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

Example 1 with TaxonImpl

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

the class StudyImporterForINaturalist method parseTaxon.

static Taxon parseTaxon(JsonNode taxonNode) {
    String name = null;
    String externalId = null;
    JsonNode nameNode = taxonNode.get("name");
    if (nameNode != null && !nameNode.isNull()) {
        name = nameNode.asText();
    }
    JsonNode idNode = taxonNode.get("id");
    if (null != idNode) {
        externalId = TaxonomyProvider.INATURALIST_TAXON.getIdPrefix() + idNode.asText();
    }
    return (name == null && externalId == null) ? null : new TaxonImpl(name, externalId);
}

Example 2 with TaxonImpl

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

the class StudyImporterForKelpForest method createSpecimen.

protected Specimen createSpecimen(LabeledCSVParser parser, Map<String, Long> nameToId, String nameLabel, String stageLabel, Study study) throws NodeFactoryException {
    String sourceName = parser.getValueByLabel(nameLabel);
    Long id = nameToId.get(sourceName);
    String taxonExternalId = id == null ? null : TaxonomyProvider.ID_PREFIX_ITIS + id;
    Specimen sourceSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(sourceName, taxonExternalId));
    String sourceLifeStage = parser.getValueByLabel(stageLabel);
    Term orCreateLifeStage = nodeFactory.getOrCreateLifeStage("KELP:" + sourceLifeStage, sourceLifeStage);
    sourceSpecimen.setLifeStage(orCreateLifeStage);
    return sourceSpecimen;
}

Example 3 with TaxonImpl

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

the class StudyImporterForRobledo method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String description = "García-Robledo C, Erickson DL, Staines CL, Erwin TL, Kress WJ. Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes Heil M, editor. PLoS ONE [Internet]. 2013 January 8;8(1):e52967. Available from: http://dx.doi.org/10.1371/journal.pone.0052967";
    String doi = "http://dx.doi.org/10.1371/journal.pone.0052967";
    Study study1 = new StudyImpl("García-Robledo et al 2013", description, doi, description);
    Study study = nodeFactory.getOrCreateStudy(study1);
    Map<String, String> abrLookup = buildPlantLookup();
    // spatial location from: http://www.ots.ac.cr/index.php?option=com_content&task=view&id=163&Itemid=348
    Double latitude = LocationUtil.parseDegrees("10°26'N");
    Double longitude = LocationUtil.parseDegrees("83°59'W");
    Location location;
    try {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, 35.0, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
    // TODO: need to map date range of collections
    String studyResource = "robledo/table_s1_extract.csv";
    try {
        LabeledCSVParser parser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String beetleName = parser.getValueByLabel("Herbivore species");
            String beetleScientificName = completeBeetleName(beetleName);
            Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(beetleScientificName, null));
            predator.caughtIn(location);
            for (String plantAbbreviation : abrLookup.keySet()) {
                String plantScientificName = abrLookup.get(plantAbbreviation);
                String valueByLabel = parser.getValueByLabel(plantAbbreviation);
                try {
                    int interactionCode = Integer.parseInt(valueByLabel);
                    if (interactionCode > 0) {
                        Specimen plant = nodeFactory.createSpecimen(study, new TaxonImpl(plantScientificName, null));
                        plant.caughtIn(location);
                        predator.ate(plant);
                    }
                } catch (NumberFormatException ex) {
                    getLogger().warn(study, "malformed or no value [" + valueByLabel + "] found for [" + plantScientificName + "(" + plantAbbreviation + ")" + "] and beetle [" + beetleScientificName + "] could be found in [" + studyResource + ":" + parser.lastLineNumber() + "]");
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem reading [" + studyResource + "]", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("cannot create specimens from [" + studyResource + "]", e);
    }
}

Example 4 with TaxonImpl

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

the class StudyImporterForRaymond method getSpecimen.

private Specimen getSpecimen(LabeledCSVParser dietParser, String nameLabel, String lifeStageLabel, Study study) throws NodeFactoryException {
    String predatorName = dietParser.getValueByLabel(nameLabel);
    Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(predatorName, null));
    String predatorLifeStage = dietParser.getValueByLabel(lifeStageLabel);
    predator.setLifeStage(nodeFactory.getOrCreateLifeStage("RAYMOND:" + predatorLifeStage, predatorLifeStage));
    return predator;
}

Example 5 with TaxonImpl

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

the class StudyImporterForSPIRE method createSpecimen.

private Specimen createSpecimen(String taxonName, Study study) throws NodeFactoryException {
    taxonName = taxonName.replaceAll("_", " ");
    Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(taxonName, null));
    if (taxonName.contains("adult")) {
        addLifeStage(specimen, "adult");
    } else if (taxonName.contains("juvenile")) {
        addLifeStage(specimen, "juvenile");
    } else if (taxonName.contains(" egg")) {
        addLifeStage(specimen, "egg");
    } else if (taxonName.contains("larvae")) {
        addLifeStage(specimen, "larvae");
    } else if (taxonName.contains("immature")) {
        addLifeStage(specimen, "immature");
    } else if (taxonName.contains("nymphs")) {
        addLifeStage(specimen, "nymphs");
    }
    return specimen;
}