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

Example 56 with Study

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

the class StudyImporterForBioInfo method createRelations.

protected void createRelations(LabeledCSVParser parser, Map<String, String> refMap, Map<String, Taxon> taxonMap) throws StudyImporterException {
    try {
        long count = 1;
        while (parser.getLine() != null) {
            if (importFilter.shouldImportRecord(count)) {
                String refIds = parser.getValueByLabel("list of reference ids");
                if (StringUtils.isNotBlank(refIds)) {
                    String[] ids = StringUtils.split(refIds, ";");
                    for (String id : ids) {
                        String trimmedId = StringUtils.trim(id);
                        Study study = createStudy(trimmedId, refMap.get(trimmedId));
                        String relationship = parser.getValueByLabel("relationship");
                        if (StringUtils.isBlank(relationship)) {
                            getLogger().warn(study, "no relationship for record on line [" + (parser.lastLineNumber() + 1) + "]");
                        }
                        InteractType interactType = INTERACTION_MAPPING.get(relationship);
                        if (null == interactType) {
                            getLogger().warn(study, "no mapping found for relationship [" + relationship + "] for record on line [" + (parser.lastLineNumber() + 1) + "]");
                        } else {
                            importInteraction(parser, study, interactType, taxonMap);
                        }
                    }
                }
            }
            count++;
        }
    } catch (IOException e1) {
        throw new StudyImporterException("problem reading trophic relations data", e1);
    }
}

Example 57 with Study

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

the class StudyImporterForBrose method importLine.

private void importLine(LabeledCSVParser parser, Map<String, String> refMap) throws StudyImporterException {
    Study localStudy = null;
    try {
        String shortReference = StringUtils.trim(parser.getValueByLabel("Link 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("BROSE-" + StringUtils.abbreviate(longReference, 20), SOURCE, null, ExternalIdUtil.toCitation(null, longReference, null)));
        String name = getName(parser, "Taxonomy consumer", "Common name(s) consumer");
        if (StringUtils.isBlank(name)) {
            getLogger().warn(localStudy, "found empty name on line [" + parser.lastLineNumber() + "]");
        } else {
            addInteractionForConsumer(parser, localStudy, name);
        }
    } 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 58 with Study

use of org.eol.globi.domain.Study 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 59 with Study

use of org.eol.globi.domain.Study 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 60 with Study

use of org.eol.globi.domain.Study 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);
    }
}