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

Example 31 with LabeledCSVParser

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

the class StudyImporterForMetaTableIT method importREEMWithStaticCSV.

@Test
public void importREEMWithStaticCSV() throws IOException, StudyImporterException {
    final List<Map<String, String>> links = new ArrayList<Map<String, String>>();
    final InteractionListener interactionListener = properties -> links.add(properties);
    final StudyImporterForMetaTable.TableParserFactory tableFactory = (config, dataset) -> {
        String firstFewLines = "Hauljoin,\" Pred_nodc\",\" Pred_specn\",\" Prey_nodc\",\" Pred_len\",\" Year\",\" Month\",\" day\",\" region\",\" Pred_name\",\" Prey_Name\",\" Vessel\",\" Cruise\",\" Haul\",\" Rlat\",\" Rlong\",\" Gear_depth\",\" Bottom_depth\",\" Start_hour\",\" Surface_temp\",\" Gear_temp\",\" INPFC_Area\",\" Stationid\",\" Start_date\",\" Prey_sz1\",\" Prey_sex\"\n" + "11012118.0,8791030401.0,5.0,9999999998.0,53.0,1994.0,7.0,11.0,AI,\"Pacific cod Gadus macrocephalus\",\"Rocks \",95.0,199401.0,148.0,51.43,178.81999999999999,222.0,228.0,11.0,0.63,0.41999999999999998,542.0,118-11,\"1994-07-11 00:00:00\",3.0,\n" + "11012118.0,8791030401.0,8.0,9999999998.0,53.0,1994.0,7.0,11.0,AI,\"Pacific cod Gadus macrocephalus\",\"Rocks \",95.0,199401.0,148.0,51.43,178.81999999999999,222.0,228.0,11.0,0.63,0.41999999999999998,542.0,118-11,\"1994-07-11 00:00:00\",3.0,\n" + "11012118.0,8791030401.0,9.0,9999999998.0,58.0,1994.0,7.0,11.0,AI,\"Pacific cod Gadus macrocephalus\",\"Rocks \",95.0,199401.0,148.0,51.43,178.81999999999999,222.0,228.0,11.0,0.63,0.41999999999999998,542.0,118-11,\"1994-07-11 00:00:00\",13.0,\n" + "11012118.0,8791030401.0,9.0,9999999998.0,58.0,1994.0,7.0,11.0,AI,\"Pacific cod Gadus macrocephalus\",\"Rocks \",95.0,199401.0,148.0,51.43,178.81999999999999,222.0,228.0,11.0,0.63,0.41999999999999998,542.0,118-11,\"1994-07-11 00:00:00\",3.0,\n";
        return new LabeledCSVParser(new CSVParser(IOUtils.toInputStream(firstFewLines)));
    };
    final String baseUrl = "https://raw.githubusercontent.com/globalbioticinteractions/noaa-reem/master";
    final String resource = baseUrl + "/globi.json";
    importAll(interactionListener, tableFactory, baseUrl, resource);
    assertThat(links.size(), is(12));
    final Map<String, String> firstLine = links.get(0);
    assertThat(firstLine.get(StudyImporterForTSV.INTERACTION_TYPE_ID), is("http://purl.obolibrary.org/obo/RO_0002470"));
    assertThat(firstLine.get(StudyImporterForTSV.INTERACTION_TYPE_NAME), is("eats"));
    assertThat(firstLine.get(StudyImporterForTSV.TARGET_TAXON_ID), is(nullValue()));
    assertThat(firstLine.get(StudyImporterForTSV.TARGET_TAXON_NAME), is("Rocks"));
    assertThat(firstLine.get(StudyImporterForTSV.SOURCE_TAXON_ID), is("NODC:8791030401"));
    assertThat(firstLine.get(StudyImporterForTSV.SOURCE_TAXON_NAME), is("Pacific cod Gadus macrocephalus"));
    assertThat(firstLine.get(StudyImporterForMetaTable.EVENT_DATE), startsWith("1994-07-11"));
    assertThat(firstLine.get(StudyImporterForMetaTable.LATITUDE), is("51.43"));
    assertThat(firstLine.get(StudyImporterForMetaTable.LONGITUDE), is("178.81999999999999"));
}

Example 32 with LabeledCSVParser

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

the class CSVTSVUtilTest method readQuotes.

@Ignore("reading with unix style csv for now")
@Test
public void readQuotes() throws IOException {
    LabeledCSVParser csvParser = CSVTSVUtil.createLabeledCSVParser(IOUtils.toInputStream("name\n\"hello \"\"world\"\"\""));
    csvParser.getLine();
    assertThat(csvParser.getValueByLabel("name"), is("hello \"world\""));
}

Example 33 with LabeledCSVParser

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

the class CSVTSVUtilTest method parseSomeMore.

@Test
public void parseSomeMore() throws IOException {
    String csvString = "\"Obs\",\"spcode\", \"sizecl\", \"cruise\", \"stcode\", \"numstom\", \"numfood\", \"pctfull\", \"predator famcode\", \"prey\", \"number\", \"season\", \"depth\", \"transect\", \"alphcode\", \"taxord\", \"station\", \"long\", \"lat\", \"time\", \"sizeclass\", \"predator\"\n";
    csvString += "1, 1, 16, 3, 2, 6, 6, 205.5, 1, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 60, \"Chandeleur Islands\", \"aabd\", 47.11, \"C2\", 348078.84, 3257617.25, 313, \"201-300\", \"Rhynchoconger flavus\"\n";
    csvString += "2, 11, 2, 1, 1, 20, 15, 592.5, 6, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 20, \"Chandeleur Islands\", \"aabd\", 47.11, \"C1\", 344445.31, 3323087.25, 144, \"26-50\", \"Halieutichthys aculeatus\"\n";
    LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(new StringReader(csvString));
    parser.getLine();
    assertThat(parser.getValueByLabel("prey"), is("Ampelisca sp. (abdita complex)"));
}

Example 34 with LabeledCSVParser

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

the class ParserFactoryLocalIT method retrieveRemoteResource.

@Test
public void retrieveRemoteResource() throws IOException {
    LabeledCSVParser parser = new ParserFactoryLocal().createParser("http://www.esapubs.org/archive/ecol/E095/124/PairwiseList.txt", "UTF-8");
    parser.changeDelimiter('\t');
    parser.getLine();
    assertThat(parser.getValueByLabel("PREDATOR"), is(notNullValue()));
    assertThat(parser.getLabels(), is(new String[] { "PREY", "PREDATOR", "CODE", "REFERENCE" }));
    assertThat(parser.getValueByLabel("PREY"), is(notNullValue()));
}

Example 35 with LabeledCSVParser

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

the class ParserFactoryLocalTest method parse.

@Test
public void parse() throws IOException {
    LabeledCSVParser lcsvp = new ParserFactory() {

        private String createString() {
            String csvString = "\"Obs\",\"spcode\", \"sizecl\", \"cruise\", \"stcode\", \"numstom\", \"numfood\", \"pctfull\", \"predator famcode\", \"prey\", \"number\", \"season\", \"depth\", \"transect\", \"alphcode\", \"taxord\", \"station\", \"long\", \"lat\", \"time\", \"sizeclass\", \"predator\"\n";
            csvString += "1, 1, 16, 3, 2, 6, 6, 205.5, 1, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 60, \"Chandeleur Islands\", \"aabd\", 47.11, \"C2\", 348078.84, 3257617.25, 313, \"201-300\", \"Rhynchoconger flavus\"\n";
            csvString += "2, 11, 2, 1, 1, 20, 15, 592.5, 6, \"Ampelisca sp. (abdita complex)\", 1, \"Summer\", 20, \"Chandeleur Islands\", \"aabd\", 47.11, \"C1\", 344445.31, 3323087.25, 144, \"26-50\", \"Halieutichthys aculeatus\"\n";
            return csvString;
        }

        public LabeledCSVParser createParser(String studyResource, String characterEncoding) throws IOException {
            return CSVTSVUtil.createLabeledCSVParser(new StringReader(createString()));
        }
    }.createParser(StudyImporterForSimons.MISSISSIPPI_ALABAMA_DATA_SOURCE, "UTF-8");
    lcsvp.getLine();
    assertFirstLine(lcsvp);
    lcsvp.getLine();
    assertSecondLine(lcsvp);
}