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

Example 51 with StudyImpl

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

the class LinkerTrustyNanoPubsTest method populateDataset.

public NodeFactoryWithDatasetContext populateDataset(DatasetImpl dataset) throws NodeFactoryException {
    TaxonIndex taxonIndex = getOrCreateTaxonIndex();
    // see https://github.com/jhpoelen/eol-globi-data/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", "some source", "http://doi.org/123.23/222", "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, dataset);
    Interaction interaction = factory.createInteraction(factory.createStudy(study));
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    Taxon mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonEOL = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonEOL, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxonEOL);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxonEOL));
    donald.ate(mickey);
    return factory;
}

Example 52 with StudyImpl

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

the class NameResolverTest method doNameResolving.

@Test
public void doNameResolving() throws NodeFactoryException, PropertyEnricherException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Animalia", "WORMS:2"));
    human.ate(animal);
    Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
    human.ate(fish);
    assertNull(taxonIndex.findTaxonById("NCBI:9606"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    assertAnimalia(taxonIndex.findTaxonById("WORMS:2"));
    assertThat(taxonIndex.findTaxonByName("Arius felis"), is(notNullValue()));
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    assertThat(homoSapiens.getExternalId(), is("NCBI:9606"));
}

Example 53 with StudyImpl

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

the class ReportGeneratorTest method generateStudyReport.

@Test
public void generateStudyReport() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("a second title", "a third source", null, null);
    study1.setSourceId("a/third/source");
    createStudy(study1);
    StudyImpl studyWithDoi = new StudyImpl("a title", "a third source", "doi:12345", "citation");
    studyWithDoi.setSourceId("a/third/source");
    createStudy(studyWithDoi);
    resolveNames();
    new ReportGenerator(getGraphDb()).generateReportForStudies();
    IndexHits<Node> reports = getGraphDb().index().forNodes("reports").get(StudyConstant.TITLE, "a title");
    assertThat(reports.size(), is(1));
    Node reportNode = reports.getSingle();
    assertThat((String) reportNode.getProperty(StudyConstant.TITLE), is("a title"));
    assertThat((String) reportNode.getProperty(StudyConstant.SOURCE_ID), is("a/third/source"));
    assertThat((String) reportNode.getProperty(StudyConstant.CITATION), is("citation"));
    assertThat((String) reportNode.getProperty(StudyConstant.DOI), is("doi:12345"));
    assertThat((String) reportNode.getProperty(PropertyAndValueDictionary.EXTERNAL_ID), is("http://dx.doi.org/12345"));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS), is(4));
    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((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(1));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(1));
    reports.close();
    reports = getGraphDb().index().forNodes("reports").get(StudyConstant.TITLE, "a second title");
    assertThat(reports.size(), is(1));
    reportNode = reports.getSingle();
    assertThat((String) reportNode.getProperty(StudyConstant.TITLE), is("a second title"));
    assertThat((String) reportNode.getProperty(StudyConstant.SOURCE_ID), is("a/third/source"));
    assertThat(reportNode.hasProperty(StudyConstant.CITATION), is(false));
    assertThat(reportNode.hasProperty(StudyConstant.DOI), is(false));
    assertThat(reportNode.hasProperty(PropertyAndValueDictionary.EXTERNAL_ID), is(false));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_INTERACTIONS), is(4));
    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((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(1));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(1));
    reports.close();
}

Example 54 with StudyImpl

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

the class ReportGeneratorTest method generateCollectionReport.

@Test
public void generateCollectionReport() throws NodeFactoryException {
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("http://example.com"));
    StudyImpl study1 = new StudyImpl("a title", "source", null, "citation");
    study1.setOriginatingDataset(originatingDataset);
    createStudy(study1);
    StudyImpl study2 = new StudyImpl("another title", "another source", null, "citation");
    study2.setOriginatingDataset(originatingDataset);
    createStudy(study2);
    resolveNames();
    new ReportGenerator(getGraphDb()).generateReportForCollection();
    IndexHits<Node> reports = getGraphDb().index().forNodes("reports").query("*:*");
    assertThat(reports.size(), is(1));
    Node reportNode = reports.getSingle();
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_SOURCES), is(2));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_DATASETS), is(1));
    assertThat((Integer) reportNode.getProperty(PropertyAndValueDictionary.NUMBER_OF_STUDIES), 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));
}

Example 55 with StudyImpl

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

the class ReportGeneratorTest method generateIndividualStudySourceReports.

@Test
public void generateIndividualStudySourceReports() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("a title", "az source", null, "citation");
    study1.setSourceId("az/source");
    createStudy(study1);
    StudyImpl study2 = new StudyImpl("another title", "az source", null, "citation");
    study2.setSourceId("az/source");
    createStudy(study2);
    StudyImpl study3 = new StudyImpl("yet another title", "zother source", null, null);
    study3.setSourceId("zother/source");
    createStudy(study3);
    resolveNames();
    new ReportGenerator(getGraphDb()).generateReportForSourceIndividuals();
    IndexHits<Node> reports = getGraphDb().index().forNodes("reports").get(StudyConstant.SOURCE_ID, "az/source");
    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(1));
    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/source"));
    reports.close();
    IndexHits<Node> otherReports = getGraphDb().index().forNodes("reports").get(StudyConstant.SOURCE_ID, "zother/source");
    Node otherReport = otherReports.getSingle();
    assertThat((String) otherReport.getProperty(StudyConstant.SOURCE_ID), is("zother/source"));
    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));
}