Examples with TermImpl org.eol.globi.domain.TermImpl used on opensource projects

Example 11 with TermImpl

use of org.eol.globi.domain.TermImpl in project eol-globi-data by jhpoelen.

the class TaxonUtilTest method copyTaxonPrefillExternalURL.

@Test
public void copyTaxonPrefillExternalURL() {
    Taxon src = new TaxonImpl("name", "GBIF:123");
    src.setStatus(new TermImpl("statusId", "statusLabel"));
    Taxon target = new TaxonImpl();
    TaxonUtil.copy(src, target);
    assertThat(target.getStatus().getId(), is("statusId"));
    assertThat(target.getStatus().getName(), is("statusLabel"));
    assertThat(target.getExternalUrl(), is("http://www.gbif.org/species/123"));
}

Example 12 with TermImpl

use of org.eol.globi.domain.TermImpl in project eol-globi-data by jhpoelen.

the class StudyImporterForSPIRETest method assertGAZMapping.

private void assertGAZMapping(TestInteractionListener listener) {
    Map<String, TermImpl> gazMap = new HashMap<String, TermImpl>() {

        {
            put("Country: New Zealand;   State: Otago;   Locality: Catlins, Craggy Tor catchment", new TermImpl("GAZ:00146864", "The Catlins"));
            put("Country: Scotland", new TermImpl("GAZ:00002639", "Scotland"));
            put("Country: USA;   State: Georgia", new TermImpl("GAZ:00002611", "State of Georgia"));
            put("Country: USA;   State: Iowa", new TermImpl("GAZ:00004438", "State of Iowa"));
            put("Country: Southern Ocean", new TermImpl("GAZ:00000373", "Southern Ocean"));
            put("Country: USA", new TermImpl("GAZ:00002459", "United States of America"));
            put("Country: USA;   State: Iowa;   Locality: Mississippi River", new TermImpl("GAZ:00004438", "State of Iowa"));
            put("Country: Japan", new TermImpl("GAZ:00002747", "Japan"));
            put("Country: Malaysia;   Locality: W. Malaysia", new TermImpl("GAZ:00003902", "Malaysia"));
            put("Country: Chile;   Locality: central Chile", new TermImpl("GAZ:00002825", "Chile"));
            put("Country: USA;   State: New Mexico;   Locality: Aden Crater", new TermImpl("GAZ:00004427", "State of New Mexico"));
            put("Country: USA;   State: Alaska;   Locality: Torch Bay", new TermImpl("GAZ:00002521", "State of Alaska"));
            put("Country: USA;   State: Pennsylvania", new TermImpl("GAZ:00002542", " Commonwealth of Pennsylvania"));
            put("Country: Costa Rica", new TermImpl("GAZ:00002901", "Costa Rica"));
            put("Country: Pacific", new TermImpl("GAZ:00000360", "Pacific Ocean"));
            put("Country: USA;   State: California;   Locality: Cabrillo Point", new TermImpl("GAZ:00002461", "State of California"));
            put("Country: USA;   State: Texas", new TermImpl("GAZ:00002580", "State of Texas"));
            put("Country: Portugal", new TermImpl("GAZ:00004125", "Autonomous Region (Portugal)"));
            put("Country: USA;   Locality: Northeastern US contintental shelf", new TermImpl("GAZ:00002459", "United States of America"));
            put("Country: Sri Lanka", new TermImpl("GAZ:00003924", "Sri Lanka"));
            put("Country: USA;   State: Maine;   Locality: Troy", new TermImpl("GAZ:00002602", "State of Maine"));
            put("Country: New Zealand", new TermImpl("GAZ:00000469", "New Zealand"));
            put("Country: USA;   State: Maine;   Locality: Gulf of Maine", new TermImpl("GAZ:00002876", "Gulf of Maine"));
            put("Country: New Zealand;   State: Otago;   Locality: Dempster's Stream, Taieri River, 3 O'Clock catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: Panama;   Locality: Gatun Lake", new TermImpl("GAZ:00002898", "Lake Gatun"));
            put("Country: USA;   State: Maryland;   Locality: Chesapeake Bay", new TermImpl("GAZ:00002604", "Chesapeake Bay"));
            put("Country: India;   Locality: Cochin", new TermImpl("GAZ:00002839", "India"));
            put("Country: Ethiopia;   Locality: Lake Abaya", new TermImpl("GAZ:00041560", "Lake Abaya"));
            put("Country: unknown;   State: Black Sea", new TermImpl("GAZ:00008171", "Black Sea"));
            put("Country: St. Martin;   Locality: Caribbean", new TermImpl("GAZ:00044587", "Saint-Martin Island"));
            put("Country: USA;   State: Yellowstone", new TermImpl("GAZ:00002534", "Yellowstone National Park"));
            put("Country: Scotland;   Locality: Loch Leven", new TermImpl("GAZ:00002639", "Scotland"));
            put("Country: New Zealand;   State: Otago;   Locality: Sutton Stream, Taieri River, Sutton catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: Alaska;   Locality: Barrow", new TermImpl("GAZ:00198344", "City Of Barrow"));
            put("Country: Malawi;   Locality: Lake Nyasa", new TermImpl("GAZ:00000058", "Lake Malawi"));
            put("Country: USA;   State: Alaska;   Locality: Aleutian Islands", new TermImpl("GAZ:00005858", "Aleutian Islands"));
            put("Country: USA;   State: California;   Locality: Southern California", new TermImpl("GAZ:00168979", "Southern California"));
            put("Country: Canada;   State: Manitoba", new TermImpl("GAZ:00002571", "Province of Manitoba"));
            put("Country: USA;   State: Maine", new TermImpl("GAZ:00002602", "State Of Maine"));
            put("Country: Polynesia", new TermImpl("GAZ:00005861", "Polynesia"));
            put("Country: South Africa", new TermImpl("GAZ:00000553", "South Africa"));
            put("Country: New Zealand;   State: Otago;   Locality: Berwick, Meggatburn", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: New Zealand;   State: Otago;   Locality: Venlaw, Mimihau catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: Montana", new TermImpl("GAZ:00002606", "State of Montana"));
            put("Country: UK;   State: Yorkshire;   Locality: Aire,  Nidd & Wharfe Rivers", new TermImpl("GAZ:00003688", "Yorkshire and the Humber"));
            put("Country: Hong Kong", new TermImpl("GAZ:00003203", "Hong Kong"));
            put("Country: Pacific;   State: Bay of Panama", new TermImpl("GAZ:00047280", "Panama Bay"));
            put("Country: Netherlands;   State: Wadden Sea;   Locality: Ems estuary", new TermImpl("GAZ:00008137", "Wadden See"));
            put("Country: New Zealand;   State: Otago;   Locality: North Col, Silver catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: North Carolina", new TermImpl("GAZ:00002520", "State of North Carolina"));
            put("Country: USA;   State: Washington", new TermImpl("GAZ:00002553", "State of Washington"));
            put("Country: USA;   State: Alaska", new TermImpl("GAZ:00002521", "State of Alaska"));
            put("Country: USA;   State: Hawaii", new TermImpl("GAZ:00003939", "State of Hawaii"));
            put("Country: Uganda;   Locality: Lake George", new TermImpl("GAZ:00001102", "Uganda"));
            put("Country: Costa Rica;   State: Guanacaste", new TermImpl("GAZ:00003210", "Guanacaste Province"));
            put("Country: USA;   State: Massachusetts;   Locality: Cape Ann", new TermImpl("GAZ:00002537", "Commonwealth of Massachusetts"));
            put("Country: USA;   State: Maine;   Locality: Martins", new TermImpl("GAZ:00002602", "State of Maine"));
            put("Country: USA;   State: New York", new TermImpl("GAZ:00002514", "State of New York"));
            put("Country: General;   Locality: General", new TermImpl("GAZ:00000448", "geographic location"));
            put("Country: New Zealand;   State: Otago;   Locality: Stony, Sutton catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: Tibet", new TermImpl("GAZ:00004219", "Tibet Autonomous Region"));
            put("Country: USA;   State: Texas;   Locality: Franklin Mtns", new TermImpl("GAZ:00002580", "State of Texas"));
            put("Country: Russia", new TermImpl("GAZ:00002721", "Russia"));
            put("Country: New Zealand;   State: Otago;   Locality: Broad, Lee catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: Africa;   Locality: Lake McIlwaine", new TermImpl("GAZ:00016177", "Lake Chivero"));
            put("Country: England;   State: River Medway", new TermImpl("GAZ:00046238", "River Medway"));
            put("Country: South Africa;   Locality: Southwest coast", new TermImpl("GAZ:00001094", "Republic of South Africa"));
            put("Country: USA;   State: Kentucky", new TermImpl("GAZ:00004440", "Commonwealth of Kentucky"));
            put("Country: USA;   State: Washington;   Locality: Cape Flattery", new TermImpl("GAZ:00049988", "Cape Flattery"));
            put("Country: USA;   State: New Jersey", new TermImpl("GAZ:00002557", "State of New Jersey"));
            put("Country: India;   Locality: Rajasthan Desert", new TermImpl("GAZ:00002839", "India"));
            put("Country: England", new TermImpl("GAZ:00002641", "England"));
            put("Country: Austria;   Locality: Hafner Lake", new TermImpl("GAZ:00002942", "Austria"));
            put("Country: USA;   State:  NE USA", new TermImpl("GAZ:00002459", "United States of America"));
            put("Country: England;   Locality: Sheffield", new TermImpl("GAZ:00004871", "City of Sheffield"));
            put("Country: Uganda", new TermImpl("GAZ:00001102", "Uganda"));
            put("Country: USA;   State:  California;   Locality: Monterey Bay", new TermImpl("GAZ:00002509", "Monterey Bay"));
            put("Country: Germany", new TermImpl("GAZ:00002646", "Germany"));
            put("Country: England;   Locality: Skipwith Pond", new TermImpl("GAZ:00002641", "England"));
            put("Country: USA;   State: Wisconsin;   Locality: Little Rock Lake", new TermImpl("GAZ:00002586", "State of Wisconsin"));
            put("Country: USA;   State: California;   Locality: Coachella Valley", new TermImpl("GAZ:00002461", "State of California"));
            put("Country: Arctic", new TermImpl("GAZ:00000323", "Arctic Ocean"));
            put("Country: USA;   State: Michigan", new TermImpl("GAZ:00003152", "State of Michigan"));
            put("Country: Mexico;   State: Guerrero", new TermImpl("GAZ:00010927", "State of Guerrero"));
            put("Country: Norway;   State: Spitsbergen", new TermImpl("GAZ:00005397", "Spitzbergen"));
            put("Country: USA;   State: Kentucky;   Locality: Station 1", new TermImpl("GAZ:00004440", "Commonwealth of Kentucky"));
            put("Country: New Zealand;   State: Otago;   Locality: Kye Burn", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: New Zealand;   State: Otago;   Locality: Little Kye, Kye Burn catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: North Carolina;   Locality: Pamlico", new TermImpl("GAZ:00002520", "State of North Carolina"));
            put("Country: Antarctic", new TermImpl("GAZ:00000462", "Antarctica"));
            put("Country: USA;   State: Arizona", new TermImpl("GAZ:00002518", "State of Arizona"));
            put("Country: England;   Locality: Lancaster", new TermImpl("GAZ:04000224", "City of Lancaster"));
            put("Country: USA;   State: Florida;   Locality: Everglades", new TermImpl("GAZ:00082878", "Everglades"));
            put("Country: Barbados", new TermImpl("GAZ:00001251", "Barbados"));
            put("Country: USA;   State: New York;   Locality: Bridge Brook", new TermImpl("GAZ:00002514", "State of New York"));
            put("Country: England;   Locality: Oxshott Heath", new TermImpl("GAZ:00002641", "England"));
            put("Country: New Zealand;   State: Otago;   Locality: Blackrock, Lee catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: Canada;   State: Ontario", new TermImpl("GAZ:00002563", "Province of Ontario"));
            put("Country: Puerto Rico;   Locality: El Verde", new TermImpl("GAZ:00006935", "Commonwealth of Puerto Rico"));
            put("Country: Quebec", new TermImpl("GAZ:00002569", "Province of Quebec"));
            put("Country: Ireland", new TermImpl("GAZ:00002943", "Republic of Ireland"));
            put("Country: Wales;   Locality: Dee River", new TermImpl("GAZ:00007857", "River Dee [Wales]"));
            put("Country: Marshall Islands", new TermImpl("GAZ:00006470", "Republic of the Marshall Islands"));
            put("Country: New Zealand;   State: South Island;   Locality: Canton Creek, Taieri River, Lee catchment", new TermImpl("GAZ:00004764", "South Island"));
            put("Country: Seychelles", new TermImpl("GAZ:00006922", "The Seychelles"));
            put("Country: Namibia;   Locality: Namib Desert", new TermImpl("GAZ:00007516", "Namib Desert"));
            put("Country: USA;   State: Rhode Island", new TermImpl("GAZ:00002531", "State of Rhode Island"));
            put("Country: USA;   State: Idaho-Utah;   Locality: Deep Creek", new TermImpl("GAZ:00000448", "geographic location"));
            put("Country: Malawi", new TermImpl("GAZ:00001105", "Malawi"));
            put("Country: Malaysia", new TermImpl("GAZ:00003902", "GAZ:00003902"));
            put("Country: Europe;   State: Central Europe", new TermImpl("GAZ:00000464", "Europe"));
            put("Country: USA;   State: Florida", new TermImpl("GAZ:00002888", "State of Florida"));
            put("Country: Norway;   State: Oppland;   Locality: Ovre Heimdalsvatn Lake", new TermImpl("GAZ:00005244", "Oppland County"));
            put("Country: Austria;   Locality: Vorderer Finstertaler Lake", new TermImpl("GAZ:00002942", "Austria"));
            put("Country: Canada;   Locality: high Arctic", new TermImpl("GAZ:00002560", "Canada"));
            put("Country: unknown", new TermImpl("GAZ:00000448", "geographic location"));
            put("Country: Peru", new TermImpl("GAZ:00002932", "Peru"));
            put("Country: USA;   State: New England", new TermImpl("GAZ:00006323", "New England Division"));
            put("Country: Great Britain", new TermImpl("GAZ:00002637", "United Kingdom"));
            put("Country: New Zealand;   State: Otago;   Locality: German, Kye Burn catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: Colorado", new TermImpl("GAZ:00006254", "State of Colorado"));
            put("Country: USA;   State: Texas;   Locality: Hueco Tanks", new TermImpl("GAZ:00002580", "State of Texas"));
            put("Country: Canada;   State: Ontario;   Locality: Mad River", new TermImpl("GAZ:00002563", "Province of Ontario"));
            put("Country: Wales;   Locality: River Rheidol", new TermImpl("GAZ:00002640", "Wales"));
            put("Country: Costa Rica;   State: de Osa", new TermImpl("GAZ:00002901", "Costa Rica"));
            put("Country: Finland", new TermImpl("GAZ:00002937", "Finland"));
            put("Country: Africa;   Locality: Crocodile Creek,  Lake Nyasa", new TermImpl("GAZ:00000058", "Lake Malawi"));
            put("Country: USA;   State: Florida;   Locality: South Florida", new TermImpl("GAZ:00004412", "Southern Florida"));
            put("Country: USA;   State: Illinois", new TermImpl("GAZ:00003142", "State of Illinois"));
            put("Country: Puerto Rico;   Locality: Puerto Rico-Virgin Islands shelf", new TermImpl("GAZ:00002822", "Puerto Rico"));
            put("Country: England;   Locality: River Thames", new TermImpl("GAZ:00007824", "River Thames"));
            put("Country: Madagascar", new TermImpl("GAZ:00006934", "Madagascar"));
            put("Country: USA;   State: New Mexico;   Locality: White Sands", new TermImpl("GAZ:00004427", "State of New Mexico"));
            put("Country: England;   Locality: River Cam", new TermImpl("GAZ:00002641", "England"));
            put("Country: Australia", new TermImpl("GAZ:00000463", "Australia"));
            put("Country: USA;   State: North Carolina;   Locality: Coweeta", new TermImpl("GAZ:00002520", "State of North Carolina"));
            put("Country: Scotland;   Locality: Ythan estuary", new TermImpl("GAZ:00002639", "Scotland"));
            put("Country: Wales;   Locality: River Clydach", new TermImpl("GAZ:00052132", "South Wales"));
            put("Country: USA;   State: Texas;   Locality: Hueco Mountains", new TermImpl("GAZ:00002580", "State of Texas"));
            put("Country: Wales", new TermImpl("GAZ:00002640", "Wales"));
            put("Country: USA;   State: Arizona;   Locality: Sonora Desert", new TermImpl("GAZ:00006847", "Sonoran Desert"));
            put("Country: England;   Locality: Silwood Park", new TermImpl("GAZ:00052254", "Silwood Park"));
            put("Country: Austria;   Locality: Neusiedler Lake", new TermImpl("GAZ:00002942", "Austria"));
            put("Country: New Zealand;   State: Otago;   Locality: Narrowdale catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: California", new TermImpl("GAZ:00002461", "State of California"));
            put("Country: England;   State: Oxfordshire;   Locality: Wytham Wood", new TermImpl("GAZ:00052249", "Wytham Woods"));
            put("Country: USA;   State: Michigan;   Locality: Tuesday Lake", new TermImpl("GAZ:00003152", "State of Michigan"));
            put("Country: USA;   State: Alabama", new TermImpl("GAZ:00006881", "State of Alabama"));
            put("Country: New Zealand;   State: Otago;   Locality: Healy Stream, Taieri River, Kye Burn catchment", new TermImpl("GAZ:00004767", "Otago Region"));
            put("Country: USA;   State: New York;   Locality: Long Island", new TermImpl("GAZ:00002584", "Long Island"));
            put("Country: Venezuela", new TermImpl("GAZ:00002931", "Venezuela"));
            put("Country: New Zealand;   State: Otago;   Locality: Akatore, Akatore catchment", new TermImpl("GAZ:00004767", "Otago Region"));
        }
    };
    int gazHit = 0;
    for (String locality : listener.localities) {
        if (gazMap.containsKey(locality) && gazMap.get(locality).getId().startsWith("GAZ:")) {
            gazHit++;
        } else {
            System.out.println("put(\"" + locality + "\", new Term(\"externalid\", \"name\"));");
        }
    }
    assertThat(gazHit, is(listener.localities.size()));
}

Example 13 with TermImpl

use of org.eol.globi.domain.TermImpl in project eol-globi-data by jhpoelen.

the class TaxonUtilTest method copyTaxon.

@Test
public void copyTaxon() {
    Taxon src = new TaxonImpl("name", "id");
    src.setStatus(new TermImpl("statusId", "statusLabel"));
    Taxon target = new TaxonImpl();
    TaxonUtil.copy(src, target);
    assertThat(target.getStatus().getId(), is("statusId"));
    assertThat(target.getStatus().getName(), is("statusLabel"));
}

Example 14 with TermImpl

use of org.eol.globi.domain.TermImpl in project eol-globi-data by jhpoelen.

the class TermLookupServiceImpl method buildMapping.

private void buildMapping(List<URI> uriList) throws TermLookupServiceException {
    mapping = new HashMap<>();
    for (URI uri : uriList) {
        try {
            String response = contentToString(uri);
            CSVParse parser = CSVTSVUtil.createCSVParse(new StringReader(response));
            parser.changeDelimiter(getDelimiter());
            if (hasHeader()) {
                parser = CSVTSVUtil.createLabeledCSVParser(parser);
            }
            String[] line;
            while ((line = parser.getLine()) != null) {
                if (line.length < 4) {
                    LOG.info("line: [" + parser.getLastLineNumber() + "] in [" + uriList + "] contains less than 4 columns");
                } else {
                    String sourceName = line[1];
                    String targetId = line[2];
                    String targetName = line[3];
                    if (StringUtils.isNotBlank(sourceName) && StringUtils.isNotBlank(targetId) && StringUtils.isNotBlank(targetName)) {
                        List<Term> terms = mapping.computeIfAbsent(sourceName, k -> new ArrayList<>());
                        terms.add(new TermImpl(targetId, targetName));
                    }
                }
            }
        } catch (IOException e) {
            throw new TermLookupServiceException("failed to retrieve mapping from [" + uriList + "]", e);
        }
    }
}

Example 15 with TermImpl

use of org.eol.globi.domain.TermImpl in project eol-globi-data by jhpoelen.

the class CMECSService method buildTermMap.

private static Map<String, Term> buildTermMap() throws IOException {
    LOG.info(CMECSService.class.getSimpleName() + " instantiating...");
    String uri = "https://cmecscatalog.org/cmecs/documents/cmecs4.accdb";
    LOG.info("CMECS data [" + uri + "] downloading ...");
    HttpGet get = new HttpGet(uri);
    try {
        HttpResponse execute = HttpUtil.getHttpClient().execute(get);
        File cmecs = File.createTempFile("cmecs", "accdb");
        cmecs.deleteOnExit();
        IOUtils.copy(execute.getEntity().getContent(), new FileOutputStream(cmecs));
        LOG.info("CMECS data [" + uri + "] downloaded.");
        Database db = new DatabaseBuilder().setFile(new File(cmecs.toURI())).setReadOnly(true).open();
        Map<String, Term> aquaticSettingsTerms = new HashMap<>();
        Table table = db.getTable("Aquatic Setting");
        Map<String, Object> row;
        while ((row = table.getNextRow()) != null) {
            Integer id = (Integer) row.get("AquaticSetting_Id");
            String name = (String) row.get("AquaticSettingName");
            String termId = TaxonomyProvider.ID_CMECS + id;
            aquaticSettingsTerms.put(name, new TermImpl(termId, name));
        }
        cmecs.delete();
        LOG.info(CMECSService.class.getSimpleName() + " instantiated.");
        return aquaticSettingsTerms;
    } finally {
        get.releaseConnection();
    }
}