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

Example 36 with LabeledCSVParser

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

the class LengthRangeParserImplTest method parse.

@Test
public void parse() throws IOException, StudyImporterException {
    LengthRangeParserImpl parser = new LengthRangeParserImpl("johnny");
    LabeledCSVParser csvParser = initParser();
    assertEquals((146d + 123d) / 2d, parser.parseLengthInMm(csvParser));
}

Example 37 with LabeledCSVParser

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

the class LengthRangeParserImplTest method initParser.

private LabeledCSVParser initParser() throws IOException {
    LabeledCSVParser csvParser = new TestParserFactory("\"johnny\"\n123-146\n324-345\n").createParser("aStudy", "UTF-8");
    csvParser.getLine();
    return csvParser;
}

Example 38 with LabeledCSVParser

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

the class LengthRangeParserImplTest method parseNoLengthUnavailable.

@Test
public void parseNoLengthUnavailable() throws IOException, StudyImporterException {
    LengthRangeParserImpl parser = new LengthRangeParserImpl("bla");
    LabeledCSVParser csvParser = initParser();
    assertNull(parser.parseLengthInMm(csvParser));
}

Example 39 with LabeledCSVParser

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

the class LengthParserImplTest method initParser.

private LabeledCSVParser initParser() throws IOException {
    LabeledCSVParser csvParser = new TestParserFactory("\"johnny\"\n123\n324\n").createParser("aStudy", "UTF-8");
    csvParser.getLine();
    return csvParser;
}

Example 40 with LabeledCSVParser

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

the class StudyImporterForRoopnarineTest method importLine.

@Test
public void importLine() throws StudyImporterException, NodeFactoryException {
    // note that this test data is a modified version of the actual data - please don't use this data for actual analysis purposes
    final String trophicGuildsToSpeciesLookup = "\"Guild Number\",\"Taxa\",\"Fish Body Length\",\"Cayman Islands\",\"Cuba\",\"Jamaica\"\n" + "1,\"something something\",,,,\n" + "2,\"Skeletonema tropicum        \",,,,\n" + "3,\"Something else        \",,,,\n" + "11,\" Epinephelus striatus          \",122,\"x \",\"x\",\"x\"\n" + "12,\" Negaprion brevirostris        \",240,\"x \",\" \",\" \"\n" + "13,\" Carcharhinus perezi           \",300,\"x \",\"x\",\"x\"\n" + "14,\" Rhizoprionodon porosus        \",75,\"x \",\"x\",\" \"\n" + "14,\" Sphyrna tiburo                \",80,\"x \",\" \",\" \"\n" + "14,\" Galeocerdo cuvieri            \",500,\"  \",,";
    final String trophicInteractions = "\"Guild Number\",\"Guild Description\",\"Foraging Habitat\",\"Number of Prey\",\"Prey\"\n" + "1,\"Planktonic bacteria   \",\".\",0,\".\"\n" + "2,\"Phytoplankton         \",\".\",0,\".\"\n" + "3,\"Nanno-zooplankton     \",\".\",30,\"1, 2\"\n" + "4,\"Filamentous macroalgae\",\".\",0,\".\"\n" + "5,\"Sheet macroalgae      \",\".\",0,\".\"\n" + "6,\"Coarsely branched macroalgae                 \",\".\",0,\".\"\n" + "7,\"Jointed calcareous macroalgae                \",\".\",0,\".\"\n" + "8,\"Thick leathery macroalgae                    \",\".\",0,\".\"\n" + "9,\"Crustose coralline algae                     \",\".\",0,\".\"\n" + "10,\"Seagrasses            \",\".\",0,\".\"\n" + "11,\"Epibenthic sponges    \",\".\",30,\"1,  2\"\n" + "12,\"Endolithic sponges    \",\".\",30,\"1,   2\"\n" + "13,\"Ahermatypic benthic corals\",\".\",35,\"1\"\n" + "14,\"Hermatypic corals\",\".\",36,\"2\"";
    StudyImporterForRoopnarine importer = new StudyImporterForRoopnarine(new ParserFactory() {

        @Override
        public LabeledCSVParser createParser(String studyResource, String characterEncoding) throws IOException {
            ParserFactory factory;
            if (studyResource.contains("4.csv")) {
                factory = new TestParserFactory(trophicGuildsToSpeciesLookup);
            } else {
                factory = new TestParserFactory(trophicInteractions);
            }
            return factory.createParser("", characterEncoding);
        }
    }, nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    assertNotNull(taxonIndex.findTaxonByName("Negaprion brevirostris"));
    assertNotNull(taxonIndex.findTaxonByName("Carcharhinus perezi"));
    assertNotNull(taxonIndex.findTaxonByName("Galeocerdo cuvieri"));
    Iterable<Relationship> collectedRels = NodeUtil.getSpecimens(study);
    int totalRels = validateSpecimen(collectedRels);
    assertThat(totalRels, Is.is(51));
}