Examples with StudyImpl org.eol.globi.domain.StudyImpl used on opensource projects

Example 21 with StudyImpl

use of org.eol.globi.domain.StudyImpl in project eol-globi-data by jhpoelen.

the class ExporterMeasurementOrFactTest method noMatchNames.

@Test
public void noMatchNames() throws IOException, NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.createStudy(new StudyImpl("myStudy", null, null, null));
    nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_NAME, "externalId1"));
    nodeFactory.createSpecimen(myStudy, new TaxonImpl("Some namus", PropertyAndValueDictionary.NO_MATCH));
    Study myStudy1 = nodeFactory.findStudy("myStudy");
    StringWriter row = new StringWriter();
    new ExporterMeasurementOrFact().exportStudy(myStudy1, row, false);
    assertThat(row.getBuffer().toString(), equalTo(""));
}

Example 22 with StudyImpl

use of org.eol.globi.domain.StudyImpl in project eol-globi-data by jhpoelen.

the class GraphExporterImplTest method exportAll.

@Test
public void exportAll() throws StudyImporterException, IOException {
    File tmpDir = FileUtils.getTempDirectory();
    File tmpDirPath = new File(tmpDir, "test" + new Random().nextLong());
    FileUtils.forceMkdir(tmpDirPath);
    assertThat(tmpDirPath.list().length, is(0));
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("a study", "a source", "doi:12345L", null));
    Specimen human = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens", "NCBI:123"));
    human.ate(nodeFactory.createSpecimen(study, new TaxonImpl("Canis familiaris", "BLA:444")));
    resolveNames();
    try {
        new GraphExporterImpl().export(getGraphDb(), tmpDirPath.getAbsolutePath() + "/");
        assertThat(tmpDirPath.list().length, is(6));
    } finally {
        FileUtils.deleteQuietly(tmpDirPath);
    }
}

Example 23 with StudyImpl

use of org.eol.globi.domain.StudyImpl in project eol-globi-data by jhpoelen.

the class ExporterSiteMapForNamesTest method writeSiteMapWithNames.

@Test
public void writeSiteMapWithNames() throws StudyImporterException, IOException {
    taxonIndex = new NonResolvingTaxonIndex(getGraphDb());
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation 123"));
    TaxonImpl homoSapiens = new TaxonImpl("Homo sapiens", "homoSapiensId");
    homoSapiens.setPath("one two three");
    final Specimen human = nodeFactory.createSpecimen(study, homoSapiens);
    TaxonImpl dogTaxon = new TaxonImpl("Canis familiaris", null);
    final Specimen dog = nodeFactory.createSpecimen(study, dogTaxon);
    human.ate(dog);
    resolveNames();
    final File baseDirNames = createBaseDir("target/sitemap/names");
    final GraphExporter siteMapForNames = new ExporterSiteMapForNames();
    siteMapForNames.export(getGraphDb(), baseDirNames.getAbsolutePath());
    assertSiteMap(baseDirNames, "http://www.globalbioticinteractions.org/?interactionType=interactsWith&sourceTaxon=Homo%20sapiens", "https://depot.globalbioticinteractions.org/snapshot/target/data/sitemap/names/sitemap.xml.gz");
}

Example 24 with StudyImpl

use of org.eol.globi.domain.StudyImpl in project eol-globi-data by jhpoelen.

the class NameResolverTest method iNaturalistTaxon.

@Test
public void iNaturalistTaxon() throws NodeFactoryException {
    Specimen someOtherOrganism = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Blaus bla", "INAT_TAXON:58831"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Redus rha", "INAT_TAXON:126777"));
    someOtherOrganism.ate(someOtherOrganism2);
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    Taxon resolvedTaxon = taxonIndex.findTaxonById("INAT_TAXON:58831");
    assertThat(resolvedTaxon, is(notNullValue()));
    assertThat(resolvedTaxon.getExternalId(), is("INAT_TAXON:58831"));
    assertThat(resolvedTaxon.getName(), is("Blaus bla"));
    Taxon resolvedTaxon2 = taxonIndex.findTaxonByName("Blaus bla");
    assertThat(resolvedTaxon2, is(notNullValue()));
    assertThat(resolvedTaxon2.getExternalId(), is("INAT_TAXON:58831"));
}

Example 25 with StudyImpl

use of org.eol.globi.domain.StudyImpl in project eol-globi-data by jhpoelen.

the class ReportGeneratorTest method generateStudySourceOrganizationReports.

@Test
public void generateStudySourceOrganizationReports() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("a title", "az source", null, "citation");
    study1.setSourceId("az/source1");
    createStudy(study1);
    StudyImpl study2 = new StudyImpl("another title", "az source", null, "citation");
    study2.setSourceId("az/source2");
    createStudy(study2);
    StudyImpl study3 = new StudyImpl("yet another title", "zother source", null, null);
    study3.setSourceId("zother/source");
    createStudy(study3);
    resolveNames();
    new ReportGenerator(getGraphDb()).generateReportForSourceOrganizations();
    IndexHits<Node> reports = getGraphDb().index().forNodes("reports").get(StudyConstant.SOURCE_ID, "az");
    Node reportNode = reports.getSingle();
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES), is(2));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(1));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(2));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS), is(8));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA), is(3));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH), is(2));
    assertThat((String) reportNode.getProperty(StudyConstant.SOURCE_ID), is("az"));
    reports.close();
    IndexHits<Node> otherReports = getGraphDb().index().forNodes("reports").get(StudyConstant.SOURCE_ID, "zother");
    Node otherReport = otherReports.getSingle();
    assertThat((String) otherReport.getProperty(StudyConstant.SOURCE_ID), is("zother"));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES), is(1));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(1));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(1));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS), is(4));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA), is(3));
    assertThat((Integer) otherReport.getProperty(PropertyAndValueDictionary.NUMBER_OF_DISTINCT_TAXA_NO_MATCH), is(2));
}