From f1b20101297a28526a936987b091a914c61cdc06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=A9r=C3=B4me=20Euzenat?= <Jerome.Euzenat@inria.fr>
Date: Mon, 20 Aug 2012 14:55:23 +0000
Subject: [PATCH] - improved the SILK output (id, Filter, DataSource,
LinkageRules)
---
.../impl/renderer/SILKRendererVisitor.java | 93 +++++++++++++++----
1 file changed, 73 insertions(+), 20 deletions(-)
diff --git a/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java b/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
index a48a30ad..d508d698 100644
--- a/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
+++ b/src/fr/inrialpes/exmo/align/impl/renderer/SILKRendererVisitor.java
@@ -28,7 +28,10 @@ import org.semanticweb.owl.align.AlignmentVisitor;
import org.semanticweb.owl.align.Cell;
import org.semanticweb.owl.align.Relation;
+import fr.inrialpes.exmo.ontowrap.Ontology;
+
import fr.inrialpes.exmo.align.impl.Namespace;
+import fr.inrialpes.exmo.align.impl.BasicAlignment;
import fr.inrialpes.exmo.align.impl.edoal.Expression;
import java.net.URI;
@@ -48,6 +51,9 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
private boolean ignoreerrors = false;
private boolean blanks = false;
private boolean weakens = false;
+ private String threshold = "";
+ private String limit = "";
+ private Random rand;
private static Namespace DEF = Namespace.ALIGNMENT;
@@ -74,10 +80,17 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
weakens = true;
if ( p.getProperty( "ignoreerrors" ) != null && !p.getProperty( "ignoreerrors" ).equals("") )
ignoreerrors = true;
+ if ( p.getProperty( "silkthreshold" ) != null && !p.getProperty( "silkthreshold" ).equals("") ) {
+ threshold = " threshold=\""+p.getProperty( "silkthreshold" )+"\"";
+ }
+ if ( p.getProperty( "silklimit" ) != null && !p.getProperty( "silklimit" ).equals("") ) {
+ limit = " limit=\""+p.getProperty( "silklimit" )+"\"";
+ }
if ( p.getProperty( "indent" ) != null )
INDENT = p.getProperty( "indent" );
if ( p.getProperty( "newline" ) != null )
NL = p.getProperty( "newline" );
+ rand = new Random( System.currentTimeMillis() );
}
public void visit(Alignment align) throws AlignmentException {
@@ -108,7 +121,7 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
}
if ( embedded == false ) {
writer.print("<?xml version='1.0' encoding='utf-8");
- writer.print("' standalone='no'?>"+NL);
+ writer.print("' standalone='no'?>"+NL+NL);
}
indentedOutputln("<SILK>");
increaseIndent();
@@ -125,6 +138,17 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
indentedOutputln("</Prefixes>"+NL);
indentedOutputln("<DataSources>");
increaseIndent();
+ indentedOutputln("<!-- These may have to be edited to proper data sources -->");
+ if ( align instanceof BasicAlignment ) {
+ printOntology( ((BasicAlignment)align).getOntologyObject1(), "source" );
+ } else {
+ printBasicOntology( align.getOntology1URI(), align.getFile1(), "source" );
+ }
+ if ( align instanceof BasicAlignment ) {
+ printOntology( ((BasicAlignment)align).getOntologyObject2(), "target" );
+ } else {
+ printBasicOntology( align.getOntology2URI(), align.getFile2(), "target" );
+ }
decreaseIndent();
indentedOutputln("</DataSources>"+NL);
indentedOutputln("<Interlinks>");
@@ -134,19 +158,34 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
indentedOutputln("</Interlinks>");
decreaseIndent();
writer.print("</SILK>"+NL);
- }
-
- public void visit(Cell cell) throws AlignmentException {
+ }
+
+ private void printBasicOntology ( URI u, URI f, String function ) {
+ indentedOutput("<DataSource id=\""+function+"\" type=\"file\">"+NL);
+ increaseIndent();
+ if ( f != null ) {
+ indentedOutputln("<Param name=\"file\" value=\""+f+"\" />");
+ } else {
+ indentedOutputln("<Param name=\"file\" value=\""+u+"\" />");
+ }
+ indentedOutputln("<Param name=\"format\" value=\"RDF/XML\" />");
+ decreaseIndent();
+ indentedOutputln("</DataSource>");
+ }
+
+ public void printOntology( Ontology onto, String function ) {
+ URI u = onto.getURI();
+ URI f = onto.getFile();
+ printBasicOntology( u, f, function );
+ }
+
+ public void visit( Cell cell ) throws AlignmentException {
if ( subsumedInvocableMethod( this, cell, Cell.class ) ) return;
// default behaviour
this.cell = cell;
- // JE: must be improved because this is an URI
- String id = cell.getId();
- if ( id == null || id.equals("") ){
- Random rand = new Random(System.currentTimeMillis());
- id = "RandomId"+Math.abs(rand.nextInt(1000));
- }
+ // JE: cannot use Cell id because it is an URI and not an id
+ String id = "RandomId"+Math.abs( rand.nextInt(100000) );
URI u1 = cell.getObject1AsURI(alignment);
URI u2 = cell.getObject2AsURI(alignment);
@@ -171,35 +210,49 @@ public class SILKRendererVisitor extends GraphPatternRendererVisitor implements
tempList = new ArrayList<String>(getCondition());
listCond2 = new ArrayList<String>(tempList);
- // JE: The link id should be either the cell id or a gensym
indentedOutputln("<Interlink id=\""+id+"\">");
increaseIndent();
indentedOutputln("<LinkType>owl:sameAs</LinkType>");
- indentedOutputln("<SourceDataSet datasource=\"\"" + " var=\"s\">");
+ indentedOutputln("<SourceDataSet dataSource=\"source\"" + " var=\"s\">");
increaseIndent();
indentedOutputln("<RestrictTo>");
-
+ increaseIndent();
indentedOutput(listBGP1.get(listBGP1.size()-1));
-
+ decreaseIndent();
indentedOutputln("</RestrictTo>");
decreaseIndent();
indentedOutputln("</SourceDataSet>");
-
- indentedOutputln("<TargetDataSet datasource=\"\"" + " var=\"x\">");
+
+ indentedOutputln("<TargetDataSet dataSource=\"target\"" + " var=\"x\">");
increaseIndent();
indentedOutputln("<RestrictTo>");
-
+ increaseIndent();
indentedOutput(listBGP2.get(listBGP2.size()-1));
-
+ decreaseIndent();
indentedOutputln("</RestrictTo>");
decreaseIndent();
- indentedOutputln("</TargetDataSet>"+NL);
+ indentedOutputln("</TargetDataSet>");
+ // This should certainly be specified in the EDOAL
indentedOutputln("<LinkageRule>");
increaseIndent();
+ indentedOutputln("<Compare metric=\"levenshtein\" threshold=\".5\">");
+ increaseIndent();
+ indentedOutputln("<TransformInput function=\"stripUriPrefix\">");
+ increaseIndent();
+ indentedOutputln("<Input path=\"?s\" />");
+ decreaseIndent();
+ indentedOutputln("</TransformInput>");
+ indentedOutputln("<TransformInput function=\"stripUriPrefix\">");
+ increaseIndent();
+ indentedOutputln("<Input path=\"?x\" />");
+ decreaseIndent();
+ indentedOutputln("</TransformInput>");
+ decreaseIndent();
+ indentedOutputln("</Compare>");
decreaseIndent();
indentedOutputln("</LinkageRule>");
- indentedOutputln("<Filter />");
+ indentedOutputln("<Filter"+threshold+limit+" />");
indentedOutputln("<Outputs>");
increaseIndent();
indentedOutputln("<Output type=\"file\">");
--
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