チェンジセット 251 : SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java

更新日時:

2015/04/08 17:05:11 (11 年 前)

更新者:

atsuko

ログメッセージ:

コスト関数導入

ファイル:

• SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (変更) (5 diff)

SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java

@@ -7 +7 @@
 package org.biohackathon.SPARQLBuilder.OWL;
 
+import java.io.*;
+import java.util.*;
 
 /**
@@ -21 +23 @@
     
     private static final String CDIR = "cdata";
-    
-    /*
+        
     public static void main(String[] args){
-        // For Test
-        //String sp = "http://data.allie.dbcls.jp/sparql";
-        //String sc = "http://purl.org/allie/ontology/201108#ShortForm";
-        //String ec = "http://purl.org/allie/ontology/201108#LongForm";
-
-        String sp = "http://www.ebi.ac.uk/rdf/services/chembl/sparql";
-        String sc = "http://rdf.ebi.ac.uk/terms/chembl#Enzyme";
-        String ec = "http://rdf.ebi.ac.uk/terms/chembl#Activity";
-
-        //String sp = "http://www.ebi.ac.uk/rdf/services/biosamples/sparql";
-        //String sc = "http://rdf.ebi.ac.uk/terms/biosd/Sample";
-        //String ec = "http://purl.obolibrary.org/obo/NCBITaxon_7955";
-        //String sp = "http://www.ebi.ac.uk/rdf/services/biosamples/sparql";
-        //String sc = "http://rdf.ebi.ac.uk/terms/biosd/Sample";
-        //String ec = "http://purl.obolibrary.org/obo/NCBITaxon_7955";
-        //String sp = "http://lsd.dbcls.jp/sparql";
-        //String sc = "http://purl.jp/bio/10/lsd/ontology/201209#EnglishCode";
-        //String ec = "http://purl.jp/bio/10/lsd/ontology/201209#JapaneseCode";
-        //QueryPathGenerator qpg = new QueryPathGenerator(sp, "c:\\cdata");
-        QueryPathGenerator qpg1 = new QueryPathGenerator(sp, "cdata/");
-        //qpg1.testOWLClassGraph();
-        //SClass[] cl = qpg.getClasses(null);
-    }*/
+        QueryPathGenerator qpg = new QueryPathGenerator();
+        //String[] elist = qpg.getFactory().getEndpointURIList();
+        List<String> elist = new LinkedList<String>();
+        File file0 = new File("eplist.txt");
+        try{
+            BufferedReader br = new BufferedReader(new FileReader(file0));
+            String buf = null;
+            while( (buf = br.readLine()) != null){
+                elist.add(buf);
+            }
+        }catch(IOException e){
+            System.err.println(e);
+        }
+        
+        ListIterator<String> eit = elist.listIterator();
+        int i = 0;
+        while(eit.hasNext()){
+            String ep = eit.next();
+            qpg.setSPARQLendpoint(ep);
+            qpg.graph = new OWLClassGraph(qpg.analyzer);
+            SClass[] classes = qpg.getClasses(null);
+            File file1 = new File("path".concat(Integer.toString(i)).concat(".txt"));
+            File file2 = new File("ptable".concat(Integer.toString(i)).concat(".txt"));
+            try{
+                BufferedWriter bw1 = new BufferedWriter(new FileWriter(file1));
+                BufferedWriter bw2 = new BufferedWriter(new FileWriter(file2));
+                String jsonstr = "[";
+                int m = 0;
+                for ( int j = 0 ; j < classes.length; j ++ ){
+                    SClass start = classes[j];
+                    for ( int k = j + 1 ; k < classes.length; k++ ){
+                        SClass end = classes[k];
+                        Path[] paths = qpg.getPaths(start.getClassURI(), end.getClassURI(), false);                        
+                        for( int l = 0; l < paths.length; l++ ){
+                            if ( paths[l] == null ){
+                                continue;
+                            }
+                            if (m > 0 ){
+                                jsonstr += ",";
+                            }
+                            double cost = paths[l].computeCost();                                                        
+                            bw2.write(Double.toString(cost));
+                            bw2.write(",");
+                            bw2.write(Boolean.toString(EndpointAccess.checkPath(paths[l], ep)));
+                            bw2.newLine();
+                            jsonstr += paths[i].toJSONString3(classes);
+                            m++;
+                        }
+                    }
+                }
+                jsonstr += "]";
+                bw1.write(jsonstr);
+                bw1.newLine();
+                
+                bw1.close();
+                bw2.close();
+            }catch(IOException e){
+                System.err.println(e);
+            }
+            i++;
+        }
+    }
     
     public QueryPathGenerator(){
@@ -58 +98 @@
     
     public void setOWLClassGraph(String startClass){
-        graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, askcheck);
+        //graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, askcheck);
+        graph = new OWLClassGraph(analyzer, sparqlEndpoint, startClass, true);
     }
-    
-/*
-    public QueryPathGenerator(String sparqlEndpoint, String crawlFileName){
-        factory = new RDFSchemaAnalyzerFactory(crawlFileName);
-        setSPARQLendpoint(sparqlEndpoint);
-        setOWLClassGraph();
-    }
-    */
     
     public SClass[] getClasses(String keyword){
@@ -86 +119 @@
     
     public Path[] getPaths(String startClass, String endClass, boolean askcheck){
-        this.askcheck = askcheck;
         if ( graph == null ){
             //System.err.println("Class graph is null."); 
             setOWLClassGraph(startClass);
         }
+        graph.askcheck = askcheck;
         return graph.getPaths(startClass, endClass);
     }
@@ -139 +172 @@
         return label;
     }
-    
-    /*
-    private void setOWLClassGraph(){
-        //graph = new OWLClassGraph(analyzer);
-        graph = new OWLClassGraph();
-    }*/
-    
+        
     public OWLClassGraph getOWLClassGraph(){
         /*if ( graph == null ){