Examples with LabeledCSVParser com.Ostermiller.util.LabeledCSVParser used on opensource projects

Example 41 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForBrose method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    dataParser.changeDelimiter('\t');
    Map<String, String> refMap = ReferenceUtil.buildRefMap(parserFactory, REFERENCE_PATH);
    try {
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                importLine(dataParser, refMap);
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem importing study at line [" + dataParser.lastLineNumber() + "]", e);
    }
}

Example 42 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser 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 43 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForBlewett method parsePredatorPreyInteraction.

private void parsePredatorPreyInteraction(Study study, Map<String, Location> locationMap, Map<String, Date> collectionTimeMap) throws IOException, NodeFactoryException, TermLookupServiceException {
    LabeledCSVParser parser = parserFactory.createParser("blewett/SnookDietData2000_02_Charlotte_Harbor_FL_Blewett_numeric_abundance.csv", CharsetConstant.UTF8);
    String[] header = parser.getLabels();
    String[] line;
    while ((line = parser.getLine()) != null) {
        if (line.length < 2) {
            break;
        }
        Specimen predatorSpecimen = addPredator(study, parser, line);
        List<Specimen> specimen = addPreyForPredator(header, line, study);
        for (Specimen prey : specimen) {
            predatorSpecimen.ate(prey);
        }
        String collectionCode = parser.getValueByLabel(COLLECTION_NO);
        if (collectionCode != null) {
            specimen.add(predatorSpecimen);
            setLocationAndDate(locationMap, collectionTimeMap, specimen, collectionCode);
        }
    }
}

Example 44 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser 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 45 with LabeledCSVParser

use of com.Ostermiller.util.LabeledCSVParser in project eol-globi-data by jhpoelen.

the class StudyImporterForBarnes method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    dataParser.changeDelimiter('\t');
    Map<String, String> refMap = ReferenceUtil.buildRefMap(parserFactory, REFERENCE_PATH);
    try {
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                importLine(dataParser, refMap);
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem importing study at line [" + dataParser.lastLineNumber() + "]", e);
    }
}