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

Example 81 with TaxonImpl

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

the class LinkerTrustyNanoPubsTest method populateDataset.

public NodeFactoryWithDatasetContext populateDataset(DatasetImpl dataset) throws NodeFactoryException {
    TaxonIndex taxonIndex = getOrCreateTaxonIndex();
    // see https://github.com/jhpoelen/eol-globi-data/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", "some source", "http://doi.org/123.23/222", "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, dataset);
    Interaction interaction = factory.createInteraction(factory.createStudy(study));
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    Taxon mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonEOL = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonEOL, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxonEOL);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxonEOL));
    donald.ate(mickey);
    return factory;
}

Example 82 with TaxonImpl

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

the class NameResolverTest method doNameResolving.

@Test
public void doNameResolving() 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("Animalia", "WORMS:2"));
    human.ate(animal);
    Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
    human.ate(fish);
    assertNull(taxonIndex.findTaxonById("NCBI:9606"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    assertAnimalia(taxonIndex.findTaxonById("WORMS:2"));
    assertThat(taxonIndex.findTaxonByName("Arius felis"), is(notNullValue()));
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    assertThat(homoSapiens.getExternalId(), is("NCBI:9606"));
}

Example 83 with TaxonImpl

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

the class TaxonLookupServiceImpl method findTaxon.

private Taxon[] findTaxon(String fieldName1, String fieldValue) throws IOException {
    Taxon[] terms = new TaxonImpl[0];
    if (StringUtils.isNotBlank(fieldValue) && indexSearcher != null) {
        PhraseQuery query = new PhraseQuery();
        query.add(new Term(fieldName1, fieldValue));
        TopDocs docs = indexSearcher.search(query, getMaxHits());
        if (docs.totalHits > 0) {
            int maxResults = Math.min(docs.totalHits, getMaxHits());
            terms = new TaxonImpl[maxResults];
            for (int i = 0; i < maxResults; i++) {
                ScoreDoc scoreDoc = docs.scoreDocs[i];
                Document foundDoc = indexSearcher.doc(scoreDoc.doc);
                Taxon term = new TaxonImpl();
                Fieldable idField = foundDoc.getFieldable(FIELD_ID);
                if (idField != null) {
                    term.setExternalId(idField.stringValue());
                }
                Fieldable rankPathField = foundDoc.getFieldable(FIELD_RANK_PATH);
                if (rankPathField != null) {
                    term.setPath(rankPathField.stringValue());
                }
                Fieldable rankPathIdsField = foundDoc.getFieldable(FIELD_RANK_PATH_IDS);
                if (rankPathIdsField != null) {
                    term.setPathIds(rankPathIdsField.stringValue());
                }
                Fieldable rankPathNamesField = foundDoc.getFieldable(FIELD_RANK_PATH_NAMES);
                if (rankPathNamesField != null) {
                    term.setPathNames(rankPathNamesField.stringValue());
                }
                Fieldable commonNamesFields = foundDoc.getFieldable(FIELD_COMMON_NAMES);
                if (commonNamesFields != null) {
                    term.setCommonNames(commonNamesFields.stringValue());
                }
                Fieldable fieldName = foundDoc.getFieldable(FIELD_RECOMMENDED_NAME);
                if (fieldName != null) {
                    term.setName(fieldName.stringValue());
                }
                terms[i] = term;
            }
        }
    }
    return terms;
}

Example 84 with TaxonImpl

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

the class TaxonCacheService method findTerms.

@Override
public void findTerms(List<Term> terms, TermMatchListener termMatchListener) throws PropertyEnricherException {
    lazyInit();
    for (Term term : terms) {
        String nodeIdAndName = term.getName();
        String[] split = StringUtils.split(nodeIdAndName, '|');
        String name = (split != null && split.length > 1) ? split[1] : nodeIdAndName;
        Long nodeId = (split != null && split.length > 1 && NumberUtils.isDigits(split[0])) ? Long.parseLong(split[0]) : null;
        if (!resolveName(termMatchListener, term.getId(), nodeId)) {
            if (StringUtils.isNotBlank(nodeIdAndName)) {
                if (!resolveName(termMatchListener, name, nodeId)) {
                    termMatchListener.foundTaxonForName(nodeId, name, new TaxonImpl(name, term.getId()), NameType.NONE);
                }
            }
        }
    }
}

Example 85 with TaxonImpl

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

the class TaxonCacheParser method parseLine.

public static Taxon parseLine(LabeledCSVParser labeledCSVParser) {
    Taxon taxa = new TaxonImpl();
    taxa.setExternalId(CSVTSVUtil.valueOrNull(labeledCSVParser, "id"));
    taxa.setName(CSVTSVUtil.valueOrNull(labeledCSVParser, "name"));
    taxa.setRank(CSVTSVUtil.valueOrNull(labeledCSVParser, "rank"));
    taxa.setPath(CSVTSVUtil.valueOrNull(labeledCSVParser, "path"));
    taxa.setPathIds(CSVTSVUtil.valueOrNull(labeledCSVParser, "pathIds"));
    taxa.setPathNames(CSVTSVUtil.valueOrNull(labeledCSVParser, "pathNames"));
    taxa.setCommonNames(CSVTSVUtil.valueOrNull(labeledCSVParser, "commonNames"));
    taxa.setExternalUrl(CSVTSVUtil.valueOrNull(labeledCSVParser, "externalUrl"));
    taxa.setThumbnailUrl(CSVTSVUtil.valueOrDefault(labeledCSVParser, "thumbnailUrl", MISSING_THUMBNAIL));
    return taxa;
}