Examples with LatLng org.eol.globi.geo.LatLng used on opensource projects

Example 1 with LatLng

use of org.eol.globi.geo.LatLng in project eol-globi-data by jhpoelen.

the class StudyImporterForRaymond method calculateCentroidOfBBox.

protected static LatLng calculateCentroidOfBBox(double left, double top, double right, double bottom) {
    LatLng latLng;
    if (left == right && top == bottom) {
        latLng = new LatLng(top, left);
    } else {
        Coordinate[] points = { GeoUtil.getCoordinate(top, left), GeoUtil.getCoordinate(top, right), GeoUtil.getCoordinate(bottom, right), GeoUtil.getCoordinate(bottom, left), GeoUtil.getCoordinate(top, left) };
        GeometryFactory geometryFactory = new GeometryFactory();
        Polygon polygon = geometryFactory.createPolygon(points);
        Point centroid = polygon.getCentroid();
        latLng = new LatLng(centroid.getCoordinate().y, centroid.getCoordinate().x);
    }
    return latLng;
}

Example 2 with LatLng

use of org.eol.globi.geo.LatLng in project eol-globi-data by jhpoelen.

the class StudyImporterForSzoboszlai method importLink.

protected Map<String, String> importLink(LabeledCSVParser parser, Map<Integer, LatLng> localeMap) throws IOException, StudyImporterException {
    TreeMap<String, String> link = new TreeMap<String, String>();
    link.put(STUDY_SOURCE_CITATION, getSourceCitationLastAccessed());
    String predNum = StringUtils.trim(parser.getValueByLabel("PredatorSciNameTSN"));
    if (StringUtils.isNotBlank(predNum)) {
        link.put(SOURCE_TAXON_ID, TaxonomyProvider.ITIS.getIdPrefix() + predNum);
    }
    String predName = StringUtils.trim(parser.getValueByLabel("PredatorSciName"));
    if (StringUtils.isNotBlank(predName)) {
        link.put(SOURCE_TAXON_NAME, predName);
    }
    String preyNum = StringUtils.trim(parser.getValueByLabel("PreySciNameTSN"));
    if (StringUtils.isNotBlank(preyNum)) {
        link.put(TARGET_TAXON_ID, TaxonomyProvider.ITIS.getIdPrefix() + preyNum);
    }
    String preyName = StringUtils.trim(parser.getValueByLabel("PreySciName"));
    if (StringUtils.isNotBlank(preyName)) {
        link.put(TARGET_TAXON_NAME, preyName);
    }
    String[] citeFields = { "CiteAuth", "CiteYear", "CiteTitle", "CiteSource", "CiteVolume", "CitePages" };
    List<String> citeValues = new ArrayList<String>();
    for (String citeField : citeFields) {
        String value = StringUtils.trim(parser.getValueByLabel(citeField));
        if (StringUtils.isNotBlank(value)) {
            String prefix;
            if ("CiteVolume".equals(citeField)) {
                prefix = "v.";
            } else if ("CitePages".equals(citeField)) {
                prefix = "pp.";
            } else {
                prefix = "";
            }
            citeValues.add(prefix + value);
        }
    }
    String referenceCitation = StringUtils.join(citeValues, ". ");
    link.put(REFERENCE_ID, getSourceDOI() + '/' + MD5.getHashString(referenceCitation));
    link.put(REFERENCE_CITATION, referenceCitation);
    link.put(INTERACTION_TYPE_NAME, "preysOn");
    link.put(INTERACTION_TYPE_ID, "RO:0002439");
    link.put(LOCALITY_NAME, StringUtils.trim(parser.getValueByLabel("LocatName")));
    String locatNum = StringUtils.trim(parser.getValueByLabel("LocatNum"));
    if (StringUtils.isNotBlank(locatNum)) {
        try {
            LatLng latLng = localeMap.get(Integer.parseInt(locatNum));
            if (latLng != null) {
                link.put(DECIMAL_LATITUDE, Double.toString(latLng.getLat()));
                link.put(DECIMAL_LONGITUDE, Double.toString(latLng.getLng()));
            }
        } catch (NumberFormatException ex) {
            throw new StudyImporterException("found invalid LocalNum [" + locatNum + "] " + parser.lastLineNumber(), ex);
        }
    }
    return link;
}

Example 3 with LatLng

use of org.eol.globi.geo.LatLng in project eol-globi-data by jhpoelen.

the class StudyImporterForSzoboszlai method importShapes.

protected Map<Integer, LatLng> importShapes() throws StudyImporterException {
    Map<Integer, LatLng> localityMap = new TreeMap<>();
    FileDataStore dataStore = null;
    try {
        InputStream shapeZipArchive = getDataset().getResource("shapes");
        File tmpFolder = new File(FileUtils.getTempDirectory(), UUID.randomUUID().toString());
        tmpFolder.deleteOnExit();
        unpackZip(shapeZipArchive, tmpFolder);
        dataStore = FileDataStoreFinder.getDataStore(new File(tmpFolder, "LocatPolygonsPoints.shp"));
        if (dataStore == null) {
            throw new StudyImporterException("failed to parse shapefiles");
        }
        FeatureReader<SimpleFeatureType, SimpleFeature> featureReader = dataStore.getFeatureReader();
        while (featureReader.hasNext()) {
            SimpleFeature feature = featureReader.next();
            Object geom = feature.getAttribute("the_geom");
            if (geom instanceof Point) {
                Coordinate coordinate = ((Point) geom).getCoordinate();
                Object localNum = feature.getAttribute("LocatNum");
                if (localNum instanceof Integer) {
                    localityMap.put((Integer) localNum, new LatLng(coordinate.y, coordinate.x));
                }
            }
        }
        featureReader.close();
    } catch (IOException e) {
        throw new StudyImporterException(e);
    } finally {
        if (dataStore != null) {
            dataStore.dispose();
        }
    }
    return localityMap;
}

Example 4 with LatLng

use of org.eol.globi.geo.LatLng in project eol-globi-data by jhpoelen.

the class StudyImporterForRoopnarine method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String suffix = ".csv";
    String prefix = "roopnarine/857470.item.";
    String trophicGuildLookup = prefix + 4 + suffix;
    final Map<Integer, List<String>> trophicGuildNumberToSpeciesMap = buildGuildLookup(trophicGuildLookup);
    Map<String, LatLng> resourceLocation = resourceLocationMap(suffix, prefix);
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Roopnarine et al 2013", "Roopnarine, P.D. & Hertog, R., 2013. Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica. DatasetImpl Papers in Ecology, 2013, pp.1–9. Available at: http://dx.doi.org/10.7167/2013/857470.", "http://dx.doi.org/10.7167/2013/857470", null));
    for (Map.Entry<String, LatLng> resourceLatLngEntry : resourceLocation.entrySet()) {
        LatLng latLng = resourceLatLngEntry.getValue();
        Location location;
        try {
            location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), 0.0, null));
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create location", e);
        }
        String studyResource = resourceLatLngEntry.getKey();
        getLogger().info(study, "import of [" + studyResource + "] started...");
        List<Specimen> predatorSpecimen = importTrophicInteractions(trophicGuildLookup, trophicGuildNumberToSpeciesMap, studyResource, study, location);
        getLogger().info(study, "import of [" + studyResource + "] done.");
    }
}

Example 5 with LatLng

use of org.eol.globi.geo.LatLng in project eol-globi-data by jhpoelen.

the class StudyImporterForRoopnarine method resourceLocationMap.

private Map<String, LatLng> resourceLocationMap(String suffix, String prefix) {
    LatLng jamaica = new LatLng(18.1315, -77.2736);
    LatLng cuba = new LatLng(22.0289, -79.9370);
    LatLng caymanIslands = new LatLng(19.30, -80.40);
    Map<String, LatLng> resourceLocation = new HashMap<String, LatLng>();
    resourceLocation.put(prefix + 1 + suffix, caymanIslands);
    resourceLocation.put(prefix + 2 + suffix, cuba);
    resourceLocation.put(prefix + 3 + suffix, jamaica);
    return resourceLocation;
}