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

Example 6 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 StudyImpl

use of org.eol.globi.domain.StudyImpl 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 StudyImpl

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

the class ExportTaxonCacheTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation"));
    Taxon taxon = new TaxonImpl("Homo sapiens");
    taxon.setExternalId("homoSapiensId");
    taxon.setPath("one\ttwo three");
    taxon.setExternalUrl("http://some/thing");
    taxon.setThumbnailUrl("http://thing/some");
    Taxon human = taxonIndex.getOrCreateTaxon(taxon);
    TaxonImpl taxon1 = new TaxonImpl("Canis lupus", "canisLupusId");
    taxon1.setPath("four five six");
    taxonIndex.getOrCreateTaxon(taxon1);
    NodeUtil.connectTaxa(new TaxonImpl("Alternate Homo sapiens no path", "alt:123"), (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    final TaxonImpl altTaxonWithPath = new TaxonImpl("Alternate Homo sapiens", "alt:123");
    altTaxonWithPath.setPath("some path here");
    NodeUtil.connectTaxa(altTaxonWithPath, (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    NodeUtil.connectTaxa(new TaxonImpl("Similar Homo sapiens", "alt:456"), (TaxonNode) human, getGraphDb(), RelTypes.SIMILAR_TO);
    StringWriter writer = new StringWriter();
    new ExportTaxonCache().exportStudy(study, writer, true);
    assertThat(writer.toString(), is("id\tname\trank\tcommonNames\tpath\tpathIds\tpathNames\texternalUrl\tthumbnailUrl" + "\nhomoSapiensId\tHomo sapiens\t\t\tone two three\t\t\thttp://some/thing\thttp://thing/some" + "\nalt:123\tAlternate Homo sapiens\t\t\tsome path here\t\t\thttp://some/thing\thttp://thing/some" + "\ncanisLupusId\tCanis lupus\t\t\tfour five six\t\t\t\t"));
}

Example 9 with StudyImpl

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

the class ExportTaxonMapTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    final PropertyEnricher taxonEnricher = new PropertyEnricher() {

        @Override
        public Map<String, String> enrich(Map<String, String> properties) {
            Taxon taxon = new TaxonImpl();
            TaxonUtil.mapToTaxon(properties, taxon);
            if ("Homo sapiens".equals(taxon.getName())) {
                taxon.setExternalId("homoSapiensId");
                taxon.setPath("one two three");
            } else if ("Canis lupus".equals(taxon.getName())) {
                taxon.setExternalId("canisLupusId");
                taxon.setPath("four\tfive six");
            }
            return TaxonUtil.taxonToMap(taxon);
        }

        @Override
        public void shutdown() {
        }
    };
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(taxonEnricher, getGraphDb());
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("title", "source", null, "citation"));
    Taxon taxon = new TaxonImpl("Homo sapiens");
    taxon.setExternalId("homoSapiensId");
    taxon.setPath("one two three");
    taxon.setExternalUrl("http://some/thing");
    taxon.setThumbnailUrl("http://thing/some");
    nodeFactory.createSpecimen(study, taxon);
    Taxon human = taxonIndex.getOrCreateTaxon(taxon);
    TaxonImpl dog = new TaxonImpl("Canis lupus");
    dog.setExternalId("canisLupusId");
    dog.setPath("four\tfive six");
    nodeFactory.createSpecimen(study, dog);
    final TaxonImpl altTaxonWithPath = new TaxonImpl("Alternate Homo sapiens", "alt:123");
    altTaxonWithPath.setPath("some path here");
    NodeUtil.connectTaxa(altTaxonWithPath, (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    NodeUtil.connectTaxa(new TaxonImpl("Alternate Homo sapiens no path", "alt:123"), (TaxonNode) human, getGraphDb(), RelTypes.SAME_AS);
    NodeUtil.connectTaxa(new TaxonImpl("Similar Homo sapiens", "alt:456"), (TaxonNode) human, getGraphDb(), RelTypes.SIMILAR_TO);
    resolveNames();
    StringWriter writer = new StringWriter();
    new ExportTaxonMap().exportStudy(study, writer, true);
    assertThat(writer.toString(), is("providedTaxonId\tprovidedTaxonName\tresolvedTaxonId\tresolvedTaxonName" + "\nhomoSapiensId\tHomo sapiens\thomoSapiensId\tHomo sapiens" + "\nhomoSapiensId\tHomo sapiens\talt:123\tAlternate Homo sapiens" + "\ncanisLupusId\tCanis lupus\tcanisLupusId\tCanis lupus"));
}

Example 10 with StudyImpl

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

the class ExportTestUtil method createTestData.

public static Study createTestData(Double length, NodeFactory factory) throws NodeFactoryException, ParseException {
    Study myStudy = factory.createStudy(new StudyImpl("myStudy", null, null, null));
    Specimen specimen1 = factory.createSpecimen(myStudy, new TaxonImpl("Homo sapiens", "EOL:45634"));
    specimen1.setStomachVolumeInMilliLiter(666.0);
    specimen1.setLifeStage(new TermImpl("GLOBI:JUVENILE", "JUVENILE"));
    specimen1.setPhysiologicalState(new TermImpl("GLOBI:DIGESTATE", "DIGESTATE"));
    specimen1.setBodyPart(new TermImpl("GLOBI:BONE", "BONE"));
    factory.setUnixEpochProperty(specimen1, ExportTestUtil.utcTestDate());
    final Specimen specimen2 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen2.setVolumeInMilliLiter(124.0);
    specimen1.ate(specimen2);
    final Specimen specimen3 = factory.createSpecimen(myStudy, new TaxonImpl("Canis lupus", "EOL:123"));
    specimen3.setVolumeInMilliLiter(18.0);
    specimen1.ate(specimen3);
    if (null != length) {
        specimen1.setLengthInMm(length);
    }
    Location location = factory.getOrCreateLocation(new LocationImpl(88.0, -120.0, -60.0, null));
    specimen1.caughtIn(location);
    return myStudy;
}