X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FClientDocument.java;fp=src%2Fuk%2Fac%2Fvamsas%2Fclient%2Fsimpleclient%2FClientDocument.java;h=dde96321791690ab0ba2dc49df86f344ec31765f;hb=5156a824b13ecd091af9f84870f41d83eb59bd71;hp=0000000000000000000000000000000000000000;hpb=43135da6463e5329abbe98a4892c50c6cd1edcfa;p=vamsas.git

diff --git a/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
new file mode 100644
index 0000000..dde9632
--- /dev/null
+++ b/src/uk/ac/vamsas/client/simpleclient/ClientDocument.java
@@ -0,0 +1,510 @@
+/*
+ *
+ */
+package uk.ac.vamsas.client.simpleclient;
+
+import java.io.IOException;
+import java.util.Vector;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.vamsas.client.ClientHandle;
+import org.vamsas.client.IClientAppdata;
+import org.vamsas.client.IClientDocument;
+import org.vamsas.client.UserHandle;
+import org.vamsas.client.Vobject;
+import org.vamsas.client.VorbaId;
+import org.vamsas.objects.core.ApplicationData;
+import org.vamsas.objects.core.User;
+import org.vamsas.objects.core.VAMSAS;
+import org.vamsas.objects.core.VamsasDocument;
+import org.vamsas.objects.utils.AppDataReference;
+import org.vamsas.test.objects.Core;
+
+/**
+ * Maintains a collection of vamsas objects, appdatas and states, and provides api for a SimpleClient's client.
+ * @author jimp 
+ */
+public class ClientDocument extends org.vamsas.client.ClientDocument implements IClientDocument {
+  private static Log log = LogFactory.getLog(ClientDocument.class);
+  private VamsasDocument doc;
+  protected SimpleClient sclient;
+  protected VamsasArchive archive = null;
+  /**
+   * indicate if new data has been incorporated
+   */
+  private boolean isModified = false;
+  /**
+   * Public method for internal use by SimpleClient.
+   * @return true if document has been modified.
+   */
+  public boolean isModified() {
+    return isModified;
+  }
+  private Vector updatedObjects=null;
+  /**
+   *
+   *  prepare Application-side dataset from the vamsas Document archive
+   * @param doc - the dataset
+   * @param docHandler - the sessionFile IO handler
+   * @param Factory - the source of current and new vorbaIds
+   * @param sclient - the simpleclient instance
+   */
+  protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler, IdFactory Factory, SimpleClient sclient) {
+    super(Factory.getVorbaIdHash(), Factory);
+    
+    
+    /**
+     * prepare Application-side dataset from the vamsas Document archive
+     */
+    this.sclient = sclient;
+    archive = docHandler;
+    this.doc = doc;
+    updatedObjects=null;  /// TODO: correct this line
+  }
+  
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.vamsas.client.IClientDocument#getObject(org.vamsas.client.VorbaId)
+   */
+  public Vobject getObject(VorbaId id) {
+    if (vamsasObjects==null) {
+      log.debug("getObject called on null objrefs list.");
+      return null;
+    }
+    if (vamsasObjects.containsKey(id))
+      return (Vobject) vamsasObjects.get(id);
+    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 (vamsasObjects==null) {
+      log.debug("getObject[]  called on null vamsasObjects list.");
+      return null;
+    }
+    Vobject[] vo = new Vobject[ids.length];
+    for (int i=0,j=ids.length; i<j;i++) 
+      if (vamsasObjects.containsKey(ids[i]))
+        vo[i] = (Vobject) vamsasObjects.get(ids[i]);
+      else
+        log.debug("Returning null Vobject reference for id "+ids[i].getId());
+    return vo;
+  }
+  /**
+   * internal reference to single copy of Document Roots array
+   */
+  private VAMSAS[] _VamsasRoots=null;
+  /*
+   * (non-Javadoc)
+   * LATER: currently there is only one Vector of roots ever passed to client - decide if this is correct (means this is not thread safe and may behave unexpectedly)
+   * @see org.vamsas.client.IClientDocument#getVamsasRoots()
+   */
+  public VAMSAS[] getVamsasRoots() {
+    if (doc==null) {
+      log.debug("Null document for getVamsasRoots(), returning null");
+      return null;
+    }
+    if (archive==null) {
+      // LATER: decide on read-only status of ClientDocument object
+      log.warn("getVamsasRoots() called on possibly read-only document.");
+    }
+    if (_VamsasRoots!=null)
+      return _VamsasRoots;
+    VAMSAS[] roots = doc.getVAMSAS();
+    if (roots == null) {
+      // Make a new one to return to client to get filled. 
+      _VamsasRoots = new VAMSAS[] { new VAMSAS() };
+      // Do provenance now. just in case.
+      doc.getProvenance().addEntry(sclient.getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
+      doc.addVAMSAS(_VamsasRoots[0]);
+    } else {
+      _VamsasRoots = new VAMSAS[roots.length];
+      for (int r=0;r<roots.length; r++)
+        _VamsasRoots[r] = roots[r];
+    }
+    return _VamsasRoots;
+  }
+  
+  private int _contains(VAMSAS root, VAMSAS[] docRoots) {
+    if (root==null)
+      return -1;
+    if (docRoots==null || docRoots.length==0)
+      return -1;
+    String r_id = root.getId();
+    for (int i=0,j=docRoots.length; i<j; i++)
+      if (docRoots[i]==root || (docRoots[i]!=null && docRoots[i].getId().equals(r_id)))
+        return i;
+    return -1;
+  }
+/**
+ * verify that newr version is really an intact version of the 
+ * @param newVersion (may be modified)
+ * @param oldVersion 
+ * @return true if newVersion is a valid root that preserves original references
+ */
+  private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion) {
+    // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
+    if (oldVersion==newVersion) {
+      // may be a virgin root element.
+      if (!newVersion.isRegistered())
+        _registerObject(newVersion);
+      // Should retrieve original version and compare - unless local hashes can be used to determine if resultSet has been truncated.
+      // just do internal validation for moment.
+      if (newVersion.isValid())
+        return true;
+      return false;
+    } else {
+      // redundant ? if (oldVersion.is__stored_in_document())
+      if (!newVersion.isRegistered())
+        _registerObject(newVersion);
+      if (newVersion.isValid())
+        return true;
+    }
+    return false;
+    /**
+     * LATER isValidUpdate : Ideally. we efficiently walk down, comparing hashes, to deal with merging and verifying provenance for objects
+    
+    // extract root objects
+    if (newroots != null) {
+      // check newroots for objects that were present in the old document
+      // check to see if the 'old' objects have been modified
+      // if they have ? we overwrite them with their new version, ensuring that
+      // provenance is updated.
+      // if they haven't ? do nothing ?
+      
+      for (int i = 0, k = newroots.length; i < k; i++) {
+        if (newroots[i].isRegistered()) {
+          // easy - just check if anything has changed and do provenance
+          Vobject oldversion = getObject(newroots[i].getVorbaId());
+          if (oldversion instanceof VAMSAS) {
+            // LATER: appropriate merging behaviour when two clients have improperly modified the same Vobject independently.
+            if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
+              // client has modified this Vobject since last retrieval.
+              if (newroots[i].get__last_hash() != oldversion.get__last_hash()) {
+                // Vobject has been modified by another client since this
+                // client's
+                // last access to document.
+              }
+            }
+          } else {
+            throw new Error(
+                "SimpleClient error when using setVamsasRoots : The vorbaId for Vobject "
+                + i
+                + " does not refer to an Vobject of type VAMSAS in the current document!");
+          }
+        } else {
+          if (!newroots[i].is__stored_in_document()) {
+            // check if Vobject is modified
+            if (newroots[i].get__last_hash() != newroots[i].hashCode()) {
+              // it is - so we add newroots[i] as a new Vobject, with updated
+              // provenance.
+            } else {
+              // do nothing
+              newroots[i] = null;
+            }
+          } else {
+            // just add newroots[i] as a new Vobject in the document
+            // - with appropriate provenance.
+          }
+        }
+      }*/
+  }
+  /**
+   * merge old and new root vectors
+   * @param newr This array may be written to
+   * @param original
+   * @param the client document (usually this) which this root set belongs to.
+   * @return merged vector of vamsas roots
+   */
+  private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original, ClientDocument modflag) {
+    Vector rts = new Vector();
+    boolean modified=false;
+    for (int i=0,j=original.length; i<j; i++) {
+      int k = _contains(original[i], newr);
+      if (k>-1) {
+        if (isValidUpdate(newr[k], original[i])) {
+          modified=true;
+          rts.add(newr[k]);
+          newr[k]=null;
+        } else {
+          // LATER: try harder to merge ducument roots.
+          log.warn("Couldn't merge new VAMSAS root "+newr[k].getId());
+          newr[k] = null; // LATER: this means we ignore mangled roots. NOT GOOD
+        }
+      } else {
+        // add in order.
+        rts.add(original[i]);
+      }
+    }
+    // add remaining (new) roots
+    for (int i=0,j=newr.length; i<j; i++) {
+      if (newr[i]!=null) {
+        rts.add(newr[i]);
+        modified=true;
+      }
+    }
+    newr = new VAMSAS[rts.size()];
+    for (int i=0,j=rts.size(); i<j; i++)
+      newr[i] = (VAMSAS) rts.get(i);
+    if (modflag!=null)
+      modflag.isModified = modified;
+    return newr;
+  }
+  
+  /**
+   * update the document with new roots.
+   * LATER: decide: this affects the next call to getVamsasRoots()
+   * @see org.vamsas.IClientDocument.setVamsasRoots
+   */
+  public void setVamsasRoots(VAMSAS[] newroots) {
+    if (doc==null) {
+      log.debug("setVamsasRoots called on null document.");
+      return;
+    }
+    VAMSAS[] newr;
+    if (newroots==null) {
+      log.debug("setVamsasRoots(null) - do nothing.");
+      return;
+    }
+    // are we dealing with same array ?
+    if (_VamsasRoots!=newroots) {
+      // merge roots into local version.
+      newr = new VAMSAS[newroots.length];
+      for (int i=0;i<newr.length;i++)
+        newr[i] = newroots[i];
+      newr=_combineRoots(newr,_VamsasRoots,this);
+    } else {
+      newr = new VAMSAS[_VamsasRoots.length];
+      for (int i=0;i<newr.length;i++)
+        newr[i]=_VamsasRoots[i];
+    }
+    //  actually compare with document root set for final combination (to ensure nothing is lost)
+    _VamsasRoots = _combineRoots(newr, doc.getVAMSAS(), this); 
+  }
+  
+  
+  /* (non-Javadoc)
+   * LATER: decide: this affects the next call to getVamsasRoots()
+   * @see org.vamsas.client.IClientDocument#addVamsasRoot(org.vamsas.objects.core.VAMSAS)
+   */
+  public void addVamsasRoot(VAMSAS newroot) {
+    if (doc==null) {
+      log.debug("addVamsasRoots called on null document.");
+      return;
+    }
+    VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, _VamsasRoots, this);
+    _VamsasRoots = newroots;  
+  }
+  
+  /*
+   * (non-Javadoc)
+   * 
+   * @see org.vamsas.client.IClientDocument#registerObjects(org.vamsas.client.Vobject[])
+   */
+  public VorbaId[] registerObjects(Vobject[] unregistered) {
+    if (doc==null) {
+      log.warn("registerObjects[] called on null document.");
+      return null;
+    }
+    if (vamsasObjects==null) {
+      log.warn("registerObjects[] called for null vamsasObjects 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 "+vamsasObjects.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 (vamsasObjects==null) {
+      log.warn("registerObjects called for null vamsasObjects hasharray.");
+      return null;
+    }
+    if (unregistered!=null) {
+      VorbaId id = _registerObject(unregistered);
+      log.debug("Registered object - total of "+vamsasObjects.size()+" ids.");
+      return id;
+    }
+    log.warn("Null Vobject passed to registerObject.");
+    return null;
+  }
+  /**
+   * IClientAppdata instance - if it exists.
+   */
+  SimpleClientAppdata scappd = null;
+  /* (non-Javadoc)
+   * @see org.vamsas.client.IClientDocument#getClientAppdata()
+   */
+  public IClientAppdata getClientAppdata() {
+    if (doc==null) {
+      log.warn("getClientAppdata called on null document.");
+      return null;
+    }
+    if (scappd==null) {
+      log.debug("Creating new SimpleClientAppdata instance for "+sclient.getSessionHandle());
+      scappd = new SimpleClientAppdata(this);
+      if (scappd==null) {
+        // LATER: may not need this as a warning message.
+        log.warn("Null appdata object for "+sclient.getSessionHandle());
+      } else {
+        log.debug("Created SimpleClientAppdata successfully.");
+      }
+    } else {
+      log.debug("Returning existing SimpleClientAppdata reference.");
+    }
+    return scappd;
+  }
+  /**
+   * access the vamsas document
+   * @return the session's vamsas document
+   */
+  protected VamsasDocument getVamsasDocument() {
+    return doc;
+  }
+  /**
+   * returns the read-only IO interface for the vamsas document Jar file
+   * @return
+   */
+  protected VamsasArchiveReader getVamsasArchiveReader() {
+    try {
+      return archive.getOriginalArchiveReader();
+    } catch (Exception e) {
+      log.warn("Unable to create OriginalArchiveReader!", e);
+    }
+    return null;
+  }
+  protected boolean updateSessionDocument() throws java.io.IOException {
+    boolean docupdate = true; // 'non-serious' problems below set this false
+    if (doc==null) {
+      log.warn("updateSessionDocument called on null document.");
+      throw new java.io.IOException("Document is closed.");
+    }
+    if (archive==null) {
+      log.warn("updateSessionDocument called document archive handler.");
+      throw new java.io.IOException("Document is closed.");
+    }
+    
+    if (!isModified() && !scappd.isModified()) {
+      log.debug("Document update not necessary. returning false.");
+      return false;
+    }
+    VamsasSession session = sclient._session;
+    log.debug("updating Session Document in "+session.sessionDir);
+    // update the VamsasDocument structure with any new appData's.
+    // try to update the sessionFile
+    log.debug("Attempting to update session "+sclient.session.getSessionUrn());
+    if (scappd.isModified()) {
+      ClientHandle client = sclient.client;
+      UserHandle user = sclient.user;
+      scappd.closeForWriting();      
+      if (scappd.appsGlobal==null) {
+        log.debug("Creating new appData entry for this application...");
+        // first write for this application - add a new section in document
+        ApplicationData appd = scappd.appsGlobal = new ApplicationData();
+        appd.setName(client.getClientName());
+        // appd.setUrn(client.getClientUrn());
+        appd.setVersion(client.getVersion());
+        doc.addApplicationData(appd);
+        // embed or jarEntry ?  - for now only jarEntry's are dealt with.
+        appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
+        log.debug("... created.");
+      }
+      if (scappd.newAppData!=null && scappd.newAppData.sessionFile.exists()) {
+        log.debug("Beginning update for new Global Appdata...");
+        // new global appdata to write.
+        if (scappd.appsGlobal.getData()!=null) {
+          scappd.appsGlobal.setData(null);
+          scappd.appsGlobal.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
+        }
+        // LATER: use a switch to decide if the data should be written as a reference or as an embedded data chunk
+        scappd.updateAnAppdataEntry(archive, scappd.appsGlobal, scappd.newAppData);
+        log.debug("...Successfully updated Global Appdata Entry.");
+      }
+      if (scappd.newUserData!=null && scappd.newUserData.sessionFile.exists()) {
+        log.debug("Beginning to update Users Appdata entry....");
+        if (scappd.usersData==null) {
+          // create new user appdata
+          scappd.usersData = new User();
+          scappd.usersData.setFullname(user.getFullName());
+          scappd.usersData.setOrganization(user.getOrganization());
+          scappd.appsGlobal.addUser(scappd.usersData);
+        }
+        User appd = scappd.usersData;
+        if (appd.getData()!=null || appd.getDataReference()==null) {
+          // LATER make standard appDataReference constructor for client+user 
+          appd.setData(null);          
+          String safe_username = user.getFullName();
+          int t = safe_username.indexOf(" ");
+          if (t!=-1) {
+            safe_username = safe_username.substring(t);
+          }
+          appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()+safe_username));
+        }
+        scappd.updateAnAppdataEntry(archive, scappd.usersData, scappd.newUserData);
+        log.debug("...Successfully updated user AppData entry.");
+      }
+    }
+    log.debug("Updating Document...");
+    // now update the document.
+    try {
+      archive.putVamsasDocument(doc);
+      log.debug("Successfully written document entry.");
+    }
+    catch (Exception e) {
+      log.error("Marshalling error for vamsas document.",e);
+      docupdate = false; // pass on the (probable) object validation error 
+    }
+    if (archive.transferRemainingAppDatas())
+      log.debug("Remaining appdatas were transferred.");
+    else
+      log.debug("No remaining appdatas were transferred. (Correct?)");
+    archive.closeArchive();
+    log.debug("...successully finished and closed.");
+    return docupdate; // no errors ?
+  }
+  /* (non-Javadoc)
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable {
+    log.debug("Garbage collecting on ClientDocument instance.");
+    if (scappd!=null) {
+      scappd.finalize();
+      scappd = null;
+    }
+    if (doc!=null) {
+      doc = null;
+    }
+    // disengage from client
+    if (sclient!=null)
+      sclient.cdocument = null;
+    sclient=null;
+    
+    super.finalize();
+  }
+  public Vector getUpdatedObjects() {
+    return updatedObjects;
+  }
+}