Examples with InvalidLocationException org.eol.globi.util.InvalidLocationException used on opensource projects

Example 1 with InvalidLocationException

use of org.eol.globi.util.InvalidLocationException 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);
    }
}

Example 2 with InvalidLocationException

use of org.eol.globi.util.InvalidLocationException in project eol-globi-data by jhpoelen.

the class InteractionListenerImpl method getOrCreateLocation.

private Location getOrCreateLocation(Study study, Map<String, String> link) throws IOException, NodeFactoryException {
    LatLng centroid = null;
    String[] latitudes = { DECIMAL_LATITUDE, StudyImporterForMetaTable.LATITUDE };
    String latitude = getFirstValueForTerms(link, latitudes);
    String[] longitudes = { DECIMAL_LONGITUDE, StudyImporterForMetaTable.LONGITUDE };
    String longitude = getFirstValueForTerms(link, longitudes);
    if (StringUtils.isNotBlank(latitude) && StringUtils.isNotBlank(longitude)) {
        try {
            centroid = LocationUtil.parseLatLng(latitude, longitude);
        } catch (InvalidLocationException e) {
            getLogger().warn(study, "found invalid location: [" + e.getMessage() + "]");
        }
    }
    String localityId = link.get(LOCALITY_ID);
    String localityName = link.get(LOCALITY_NAME);
    if (centroid == null) {
        if (StringUtils.isNotBlank(localityId)) {
            centroid = getGeoNamesService().findLatLng(localityId);
        }
    }
    LocationImpl location = null;
    if (centroid != null) {
        location = new LocationImpl(centroid.getLat(), centroid.getLng(), null, null);
        if (StringUtils.isNotBlank(localityId)) {
            location.setLocalityId(localityId);
        }
        if (StringUtils.isNotBlank(localityName)) {
            location.setLocality(localityName);
        }
    }
    return location == null ? null : nodeFactory.getOrCreateLocation(location);
}

Example 3 with InvalidLocationException

use of org.eol.globi.util.InvalidLocationException in project eol-globi-data by jhpoelen.

the class LocationUtil method parseLatLng.

public static LatLng parseLatLng(String latitude, String longitude) throws InvalidLocationException {
    LatLng point = null;
    try {
        double lat = Double.parseDouble(latitude);
        double lng = Double.parseDouble(longitude);
        if (!isValidLatitude(lat)) {
            throw new InvalidLocationException("range of latitude [" + latitude + "] not valid");
        } else if (!isValidLongitude(lng)) {
            throw new InvalidLocationException("range of longitude [" + longitude + "] not valid");
        }
        if (isValidLatitude(lat) && isValidLongitude(lng)) {
            point = new LatLng(lat, lng);
        }
    } catch (NumberFormatException ex) {
        throw new InvalidLocationException("invalid (latitude, longitude) = (" + latitude + "," + longitude + ")", ex);
    }
    return point;
}