Java tutorial
/****************************************************************************** * Copyright 2013-2014 LASIGE * * * * Licensed under the Apache License, Version 2.0 (the "License"); you may * * not use this file except in compliance with the License. You may obtain a * * copy of the License at http://www.apache.org/licenses/LICENSE-2.0 * * * * Unless required by applicable law or agreed to in writing, software * * distributed under the License is distributed on an "AS IS" BASIS, * * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * * See the License for the specific language governing permissions and * * limitations under the License. * * * ******************************************************************************* * An alignment between two Ontologies, stored both as a list of Mappings and * * as a Table of indexes, and including methods for input and output. * * * * @author Daniel Faria * * @date 12-09-2014 * * @version 2.1 * ******************************************************************************/ package aml.match; import java.io.BufferedReader; import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; import java.io.FileReader; import java.io.PrintWriter; import java.util.Collections; import java.util.Comparator; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Set; import java.util.Vector; import org.apache.commons.lang.StringEscapeUtils; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.Element; import org.dom4j.io.SAXReader; import aml.AML; import aml.ontology.Ontology; import aml.ontology.RelationshipMap; import aml.ontology.URIMap; import aml.settings.MappingRelation; import aml.util.Table2Map; public class Alignment implements Iterable<Mapping> { //Attributes //Term mappings organized in list private Vector<Mapping> maps; //Term mappings organized by source class private Table2Map<Integer, Integer, Mapping> sourceMaps; //Term mappings organized by target class private Table2Map<Integer, Integer, Mapping> targetMaps; // private boolean internal; //Constructors /** * Creates a new empty Alignment */ public Alignment() { maps = new Vector<Mapping>(0, 1); sourceMaps = new Table2Map<Integer, Integer, Mapping>(); targetMaps = new Table2Map<Integer, Integer, Mapping>(); internal = false; } /** * Creates a new empty Alignment */ public Alignment(boolean internal) { maps = new Vector<Mapping>(0, 1); sourceMaps = new Table2Map<Integer, Integer, Mapping>(); targetMaps = new Table2Map<Integer, Integer, Mapping>(); this.internal = internal; } /** * Reads an Alignment from an input file * @param file: the path to the input file */ public Alignment(String file) throws Exception { this(); if (file.endsWith(".rdf")) loadMappingsRDF2(file); else if (file.endsWith(".tsv")) loadMappingsTSV(file); else throw new Exception("Unrecognized alignment format!"); } /** * Creates a new Alignment that is a copy of the input alignment * @param a: the Alignment to copy */ public Alignment(Alignment a) { this(); addAll(a); } //Public Methods /** * Adds a new Mapping to the alignment if it is non-redundant * Otherwise, updates the similarity of the already present Mapping * to the maximum similarity of the two redundant Mappings * @param sourceId: the index of the source class to add to the alignment * @param targetId: the index of the target class to add to the alignment * @param sim: the similarity between the classes */ public void add(int sourceId, int targetId, double sim) { //Unless the alignment is internal, we can't have a mapping //between entities with the same id (which corresponds to URI) if (!internal && sourceId == targetId) return; //Construct the Mapping Mapping m = new Mapping(sourceId, targetId, sim, MappingRelation.EQUIVALENCE); //If it isn't listed yet, add it if (!sourceMaps.contains(sourceId, targetId)) { maps.add(m); sourceMaps.add(sourceId, targetId, m); targetMaps.add(targetId, sourceId, m); } //Otherwise update the similarity else { m = sourceMaps.get(sourceId, targetId); if (m.getSimilarity() < sim) m.setSimilarity(sim); if (!m.getRelationship().equals(MappingRelation.EQUIVALENCE)) m.setRelationship(MappingRelation.EQUIVALENCE); } } public void add(int sourceId, int targetId, double sim, List<SubMapping> s) { //Unless the alignment is internal, we can't have a mapping //between entities with the same id (which corresponds to URI) if (!internal && sourceId == targetId) return; //Construct the Mapping Mapping m = new Mapping(sourceId, targetId, sim, MappingRelation.EQUIVALENCE); m.setSubMap(s); //If it isn't listed yet, add it if (!sourceMaps.contains(sourceId, targetId)) { maps.add(m); sourceMaps.add(sourceId, targetId, m); targetMaps.add(targetId, sourceId, m); } //Otherwise update the similarity else { m = sourceMaps.get(sourceId, targetId); if (m.getSimilarity() < sim) m.setSimilarity(sim); if (!m.getRelationship().equals(MappingRelation.EQUIVALENCE)) m.setRelationship(MappingRelation.EQUIVALENCE); } } /** * Adds a new Mapping to the alignment if it is non-redundant * Otherwise, updates the similarity of the already present Mapping * to the maximum similarity of the two redundant Mappings * @param sourceId: the index of the source class to add to the alignment * @param targetId: the index of the target class to add to the alignment * @param sim: the similarity between the classes * @param r: the mapping relationship between the classes */ public void add(int sourceId, int targetId, double sim, MappingRelation r) { //We can't have a mapping between entities with the same URI if (sourceId == targetId) return; //Construct the Mapping Mapping m = new Mapping(sourceId, targetId, sim, r); //If it isn't listed yet, add it if (!sourceMaps.contains(sourceId, targetId)) { maps.add(m); sourceMaps.add(sourceId, targetId, m); targetMaps.add(targetId, sourceId, m); } //Otherwise update the similarity else { m = sourceMaps.get(sourceId, targetId); if (m.getSimilarity() < sim) m.setSimilarity(sim); if (!m.getRelationship().equals(r)) m.setRelationship(r); } } public void add(int sourceId, int targetId, double sim, MappingRelation r, List<SubMapping> s) { //We can't have a mapping between entities with the same URI if (sourceId == targetId) return; //Construct the Mapping Mapping m = new Mapping(sourceId, targetId, sim, r); m.setSubMap(s); //If it isn't listed yet, add it if (!sourceMaps.contains(sourceId, targetId)) { maps.add(m); sourceMaps.add(sourceId, targetId, m); targetMaps.add(targetId, sourceId, m); } //Otherwise update the similarity else { m = sourceMaps.get(sourceId, targetId); if (m.getSimilarity() < sim) m.setSimilarity(sim); if (!m.getRelationship().equals(r)) m.setRelationship(r); } } /** * Adds a clone of the given Mapping to the alignment if it is non-redundant * Otherwise, updates the similarity of the already present Mapping * to the maximum similarity of the two redundant Mappings * @param m: the Mapping to add to the alignment */ public void add(Mapping m) { add(m.getSourceId(), m.getTargetId(), m.getSimilarity(), m.getRelationship(), m.getSubMappings()); } /** * Adds all Mappings in a to this Alignment * @param a: the Alignment to add to this Alignment */ public void addAll(Alignment a) { addAll(a.maps); } /** * Adds all Mappings in the given list to this Alignment * @param maps: the list of Mappings to add to this Alignment */ public void addAll(List<Mapping> maps) { for (Mapping m : maps) add(m); } /** * Adds all Mappings in a to this Alignment as long as * they don't conflict with any Mapping in a * @param a: the Alignment to add to this Alignment */ public void addAllNonConflicting(Alignment a) { Vector<Mapping> nonConflicting = new Vector<Mapping>(); for (Mapping m : a.maps) if (!this.containsConflict(m)) nonConflicting.add(m); addAll(nonConflicting); } /** * Adds all Mappings in a to this Alignment as long as * they don't conflict with any Mapping in a * @param a: the Alignment to add to this Alignment */ public void addAllOneToOne(Alignment a) { a.sort(); for (Mapping m : a.maps) if (!this.containsConflict(m)) add(m); } /** * @return the average cardinality of this alignment */ public double cardinality() { double cardinality = 0.0; Set<Integer> sources = sourceMaps.keySet(); for (Integer i : sources) cardinality += sourceMaps.keySet(i).size(); Set<Integer> targets = targetMaps.keySet(); for (Integer i : targets) cardinality += targetMaps.keySet(i).size(); cardinality /= sources.size() + targets.size(); return cardinality; } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return whether the alignment contains a Mapping that is ancestral to the given pair of classes * (i.e. includes one ancestor of sourceId and one ancestor of targetId) */ public boolean containsAncestralMapping(int sourceId, int targetId) { AML aml = AML.getInstance(); RelationshipMap rels = aml.getRelationshipMap(); Set<Integer> sourceAncestors = rels.getAncestors(sourceId); Set<Integer> targetAncestors = rels.getAncestors(targetId); for (Integer sa : sourceAncestors) { Set<Integer> over = getSourceMappings(sa); for (Integer ta : targetAncestors) if (over.contains(ta)) return true; } return false; } /** * @param m: the Mapping to check in the alignment * @return whether the Alignment contains a Mapping that conflicts with the given * Mapping and has a higher similarity */ public boolean containsBetterMapping(Mapping m) { int source = m.getSourceId(); int target = m.getTargetId(); double sim = m.getSimilarity(); if (containsSource(source)) { Set<Integer> targets = sourceMaps.keySet(source); for (Integer i : targets) if (getSimilarity(source, i) > sim) return true; } if (containsTarget(target)) { Set<Integer> sources = targetMaps.keySet(target); for (Integer i : sources) if (getSimilarity(i, target) > sim) return true; } return false; } /** * @param classId: the index of the class to check in the alignment * @return whether the Alignment contains a Mapping with that class * (either as a source or as a target class) */ public boolean containsClass(int classId) { return containsSource(classId) || containsTarget(classId); } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return whether the Alignment contains a Mapping for sourceId or for targetId */ public boolean containsConflict(int sourceId, int targetId) { return containsSource(sourceId) || containsTarget(targetId); } /** * @param m: the Mapping to check in the alignment * @return whether the Alignment contains a Mapping involving either class in m */ public boolean containsConflict(Mapping m) { return containsConflict(m.getSourceId(), m.getTargetId()); } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return whether the alignment contains a Mapping that is descendant of the given pair of classes * (i.e. includes one descendant of sourceId and one descendant of targetId) */ public boolean containsDescendantMapping(int sourceId, int targetId) { AML aml = AML.getInstance(); RelationshipMap rels = aml.getRelationshipMap(); Set<Integer> sourceDescendants = rels.getDescendants(sourceId); Set<Integer> targetDescendants = rels.getDescendants(targetId); for (Integer sa : sourceDescendants) { Set<Integer> over = getSourceMappings(sa); for (Integer ta : targetDescendants) if (over.contains(ta)) return true; } return false; } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return whether the Alignment contains a Mapping between sourceId and targetId */ public boolean containsMapping(int sourceId, int targetId) { return sourceMaps.contains(sourceId, targetId); } /** * @param m: the Mapping to check in the alignment * @return whether the Alignment contains a Mapping equivalent to m */ public boolean containsMapping(Mapping m) { return sourceMaps.contains(m.getSourceId(), m.getTargetId()); } /** * @param lm: the List of Mapping to check in the alignment * @return whether the Alignment contains all the Mapping listed in m */ public boolean containsMappings(List<Mapping> lm) { for (Mapping m : lm) if (!containsMapping(m)) return false; return true; } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return whether the alignment contains a Mapping that is parent to the * given pair of classes on one side only */ public boolean containsParentMapping(int sourceId, int targetId) { AML aml = AML.getInstance(); RelationshipMap rels = aml.getRelationshipMap(); Set<Integer> sourceAncestors = rels.getParents(sourceId); Set<Integer> targetAncestors = rels.getParents(targetId); for (Integer sa : sourceAncestors) if (containsMapping(sa, targetId)) return true; for (Integer ta : targetAncestors) if (containsMapping(sourceId, ta)) return true; return false; } /** * @param sourceId: the index of the source class to check in the alignment * @return whether the Alignment contains a Mapping for sourceId */ public boolean containsSource(int sourceId) { return sourceMaps.contains(sourceId); } /** * @param targetId: the index of the target class to check in the alignment * @return whether the Alignment contains a Mapping for targetId */ public boolean containsTarget(int targetId) { return targetMaps.contains(targetId); } /** * @param a: the Alignment to subtract from this Alignment * @return the Alignment corresponding to the difference between this Alignment and a */ public Alignment difference(Alignment a) { Alignment diff = new Alignment(); for (Mapping m : maps) if (!a.containsMapping(m)) diff.add(m); return diff; } /** * @param ref: the reference Alignment to evaluate this Alignment * @param forGUI: whether the evaluation is for display in the GUI * or for output to the console * @return the evaluation of this Alignment */ public String evaluate(Alignment ref, boolean forGUI) { int found = size(); int correct = 0; int total = 0; int conflict = 0; for (Mapping m : maps) { if (ref.containsMapping(m)) { if (ref.getRelationship(m.getSourceId(), m.getTargetId()).equals(MappingRelation.UNKNOWN)) conflict++; else correct++; } } for (Mapping m : ref) if (!m.getRelationship().equals(MappingRelation.UNKNOWN)) total++; double precision = 1.0 * correct / (found - conflict); String prc = Math.round(precision * 1000) / 10.0 + "%"; double recall = 1.0 * correct / total; String rec = Math.round(recall * 1000) / 10.0 + "%"; double fmeasure = 2 * precision * recall / (precision + recall); String fms = Math.round(fmeasure * 1000) / 10.0 + "%"; if (forGUI) return "Precision: " + prc + "; Recall: " + rec + "; F-measure: " + fms; else return "Precision\tRecall\tF-measure\tFound\tCorrect\tReference\n" + prc + "\t" + rec + "\t" + fms + "\t" + found + "\t" + correct + "\t" + total; } public Double[] evaluateNoPrint(Alignment ref, boolean forGUI) { double found = size(); double correct = 0; double total = 0; double conflict = 0; for (Mapping m : maps) { if (ref.containsMapping(m)) { if (ref.getRelationship(m.getSourceId(), m.getTargetId()).equals(MappingRelation.UNKNOWN)) conflict++; else correct++; } } for (Mapping m : ref) if (!m.getRelationship().equals(MappingRelation.UNKNOWN)) total++; double precision = 1.0 * correct / (found - conflict); double recall = 1.0 * correct / total; double fmeasure = 2 * precision * recall / (precision + recall); return new Double[] { precision, recall, fmeasure, found, correct, total, }; } /** * @param a: the base Alignment to which this Alignment will be compared * @return the gain (i.e. the fraction of new Mappings) of this Alignment * in comparison with the base Alignment */ public double gain(Alignment a) { double gain = 0.0; for (Mapping m : maps) if (!a.containsMapping(m)) gain++; gain /= a.size(); return gain; } /** * @param a: the base Alignment to which this Alignment will be compared * @return the gain (i.e. the fraction of new Mappings) of this Alignment * in comparison with the base Alignment */ public double gainOneToOne(Alignment a) { double sourceGain = 0.0; Set<Integer> sources = sourceMaps.keySet(); for (Integer i : sources) if (!a.containsSource(i)) sourceGain++; sourceGain /= a.sourceCount(); double targetGain = 0.0; Set<Integer> targets = targetMaps.keySet(); for (Integer i : targets) if (!a.containsTarget(i)) targetGain++; targetGain /= a.targetCount(); return Math.min(sourceGain, targetGain); } /** * @param index: the index of the Mapping to return in the list of Mappings * @return the Mapping at the input index (note that the index will change * during sorting) or null if the index falls outside the list */ public Mapping get(int index) { if (index < 0 || index >= maps.size()) return null; return maps.get(index); } /** * @param sourceId: the index of the source class to check in the alignment * @param targetId: the index of the target class to check in the alignment * @return the Mapping between the source and target classes or null if no * such Mapping exists */ public Mapping get(int sourceId, int targetId) { return sourceMaps.get(sourceId, targetId); } /** * @param id1: the index of the first class to check in the alignment * @param targetId: the index of the second class to check in the alignment * @return the Mapping between the classes or null if no such Mapping exists * in either direction */ public Mapping getBidirectional(int id1, int id2) { if (sourceMaps.contains(id1, id2)) return sourceMaps.get(id1, id2); else if (sourceMaps.contains(id2, id1)) return sourceMaps.get(id2, id1); else return null; } /** * @param sourceId: the index of the source class to check in the alignment * @return the index of the target class that best matches source */ public int getBestSourceMatch(int sourceId) { double max = 0; int target = -1; Set<Integer> targets = sourceMaps.keySet(sourceId); for (Integer i : targets) { double sim = getSimilarity(sourceId, i); if (sim > max) { max = sim; target = i; } } return target; } /** * @param targetId: the index of the target class to check in the alignment * @return the index of the source class that best matches target */ public int getBestTargetMatch(int targetId) { double max = 0; int source = -1; Set<Integer> sources = sourceMaps.keySet(targetId); for (Integer i : sources) { double sim = getSimilarity(i, targetId); if (sim > max) { max = sim; source = i; } } return source; } /** * @return the high level Alignment induced from this alignment */ public Alignment getHighLevelAlignment() { AML aml = AML.getInstance(); RelationshipMap rels = aml.getRelationshipMap(); Alignment a = new Alignment(); int total = maps.size(); for (Mapping m : maps) { Set<Integer> sourceAncestors = rels.getHighLevelAncestors(m.getSourceId()); Set<Integer> targetAncestors = rels.getHighLevelAncestors(m.getTargetId()); for (int i : sourceAncestors) { for (int j : targetAncestors) { double sim = a.getSimilarity(i, j) + 1.0 / total; a.add(i, j, sim, MappingRelation.OVERLAP); } } } Alignment b = new Alignment(); for (Mapping m : a) if (m.getSimilarity() >= 0.01) b.add(m); return b; } /** * @param sourceId: the index of the source class * @param targetId: the index of the target class * @return the index of the Mapping between the given classes in * the list of Mappings, or -1 if the Mapping doesn't exist */ public int getIndex(int sourceId, int targetId) { if (sourceMaps.contains(sourceId, targetId)) return maps.indexOf(sourceMaps.get(sourceId, targetId)); else return -1; } /** * @param id1: the index of the first class * @param id2: the index of the second class * @return the index of the Mapping between the given classes in * the list of Mappings (in any order), or -1 if the Mapping doesn't exist */ public int getIndexBidirectional(int id1, int id2) { if (sourceMaps.contains(id1, id2)) return maps.indexOf(sourceMaps.get(id1, id2)); else if (targetMaps.contains(id1, id2)) return maps.indexOf(targetMaps.get(id1, id2)); else return -1; } /** * @param id: the index of the class to check in the alignment * @return the list of all classes mapped to the given class */ public Set<Integer> getMappingsBidirectional(int id) { HashSet<Integer> mappings = new HashSet<Integer>(); if (sourceMaps.contains(id)) mappings.addAll(sourceMaps.keySet(id)); if (targetMaps.contains(id)) mappings.addAll(targetMaps.keySet(id)); return mappings; } /** * @param sourceId: the index of the source class to check in the alignment * @return the index of the target class that best matches source */ public double getMaxSourceSim(int sourceId) { double max = 0; Set<Integer> targets = sourceMaps.keySet(sourceId); for (Integer i : targets) { double sim = getSimilarity(sourceId, i); if (sim > max) max = sim; } return max; } /** * @param targetId: the index of the target class to check in the alignment * @return the index of the source class that best matches target */ public double getMaxTargetSim(int targetId) { double max = 0; Set<Integer> sources = targetMaps.keySet(targetId); for (Integer i : sources) { double sim = getSimilarity(i, targetId); if (sim > max) max = sim; } return max; } /** * @param sourceId: the index of the source class in the alignment * @param targetId: the index of the target class in the alignment * @return the mapping relationship between source and target */ public MappingRelation getRelationship(int sourceId, int targetId) { Mapping m = sourceMaps.get(sourceId, targetId); if (m == null) return null; return m.getRelationship(); } /** * @param sourceId: the index of the source class in the alignment * @param targetId: the index of the target class in the alignment * @return the similarity between source and target */ public double getSimilarity(int sourceId, int targetId) { Mapping m = sourceMaps.get(sourceId, targetId); if (m == null) return 0.0; return m.getSimilarity(); } /** * @param sourceId: the index of the source class to check in the alignment * @return the list of all target classes mapped to the source class */ public Set<Integer> getSourceMappings(int sourceId) { if (sourceMaps.contains(sourceId)) return sourceMaps.keySet(sourceId); return new HashSet<Integer>(); } /** * @return the list of all source classes that have mappings */ public Set<Integer> getSources() { HashSet<Integer> sMaps = new HashSet<Integer>(); sMaps.addAll(sourceMaps.keySet()); return sMaps; } /** * @param targetId: the index of the target class to check in the alignment * @return the list of all source classes mapped to the target class */ public Set<Integer> getTargetMappings(int targetId) { if (targetMaps.contains(targetId)) return targetMaps.keySet(targetId); return new HashSet<Integer>(); } /** * @return the list of all target classes that have mappings */ public Set<Integer> getTargets() { HashSet<Integer> tMaps = new HashSet<Integer>(); tMaps.addAll(targetMaps.keySet()); return tMaps; } /** * @param a: the Alignment to intersect with this Alignment * @return the Alignment corresponding to the intersection between this Alignment and a */ public Alignment intersection(Alignment a) { //Otherwise, compute the intersection Alignment intersection = new Alignment(); for (Mapping m : maps) if (a.containsMapping(m)) intersection.add(m); return intersection; } @Override /** * @return an Iterator over the list of class Mappings */ public Iterator<Mapping> iterator() { return maps.iterator(); } /** * @return the maximum cardinality of this alignment */ public double maxCardinality() { double cardinality; double max = 0.0; Set<Integer> sources = sourceMaps.keySet(); for (Integer i : sources) { cardinality = sourceMaps.keySet(i).size(); if (cardinality > max) max = cardinality; } Set<Integer> targets = targetMaps.keySet(); for (Integer i : targets) { cardinality = targetMaps.keySet(i).size(); if (cardinality > max) max = cardinality; } return max; } /** * Removes the given Mapping from the Alignment * @param m: the Mapping to remove from the Alignment */ public void remove(Mapping m) { int sourceId = m.getSourceId(); int targetId = m.getTargetId(); sourceMaps.remove(sourceId, targetId); targetMaps.remove(targetId, sourceId); maps.remove(m); } /** * Removes the Mapping between the given classes from the Alignment * @param sourceId: the source class to remove from the Alignment * @param targetId: the target class to remove from the Alignment */ public void remove(int sourceId, int targetId) { Mapping m = new Mapping(sourceId, targetId, 1.0); sourceMaps.remove(sourceId, targetId); targetMaps.remove(targetId, sourceId); maps.remove(m); } /** * Removes a list of Mappings from the alignment. * @param maps: the list of Mappings to remove to this Alignment */ public void removeAll(List<Mapping> maps) { for (Mapping m : maps) remove(m); } /** * Saves the alignment into an .rdf file in OAEI format * @param file: the output file */ public void saveRDF(String file) throws FileNotFoundException { AML aml = AML.getInstance(); String sourceURI = aml.getSource().getURI(); String targetURI = aml.getTarget().getURI(); URIMap uris = aml.getURIMap(); PrintWriter outStream = new PrintWriter(new FileOutputStream(file)); outStream.println("<?xml version='1.0' encoding='utf-8'?>"); outStream.println("<rdf:RDF xmlns='http://knowledgeweb.semanticweb.org/heterogeneity/alignment'"); outStream.println("\t xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#' "); outStream.println("\t xmlns:xsd='http://www.w3.org/2001/XMLSchema#' "); outStream.println("\t alignmentSource='AgreementMakerLight'>\n"); outStream.println("<Alignment>"); outStream.println("\t<xml>yes</xml>"); outStream.println("\t<level>0</level>"); double card = cardinality(); if (card < 1.02) outStream.println("\t<type>11</type>"); else outStream.println("\t<type>??</type>"); outStream.println("\t<onto1>" + sourceURI + "</onto1>"); outStream.println("\t<onto2>" + targetURI + "</onto2>"); outStream.println("\t<uri1>" + sourceURI + "</uri1>"); outStream.println("\t<uri2>" + targetURI + "</uri2>"); for (Mapping m : maps) { outStream.println("\t<map>"); outStream.println("\t\t<Cell>"); outStream.println("\t\t\t<entity1 rdf:resource=\"" + uris.getURI(m.getSourceId()) + "\"/>"); outStream.println("\t\t\t<entity2 rdf:resource=\"" + uris.getURI(m.getTargetId()) + "\"/>"); outStream.println("\t\t\t<measure rdf:datatype=\"http://www.w3.org/2001/XMLSchema#float\">" + m.getSimilarity() + "</measure>"); outStream.println("\t\t\t<relation>" + StringEscapeUtils.escapeXml(m.getRelationship().toString()) + "</relation>"); outStream.println("\t\t</Cell>"); outStream.println("\t</map>"); } outStream.println("</Alignment>"); outStream.println("</rdf:RDF>"); outStream.close(); } /** * Saves the alignment into a .tsv file in AML format * @param file: the output file */ public void saveTSV(String file) throws FileNotFoundException { AML aml = AML.getInstance(); Ontology source = aml.getSource(); Ontology target = aml.getTarget(); URIMap uris = aml.getURIMap(); PrintWriter outStream = new PrintWriter(new FileOutputStream(file)); outStream.println("#AgreementMakerLight Alignment File"); outStream.println("#Source ontology:\t" + source.getURI()); outStream.println("#Target ontology:\t" + target.getURI()); outStream.println("Source URI\tSource Label\tTarget URI\tTarget Label\tSimilarity\tRelationship"); for (Mapping m : maps) outStream.println(uris.getURI(m.getSourceId()) + "\t" + source.getName(m.getSourceId()) + "\t" + uris.getURI(m.getTargetId()) + "\t" + target.getName(m.getTargetId()) + "\t" + m.getSimilarity() + "\t" + m.getRelationship().toString()); outStream.close(); } /** * @return the number of Mappings in this Alignment */ public int size() { return maps.size(); } /** * Sorts the Alignment descendingly, by similarity */ public void sort() { Collections.sort(maps, new Comparator<Mapping>() { public int compare(Mapping m1, Mapping m2) { double diff = m2.getSimilarity() - m1.getSimilarity(); if (diff < 0) return -1; if (diff > 0) return 1; return 0; } }); } /** * @return the number of source classes mapped in this Alignment */ public int sourceCount() { return sourceMaps.keyCount(); } /** * @return the fraction of source classes mapped in this Alignment */ public double sourceCoverage() { AML aml = AML.getInstance(); double coverage = sourceMaps.keyCount(); int count = aml.getSource().classCount(); coverage /= count; return coverage; } /** * @return the number of target classes mapped in this Alignment */ public int targetCount() { return targetMaps.keyCount(); } /** * @return the fraction of target classes mapped in this Alignment */ public double targetCoverage() { AML aml = AML.getInstance(); double coverage = targetMaps.keyCount(); int count = aml.getTarget().classCount(); coverage /= count; return coverage; } //Private Methods private void loadMappingsRDF(String file) throws DocumentException { AML aml = AML.getInstance(); URIMap uris = aml.getURIMap(); //Open the alignment file using SAXReader SAXReader reader = new SAXReader(); File f = new File(file); Document doc = reader.read(f); //Read the root, then go to the "Alignment" element Element root = doc.getRootElement(); Element align = root.element("Alignment"); //Get an iterator over the mappings Iterator<?> map = align.elementIterator("map"); while (map.hasNext()) { //Get the "Cell" in each mapping Element e = ((Element) map.next()).element("Cell"); if (e == null) continue; //Get the source class String sourceURI = e.element("entity1").attributeValue("resource"); //Get the target class String targetURI = e.element("entity2").attributeValue("resource"); //Get the similarity measure String measure = e.elementText("measure"); //Parse it, assuming 1 if a valid measure is not found double similarity = 1; if (measure != null) { try { similarity = Double.parseDouble(measure); if (similarity < 0 || similarity > 1) similarity = 1; } catch (Exception ex) { /*Do nothing - use the default value*/} ; } //Get the relation String r = e.elementText("relation"); if (r == null) r = "?"; MappingRelation rel = MappingRelation.parseRelation(StringEscapeUtils.unescapeXml(r)); //Check if the URIs are listed in the URI map int sourceIndex = uris.getIndex(sourceURI); int targetIndex = uris.getIndex(targetURI); //If they are, add the mapping to the maps and proceed to next mapping if (sourceIndex > -1 && targetIndex > -1) { if (sourceIndex < targetIndex) add(sourceIndex, targetIndex, similarity, rel); else add(targetIndex, sourceIndex, similarity, rel); } } } private void loadMappingsRDF2(String file) throws DocumentException { AML aml = AML.getInstance(); URIMap uris = aml.getURIMap(); //Open the alignment file using SAXReader SAXReader reader = new SAXReader(); File f = new File(file); Document doc = reader.read(f); //Read the root, then go to the "Alignment" element Element root = doc.getRootElement(); Element align = root.element("Alignment"); //Get an iterator over the mappings Iterator<?> map = align.elementIterator("map"); while (map.hasNext()) { //Get the "Cell" in each mapping Element e = ((Element) map.next()).element("Cell"); if (e == null) continue; //Get the source class String sourceURI = e.element("entity1").element("Class").attributeValue("about"); //Get the target class String targetURI = e.element("entity2").element("Class").element("and").element("Class") .attributeValue("about"); //Get the similarity measure String measure = e.elementText("measure"); //Parse it, assuming 1 if a valid measure is not found double similarity = 1; if (measure != null) { try { similarity = Double.parseDouble(measure); if (similarity < 0 || similarity > 1) similarity = 1; } catch (Exception ex) { /*Do nothing - use the default value*/} ; } //Get the relation String r = e.elementText("relation"); if (r == null) r = "?"; MappingRelation rel = MappingRelation.parseRelation(StringEscapeUtils.unescapeXml(r)); //Check if the URIs are listed in the URI map int sourceIndex = uris.getIndex(sourceURI); int targetIndex = uris.getIndex(targetURI); //If they are, add the mapping to the maps and proceed to next mapping if (sourceIndex > -1 && targetIndex > -1) { if (sourceIndex < targetIndex) add(sourceIndex, targetIndex, similarity, rel); else add(targetIndex, sourceIndex, similarity, rel); } } } private void loadMappingsTSV(String file) throws Exception { AML aml = AML.getInstance(); URIMap uris = aml.getURIMap(); BufferedReader inStream = new BufferedReader(new FileReader(file)); //First line contains the reference to AML inStream.readLine(); //Second line contains the source ontology inStream.readLine(); //Third line contains the target ontology inStream.readLine(); //Fourth line contains the headers inStream.readLine(); //And from the fifth line forward we have mappings String line; while ((line = inStream.readLine()) != null) { String[] col = line.split("\t"); //First column contains the source uri String sourceURI = col[0]; //Third contains the target uri String targetURI = col[2]; //Fifth contains the similarity String measure = col[4]; //Parse it, assuming 1 if a valid measure is not found double similarity = 1; if (measure != null) { try { similarity = Double.parseDouble(measure); if (similarity < 0 || similarity > 1) similarity = 1; } catch (Exception ex) { /*Do nothing - use the default value*/} ; } //Finally, sixth column contains the type of relation MappingRelation rel; if (col.length > 5) rel = MappingRelation.parseRelation(col[5]); //For compatibility with previous tsv format without listed relation else rel = MappingRelation.EQUIVALENCE; //Get the indexes int sourceIndex = uris.getIndex(sourceURI); int targetIndex = uris.getIndex(targetURI); if (sourceIndex > -1 && targetIndex > -1) { if (sourceIndex < targetIndex) add(sourceIndex, targetIndex, similarity, rel); else add(targetIndex, sourceIndex, similarity, rel); } } inStream.close(); } }