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

Example 21 with Dataset

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

the class NodeFactoryNeo4jTest method addDatasetToStudy.

@Test
public void addDatasetToStudy() throws NodeFactoryException, IOException {
    StudyImpl study1 = new StudyImpl("my title", SOME_DOI, "some citation");
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, false);
    dataset.setConfig(objectNode);
    study1.setOriginatingDataset(dataset);
    StudyNode study = getNodeFactory().getOrCreateStudy(study1);
    Dataset origDataset = study.getOriginatingDataset();
    assertThat(origDataset, is(notNullValue()));
    assertThat(origDataset.getArchiveURI().toString(), is("some:uri"));
    assertThat(origDataset.getOrDefault(DatasetConstant.SHOULD_RESOLVE_REFERENCES, "true"), is("false"));
    String expectedConfig = new ObjectMapper().writeValueAsString(objectNode);
    assertThat(new ObjectMapper().writeValueAsString(origDataset.getConfig()), is(expectedConfig));
    Node datasetNode = NodeUtil.getDataSetForStudy(study);
    assertThat(datasetNode.getProperty(DatasetConstant.NAMESPACE), is("some/namespace"));
    assertThat(datasetNode.getProperty("archiveURI"), is("some:uri"));
    assertThat(datasetNode.getProperty(DatasetConstant.SHOULD_RESOLVE_REFERENCES), is("false"));
    StudyImpl otherStudy = new StudyImpl("my other title", SOME_DOI, "some citation");
    otherStudy.setOriginatingDataset(dataset);
    StudyNode studySameDataset = getNodeFactory().getOrCreateStudy(otherStudy);
    Node datasetNodeOther = NodeUtil.getDataSetForStudy(studySameDataset);
    assertThat(datasetNode.getId(), is(datasetNodeOther.getId()));
}

Example 22 with Dataset

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

the class NodeFactoryNeo4jTest method assertDataset.

protected void assertDataset(String citationKey) {
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, false);
    objectNode.put(citationKey, "some citation");
    dataset.setConfig(objectNode);
    Dataset origDataset = getNodeFactory().getOrCreateDataset(dataset);
    assertThat(origDataset, is(notNullValue()));
    assertThat(origDataset.getArchiveURI().toString(), is("some:uri"));
    assertThat(origDataset.getOrDefault(DatasetConstant.SHOULD_RESOLVE_REFERENCES, "true"), is("false"));
    assertThat(origDataset.getOrDefault(DatasetConstant.CITATION, "no citation"), is("some citation"));
    assertThat(origDataset.getCitation(), is("some citation"));
    assertThat(origDataset.getOrDefault(DatasetConstant.LAST_SEEN_AT, "1"), is(not("1")));
    Dataset datasetAnother = getNodeFactory().getOrCreateDataset(dataset);
    assertThat(((DatasetNode) datasetAnother).getNodeID(), is(((DatasetNode) origDataset).getNodeID()));
}

Example 23 with Dataset

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

the class DatasetImporterForSzoboszlaiTest method importShapes2.

@Test
public void importShapes2() throws IOException {
    Dataset testDataset = getTestDataset();
    ParserFactory parserFactory = new ParserFactoryForDataset(testDataset);
    DatasetImporterForSzoboszlai studyImporterForSzoboszlai = new DatasetImporterForSzoboszlai(parserFactory, nodeFactory);
    studyImporterForSzoboszlai.setDataset(testDataset);
    Map<Integer, LatLng> localityMap = studyImporterForSzoboszlai.importShapes2();
    assertLocalityMap(localityMap);
}

Example 24 with Dataset

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

the class DatasetImporterForSzoboszlaiTest method getTestDataset.

private Dataset getTestDataset() throws 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\": \"szoboszlai/CCPDDlinkdata_v2.csv\",\n" + "    \"shapes\": \"szoboszlai/CCPDDlocationdata_test.zip\"\n" + "  }\n" + "}");
    Dataset dataset = new DatasetLocal(inStream -> inStream);
    dataset.setConfig(config);
    return dataset;
}

Example 25 with Dataset

use of org.globalbioticinteractions.dataset.Dataset 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));
}