/*
- *
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
package uk.ac.vamsas.client.simpleclient;
import uk.ac.vamsas.test.objects.Core;
/**
- * Maintains a collection of vamsas objects, appdatas and states,
- * and provides api for a SimpleClient's client.
- * TODO: test and migrate ArchiveClient.getAppData methods to here and retest in ExampleApplication
- * @author jimp
+ * Maintains a collection of vamsas objects, appdatas and states, and provides
+ * api for a SimpleClient's client. TODO: test and migrate
+ * ArchiveClient.getAppData methods to here and retest in ExampleApplication
+ *
+ * @author jimp
*/
-public class ClientDocument extends uk.ac.vamsas.client.ClientDocument implements IClientDocument {
+public class ClientDocument extends uk.ac.vamsas.client.ClientDocument
+ implements IClientDocument {
private static Log log = LogFactory.getLog(ClientDocument.class);
+
private VamsasDocument doc;
+
protected SimpleClient sclient;
+
protected VamsasArchive iohandler = 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;
}
+
/**
- *
- * prepare Application-side dataset from the vamsas Document iohandler
- * @param doc - the dataset
- * @param docHandler - the sessionFile IO handler
- * @param Factory - the source of current and new vorbaIds
- * @param sclient - the simpleclient instance
+ *
+ * prepare Application-side dataset from the vamsas Document iohandler
+ *
+ * @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) {
+ protected ClientDocument(VamsasDocument doc, VamsasArchive docHandler,
+ IdFactory Factory, SimpleClient sclient) {
super(Factory.getVorbaIdHash(), Factory);
-
-
+
/**
* prepare Application-side dataset from the vamsas Document iohandler
*/
this.sclient = sclient;
iohandler = docHandler;
this.doc = doc;
- _VamsasRoots=doc.getVAMSAS();
+ _VamsasRoots = doc.getVAMSAS();
}
-
+
/*
* (non-Javadoc)
*
- * @see uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#getObject(uk.ac.vamsas.client.VorbaId)
*/
public Vobject getObject(VorbaId id) {
- if (vamsasObjects==null) {
+ 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());
+ log.debug("Returning null Vobject reference for id " + id.getId());
return null;
}
-
+
/*
* (non-Javadoc)
*
- * @see uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId[])
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#getObjects(uk.ac.vamsas.client.VorbaId
+ * [])
*/
public Vobject[] getObjects(VorbaId[] ids) {
- if (vamsasObjects==null) {
+ 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++)
+ 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());
+ 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;
+ private VAMSAS[] _VamsasRoots = null;
+
/**
- * set if the client has corrupted the Vamsas Document structure somehow.
- * if this is set the document will never be written back to the session unless the corruption is fixed.
+ * set if the client has corrupted the Vamsas Document structure somehow. if
+ * this is set the document will never be written back to the session unless
+ * the corruption is fixed.
*/
- private boolean invalidModification=false;
+ private boolean invalidModification = false;
protected void updateDocumentRoots() {
- if (doc==null) {
- log.error("updateDocumentRoots called on null document. Probably an implementation error.");
+ if (doc == null) {
+ log
+ .error("updateDocumentRoots called on null document. Probably an implementation error.");
return;
}
if (isModified) {
- if (_VamsasRoots!=null) {
+ if (_VamsasRoots != null) {
doc.setVAMSAS(_VamsasRoots);
- _VamsasRoots=null;
+ _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)
+
+ /*
+ * (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 uk.ac.vamsas.client.IClientDocument#getVamsasRoots()
*/
public VAMSAS[] getVamsasRoots() {
- if (doc==null) {
+ if (doc == null) {
log.debug("Null document for getVamsasRoots(), returning null");
return null;
}
- if (iohandler==null) {
+ if (iohandler == null) {
// LATER: decide on read-only status of ClientDocument object
log.warn("getVamsasRoots() called on possibly read-only document.");
}
- if (_VamsasRoots!=null)
+ if (_VamsasRoots != null)
return _VamsasRoots;
VAMSAS[] roots = doc.getVAMSAS();
if (roots == null) {
- // Make a new one to return to client to get filled.
+ // Make a new one to return to client to get filled.
_VamsasRoots = new VAMSAS[] { new VAMSAS() };
registerObject(_VamsasRoots[0]);
// Do provenance now. just in case.
- doc.getProvenance().addEntry(sclient.getProvenanceEntry("Created new document root [id="+_VamsasRoots[0].getId()+"]"));
+ 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++)
+ for (int r = 0; r < roots.length; r++)
_VamsasRoots[r] = roots[r];
}
return _VamsasRoots;
}
-
+
private int _contains(VAMSAS root, VAMSAS[] docRoots) {
- if (root==null)
+ if (root == null)
return -1;
- if (docRoots==null || docRoots.length==0)
+ if (docRoots == null || docRoots.length == 0)
return -1;
- VorbaId d_id=null,r_id = root.getVorbaId();
- for (int i=0,j=docRoots.length; i<j; i++)
- if (docRoots[i]==root || (docRoots[i]!=null && (d_id=docRoots[i].getVorbaId())!=null) && d_id.equals(r_id))
+ VorbaId d_id = null, r_id = root.getVorbaId();
+ for (int i = 0, j = docRoots.length; i < j; i++)
+ if (docRoots[i] == root
+ || (docRoots[i] != null && (d_id = docRoots[i].getVorbaId()) != null)
+ && d_id.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
- * @param modflag
- * @return true if newVersion is a valid root that preserves original references
- */
- private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion, ClientDocument modflag) {
- // ideal - this cascades down the two structures, ensuring that all ID'd objects in one are present in the other.
- if (oldVersion==newVersion) {
+
+ /**
+ * verify that newr version is really an intact version of the
+ *
+ * @param newVersion
+ * (may be modified)
+ * @param oldVersion
+ * @param modflag
+ * @return true if newVersion is a valid root that preserves original
+ * references
+ */
+ private boolean isValidUpdate(VAMSAS newVersion, final VAMSAS oldVersion,
+ ClientDocument modflag) {
+ // 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); // TODO: check - this call hasn't been tested. (seems to work now)
- modflag.isModified=true;
+ if (!newVersion.isRegistered()) {
+ _registerObject(newVersion); // TODO: check - this call hasn't been
+ // tested. (seems to work now)
+ modflag.isModified = true;
}
- // TODO: Should attempt to repair document if client app has deleted/broken bits of it
+ // TODO: Should attempt to repair document if client app has
+ // deleted/broken bits of it
if (oldVersion.is__stored_in_document()) {
// retrieve compare hashCodes to detect update.
- if (oldVersion.get__last_hash()!=oldVersion.hashCode())
- {
- log.debug("Modified hashcode for vamsas root "+oldVersion.getVorbaId());
+ if (oldVersion.get__last_hash() != oldVersion.hashCode()) {
+ log.debug("Modified hashcode for vamsas root "
+ + oldVersion.getVorbaId());
modflag.isModified = true;
} else {
- log.debug("Unmodified vamsas root "+oldVersion.getVorbaId());
+ log.debug("Unmodified vamsas root " + oldVersion.getVorbaId());
}
}
// just do internal validation for moment.
try {
- if (getSimpleClientConfig().validateUpdatedRoots())
- {
+ if (getSimpleClientConfig().validateUpdatedRoots()) {
newVersion.validate();
}
return true;
- }
- catch (Exception e)
- {
- log.error("Validation Exception for new vamsas root :"+newVersion.getVorbaId(),e);
- modflag.invalidModification=true;
+ } catch (Exception e) {
+ log.error("Validation Exception for new vamsas root :"
+ + newVersion.getVorbaId(), e);
+ modflag.invalidModification = true;
}
return false;
} else {
// redundant ? if (oldVersion.is__stored_in_document())
- if (!newVersion.isRegistered())
- {
+ if (!newVersion.isRegistered()) {
_registerObject(newVersion);
- modflag.isModified=true;
+ modflag.isModified = true;
}
try {
- if (getSimpleClientConfig().validateMergedRoots())
- {
+ if (getSimpleClientConfig().validateMergedRoots()) {
newVersion.validate();
}
- modflag.isModified=true;
+ modflag.isModified = true;
return true;
- }
- catch (Exception e)
- {
- log.error("Validation Exception for new vamsas root :"+newVersion.getVorbaId(),e);
+ } catch (Exception e) {
+ log.error("Validation Exception for new vamsas root :"
+ + newVersion.getVorbaId(), e);
}
}
return false;
/**
- * LATER: MUCH LATER! - not needed for simple case and this routine shouldn't live in this class anymore
- * 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.
- }
- }
- }*/
+ * LATER: MUCH LATER! - not needed for simple case and this routine
+ * shouldn't live in this class anymore 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. } } }
+ */
}
+
private SimpleClientConfig getSimpleClientConfig() {
return sclient.getSimpleClientConfig();
-}
+ }
+
/**
* merge old and new root vectors
- * @param newr This array may be written to
+ *
+ * @param newr
+ * This array may be written to
* @param original
- * @param the client document (usually this) which this root set belongs to.
+ * @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) {
+ private VAMSAS[] _combineRoots(VAMSAS[] newr, final VAMSAS[] original,
+ ClientDocument modflag) {
Vector rts = new Vector();
- for (int i=0,j=original.length; i<j; i++) {
+ for (int i = 0, j = original.length; i < j; i++) {
int k = _contains(original[i], newr);
- if (k>-1) {
+ if (k > -1) {
if (isValidUpdate(newr[k], original[i], modflag)) {
- // set by isValidUpdate if the hashcodes were really different from last store
+ // set by isValidUpdate if the hashcodes were really different from
+ // last store
rts.add(newr[k]);
- newr[k]=null;
+ newr[k] = null;
} else {
// LATER: try harder to merge ducument roots.
- log.warn("Couldn't merge new VAMSAS root "+newr[k].getId());
+ 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 remaining (new) roots
- for (int i=0,j=newr.length; i<j; i++) {
- if (newr[i]!=null) {
+ for (int i = 0, j = newr.length; i < j; i++) {
+ if (newr[i] != null) {
rts.add(newr[i]);
- modflag.isModified=true;
+ modflag.isModified = true;
}
}
newr = new VAMSAS[rts.size()];
- for (int i=0,j=rts.size(); i<j; i++)
+ for (int i = 0, j = rts.size(); i < j; i++)
newr[i] = (VAMSAS) rts.get(i);
return newr;
}
-
+
/**
- * update the document with new roots.
- * LATER: decide: this affects the next call to getVamsasRoots()
+ * 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) {
+ if (doc == null) {
log.debug("setVamsasRoots called on null document.");
return;
}
VAMSAS[] newr;
- if (newroots==null) {
+ if (newroots == null) {
log.debug("setVamsasRoots(null) - do nothing.");
return;
}
// are we dealing with same array ?
- if (_VamsasRoots!=newroots) {
+ if (_VamsasRoots != newroots) {
// merge roots into local version.
newr = new VAMSAS[newroots.length];
- for (int i=0;i<newr.length;i++)
+ for (int i = 0; i < newr.length; i++)
newr[i] = newroots[i];
- newr=_combineRoots(newr,_VamsasRoots,this);
+ newr = _combineRoots(newr, _VamsasRoots, this);
} else {
newr = new VAMSAS[_VamsasRoots.length];
- for (int i=0;i<newr.length;i++)
- newr[i]=_VamsasRoots[i];
+ 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);
+ // 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 uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.vamsas.objects.core.VAMSAS)
+
+ /*
+ * (non-Javadoc) LATER: decide: this affects the next call to getVamsasRoots()
+ *
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#addVamsasRoot(uk.ac.vamsas.objects.
+ * core.VAMSAS)
*/
public void addVamsasRoot(VAMSAS newroot) {
- if (doc==null) {
+ if (doc == null) {
log.debug("addVamsasRoots called on null document.");
return;
}
- VAMSAS[] newroots = _combineRoots(new VAMSAS[] {newroot}, getVamsasRoots(), this);
- _VamsasRoots = newroots;
+ VAMSAS[] newroots = _combineRoots(new VAMSAS[] { newroot },
+ getVamsasRoots(), this);
+ _VamsasRoots = newroots;
}
-
+
/*
* (non-Javadoc)
*
- * @see uk.ac.vamsas.client.IClientDocument#registerObjects(uk.ac.vamsas.client.Vobject[])
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#registerObjects(uk.ac.vamsas.client
+ * .Vobject[])
*/
public VorbaId[] registerObjects(Vobject[] unregistered) {
- if (doc==null) {
+ if (doc == null) {
log.warn("registerObjects[] called on null document.");
return null;
}
- if (vamsasObjects==null) {
+ if (vamsasObjects == null) {
log.warn("registerObjects[] called for null vamsasObjects hasharray.");
return null;
}
- if (unregistered!=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);
+ 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]);
+ ids[i] = registerObject(unregistered[i]);
}
- log.debug("Registered "+unregistered.length+" objects - total of "+vamsasObjects.size()+" ids.");
+ log.debug("Registered " + unregistered.length + " objects - total of "
+ + vamsasObjects.size() + " ids.");
return ids;
}
return null;
}
- /* (non-Javadoc)
- * @see uk.ac.vamsas.client.IClientDocument#registerObject(uk.ac.vamsas.client.Vobject)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * uk.ac.vamsas.client.IClientDocument#registerObject(uk.ac.vamsas.client.
+ * Vobject)
*/
public VorbaId registerObject(Vobject unregistered) {
- if (doc==null) {
+ if (doc == null) {
log.warn("registerObjects called on null document.");
return null;
}
- if (vamsasObjects==null) {
+ if (vamsasObjects == null) {
log.warn("registerObjects called for null vamsasObjects hasharray.");
return null;
}
- if (iohandler==null) {
+ if (iohandler == null) {
log.warn("registerObjects called for read only document.");
return null;
}
-
- if (unregistered!=null) {
+
+ if (unregistered != null) {
VorbaId id = _registerObject(unregistered);
- log.debug("Registered object - total of "+vamsasObjects.size()+" ids.");
+ 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)
+
+ /*
+ * (non-Javadoc)
+ *
* @see uk.ac.vamsas.client.IClientDocument#getClientAppdata()
*/
public IClientAppdata getClientAppdata() {
// TODO: getClientAppdata not tested in ArchiveClient mockup
log.error("TODO: TEST Client Appdata access methods");
- if (doc==null) {
+ if (doc == null) {
log.warn("getClientAppdata called on null document.");
return null;
}
- if (scappd==null) {
- log.debug("Creating new SimpleClientAppdata instance for "+sclient.getSessionHandle());
+ if (scappd == null) {
+ log.debug("Creating new SimpleClientAppdata instance for "
+ + sclient.getSessionHandle());
scappd = new SimpleClientAppdata(this);
- if (scappd==null) {
+ if (scappd == null) {
// LATER: may not need this as a warning message.
- log.warn("Null appdata object for "+sclient.getSessionHandle());
+ log.warn("Null appdata object for " + sclient.getSessionHandle());
} else {
log.debug("Created SimpleClientAppdata successfully.");
}
}
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() {
- if (iohandler==null) {
- log.error("Near fatal. Null VamsasArchive iohandler so can't get VamsasArchiveReader");
+ if (iohandler == null) {
+ log
+ .error("Near fatal. Null VamsasArchive iohandler so can't get VamsasArchiveReader");
return null;
}
try {
}
return null;
}
+
/**
* called by vamsas api to write updated document to session
+ *
* @return true if update was successful
* @throws java.io.IOException
*/
protected boolean updateSessionDocument() throws java.io.IOException {
boolean docupdate = true; // 'non-serious' problems below set this false
- if (doc==null) {
+ if (doc == null) {
log.warn("updateSessionDocument called on null document.");
throw new java.io.IOException("Document is closed.");
}
- if (iohandler==null) {
- log.warn("updateSessionDocument called on null document iohandler handler.");
+ if (iohandler == null) {
+ log
+ .warn("updateSessionDocument called on null document iohandler 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);
+ 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!=null && scappd.isModified()) {
+ log
+ .debug("Attempting to update session "
+ + sclient.session.getSessionUrn());
+ if (scappd != null && scappd.isModified()) {
ClientHandle client = sclient.client;
UserHandle user = sclient.user;
- scappd.closeForWriting();
- if (scappd.appsGlobal==null) {
+ 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.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()));
+ // 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()) {
+ 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) {
+ if (scappd.appsGlobal.getData() != null) {
scappd.appsGlobal.setData(null);
- scappd.appsGlobal.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()));
+ 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(iohandler, scappd.appsGlobal, scappd.newAppData);
+ // LATER: use a switch to decide if the data should be written as a
+ // reference or as an embedded data chunk
+ scappd.updateAnAppdataEntry(iohandler, scappd.appsGlobal,
+ scappd.newAppData);
log.debug("...Successfully updated Global Appdata Entry.");
}
- if (scappd.newUserData!=null && scappd.newUserData.sessionFile.exists()) {
+ if (scappd.newUserData != null && scappd.newUserData.sessionFile.exists()) {
log.debug("Beginning to update Users Appdata entry....");
- if (scappd.usersData==null) {
+ if (scappd.usersData == null) {
// create new user appdata
scappd.usersData = new User();
scappd.usersData.setFullname(user.getFullName());
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);
+ 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) {
+ if (t != -1) {
safe_username = safe_username.substring(t);
}
- appd.setDataReference(AppDataReference.uniqueAppDataReference(doc, sclient.client.getClientUrn()+safe_username));
+ appd.setDataReference(AppDataReference.uniqueAppDataReference(doc,
+ sclient.client.getClientUrn() + safe_username));
}
- scappd.updateAnAppdataEntry(iohandler, scappd.usersData, scappd.newUserData);
+ scappd.updateAnAppdataEntry(iohandler, scappd.usersData,
+ scappd.newUserData);
log.debug("...Successfully updated user AppData entry.");
}
}
log.error("While transferring remaining AppDatas", e);
}
log.debug("Updating Document...");
- // now update the document. - this was basically the doUpdate method in test.ArchiveClient
+ // now update the document. - this was basically the doUpdate method in
+ // test.ArchiveClient
updateDocumentRoots();
try {
iohandler.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
+ } catch (Exception e) {
+ log.error("Marshalling error for vamsas document.", e);
+ docupdate = false; // pass on the (probable) object validation error
}
iohandler.closeArchive();
- iohandler=null; // so this method cannot be called again for this instance
+ iohandler = null; // so this method cannot be called again for this instance
log.debug("...successully finished and closed.");
return docupdate; // no errors ?
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable {
log.debug("Garbage collecting on ClientDocument instance.");
- if (scappd!=null) {
+ if (scappd != null) {
scappd.finalize();
scappd = null;
}
- if (doc!=null) {
+ if (doc != null) {
doc = null;
}
// disengage from client
- if (sclient!=null && sclient.cdocument==this)
+ if (sclient != null && sclient.cdocument == this)
sclient.cdocument = null;
- sclient=null;
-
+ sclient = null;
+
super.finalize();
}
+
public Vector getUpdatedObjects() {
- // TODO: WALK through the document objects calling the update mechanism for each one, or just pass this vector back to client ?return updatedObjects;
+ // TODO: WALK through the document objects calling the update mechanism for
+ // each one, or just pass this vector back to client ?return updatedObjects;
return null;
}
+
/**
- * if this is set the document will never be written back to the session unless the corruption is fixed.
+ * if this is set the document will never be written back to the session
+ * unless the corruption is fixed.
+ *
* @return the invalidModification
*/
public boolean isInvalidModification() {
return invalidModification;
}
+
/**
- * set if the client has corrupted the Vamsas Document structure somehow.
- * if this is set the document will never be written back to the session unless the corruption is fixed.
- * @param invalidModification the invalidModification to set
+ * set if the client has corrupted the Vamsas Document structure somehow. if
+ * this is set the document will never be written back to the session unless
+ * the corruption is fixed.
+ *
+ * @param invalidModification
+ * the invalidModification to set
*/
public void setInvalidModification(boolean invalidModification) {
this.invalidModification = invalidModification;
git://source.jalview.org / vamsas.git / blobdiff