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

Example 36 with DatasetImpl

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

the class NodeFactoryNeo4jTest method datasetWithNamespace.

private DatasetImpl datasetWithNamespace(String namespace) {
    DatasetImpl dataset = new DatasetImpl(namespace, URI.create("some:uri"), inStream -> inStream);
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, false);
    dataset.setConfig(objectNode);
    return dataset;
}

Example 37 with DatasetImpl

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

the class CmdGenerateReportTest method generateCollectionReport.

@Test
public void generateCollectionReport() throws NodeFactoryException {
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    Dataset originatingDatasetNode = nodeFactory.getOrCreateDataset(originatingDataset);
    StudyImpl study1 = new StudyImpl("a title", null, "citation");
    study1.setOriginatingDataset(originatingDatasetNode);
    createStudy(study1);
    StudyImpl study2 = new StudyImpl("another title", null, "citation");
    study2.setOriginatingDataset(originatingDatasetNode);
    createStudy(study2);
    resolveNames();
    new CmdGenerateReport(getGraphDb(), cacheService).generateReportForCollection();
    IndexHits<Node> reports = getGraphDb().index().forNodes("reports").query("*", "*");
    assertThat(reports.size(), is(1));
    Node reportNode = reports.getSingle();
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(1));
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(1));
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES), is(2));
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS), is(8));
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA), is(3));
    assertThat(reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH), is(2));
}

Example 38 with DatasetImpl

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

the class NodeFactoryNeo4jTest method addDatasetToStudyNulls2.

@Test
public void addDatasetToStudyNulls2() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("my title", SOME_DOI, "some citation");
    DatasetImpl dataset = new DatasetImpl("some/namespace", null, inStream -> inStream);
    study1.setOriginatingDataset(dataset);
    StudyNode study = getNodeFactory().getOrCreateStudy(study1);
    Node datasetNode = NodeUtil.getDataSetForStudy(study);
    assertThat(datasetNode.getProperty(DatasetConstant.NAMESPACE), is("some/namespace"));
    assertThat(datasetNode.hasProperty(DatasetConstant.ARCHIVE_URI), is(false));
    assertThat(datasetNode.getProperty(DatasetConstant.SHOULD_RESOLVE_REFERENCES), is("true"));
}

Example 39 with DatasetImpl

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

the class DatasetImporterForDunneIT method importStudy2.

@Test
public void importStudy2() throws StudyImporterException, IOException {
    String configJson = "{ \"citation\": \"blabla\",\n" + "  \"format\": \"dunne\",\n" + "  \"resources\": {\n" + "    \"nodes\": \"https://raw.githubusercontent.com/globalbioticinteractions/dunne2016SanakNearshore/main/nodes.tsv\",\n" + "    \"links\": \"https://raw.githubusercontent.com/globalbioticinteractions/dunne2016SanakNearshore/main/links.tsv\"\n" + "  },\n" + "  \"location\": {\n" + "    \"locality\": {\n" + "      \"id\": \"GEONAMES:5873327\",\n" + "      \"name\": \"Sanak Island, Alaska, USA\"\n" + "    },\n" + "    \"latitude\": 60,\n" + "    \"longitude\": 60\n" + "  }\n" + "}";
    DatasetImpl dunne2016 = new DatasetImpl("dunne2016", URI.create("http://example.com"), inStream -> inStream);
    dunne2016.setConfig(new ObjectMapper().readTree(configJson));
    ParserFactory parserFactory = new ParserFactoryForDataset(dunne2016);
    DatasetImporterForDunne importer = new DatasetImporterForDunne(parserFactory, nodeFactory);
    importer.setDataset(dunne2016);
    importStudy(importer);
    StudyNode study = getStudySingleton(getGraphDb());
    assertThat(study, is(notNullValue()));
    assertThat(study.getCitation(), is(notNullValue()));
    assertThat(getSpecimenCount(study), is(6774 * 2));
}

Example 40 with DatasetImpl

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

the class DatasetImporterForSzoboszlaiIT method importAll.

@Test
public void importAll() throws StudyImporterException, IOException {
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Szoboszlai AI, Thayer JA, Wood SA, Sydeman WJ, Koehn LE (2015) Data from: Forage species in predator diets: synthesis of data from the California Current. Dryad Digital Repository. https://doi.org/10.5061/dryad.nv5d2\",\n" + "  \"doi\": \"https://doi.org/10.5061/dryad.nv5d2\",\n" + "  \"format\": \"szoboszlai\",\n" + "  \"resources\": {\n" + "    \"links\": \"http://datadryad.org/bitstream/handle/10255/dryad.94536/CCPDDlinkdata_v1.csv\",\n" + "    \"shapes\": \"http://datadryad.org/bitstream/handle/10255/dryad.94535/CCPDDlocationdata_v1.zip\"\n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("someRepo", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(config);
    ParserFactory parserFactory = new ParserFactoryForDataset(dataset);
    DatasetImporterForSzoboszlai importer = new DatasetImporterForSzoboszlai(parserFactory, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(getStudySingleton(getGraphDb()).getUnderlyingNode()), relationship -> {
        Specimen specimenNode = new SpecimenNode(relationship.getEndNode());
        Location sampleLocation = specimenNode.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getLatitude(), is(notNullValue()));
        assertThat(sampleLocation.getLongitude(), is(notNullValue()));
    });
    assertThat(taxonIndex.findTaxonByName("Thunnus thynnus"), is(notNullValue()));
    assertThat(nodeFactory.findLocation(new LocationImpl(34.00824202376044, -120.72716166720323, null, null)), is(notNullValue()));
}