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

Example 36 with Location

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

the class StudyImporterForRaymond method parseDietObservation.

private void parseDietObservation(LabeledCSVParser dietParser, Study study) throws StudyImporterException {
    try {
        Specimen predator = getSpecimen(dietParser, "PREDATOR_NAME", "PREDATOR_LIFE_STAGE", study);
        dietParser.getValueByLabel("ALTITUDE_MIN");
        dietParser.getValueByLabel("ALTITUDE_MAX");
        dietParser.getValueByLabel("DEPTH_MIN");
        dietParser.getValueByLabel("DEPTH_MAX");
        Location sampleLocation = parseLocation(dietParser, study);
        predator.caughtIn(sampleLocation);
        Specimen prey = getSpecimen(dietParser, "PREY_NAME", "PREY_LIFE_STAGE", study);
        prey.caughtIn(sampleLocation);
        predator.ate(prey);
        Date date = parseCollectionDate(dietParser);
        nodeFactory.setUnixEpochProperty(prey, date);
        nodeFactory.setUnixEpochProperty(predator, date);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import data", e);
    }
}

Example 37 with Location

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

the class StudyImporterForRaymond method locationFromLocale.

private Location locationFromLocale(LabeledCSVParser dietParser, Study study) throws NodeFactoryException {
    Location loc = null;
    LatLng centroid;
    String location = dietParser.getValueByLabel("LOCATION");
    if (StringUtils.isNotBlank(location)) {
        String cleanedLocationString = location.replaceAll("\\.$", "");
        getLocations().add(cleanedLocationString);
        try {
            centroid = getGeoNamesService().findLatLng(cleanedLocationString);
            if (centroid == null) {
                getLogger().warn(study, "missing lat/lng bounding box [" + dietParser.lastLineNumber() + "] and attempted to using location [" + location + "] failed.");
            } else {
                loc = nodeFactory.getOrCreateLocation(new LocationImpl(centroid.getLat(), centroid.getLng(), null, null));
            }
        } catch (IOException e) {
            getLogger().warn(study, "failed to lookup point for location [" + location + "] on line [" + dietParser.lastLineNumber() + "]");
        }
    }
    return loc;
}

Example 38 with Location

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

the class StudyImporterForRaymond method parseLocation.

private Location parseLocation(LabeledCSVParser dietParser, Study study) throws StudyImporterException {
    /**
     * left, top ------- right, top
     *  |                 |
     *  |                 |
     * left, bottom  -- right, bottom
     */
    String westString = dietParser.getValueByLabel(WEST);
    String eastString = dietParser.getValueByLabel(EAST);
    String northString = dietParser.getValueByLabel(NORTH);
    String southString = dietParser.getValueByLabel(SOUTH);
    Location loc = null;
    if (StringUtils.isBlank(westString) || StringUtils.isBlank(eastString) || StringUtils.isBlank(northString) || StringUtils.isBlank(southString)) {
        try {
            loc = locationFromLocale(dietParser, study);
        } catch (NodeFactoryException ex) {
            throw new StudyImporterException("found invalid location on line [" + dietParser.lastLineNumber() + "]", ex);
        }
    } else {
        double left = Double.parseDouble(westString);
        double top = Double.parseDouble(northString);
        double right = Double.parseDouble(eastString);
        double bottom = Double.parseDouble(southString);
        LatLng centroid = calculateCentroidOfBBox(left, top, right, bottom);
        try {
            loc = nodeFactory.getOrCreateLocation(new LocationImpl(centroid.getLat(), centroid.getLng(), null, null));
        } catch (NodeFactoryException ex) {
            String locationString = StringUtils.join(Arrays.asList(westString, northString, eastString, southString), ",");
            LOG.warn("found invalid locations [" + locationString + "] on line [" + (dietParser.lastLineNumber() + 1) + "]: " + ex.getMessage());
        }
    }
    return loc;
}

Example 39 with Location

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

the class StudyImporterForINaturalist method parseLocation.

private Location parseLocation(JsonNode observation) throws NodeFactoryException {
    Location location = null;
    String latitudeString = observation.get("latitude").getTextValue();
    String longitudeString = observation.get("longitude").getTextValue();
    if (latitudeString != null && longitudeString != null) {
        double latitude = Double.parseDouble(latitudeString);
        double longitude = Double.parseDouble(longitudeString);
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, null, null));
    }
    return location;
}

Example 40 with Location

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

the class StudyImporterForRobledoTest method createAndPopulateStudy.

@Test
public void createAndPopulateStudy() throws StudyImporterException, NodeFactoryException {
    StudyImporterForRobledo importer = new StudyImporterForRobledo(new ParserFactoryLocal(), nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    assertNotNull(taxonIndex.findTaxonByName("Heliconia imbricata"));
    assertNotNull(taxonIndex.findTaxonByName("Renealmia alpinia"));
    assertNotNull(nodeFactory.findStudy(study.getTitle()));
    int count = 0;
    Iterable<Relationship> specimenRels = NodeUtil.getSpecimens(study);
    for (Relationship specimenRel : specimenRels) {
        Specimen specimen1 = new SpecimenNode(specimenRel.getEndNode());
        Location sampleLocation = specimen1.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getAltitude(), is(35.0));
        assertThat(Math.round(sampleLocation.getLongitude()), is(-84L));
        assertThat(Math.round(sampleLocation.getLatitude()), is(10L));
        count++;
    }
    assertThat(count, is(93));
}