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

Example 41 with Dataset

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

the class DatasetImporterForRSSTest method readRSS.

@Test
public void readRSS() throws StudyImporterException, IOException {
    final Dataset dataset = getDatasetGroup();
    List<Dataset> datasets = DatasetImporterForRSS.getDatasetsForFeed(dataset);
    assertThat(datasets.size(), is(3));
    assertThat(datasets.get(0).getOrDefault("hasDependencies", null), is("false"));
}

Example 42 with Dataset

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

the class DatasetImporterForRSSTest method readFieldMuseum.

@Test
public void readFieldMuseum() throws StudyImporterException, IOException {
    String configJson = "{ \"url\": \"classpath:/org/eol/globi/data/rss_fieldmuseum.xml\" }";
    final Dataset dataset = datasetFor(configJson);
    List<Dataset> datasets = DatasetImporterForRSS.getDatasetsForFeed(dataset);
    assertThat(datasets.size(), is(14));
    assertThat(datasets.get(0).getOrDefault("hasDependencies", null), is("false"));
}

Example 43 with Dataset

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

the class DatasetImporterForRSSTest method titleIncludePatternOnly.

@Test
public void titleIncludePatternOnly() throws StudyImporterException, IOException {
    String configJson = "{ \"url\": \"classpath:/org/eol/globi/data/rss_vertnet.xml\", " + "\"include\": \".*(Arctos).*\", " + "\"hasDependencies\": true }";
    final Dataset dataset = datasetFor(configJson);
    assertTrue(DatasetImporterForRSS.shouldIncludeTitleInDatasetCollection("bla (Arctos) GGBN", dataset));
    assertTrue(DatasetImporterForRSS.shouldIncludeTitleInDatasetCollection("bla (Arctos)", dataset));
    assertFalse(DatasetImporterForRSS.shouldIncludeTitleInDatasetCollection("bla", dataset));
}

Example 44 with Dataset

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

the class DatasetImporterForRSSTest method embeddedDatasetWithConfig.

@Test
public void embeddedDatasetWithConfig() throws IOException {
    Dataset embeddedDataset = embeddedDatasetFor(getDatasetGroupWithProperty(), URI.create("http://example.com/archive.zip"));
    assertThat(embeddedDataset.getCitation(), is("some other citation"));
    assertThat(embeddedDataset.getOrDefault(DatasetConstant.SHOULD_RESOLVE_REFERENCES, "true"), is("false"));
    assertThat(embeddedDataset.getArchiveURI().toString(), is("http://example.com/archive.zip"));
}

Example 45 with Dataset

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

the class DatasetImporterForTSVTest method withGenus.

@Test
public void withGenus() throws StudyImporterException {
    String firstFewLines = "sourceTaxonFamily\tsourceTaxonGenus\tinteractionTypeId\ttargetTaxonName\n" + "Bacillaceae\tBacillus\tRO:0002454\tMorus alba\n";
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    Taxon taxon = taxonIndex.findTaxonByName("Bacillus");
    assertThat(taxon, is(notNullValue()));
    assertThat(taxon.getName(), is("Bacillus"));
    assertThat(taxon.getPath(), is("Bacillaceae | Bacillus"));
    assertThat(taxon.getPathNames(), is("family | genus"));
    final List<StudyNode> allStudies = NodeUtil.findAllStudies(getGraphDb());
}