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

Example 11 with StudyImpl

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

the class ExporterAssociationAggregatesTest method exportNoMatchTaxa.

@Test
public void exportNoMatchTaxa() throws IOException, NodeFactoryException, ParseException {
    String[] studyTitles = { "myStudy1", "myStudy2" };
    for (String studyTitle : studyTitles) {
        Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl(studyTitle, "data source description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
        Specimen specimen = nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, null));
        specimen.ate(nodeFactory.createSpecimen(myStudy, new TaxonImpl(PropertyAndValueDictionary.NO_MATCH, null)));
    }
    resolveNames();
    ExporterAssociationAggregates exporter = new ExporterAssociationAggregates();
    StringWriter row = new StringWriter();
    for (String studyTitle : studyTitles) {
        Study myStudy1 = nodeFactory.findStudy(studyTitle);
        exporter.exportStudy(myStudy1, row, false);
    }
    assertThat(row.getBuffer().toString(), equalTo(""));
}

Example 12 with StudyImpl

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

the class ExporterAssociationAggregatesTest method createTestData.

private void createTestData(Double length, String studyTitle) throws NodeFactoryException, ParseException {
    Study myStudy = nodeFactory.getOrCreateStudy(new StudyImpl(studyTitle, "data source description", null, ExternalIdUtil.toCitation("contributor", "description", "pubYear")));
    Specimen specimen = nodeFactory.createSpecimen(myStudy, setPathAndId(new TaxonImpl("Homo sapiens", null)));
    specimen.setStomachVolumeInMilliLiter(666.0);
    specimen.setLifeStage(new TermImpl("GlOBI:JUVENILE", "JUVENILE"));
    specimen.setPhysiologicalState(new TermImpl("GlOBI:DIGESTATE", "DIGESTATE"));
    specimen.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    nodeFactory.setUnixEpochProperty(specimen, new Date(ExportTestUtil.utcTestTime()));
    TaxonImpl taxon = new TaxonImpl("Canis lupus", null);
    Specimen otherSpecimen = nodeFactory.createSpecimen(myStudy, setPathAndId(taxon));
    otherSpecimen.setVolumeInMilliLiter(124.0);
    specimen.ate(otherSpecimen);
    specimen.ate(otherSpecimen);
    if (null != length) {
        specimen.setLengthInMm(length);
    }
    Location location = nodeFactory.getOrCreateLocation(new LocationImpl(44.0, 120.0, -60.0, null));
    specimen.caughtIn(location);
}

Example 13 with StudyImpl

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

the class ExportUnmatchedTaxonNamesTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    String title = "my study\"";
    String citation = "citation my study";
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl(title, "my first source", null, citation));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null));
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, human());
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis lupus", null));
    Specimen preySpecimen6 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen6, InteractType.ATE);
    Specimen preySpecimen5 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen5, InteractType.ATE);
    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Caniz", null));
    predatorSpecimen.ate(preySpecimen);
    Specimen predatorSpecimen23 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen4 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen23.interactsWith(preySpecimen4, InteractType.ATE);
    Specimen predatorSpecimen22 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen3 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen22.interactsWith(preySpecimen3, InteractType.ATE);
    Study study2 = nodeFactory.getOrCreateStudy(new StudyImpl("my study2", "my source2", null, "citation study2"));
    Specimen predatorSpecimen21 = nodeFactory.createSpecimen(study2, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen2 = nodeFactory.createSpecimen(study2, dog());
    predatorSpecimen21.interactsWith(preySpecimen2, InteractType.ATE);
    Specimen predatorSpecimen2 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens3", PropertyAndValueDictionary.NO_MATCH));
    Specimen preySpecimen1 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen2.interactsWith(preySpecimen1, InteractType.ATE);
    resolveNames();
    StringWriter writer = new StringWriter();
    new ExportUnmatchedTaxonNames().exportStudy(study, writer, true);
    assertThat(writer.toString(), is("unmatched taxon name\tunmatched taxon id\tname status\tsimilar to taxon name\tsimilar to taxon path\tsimilar to taxon id\tstudy\tsource" + "\nCaniz\t\t\t\t\t\tcitation my study\tmy first source" + "\nHomo sapiens2\t\t\t\t\t\tcitation my study\tmy first source" + "\nHomo sapiens3\tno:match\t\t\t\t\tcitation my study\tmy first source"));
}

Example 14 with StudyImpl

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

the class InteractionListenerImpl method studyFromLink.

private StudyImpl studyFromLink(Map<String, String> link) {
    String referenceCitation = link.get(REFERENCE_CITATION);
    StudyImpl study1 = new StudyImpl(link.get(REFERENCE_ID), link.get(STUDY_SOURCE_CITATION), link.get(REFERENCE_DOI), referenceCitation);
    final String referenceUrl = link.get(REFERENCE_URL);
    if (StringUtils.isBlank(study1.getExternalId()) && StringUtils.isNotBlank(referenceUrl)) {
        study1.setExternalId(referenceUrl);
    }
    return study1;
}

Example 15 with StudyImpl

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

the class StudyImporterForHurlbert method importRecords.

private void importRecords(Set<String> regions, Set<String> locales, Set<String> habitats, Record record, String sourceCitation) throws StudyImporterException {
    String namespace = getDataset() == null ? "" : getDataset().getNamespace();
    StudyImpl study1 = new StudyImpl(namespace + sourceCitation, "Allen Hurlbert. Avian Diet Database (https://github.com/hurlbertlab/dietdatabase/). " + CitationUtil.createLastAccessedString(RESOURCE), null, sourceCitation);
    study1.setOriginatingDataset(getDataset());
    Study study = nodeFactory.getOrCreateStudy(study1);
    // ID,Common_Name,Scientific_Name,,,,Prey_Common_Name,Fraction_Diet_By_Wt_or_Vol,Fraction_Diet_By_Items,Fraction_Occurrence,Fraction_Diet_Unspecified,Item Sample Size,Bird Sample size,Sites,StudyNode Type,Notes,Source
    String[] preyLabels = { "Prey_Kingdom", "Prey_Phylum", "Prey_Class", "Prey_Order", "Prey_Suborder", "Prey_Family", "Prey_Genus", "Prey_Scientific_Name" };
    ArrayUtils.reverse(preyLabels);
    String preyTaxonName = null;
    for (String preyLabel : preyLabels) {
        preyTaxonName = columnValueOrNull(record, preyLabel);
        if (StringUtils.isNotBlank(preyTaxonName) && !"NA".equalsIgnoreCase(preyTaxonName)) {
            break;
        }
    }
    String predatorTaxonName = StringUtils.trim(columnValueOrNull(record, "Scientific_Name"));
    if (StringUtils.isNotBlank(StringUtils.trim(predatorTaxonName)) && StringUtils.isNotBlank(StringUtils.trim(preyTaxonName))) {
        importInteraction(regions, locales, habitats, record, study, preyTaxonName, predatorTaxonName);
    }
}