Examples with TermLookupServiceException org.eol.globi.service.TermLookupServiceException used on opensource projects

Example 1 with TermLookupServiceException

use of org.eol.globi.service.TermLookupServiceException in project eol-globi-data by jhpoelen.

the class StudyImporterForBlewett method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String citation = "Blewett DA, Hensley RA, and Stevens PW, Feeding Habits of Common Snook, Centropomus Undecimalis, in Charlotte Harbor, Florida, Gulf and Caribbean Research Vol 18, 1–13, 2006. doi:10.18785/gcr.1801.01 ";
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Blewett 2006", StudyImporterForGoMexSI2.GOMEXI_SOURCE_DESCRIPTION, null, citation));
    try {
        Map<String, Location> collectionLocationMap = new HashMap<>();
        Map<String, Date> collectionTimeMap = new HashMap<String, Date>();
        buildLocationTimeMaps(collectionLocationMap, collectionTimeMap, study);
        parsePredatorPreyInteraction(study, collectionLocationMap, collectionTimeMap);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create taxon", e);
    } catch (TermLookupServiceException e) {
        throw new StudyImporterException("failed to map terms", e);
    }
}

Example 2 with TermLookupServiceException

use of org.eol.globi.service.TermLookupServiceException in project eol-globi-data by jhpoelen.

the class StudyImporterForAkin method addPrey.

private void addPrey(Study study, LabeledCSVParser parser, String[] header, String[] line, Specimen specimen, Location location) throws StudyImporterException {
    int firstPreyIndex = findIndexForColumnWithNameThrowOnMissing("Detritus", header);
    for (int i = firstPreyIndex; i < line.length; i++) {
        String preySpeciesName = header[i];
        if (StringUtils.isNotBlank(preySpeciesName)) {
            String preyVolumeString = line[i];
            try {
                if (StringUtils.isNotBlank(preyVolumeString)) {
                    double volume = Double.parseDouble(preyVolumeString);
                    if (volume > 0) {
                        Specimen prey = nodeFactory.createSpecimen(study, new TaxonImpl(preySpeciesName, null));
                        prey.setLifeStage(parseLifeStage(nodeFactory.getTermLookupService(), preySpeciesName));
                        prey.setVolumeInMilliLiter(volume);
                        prey.caughtIn(location);
                        specimen.ate(prey);
                    }
                }
            } catch (NumberFormatException ex) {
                throw new StudyImporterException("failed to parse volume of prey [" + preySpeciesName + "] in stomach [" + preyVolumeString + "] on line [" + parser.getLastLineNumber() + "]");
            } catch (TermLookupServiceException e) {
                throw new StudyImporterException("failed to parse life stage of prey [" + preySpeciesName + "] in stomach [" + preyVolumeString + "] on line [" + parser.getLastLineNumber() + "]");
            }
        }
    }
}

Example 3 with TermLookupServiceException

use of org.eol.globi.service.TermLookupServiceException in project eol-globi-data by jhpoelen.

the class TermLookupServiceImpl method buildMapping.

private void buildMapping(List<URI> uriList) throws TermLookupServiceException {
    mapping = new HashMap<>();
    for (URI uri : uriList) {
        try {
            String response = contentToString(uri);
            CSVParse parser = CSVTSVUtil.createCSVParse(new StringReader(response));
            parser.changeDelimiter(getDelimiter());
            if (hasHeader()) {
                parser = CSVTSVUtil.createLabeledCSVParser(parser);
            }
            String[] line;
            while ((line = parser.getLine()) != null) {
                if (line.length < 4) {
                    LOG.info("line: [" + parser.getLastLineNumber() + "] in [" + uriList + "] contains less than 4 columns");
                } else {
                    String sourceName = line[1];
                    String targetId = line[2];
                    String targetName = line[3];
                    if (StringUtils.isNotBlank(sourceName) && StringUtils.isNotBlank(targetId) && StringUtils.isNotBlank(targetName)) {
                        List<Term> terms = mapping.computeIfAbsent(sourceName, k -> new ArrayList<>());
                        terms.add(new TermImpl(targetId, targetName));
                    }
                }
            }
        } catch (IOException e) {
            throw new TermLookupServiceException("failed to retrieve mapping from [" + uriList + "]", e);
        }
    }
}

Example 4 with TermLookupServiceException

use of org.eol.globi.service.TermLookupServiceException in project eol-globi-data by jhpoelen.

the class NodeFactoryNeo4jTest method createAndFindEnvironment.

@Test
public void createAndFindEnvironment() throws NodeFactoryException {
    getNodeFactory().setEnvoLookupService(new TermLookupService() {

        @Override
        public List<Term> lookupTermByName(String name) throws TermLookupServiceException {
            ArrayList<Term> terms = new ArrayList<>();
            terms.add(new TermImpl("NS:" + name, StringUtils.replace(name, " ", "_")));
            return terms;
        }
    });
    Location location = getNodeFactory().getOrCreateLocation(new LocationImpl(0.0, 1.0, 2.0, null));
    List<Environment> first = getNodeFactory().getOrCreateEnvironments(location, "BLA:123", "this and that");
    location = getNodeFactory().getOrCreateLocation(new LocationImpl(0.0, 1.0, 2.0, null));
    List<Environment> second = getNodeFactory().getOrCreateEnvironments(location, "BLA:123", "this and that");
    assertThat(first.size(), is(second.size()));
    assertThat(((NodeBacked) first.get(0)).getNodeID(), is(((NodeBacked) second.get(0)).getNodeID()));
    EnvironmentNode foundEnvironment = getNodeFactory().findEnvironment("this_and_that");
    assertThat(foundEnvironment, is(notNullValue()));
    List<Environment> environments = location.getEnvironments();
    assertThat(environments.size(), is(1));
    Environment environment = environments.get(0);
    NodeBacked environmentNode = (NodeBacked) environment;
    assertThat(environmentNode.getNodeID(), is(foundEnvironment.getNodeID()));
    assertThat(environment.getName(), is("this_and_that"));
    assertThat(environment.getExternalId(), is("NS:this and that"));
    Location anotherLocation = getNodeFactory().getOrCreateLocation(new LocationImpl(48.2, 123.1, null, null));
    LocationNode anotherLocationNode = (LocationNode) anotherLocation;
    assertThat(anotherLocationNode.getEnvironments().size(), is(0));
    anotherLocationNode.addEnvironment((EnvironmentNode) environment);
    assertThat(anotherLocationNode.getEnvironments().size(), is(1));
    // don't add environment that has already been associated
    anotherLocationNode.addEnvironment(environment);
    assertThat(anotherLocationNode.getEnvironments().size(), is(1));
    getNodeFactory().getOrCreateEnvironments(anotherLocation, "BLA:124", "that");
    assertThat(anotherLocationNode.getEnvironments().size(), is(2));
}