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

Example 6 with LabeledCSVParser

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

the class StudyImporterForWrast method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String citation = "Wrast JL. Spatiotemporal And Habitat-mediated Food Web Dynamics in Lavaca Bay, Texas. 2008. Master Thesis.";
    StudyImpl study1 = new StudyImpl("Wrast 2008", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, citation);
    study1.setExternalId("http://www.fisheries.tamucc.edu/people_files/FINAL%20WRAST%20THESIS.pdf");
    Study study = nodeFactory.getOrCreateStudy(study1);
    try {
        LabeledCSVParser csvParser = parserFactory.createParser(LAVACA_BAY_DATA_SOURCE, CharsetConstant.UTF8);
        LengthParser parser = new LengthParserImpl(COLUMN_MAPPER.get(LENGTH_IN_MM));
        getPredatorSpecimenMap().clear();
        while (csvParser.getLine() != null) {
            addNextRecordToStudy(csvParser, study, COLUMN_MAPPER, parser);
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to create study [" + LAVACA_BAY_DATA_SOURCE + "]", e);
    } finally {
        getPredatorSpecimenMap().clear();
    }
}

Example 7 with LabeledCSVParser

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

the class StudyImporterForINaturalistTest method loadIgnoredInteractions.

@Test
public void loadIgnoredInteractions() throws IOException {
    LabeledCSVParser labeledCSVParser = importer.parserFactory.createParser(StudyImporterForINaturalist.TYPE_IGNORED_URI_DEFAULT, CharsetConstant.UTF8);
    List<Integer> typeMap1 = StudyImporterForINaturalist.buildTypesIgnored(labeledCSVParser);
    assertThat(typeMap1.contains(13), is(false));
    assertThat(typeMap1.contains(1378), is(true));
}

Example 8 with LabeledCSVParser

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

the class StudyImporterForINaturalistTest method loadInteractionMap.

@Test
public void loadInteractionMap() throws IOException {
    String resourceName = StudyImporterForINaturalist.TYPE_MAP_URI_DEFAULT;
    LabeledCSVParser labeledCSVParser = importer.parserFactory.createParser(resourceName, CharsetConstant.UTF8);
    Map<Integer, InteractType> typeMap = StudyImporterForINaturalist.buildTypeMap(resourceName, labeledCSVParser);
    assertThat(typeMap.get(13), is(InteractType.ATE));
    assertThat(typeMap.get(1685), is(InteractType.ATE));
    assertThat(typeMap.get(839), is(InteractType.PREYS_UPON));
}

Example 9 with LabeledCSVParser

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

the class SchemaControllerTest method interactionTypesCSV.

@Test
public void interactionTypesCSV() throws IOException {
    HttpServletRequest request = Mockito.mock(HttpServletRequest.class);
    when(request.getParameter("type")).thenReturn("csv");
    String interactionTypes = new SchemaController().getInteractionTypes(request);
    LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(IOUtils.toInputStream(interactionTypes));
    assertThat(parser.getLabels(), is(new String[] { "interaction", "source", "target", "termIRI" }));
    while (parser.getLine() != null) {
        assertThat(parser.getValueByLabel("interaction"), is(notNullValue()));
        assertThat(parser.getValueByLabel("source"), is(notNullValue()));
        assertThat(parser.getValueByLabel("target"), is(notNullValue()));
        assertThat(parser.getValueByLabel("termIRI"), is(notNullValue()));
    }
}

Example 10 with LabeledCSVParser

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

the class TaxonMapParserTest method parse.

public static void parse(BufferedReader reader, TaxonMapListener listener) throws IOException {
    LabeledCSVParser labeledCSVParser = CSVTSVUtil.createLabeledCSVParser(reader);
    listener.start();
    while (labeledCSVParser.getLine() != null) {
        Taxon providedTaxon = TaxonMapParser.parseProvidedTaxon(labeledCSVParser);
        Taxon resolvedTaxon = TaxonMapParser.parseResolvedTaxon(labeledCSVParser);
        listener.addMapping(providedTaxon, resolvedTaxon);
    }
    listener.finish();
}