Mentions légales du service

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Commit 68c15efc authored by Luz-Maria Priego's avatar Luz-Maria Priego
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ontology network functionalities added

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src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+ 186
− 108
View file @ 68c15efc
...@@ -22,6 +22,7 @@ ...@@ -22,6 +22,7 @@
package fr.inrialpes.exmo.align.service; package fr.inrialpes.exmo.align.service;
import fr.inrialpes.exmo.align.parser.AlignmentParser; 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.Annotations;
import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork; import fr.inrialpes.exmo.align.impl.BasicOntologyNetwork;
import fr.inrialpes.exmo.align.impl.Namespace; import fr.inrialpes.exmo.align.impl.Namespace;
...@@ -65,6 +66,9 @@ import org.semanticweb.owl.align.OntologyNetwork; ...@@ -65,6 +66,9 @@ import org.semanticweb.owl.align.OntologyNetwork;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; 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.ClassNotFoundException;
import java.lang.InstantiationException; import java.lang.InstantiationException;
import java.lang.NoSuchMethodException; import java.lang.NoSuchMethodException;
...@@ -87,6 +91,7 @@ import java.io.OutputStreamWriter; ...@@ -87,6 +91,7 @@ import java.io.OutputStreamWriter;
import java.io.IOException; import java.io.IOException;
import java.io.File; import java.io.File;
import java.io.UnsupportedEncodingException; import java.io.UnsupportedEncodingException;
import java.net.HttpURLConnection;
import java.net.URI; import java.net.URI;
import java.net.URL; import java.net.URL;
import java.net.JarURLConnection; import java.net.JarURLConnection;
...@@ -108,6 +113,11 @@ import java.util.jar.JarFile; ...@@ -108,6 +113,11 @@ import java.util.jar.JarFile;
import java.util.jar.JarEntry; import java.util.jar.JarEntry;
import java.util.zip.ZipEntry; 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 * This is the main class which controls the behaviour of the Alignment Server
* It is as independent from the OWL API as possible. * It is as independent from the OWL API as possible.
...@@ -1254,8 +1264,7 @@ public class AServProtocolManager implements Service { ...@@ -1254,8 +1264,7 @@ public class AServProtocolManager implements Service {
try { try {
noo = alignmentCache.getOntologyNetwork(id); noo = alignmentCache.getOntologyNetwork(id);
} catch (AlignmentException e) { } catch (AlignmentException e) {
// TODO Auto-generated catch block return new UnreachableOntologyNetwork( params, newId(), serverId, id );
e.printStackTrace();
} }
BasicOntologyNetwork newnoo = (BasicOntologyNetwork)noo; BasicOntologyNetwork newnoo = (BasicOntologyNetwork)noo;
...@@ -1269,14 +1278,12 @@ public class AServProtocolManager implements Service { ...@@ -1269,14 +1278,12 @@ public class AServProtocolManager implements Service {
new BufferedWriter( new BufferedWriter(
new OutputStreamWriter( result, "UTF-8" )), true); new OutputStreamWriter( result, "UTF-8" )), true);
} catch (UnsupportedEncodingException e) { } catch (UnsupportedEncodingException e) {
// TODO Auto-generated catch block return new ErrorMsg( params, newId(), serverId,"Network encoding error" );
e.printStackTrace();
} }
try { try {
newnoo.write( writer ); newnoo.write( writer );
} catch (AlignmentException e) { } catch (AlignmentException e) {
// TODO Auto-generated catch block return new ErrorMsg( params, newId(), serverId,"Network writing error" );
e.printStackTrace();
} finally { } finally {
writer.flush(); writer.flush();
writer.close(); writer.close();
...@@ -1285,13 +1292,12 @@ public class AServProtocolManager implements Service { ...@@ -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 // Retrieve the alignment
String result = new String(); String result = new String();
String idON = new String(); String idON = new String();
String pidON = new String(); String pidON = new String();
String id = params.getProperty( "id" ); String id = params.getProperty( "id" );
//String id = idON;
BasicOntologyNetwork noo = null; BasicOntologyNetwork noo = null;
try { try {
logger.trace("Network sought for {}", id); logger.trace("Network sought for {}", id);
...@@ -1367,89 +1373,33 @@ public class AServProtocolManager implements Service { ...@@ -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 ) { public 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 ) {
//parameters: onID, method, reflexive, symmetric //parameters: onID, method, reflexive, symmetric
OntologyNetwork noo = null; OntologyNetwork noo = null;
Boolean reflexive = false; Boolean reflexive = false;
Boolean symmetric = false; Boolean symmetric = false;
Boolean newnet = false;
String id = params.getProperty("id"); String id = params.getProperty("id");
String pretty = params.getProperty("pretty"); String pretty = params.getProperty("pretty");
String method = params.getProperty("method"); String method = params.getProperty("method");
if (params.getProperty("reflexive") != null) reflexive = true; if (params.getProperty("reflexive") != null) reflexive = true;
if (params.getProperty("symmetric") != null) symmetric = true; if (params.getProperty("symmetric") != null) symmetric = true;
if (params.getProperty("new") != null) newnet = true;
try { try {
noo = alignmentCache.getOntologyNetwork( id ); noo = alignmentCache.getOntologyNetwork( id );
} catch (AlignmentException e1) { if (newnet) noo = ((BasicOntologyNetwork) noo).clone();
return new UnknownOntologyNetwork( params, newId(), serverId,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()); }
try { try {
((BasicOntologyNetwork)noo).match( method, reflexive, symmetric, params ); ((BasicOntologyNetwork)noo).match( method, reflexive, symmetric, params );
} catch (AlignmentException e) { } catch (AlignmentException e) {
return new ErrorMsg( params, newId(), serverId,"Network alignment error" ); 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()); logger.debug(" Network alignments results, id: {} total ontologies: {} total alignments: {}",id, noo.getOntologies().size(),noo.getAlignments().size());
Set<Alignment> networkAlignments = networkAlignmentUri(id); Set<Alignment> networkAlignments = networkAlignmentUri(id);
...@@ -1459,24 +1409,38 @@ public List<Message> alignonet( Properties params ) { ...@@ -1459,24 +1409,38 @@ public List<Message> alignonet( Properties params ) {
al.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty ); 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 )); ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
} }
public Message trimonet( Properties params ) { public Message trimonet( Properties params ) {
//parameters: onID, method, reflexive, symmetric BasicOntologyNetwork noo = new BasicOntologyNetwork();
OntologyNetwork noo = null;
OntologyNetwork nooClone = null;
String id = params.getProperty("id"); String id = params.getProperty("id");
String method = params.getProperty("type"); String method = params.getProperty("type");
String idClone = new String();
double threshold = Double.parseDouble(params.getProperty("threshold")); double threshold = Double.parseDouble(params.getProperty("threshold"));
try { try {
noo = alignmentCache.getOntologyNetwork( id ); noo = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id);
} catch (AlignmentException e1) { 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 ); return new UnknownOntologyNetwork( params, newId(), serverId,id );
} }
...@@ -1485,31 +1449,145 @@ public List<Message> alignonet( Properties params ) { ...@@ -1485,31 +1449,145 @@ public List<Message> alignonet( Properties params ) {
} catch (AlignmentException e) { } catch (AlignmentException e) {
return new ErrorMsg( params, newId(), serverId,"Network alignment error" ); 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 )); ((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 );
}
}
} }
src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+ 114
− 56
View file @ 68c15efc
...@@ -204,7 +204,6 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -204,7 +204,6 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
String id = ""; String id = "";
String pid = ""; String pid = "";
msg = "<h1>Available networks</h1>"; msg = "<h1>Available networks</h1>";
//msg += "<form action=\"listNetOnto\"><ul compact=\"1\">";
msg += "<form action=\"listnetwork\"><ul compact=\"1\">"; msg += "<form action=\"listnetwork\"><ul compact=\"1\">";
for ( OntologyNetwork oNetwork : ontologyNetworks ) { for ( OntologyNetwork oNetwork : ontologyNetworks ) {
noo = (BasicOntologyNetwork) oNetwork; noo = (BasicOntologyNetwork) oNetwork;
...@@ -215,20 +214,23 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -215,20 +214,23 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} }
msg += "</ul></form>"; 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 ); Message answer = manager.renderHTMLNetwork( params );
if ( answer instanceof ErrorMsg ) { if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource ); msg = testErrorMessages( answer, params, eSource );
} else { } else {
return answer.getContent(); 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 = "<h1>Ontologies</h1>";
msg += "<form action=\"listNetAlig\">"; msg += "<form action=\"listNetAlig\">";
String uriON = params.getProperty("uriON"); //send as parameter uriON for listNetAlig String uriON = params.getProperty("uriON");
int numOnto = 0; int numOnto = 0;
Collection<URI> networkOntology = manager.networkOntologyUri(uriON); Collection<URI> networkOntology = manager.networkOntologyUri(uriON);
msg += "<p>" + uriON + " "; msg += "<p>" + uriON + " ";
...@@ -239,6 +241,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -239,6 +241,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<li><a href=\""+onto.toString()+"\"> ("+String.format("%05d", numOnto)+") "+onto.toString()+"</a></li>"; msg += "<li><a href=\""+onto.toString()+"\"> ("+String.format("%05d", numOnto)+") "+onto.toString()+"</a></li>";
} }
//msg += "&nbsp;<input type=\"submit\" value=\"List alignments\"/></form><ul compact=\"1\">"; //msg += "&nbsp;<input type=\"submit\" value=\"List alignments\"/></form><ul compact=\"1\">";
*/
/*
} else if ( perf.equals("listNetAlig") ){ } else if ( perf.equals("listNetAlig") ){
...@@ -252,6 +256,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -252,6 +256,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
numAlig ++; numAlig ++;
msg += "<li><a href=\""+"idAlign" + "\"> ("+String.format("%05d", numAlig)+") " +"idAlign:"+"</a>&nbsp;&nbsp;&nbsp; "+ al.getFile1() + "&nbsp;&nbsp;&nbsp;" + al.getFile2() + "</li>"; msg += "<li><a href=\""+"idAlign" + "\"> ("+String.format("%05d", numAlig)+") " +"idAlign:"+"</a>&nbsp;&nbsp;&nbsp; "+ al.getFile1() + "&nbsp;&nbsp;&nbsp;" + al.getFile2() + "</li>";
} }
*/
} else if ( perf.equals("prmloadonet") ){ } else if ( perf.equals("prmloadonet") ){
//TODO add two more parameters TYPE of file (json/html, etc) and STRUCTURE of the file //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 { ...@@ -267,6 +272,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />"; msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />";
msg += "<input type=\"submit\" Value=\"Upload\">"; msg += "<input type=\"submit\" Value=\"Upload\">";
msg += " </form>"; msg += " </form>";
} else if ( perf.equals("loadonet") ) { } else if ( perf.equals("loadonet") ) {
Message answer = manager.loadonet( params ); Message answer = manager.loadonet( params );
...@@ -276,6 +282,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -276,6 +282,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Ontology Network loaded</h1>"; msg = "<h1>Ontology Network loaded</h1>";
msg += displayAnswerON( answer, params ); msg += displayAnswerON( answer, params );
} }
} else if ( perf.equals("storeonet") ){ } else if ( perf.equals("storeonet") ){
// here should be done the switch between store and load/store // here should be done the switch between store and load/store
...@@ -295,7 +302,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -295,7 +302,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = testErrorMessages( answer, params, eSource ); msg = testErrorMessages( answer, params, eSource );
} else { } else {
msg = "<h1>Ontology Network stored</h1>"; 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 { ...@@ -340,8 +347,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Store an ontology network</h1><form action=\"storeonet\">"; msg = "<h1>Store an ontology network</h1><form action=\"storeonet\">";
msg += "Network: <select name=\"id\">"; msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) { for ( OntologyNetwork on : manager.ontologyNetworks() ) {
String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")"; if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){ if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>"; msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
...@@ -356,8 +363,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -356,8 +363,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg ="<h1>Trim networks</h1><form action=\"trimonet\">"; msg ="<h1>Trim networks</h1><form action=\"trimonet\">";
msg += "Network: <select name=\"id\">"; msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) { for ( OntologyNetwork on : manager.ontologyNetworks() ) {
String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")"; if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){ if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>"; msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
...@@ -369,34 +376,26 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -369,34 +376,26 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("trimonet") ){ } else if ( perf.equals("trimonet") ){
Message answer = manager.trimonet( params ); Message answer = manager.trimonet( params );
if ( answer instanceof ErrorMsg ) { if ( answer instanceof ErrorMsg ) {
System.out.println("answer error "); msg = testErrorMessages( answer, params, eSource );
msg = testErrorMessages( answer, params, eSource );
} else { } else {
msg ="<h1>Trimed network</h1><form action=\"trimonet\">"; msg ="<h1>Trimmed network</h1>";
msg += "<a href=\"" + answer.getContent() +"\">" + answer.getContent() + "</a>"; msg += displayAnswerON( answer, params );
}
System.out.println("answer: "+ answer.getContent());
}
} else if ( perf.equals("prmmatchonet") ){ } else if ( perf.equals("prmmatchonet") ){
msg = "<h1>Match an ontology network</h1><form action=\"matchonet\">"; 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\">"; msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id"); String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) { for ( OntologyNetwork on : manager.ontologyNetworks() ) {
String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")"; if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){ if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>"; msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
} else { msg += "<option value=\""+id+"\">"+pid+"</option>";} } else { msg += "<option value=\""+id+"\">"+pid+"</option>";}
} }
msg += "</select><br />"; msg += "</select><br />";
// msg += "<!--input type=\"submit\" name=\"action\" value=\"Find\"/>";
// msg += "<br /-->Methods: <select name=\"method\">";
msg += "<br />Methods: <select name=\"method\">"; msg += "<br />Methods: <select name=\"method\">";
for( String idMethod : manager.listmethods() ) { for( String idMethod : manager.listmethods() ) {
msg += "<option value=\""+idMethod+"\">"+idMethod+"</option>"; msg += "<option value=\""+idMethod+"\">"+idMethod+"</option>";
...@@ -415,24 +414,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -415,24 +414,10 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("matchonet") ) { } 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 // DO MATCHING
String idON = params.getProperty("id"); String idON = params.getProperty("id");
logger.debug("Matching network {}", idON); logger.debug("Matching network {}", idON);
Message answer = manager.alignonet2( params ); Message answer = manager.alignonet( params );
if ( answer instanceof ErrorMsg ) { if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource ); msg = testErrorMessages( answer, params, eSource );
} else { } else {
...@@ -457,8 +442,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -457,8 +442,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = "<h1>Retrieve ontology network</h1><form action=\"retrieveonet\">"; msg = "<h1>Retrieve ontology network</h1><form action=\"retrieveonet\">";
msg += "Network: <select name=\"id\">"; msg += "Network: <select name=\"id\">";
for ( OntologyNetwork on : manager.ontologyNetworks() ) { for ( OntologyNetwork on : manager.ontologyNetworks() ) {
String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")"; if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){ if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>"; msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
...@@ -474,23 +459,17 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -474,23 +459,17 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg = testErrorMessages( answer, params, eSource ); msg = testErrorMessages( answer, params, eSource );
} else { } else {
// Depending on the type we should change the MIME type // Depending on the type we should change the MIME type
//return answer.getContent().replaceAll("&", "&amp;").replaceAll("<", "&lt;");
return answer.getContent(); return answer.getContent();
} }
} else if ( perf.equals("prmcloseonet") ){ } else if ( perf.equals("prmcloseonet") ){
msg = "<h1>Close an ontology network</h1><form action=\"matchonet\">"; msg = "<h1>Close an ontology network</h1><form action=\"closeonet\">";
msg += "<h2><font color=\"red\">(not implemented yet)</font></h2>";
msg += "Network: <select name=\"id\">"; msg += "Network: <select name=\"id\">";
String sel = params.getProperty("id"); String sel = params.getProperty("id");
for ( OntologyNetwork on : manager.ontologyNetworks() ) { for ( OntologyNetwork on : manager.ontologyNetworks() ) {
String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID ); //TODO eliminate BasicOntologyNetwork String id = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ); //TODO eliminate BasicOntologyNetwork String pid = ((BasicOntologyNetwork)on).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
if ( pid == null ) pid = id; else pid = id+" ("+pid+")"; if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
if ( sel != null && sel.equals( id ) ){ if ( sel != null && sel.equals( id ) ){
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>"; msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
...@@ -498,11 +477,89 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -498,11 +477,89 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} }
msg += "</select><br />"; msg += "</select><br />";
msg += "<input type=\"submit\" name=\"action\" value=\"Invert\" /> "; msg += "<input type=\"submit\" name=\"invert\" value=\"Invert\" /> ";
msg += "<input type=\"submit\" name=\"action\" value=\"Compose\"/> "; //msg += "<input type=\"submit\" name=\"compose\" value=\"Compose\"/> ";
msg += "<input type=\"checkbox\" name=\"new\" /> New "; //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") ){ } 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("") ) { } else if ( perf.equals("") ) {
msg = "<h1>Ontology network commands</h1>"; msg = "<h1>Ontology network commands</h1>";
...@@ -512,6 +569,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -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=\"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=\"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=\"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=\"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=\"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>"; 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 { ...@@ -667,7 +725,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
if ( answer instanceof ErrorMsg ) { if ( answer instanceof ErrorMsg ) {
msg = testErrorMessages( answer, params, eSource ); msg = testErrorMessages( answer, params, eSource );
} else { } else {
msg = "<h1>Alignment trimed</h1>"; msg = "<h1>Alignment trimmed</h1>";
msg += displayAnswer( answer, params ); msg += displayAnswer( answer, params );
} }
} }
...@@ -1021,7 +1079,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile { ...@@ -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=\"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 += "<td><form action=\"metadata\"><input type=\"hidden\" name=\"id\" value=\""+answer.getContent()+"\"/><input type=\"submit\" name=\"action\" value=\"Metadata\"/></form></td>";
result += "</tr></table>"; 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(); result = answer.HTMLRESTString();
} }
} else { } else {
......
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