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

Example 31 with StudyImpl

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

the class StudyImporterForByrnes method importLine.

private void importLine(LabeledCSVParser parser, Map<String, String> refMap) throws StudyImporterException {
    Study localStudy = null;
    try {
        String refList = StringUtils.trim(parser.getValueByLabel("Reference"));
        String[] refs;
        if (StringUtils.isBlank(refList)) {
            refs = new String[] { "Byrnes, J.E. et al., 2011. Climate-driven increases in storm frequency simplify kelp forest food webs. Global Change Biology, 17(8), pp.2513–2524. Available at: http://dx.doi.org/10.1111/j.1365-2486.2011.02409.x." };
        } else {
            refs = StringUtils.split(refList, ",");
        }
        for (String ref : refs) {
            String singleShortRef = StringUtils.trim(ref);
            String longRef = refMap.get(singleShortRef);
            String citation = StringUtils.isBlank(longRef) ? singleShortRef : longRef;
            localStudy = nodeFactory.getOrCreateStudy(new StudyImpl("BYRNES-" + StringUtils.abbreviate(citation, 32), SOURCE, null, citation));
            String predatorName = parser.getValueByLabel("Predator");
            if (StringUtils.isBlank(predatorName)) {
                getLogger().warn(localStudy, "found empty predator name on line [" + parser.lastLineNumber() + "]");
            } else {
                addInteractionForPredator(parser, localStudy, predatorName);
            }
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("problem creating nodes at line [" + parser.lastLineNumber() + "]", e);
    } catch (NumberFormatException e) {
        String message = "skipping record, found malformed field at line [" + parser.lastLineNumber() + "]: ";
        if (localStudy != null) {
            getLogger().warn(localStudy, message + e.getMessage());
        }
    }
}

Example 32 with StudyImpl

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

the class StudyImporterForBarnes method importLine.

private void importLine(LabeledCSVParser parser, Map<String, String> refMap) throws StudyImporterException {
    Study localStudy = null;
    try {
        String shortReference = StringUtils.trim(parser.getValueByLabel("Reference"));
        if (!refMap.containsKey(shortReference)) {
            throw new StudyImporterException("failed to find ref [" + shortReference + "] on line [" + parser.lastLineNumber() + "]");
        }
        String longReference = refMap.get(shortReference);
        localStudy = nodeFactory.getOrCreateStudy(new StudyImpl("BARNES-" + shortReference, SOURCE, null, ExternalIdUtil.toCitation(null, longReference, null)));
        String predatorName = parser.getValueByLabel("Predator");
        if (StringUtils.isBlank(predatorName)) {
            getLogger().warn(localStudy, "found empty predator name on line [" + parser.lastLineNumber() + "]");
        } else {
            addInteractionForPredator(parser, localStudy, predatorName);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("problem creating nodes at line [" + parser.lastLineNumber() + "]", e);
    } catch (NumberFormatException e) {
        String message = "skipping record, found malformed field at line [" + parser.lastLineNumber() + "]: ";
        if (localStudy != null) {
            getLogger().warn(localStudy, message + e.getMessage());
        }
    }
}

Example 33 with StudyImpl

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

the class StudyImporterForBioInfo method createStudy.

protected Study createStudy(String refId, String citation) throws NodeFactoryException {
    String sourceCitation = "Food Webs and Species Interactions in the Biodiversity of UK and Ireland (Online). 2015. Data provided by Malcolm Storey. Also available from " + BIOINFO_URL + ".";
    String bioInfoId = TaxonomyProvider.BIO_INFO + "ref:" + refId;
    StudyImpl study1 = new StudyImpl(bioInfoId, sourceCitation, null, citation);
    study1.setExternalId(ExternalIdUtil.urlForExternalId(bioInfoId));
    return nodeFactory.getOrCreateStudy(study1);
}

Example 34 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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 35 with StudyImpl

use of org.eol.globi.domain.StudyImpl 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"));
}