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

Example 21 with LocationImpl

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

the class StudyImporterForBaremore method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study;
    try {
        LabeledCSVParser parser = parserFactory.createParser(DATA_SOURCE, CharsetConstant.UTF8);
        String[] line;
        study = nodeFactory.getOrCreateStudy(new StudyImpl("Baremore 2010", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, "doi:10.3354/ab00214", ExternalIdUtil.toCitation("Ivy E. Baremore", "Prey Selection By The Atlantic Angel Shark Squatina Dumeril In The Northeastern Gulf Of Mexico.", "2010")));
        Location collectionLocation = nodeFactory.getOrCreateLocation(new LocationImpl(29.219302, -87.06665, null, null));
        Map<Integer, Specimen> specimenMap = new HashMap<Integer, Specimen>();
        while ((line = parser.getLine()) != null) {
            Integer sharkId = Integer.parseInt(line[0]);
            String collectionDateString = line[1];
            if (isBlank(collectionDateString)) {
                getLogger().warn(study, "line [" + parser.getLastLineNumber() + "] in [" + DATA_SOURCE + "]: missing collection date");
            } else {
                Specimen predatorSpecimen = specimenMap.get(sharkId);
                if (predatorSpecimen == null) {
                    predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Squatina dumeril", null));
                    predatorSpecimen.caughtIn(collectionLocation);
                    addLifeStage(parser, predatorSpecimen);
                    addCollectionDate(collectionDateString, predatorSpecimen);
                }
                specimenMap.put(sharkId, predatorSpecimen);
                String totalLengthInCm = line[3];
                try {
                    Double lengthInMm = Double.parseDouble(totalLengthInCm) * 10.0;
                    predatorSpecimen.setLengthInMm(lengthInMm);
                } catch (NumberFormatException ex) {
                    throw new StudyImporterException("failed to parse length [" + totalLengthInCm);
                }
                String preySpeciesDescription = line[7];
                if (StringUtils.isBlank(preySpeciesDescription)) {
                    getLogger().info(study, "found blank prey species description [" + preySpeciesDescription + "] on line [" + parser.lastLineNumber() + "]");
                } else {
                    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preySpeciesDescription, null));
                    preySpecimen.caughtIn(collectionLocation);
                    predatorSpecimen.ate(preySpecimen);
                    nodeFactory.setUnixEpochProperty(preySpecimen, nodeFactory.getUnixEpochProperty(predatorSpecimen));
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to parse labels", e);
    }
}

Example 22 with LocationImpl

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

the class StudyImporterForAkin method parseLocation.

private Location parseLocation(String[] siteInfo) throws StudyImporterException, IOException, NodeFactoryException {
    Double longitude;
    Double latitude;
    // TODO note that this study was taken in shallow water ~ 0.7m, probably better to include a depth range?
    Double altitude = -0.7d;
    String latitudeString = siteInfo[7];
    try {
        latitude = Double.parseDouble(latitudeString);
    } catch (NumberFormatException ex) {
        throw new StudyImporterException("failed to parse latitude [" + latitudeString + "]");
    }
    String longitudeString = siteInfo[8];
    try {
        longitude = Double.parseDouble(longitudeString);
    } catch (NumberFormatException ex) {
        throw new StudyImporterException("failed to parse longitude [" + longitudeString + "]");
    }
    return nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, altitude, null));
}

Example 23 with LocationImpl

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

the class StudyImporterForBlewett method buildLocationTimeMaps.

private void buildLocationTimeMaps(Map<String, Location> collectionLocationMap, Map<String, Date> collectionTimeMap, Study study) throws IOException, StudyImporterException {
    LabeledCSVParser locationParser = parserFactory.createParser("blewett/SnookDietData2000_02_Charlotte_Harbor_FL_Blewett_date_and_abiotic.csv", CharsetConstant.UTF8);
    String[] line;
    while ((line = locationParser.getLine()) != null) {
        if (line.length < 3) {
            getLogger().warn(study, "line:" + locationParser.getLastLineNumber() + " [" + StringUtils.join(line, ",") + "] has missing location information");
        }
        String collectionCode = locationParser.getValueByLabel(COLLECTION_NO);
        if (StringUtils.isBlank(collectionCode)) {
            getLogger().warn(study, "blank location code for line: [" + locationParser.getLastLineNumber() + "]");
        }
        String latitude = locationParser.getValueByLabel("Latitude");
        if (StringUtils.isBlank(latitude)) {
            getLogger().warn(study, "blank value for lattitude for line: [" + locationParser.getLastLineNumber() + "]");
        }
        String longitude = locationParser.getValueByLabel("Longitude");
        if (StringUtils.isBlank(longitude)) {
            getLogger().warn(study, "blank value for longitude for line: [" + locationParser.getLastLineNumber() + "]");
        }
        Location location;
        try {
            location = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), 0.0, null));
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create location", e);
        }
        collectionLocationMap.put(collectionCode, location);
        String timeString = locationParser.getValueByLabel("Time");
        if (StringUtils.isBlank(timeString)) {
            getLogger().warn(study, "blank value for time for line: [" + locationParser.getLastLineNumber() + "]");
        }
        String dateString = locationParser.getValueByLabel("Date");
        if (StringUtils.isBlank(dateString)) {
            getLogger().warn(study, "blank value for date for line: [" + locationParser.getLastLineNumber() + "]");
        }
        String dateTimeString = dateString + " " + timeString;
        try {
            Date dateTime = parseDateString(dateTimeString);
            collectionTimeMap.put(collectionCode, dateTime);
        } catch (ParseException e) {
            throw new StudyImporterException("failed to parse date time [" + dateTimeString + "] for collection [" + collectionCode + "] on line [" + locationParser.getLastLineNumber() + "]");
        }
    }
}

Example 24 with LocationImpl

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

the class StudyImporterForBarnes method addInteractionForPredator.

private void addInteractionForPredator(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Specimen predator = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    addLifeStage(parser, predator);
    Double latitude = LocationUtil.parseDegrees(parser.getValueByLabel("Latitude"));
    Double longitude = LocationUtil.parseDegrees(parser.getValueByLabel("Longitude"));
    String depth = parser.getValueByLabel("Depth");
    Double altitudeInMeters = -1.0 * Double.parseDouble(depth);
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, altitudeInMeters, null));
    predator.caughtIn(location);
    String preyName = parser.getValueByLabel("Prey");
    if (StringUtils.isBlank(preyName)) {
        getLogger().warn(localStudy, "found empty prey name on line [" + parser.lastLineNumber() + "]");
    } else {
        Specimen prey = nodeFactory.createSpecimen(localStudy, new TaxonImpl(preyName, null));
        prey.caughtIn(location);
        predator.ate(prey);
    }
}

Example 25 with LocationImpl

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

the class StudyImporterForSeltmann method createInteraction.

protected void createInteraction(LabeledCSVParser occurrence, Study study, Map<String, String> assoc, String targetName, String sourceName, Date date, InteractType interactType) throws StudyImporterException {
    Specimen source = nodeFactory.createSpecimen(study, new TaxonImpl(sourceName, null));
    Specimen target = nodeFactory.createSpecimen(study, new TaxonImpl(targetName, null));
    source.interactsWith(target, interactType);
    String sourceBasisOfRecord = occurrence.getValueByLabel("basisOfRecord");
    source.setBasisOfRecord(nodeFactory.getOrCreateBasisOfRecord(sourceBasisOfRecord, sourceBasisOfRecord));
    final String recordId = occurrence.getValueByLabel(FIELD_IDIGBIO_RECORD_ID);
    source.setProperty(FIELD_IDIGBIO_RECORD_ID, recordId);
    source.setExternalId(recordId);
    source.setProperty(FIELD_OCCURRENCE_ID, occurrence.getValueByLabel(FIELD_OCCURRENCE_ID));
    source.setProperty(FIELD_CATALOG_NUMBER, occurrence.getValueByLabel(FIELD_CATALOG_NUMBER));
    String targetBasisOfRecord = assoc.get("dwc:basisOfRecord");
    target.setBasisOfRecord(nodeFactory.getOrCreateBasisOfRecord(targetBasisOfRecord, targetBasisOfRecord));
    final String assocRecordId = assoc.get(FIELD_IDIGBIO_RECORD_ID);
    target.setProperty(FIELD_IDIGBIO_RECORD_ID, assocRecordId);
    target.setExternalId(assocRecordId);
    nodeFactory.setUnixEpochProperty(source, date);
    nodeFactory.setUnixEpochProperty(target, date);
    String latitude = occurrence.getValueByLabel("decimalLatitude");
    String longitude = occurrence.getValueByLabel("decimalLongitude");
    if (StringUtils.isNotBlank(latitude) && StringUtils.isNotBlank(longitude)) {
        Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(Double.parseDouble(latitude), Double.parseDouble(longitude), null, null));
        source.caughtIn(loc);
    }
}