Examples with DatasetLocal org.eol.globi.service.DatasetLocal used on opensource projects

Example 1 with DatasetLocal

use of org.eol.globi.service.DatasetLocal in project eol-globi-data by jhpoelen.

the class StudyImporterForJSONLD method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Model model;
    try {
        model = buildModel();
    } catch (IOException e) {
        throw new StudyImporterException("failed to import [" + getResourceURI() + "]", e);
    }
    Query query;
    try {
        query = QueryFactory.create(IOUtils.toString(new DatasetLocal().getResource("find-jsonld-interactions.rq"), CharsetConstant.UTF8));
    } catch (IOException e) {
        throw new StudyImporterException("failed to find sparql query", e);
    }
    QueryExecution exec = QueryExecutionFactory.create(query, model);
    try {
        ResultSet results = exec.execSelect();
        while (results.hasNext()) {
            QuerySolution solution = results.nextSolution();
            String subj = solution.get("subj").asResource().getURI();
            String creationDate = solution.get("creationDate").asLiteral().getString();
            String authorURI = solution.get("author").toString();
            String author;
            try {
                author = nodeFactory.getAuthorResolver().findFullName(authorURI);
            } catch (IOException e) {
                throw new StudyImporterException("failed to resolve author URI [" + authorURI + "]");
            }
            final String source1 = author + ". " + new DateTime(parseDate(creationDate)).getYear() + ". " + CitationUtil.createLastAccessedString(getResourceURI().toString());
            Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getResourceURI() + subj, source1, null, subj));
            study.setExternalId(subj);
            Specimen source = createSpecimen(solution, study, "subjTaxon");
            Specimen target = createSpecimen(solution, study, "targetTaxon");
            String interactType = solution.get("p").asResource().getLocalName();
            InteractType interactType1 = InteractType.typeOf(StringUtils.replace(interactType, "RO_", "RO:"));
            if (interactType1 == null) {
                throw new StudyImporterException("failed to map interaction type [" + interactType + "]");
            }
            String collTime = solution.get("collTime").asLiteral().getString();
            Date date = parseDate(collTime);
            nodeFactory.setUnixEpochProperty(source, date);
            nodeFactory.setUnixEpochProperty(target, date);
            Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(solution.get("collLat").asLiteral().getDouble(), solution.get("collLng").asLiteral().getDouble(), null, null));
            target.caughtIn(loc);
            source.caughtIn(loc);
            source.interactsWith(target, interactType1);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import jsonld data in [" + getResourceURI() + "]", e);
    } finally {
        exec.close();
    }
}

Example 2 with DatasetLocal

use of org.eol.globi.service.DatasetLocal in project eol-globi-data by jhpoelen.

the class StudyImporterForRaymondIT method importStudy.

@Test
public void importStudy() throws StudyImporterException {
    StudyImporterForRaymond importer = new StudyImporterForRaymond(new ParserFactoryLocal(), nodeFactory);
    importer.setGeoNamesService(new GeoNamesService() {

        @Override
        public boolean hasTermForLocale(String locality) {
            return true;
        }

        @Override
        public LatLng findLatLng(String locality) throws IOException {
            return new LatLng(0, 0);
        }
    });
    importer.setDataset(new DatasetLocal());
    importStudy(importer);
    importer.setGeoNamesService(new GeoNamesServiceImpl());
    Collection<String> unmappedLocations = new HashSet<String>();
    for (String location : importer.getLocations()) {
        if (!importer.getGeoNamesService().hasTermForLocale(location)) {
            unmappedLocations.add(location);
        }
    }
    assertThat(unmappedLocations, containsInAnyOrder("Not described", "South African waters", "Ocean location", "subantarctic waters", "oceanic habitat in Southern Ocean. 68� 07\u0019 S & 70�13\u0019 S", "Subantarctic Pacific Ocean"));
}

Example 3 with DatasetLocal

use of org.eol.globi.service.DatasetLocal in project eol-globi-data by jhpoelen.

the class ParserFactoryForDatasetTest method parserWithDatasetContextLocalResource.

@Test
public void parserWithDatasetContextLocalResource() throws IOException {
    ParserFactoryForDataset parserFactory = new ParserFactoryForDataset(new DatasetLocal());
    LabeledCSVParser parser = parserFactory.createParser("classpath:/org/eol/globi/data/someResource.csv", "UTF-8");
    assertThat(parser.getLine(), is(new String[] { "valueA", "valueB" }));
}

Example 4 with DatasetLocal

use of org.eol.globi.service.DatasetLocal in project eol-globi-data by jhpoelen.

the class StudyImporterForCoetzerTest method importSome.

@Test
public void importSome() throws StudyImporterException, IOException {
    StudyImporterForCoetzer importer = new StudyImporterForCoetzer(null, nodeFactory);
    DatasetImpl dataset = new DatasetLocal();
    JsonNode config = new ObjectMapper().readTree("{\"citation\": \"source citation\", \"resources\": {\"archive\": \"coetzer/CatalogOfAfrotropicalBees.zip\"}}");
    dataset.setConfig(config);
    importer.setDataset(dataset);
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study allStudy : allStudies) {
        assertThat(allStudy.getSource(), startsWith("source citation"));
        assertThat(allStudy.getSource(), containsString("Accessed at"));
    }
    assertThat(taxonIndex.findTaxonByName("Agrostis tremula"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Coelioxys erythrura"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Patellapis namaquensis"), is(notNullValue()));
}

Example 5 with DatasetLocal

use of org.eol.globi.service.DatasetLocal in project eol-globi-data by jhpoelen.

the class StudyImporterForSeltmannTest method importSome.

@Test
public void importSome() throws StudyImporterException, IOException {
    StudyImporterForSeltmann importer = new StudyImporterForSeltmann(null, nodeFactory);
    Dataset dataset = new DatasetLocal();
    JsonNode config = new ObjectMapper().readTree("{\"citation\": \"some citation\", \"resources\": {\"archive\": \"seltmann/testArchive.zip\"}}");
    dataset.setConfig(config);
    importer.setDataset(dataset);
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study allStudy : allStudies) {
        assertThat(allStudy.getSource(), startsWith("Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388"));
        assertThat(allStudy.getCitation(), is("Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388"));
        Iterable<Relationship> specimens = NodeUtil.getSpecimens(allStudy);
        for (Relationship specimen : specimens) {
            SpecimenNode spec = new SpecimenNode(specimen.getEndNode());
            final String recordId = (String) spec.getUnderlyingNode().getProperty("idigbio:recordID");
            assertThat(recordId, is(notNullValue()));
            assertThat(spec.getExternalId(), is(recordId));
            Term basisOfRecord = spec.getBasisOfRecord();
            assertThat(basisOfRecord.getId(), either(is("TEST:PreservedSpecimen")).or(is("TEST:LabelObservation")));
            assertThat(basisOfRecord.getName(), either(is("PreservedSpecimen")).or(is("LabelObservation")));
        }
    }
    assertThat(taxonIndex.findTaxonByName("Megandrena mentzeliae"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Mentzelia tricuspis"), is(notNullValue()));
}