Examples with Taxon org.eol.globi.domain.Taxon used on opensource projects

Example 1 with Taxon

use of org.eol.globi.domain.Taxon in project eol-globi-data by jhpoelen.

the class TaxonUtil method mapToTaxon.

public static Taxon mapToTaxon(Map<String, String> properties) {
    Taxon taxon = new TaxonImpl();
    mapToTaxon(properties, taxon);
    return taxon;
}

Example 2 with Taxon

use of org.eol.globi.domain.Taxon in project eol-globi-data by jhpoelen.

the class TaxonUtilTest method toTaxonImage.

@Test
public void toTaxonImage() {
    TaxonImage image = new TaxonImage();
    Taxon taxon = new TaxonImpl("Donald duckus", "EOL:123");
    taxon.setCommonNames("bla @en | boo @de");
    taxon.setPath("one | two | three");
    Map<String, String> taxonMap = new TreeMap<String, String>(TaxonUtil.taxonToMap(taxon));
    taxonMap.put(PropertyAndValueDictionary.THUMBNAIL_URL, "http://foo/bar/thumb");
    taxonMap.put(PropertyAndValueDictionary.EXTERNAL_URL, "http://foo/bar");
    TaxonImage enrichedImage = TaxonUtil.enrichTaxonImageWithTaxon(taxonMap, image);
    assertThat(enrichedImage.getCommonName(), is("bla"));
    assertThat(enrichedImage.getTaxonPath(), is("one | two | three"));
    assertThat(enrichedImage.getInfoURL(), is("http://foo/bar"));
    assertThat(enrichedImage.getThumbnailURL(), is("http://foo/bar/thumb"));
    assertThat(enrichedImage.getPageId(), is("123"));
    assertThat(enrichedImage.getImageURL(), is(nullValue()));
}

Example 3 with Taxon

use of org.eol.globi.domain.Taxon in project eol-globi-data by jhpoelen.

the class LinkerTermMatcher method handleBatch.

private void handleBatch(final GraphDatabaseService graphDb, TermMatcher termMatcher, final Map<Long, TaxonNode> nodeMap, int counter) {
    StopWatch stopWatch = new StopWatch();
    stopWatch.start();
    String msgPrefix = "batch #" + counter / BATCH_SIZE;
    LOG.info(msgPrefix + " preparing...");
    List<String> nodeIdAndNames = new ArrayList<String>();
    for (Map.Entry<Long, TaxonNode> entry : nodeMap.entrySet()) {
        String name = entry.getKey() + "|" + entry.getValue().getName();
        nodeIdAndNames.add(name);
    }
    try {
        if (nodeIdAndNames.size() > 0) {
            termMatcher.findTermsForNames(nodeIdAndNames, new TermMatchListener() {

                @Override
                public void foundTaxonForName(Long nodeId, String name, Taxon taxon, NameType relType) {
                    TaxonNode taxonNode = nodeMap.get(nodeId);
                    if (taxonNode != null && NameType.NONE != relType && !TaxonUtil.likelyHomonym(taxon, taxonNode)) {
                        NodeUtil.connectTaxa(taxon, taxonNode, graphDb, RelTypes.forType(relType));
                    }
                }
            });
        }
    } catch (PropertyEnricherException ex) {
        LOG.error(msgPrefix + " problem matching terms", ex);
    }
    stopWatch.stop();
    LOG.info(msgPrefix + " completed in [" + stopWatch.getTime() + "] ms (" + (1.0 * stopWatch.getTime() / BATCH_SIZE) + " ms/name )");
    nodeMap.clear();
}

Example 4 with Taxon

use of org.eol.globi.domain.Taxon in project eol-globi-data by jhpoelen.

the class NonResolvingTaxonIndex method addNoMatchTaxon.

protected TaxonNode addNoMatchTaxon(Taxon origTaxon) throws NodeFactoryException {
    Taxon noMatchTaxon = TaxonUtil.copy(origTaxon);
    noMatchTaxon.setName(isNonEmptyTaxonNameOrId(origTaxon.getName()) ? origTaxon.getName() : PropertyAndValueDictionary.NO_NAME);
    noMatchTaxon.setExternalId(isNonEmptyTaxonNameOrId(origTaxon.getExternalId()) ? origTaxon.getExternalId() : PropertyAndValueDictionary.NO_MATCH);
    return createAndIndexTaxon(origTaxon, noMatchTaxon);
}

Example 5 with Taxon

use of org.eol.globi.domain.Taxon in project eol-globi-data by jhpoelen.

the class StudyImporterForGoMexSI2IT method assertThatSomeDataIsImported.

private static void assertThatSomeDataIsImported(NodeFactory nodeFactory, TaxonIndex taxonIndex) throws StudyImporterException, NodeFactoryException {
    Study study = nodeFactory.findStudy("Divita et al 1983");
    assertSpecimenProperties(((NodeBacked) study).getUnderlyingNode().getGraphDatabase());
    assertNotNull(study);
    assertThat(study.getTitle(), is("Divita et al 1983"));
    assertThat(study.getExternalId(), is(ExternalIdUtil.urlForExternalId("GAME:2689")));
    assertThat(study.getCitation(), is("Regina Divita, Mischelle Creel, Peter Sheridan. 1983. Foods of coastal fishes during brown shrimp Penaeus aztecus, migration from Texas estuaries (June - July 1981)."));
    assertNotNull(nodeFactory.findStudy("Beaumariage 1973"));
    assertNotNull(nodeFactory.findStudy("Baughman, 1943"));
    assertNotNull(taxonIndex.findTaxonByName("Chloroscombrus chrysurus"));
    assertNotNull(taxonIndex.findTaxonByName("Micropogonias undulatus"));
    assertNotNull(taxonIndex.findTaxonByName("Amphipoda"));
    assertNotNull(taxonIndex.findTaxonByName("Crustacea"));
    Taxon taxon = taxonIndex.findTaxonByName("Scomberomorus cavalla");
    List<String> preyList = new ArrayList<String>();
    final List<String> titles = new ArrayList<String>();
    Iterable<Relationship> classifiedAsRels = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    int count = 0;
    for (Relationship classifiedAsRel : classifiedAsRels) {
        Node predatorSpecimen = classifiedAsRel.getStartNode();
        Specimen predator = new SpecimenNode(predatorSpecimen);
        Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(predator);
        for (Relationship prey : stomachContents) {
            Relationship singleRelationship = prey.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
            preyList.add((String) singleRelationship.getEndNode().getProperty("name"));
        }
        count++;
        Relationship collectedBy = predatorSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat(collectedBy, is(notNullValue()));
        String title = (String) collectedBy.getStartNode().getProperty("title");
        titles.add(title);
    }
    assertThat(count > 7, is(true));
    assertThat(preyList, hasItem("Organic matter"));
    assertThat(preyList, hasItem("Triglidae"));
    assertThat(preyList, hasItem("Sparidae"));
    assertThat(titles, hasItem("Beaumariage 1973"));
    assertThat(titles, hasItem("Blanton et al 1972"));
    assertNotNull(taxon);
    final String footprintWKT = WKT_FOOTPRINT2;
    LocationImpl expectedLocation = new LocationImpl(29.346953, -92.980614, -13.641, footprintWKT);
    expectedLocation.setLocality("Louisiana inner continental shelf");
    Location location = nodeFactory.findLocation(expectedLocation);
    assertThat(location, is(notNullValue()));
    assertThat(location.getFootprintWKT(), is(footprintWKT));
    assertThat(location.getLocality(), is("Louisiana inner continental shelf"));
    assertNotNull(location);
    List<Environment> environments = location.getEnvironments();
    assertThat(environments.size(), not(is(0)));
    assertThat(environments.get(0).getExternalId(), is("http://cmecscatalog.org/classification/aquaticSetting/13"));
    assertThat(environments.get(0).getName(), is("Marine Nearshore Subtidal"));
    assertNotNull(nodeFactory.findStudy("GoMexSI"));
}