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

Example 86 with Study

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

the class StudyImporterForDunne method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study = createStudy();
    try {
        LabeledCSVParser nodes = parserFactory.createParser(getNodesResourceName(), CharsetConstant.UTF8);
        nodes.changeDelimiter(getDelimiter());
        Map<Integer, Taxon> taxonForNode = new HashMap<Integer, Taxon>();
        while (nodes.getLine() != null) {
            Integer nodeId = getNodeId(nodes);
            if (nodeId != null) {
                final String tsn = nodes.getValueByLabel("TSN");
                taxonForNode.put(nodeId, new TaxonImpl(nodes.getValueByLabel("Name"), TaxonomyProvider.ID_PREFIX_ITIS + tsn));
            }
        }
        LabeledCSVParser links = parserFactory.createParser(getLinksResourceName(), CharsetConstant.UTF8);
        links.changeDelimiter(getDelimiter());
        while (links.getLine() != null) {
            List<Location> locations = new ArrayList<>();
            if (getLocation() != null) {
                Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(getLocation().getLat(), getLocation().getLng(), null, null));
                if (loc != null) {
                    locations.add(loc);
                }
            }
            for (Location location : locations) {
                addLink(study, taxonForNode, links, location);
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to find data file(s)", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create nodes", e);
    }
}

Example 87 with Study

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

the class StudyImporterForGoMexSI2 method addReferences.

protected void addReferences(Map<String, Study> referenceIdToStudy) throws StudyImporterException {
    String referenceResource = getReferencesResourcePath();
    try {
        LabeledCSVParser parser = parserFactory.createParser(referenceResource, CharsetConstant.UTF8);
        Map<String, String> studyContributorMap = collectContributors(referenceResource, parser);
        parser = parserFactory.createParser(referenceResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String refId = getMandatoryValue(referenceResource, parser, "DATA_ID");
            Study study = referenceIdToStudy.get(refId);
            if (study == null) {
                addNewStudy(referenceIdToStudy, referenceResource, parser, refId, studyContributorMap.get(refId));
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("failed to open resource [" + referenceResource + "]", e);
    }
}

Example 88 with Study

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

the class StudyImporterForGemina method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String studyResource = "gemina_search_2008-01-03.txt";
    try {
        String source = "Schriml, L. M., Arze, C., Nadendla, S., Ganapathy, A., Felix, V., Mahurkar, A., … Hall, N. (2009). GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Research, 38(Database), D754–D764. doi:10.1093/nar/gkp832";
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl(source, source, "doi:10.1093/nar/gkp832", source));
        LabeledCSVParser parser = parserFactory.createParser(studyResource, "UTF-8");
        parser.changeDelimiter('\t');
        String[] line;
        while ((line = parser.getLine()) != null) {
            if (line.length > 7) {
                String pathogenId = parser.getValueByLabel("Pathogen Taxonomy");
                String pathogenExternalId = StringUtils.isBlank(pathogenId) ? null : TaxonomyProvider.NCBI.getIdPrefix() + pathogenId;
                Specimen pathogen = nodeFactory.createSpecimen(study, new TaxonImpl(parser.getValueByLabel("Pathogen"), pathogenExternalId));
                String hostId = line[7];
                String hostReservoirExternalId = StringUtils.isBlank(hostId) ? null : TaxonomyProvider.NCBI.getIdPrefix() + hostId;
                Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(parser.getValueByLabel("Host/Reservoir"), hostReservoirExternalId));
                pathogen.interactsWith(host, InteractType.PATHOGEN_OF);
            }
        }
    } catch (IOException | NodeFactoryException e) {
        throw new StudyImporterException("failed to import [" + studyResource + "]", e);
    }
}

Example 89 with Study

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

the class StudyImporterForGoMexSI2 method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("GoMexSI", GOMEXI_SOURCE_DESCRIPTION, null, ExternalIdUtil.toCitation("James D. Simons", "<a href=\"http://www.ingentaconnect.com/content/umrsmas/bullmar/2013/00000089/00000001/art00009\">Building a Fisheries Trophic Interaction Database for Management and Modeling Research in the Gulf of Mexico Large Marine Ecosystem.</a>", null)));
    final Map<String, Map<String, String>> predatorIdToPredatorNames = new HashMap<String, Map<String, String>>();
    final Map<String, List<Map<String, String>>> predatorIdToPreyNames = new HashMap<String, List<Map<String, String>>>();
    Map<String, Study> referenceIdToStudy = new HashMap<String, Study>();
    addSpecimen(getPredatorResourcePath(), "PRED_", new ParseEventHandler() {

        @Override
        public void onSpecimen(String predatorUID, Map<String, String> properties) {
            predatorIdToPredatorNames.put(predatorUID, properties);
        }
    });
    addSpecimen(getPreyResourcePath(), "PREY_", new ParseEventHandler() {

        @Override
        public void onSpecimen(String predatorUID, Map<String, String> properties) {
            List<Map<String, String>> preyList = predatorIdToPreyNames.get(predatorUID);
            if (preyList == null) {
                preyList = new ArrayList<Map<String, String>>();
                predatorIdToPreyNames.put(predatorUID, preyList);
            }
            preyList.add(properties);
        }
    });
    addReferences(referenceIdToStudy);
    addObservations(predatorIdToPredatorNames, referenceIdToStudy, predatorIdToPreyNames, study);
}

Example 90 with Study

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

the class StudyImporterForGoMexSI2 method addNewStudy.

private void addNewStudy(Map<String, Study> referenceIdToStudy, String referenceResource, LabeledCSVParser parser, String refId, String contributors) throws StudyImporterException {
    Study study;
    String refTag = getMandatoryValue(referenceResource, parser, "REF_TAG");
    String externalId = getMandatoryValue(referenceResource, parser, "GAME_ID");
    String description = getMandatoryValue(referenceResource, parser, "TITLE_REF");
    String publicationYear = getMandatoryValue(referenceResource, parser, "YEAR_PUB");
    study = nodeFactory.getOrCreateStudy(new StudyImpl(refTag, getSourceCitation(), null, ExternalIdUtil.toCitation(contributors, description, publicationYear)));
    if (StringUtils.isNotBlank(externalId)) {
        study.setExternalId(ExternalIdUtil.urlForExternalId(TaxonomyProvider.ID_PREFIX_GAME + externalId));
    }
    referenceIdToStudy.put(refId, study);
}