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

Example 6 with Study

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

the class StudyImporterForSPIRE method importValidLink.

private void importValidLink(Map<String, String> properties) throws NodeFactoryException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl(properties.get(StudyConstant.TITLE), SOURCE_SPIRE, null, properties.get(StudyConstant.DESCRIPTION)));
    try {
        Specimen predator = createSpecimen(properties.get(PREDATOR_NAME), study);
        String locality = properties.get(LOCALITY_ORIGINAL);
        LatLng latLng = getGeoNamesService().findLatLng(locality);
        if (latLng == null) {
            getLogger().warn(study, "failed to find location for county [" + locality + "]");
        } else {
            Location location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
            predator.caughtIn(location);
            String habitat = properties.get(OF_HABITAT);
            if (StringUtils.isNotBlank(habitat)) {
                addEnvironment(location, "SPIRE:" + habitat, habitat);
            }
        }
        Specimen prey = createSpecimen(properties.get(PREY_NAME), study);
        predator.ate(prey);
    } catch (NodeFactoryException e) {
        getLogger().warn(study, "failed to import trophic link with properties [" + properties + "]: " + e.getMessage());
    } catch (IOException e) {
        getLogger().warn(study, "failed to import trophic link with properties [" + properties + "]: " + e.getMessage());
    }
}

Example 7 with Study

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

the class StudyImporterForWrast method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String citation = "Wrast JL. Spatiotemporal And Habitat-mediated Food Web Dynamics in Lavaca Bay, Texas. 2008. Master Thesis.";
    StudyImpl study1 = new StudyImpl("Wrast 2008", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, citation);
    study1.setExternalId("http://www.fisheries.tamucc.edu/people_files/FINAL%20WRAST%20THESIS.pdf");
    Study study = nodeFactory.getOrCreateStudy(study1);
    try {
        LabeledCSVParser csvParser = parserFactory.createParser(LAVACA_BAY_DATA_SOURCE, CharsetConstant.UTF8);
        LengthParser parser = new LengthParserImpl(COLUMN_MAPPER.get(LENGTH_IN_MM));
        getPredatorSpecimenMap().clear();
        while (csvParser.getLine() != null) {
            addNextRecordToStudy(csvParser, study, COLUMN_MAPPER, parser);
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to create study [" + LAVACA_BAY_DATA_SOURCE + "]", e);
    } finally {
        getPredatorSpecimenMap().clear();
    }
}

Example 8 with Study

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

the class StudyImporterForGoMexSI2IT method assertThatSomeDataIsImported.

private static void assertThatSomeDataIsImported(NodeFactory nodeFactory, TaxonIndex taxonIndex) throws StudyImporterException, NodeFactoryException {
    Study study = nodeFactory.findStudy("Divita et al 1983");
    assertSpecimenProperties(((NodeBacked) study).getUnderlyingNode().getGraphDatabase());
    assertNotNull(study);
    assertThat(study.getTitle(), is("Divita et al 1983"));
    assertThat(study.getExternalId(), is(ExternalIdUtil.urlForExternalId("GAME:2689")));
    assertThat(study.getCitation(), is("Regina Divita, Mischelle Creel, Peter Sheridan. 1983. Foods of coastal fishes during brown shrimp Penaeus aztecus, migration from Texas estuaries (June - July 1981)."));
    assertNotNull(nodeFactory.findStudy("Beaumariage 1973"));
    assertNotNull(nodeFactory.findStudy("Baughman, 1943"));
    assertNotNull(taxonIndex.findTaxonByName("Chloroscombrus chrysurus"));
    assertNotNull(taxonIndex.findTaxonByName("Micropogonias undulatus"));
    assertNotNull(taxonIndex.findTaxonByName("Amphipoda"));
    assertNotNull(taxonIndex.findTaxonByName("Crustacea"));
    Taxon taxon = taxonIndex.findTaxonByName("Scomberomorus cavalla");
    List<String> preyList = new ArrayList<String>();
    final List<String> titles = new ArrayList<String>();
    Iterable<Relationship> classifiedAsRels = ((NodeBacked) taxon).getUnderlyingNode().getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    int count = 0;
    for (Relationship classifiedAsRel : classifiedAsRels) {
        Node predatorSpecimen = classifiedAsRel.getStartNode();
        Specimen predator = new SpecimenNode(predatorSpecimen);
        Iterable<Relationship> stomachContents = NodeUtil.getStomachContents(predator);
        for (Relationship prey : stomachContents) {
            Relationship singleRelationship = prey.getEndNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS), Direction.OUTGOING);
            preyList.add((String) singleRelationship.getEndNode().getProperty("name"));
        }
        count++;
        Relationship collectedBy = predatorSpecimen.getSingleRelationship(NodeUtil.asNeo4j(RelTypes.COLLECTED), Direction.INCOMING);
        assertThat(collectedBy, is(notNullValue()));
        String title = (String) collectedBy.getStartNode().getProperty("title");
        titles.add(title);
    }
    assertThat(count > 7, is(true));
    assertThat(preyList, hasItem("Organic matter"));
    assertThat(preyList, hasItem("Triglidae"));
    assertThat(preyList, hasItem("Sparidae"));
    assertThat(titles, hasItem("Beaumariage 1973"));
    assertThat(titles, hasItem("Blanton et al 1972"));
    assertNotNull(taxon);
    final String footprintWKT = WKT_FOOTPRINT2;
    LocationImpl expectedLocation = new LocationImpl(29.346953, -92.980614, -13.641, footprintWKT);
    expectedLocation.setLocality("Louisiana inner continental shelf");
    Location location = nodeFactory.findLocation(expectedLocation);
    assertThat(location, is(notNullValue()));
    assertThat(location.getFootprintWKT(), is(footprintWKT));
    assertThat(location.getLocality(), is("Louisiana inner continental shelf"));
    assertNotNull(location);
    List<Environment> environments = location.getEnvironments();
    assertThat(environments.size(), not(is(0)));
    assertThat(environments.get(0).getExternalId(), is("http://cmecscatalog.org/classification/aquaticSetting/13"));
    assertThat(environments.get(0).getName(), is("Marine Nearshore Subtidal"));
    assertNotNull(nodeFactory.findStudy("GoMexSI"));
}

Example 9 with Study

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

the class StudyImporterForGitHubDataIT method importGoMexSI.

@Test
public void importGoMexSI() throws StudyImporterException {
    StudyImporterForGitHubData importer = createImporter();
    importer.importData("gomexsi/interaction-data");
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study study : allStudies) {
        assertThat(study.getSource(), is(Matchers.notNullValue()));
    }
}

Example 10 with Study

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

the class StudyImporterForGitHubDataIT method importSmithsonian.

@Test
public void importSmithsonian() throws StudyImporterException {
    StudyImporterForGitHubData importer = createImporter();
    importer.importData("millerse/Smithsonian-Repository-Interactions");
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    Map<String, String> citationDOIs = new TreeMap<String, String>();
    for (Study study : allStudies) {
        citationDOIs.put(study.getCitation(), study.getDOI());
    }
    String citation = "Raboy, Becky E., and James M. Dietz. Diet, Foraging, and Use of Space in Wild Golden-headed Lion Tamarins. American Journal of Primatology, 63(1):, 2004, 1-15. Accessed April 20, 2015. http://hdl.handle.net/10088/4251.";
    assertThat(citationDOIs.keySet(), hasItem(citation));
    String doi = citationDOIs.get(citation);
    assertThat(doi, startsWith("doi:Raboy"));
    assertThat(allStudies.get(0).getSource(), containsString("Miller"));
    assertThat(taxonIndex.findTaxonByName("Leontopithecus chrysomelas"), is(notNullValue()));
}