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

Example 76 with TaxonImpl

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

the class StudyImporterForSIAD method downloadAndImportResource.

private void downloadAndImportResource(String resource, String source) throws StudyImporterException {
    try {
        LabeledCSVParser labeledCSVParser = parserFactory.createParser(resource, "UTF-8");
        labeledCSVParser.changeDelimiter('\t');
        while (labeledCSVParser.getLine() != null) {
            String name = labeledCSVParser.getValueByLabel("name");
            String ref = labeledCSVParser.getValueByLabel("source");
            String title = "SIAD-" + ref;
            String citation = "ABRS 2009. Australian Faunal Directory. " + name + ". Australian Biological Resources StudyNode, Canberra. " + CitationUtil.createLastAccessedString(ref);
            StudyImpl study1 = new StudyImpl(title, source, null, citation);
            study1.setExternalId(ref);
            Study study = nodeFactory.getOrCreateStudy(study1);
            Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(name, null));
            String hostName = labeledCSVParser.getValueByLabel("host name");
            Specimen hostSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
            InteractType type = map.get(labeledCSVParser.getValueByLabel("interaction"));
            specimen.interactsWith(hostSpecimen, type);
        }
    } catch (FileNotFoundException e) {
        throw new StudyImporterException("failed to open tmp file", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to map data", e);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + resource + "]", e);
    }
}

Example 77 with TaxonImpl

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

the class TaxonUtil method enrich.

public static Taxon enrich(PropertyEnricher enricher, Taxon taxon) throws PropertyEnricherException {
    Map<String, String> properties = taxonToMap(taxon);
    Taxon enrichedTaxon = new TaxonImpl();
    mapToTaxon(enricher.enrich(properties), enrichedTaxon);
    return enrichedTaxon;
}

Example 78 with TaxonImpl

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

the class ResolvingTaxonIndex method resolveAndIndex.

private TaxonNode resolveAndIndex(Taxon origTaxon, Taxon taxon) throws NodeFactoryException {
    TaxonNode indexedTaxon = findTaxon(taxon);
    while (indexedTaxon == null) {
        try {
            taxon = TaxonUtil.enrich(enricher, taxon);
        } catch (PropertyEnricherException e) {
            throw new NodeFactoryException("failed to enrich taxon with name [" + taxon.getName() + "]", e);
        }
        indexedTaxon = findTaxon(taxon);
        if (indexedTaxon == null) {
            if (TaxonUtil.isResolved(taxon)) {
                indexedTaxon = createAndIndexTaxon(origTaxon, taxon);
            } else {
                String truncatedName = NodeUtil.truncateTaxonName(taxon.getName());
                if (StringUtils.equals(truncatedName, taxon.getName())) {
                    if (isIndexResolvedOnly()) {
                        break;
                    } else {
                        indexedTaxon = addNoMatchTaxon(origTaxon);
                    }
                } else {
                    taxon = new TaxonImpl();
                    taxon.setName(truncatedName);
                    indexedTaxon = findTaxonByName(taxon.getName());
                }
            }
        }
    }
    return indexedTaxon;
}

Example 79 with TaxonImpl

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

the class TaxonInteractionIndexerTest method indexNoNameNoMatch.

@Test
public void indexNoNameNoMatch() throws NodeFactoryException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", PropertyAndValueDictionary.NO_MATCH));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Canis lupus", PropertyAndValueDictionary.NO_MATCH));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", null));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb())).resolve();
    assertNotNull(taxonIndex.findTaxonByName("Homo sapiens"));
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName(PropertyAndValueDictionary.NO_NAME));
}

Example 80 with TaxonImpl

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

the class TaxonInteractionIndexerTest method buildTaxonInterIndex.

@Test
public void buildTaxonInterIndex() throws NodeFactoryException, PropertyEnricherException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Canis lupus", "WORMS:2"));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById("WORMS:2"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb())).resolve();
    new TaxonInteractionIndexer(getGraphDb()).index();
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    Iterable<Relationship> rels = ((NodeBacked) homoSapiens).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
    List<String> humanFood = new ArrayList<String>();
    List<Long> counts = new ArrayList<Long>();
    List<String> labels = new ArrayList<>();
    for (Relationship rel : rels) {
        humanFood.add((String) rel.getEndNode().getProperty("name"));
        counts.add((Long) rel.getProperty("count"));
        labels.add((String) rel.getProperty("label"));
    }
    assertThat(humanFood.size(), is(4));
    assertThat(humanFood, hasItems("Arius felis", "Canis lupus"));
    assertThat(counts, hasItems(10L, 1L));
    assertThat(labels, hasItems("eats"));
}