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

Example 41 with Specimen

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

the class StudyImporterForSeltmannIT method importArchive.

protected void importArchive(String archiveName) throws StudyImporterException {
    StudyImporterForSeltmann importer = new StudyImporterForSeltmann(null, nodeFactory);
    importer.setDataset(new DatasetImpl(null, URI.create(ARCHIVE_URI_PREFIX + archiveName)));
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study allStudy : allStudies) {
        assertThat(allStudy.getSource(), startsWith("Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388"));
        assertThat(allStudy.getCitation(), is("Digital Bee Collections Network, 2014 (and updates). Version: 2015-03-18. National Science Foundation grant DBI 0956388"));
        Iterable<Relationship> specimens = NodeUtil.getSpecimens(allStudy);
        for (Relationship specimen : specimens) {
            Specimen spec = new SpecimenNode(specimen.getEndNode());
            Term basisOfRecord = spec.getBasisOfRecord();
            assertThat(basisOfRecord.getId(), either(is("TEST:PreservedSpecimen")).or(is("TEST:LabelObservation")));
            assertThat(basisOfRecord.getName(), either(is("PreservedSpecimen")).or(is("LabelObservation")));
        }
    }
    assertThat(taxonIndex.findTaxonByName("Megandrena mentzeliae"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Mentzelia tricuspis"), is(notNullValue()));
}

Example 42 with Specimen

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

the class StudyImporterForSzoboszlaiIT method importAll.

@Test
public void importAll() throws StudyImporterException, IOException {
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Szoboszlai AI, Thayer JA, Wood SA, Sydeman WJ, Koehn LE (2015) Data from: Forage species in predator diets: synthesis of data from the California Current. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"doi\": \"http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"format\": \"szoboszlai\",\n" + "  \"resources\": {\n" + "    \"links\": \"http://datadryad.org/bitstream/handle/10255/dryad.94536/CCPDDlinkdata_v1.csv\",\n" + "    \"shapes\": \"http://datadryad.org/bitstream/handle/10255/dryad.94535/CCPDDlocationdata_v1.zip\"\n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("someRepo", URI.create("http://example.com"));
    dataset.setConfig(config);
    ParserFactory parserFactory = new ParserFactoryForDataset(dataset);
    StudyImporterForSzoboszlai importer = new StudyImporterForSzoboszlai(parserFactory, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(allStudies.size(), is(not(0)));
    Study firstStudy = allStudies.get(0);
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(firstStudy);
    for (Relationship specimen : specimens) {
        Specimen specimenNode = new SpecimenNode(specimen.getEndNode());
        Location sampleLocation = specimenNode.getSampleLocation();
        assertThat(sampleLocation, is(notNullValue()));
        assertThat(sampleLocation.getLatitude(), is(notNullValue()));
        assertThat(sampleLocation.getLongitude(), is(notNullValue()));
    }
    assertThat(taxonIndex.findTaxonByName("Thunnus thynnus"), is(notNullValue()));
    assertThat(nodeFactory.findLocation(new LocationImpl(34.00824202376044, -120.72716166720323, null, null)), is(notNullValue()));
}

Example 43 with Specimen

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

the class IndexInteractionsTest method indexInteractions.

@Test
public void indexInteractions() 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, new DatasetImpl("some/namespace", URI.create("https://some.uri")));
    Study interaction = factory.getOrCreateStudy(study);
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    TaxonImpl mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonNCBI = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonNCBI, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxon);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxon));
    donald.ate(mickey);
    new IndexInteractions(getGraphDb()).link();
    NodeFactoryNeo4j nodeFactoryNeo4j = new NodeFactoryNeo4j(getGraphDb());
    StudyImpl study1 = new StudyImpl("some study", "some source", null, "come citation");
    study1.setOriginatingDataset(new DatasetImpl("some/namespace", URI.create("some:uri")));
    StudyNode someStudy = nodeFactoryNeo4j.getOrCreateStudy(study1);
    assertThat(interaction.getOriginatingDataset().getNamespace(), is(someStudy.getOriginatingDataset().getNamespace()));
    assertThat(interaction.getTitle(), is(someStudy.getTitle()));
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(someStudy);
    RelationshipType hasParticipant = NodeUtil.asNeo4j(RelTypes.HAS_PARTICIPANT);
    Set<Long> ids = new HashSet<>();
    List<Long> idList = new ArrayList<>();
    for (Relationship specimen : specimens) {
        assertThat(specimen.getEndNode().hasRelationship(Direction.INCOMING, hasParticipant), Is.is(true));
        Relationship singleRelationship = specimen.getEndNode().getSingleRelationship(hasParticipant, Direction.INCOMING);
        long id = singleRelationship.getStartNode().getId();
        ids.add(id);
        idList.add(id);
    }
    assertThat(ids.size(), Is.is(1));
    assertThat(idList.size(), Is.is(2));
    Node interactionNode = getGraphDb().getNodeById(idList.get(0));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.DERIVED_FROM)));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.ACCESSED_AT)));
}

Example 44 with Specimen

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

the class StudyImporterForBlewett method addPreyForPredator.

private List<Specimen> addPreyForPredator(String[] header, String[] line, Study study) throws NodeFactoryException {
    List<Specimen> preyItems = new ArrayList<Specimen>();
    int preyColumn = 4;
    for (int i = preyColumn; i < header.length; i++) {
        if (i < line.length) {
            String preyCountString = line[i];
            if (preyCountString.trim().length() > 0) {
                try {
                    int preyCount = Integer.parseInt(preyCountString);
                    String preyName = header[i];
                    for (int j = 0; j < preyCount; j++) {
                        Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(preyName, null));
                        preyItems.add(preySpecimen);
                    }
                } catch (NumberFormatException e) {
                    getLogger().warn(study, "failed to parse prey count line/column:");
                }
            }
        }
    }
    return preyItems;
}

Example 45 with Specimen

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

the class StudyImporterForBrose method addInteractionForConsumer.

private void addInteractionForConsumer(LabeledCSVParser parser, Study localStudy, String predatorName) throws NodeFactoryException, StudyImporterException {
    Location location = null;
    String locationString = parser.getValueByLabel("Geographic location");
    LatLng latLng = LOC_MAP.get(StringUtils.trim(locationString));
    if (latLng == null) {
        getLogger().warn(localStudy, "failed to find location for [" + locationString + "]");
    } else {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
        String habitat = StringUtils.join(parser.getValueByLabel("General habitat"), " ", parser.getValueByLabel("Specific habitat"));
        String habitatId = "BROSE:" + habitat.replaceAll("\\W", "_");
        nodeFactory.getOrCreateEnvironments(location, habitatId, habitat);
    }
    Specimen consumer = nodeFactory.createSpecimen(localStudy, new TaxonImpl(predatorName, null));
    consumer.caughtIn(location);
    addLifeStage(parser, consumer, "Lifestage consumer");
    String name = getName(parser, "Taxonomy resource", "Common name(s) resource");
    if (StringUtils.isBlank(name) || StringUtils.length(name) < 2) {
        String message = "found (near) empty prey name on line [" + parser.lastLineNumber() + "] + [" + name + "]";
        LOG.warn(message);
        getLogger().warn(localStudy, message);
    } else {
        Specimen resource = nodeFactory.createSpecimen(localStudy, new TaxonImpl(name, null));
        resource.caughtIn(location);
        addLifeStage(parser, resource, "Lifestage - resource");
        String interactionType = parser.getValueByLabel("Type of feeding interaction");
        Map<String, InteractType> typeMapping = new HashMap<String, InteractType>() {

            {
                put("predacious", InteractType.PREYS_UPON);
                put("predator", InteractType.PREYS_UPON);
                put("herbivorous", InteractType.ATE);
                put("parasitoid", InteractType.PARASITE_OF);
                put("parasitic", InteractType.PARASITE_OF);
                put("bacterivorous", InteractType.ATE);
                put("omnivore", InteractType.ATE);
                put("detritivorous", InteractType.ATE);
                put("pathogen", InteractType.PATHOGEN_OF);
            }
        };
        InteractType interactType = typeMapping.get(interactionType);
        if (interactType == null) {
            throw new StudyImporterException("found unsupported interaction type [" + interactionType + "]");
        }
        consumer.interactsWith(resource, interactType);
    }
}