From 68c15efcd49df6257cd7047029b21cd4afff3713 Mon Sep 17 00:00:00 2001
From: Luz-Maria Priego <lpriego2003@hotmail.com>
Date: Mon, 26 May 2014 16:05:06 +0000
Subject: [PATCH] ontology network functionalities added
---
.../align/service/AServProtocolManager.java | 294 +++++++++++-------
.../exmo/align/service/HTMLAServProfile.java | 170 ++++++----
2 files changed, 300 insertions(+), 164 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index 1e38b33f..0552646b 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -22,6 +22,7 @@
package fr.inrialpes.exmo.align.service;
import fr.inrialpes.exmo.align.parser.AlignmentParser;
+import fr.inrialpes.exmo.align.parser.SyntaxElement;
import fr.inrialpes.exmo.align.impl.Annotations;
import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
import fr.inrialpes.exmo.align.impl.Namespace;
@@ -65,6 +66,9 @@ import org.semanticweb.owl.align.OntologyNetwork;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+
import java.lang.ClassNotFoundException;
import java.lang.InstantiationException;
import java.lang.NoSuchMethodException;
@@ -87,6 +91,7 @@ import java.io.OutputStreamWriter;
import java.io.IOException;
import java.io.File;
import java.io.UnsupportedEncodingException;
+import java.net.HttpURLConnection;
import java.net.URI;
import java.net.URL;
import java.net.JarURLConnection;
@@ -108,6 +113,11 @@ import java.util.jar.JarFile;
import java.util.jar.JarEntry;
import java.util.zip.ZipEntry;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
+
/**
* This is the main class which controls the behaviour of the Alignment Server
* It is as independent from the OWL API as possible.
@@ -1254,8 +1264,7 @@ public class AServProtocolManager implements Service {
try {
noo = alignmentCache.getOntologyNetwork(id);
} catch (AlignmentException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ return new UnreachableOntologyNetwork( params, newId(), serverId, id );
}
BasicOntologyNetwork newnoo = (BasicOntologyNetwork)noo;
@@ -1269,14 +1278,12 @@ public class AServProtocolManager implements Service {
new BufferedWriter(
new OutputStreamWriter( result, "UTF-8" )), true);
} catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ return new ErrorMsg( params, newId(), serverId,"Network encoding error" );
}
try {
newnoo.write( writer );
} catch (AlignmentException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ return new ErrorMsg( params, newId(), serverId,"Network writing error" );
} finally {
writer.flush();
writer.close();
@@ -1285,13 +1292,12 @@ public class AServProtocolManager implements Service {
}
- public Message renderHTMLNetwork( Properties params ){
+ public Message renderHTMLNetwork( Properties params ){ //called by HTTPTransport
// Retrieve the alignment
String result = new String();
String idON = new String();
String pidON = new String();
String id = params.getProperty( "id" );
- //String id = idON;
BasicOntologyNetwork noo = null;
try {
logger.trace("Network sought for {}", id);
@@ -1367,89 +1373,33 @@ public class AServProtocolManager implements Service {
}
}
-
- private Message retrieveAlignmentON( Properties params, URI uri1, URI uri2 ){
- String method = params.getProperty("method");
-
- Set<Alignment> alignments = alignmentCache.getAlignments( uri1, uri2 );
- if ( alignments != null && params.getProperty("force") == null ) {
- for ( Alignment al: alignments ){
- String meth2 = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.METHOD );
- if ( meth2 != null && meth2.equals(method) ) {
- return new AlignmentId( params, newId(), serverId,
- al.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ) ,
- al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ) );
- }
- }
- }
- return (Message)null;
- }
-public List<Message> alignonet( Properties params ) {
-
-
- List<Message> result = new ArrayList<>();
- //not finished
- //parameters: onID, method, reflexive, symmetric
- for ( Enumeration<String> e = (Enumeration<String>)commandLineParams.propertyNames(); e.hasMoreElements();) {
- String key = e.nextElement();
- if ( params.getProperty( key ) == null ){
- params.setProperty( key , commandLineParams.getProperty( key ) );
- }
- }
- //prepare for
- String id = params.getProperty("id");
- Boolean reflexive = false;
- if (params.getProperty("reflexive") != null) reflexive = true;
- Boolean symmetric = false;
- if (params.getProperty("symmetric") != null) symmetric = true;
-
- Collection<URI> networkOntologyA = networkOntologyUri(id);
- Collection<URI> networkOntologyB = networkOntologyUri(id);
-
- // Reflexive and Symmetric
- if ( reflexive && symmetric ) {
- for ( URI ontoA : networkOntologyA ) {
- for ( URI ontoB : networkOntologyB ) {
- params.setProperty("onto1", ontoA.toString());
- params.setProperty("onto2", ontoB.toString());
- Message answer = align( params );
- if ( answer != null || answer.toString().contains("AlignmentId")) {
- result.add(answer);
- };
- }
- }
- }
- return result;
-}
-
-
- // TO VERIFY
- public Message alignonet2( Properties params ) {
+ public Message alignonet( Properties params ) {
//parameters: onID, method, reflexive, symmetric
OntologyNetwork noo = null;
Boolean reflexive = false;
Boolean symmetric = false;
+ Boolean newnet = false;
String id = params.getProperty("id");
- String pretty = params.getProperty("pretty");
+ String pretty = params.getProperty("pretty");
String method = params.getProperty("method");
if (params.getProperty("reflexive") != null) reflexive = true;
if (params.getProperty("symmetric") != null) symmetric = true;
+ if (params.getProperty("new") != null) newnet = true;
try {
- noo = alignmentCache.getOntologyNetwork( id );
- } catch (AlignmentException e1) {
- return new UnknownOntologyNetwork( params, newId(), serverId,id );
- }
- logger.debug(" Before Network alignments results, id: {} total ontologies: {} total alignments: {}",id, noo.getOntologies().size(),noo.getAlignments().size());
-
+ noo = alignmentCache.getOntologyNetwork( id );
+ if (newnet) noo = ((BasicOntologyNetwork) noo).clone();
+ } catch (AlignmentException e1) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
try {
- ((BasicOntologyNetwork)noo).match( method, reflexive, symmetric, params );
- } catch (AlignmentException e) {
- return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
- }
+ ((BasicOntologyNetwork)noo).match( method, reflexive, symmetric, params );
+ } catch (AlignmentException e) {
+ return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
+ }
logger.debug(" Network alignments results, id: {} total ontologies: {} total alignments: {}",id, noo.getOntologies().size(),noo.getAlignments().size());
Set<Alignment> networkAlignments = networkAlignmentUri(id);
@@ -1459,24 +1409,38 @@ public List<Message> alignonet( Properties params ) {
al.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
}
}
-
- return new OntologyNetworkId( params, newId(), serverId, id,
+
+ return new OntologyNetworkId( params, newId(), serverId, id,
((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
}
- public Message trimonet( Properties params ) {
-
- //parameters: onID, method, reflexive, symmetric
- OntologyNetwork noo = null;
- OntologyNetwork nooClone = null;
+public Message trimonet( Properties params ) {
+
+ BasicOntologyNetwork noo = new BasicOntologyNetwork();
String id = params.getProperty("id");
String method = params.getProperty("type");
+ String idClone = new String();
double threshold = Double.parseDouble(params.getProperty("threshold"));
try {
- noo = alignmentCache.getOntologyNetwork( id );
- } catch (AlignmentException e1) {
+ noo = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id);
+ noo = (BasicOntologyNetwork) noo.clone();
+
+ // We preserve the pretty tag within the loaded ontology network
+ String pretty = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pretty == null ) pretty = params.getProperty("pretty");
+ if ( pretty != null && !pretty.equals("") ) {
+ noo.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
+ }
+ // register it
+ idClone = alignmentCache.recordNewNetwork( noo, true );
+ // Generate new ids to trimmed alignments
+ Set<Alignment> networkAlignments = networkAlignmentUri(idClone);
+ for (Alignment al : networkAlignments) {
+ String idAl = alignmentCache.recordNewAlignment( al, true );
+ }
+ } catch (AlignmentException e) {
return new UnknownOntologyNetwork( params, newId(), serverId,id );
}
@@ -1485,31 +1449,145 @@ public List<Message> alignonet( Properties params ) {
} catch (AlignmentException e) {
return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
}
- return new OntologyNetworkId( params, newId(), serverId, id,
+ logger.debug(" Ontology network trimmed from id: {}, to new id: {} total ontologies: {} total alignments: {}",id, idClone, noo.getOntologies().size(),noo.getAlignments().size());
+ return new OntologyNetworkId( params, newId(), serverId, idClone,
((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
}
+public Message closeonet( Properties params ) {
+
+ BasicOntologyNetwork noo = new BasicOntologyNetwork();
+ Boolean invert = false;
+ Boolean compose = false; //what should it do?
+ Boolean newnet = false; //would always be a network, what is the behaviour with compose?
+ String id = params.getProperty("id");
+ if (params.getProperty("invert") != null) invert = true;
+ if (params.getProperty("compose") != null) compose = true;
+ if (params.getProperty("new") != null) newnet = true;
+
+ String idClone = new String();
+
+ try {
+ noo = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id);
+ noo = (BasicOntologyNetwork) noo.clone();
+
+ // We preserve the pretty tag within the loaded ontology network
+ String pretty = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pretty == null ) pretty = params.getProperty("pretty");
+ if ( pretty != null && !pretty.equals("") ) {
+ noo.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
+ }
+ // register it
+ idClone = alignmentCache.recordNewNetwork( noo, true );
+ // Generate new ids to trimmed alignments
+ Set<Alignment> networkAlignments = networkAlignmentUri(idClone);
+ for (Alignment al : networkAlignments) {
+ String idAl = alignmentCache.recordNewAlignment( al, true );
+ }
+ } catch (AlignmentException e) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+
+ try {
+ if (invert) ((BasicOntologyNetwork) noo).invert();
+ } catch (AlignmentException e) {
+ return new ErrorMsg( params, newId(), serverId,"Invert network alignment error" );
+ }
+ logger.debug(" Ontology network inverted from id: {}, to new id: {} total ontologies: {} total alignments: {}",id, idClone, noo.getOntologies().size(),noo.getAlignments().size());
+ return new OntologyNetworkId( params, newId(), serverId, idClone,
+ ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+}
+
+public Message normonet( Properties params ) {
+
+ BasicOntologyNetwork noo = new BasicOntologyNetwork();
+ Boolean normalize = false;
+ String id = params.getProperty("id");
+ if (params.getProperty("normalize") != null) normalize = true;
+
+ String idClone = new String();
+
+ try {
+ noo = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id);
+ noo = (BasicOntologyNetwork) noo.clone();
+
+ // We preserve the pretty tag within the loaded ontology network
+ String pretty = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pretty == null ) pretty = params.getProperty("pretty");
+ if ( pretty != null && !pretty.equals("") ) {
+ noo.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
+ }
+ // register it
+ idClone = alignmentCache.recordNewNetwork( noo, true );
+ // Generate new ids to normalized alignments
+ Set<Alignment> networkAlignments = networkAlignmentUri(idClone);
+ for (Alignment al : networkAlignments) {
+ String idAl = alignmentCache.recordNewAlignment( al, true );
+ }
+ } catch (AlignmentException e) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+
+ try {
+ ((BasicOntologyNetwork) noo).normalize();
+ } catch (AlignmentException e) {
+ return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
+ }
+ logger.debug(" Ontology network normalized from id: {}, to new id: {} total ontologies: {} total alignments: {}",id, idClone, noo.getOntologies().size(),noo.getAlignments().size());
+ return new OntologyNetworkId( params, newId(), serverId, idClone,
+ ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+}
+
+
+public Message opsetonet( Properties params ) {
+
+ BasicOntologyNetwork noo = new BasicOntologyNetwork();
+ BasicOntologyNetwork noo1 = new BasicOntologyNetwork();
+ BasicOntologyNetwork noo2 = new BasicOntologyNetwork();
+ Boolean meet = false;
+ Boolean join = false;
+ Boolean diff = false;
+ String id = new String();
+ String id1 = params.getProperty("id1");
+ String id2 = params.getProperty("id2");
+ if (params.getProperty("meet") != null) meet = true;
+ if (params.getProperty("join") != null) join = true;
+ if (params.getProperty("diff") != null) diff = true;
+
+ try {
+ noo1 = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id1);
+ noo2 = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id2);
+ if (meet) ((BasicOntologyNetwork) noo).meet(noo1, noo2);
+ else if (join) ((BasicOntologyNetwork) noo).join(noo1, noo2);
+ else if (diff) ((BasicOntologyNetwork) noo).diff(noo1, noo2);
+
+ // We preserve the pretty tag within the loaded ontology network
+ String pretty = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pretty == null ) pretty = params.getProperty("pretty");
+ if ( pretty != null && !pretty.equals("") ) {
+ noo.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
+ }
+ // register it
+ id = alignmentCache.recordNewNetwork( noo, true );
+ // Generate new ids to operation set alignments
+ Set<Alignment> networkAlignments = networkAlignmentUri(id);
+ for (Alignment al : networkAlignments) {
+ String idAl = alignmentCache.recordNewAlignment( al, true );
+ }
+ } catch (AlignmentException e) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+
+ try {
+ ((BasicOntologyNetwork) noo).normalize();
+ } catch (AlignmentException e) {
+ return new ErrorMsg( params, newId(), serverId,"Network alignment error" );
+ }
+ logger.debug(" Ontology network operation set from id1: {}, id2: {} to new id: {}total ontologies: {} total alignments: {}",id1, id2, id, noo.getOntologies().size(),noo.getAlignments().size());
+ return new OntologyNetworkId( params, newId(), serverId, id,
+ ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+}
+
- public Message listNetworkOntology( Properties params ) { //not UsED??
- String result = "";
-
- OntologyNetwork noo = null;
- noo = new BasicOntologyNetwork();
- String id = params.getProperty( "id" );
- //URI onto2 = null;
-
- try {
- noo = alignmentCache.getOntologyNetwork(id);
- noo.getOntologies().size();
- Iterator<URI> iterator2 = noo.getOntologies().iterator();
- while (iterator2.hasNext()){
- URI onto2 = (URI) iterator2.next();
- result += "<li><a href=\""+onto2+"\">"+onto2+"</a></li>";
- }
- return new OntologyNetworkId( params, newId(), serverId, id ,result );
- } catch (AlignmentException e) {
- return new UnknownOntologyNetwork( params, newId(), serverId, id );
- }
- }
}
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 6ba944d6..d0444440 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -204,7 +204,6 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String id = "";
String pid = "";
msg = "<h1>Available networks</h1>";
- //msg += "<form action=\"listNetOnto\"><ul compact=\"1\">";
msg += "<form action=\"listnetwork\"><ul compact=\"1\">";
for ( OntologyNetwork oNetwork : ontologyNetworks ) {
noo = (BasicOntologyNetwork) oNetwork;
@@ -215,20 +214,23 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</ul></form>";
- } else if ( perf.equals("listNetOnto") ){ //TODO eliminate this
- //Message answer = manager.renderHTMLON( params );
+ /*
+ } else if ( perf.equals("listNetOnto") ){ //TODO verify if will it be used
+
Message answer = manager.renderHTMLNetwork( params );
if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource );
} else {
return answer.getContent();
}
-
- } else if ( perf.equals("listNetOnto2") ){
+ */
+ /*
+
+ } else if ( perf.equals("listNetOnto2") ){//TODO verify if will it be used
msg = "<h1>Ontologies</h1>";
msg += "<form action=\"listNetAlig\">";
- String uriON = params.getProperty("uriON"); //send as parameter uriON for listNetAlig
+ String uriON = params.getProperty("uriON");
int numOnto = 0;
Collection<URI> networkOntology = manager.networkOntologyUri(uriON);
msg += "<p>" + uriON + " ";
@@ -239,6 +241,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<li><a href=\""+onto.toString()+"\"> ("+String.format("%05d", numOnto)+") "+onto.toString()+"</a></li>";
}
//msg += " <input type=\"submit\" value=\"List alignments\"/></form><ul compact=\"1\">";
+ */
+ /*
} else if ( perf.equals("listNetAlig") ){
@@ -252,6 +256,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
numAlig ++;
msg += "<li><a href=\""+"idAlign" + "\"> ("+String.format("%05d", numAlig)+") " +"idAlign:"+"</a> "+ al.getFile1() + " " + al.getFile2() + "</li>";
}
+ */
} else if ( perf.equals("prmloadonet") ){
//TODO add two more parameters TYPE of file (json/html, etc) and STRUCTURE of the file
@@ -267,6 +272,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />";
msg += "<input type=\"submit\" Value=\"Upload\">";
msg += " </form>";
+
} else if ( perf.equals("loadonet") ) {
Message answer = manager.loadonet( params );
@@ -276,6 +282,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Ontology Network loaded</h1>";
msg += displayAnswerON( answer, params );
}
+
} else if ( perf.equals("storeonet") ){
// here should be done the switch between store and load/store
@@ -295,7 +302,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = testErrorMessages( answer, params, eSource );
} else {
msg = "<h1>Ontology Network stored</h1>";
- msg += displayAnswer( answer, params );
+ msg += displayAnswerON( answer, params ); //it was msg += displayAnswer( answer, params );
}
}
@@ -340,8 +347,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Store an ontology network</h1><form action=\"storeonet\">";
msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
- String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
- String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
@@ -356,8 +363,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Trim networks</h1><form action=\"trimonet\">";
msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
- String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
- String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
@@ -369,34 +376,26 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("trimonet") ){
Message answer = manager.trimonet( params );
if ( answer instanceof ErrorMsg ) {
- System.out.println("answer error ");
- msg = testErrorMessages( answer, params, eSource );
+ msg = testErrorMessages( answer, params, eSource );
} else {
- msg ="<h1>Trimed network</h1><form action=\"trimonet\">";
- msg += "<a href=\"" + answer.getContent() +"\">" + answer.getContent() + "</a>";
-
- System.out.println("answer: "+ answer.getContent());
- }
+ msg ="<h1>Trimmed network</h1>";
+ msg += displayAnswerON( answer, params );
+ }
} else if ( perf.equals("prmmatchonet") ){
msg = "<h1>Match an ontology network</h1><form action=\"matchonet\">";
- msg += "<h2><font color=\"red\">(not implemented yet)</font></h2>";
msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
- String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
- String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
} else { msg += "<option value=\""+id+"\">"+pid+"</option>";}
}
msg += "</select><br />";
-
-// msg += "<!--input type=\"submit\" name=\"action\" value=\"Find\"/>";
-// msg += "<br /-->Methods: <select name=\"method\">";
-
msg += "<br />Methods: <select name=\"method\">";
for( String idMethod : manager.listmethods() ) {
msg += "<option value=\""+idMethod+"\">"+idMethod+"</option>";
@@ -415,24 +414,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("matchonet") ) {
- // DO MATCHING version 1
-/*
- List<Message> answer = manager.alignonet( params );
- msg = "<h1>Network Alignments results</h1>";
- Iterator<Message> it = answer.iterator();
- msg += "<ul>";
- while (it.hasNext()) {
- final Message alignment = it.next();
- msg += "<li><a href=\"" + alignment.getContent() +"\">" + alignment.getContent() + "</a></li>";
- }
- msg += "</ul>";
-
-*/
-
// DO MATCHING
String idON = params.getProperty("id");
logger.debug("Matching network {}", idON);
- Message answer = manager.alignonet2( params );
+ Message answer = manager.alignonet( params );
if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource );
} else {
@@ -457,8 +442,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve ontology network</h1><form action=\"retrieveonet\">";
msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
- String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
- String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
@@ -474,23 +459,17 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = testErrorMessages( answer, params, eSource );
} else {
// Depending on the type we should change the MIME type
- //return answer.getContent().replaceAll("&", "&").replaceAll("<", "<");
return answer.getContent();
}
-
-
-
-
} else if ( perf.equals("prmcloseonet") ){
- msg = "<h1>Close an ontology network</h1><form action=\"matchonet\">";
- msg += "<h2><font color=\"red\">(not implemented yet)</font></h2>";
+ msg = "<h1>Close an ontology network</h1><form action=\"closeonet\">";
msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) {
- String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork
- String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
@@ -498,11 +477,89 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
}
msg += "</select><br />";
- msg += "<input type=\"submit\" name=\"action\" value=\"Invert\" /> ";
- msg += "<input type=\"submit\" name=\"action\" value=\"Compose\"/> ";
- msg += "<input type=\"checkbox\" name=\"new\" /> New ";
+ msg += "<input type=\"submit\" name=\"invert\" value=\"Invert\" /> ";
+ //msg += "<input type=\"submit\" name=\"compose\" value=\"Compose\"/> ";
+ //msg += "<input type=\"checkbox\" name=\"new\" /> New ";
+ msg += "</form>";
+
+ } else if ( perf.equals("closeonet") ){
+ Message answer = manager.closeonet( params );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ msg ="<h1>Closed network</h1>";
+ msg += displayAnswerON( answer, params );
+ }
} else if ( perf.equals("prmnormalizeonet") ){
+
+ msg = "<h1>Normalize an ontology network</h1><form action=\"normonet\">";
+ msg += "Network: <select name=\"id\">";
+ String sel = params.getProperty("id");
+ for ( OntologyNetwork on : manager.ontologyNetworks() ) {
+ String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ if ( sel != null && sel.equals( id ) ){
+ msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
+ } else { msg += "<option value=\""+id+"\">"+pid+"</option>";}
+ }
+
+ msg += "</select><br />";
+ msg += "<input type=\"submit\" name=\"action\" value=\"Normalize\" /> ";
+ msg += "</form>";
+
+ } else if ( perf.equals("normonet") ){
+ Message answer = manager.normonet( params );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ msg ="<h1>Normalized network</h1>";
+ msg += displayAnswerON( answer, params );
+ }
+
+ } else if ( perf.equals("prmopersetonet") ){
+
+ msg = "<h1>Operations on ontology network sets</h1><form action=\"opsetonet\">";
+ msg += "Network 1: <select name=\"id1\">";
+ String sel1 = params.getProperty("id1");
+ for ( OntologyNetwork on : manager.ontologyNetworks() ) {
+ String id1 = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid1 = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid1 == null ) pid1 = id1; else pid1 = id1+" ("+pid1+")";
+ if ( sel1 != null && sel1.equals( id1 ) ){
+ msg += "<option selected=\"1\" value=\""+id1+"\">"+pid1+"</option>";
+ } else { msg += "<option value=\""+id1+"\">"+pid1+"</option>";}
+ }
+ msg += "</select><br />";
+ msg += "Network 2: <select name=\"id2\">";
+ String sel2 = params.getProperty("id2");
+ for ( OntologyNetwork on : manager.ontologyNetworks() ) {
+ String id2 = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid2 = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid2 == null ) pid2 = id2; else pid2 = id2+" ("+pid2+")";
+ if ( sel2 != null && sel2.equals( id2 ) ){
+ msg += "<option selected=\"1\" value=\""+id2+"\">"+pid2+"</option>";
+ } else { msg += "<option value=\""+id2+"\">"+pid2+"</option>";}
+ }
+ msg += "</select><br />";
+
+ msg += "<br /><input type=\"checkbox\" name=\"meet\" /> Meet ";
+ msg += "<input type=\"checkbox\" name=\"join\" /> Join ";
+ msg += "<input type=\"checkbox\" name=\"diff\" /> Diff ";
+ msg += "<br /><br />";
+ msg += "<input type=\"submit\" name=\"action\" value=\"Execute\"/> ";
+ msg += "<br /><br /></form>";
+
+
+ } else if ( perf.equals("opsetonet") ){
+ Message answer = manager.opsetonet( params );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ msg ="<h1>Operation on network done</h1>";
+ msg += displayAnswerON( answer, params );
+ }
} else if ( perf.equals("") ) {
msg = "<h1>Ontology network commands</h1>";
@@ -512,6 +569,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<form action=\"prmmatchonet\"><button title=\"Match an ontology network\" type=\"submit\">Match network </button></form>";
msg += "<form action=\"prmtrimonet\"><button title=\"Trim a network\" type=\"submit\">Trim network</button></form>";
msg += "<form action=\"prmnormalizeonet\"><button title=\"Normalize an ontology network\" type=\"submit\">Normalize network</button></form>";
+ msg += "<form action=\"prmopersetonet\"><button title=\"Operations on ontology network sets\" type=\"submit\">Operations on network sets</button></form>";
msg += "<form action=\"prmcloseonet\"><button title=\"Close an ontology network\" type=\"submit\">Close network</button></form>";
msg += "<form action=\"prmretreiveonet\"><button title=\"Render an ontology network in a particular format\" type=\"submit\">Render network</button></form>";
msg += "<form action=\"prmstoreonet\"><button title=\"Store a network in the server\" type=\"submit\">Store network</button></form>";
@@ -667,7 +725,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource );
} else {
- msg = "<h1>Alignment trimed</h1>";
+ msg = "<h1>Alignment trimmed</h1>";
msg += displayAnswer( answer, params );
}
}
@@ -1021,7 +1079,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
result += "<td><form action=\"getID\"><input type=\"hidden\" name=\"id\" value=\""+answer.getContent()+"\"/><input type=\"submit\" name=\"action\" value=\"GetID\" disabled=\"disabled\"/></form></td>";
result += "<td><form action=\"metadata\"><input type=\"hidden\" name=\"id\" value=\""+answer.getContent()+"\"/><input type=\"submit\" name=\"action\" value=\"Metadata\"/></form></td>";
result += "</tr></table>";
- //} else if( answer instanceof OntologyNetworkIds && ( answer.getParameters() == null || answer.getParameters().getProperty("async") == null )) { //TODO is it needed??create public class OntologyNetworkIds extends Success {
+ //} else if( answer instanceof OntologyNetworkIds && ( answer.getParameters() == null || answer.getParameters().getProperty("async") == null )) { }
result = answer.HTMLRESTString();
}
} else {
--
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