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

Example 61 with Study

use of org.eol.globi.domain.Study 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 62 with Study

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

the class NodeFactoryIT method createLogMessage.

@Test
public void createLogMessage() throws NodeFactoryException {
    Study bla = nodeFactory.createStudy(new StudyImpl("bla", null, null, null));
    bla.appendLogMessage("one two three", Level.INFO);
    List<LogMessage> logMessages = bla.getLogMessages();
    assertThat(logMessages.size(), is(1));
    assertThat(logMessages.get(0).getMessage(), is("one two three"));
    assertThat(logMessages.get(0).getLevel(), is("INFO"));
}

Example 63 with Study

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

the class StudyImporterForRoopnarineTest method importLine.

@Test
public void importLine() throws StudyImporterException, NodeFactoryException {
    // note that this test data is a modified version of the actual data - please don't use this data for actual analysis purposes
    final String trophicGuildsToSpeciesLookup = "\"Guild Number\",\"Taxa\",\"Fish Body Length\",\"Cayman Islands\",\"Cuba\",\"Jamaica\"\n" + "1,\"something something\",,,,\n" + "2,\"Skeletonema tropicum        \",,,,\n" + "3,\"Something else        \",,,,\n" + "11,\" Epinephelus striatus          \",122,\"x \",\"x\",\"x\"\n" + "12,\" Negaprion brevirostris        \",240,\"x \",\" \",\" \"\n" + "13,\" Carcharhinus perezi           \",300,\"x \",\"x\",\"x\"\n" + "14,\" Rhizoprionodon porosus        \",75,\"x \",\"x\",\" \"\n" + "14,\" Sphyrna tiburo                \",80,\"x \",\" \",\" \"\n" + "14,\" Galeocerdo cuvieri            \",500,\"  \",,";
    final String trophicInteractions = "\"Guild Number\",\"Guild Description\",\"Foraging Habitat\",\"Number of Prey\",\"Prey\"\n" + "1,\"Planktonic bacteria   \",\".\",0,\".\"\n" + "2,\"Phytoplankton         \",\".\",0,\".\"\n" + "3,\"Nanno-zooplankton     \",\".\",30,\"1, 2\"\n" + "4,\"Filamentous macroalgae\",\".\",0,\".\"\n" + "5,\"Sheet macroalgae      \",\".\",0,\".\"\n" + "6,\"Coarsely branched macroalgae                 \",\".\",0,\".\"\n" + "7,\"Jointed calcareous macroalgae                \",\".\",0,\".\"\n" + "8,\"Thick leathery macroalgae                    \",\".\",0,\".\"\n" + "9,\"Crustose coralline algae                     \",\".\",0,\".\"\n" + "10,\"Seagrasses            \",\".\",0,\".\"\n" + "11,\"Epibenthic sponges    \",\".\",30,\"1,  2\"\n" + "12,\"Endolithic sponges    \",\".\",30,\"1,   2\"\n" + "13,\"Ahermatypic benthic corals\",\".\",35,\"1\"\n" + "14,\"Hermatypic corals\",\".\",36,\"2\"";
    StudyImporterForRoopnarine importer = new StudyImporterForRoopnarine(new ParserFactory() {

        @Override
        public LabeledCSVParser createParser(String studyResource, String characterEncoding) throws IOException {
            ParserFactory factory;
            if (studyResource.contains("4.csv")) {
                factory = new TestParserFactory(trophicGuildsToSpeciesLookup);
            } else {
                factory = new TestParserFactory(trophicInteractions);
            }
            return factory.createParser("", characterEncoding);
        }
    }, nodeFactory);
    importStudy(importer);
    Study study = getStudySingleton(getGraphDb());
    assertNotNull(taxonIndex.findTaxonByName("Negaprion brevirostris"));
    assertNotNull(taxonIndex.findTaxonByName("Carcharhinus perezi"));
    assertNotNull(taxonIndex.findTaxonByName("Galeocerdo cuvieri"));
    Iterable<Relationship> collectedRels = NodeUtil.getSpecimens(study);
    int totalRels = validateSpecimen(collectedRels);
    assertThat(totalRels, Is.is(51));
}

Example 64 with Study

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

the class StudyImporterForRoopnarineTest method importAll.

@Ignore("roopnarine imports eats more memory that other study imports")
@Test
public void importAll() throws StudyImporterException {
    StudyImporterForRoopnarine studyImporterFor = new StudyImporterForRoopnarine(new ParserFactoryLocal(), nodeFactory);
    studyImporterFor.importStudy();
    List<Study> studies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(studies.size(), is(1));
    Study study = studies.get(0);
    Iterable<Relationship> collectedRels = NodeUtil.getSpecimens(study);
    int totalRels = validateSpecimen(collectedRels);
    assertThat(totalRels, Is.is(1939));
    assertNotNull(taxonIndex.findTaxonByName("Lestrigonus bengalensis"));
    assertNotNull(taxonIndex.findTaxonByName("Bracyscelus crusculum"));
}

Example 65 with Study

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

the class StudyImporterForSIADIT method importAll.

@Test
public void importAll() throws StudyImporterException {
    StudyImporterForSIAD importer = new StudyImporterForSIAD(new ParserFactoryLocal(), nodeFactory);
    importStudy(importer);
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    assertThat(allStudies.size() > 1, is(true));
    Taxon taxon = taxonIndex.findTaxonByName("Anisakis");
    assertThat(taxon, is(notNullValue()));
    taxon = taxonIndex.findTaxonByName("Abbreviata");
    assertThat(taxon, is(notNullValue()));
}