From 4c30b8007d3e3b640384e7e2258682e35560a776 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Thu, 22 May 2014 19:09:14 +0000
Subject: [PATCH] - implemented semi-deep cloning in BasicOntologyNetwork -
moved convertExtensions to Extensions
---
.../exmo/align/impl/BasicAlignment.java | 25 +++----------------
.../exmo/align/impl/BasicOntologyNetwork.java | 19 +++++++++++---
.../inrialpes/exmo/align/impl/Extensions.java | 19 ++++++++++++++
.../exmo/align/impl/ObjectAlignment.java | 6 ++---
.../exmo/align/impl/edoal/EDOALAlignment.java | 8 +++---
5 files changed, 46 insertions(+), 31 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
index 8657fc7c..c1d65f9d 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicAlignment.java
@@ -218,6 +218,8 @@ public class BasicAlignment implements Alignment {
public Collection<String[]> getExtensions(){ return extensions.getValues(); }
+ public Extensions getExtensionsObject(){ return extensions; }
+
public void setExtensions( Extensions ext ){ extensions = ext; }
public void setExtension( String uri, String label, String value ) {
@@ -667,25 +669,6 @@ public class BasicAlignment implements Alignment {
return result;
}
- public Extensions convertExtension( String label, String method ) {
- Extensions newext = (Extensions)extensions.clone();
- String oldid = extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
- if ( oldid != null && !oldid.equals("") ) {
- newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.DERIVEDFROM, oldid );
- newext.unsetExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
- }
- String pretty = getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
- if ( pretty != null ){
- newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty+"/"+label );
- };
- if ( extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) != null ) {
- newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE,
- extensions.getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) );
- }
- newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.METHOD, method );
- return newext;
- }
-
/**
* A new alignment is created such that for
* any pair (o, o', n, r) in O the resulting alignment will contain:
@@ -699,7 +682,7 @@ public class BasicAlignment implements Alignment {
// We must inverse getType
result.setType( getType() );
result.setLevel( getLevel() );
- result.setExtensions( convertExtension( "inverted", "http://exmo.inrialpes.fr/align/impl/BasicAlignment#inverse" ) );
+ result.setExtensions( extensions.convertExtension( "inverted", "http://exmo.inrialpes.fr/align/impl/BasicAlignment#inverse" ) );
//for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
// String label = (String)e.nextElement();
for ( String label : namespaces.stringPropertyNames() ) {
@@ -743,7 +726,7 @@ public class BasicAlignment implements Alignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- align.setExtensions( convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
+ align.setExtensions( extensions.convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
//for ( Enumeration e = namespaces.getNames() ; e.hasMoreElements(); ){
// String label = (String)e.nextElement();
for ( String label : namespaces.stringPropertyNames() ) {
diff --git a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
index 43982ad9..7dcd086f 100644
--- a/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
+++ b/src/fr/inrialpes/exmo/align/impl/BasicOntologyNetwork.java
@@ -20,7 +20,6 @@
package fr.inrialpes.exmo.align.impl;
-//import java.lang.Cloneable; // JE: what happens when I do a clone() ??
import java.lang.Iterable;
import java.util.Collections;
import java.util.Collection;
@@ -168,9 +167,23 @@ public class BasicOntologyNetwork implements OntologyNetwork {
/**
- * Clone?
+ * Clone does some deeper cloning
+ * It has the same content but a different id (no id indeed)
*/
- //public BasicOntologyNetwork clone() {}
+ public BasicOntologyNetwork clone() {
+ //public Object clone() {
+ BasicOntologyNetwork network = new BasicOntologyNetwork();
+ network.setExtensions( extensions.convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
+ for ( URI onto : ontologies.keySet() ) network.addOntology( onto );
+ for ( Alignment al : alignments ) {
+ try {
+ network.addAlignment( al );
+ } catch (AlignmentException alex) {
+ logger.debug( "IGNORED Exception : should not happen {}", al );
+ }
+ }
+ return network;
+ }
/**
* Normalizes an ontology network for it to have exactly one alignment between each pair of ontologies.
diff --git a/src/fr/inrialpes/exmo/align/impl/Extensions.java b/src/fr/inrialpes/exmo/align/impl/Extensions.java
index aad1e69b..1331b309 100644
--- a/src/fr/inrialpes/exmo/align/impl/Extensions.java
+++ b/src/fr/inrialpes/exmo/align/impl/Extensions.java
@@ -72,6 +72,25 @@ public class Extensions {
return table.values();
}
+ public Extensions convertExtension( String label, String method ) {
+ Extensions newext = (Extensions)clone();
+ String oldid = getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ if ( oldid != null && !oldid.equals("") ) {
+ newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.DERIVEDFROM, oldid );
+ newext.unsetExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ }
+ String pretty = getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pretty != null ){
+ newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty+"/"+label );
+ };
+ if ( getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) != null ) {
+ newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE,
+ getExtension( Namespace.ALIGNMENT.uri, Annotations.PROVENANCE ) );
+ }
+ newext.setExtension( Namespace.ALIGNMENT.uri, Annotations.METHOD, method );
+ return newext;
+ }
+
@SuppressWarnings( "unchecked" )
public Object clone() {
return new Extensions( (Hashtable<String,String[]>)table.clone() ); //[W:unchecked]
diff --git a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
index ab3334af..ada4592c 100644
--- a/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/ObjectAlignment.java
@@ -1,7 +1,7 @@
/*
* $Id$
*
- * Copyright (C) INRIA, 2003-2011, 2013
+ * Copyright (C) INRIA, 2003-2011, 2013-2014
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -119,7 +119,7 @@ public class ObjectAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- align.setExtensions( convertExtension( "EDOALURIConverted", this.getClass().getName()+"#toURI" ) );
+ align.setExtensions( extensions.convertExtension( "EDOALURIConverted", this.getClass().getName()+"#toURI" ) );
for (Enumeration e = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
try {
@@ -147,7 +147,7 @@ public class ObjectAlignment extends BasicAlignment {
}
alignment.setType( al.getType() );
alignment.setLevel( al.getLevel() );
- alignment.setExtensions( al.convertExtension( "ObjectURIConverted", "fr.inrialpes.exmo.align.ObjectAlignment#toObject" ) );
+ alignment.setExtensions( al.extensions.convertExtension( "ObjectURIConverted", "fr.inrialpes.exmo.align.ObjectAlignment#toObject" ) );
LoadedOntology<Object> o1 = (LoadedOntology<Object>)alignment.getOntologyObject1(); // [W:unchecked]
LoadedOntology<Object> o2 = (LoadedOntology<Object>)alignment.getOntologyObject2(); // [W:unchecked]
Object obj1 = null;
diff --git a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
index 108771a9..6db026de 100644
--- a/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
+++ b/src/fr/inrialpes/exmo/align/impl/edoal/EDOALAlignment.java
@@ -2,7 +2,7 @@
* $Id$
*
* Sourceforge version 1.6 - 2008 - was OMWGAlignment
- * Copyright (C) INRIA, 2007-2013
+ * Copyright (C) INRIA, 2007-2014
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
@@ -233,7 +233,7 @@ public class EDOALAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- align.setExtensions( convertExtension( "EDOALURIConverted", "http://exmo.inrialpes.fr/align/impl/edoal/EDOALAlignment#toURI" ) );
+ align.setExtensions( extensions.convertExtension( "EDOALURIConverted", "http://exmo.inrialpes.fr/align/impl/edoal/EDOALAlignment#toURI" ) );
for (Enumeration e = getElements(); e.hasMoreElements();) {
Cell c = (Cell)e.nextElement();
try {
@@ -306,7 +306,7 @@ public class EDOALAlignment extends BasicAlignment {
*/
public void convertToEDOAL( BasicAlignment al ) throws AlignmentException {
setType( al.getType() );
- setExtensions( al.convertExtension( "toEDOAL", "fr.inrialpes.exmo.align.edoal.EDOALAlignment#toEDOAL" ) );
+ setExtensions( al.getExtensionsObject().convertExtension( "toEDOAL", "fr.inrialpes.exmo.align.edoal.EDOALAlignment#toEDOAL" ) );
LoadedOntology<Object> o1 = (LoadedOntology<Object>)getOntologyObject1(); // [W:unchecked]
LoadedOntology<Object> o2 = (LoadedOntology<Object>)getOntologyObject2(); // [W:unchecked]
for ( Cell c : al ) {
@@ -360,7 +360,7 @@ public class EDOALAlignment extends BasicAlignment {
align.setLevel( getLevel() );
align.setFile1( getFile1() );
align.setFile2( getFile2() );
- align.setExtensions( convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
+ align.setExtensions( extensions.convertExtension( "cloned", this.getClass().getName()+"#clone" ) );
try {
align.ingest( this );
} catch (AlignmentException ex) {
--
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