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

Example 1 with TermImpl

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

the class TaxonUtil method mapToTaxon.

public static void mapToTaxon(Map<String, String> properties, Taxon taxon) {
    taxon.setName(properties.get(NAME));
    taxon.setRank(properties.get(RANK));
    final String externalId = properties.get(EXTERNAL_ID);
    taxon.setExternalId(externalId);
    taxon.setPath(properties.get(PATH));
    taxon.setPathIds(properties.get(PATH_IDS));
    taxon.setPathNames(properties.get(PATH_NAMES));
    taxon.setCommonNames(properties.get(COMMON_NAMES));
    final String externalUrl = properties.get(EXTERNAL_URL);
    if (StringUtils.isBlank(externalUrl) && StringUtils.isNotBlank(externalId)) {
        taxon.setExternalUrl(ExternalIdUtil.urlForExternalId(externalId));
    } else {
        taxon.setExternalUrl(externalUrl);
    }
    taxon.setThumbnailUrl(properties.get(THUMBNAIL_URL));
    String statusId = properties.get(STATUS_ID);
    String statusLabel = properties.get(STATUS_LABEL);
    if (StringUtils.isNotBlank(statusId) && StringUtils.isNotBlank(statusLabel)) {
        taxon.setStatus(new TermImpl(statusId, statusLabel));
    }
    taxon.setNameSource(properties.get(NAME_SOURCE));
    taxon.setNameSourceURL(properties.get(NAME_SOURCE_URL));
    taxon.setNameSourceAccessedAt(properties.get(NAME_SOURCE_ACCESSED_AT));
}

Example 2 with TermImpl

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

the class ExportTestUtil method createTestData.

public static Study createTestData(Double length, NodeFactory factory) throws NodeFactoryException, ParseException {
    Study myStudy = factory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen1 = factory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:45634"));
    specimen1.setStomachVolumeInMilliLiter(666.0);
    specimen1.setLifeStage(new TermImpl("GLOBI:JUVENILE", "JUVENILE"));
    specimen1.setPhysiologicalState(new TermImpl("GLOBI:DIGESTATE", "DIGESTATE"));
    specimen1.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    factory.setUnixEpochProperty(specimen1, ExportTestUtil.utcTestDate());
    final Specimen specimen2 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen2.setVolumeInMilliLiter(124.0);
    specimen1.ate(specimen2);
    final Specimen specimen3 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen3.setVolumeInMilliLiter(18.0);
    specimen1.ate(specimen3);
    if (null != length) {
        specimen1.setLengthInMm(length);
    }
    Location location = factory.getOrCreateLocation(new LocationImpl(88.0, -120.0, -60.0, null));
    specimen1.caughtIn(location);
    return myStudy;
}

Example 3 with TermImpl

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

the class ExporterAssociationAggregatesTest method createTestData.

private void createTestData(Double length, String studyTitle) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl(studyTitle, "data source description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, setPathAndId(new TaxonImpl("Homo sapiens", null)));
    specimen.setStomachVolumeInMilliLiter(666.0);
    specimen.setLifeStage(new TermImpl("GlOBI:JUVENILE", "JUVENILE"));
    specimen.setPhysiologicalState(new TermImpl("GlOBI:DIGESTATE", "DIGESTATE"));
    specimen.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    nodeFactory.setUnixEpochProperty(specimen, new Date(ExportTestUtil.utcTestTime()));
    TaxonImpl taxon = new TaxonImpl("Canis lupus", null);
    Specimen otherSpecimen = nodeFactory.createSpecimen(myStudy, setPathAndId(taxon));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    specimen.ate(otherSpecimen);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(44.0, 120.0, -60.0, null));
    specimen.caughtIn(location);
}

Example 4 with TermImpl

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

the class InteractionListenerImpl method setBasisOfRecordIfAvailable.

private void setBasisOfRecordIfAvailable(Map<String, String> link, Specimen specimen) {
    final String basisOfRecordName = link.get(BASIS_OF_RECORD_NAME);
    final String basisOfRecordId = link.get(BASIS_OF_RECORD_ID);
    if (StringUtils.isNotBlank(basisOfRecordName) || StringUtils.isNotBlank(basisOfRecordId)) {
        specimen.setBasisOfRecord(new TermImpl(basisOfRecordId, basisOfRecordName));
    }
}

Example 5 with TermImpl

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

the class StudyImporterForHurlbert method importInteraction.

protected void importInteraction(Set<String> regions, Set<String> locales, Set<String> habitats, Record record, Study study, String preyTaxonName, String predatorName) throws StudyImporterException {
    try {
        Taxon predatorTaxon = new TaxonImpl(predatorName);
        Specimen predatorSpecimen = nodeFactory.createSpecimen(study, predatorTaxon);
        setBasisOfRecordAsLiterature(predatorSpecimen);
        Taxon preyTaxon = new TaxonImpl(preyTaxonName);
        String preyNameId = StringUtils.trim(columnValueOrNull(record, "Prey_Name_ITIS_ID"));
        if (NumberUtils.isDigits(preyNameId)) {
            preyTaxon.setExternalId(TaxonomyProvider.ITIS.getIdPrefix() + preyNameId);
        }
        Specimen preySpecimen = nodeFactory.createSpecimen(study, preyTaxon);
        setBasisOfRecordAsLiterature(preySpecimen);
        String preyStage = StringUtils.trim(columnValueOrNull(record, "Prey_Stage"));
        if (StringUtils.isNotBlank(preyStage)) {
            Term lifeStage = nodeFactory.getOrCreateLifeStage("HULBERT:" + StringUtils.replace(preyStage, " ", "_"), preyStage);
            preySpecimen.setLifeStage(lifeStage);
        }
        String preyPart = StringUtils.trim(columnValueOrNull(record, "Prey_Part"));
        if (StringUtils.isNotBlank(preyPart)) {
            Term term = nodeFactory.getOrCreateBodyPart("HULBERT:" + StringUtils.replace(preyPart, " ", "_"), preyPart);
            preySpecimen.setBodyPart(term);
        }
        Date date = addCollectionDate(record, study);
        nodeFactory.setUnixEpochProperty(predatorSpecimen, date);
        nodeFactory.setUnixEpochProperty(preySpecimen, date);
        LocationImpl location = new LocationImpl(null, null, null, null);
        String longitude = columnValueOrNull(record, "Longitude_dd");
        String latitude = columnValueOrNull(record, "Latitude_dd");
        if (NumberUtils.isNumber(latitude) && NumberUtils.isNumber(longitude)) {
            try {
                LatLng latLng = LocationUtil.parseLatLng(latitude, longitude);
                String altitude = columnValueOrNull(record, "Altitude_mean_m");
                Double altitudeD = NumberUtils.isNumber(altitude) ? Double.parseDouble(altitude) : null;
                location = new LocationImpl(latLng.getLat(), latLng.getLng(), altitudeD, null);
            } catch (InvalidLocationException e) {
                getLogger().warn(study, "found invalid (lat,lng) pair: (" + latitude + "," + longitude + ")");
            }
        }
        String locationRegion = columnValueOrNull(record, "Location_Region");
        String locationSpecific = columnValueOrNull(record, "Location_Specific");
        location.setLocality(StringUtils.join(Arrays.asList(locationRegion, locationSpecific), ":"));
        Location locationNode = nodeFactory.getOrCreateLocation(location);
        String habitat_type = columnValueOrNull(record, "Habitat_type");
        List<Term> habitatList = Arrays.stream(StringUtils.split(StringUtils.defaultIfBlank(habitat_type, ""), ";")).map(StringUtils::trim).map(habitat -> new TermImpl(idForHabitat(habitat), habitat)).collect(Collectors.toList());
        nodeFactory.addEnvironmentToLocation(locationNode, habitatList);
        preySpecimen.caughtIn(locationNode);
        predatorSpecimen.caughtIn(locationNode);
        predatorSpecimen.ate(preySpecimen);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create interaction between [" + predatorName + "] and [" + preyTaxonName + "]", e);
    }
}