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

Example 76 with Specimen

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

the class ExporterTaxaDistinctTest method excludeNoMatchNames.

@Test
public void excludeNoMatchNames() throws NodeFactoryException, IOException {
    Study study = nodeFactory.createStudy(new StudyImpl("bla", null, null, null));
    Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, "EOL:1234"));
    Specimen prey = nodeFactory.createSpecimen(study, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, "EOL:122"));
    predator.ate(prey);
    assertThat(exportStudy(study), not(containsString(PropertyAndValueDictionary.NO_MATCH)));
}

Example 77 with Specimen

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

the class InteractionListenerImpl method createSpecimen.

private Specimen createSpecimen(Map<String, String> link, Study study, String taxonNameLabel, String taxonIdLabel, String bodyPartName, String bodyPartId) throws StudyImporterException {
    String sourceTaxonName = link.get(taxonNameLabel);
    String sourceTaxonId = link.get(taxonIdLabel);
    Specimen source = nodeFactory.createSpecimen(study, new TaxonImpl(sourceTaxonName, sourceTaxonId));
    setBasisOfRecordIfAvailable(link, source);
    setDateTimeIfAvailable(link, source);
    setBodyPartIfAvailable(link, source, bodyPartName, bodyPartId);
    return source;
}

Example 78 with Specimen

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

the class StudyImporterForPlanque method addInteractionForPredator.

private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(normalizeName(predatorName), null));
    // from http://www.geonames.org/630674/barents-sea.html
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(74.0, 36.0, null, null));
    predator.caughtIn(location);
    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(normalizeName(preyName), null));
        prey.caughtIn(location);
        predator.ate(prey);
    }
}

Example 79 with Specimen

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

the class StudyImporterForKelpForest method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    try {
        String source = "Beas-Luna, R., Novak, M., Carr, M. H., Tinker, M. T., Black, A., Caselle, J. E., … Iles, A. (2014). An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu. PLoS ONE, 9(10), e109356. doi:10.1371/journal.pone.0109356";
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl(source, source, "doi:10.1371/journal.pone.0109356", source));
        LabeledCSVParser parser = parserFactory.createParser(NODES, "UTF-8");
        String[] line;
        Map<String, Long> nameToId = new HashMap<String, Long>();
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String name = parser.getValueByLabel("working_name");
                String itisId = parser.getValueByLabel("itis_id");
                Long id = StringUtils.isBlank(itisId) ? null : Long.parseLong(itisId);
                id = (id != null && id > 0L) ? id : null;
                nameToId.put(name, id);
            }
        }
        Map<String, InteractType> typeToType = new HashMap<String, InteractType>() {

            {
                put("trophic", InteractType.ATE);
                put("parasitic", InteractType.PARASITE_OF);
            }
        };
        parser = parserFactory.createParser(LINKS, "UTF-8");
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String interactionType = parser.getValueByLabel("type");
                InteractType interactType = typeToType.get(interactionType);
                if (null == interactType) {
                    LOG.warn("ignoring type [" + interactionType + "] on line: [" + (parser.getLastLineNumber() + 1) + "]");
                } else {
                    Specimen sourceSpecimen = createSpecimen(parser, nameToId, "node_1_working_name", "node1_stage", study);
                    Specimen targetSpecimen = createSpecimen(parser, nameToId, "node_2_working_name", "node2_stage", study);
                    sourceSpecimen.interactsWith(targetSpecimen, interactType);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed to import", e);
    }
}

Example 80 with Specimen

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

the class StudyImporterForJRFerrerParis method addAssociation.

private void addAssociation(Study study, LabeledCSVParser parser, String butterflyName, String plantName) throws StudyImporterException {
    Specimen instigatorSpecimen;
    try {
        instigatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(butterflyName, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create butterfly specimen [" + butterflyName + "] on line [" + parser.lastLineNumber() + "]", e);
    }
    Specimen targetSpecimen;
    try {
        targetSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(plantName, null));
        instigatorSpecimen.ate(targetSpecimen);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to associate butterfly [" + butterflyName + "] to plant [" + plantName + "] on line [" + parser.lastLineNumber() + "]", e);
    }
}