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

Example 46 with TaxonImpl

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

the class StudyImporterForBioInfo method createSpecimen.

private Specimen createSpecimen(Study study, LabeledCSVParser labeledCSVParser, String externalId) throws StudyImporterException {
    try {
        Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(null, TaxonomyProvider.NBN.getIdPrefix() + externalId));
        setSpecimenExternalId(labeledCSVParser, specimen);
        return specimen;
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create taxon with scientific name [" + externalId + "]", e);
    }
}

Example 47 with TaxonImpl

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

the class StudyImporterForByrnes method addInteractionForPredator.

private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    String preyName = parser.getValueByLabel("Prey");
    if (StringUtils.isBlank(preyName)) {
        getLogger().warn(localStudy, "found empty prey name on line [" + parser.lastLineNumber() + "]");
    } else {
        Specimen prey = nodeFactory.createSpecimen(localStudy, new TaxonImpl(preyName, null));
        String feedingLink = parser.getValueByLabel("Feeding Link?");
        if (StringUtils.equals("1", StringUtils.trim(feedingLink))) {
            predator.ate(prey);
        } else {
            predator.interactsWith(prey, InteractType.INTERACTS_WITH);
        }
    }
}

Example 48 with TaxonImpl

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

the class StudyImporterForBioInfo method buildTaxonMap.

protected static Map<String, Taxon> buildTaxonMap(LabeledCSVParser parser) throws IOException {
    Map<String, Taxon> taxonMap = new HashMap<String, Taxon>();
    while (parser.getLine() != null) {
        if (StringUtils.isBlank(parser.getValueByLabel("NBN Code"))) {
            Taxon taxon = new TaxonImpl();
            taxon.setRank(parser.getValueByLabel("rank"));
            taxon.setName(StringUtils.replaceChars(parser.getValueByLabel("latin"), "'", ""));
            String bioInfoTaxonId = parser.getValueByLabel("my taxon id");
            taxon.setExternalId(TaxonomyProvider.BIO_INFO + "taxon:" + bioInfoTaxonId);
            taxonMap.put(bioInfoTaxonId, taxon);
        }
    }
    return taxonMap;
}

Example 49 with TaxonImpl

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

the class StudyImporterForBlewett method addPredator.

private Specimen addPredator(Study study, LabeledCSVParser parser, String[] line) throws NodeFactoryException, TermLookupServiceException {
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Centropomus undecimalis", null));
    predatorSpecimen.setLifeStage(nodeFactory.getTermLookupService().lookupTermByName("adult"));
    try {
        String length = parser.getValueByLabel("Standard Length");
        predatorSpecimen.setLengthInMm(Double.parseDouble(length));
    } catch (NumberFormatException ex) {
        getLogger().warn(study, "found malformed length in line:" + parser.lastLineNumber() + " [" + StringUtils.join(line, ",") + "]");
    }
    return predatorSpecimen;
}

Example 50 with TaxonImpl

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

the class TaxonUtilTest method toTaxonImageNonEOL.

@Test
public void toTaxonImageNonEOL() {
    TaxonImage image = new TaxonImage();
    Taxon taxon = new TaxonImpl("Donald duckus", "ZZZ: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(nullValue()));
    assertThat(enrichedImage.getImageURL(), is(nullValue()));
}