Examples with DatasetImpl org.globalbioticinteractions.dataset.DatasetImpl used on opensource projects

Example 41 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method importMinimal.

@Test
public void importMinimal() throws StudyImporterException {
    String minimalLines = "sourceTaxonId\tsourceTaxonName\tinteractionTypeId\tinteractionTypeName\ttargetTaxonId\ttargetTaxonName\tlocalityId\tlocalityName\tdecimalLatitude\tdecimalLongitude\tobservationDateTime\treferenceDoi\treferenceCitation\n" + "EOL:123\t\tRO:0002444\t\tEOL:111\t\t\t\t\t\t\t\tGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1\n" + "EOL:456\t\tRO:0002444\t\tEOL:222\t\t\t\t\t\t\t\tGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1\n" + "EOL:678\t\tRO:0002444\t\tEOL:333\t\t\t\t\t\t\t\tGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1\n" + "EOL:912\t\tRO:0002444\t\tEOL:444\t\t\t\t\t\t\t\tGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1\n";
    DatasetImpl dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), minimalLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    Taxon taxon = taxonIndex.findTaxonById("EOL:123");
    assertThat(taxon, is(notNullValue()));
    assertThat(taxon.getName(), is("no name"));
    assertThat(taxon.getExternalId(), is("EOL:123"));
    assertStudyTitles("someRepoGittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1");
}

Example 42 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method importFewLinesCSVAndTSV.

@Test
public void importFewLinesCSVAndTSV() throws StudyImporterException {
    DatasetImpl dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLinesTSV);
            put(URI.create("/interactions.csv"), firstFewLinesCSV);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    assertExists("Leptoconchus incycloseris");
    assertExists("TESTLeptoconchus incycloseris");
    assertExists("Sandalolitha dentata");
    assertStudyTitles("someRepodoi:10.1007/s13127-011-0039-1");
}

Example 43 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method assertArgumentType.

private void assertArgumentType(String firstFewLines, final RelTypes argumentType) throws StudyImporterException {
    DatasetImpl dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    final AtomicBoolean foundStudy = new AtomicBoolean(false);
    NodeUtil.findStudies(getGraphDb(), new NodeListener() {

        @Override
        public void on(Node node) {
            assertTrue(node.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(argumentType)));
            foundStudy.set(true);
        }
    });
    assertThat(foundStudy.get(), is(true));
}

Example 44 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForPlanqueIT method importAll.

@Test
public void importAll() throws StudyImporterException, IOException {
    final List<String> errorMessages = new ArrayList<String>();
    BaseDatasetImporter importer = new DatasetImporterForPlanque(new ParserFactoryLocal(), nodeFactory);
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Benjamin Planque, Raul Primicerio, Kathrine Michalsen, Michaela Aschan, Grégoire Certain, Padmini Dalpadado, Harald Gjøsæater, Cecilie Hansen, Edda Johannesen, Lis Lindal Jørgensen, Ina Kolsum, Susanne Kortsch, Lise-Marie Leclerc, Lena Omli, Mette Skern-Mauritzen, and Magnus Wiedmann 2014. Who eats whom in the Barents Sea: a food web topology from plankton to whales. Ecology 95:1430–1430. https://doi.org/10.1890/13-1062.1\",\n" + "  \"doi\": \"https://doi.org/10.1890/13-1062.1\",\n" + "  \"format\": \"planque\",\n" + "  \"resources\": {\n" + "    \"links\": \"http://www.esapubs.org/archive/ecol/E095/124/revised/PairwiseList.txt\",\n" + "    \"references\": \"http://www.esapubs.org/archive/ecol/E095/124/revised/References.txt\",\n" + "    \"referencesForLinks\": \"http://www.esapubs.org/archive/ecol/E095/124/revised/PairWise2References.txt\"\n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(config);
    importer.setDataset(dataset);
    importer.setLogger(new NullImportLogger() {

        @Override
        public void warn(LogContext ctx, String message) {
            errorMessages.add(message);
        }
    });
    importStudy(importer);
    int interactionCount = 0;
    List<StudyNode> studies = NodeUtil.findAllStudies(getGraphDb());
    for (StudyNode study : studies) {
        interactionCount += getSpecimenCount(study);
    }
    assertThat(interactionCount, is(4900));
    int uniqueReference = 236;
    // note that the +1 is for all links that had no reference associated to it
    assertThat(studies.size(), is(uniqueReference + 1));
    assertThat(taxonIndex.findTaxonByName("Trisopterus esmarkii"), is(notNullValue()));
    assertThat(errorMessages.size(), is(0));
}

Example 45 with DatasetImpl

use of org.globalbioticinteractions.dataset.DatasetImpl in project eol-globi-data by jhpoelen.

the class DatasetImporterForJSONLDTest method importStaticInvalid.

@Test(expected = StudyImporterException.class)
public void importStaticInvalid() throws StudyImporterException, URISyntaxException {
    DatasetImporter importer = new DatasetImporterForJSONLD(null, nodeFactory);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfigURI(URI.create("classpath:/org/eol/globi/data/globi-jsonld/globi-dataset.jsonld.invalid"));
    importer.setDataset(dataset);
    importStudy(importer);
}