diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index c2adc682ff9e0707875fcae7672d0c150a9ec91b..b143db3e7ea20cf37d0663a983fac426dbf41801 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -432,12 +432,12 @@ public class AServProtocolManager {
*********************************************************************/
// Implementation specific
- public Message store( Message mess ){
+ public Message store( Message mess ) {
String id = mess.getContent();
Alignment al=null;
try {
- try{
+ try {
al = alignmentCache.getAlignment( id );
} catch(Exception ex) {
//System.err.println("Unknown Id in Store :=" + id );
@@ -454,7 +454,7 @@ public class AServProtocolManager {
for ( Directory d : directories.values() ){
// Declare the alignment in the directory
try { d.register( al ); }
- catch (AServException e) { e.printStackTrace(); }// ignore
+ catch ( AServException e ) { e.printStackTrace(); }// ignore
}
}
// register by them
@@ -466,6 +466,29 @@ public class AServProtocolManager {
}
}
+ // Implementation specific
+ public Message erase( Message mess ) {
+ String id = mess.getContent();
+ Alignment al = null;
+ try {
+ al = alignmentCache.getAlignment( id );
+ // Erase it from directories
+ for ( Directory d : directories.values() ){
+ try { d.register( al ); }
+ catch ( AServException e ) { e.printStackTrace(); }// ignore
+ }
+ // Erase it from storage
+ try {
+ alignmentCache.eraseAlignment( id );
+ } catch ( Exception ex ) { ex.printStackTrace(); }// ignore
+ // Should be a SuppressedAlignment
+ return new AlignmentId(newId(),mess,myId,mess.getSender(),id,(Properties)null,
+ al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+ } catch ( Exception ex ) {
+ return new UnknownAlignment(newId(),mess,myId,mess.getSender(),id,(Properties)null);
+ }
+ }
+
/*
* Returns only the metadata of an alignment and returns it in
* parameters
@@ -682,11 +705,7 @@ public class AServProtocolManager {
} catch (Exception e) {
return false;
}
- if ( al.getExtension(CacheImpl.SVCNS, CacheImpl.STORED) != null && al.getExtension(CacheImpl.SVCNS, CacheImpl.STORED) != "" ) {
- return true;
- } else {
- return false;
- }
+ return alignmentCache.isAlignmentStored( al );
}
/*********************************************************************
diff --git a/src/fr/inrialpes/exmo/align/service/CacheImpl.java b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
index d8c3a277b1facc972c613758f3e7468c13a7ff68..08dbd66762f4666a844e7cb5bb95dd5384177075 100644
--- a/src/fr/inrialpes/exmo/align/service/CacheImpl.java
+++ b/src/fr/inrialpes/exmo/align/service/CacheImpl.java
@@ -2,7 +2,7 @@
* $Id$
*
* Copyright (C) Seungkeun Lee, 2006
- * Copyright (C) INRIA, 2006-2010
+ * Copyright (C) INRIA, 2006-2011
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -90,11 +90,11 @@ public class CacheImpl {
final int INIT_ERROR = 3;
//static public final String SVCNS = "http://exmo.inrialpes.fr/align/service#";
- static public final String SVCNS = Namespace.ALIGNSVC.getUriPrefix();
- static public final String CACHED = "cached";
- static public final String STORED = "stored";
- static public final String OURI1 = "ouri1";
- static public final String OURI2 = "ouri2";
+ static private final String SVCNS = Namespace.ALIGNSVC.getUriPrefix();
+ static private final String CACHED = "cached";
+ static private final String STORED = "stored";
+ static private final String OURI1 = "ouri1";
+ static private final String OURI2 = "ouri2";
//**********************************************************************
@@ -458,7 +458,7 @@ public class CacheImpl {
/**
* records alignment identified by id
*/
- public String recordAlignment( String id, Alignment alignment, boolean force ){
+ public String recordAlignment( String id, Alignment alignment, boolean force ) {
// record the Id!
//CLD put in comment this line for allowing to create a new ID for any alignment
//if ( alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) == null )
@@ -490,7 +490,23 @@ public class CacheImpl {
return null;
}
}
-
+
+ /**
+ * suppresses the record for an alignment
+ */
+ public void unRecordAlignment( Alignment alignment ) {
+ String id = alignment.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ try {
+ Set<Alignment> s1 = ontologyTable.get( new URI( alignment.getExtension( SVCNS, OURI1) ) );
+ if ( s1 != null ) s1.remove( alignment );
+ Set<Alignment> s2 = ontologyTable.get( new URI( alignment.getExtension( SVCNS, OURI2) ) );
+ if ( s2 != null ) s2.remove( alignment );
+ } catch ( URISyntaxException uriex ) {
+ uriex.printStackTrace(); // should never happen
+ }
+ alignmentTable.remove( id );
+ }
+
//**********************************************************************
// STORING IN DATABASE
/**
@@ -529,24 +545,41 @@ public class CacheImpl {
else return false;
}
+
+ /**
+ * Non publicised class
+ */
+ public void eraseAlignment( String id ) throws SQLException, AlignmentException {
+ Alignment alignment = getAlignment( id );
+ if ( alignment != null ) {
+ unstoreAlignment( id, alignment );
+ // Suppress it from the cache...
+ unRecordAlignment( alignment );
+ }
+ }
+
/**
* Non publicised class
*/
public void unstoreAlignment( String id ) throws SQLException, AlignmentException {
Alignment alignment = getAlignment( id );
if ( alignment != null ) {
- Statement st = createStatement();
- String query = "DELETE FROM extension WHERE id='"+id+"'";
- st.executeUpdate(query);
- query = "DELETE FROM alignment WHERE id='"+id+"'";
- st.executeUpdate(query);
- query = "DELETE FROM cell WHERE id='"+id+"'";
- st.executeUpdate(query);
- alignment.setExtension( SVCNS, STORED, (String)null);
- st.close();
+ unstoreAlignment( id, alignment );
}
}
+ public void unstoreAlignment( String id, Alignment alignment ) throws SQLException, AlignmentException {
+ Statement st = createStatement();
+ String query = "DELETE FROM extension WHERE id='"+id+"'";
+ st.executeUpdate(query);
+ query = "DELETE FROM alignment WHERE id='"+id+"'";
+ st.executeUpdate(query);
+ query = "DELETE FROM cell WHERE id='"+id+"'";
+ st.executeUpdate(query);
+ alignment.setExtension( SVCNS, STORED, (String)null);
+ st.close();
+ }
+
public void storeAlignment( String id ) throws AlignmentException, SQLException {
String query = null;
Alignment alignment = getAlignment( id );
diff --git a/src/fr/inrialpes/exmo/align/service/Directory.java b/src/fr/inrialpes/exmo/align/service/Directory.java
index 9f71ccbf49b454250d78b863d8fb746ef2a56750..f5cc91e3c118d85f474dfa33519f0988fcf1186a 100644
--- a/src/fr/inrialpes/exmo/align/service/Directory.java
+++ b/src/fr/inrialpes/exmo/align/service/Directory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007, 2009
+ * Copyright (C) INRIA, 2007, 2009, 2011
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -39,6 +39,11 @@ public interface Directory {
*/
public void register( Alignment al ) throws AServException;
+ /**
+ * Unregister an alignment to the directory (if necessary)
+ */
+ public void unregister( Alignment al ) throws AServException;
+
/**
* Shutdown the connection and/or registration to the directory
*/
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index fa14b4953d7512f78ff08c1d8f5a364bab7845fb..1ce3bf8049f50fa3f558d397ac95f380aae85ebd 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -501,6 +501,26 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+pid+"</a></li>";
}
msg += "</ul>";
+ } if ( perf.equals("manalignments") ){ // Manage ailignments
+ msg = "<h1>Available alignments</h1><ul compact=\"1\">";
+ for ( Alignment al : manager.alignments() ) {
+ String id = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<li><a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+id+"\">"+pid+"</a> "+al.nbCells()+" <a href=\"../html/errrazze?id="+id+"\">DEL</a></li>";
+ }
+ msg += "</ul>";
+ } if ( perf.equals("errrazze") ){ // Suppress an alignment
+ String id = params.getProperty("id");
+ if ( id != null && !id.equals("") ) { // Erase it
+ Message answer = manager.erase( new Message(newId(),(Message)null,myId,serverId,id, params) );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params );
+ } else {
+ msg = "<h1>Alignment deleted</h1>";
+ msg += displayAnswer( answer, params );
+ }
+ }
} else if ( perf.equals("prmstore") ) {
msg = "<h1>Store an alignment</h1><form action=\"store\">";
msg += "Alignment id: <select name=\"id\">";
diff --git a/src/fr/inrialpes/exmo/align/service/OysterDirectory.java b/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
index b6ea6a7b1257210725288c103a67bb4d79e631e9..2029b696e91affec7e70a725465e52037cd77b19 100644
--- a/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
+++ b/src/fr/inrialpes/exmo/align/service/OysterDirectory.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2007-2010
+ * Copyright (C) INRIA, 2007-2011
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
@@ -91,6 +91,13 @@ public class OysterDirectory implements Directory {
public void getAlignmentReferences( Ontology o1, Ontology o2 ){
}
+ /**
+ * unregister an alignment from the directory (if necessary)
+ * This is not implemented
+ */
+ public void unregister( Alignment al ) {
+ }
+
/**
* Shutdown the connection and/or registration to the directory
*/