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

Example 11 with CSVParser

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

the class StudyImporterForLifeWatchGreece method handleTable.

protected void handleTable(RowListener listener, String tableName) throws IOException {
    InputStream is = getDataset().getResource("polytraits.lifewatchgreece.eu/" + tableName);
    CSVParser parser = new CSVParser(is);
    String[] line;
    while ((line = parser.getLine()) != null) {
        listener.nextLine(line);
    }
}

Example 12 with CSVParser

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

the class StudyImporterForGoMexSI2Test method importSinglePreyMissingDatabaseName.

@Test
public void importSinglePreyMissingDatabaseName() throws IOException, StudyImporterException {
    final Map<String, String> parsedProperties = new HashMap<String, String>();
    String predOneLine = "DATA_ID,PRED_ID,PREY_SOURCE_NAME,PREY_DATABASE_NAME,PHYSIOLOG_STATE,SED_ORIGIN,PREY_PARTS,PREY_LIFE_HIST_STAGE,PREY_COND_INDEX,PREY_SEX,PREY_SEX_RATIO,PREY_LEN_TYPE,PREY_MIN_LEN,PREY_MAX_LEN,PREY_MN_LEN,PREY_MIN_WIDTH,PREY_MAX_WIDTH,PREY_MN_WIDTH,BIOMASS,BIOMASS_QUALIFIER,PCT_BIOMASS,PCT_BIOMASS_QUALIFIER,N_CONS,N_CONS_QUALIFIER,PCT_N_CONS,PCT_N_CONS_QUALIFIER,VOL_CONS,VOL_CONS_QUALIFIER,PCT_VOL_CONS,PCT_VOL_CONS_QUALIFIER,FREQ_OCC,FREQ_OCC_QUALIFIER,PCT_FREQ_OCC,PCT_FREQ_OCC_QUALIFIER,IRI,PCT_IRI,IRIa,IIR,E,PREY_NOTES,ENTRY_DATE,ENTRY_PERSON,EDITED_DATE,DATA_EDITOR,MODIFY_DATE,DATA_MODIFIER\n" + "ACT_16R,Cchr.1,Crustacea,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,1.245,NA,0.15,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Jim Simons,NA,Jim Simons,27/06/2016,Theresa Mitchell\n";
    StudyImporterForGoMexSI2.parseSpecimen("test.txt", "PREY_", new ParseEventHandler() {

        @Override
        public void onSpecimen(String predatorUID, Map<String, String> properties) {
            parsedProperties.putAll(properties);
        }
    }, new LabeledCSVParser(new CSVParser(new StringReader(predOneLine))));
    assertThat(parsedProperties.get("name"), is("Crustacea"));
    assertThat(parsedProperties.get("GOMEXSI:PREY_SOURCE_NAME"), is("Crustacea"));
    assertThat(parsedProperties.get("GOMEXSI:PREY_DATABASE_NAME"), is(""));
}

Example 13 with CSVParser

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

the class StudyImporterForMetaTableIT method importNHMStatic.

@Test
public void importNHMStatic() 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 = "\"InteractionID\",\"InteractionURL\",\"Species1UUID\",\"Species1Name\",\"Species1LifeCycleStage\",\"Species1OrganismPart\",\"Species1Status\",\"InteractionType\",\"InteractionOntologyURL\",\"Species2UUID\",\"Species2Name\",\"Species2LifeCycleStage\",\"Species2OrganismPart\",\"Species2Status\",\"LocationUUID\",\"LocationName\",\"LocationCountryName\",\"ISO2\",\"Importance\",\"InteractionRecordType\",\"Reference\",\"ReferenceDOI\",\"Reference Page\",\"Notes\"\n" + "\"4bee827f-c9f5-4c0e-9db3-e40a6e4d8008\",\"http://phthiraptera.info/node/94209\",\"c8faa033-237b-40b9-9b76-d9e7fcff9238\",\"Menacanthus alaudae\",\"\",\"\",\"\",\"ectoparasite of\",\"http://purl.obolibrary.org/obo/RO_0002632\",\"e275d77c-e993-4de0-981f-b3f39fd4da9b\",\"Acanthis flavirostris\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"310\",\"[REF: Palma, Price & Hellenthal, 1998:310]\"\n" + "\"80e66e7c-75db-467f-9a89-a11f94d58eb3\",\"http://phthiraptera.info/node/94210\",\"fe5b2e50-b414-41d9-840d-189e732b2ea5\",\"Ricinus fringillae flammeae\",\"\",\"\",\"\",\"ectoparasite of\",\"http://purl.obolibrary.org/obo/RO_0002632\",\"f26a1199-c0bb-4d7c-a511-2fe6284c5378\",\"Acanthis flammea flammea\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Self citation to checklist added. Requires page number.\"\n" + "\"001ee8aa-dbab-43b8-9137-a61565ccf41b\",\"http://phthiraptera.info/node/94211\",\"ee17d179-9f60-4198-ac49-dc9dab3ae529\",\"Brueelia sibirica\",\"\",\"\",\"\",\"ectoparasite of\",\"http://purl.obolibrary.org/obo/RO_0002632\",\"f26a1199-c0bb-4d7c-a511-2fe6284c5378\",\"Acanthis flammea flammea\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"Self citation to checklist added. Requires page number.\"\n" + "\"d0929673-2f4c-49ec-877f-116e74ea360e\",\"http://phthiraptera.info/node/94212\",\"46084bc3-cfbf-4e01-96f8-5ecb50bc5ff9\",\"Ricinus fringillae\",\"\",\"\",\"\",\"ectoparasite of\",\"http://purl.obolibrary.org/obo/RO_0002632\",\"2027cf09-f15d-4c2b-be28-9cb00fabf308\",\"Acanthis flammea\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"\",\"204\",\"[REF: Rheinwald, 1968:204]\"\n";
        return new LabeledCSVParser(new CSVParser(IOUtils.toInputStream(firstFewLines)));
    };
    final String baseUrl = "https://raw.githubusercontent.com/globalbioticinteractions/natural-history-museum-london-interactions-bank/master";
    final String resource = baseUrl + "/globi.json";
    importAll(interactionListener, tableFactory, baseUrl, resource);
    assertThat(links.size(), is(4));
    for (Map<String, String> firstLine : links) {
        assertNotNull(firstLine.get(StudyImporterForTSV.INTERACTION_TYPE_NAME));
        assertNotNull(firstLine.get(StudyImporterForTSV.TARGET_TAXON_ID));
        assertNotNull(firstLine.get(StudyImporterForTSV.TARGET_TAXON_NAME));
        assertNotNull(firstLine.get(StudyImporterForTSV.SOURCE_TAXON_ID));
        assertNotNull(firstLine.get(StudyImporterForTSV.SOURCE_TAXON_NAME));
    }
}

Example 14 with CSVParser

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

the class StudyImporterFelderTest method importData.

@Test
public void importData() throws IOException {
    FilterInputStream fis = convertToTSV(getClass().getResourceAsStream("felder/BIRDS.BDT"));
    CSVParser parser = new CSVParser(fis);
    parser.changeDelimiter('\t');
    String[] line = parser.getLine();
    assertThat(line, is(notNullValue()));
    assertThat(line[1], is("*Dawson, W. L."));
    assertThat(line[2], is("1923"));
}