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

Example 6 with LocationImpl

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

the class StudyImporterForSimons method getOrCreateSampleLocation.

private Location getOrCreateSampleLocation(LabeledCSVParser csvParser, Map<String, String> columnToNormalizedTermMapper) throws StudyImporterException {
    Double northing = parseAsDouble(csvParser, columnToNormalizedTermMapper.get(NORTHING));
    Double easting = parseAsDouble(csvParser, columnToNormalizedTermMapper.get(EASTING));
    Double latitude = null;
    Double longitude = null;
    if (easting != null && northing != null) {
        UTMRef utmRef = new UTMRef(easting, northing, 'R', 16);
        LatLng latLng = utmRef.toLatLng();
        latitude = latLng.getLat();
        longitude = latLng.getLng();
    }
    Double depth = parseAsDouble(csvParser, columnToNormalizedTermMapper.get(DEPTH));
    Double altitude = depth == null ? null : -depth;
    try {
        return nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, altitude, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
}

Example 7 with LocationImpl

use of org.eol.globi.domain.LocationImpl 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 8 with LocationImpl

use of org.eol.globi.domain.LocationImpl 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;
}

Example 9 with LocationImpl

use of org.eol.globi.domain.LocationImpl 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 10 with LocationImpl

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

the class StudyImporterForHurlbert method importInteraction.

protected void importInteraction(Set<String> regions, Set<String> locales, Set<String> habitats, Record record, Study study, String preyTaxonName, String predatorName) throws StudyImporterException {
    try {
        Taxon predatorTaxon = new TaxonImpl(predatorName);
        Specimen predatorSpecimen = nodeFactory.createSpecimen(study, predatorTaxon);
        setBasisOfRecordAsLiterature(predatorSpecimen);
        Taxon preyTaxon = new TaxonImpl(preyTaxonName);
        String preyNameId = StringUtils.trim(columnValueOrNull(record, "Prey_Name_ITIS_ID"));
        if (NumberUtils.isDigits(preyNameId)) {
            preyTaxon.setExternalId(TaxonomyProvider.ITIS.getIdPrefix() + preyNameId);
        }
        Specimen preySpecimen = nodeFactory.createSpecimen(study, preyTaxon);
        setBasisOfRecordAsLiterature(preySpecimen);
        String preyStage = StringUtils.trim(columnValueOrNull(record, "Prey_Stage"));
        if (StringUtils.isNotBlank(preyStage)) {
            Term lifeStage = nodeFactory.getOrCreateLifeStage("HULBERT:" + StringUtils.replace(preyStage, " ", "_"), preyStage);
            preySpecimen.setLifeStage(lifeStage);
        }
        String preyPart = StringUtils.trim(columnValueOrNull(record, "Prey_Part"));
        if (StringUtils.isNotBlank(preyPart)) {
            Term term = nodeFactory.getOrCreateBodyPart("HULBERT:" + StringUtils.replace(preyPart, " ", "_"), preyPart);
            preySpecimen.setBodyPart(term);
        }
        Date date = addCollectionDate(record, study);
        nodeFactory.setUnixEpochProperty(predatorSpecimen, date);
        nodeFactory.setUnixEpochProperty(preySpecimen, date);
        LocationImpl location = new LocationImpl(null, null, null, null);
        String longitude = columnValueOrNull(record, "Longitude_dd");
        String latitude = columnValueOrNull(record, "Latitude_dd");
        if (NumberUtils.isNumber(latitude) && NumberUtils.isNumber(longitude)) {
            try {
                LatLng latLng = LocationUtil.parseLatLng(latitude, longitude);
                String altitude = columnValueOrNull(record, "Altitude_mean_m");
                Double altitudeD = NumberUtils.isNumber(altitude) ? Double.parseDouble(altitude) : null;
                location = new LocationImpl(latLng.getLat(), latLng.getLng(), altitudeD, null);
            } catch (InvalidLocationException e) {
                getLogger().warn(study, "found invalid (lat,lng) pair: (" + latitude + "," + longitude + ")");
            }
        }
        String locationRegion = columnValueOrNull(record, "Location_Region");
        String locationSpecific = columnValueOrNull(record, "Location_Specific");
        location.setLocality(StringUtils.join(Arrays.asList(locationRegion, locationSpecific), ":"));
        Location locationNode = nodeFactory.getOrCreateLocation(location);
        String habitat_type = columnValueOrNull(record, "Habitat_type");
        List<Term> habitatList = Arrays.stream(StringUtils.split(StringUtils.defaultIfBlank(habitat_type, ""), ";")).map(StringUtils::trim).map(habitat -> new TermImpl(idForHabitat(habitat), habitat)).collect(Collectors.toList());
        nodeFactory.addEnvironmentToLocation(locationNode, habitatList);
        preySpecimen.caughtIn(locationNode);
        predatorSpecimen.caughtIn(locationNode);
        predatorSpecimen.ate(preySpecimen);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create interaction between [" + predatorName + "] and [" + preyTaxonName + "]", e);
    }
}