {
- if (((Vobject) child).V_parent==null) {
- // System.err.println("Setting parent of "+fieldName);
- ((Vobject) child).setV_parent((Vobject) parent);
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.exolab.castor.xml.UnmarshalListener#initialized(java.lang.Object)
- */
- public void initialized(Object object) {
- }
-
- /*
- * Check if the object has an 'id' field - if it does, copy the value into
- * the VorbaId field of Vobject, and add the Vobject to the VorbaId hash.
- *
- * @see org.exolab.castor.xml.UnmarshalListener#unmarshalled(java.lang.Object)
- */
- public void unmarshalled(Object newobj) {
- if (newobj instanceof Vobject) {
- Vobject nobj = (Vobject) newobj;
- nobj.set__stored_in_document(true);
- try {
- if (nobj.isRegisterable() && nobj.___id_field!=null) {
- VorbaId nobj_id=null;
- // look for the id field (should be an NCName string)
- nobj.__vorba = vorbafactory;
- // use the Vobject accessor method to avoid unpleasant security exceptions.
- String idstring = nobj.__getInstanceIdField();
- if (idstring!=null) {
- if (idstring.length() > 0) {
- nobj.setVorbaId(VorbaId.newId(idstring));
- if (objrefs.containsKey(nobj_id=nobj.getVorbaId()) && !objrefs.get(nobj.getVorbaId()).equals(nobj)) {
- System.err.println("Serious problem : duplicate id '"+idstring+"' found! expect badness.");
- // TODO: HANDLE duplicate XML ids correctly
- }
- objrefs.put(nobj_id, nobj);
- } else {
- // add to list of objects without a valid vorbaId
- obj.add(nobj);
- }
- } else {
- // TODO: add to list of objects without a valid vorbaId
- obj.add(nobj);
- }
-
- nobj.doHash();
- // check to see if new object was present in old object hash
- if (oldobjhashes.containsKey(nobj.getVorbaId())) {
- Vobjhash oldhash = (Vobjhash) oldobjhashes.get(nobj.getVorbaId());
- if (oldhash.isUpdated(nobj)) {
- // mark the object as updated in this document read.
- nobj.set__updated_since_last_read(true);
- oldobjhashes.put(nobj_id, new Vobjhash(nobj));
- updatedobjs.addElement(nobj);
- }
- }
- }
- } catch (Exception e) {
- return;
- };
-
- }
- }
-
- /**
- * 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
- */
- public static void putVamsasDocument(PrintWriter outstream, VorbaIdFactory vorba, VamsasDocument doc)
- throws IOException, MarshalException, ValidationException {
- // Ensure references
- if (vorba==null)
- throw new Error("Null VorbaIdFactory Parameter");
- if (doc.__vorba==null)
- doc.__vorba = vorba;
- doc.__ensure_instance_ids(); // this may take a while. Do we allow for cyclic references ?
- doc.marshal(outstream);
-
- }
- /**
- * creates new VorbaId references where necessary for newly unmarshalled objects
- * @param unrefed
- * @param objrefs
- * @return false if any new object references were made
- */
- 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()) {
- Vobject o = (Vobject) newobj.next();
- // forces registration and id field update.
- VorbaId id = o.getVorbaId();
- if (!objrefs.containsKey(id)) {
- objrefs.put(id, o);
- } else {
- if (!objrefs.get(id).equals(o))
- throw new Error("Serious! Duplicate reference made by vorbaIdFactory!");
- }
- }
- }
- return sync;
- }
- /**
- * Unmarshals a vamsasDocument Vobject from a stream, registers
- * unregistered objects, records existing VorbaIds, and completes
- * the org.vamsas.client.Vobject housekeeping fields.
- * For a valid unmarshalling, the array of returned objects also includes
- * a <return>sync</return> parameter which is true if new VorbaIds
- * were created. If sync is false, then the caller should ensure that the
- * vamsasDocument is written back to disk to propagate the new VorbaIds.
- * TODO: ensure that provenance is correct for newly registered objects
- * as getVamsasObjects but will detect updated objects based on differing hash values
- * obtained from the VorbaIdFactory's VorbaId, Vobject.get__last_Hash() pairs (if any)
- * @param instream - the XML input stream
- * @param factory - the SimpleClient's properly configured VorbaId factory to make new references.
- * @param root the root element's org.vamsas.objects.core Vobject.
- * @return null or {(Object) VamsasDocument Vobject, (Object) Hashtable of Vobject references, (Object) Boolean(sync), (Object) Vector of updated objects in document }
- */
- public static Object[] getVamsasObjects(Reader instream,
- VorbaIdFactory factory, Vobject root) {
- Unmarshaller unmarshaller = new Unmarshaller(root);
- unmarshaller.setIDResolver(new IDResolver() {
- public Object resolve(String id) {
- VorbaXmlBinder.log.warn("Warning - id " + id
- + " is not found in the Vamsas XML!");
- return null;
- }
- });
- final Hashtable objrefs = new Hashtable();
- if (factory.extanthashv==null)
- factory.extanthashv=new Hashtable();
- final Hashtable oobjhashes=factory.extanthashv;
- final VorbaIdFactory vorbafactory = factory;
- final Vector unrefedObj = new Vector();
- final Vector updatedObj = new Vector();
- unmarshaller.setUnmarshalListener(new VorbaXmlBinder(vorbafactory, unrefedObj, objrefs, oobjhashes, updatedObj));
- // Call the unmarshaller.
- try {
- while (instream.ready()) {
- // TODO: mark objects in oobjhash prior to unmarshalling, to detect when objects have been lost through an update.
- //tohere
- Object obj = unmarshaller.unmarshal(instream);
- boolean sync=ensure_references(unrefedObj, objrefs);
- if (!(obj instanceof Vobject))
- return null;
- vorbafactory.setNewIdHash(objrefs); // update the Document IO Handler's set of vorbaId<>Object bindings.
- return new Object[] { obj, objrefs, new Boolean(sync),updatedObj};
- }
- } catch (MarshalException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (ValidationException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-}
\ No newline at end of file
git://source.jalview.org / vamsas.git / commitdiff