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

Example 66 with LabeledCSVParser

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

the class OpenTreeUtil method readTaxonomy.

public static void readTaxonomy(OpenTreeListener listener, InputStream inputStream) throws IOException {
    LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(new CSVParser(IOUtils.toBufferedInputStream(inputStream), '\t'));
    while (parser.getLine() != null) {
        String taxonId = parser.getValueByLabel("uid");
        String[] externalIds = StringUtils.split(parser.getValueByLabel("sourceinfo"), ",");
        for (String otherTaxonId : externalIds) {
            listener.taxonSameAs(taxonId, otherTaxonId);
        }
    }
}

Example 67 with LabeledCSVParser

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

the class TaxonCacheParserTest method parse.

public static void parse(BufferedReader reader, TaxonCacheListener listener) throws IOException {
    LabeledCSVParser labeledCSVParser = CSVTSVUtil.createLabeledCSVParser(reader);
    listener.start();
    while (labeledCSVParser.getLine() != null) {
        Taxon taxa = TaxonCacheParser.parseLine(labeledCSVParser);
        listener.addTaxon(taxa);
    }
    listener.finish();
}

Example 68 with LabeledCSVParser

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

the class StudyImporterForRaymond method importData.

private void importData(InputStream inputStream) throws IOException, StudyImporterException {
    File dietFile = null;
    File sourcesFile = null;
    LabeledCSVParser sourcesParser = null;
    LabeledCSVParser dietParser = null;
    try {
        ZipInputStream zis = new ZipInputStream(inputStream);
        ZipEntry entry;
        while ((entry = zis.getNextEntry()) != null) {
            if (DIET_CSV.equals(entry.getName())) {
                dietFile = File.createTempFile("raymondDiet", ".csv");
                dietParser = CSVTSVUtil.createParser(dietFile, zis);
            } else if (SOURCES_CSV.equals(entry.getName())) {
                sourcesFile = File.createTempFile("raymondSources", ".csv");
                sourcesParser = CSVTSVUtil.createParser(sourcesFile, zis);
            } else {
                IOUtils.copy(zis, new NullOutputStream());
            }
        }
        if (sourcesParser == null) {
            throw new StudyImporterException("failed to find [" + SOURCES_CSV + "] in [" + RESOURCE_URL + "]");
        }
        if (dietParser == null) {
            throw new StudyImporterException("failed to find [" + DIET_CSV + "] in [" + RESOURCE_URL + "]");
        }
        importData(sourcesParser, dietParser);
    } finally {
        org.apache.commons.io.FileUtils.deleteQuietly(dietFile);
        org.apache.commons.io.FileUtils.deleteQuietly(sourcesFile);
    }
}

Example 69 with LabeledCSVParser

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

the class StudyImporterForKelpForest method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    try {
        String source = "Beas-Luna, R., Novak, M., Carr, M. H., Tinker, M. T., Black, A., Caselle, J. E., … Iles, A. (2014). An Online Database for Informing Ecological Network Models: http://kelpforest.ucsc.edu. PLoS ONE, 9(10), e109356. doi:10.1371/journal.pone.0109356";
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl(source, source, "doi:10.1371/journal.pone.0109356", source));
        LabeledCSVParser parser = parserFactory.createParser(NODES, "UTF-8");
        String[] line;
        Map<String, Long> nameToId = new HashMap<String, Long>();
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String name = parser.getValueByLabel("working_name");
                String itisId = parser.getValueByLabel("itis_id");
                Long id = StringUtils.isBlank(itisId) ? null : Long.parseLong(itisId);
                id = (id != null && id > 0L) ? id : null;
                nameToId.put(name, id);
            }
        }
        Map<String, InteractType> typeToType = new HashMap<String, InteractType>() {

            {
                put("trophic", InteractType.ATE);
                put("parasitic", InteractType.PARASITE_OF);
            }
        };
        parser = parserFactory.createParser(LINKS, "UTF-8");
        while ((line = parser.getLine()) != null) {
            if (line.length > 2) {
                String interactionType = parser.getValueByLabel("type");
                InteractType interactType = typeToType.get(interactionType);
                if (null == interactType) {
                    LOG.warn("ignoring type [" + interactionType + "] on line: [" + (parser.getLastLineNumber() + 1) + "]");
                } else {
                    Specimen sourceSpecimen = createSpecimen(parser, nameToId, "node_1_working_name", "node1_stage", study);
                    Specimen targetSpecimen = createSpecimen(parser, nameToId, "node_2_working_name", "node2_stage", study);
                    sourceSpecimen.interactsWith(targetSpecimen, interactType);
                }
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed to import", e);
    }
}

Example 70 with LabeledCSVParser

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

the class StudyImporterForJRFerrerParis method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String citation = "Ferrer-Paris, José R.; Sánchez-Mercado, Ada Y.; Lozano, Cecilia; Zambrano, Liset; Soto, José; Baettig, Jessica; Leal, María (2014): A compilation of larval host-plant records for six families of butterflies (Lepidoptera: Papilionoidea) from available electronic resources. figshare. http://dx.doi.org/10.6084/m9.figshare.1168861 . " + CitationUtil.createLastAccessedString(RESOURCE);
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Ferrer-Paris 2014", citation, "http://dx.doi.org/10.6084/m9.figshare.1168861", citation));
    try {
        LabeledCSVParser parser = parserFactory.createParser(RESOURCE, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String butterflyName = createTaxon(parser, "Lepidoptera Name");
            String plantName = createTaxon(parser, "Hostplant Name");
            if (validNames(butterflyName, plantName, study, parser.lastLineNumber())) {
                addAssociation(study, parser, butterflyName, plantName);
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to access resource [" + RESOURCE + "]");
    }
}