From 9cc84d160fa47d88e7d3f8a267957ced8ad261c6 Mon Sep 17 00:00:00 2001
From: Luz-Maria Priego <lpriego2003@hotmail.com>
Date: Mon, 19 May 2014 16:20:48 +0000
Subject: [PATCH] implemented Available Networks functionality
---
.../align/service/AServProtocolManager.java | 131 +++++++++++++++---
.../exmo/align/service/HTMLAServProfile.java | 118 +++++++++++-----
.../exmo/align/service/HTTPTransport.java | 25 ++++
.../align/service/msg/OntologyNetworkId.java | 2 +-
4 files changed, 214 insertions(+), 62 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
index f43ba22e..36239172 100644
--- a/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
+++ b/src/fr/inrialpes/exmo/align/service/AServProtocolManager.java
@@ -91,7 +91,9 @@ import java.net.URI;
import java.net.URL;
import java.net.JarURLConnection;
import java.net.URISyntaxException;
+import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Set;
import java.util.HashSet;
import java.util.Collection;
@@ -226,12 +228,12 @@ public class AServProtocolManager implements Service {
public Set<Alignment> networkAlignmentUri(String uri) {
OntologyNetwork noo = null;
- try {
- noo = alignmentCache.getOntologyNetwork(uri);
- } catch (AlignmentException e) {
- e.printStackTrace();
- }
- return ((BasicOntologyNetwork) noo).getAlignments();
+ try {
+ noo = alignmentCache.getOntologyNetwork(uri);
+ } catch (AlignmentException e) {
+ e.printStackTrace();
+ }
+ return ((BasicOntologyNetwork) noo).getAlignments();
}
public Collection<Alignment> alignments( URI uri1, URI uri2 ) {
@@ -1221,29 +1223,31 @@ public class AServProtocolManager implements Service {
try {
noo = (BasicOntologyNetwork) BasicOntologyNetwork.read( name );
logger.trace(" Ontology network parsed");
- } catch (Exception e) {
- return new UnreachableOntologyNetwork( params, newId(), serverId, name );
- }
+ } catch (Exception e) {
+ return new UnreachableOntologyNetwork( params, newId(), serverId, name );
+ }
// 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 );
- }
+ noo.setExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY, pretty );
+ }
// register it
String id = alignmentCache.recordNewNetwork( noo, true );
logger.debug(" Ontology network loaded, id: {} total ontologies: {} total alignments: {}",id, noo.getOntologies().size(),noo.getAlignments().size());
- //=== The alignment has the id of the source file (e.g. file:///path/FileName.rdf)
- for ( Alignment al : noo.getAlignments() ) {
- alignmentCache.recordNewAlignment( al, true );
+ //=== The alignment has the id of the source file (e.g. file:///path/FileName.rdf)
+ Set<Alignment> networkAlignments = networkAlignmentUri(id);
+ for (Alignment al : networkAlignments) {
+ String idAl = alignmentCache.recordNewAlignment( al, true );
}
+
return new OntologyNetworkId( params, newId(), serverId, id ,pretty );
}
public Message renderonet(Properties params) {
-
+ //rdf render
OntologyNetwork noo = null;
noo = new BasicOntologyNetwork();
String id = params.getProperty( "id" );
@@ -1281,7 +1285,43 @@ public class AServProtocolManager implements Service {
}
-
+ public Message renderHTMLNetwork( Properties params ){
+ // Retrieve the alignment
+ String result = new String();
+ String id = params.getProperty( "id" );
+ //String id = idON;
+ BasicOntologyNetwork noo = null;
+ try {
+ logger.trace("Network sought for {}", id);
+ noo = (BasicOntologyNetwork) alignmentCache.getOntologyNetwork(id);
+ logger.trace("Network found");
+ } catch (Exception e) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+ result = "<h1>" + id + "</h1>";
+
+ result += "<table border=\"0\">\n";
+ result += "<h2>Ontologies of the Network</h2>\n";
+ Collection<URI> networkOntology = networkOntologyUri(id);
+ result += "<p><tr><th><b>Total ontologies: </b>" + networkOntology.size() + "</th></tr></p>";
+ result += "<table>\n";
+ for ( URI onto : networkOntology ) {
+ result += "<tr><td>" + "<a href=\"" + onto.toString() +"\">"+ onto.toString() + "</a>" + "</td></tr>\n";
+ }
+ result += "</table>\n";
+
+ result += "<h2>Alignments of the Network</h2>\n";
+ Set<Alignment> networkAlignments = networkAlignmentUri(id);
+ result += "<table>\n";
+ result += "<p><tr><th><b>Total alignments: </b>" + networkAlignments.size() + "</th></tr></p>";
+ for (Alignment al : networkAlignments) {
+ String idAl = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pidAl = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pidAl == null ) pidAl = idAl; else pidAl = idAl+" ("+pidAl+")";
+ result += "<tr><td>" + "<a href=\""+idAl+"\">"+pidAl+"</a>" + "</td></tr>\n";
+ }
+ return new RenderedAlignment( params, newId(), serverId, result );
+ }
public boolean storedOntologyNetwork( Properties params ) {
// Retrieve the ontology network
@@ -1335,9 +1375,12 @@ public class AServProtocolManager implements Service {
}
return (Message)null;
}
+
- public Message alignonet( Properties params ) {
- Message result = 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();) {
@@ -1355,16 +1398,58 @@ public class AServProtocolManager implements Service {
Collection<URI> networkOntologyA = networkOntologyUri(id);
Collection<URI> networkOntologyB = networkOntologyUri(id);
- for ( URI ontoA : networkOntologyA ) {
- for ( URI ontoB : networkOntologyB ) {
- result = retrieveAlignmentON( params ,ontoA, ontoB);
- if ( result != null ) return result;
+
+ // 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 (Message)null;
+
+ return result;
}
+
+ /* TO VERIFY
+ public Message alignonet( Properties params ) {
+
+ //parameters: onID, method, reflexive, symmetric
+ OntologyNetwork noo = null;
+ Boolean reflexive = false;
+ Boolean symmetric = false;
+ String id = params.getProperty("id");
+ String method = params.getProperty("method");
+ if (params.getProperty("reflexive") != null) reflexive = true;
+ if (params.getProperty("symmetric") != null) symmetric = true;
+
+ try {
+ noo = alignmentCache.getOntologyNetwork( id );
+ } catch (AlignmentException e1) {
+ return new UnknownOntologyNetwork( params, newId(), serverId,id );
+ }
+
+ try {
+ ((BasicOntologyNetwork) noo).match(method, reflexive, symmetric);
+ } 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());
+ return new OntologyNetworkId( params, newId(), serverId, id,
+ ((BasicOntologyNetwork) noo).getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY ));
+
+ }
+
+ */
+
public Message listNetworkOntology( Properties params ) { //not UsED??
String result = "";
diff --git a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
index 8cf64653..fddd19dd 100644
--- a/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
+++ b/src/fr/inrialpes/exmo/align/service/HTMLAServProfile.java
@@ -46,6 +46,7 @@ import java.io.ByteArrayInputStream;
import java.io.OutputStream;
import java.io.BufferedInputStream;
import java.io.FileOutputStream;
+import java.util.List;
import java.util.Locale;
import java.util.Set;
import java.util.TimeZone;
@@ -195,35 +196,38 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
logger.trace( "ONTONET[{}]", perf);
String msg = "";
String eSource = "on";
- if ( perf.equals("prmlistonet") ){
- URI uriON = null;
- String uON = params.getProperty("uri");
- try {
- if ( uON != null && !uON.equals("all") ) uriON = new URI( uON );
- } catch ( URISyntaxException usex ) {
- logger.debug( "IGNORED Invalid URI parameter", usex );
- };
-
- Collection<URI> ontologyNetworksURI = manager.ontologyNetworkUris();
+ if ( perf.equals("listnetwork") ){
+
+ Collection<OntologyNetwork> ontologyNetworks = manager.ontologyNetworks();
+ BasicOntologyNetwork noo = null;
+ String id = "";
+ String pid = "";
msg = "<h1>Available networks</h1>";
- msg += "<form action=\"listNetOnto\">";
- msg += "Network: <select name=\"uri\"><option value=\"all\">all</option>";
- if ( uriON == null ) msg += " selected=\"1\"";
- for ( URI onet : ontologyNetworksURI ) {
- msg += "<option";
- if ( onet.equals( uriON ) ) msg += " selected =\"1\"";
- msg += " value=\""+onet+"\">"+onet+"</option>";
+ //msg += "<form action=\"listNetOnto\"><ul compact=\"1\">";
+ msg += "<form action=\"listnetwork\"><ul compact=\"1\">";
+ for ( OntologyNetwork oNetwork : ontologyNetworks ) {
+ noo = (BasicOntologyNetwork) oNetwork;
+ id = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ pid = noo.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<li><a href=\"" + id +"\">" + pid + "</a></li>";
+ }
+ msg += "</ul></form>";
+
+ } else if ( perf.equals("listNetOnto") ){ //TODO eliminate this
+ //Message answer = manager.renderHTMLON( params );
+ Message answer = manager.renderHTMLNetwork( params ); // "http://localhost:8089/onid/1400170347760/525" );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ return answer.getContent();
}
- msg += "</select>";
- msg += " <input type=\"submit\" value=\"List ontologies\"/></form><ul compact=\"1\">";
- //msg += "<table><tr><td><input type=\"submit\" value=\"List ontologies\"name=\"listNetOnto\"/></form>";
- //msg += "<input type=\"submit\" value=\"List alignments\"/ name=\"listNetAlig\"></form></td></tr></table/>";
-
- } else if ( perf.equals("listNetOnto") ){
+
+ } else if ( perf.equals("listNetOnto2") ){
msg = "<h1>Ontologies of the Network</h1>";
msg += "<form action=\"listNetAlig\">";
- String uriON = params.getProperty("uri"); //send as parameter uriON for listNetAlig
+ String uriON = params.getProperty("uriON"); //send as parameter uriON for listNetAlig
int numOnto = 0;
Collection<URI> networkOntology = manager.networkOntologyUri(uriON);
msg += "<p>" + uriON + " ";
@@ -358,32 +362,68 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<option selected=\"1\" value=\""+id+"\">"+pid+"</option>";
} else { msg += "<option value=\""+id+"\">"+pid+"</option>";}
}
- msg += "<!--input type=\"submit\" name=\"action\" value=\"Find\"/>";
- msg += "<br /-->Methods: <select name=\"method\">";
+ 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>";
}
+ msg += "</select><br /><br />";
- msg += "</select><br />";
- msg += "<input type=\"checkbox\" name=\"reflexive\" /> Reflexive ";
+ msg += "Pretty name: <input type=\"text\" name=\"pretty\" size=\"80\"/><br />";
+ msg += " <input type=\"checkbox\" name=\"force\" /> Force <input type=\"checkbox\" name=\"async\" /> Asynchronous<br />";
+ msg += "Additional parameters:<br /><input type=\"text\" name=\"paramn1\" size=\"15\"/> = <input type=\"text\" name=\"paramv1\" size=\"65\"/><br /><input type=\"text\" name=\"paramn2\" size=\"15\"/> = <input type=\"text\" name=\"paramv2\" size=\"65\"/><br /><input type=\"text\" name=\"paramn3\" size=\"15\"/> = <input type=\"text\" name=\"paramv3\" size=\"65\"/><br /><input type=\"text\" name=\"paramn4\" size=\"15\"/> = <input type=\"text\" name=\"paramv4\" size=\"65\"/>";
+
+ msg += "<br /><input type=\"checkbox\" name=\"reflexive\" /> Reflexive ";
msg += "<input type=\"checkbox\" name=\"symmetric\" /> Symmetric ";
msg += "<input type=\"checkbox\" name=\"new\" /> New ";
- msg += "<br /><input type=\"submit\" name=\"action\" value=\"Match\"/> ";
+ msg += "<br /><br /><input type=\"submit\" name=\"action\" value=\"Match\"/> ";
+ msg += "</form>";
} else if ( perf.equals("matchonet") ) {
+
// DO MATCHING
- Message answer = manager.alignonet( params );
- if ( answer instanceof ErrorMsg ) {
- msg = testErrorMessages( answer, params, eSource );
- } else {
+ List<Message> answer = manager.alignonet( params );
msg = "<h1>Network Alignments results</h1>";
- msg += displayAnswer( answer, params );
- }
+ 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.alignonet( params );
+ if ( answer instanceof ErrorMsg ) {
+ msg = testErrorMessages( answer, params, eSource );
+ } else {
+ //return answer.getContent();
+ msg = "<h1>Network alignments results</h1>";
+
+ //String idON = "http://localhost:8089/onid/1400144735513/788";
+ Set<Alignment> networkAlignments = manager.networkAlignmentUri(idON);
+ msg += "<p> Network ID: <a href=\""+idON+"\">"+idON+"</a></p>";
+ msg += "<p><tr><th><b>Total alignments: </b>" + networkAlignments.size() + "</th></tr></p>";
+ msg += "<ul>";
+ for ( Alignment al : networkAlignments ) {
+ String id = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.ID );
+ String pid = al.getExtension( Namespace.ALIGNMENT.uri, Annotations.PRETTY );
+ if ( pid == null ) pid = id; else pid = id+" ("+pid+")";
+ msg += "<li><a href=\""+id+"\">"+pid+"</a></li>";
+ }
+ msg += "</ul>";
+ }
+ */
} else if ( perf.equals("prmretreiveonet") ){
-
String sel = params.getProperty("id");
msg = "<h1>Retrieve ontology network</h1><form action=\"retrieveonet\">";
msg += "Network: <select name=\"id\">";
@@ -436,7 +476,8 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
} else if ( perf.equals("") ) {
msg = "<h1>Ontology Network commands</h1>";
- msg += "<form action=\"prmlistonet\"><button title=\"List networks stored in the server\" type=\"submit\">Available networks</button></form>";
+ msg += "<form action=\"../ontonet/listnetwork\"><button title=\"List networks stored in the server\" type=\"submit\">Available networks</button></form>";
+ // msg += "<form action=\"prmlistonet\"><button title=\"List networks stored in the server\" type=\"submit\">Available networks</button></form>";
msg += "<form action=\"prmloadonet\"><button title=\"Load a network from a valid source\" type=\"submit\">Load a network</button></form>";
msg += "<form action=\"prmstoreonet\"><button title=\"Store a network in the server\" type=\"submit\">Store network</button></form>";
msg += "<form action=\"prmmatchonet\"><button title=\"Match an ontology network\" type=\"submit\">Match network </button></form>";
@@ -455,7 +496,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
* uses the protocol but offers user-targeted interaction
*/
public String htmlAnswer( String uri, String perf, Properties header, Properties params ) {
- //logger.trace("HTML[{}]", perf );
+ logger.trace("HTML[{}]", perf );
// REST get
String msg = "";
String eSource = "al";
@@ -512,6 +553,7 @@ public class HTMLAServProfile implements AlignmentServiceProfile {
msg += "<li><a href=\""+id+"\">"+pid+"</a></li>";
}
msg += "</ul>";
+
} else if ( perf.equals("manalignments") ){ // Manage alignments
msg = "<h1>Available alignments</h1><ul compact=\"1\">";
for ( Alignment al : manager.alignments() ) {
diff --git a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
index fba20953..c6204208 100644
--- a/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
+++ b/src/fr/inrialpes/exmo/align/service/HTTPTransport.java
@@ -319,6 +319,8 @@ public class HTTPTransport {
if ( oper.equals( "alid" ) ){ // Asks for an alignment by URI
return returnAlignment( uri, returnType );
+ } else if ( oper.equals( "onid" ) ){ // Asks for a network by URI
+ return returnNetwork( uri, returnType );
} else if ( oper.equals( "" ) ) {
// SHOULD BE ASSIGNED TO CONTENT NEGOCIATION AS WELL... (DEFAULT IN SERVERS)
//return serveFile( uri, header, new File("."), true );
@@ -366,6 +368,29 @@ public class HTTPTransport {
}
}
+
+ /**
+ * Returns the network in HTML format
+ */
+
+ public HTTPResponse returnNetwork( String uri, String mimeType ) {
+ Properties params = new Properties();
+ params.setProperty( "id", manager.serverURL()+uri );
+ if ( returnType == HTTPResponse.MIME_JSON ) { // YES string compared by ==.
+ params.setProperty( "method", "fr.inrialpes.exmo.align.impl.renderer.JSONRendererVisitor" );
+ } else if ( returnType == HTTPResponse.MIME_RDFXML ) {
+ params.setProperty( "method", "fr.inrialpes.exmo.align.impl.renderer.RDFRendererVisitor" );
+ } else {
+ params.setProperty( "method", "fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor" );
+ }
+ logger.trace( "Bloody Network URI : {}", manager.serverURL()+uri);
+ Message answer = manager.renderHTMLNetwork(params);
+ if ( answer instanceof ErrorMsg ) {
+ return new HTTPResponse( HTTPResponse.HTTP_NOTFOUND, HTTPResponse.MIME_PLAINTEXT, "Alignment server: unknown network : "+answer.getContent() );
+ } else {
+ return new HTTPResponse( HTTPResponse.HTTP_OK, mimeType, answer.getContent() );
+ }
+ }
// ===============================================
// Util
diff --git a/src/fr/inrialpes/exmo/align/service/msg/OntologyNetworkId.java b/src/fr/inrialpes/exmo/align/service/msg/OntologyNetworkId.java
index d4c80c16..c44c7438 100644
--- a/src/fr/inrialpes/exmo/align/service/msg/OntologyNetworkId.java
+++ b/src/fr/inrialpes/exmo/align/service/msg/OntologyNetworkId.java
@@ -56,7 +56,7 @@ public class OntologyNetworkId extends Success {
}
};
public String HTMLString(){
- //return "Alignment ID: <a href=\"../html/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+getContent()+"\">"+getPretty(getContent())+"</a> ";
+ //return "Ontology Network ID: <a href=\"../ontonet/retrieve?method=fr.inrialpes.exmo.align.impl.renderer.HTMLRendererVisitor&id="+getContent()+"\">"+getPretty(getContent())+"</a> ";
return "Ontology Network ID: <a href=\""+getContent()+"\">"+getPretty(getContent())+"</a> ";
}
public String HTMLRESTString(){
--
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