From c59fb24fe46a6e0f13bcf4784cd49130568474b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Mon, 28 Apr 2014 21:37:02 +0000
Subject: [PATCH] - implemented OntologyNetwork management (volatil) for the
server
---
.../inrialpes/exmo/align/service/Cache.java | 44 +++++--
.../exmo/align/service/SQLCache.java | 8 ++
.../exmo/align/service/VolatilCache.java | 124 +++++++++++++++---
3 files changed, 148 insertions(+), 28 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/service/Cache.java b/src/fr/inrialpes/exmo/align/service/Cache.java
index 9f9178fc..55cc4ae7 100644
--- a/src/fr/inrialpes/exmo/align/service/Cache.java
+++ b/src/fr/inrialpes/exmo/align/service/Cache.java
@@ -28,6 +28,7 @@ import java.net.URI;
import java.net.URISyntaxException;
import org.semanticweb.owl.align.Alignment;
+import org.semanticweb.owl.align.OntologyNetwork;
import org.semanticweb.owl.align.AlignmentException;
/**
@@ -46,17 +47,12 @@ public interface Cache {
public void close() throws AlignmentException;
- public void flushCache();
-
// **********************************************************************
- // LOADING FROM DATABASE
- /**
- * loads the alignment descriptions from the database and put them in the
- * alignmentTable hashtable
- * index them under the ontology URIs
- */
+ // INDEXES
+
public Collection<Alignment> alignments();
public Collection<URI> ontologies();
+ public Collection<OntologyNetwork> ontologyNetworks();
public Collection<Alignment> alignments( URI u1, URI u2 );
//**********************************************************************
@@ -65,6 +61,8 @@ public interface Cache {
// Public because this is now used by AServProtocolManager
public String generateAlignmentUri();
+ public String generateOntologyNetworkUri();
+
//**********************************************************************
// FETCHING FROM CACHE
/**
@@ -79,6 +77,11 @@ public interface Cache {
*/
public Alignment getAlignment( String uri ) throws AlignmentException;
+ /**
+ * retrieve network of ontologies from id
+ */
+ public OntologyNetwork getOntologyNetwork( String uri ) throws AlignmentException;
+
public Set<Alignment> getAlignments( URI uri );
/**
@@ -87,8 +90,16 @@ public interface Cache {
*/
public Set<Alignment> getAlignments( URI uri1, URI uri2 );
+ /**
+ * The equivalent primitives to both getAlignments()
+ * within a network of ontologies are available from the network itself
+ */
+
+ public void flushCache();
+
//**********************************************************************
- // RECORDING ALIGNMENTS
+ // RECORDING ALIGNMENTS AND NETWORKS
+
/**
* records newly created alignment
*/
@@ -99,16 +110,31 @@ public interface Cache {
*/
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException;
+ /**
+ * records newly created alignment
+ */
+ public String recordNewNetwork( OntologyNetwork network, boolean force );
+
+ /**
+ * records alignment identified by id
+ */
+ public String recordNewNetwork( String uri, OntologyNetwork network, boolean force ) throws AlignmentException;
+
//**********************************************************************
// STORING IN DATABASE
public boolean isAlignmentStored( Alignment alignment );
+ public boolean isNetworkStored( OntologyNetwork network );
+
/**
* Non publicised class
*/
public void eraseAlignment( String uri, boolean eraseFromDB ) throws AlignmentException;
+ public void eraseOntologyNetwork( String uri, boolean eraseFromDB ) throws AlignmentException;
+
public void storeAlignment( String uri ) throws AlignmentException;
+ public void storeOntologyNetwork( String uri ) throws AlignmentException;
}
diff --git a/src/fr/inrialpes/exmo/align/service/SQLCache.java b/src/fr/inrialpes/exmo/align/service/SQLCache.java
index 72702036..38975a47 100644
--- a/src/fr/inrialpes/exmo/align/service/SQLCache.java
+++ b/src/fr/inrialpes/exmo/align/service/SQLCache.java
@@ -520,6 +520,14 @@ public class SQLCache extends VolatilCache implements Cache {
st.executeUpdate(query);
}
+ public void storeOntologyNetwork( String uri ) throws AlignmentException {
+ // TODO
+ }
+
+ public void unstoreOntologyNetwork( String uri, OntologyNetwork network ) throws AlignmentException {
+ // TODO
+ }
+
// **********************************************************************
// DATABASE CREATION AND UPDATING
/*
diff --git a/src/fr/inrialpes/exmo/align/service/VolatilCache.java b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
index 65ef5c96..5feea5a9 100644
--- a/src/fr/inrialpes/exmo/align/service/VolatilCache.java
+++ b/src/fr/inrialpes/exmo/align/service/VolatilCache.java
@@ -39,6 +39,7 @@ import org.slf4j.LoggerFactory;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.Namespace;
+import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
import org.semanticweb.owl.align.OntologyNetwork;
import org.semanticweb.owl.align.Alignment;
@@ -99,7 +100,7 @@ public class VolatilCache implements Cache {
}
// **********************************************************************
- // LOADING FROM DATABASE
+ // INDEXES
protected Enumeration<Alignment> listAlignments() {
return alignmentTable.elements();
@@ -113,6 +114,14 @@ public class VolatilCache implements Cache {
return ontologyTable.keySet();
}
+ public Collection<URI> ontologyNetworkUris() {
+ return onetworkTable.keySet();
+ }
+
+ public Collection<OntologyNetwork> ontologyNetworks() {
+ return onetworkTable.values();
+ }
+
public Set<Alignment> getAlignments( URI uri ) {
return ontologyTable.get( uri );
}
@@ -154,14 +163,6 @@ public class VolatilCache implements Cache {
return result;
}
- public Collection<URI> ontologynetworks() {
- return onetworkTable.keySet();
- }
-
- public Collection<OntologyNetwork> ontologyNetworks() {
- return onetworkTable.values();
- }
-
public Collection<Alignment> alignments( URI u1, URI u2 ) {
Collection<Alignment> results = new HashSet<Alignment>();
if ( u1 != null ) {
@@ -202,7 +203,7 @@ public class VolatilCache implements Cache {
return alid.substring( alid.indexOf( ALID )+5 );
}
- public String generateNetworkUri() { //For Ontology and Ontology Networks
+ public String generateOntologyNetworkUri() { //For Ontology and Ontology Networks
// Generate an id based on a URI prefix + Date + random number
return recoverNetworkUri( generateId() );
}
@@ -291,6 +292,16 @@ public class VolatilCache implements Cache {
return result;
}
+ /**
+ * retrieve network of ontologies from id
+ */
+ public OntologyNetwork getOntologyNetwork( String uri ) throws AlignmentException {
+ OntologyNetwork result = onetworkTable.get( uri );
+ if ( result == null )
+ throw new AlignmentException("Cannot find ontology network "+uri);
+ return result;
+ }
+
public void flushCache() { // throws AlignmentException
for ( Alignment al : alignmentTable.values() ){
if ( al.getExtension(SVCNS, CACHED ) != null &&
@@ -329,16 +340,14 @@ public class VolatilCache implements Cache {
* records alignment identified by id
*/
public String recordNewAlignment( String uri, Alignment al, boolean force ) throws AlignmentException {
- Alignment alignment = al;
-
- alignment.setExtension(SVCNS, OURI1, alignment.getOntology1URI().toString());
- alignment.setExtension(SVCNS, OURI2, alignment.getOntology2URI().toString());
+ al.setExtension(SVCNS, OURI1, al.getOntology1URI().toString());
+ al.setExtension(SVCNS, OURI2, al.getOntology2URI().toString());
// Index
- recordAlignment( uri, alignment, force );
+ recordAlignment( uri, al, force );
// Not yet stored
- alignment.setExtension(SVCNS, STORED, (String)null);
+ al.setExtension(SVCNS, STORED, (String)null);
// Cached now
- resetCacheStamp(alignment);
+ resetCacheStamp( al );
return uri;
}
@@ -391,6 +400,57 @@ public class VolatilCache implements Cache {
alignmentTable.remove( id );
}
+ //**********************************************************************
+ // RECORDING NETWORKS OF ONTOLOGIES
+
+ /**
+ * records a newly created network
+ */
+ public String recordNewNetwork( OntologyNetwork network, boolean force ) {
+ try { return recordNewNetwork( generateOntologyNetworkUri(), network, force );
+ } catch ( AlignmentException ae ) { return (String)null; }
+ }
+
+ /**
+ * records alignment identified by id
+ */
+ public String recordNewNetwork( String uri, OntologyNetwork network, boolean force ) throws AlignmentException {
+ // Index
+ recordNetwork( uri, network, force );
+ // Not yet stored
+ ((BasicOntologyNetwork)network).setExtension( SVCNS, STORED, (String)null );
+ // Cached now
+ resetCacheStamp( network );
+ return uri;
+ }
+
+ /**
+ * records a network identified by id
+ */
+ public String recordNetwork( String uri, OntologyNetwork network, boolean force ) {
+ // record the network at the corresponding Uri in tables!
+ ((BasicOntologyNetwork)network).setExtension( Namespace.ALIGNMENT.uri, Annotations.ID, uri );
+
+ // Store it
+ if ( force || onetworkTable.get( uri ) == null ) {
+ try {
+ onetworkTable.put( new URI( uri ), network );
+ } catch ( URISyntaxException uriex ) {
+ logger.debug( "IGNORED: Unlikely URI exception", uriex );
+ return null;
+ }
+ }
+ return uri;
+ }
+
+ /**
+ * suppresses the record for a network of ontologies
+ */
+ public void unRecordNetwork( OntologyNetwork network ) {
+ String id = ((BasicOntologyNetwork)network).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ onetworkTable.remove( id );
+ }
+
//**********************************************************************
// STORING IN DATABASE
@@ -399,6 +459,11 @@ public class VolatilCache implements Cache {
!alignment.getExtension( SVCNS, STORED ).equals("") );
}
+ public boolean isNetworkStored( OntologyNetwork network ) {
+ return ( ((BasicOntologyNetwork)network).getExtension( SVCNS, STORED ) != null &&
+ !((BasicOntologyNetwork)network).getExtension( SVCNS, STORED ).equals("") );
+ }
+
/**
* Non publicised class
*/
@@ -416,10 +481,31 @@ public class VolatilCache implements Cache {
public void storeAlignment( String uri ) throws AlignmentException {
}
+ /**
+ * Non publicised class
+ */
+ public void eraseOntologyNetwork( String uri, boolean eraseFromDB ) throws AlignmentException {
+ OntologyNetwork network = getOntologyNetwork( uri );
+ if ( network != null ) {
+ if ( eraseFromDB ) unstoreOntologyNetwork( uri, network );
+ unRecordNetwork( network );
+ }
+ }
+
+ public void unstoreOntologyNetwork( String uri, OntologyNetwork network ) throws AlignmentException {
+ }
+
+ public void storeOntologyNetwork( String uri ) throws AlignmentException {
+ }
+
//**********************************************************************
// CACHE MANAGEMENT (Not implemented yet)
- public void resetCacheStamp( Alignment result ){
- result.setExtension(SVCNS, CACHED, new Date().toString() );
+ public void resetCacheStamp( Alignment al ){
+ al.setExtension(SVCNS, CACHED, new Date().toString() );
+ }
+
+ public void resetCacheStamp( OntologyNetwork network ){
+ ((BasicOntologyNetwork)network).setExtension(SVCNS, CACHED, new Date().toString() );
}
public void cleanUpCache() {
--
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