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

Example 1 with SpecimenNode

use of org.eol.globi.domain.SpecimenNode 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 2 with SpecimenNode

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

the class StudyImporterForBioInfoTest method importAbout600Records.

@Test
public void importAbout600Records() throws StudyImporterException {
    StudyImporter importer = new StudyImporterTestFactory(nodeFactory).instantiateImporter((Class) StudyImporterForBioInfo.class);
    final List<String> msgs = new ArrayList<String>();
    importer.setLogger(new ImportLogger() {

        @Override
        public void warn(LogContext study, String message) {
            msgs.add(message);
        }

        @Override
        public void info(LogContext study, String message) {
            msgs.add(message);
        }

        @Override
        public void severe(LogContext study, String message) {
            msgs.add(message);
        }
    });
    // limit the number of line to be imported to make test runs reasonably fast
    importer.setFilter(recordNumber -> recordNumber < 1000 || recordNumber == 4585 || (recordNumber > 47310 && recordNumber < 47320) || (recordNumber > 24220 && recordNumber < 24340));
    importStudy(importer);
    Study vectorStudy = nodeFactory.findStudy(TaxonomyProvider.BIO_INFO + "ref:153303");
    assertThat(vectorStudy, is(notNullValue()));
    Study study = nodeFactory.findStudy(TaxonomyProvider.BIO_INFO + "ref:60527");
    for (Relationship collectedRel : NodeUtil.getSpecimens(study)) {
        SpecimenNode specimen = new SpecimenNode(collectedRel.getEndNode());
        String externalId = specimen.getExternalId();
        assertThat(externalId, is(notNullValue()));
        assertThat(externalId, containsString(TaxonomyProvider.BIO_INFO + "rel:"));
    }
    ExecutionEngine engine = new ExecutionEngine(getGraphDb());
    ExecutionResult result = engine.execute("START taxon = node:taxons('*:*') MATCH taxon<-[:CLASSIFIED_AS]-specimen-[r]->targetSpecimen-[:CLASSIFIED_AS]->targetTaxon RETURN taxon.externalId + ' ' + lower(type(r)) + ' ' + targetTaxon.externalId as interaction");
    ResourceIterator<Map<String, Object>> iterator = result.iterator();
    List<String> interactions = new ArrayList<String>();
    while (iterator.hasNext()) {
        Map<String, Object> next = iterator.next();
        interactions.add((String) next.get("interaction"));
    }
    assertThat(interactions, hasItem("NBN:NHMSYS0000455771 interacts_with NBN:NBNSYS0000024890"));
    assertThat(interactions, hasItem("NBN:NBNSYS0000030148 endoparasitoid_of NBN:NHMSYS0000502366"));
    assertThat(interactions, hasItem("NBN:NHMSYS0000500943 has_endoparasitoid NBN:NBNSYS0000030148"));
    assertThat(interactions, hasItem("bioinfo:taxon:160260 has_vector bioinfo:taxon:162065"));
    assertThat(study.getTitle(), is("bioinfo:ref:60527"));
    assertThat(study.getSource(), is("Food Webs and Species Interactions in the Biodiversity of UK and Ireland (Online). 2015. Data provided by Malcolm Storey. Also available from http://bioinfo.org.uk."));
    assertThat("found unexpected log messages: [" + StringUtils.join(msgs, "\n") + "]", msgs.size(), is(1));
    assertThat(msgs.get(0), is("empty/no taxon name for bioinfo taxon id [149359] on line [4171]"));
}

Example 3 with SpecimenNode

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

the class ExporterRDF method writeParticipantStatements.

public void writeParticipantStatements(Writer writer, Relationship ixnR, Node participant1) throws IOException {
    writeStatement(writer, Arrays.asList(blankNode(ixnR), iriNode(HAS_PARTICIPANT), blankNode(participant1)));
    writeStatement(writer, Arrays.asList(blankNode(participant1), iriNode(HAS_TYPE), iriNode(ORGANISM)));
    writeStatements(writer, taxonOfSpecimen(participant1));
    LocationNode location = new SpecimenNode(participant1).getSampleLocation();
    if (location != null) {
        for (Environment env : location.getEnvironments()) {
            String envoId = ExternalIdUtil.urlForExternalId(env.getExternalId());
            if (StringUtils.isNotBlank(envoId)) {
                writeStatement(writer, Arrays.asList(blankNode(participant1), iriNode(OCCURS_IN), iriNode(envoId)));
            }
        }
    }
}

Example 4 with SpecimenNode

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

the class InteractionListenerImplTest method importAssociatedTaxa.

@Test
public void importAssociatedTaxa() throws StudyImporterException {
    final InteractionListenerImpl listener = new InteractionListenerImpl(nodeFactory, null, new ImportLogger() {

        @Override
        public void warn(LogContext study, String message) {
            fail("got message: " + message);
        }

        @Override
        public void info(LogContext study, String message) {
        }

        @Override
        public void severe(LogContext study, String message) {
            fail("got message: " + message);
        }
    });
    final HashMap<String, String> link = new HashMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(SOURCE_BODY_PART_ID, "bla:123");
    link.put(SOURCE_BODY_PART_NAME, "snout");
    link.put("associatedTaxa", "parasite of: Mini mouse");
    link.put(StudyImporterForMetaTable.EVENT_DATE, "20160404T21:31:40Z");
    link.put(StudyImporterForMetaTable.LATITUDE, "12.1");
    link.put(StudyImporterForMetaTable.LONGITUDE, "13.2");
    link.put(REFERENCE_ID, "123");
    link.put(STUDY_SOURCE_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:1234");
    listener.newLink(link);
    final List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(allStudies.size(), is(1));
    final Study study = allStudies.get(0);
    assertThat(study.getCitation(), is(""));
    boolean foundPair = false;
    for (Relationship specimenRel : NodeUtil.getSpecimens(study)) {
        final SpecimenNode predator = new SpecimenNode(specimenRel.getEndNode());
        for (Relationship hosts : ((NodeBacked) predator).getUnderlyingNode().getRelationships(NodeUtil.asNeo4j(InteractType.PARASITE_OF), Direction.OUTGOING)) {
            final SpecimenNode host = new SpecimenNode(hosts.getEndNode());
            final TaxonNode hostTaxon = getOrigTaxon(host);
            final TaxonNode predTaxon = getOrigTaxon(predator);
            assertThat(hostTaxon.getName(), is("Mini mouse"));
            assertThat(predTaxon.getName(), is("donald"));
            assertThat(predTaxon.getExternalId(), is("duck"));
            foundPair = true;
        }
    }
    assertThat(foundPair, is(true));
}

Example 5 with SpecimenNode

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

the class TaxonInteractionIndexer method collectTaxonInteractions.

public void collectTaxonInteractions(Map<Fun.Tuple3<Long, String, Long>, Long> taxonInteractions) {
    StopWatch watchForEntireRun = new StopWatch();
    watchForEntireRun.start();
    StopWatch watchForBatch = new StopWatch();
    watchForBatch.start();
    long count = 0L;
    int batchSize = 1000;
    Index<Node> taxonIndex = graphService.index().forNodes("taxons");
    IndexHits<Node> taxa = taxonIndex.query("name", "*");
    for (Node sourceTaxon : taxa) {
        final Iterable<Relationship> classifiedAs = sourceTaxon.getRelationships(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
        for (Relationship classifiedA : classifiedAs) {
            Node specimenNode = classifiedA.getStartNode();
            final Iterable<Relationship> interactions = specimenNode.getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.values()));
            for (Relationship interaction : interactions) {
                final Iterable<Relationship> targetClassifications = interaction.getEndNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
                for (Relationship targetClassification : targetClassifications) {
                    final Node targetTaxonNode = targetClassification.getEndNode();
                    final Fun.Tuple3<Long, String, Long> interactionKey = new Fun.Tuple3<Long, String, Long>(sourceTaxon.getId(), interaction.getType().name(), targetTaxonNode.getId());
                    final Long distinctInteractions = taxonInteractions.get(interactionKey);
                    taxonInteractions.put(interactionKey, distinctInteractions == null ? 1L : (distinctInteractions + 1L));
                    count++;
                }
            }
        }
        if (count % batchSize == 0) {
            watchForBatch.stop();
            final long duration = watchForBatch.getTime();
            if (duration > 0) {
                LOG.info("walked [" + batchSize + "] interactions in " + getProgressMsg(batchSize, duration));
            }
            watchForBatch.reset();
            watchForBatch.start();
        }
    }
    taxa.close();
    watchForEntireRun.stop();
    LOG.info("walked [" + count + "] interactions in " + getProgressMsg(count, watchForEntireRun.getTime()));
}