root/SPARQLBuilderWWW2016/src/java/org/biohackathon/SPARQLBuilder/OWL/StructureCrawler.java

package org.biohackathon.SPARQLBuilder.OWL;

import java.io.File;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;

import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.SchemaCategory;
import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.JenaModelGenerator;
import jp.riken.accc.db.sparqlBuilderMetadata.crawler.dataStructure.sparql.RDFsCrawlerImpl;

public class StructureCrawler {

        private File dataDir = null;

        // this is just for a test
        /*
        public static void main(String[] args) throws Exception{
                StructureCrawler sc = new StructureCrawler(new File("c:\\cdata"));
//              sc.crawl("http://dbe-rdf.biosciencedbc.jp/sparql", "biosciencedbc.ttl");
                
//              System.out.println("done");
                
                
                Map<String,String> acTable = sc.getAcquiredStructureFiles();
                Set<String> keySet = acTable.keySet();
                for(String key: keySet){
                        String val = acTable.get(key);
                        System.out.println("File: " + key + " --- " + val);
                }
        }
        */
        
        
        public Map<String, String> getAcquiredStructureFiles(){
                Map<String, String> table = new HashMap<String, String>();
                if( dataDir.isDirectory() ){
                        // read files
                        File[] files = dataDir.listFiles();
                        for(File file: files){
                                String uri = null;
                                try{
                                        JenaModelGenerator jmGene = new JenaModelGenerator(file.getAbsolutePath());
                                        uri = jmGene.getEndpointURI();
System.out.println("URI: "+ uri);
                                }catch(Exception ex){
                                        //
                                }
                                if( uri != null ){
                                        table.put(uri, file.getAbsolutePath());
                                }
                        }
                }else{
                        if( dataDir.isFile() ){
                                String uri = null;
                                try{
                                        JenaModelGenerator jmGene = new JenaModelGenerator(dataDir.getAbsolutePath());
                                        uri = jmGene.getEndpointURI();
                                
                                }catch(Exception ex){
                                        //
                                }
                                if( uri != null ){
                                        table.put(uri, dataDir.getAbsolutePath());
                                }
                        }
                }
                return table;
        }
        
        
        
        public StructureCrawler(File dataDir) throws Exception {
                this.dataDir = dataDir;
        }

        public void crawl(String endPURI, String crawlName, String outFileName) throws Exception {
                RDFsCrawlerImpl impl = new RDFsCrawlerImpl(endPURI, crawlName);
                SchemaCategory sc = impl.determineSchemaCategory();

                // RDF/XML, RDF/XML-ABBREV, N-TRIPLE, N3
                File outFile = null;
                if (outFileName == null) {
                        String tFileName = null;
                        if (endPURI.lastIndexOf("/", endPURI.length() - 2) > 0) {
                                tFileName = endPURI.substring(
                                                endPURI.lastIndexOf("/", endPURI.length() - 2) + 1,
                                                endPURI.length());
                        } else {
                                tFileName = endPURI;
                        }
                        outFile = new File(dataDir, tFileName);
                        if (outFile.exists()) {
                                outFile = File.createTempFile(tFileName, "", dataDir);
                        }
                } else {
                        outFile = new File(dataDir, outFileName);
                }
                sc.write2File(outFile.getAbsolutePath(), "Turtle");
                // System.out.println("Category:" + sc.getCategory());
        }

}