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Revision 50781539

Added by Andreas Kohlbecker over 8 years ago

easier switching between rdf download locations & adding support for genus resolution

View differences:

src/main/java/org/cybertaxonomy/utis/checklist/EEA_BDC_Client.java
46 46 
    public static final String DOC_URL = "http://semantic.eea.europa.eu/documentation";
47 47 
    public static final String COPYRIGHT_URL = "http://www.eea.europa.eu/legal/eea-data-policy";
48 48 

  		




  49
  
  
    
    private static final String SPECIES_RDF_FILE_URL = "http://localhost/download/species.rdf.gz"; // http://eunis.eea.europa.eu/rdf/species.rdf.gz


  		




  50
  
  
    
    private static final String TAXONOMY_RDF_FILE_URL = "http://localhost/download/taxonomy.rdf.gz"; // http://eunis.eea.europa.eu/rdf/taxonomy.rdf.gz


  		




  51
  
  
    
    private static final String LEGALREFS_RDF_FILE_URL = "http://localhost/download/legalrefs.rdf.gz"; // http://eunis.eea.europa.eu/rdf/legalrefs.rdf.gz


  		




  52
  
  
    
    private static final String REFERENCES_RDF_FILE_URL = "http://localhost/download/references.rdf.gz"; // http://eunis.eea.europa.eu/rdf/references.rdf.gz


  		




  
  49
  
    
//    private static final String DOWNLOAD_BASE_URL = "http://localhost/download/";


  		




  
  50
  
    
    private static final String DOWNLOAD_BASE_URL = "http://eunis.eea.europa.eu/rdf/";


  		




  
  51
  
    

  		




  
  52
  
    
    private static final String SPECIES_RDF_FILE_URL = DOWNLOAD_BASE_URL + "species.rdf.gz";


  		




  
  53
  
    
    private static final String TAXONOMY_RDF_FILE_URL = DOWNLOAD_BASE_URL + "taxonomy.rdf.gz";


  		




  
  54
  
    
    private static final String LEGALREFS_RDF_FILE_URL = DOWNLOAD_BASE_URL + "legalrefs.rdf.gz";


  		




  
  55
  
    
    private static final String REFERENCES_RDF_FILE_URL = DOWNLOAD_BASE_URL + "references.rdf.gz";


  		




  53
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  54
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    /**


  		




  55
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     * check for updates once a day


  		




  ......




  384
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  385
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            GremlinPipeline<Graph, Vertex> pipe = null;


  		




  386
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  387
  
  
    
            Profiler profiler = Profiler.newCpuProfiler(false);


  		




  
  390
  
    
//            Profiler profiler = Profiler.newCpuProfiler(false);


  		




  388
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  389
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            logger.debug("Neo4jINDEX");


  		




  390
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  ......




  392
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            pipe = new GremlinPipeline<Graph, Vertex>(hitVs);


  		




  393
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  394
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            List<Vertex> vertices = new ArrayList<Vertex>();


  		




  395
  
  
    
            pipe.in(RdfSchema.EUNIS_SPECIES.property("binomialName")).fill(vertices);


  		




  
  398
  
    
            pipe.in(RdfSchema.EUNIS_SPECIES.property("binomialName"),


  		




  
  399
  
    
                    RdfSchema.DWC.property("subgenus"), // EUNIS has no subgenera but this is added for future compatibility


  		




  
  400
  
    
                    RdfSchema.DWC.property("genus")


  		




  
  401
  
    
                    // no taxa for higher ranks in EUNIS


  		




  
  402
  
    
                    ).fill(vertices);


  		




  396
  403
  
    

  		




  397
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            updateQueriesWithResponse(vertices, null, null, checklistInfo, query);


  		




  398
  
  
    
            profiler.end(System.err);


  		




  
  405
  
    
//            profiler.end(System.err);


  		




  399
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        }


  		




  400
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    }


  		




  401
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      src/main/java/org/cybertaxonomy/utis/query/TinkerPopClient.java
    
  





  202
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    public ArrayList<Vertex> vertexIndexQuery(String luceneQuery) {


  		




  203
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        Neo4j2Graph graph = (Neo4j2Graph)graph();


  		




  204
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        AutoIndexer<Node> nodeAutoIndex = graph.getRawGraph().index().getNodeAutoIndexer();


  		




  
  205
  
    
        graph.autoStartTransaction(false);


  		




  205
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        IndexHits<Node> nodes = nodeAutoIndex.getAutoIndex().query(luceneQuery);


  		




  206
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        ArrayList<Vertex> hitVs = new ArrayList<Vertex>();


  		




  207
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        while(nodes.hasNext()) {


  		




  208
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            hitVs.add(new Neo4j2Vertex(nodes.next(), graph));


  		




  209
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        }


  		




  
  211
  
    
        graph.commit();


  		




  210
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        return hitVs;


  		




  211
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    }


  		




  212
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      src/main/java/org/cybertaxonomy/utis/store/Store.java
    
  





  35
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 */


  		




  36
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public abstract class Store {


  		




  37
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  38
  
  
    
    protected Logger logger = LoggerFactory.getLogger(Neo4jStore.class);


  		




  
  38
  
    
    protected Logger logger = LoggerFactory.getLogger(Store.class);


  		




  39
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    private static final File tmpDir = new File(System.getProperty("java.io.tmpdir"));


  		




  40
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    private static final File userHomeDir = new File(System.getProperty("user.home"));


  		




  41
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    private static final File utisHome = new File(userHomeDir, ".utis");


  		












  

    
      src/test/java/org/cybertaxonomy/utis/checklist/EEA_BDC_ClientTest.java
    
  





  3
  3
  
    
import static org.junit.Assert.assertEquals;


  		




  4
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import static org.junit.Assert.assertTrue;


  		




  5
  5
  
    

  		




  6
  
  
    
import org.cybertaxonomy.utis.checklist.DRFChecklistException;


  		




  7
  
  
    
import org.cybertaxonomy.utis.checklist.EEA_BDC_Client;


  		




  8
  
  
    
import org.cybertaxonomy.utis.checklist.SearchMode;


  		




  9
  6
  
    
import org.cybertaxonomy.utis.tnr.msg.Classification;


  		




  10
  7
  
    
import org.cybertaxonomy.utis.tnr.msg.NameType;


  		




  11
  8
  
    
import org.cybertaxonomy.utis.tnr.msg.Response;


  		




  ......




  59
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        assertEquals("Animalia", c.getKingdom());


  		




  60
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    }


  		




  61
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  59
  
    
    @Test


  		




  
  60
  
    
    public void genus_Test() throws DRFChecklistException, TnrMsgException {


  		




  
  61
  
    

  		




  
  62
  
    
        TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Prionus", true);


  		




  
  63
  
    
        client.queryChecklist(tnrMsg);


  		




  
  64
  
    
        String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg);


  		




  
  65
  
    
        System.out.println(outputXML);


  		




  
  66
  
    
        assertEquals(8, tnrMsg.getQuery().get(0).getResponse().size());


  		




  
  67
  
    
        Response response = tnrMsg.getQuery().get(0).getResponse().get(0);


  		




  
  68
  
    
        assertEquals("Prionus", response.getMatchingNameString());


  		




  
  69
  
    
        assertEquals("Prionus", response.getTaxon().getTaxonName().getCanonicalName());


  		




  
  70
  
    
        Classification c = response.getTaxon().getClassification();


  		




  
  71
  
    
        assertEquals("Cerambycidae", c.getFamily());


  		




  
  72
  
    
        assertEquals("Coleoptera", c.getOrder());


  		




  
  73
  
    
        assertEquals("Arthropoda", c.getPhylum());


  		




  
  74
  
    
        assertEquals("Animalia", c.getKingdom());


  		




  
  75
  
    
    }


  		




  
  76
  
    

  		




  
  77
  
    

  		




  
  78
  
    
    @Test


  		




  
  79
  
    
    public void family_Test() throws DRFChecklistException, TnrMsgException {


  		




  
  80
  
    

  		




  
  81
  
    
        TnrMsg tnrMsg = TnrMsgUtils.createRequest(SearchMode.scientificNameExact, "Cerambycidae", true);


  		




  
  82
  
    
        client.queryChecklist(tnrMsg);


  		




  
  83
  
    
        String outputXML = TnrMsgUtils.convertTnrMsgToXML(tnrMsg);


  		




  
  84
  
    
        System.out.println(outputXML);


  		




  
  85
  
    
        assertTrue(tnrMsg.getQuery().get(0).getResponse().size() > 20);


  		




  
  86
  
    
        Response response = tnrMsg.getQuery().get(0).getResponse().get(0);


  		




  
  87
  
    
        Classification c = response.getTaxon().getClassification();


  		




  
  88
  
    
        assertEquals("Cerambycidae", c.getFamily());


  		




  
  89
  
    
        assertEquals("Coleoptera", c.getOrder());


  		




  
  90
  
    
        assertEquals("Arthropoda", c.getPhylum());


  		




  
  91
  
    
        assertEquals("Animalia", c.getKingdom());


  		




  
  92
  
    
    }


  		




  
  93
  
    

  		




  62
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    @Test


  		




  63
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    public void scientificNameLikeTest_1() throws DRFChecklistException, TnrMsgException {


  		




  64
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        String queryString = "Cani";


  		












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