Examples with Record com.univocity.parsers.common.record.Record used on opensource projects

Example 1 with Record

use of com.univocity.parsers.common.record.Record 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 Record

use of com.univocity.parsers.common.record.Record in project eol-globi-data by jhpoelen.

the class StudyImporterForHurlbert method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    InputStream resource;
    try {
        resource = getDataset().getResource(RESOURCE);
    } catch (IOException e) {
        throw new StudyImporterException("failed to access [" + RESOURCE + "]", e);
    }
    Set<String> regions = new HashSet<String>();
    Set<String> locales = new HashSet<String>();
    Set<String> habitats = new HashSet<String>();
    TsvParserSettings settings = new TsvParserSettings();
    settings.getFormat().setLineSeparator("\n");
    settings.setHeaderExtractionEnabled(true);
    TsvParser parser = new TsvParser(settings);
    parser.beginParsing(resource, CharsetConstant.UTF8);
    Record record;
    while ((record = parser.parseNextRecord()) != null) {
        String columnNameSource = "Source";
        String sourceCitation = columnValueOrNull(record, columnNameSource);
        if (StringUtils.isBlank(sourceCitation)) {
            LOG.warn("failed to extract source from column [" + columnNameSource + "] in [" + RESOURCE + "] on line [" + (parser.getContext().currentLine() + 1) + "]");
        } else {
            importRecords(regions, locales, habitats, record, sourceCitation);
        }
    }
}

Example 3 with Record

use of com.univocity.parsers.common.record.Record in project eol-globi-data by jhpoelen.

the class StudyImporterForFishbase3 method handleTsvInputStream.

public static void handleTsvInputStream(RecordListener listener, InputStream is) throws StudyImporterException {
    TsvParserSettings settings = new TsvParserSettings();
    settings.getFormat().setLineSeparator("\n");
    settings.setMaxCharsPerColumn(4096 * 8);
    settings.setHeaderExtractionEnabled(true);
    TsvParser parser = new TsvParser(settings);
    parser.beginParsing(is, CharsetConstant.UTF8);
    Record record;
    while ((record = parser.parseNextRecord()) != null) {
        listener.onRecord(record);
    }
}