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

Example 86 with TaxonImpl

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

the class StudyImporterForCruaud method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    LabeledCSVParser dataParser;
    try {
        dataParser = parserFactory.createParser(RESOURCE_PATH, CharsetConstant.UTF8);
    } catch (IOException e) {
        throw new StudyImporterException("failed to read resource [" + RESOURCE_PATH + "]", e);
    }
    try {
        Study study = nodeFactory.getOrCreateStudy(new StudyImpl("cruaud", SOURCE, "http://dx.doi.org/10.1093/sysbio/sys068", null));
        while (dataParser.getLine() != null) {
            if (importFilter.shouldImportRecord((long) dataParser.getLastLineNumber())) {
                try {
                    String parasiteName = StringUtils.trim(dataParser.getValueByLabel("Family and Species"));
                    String hostName = StringUtils.trim(dataParser.getValueByLabel("Natural host Ficus species"));
                    hostName = StringUtils.replace(hostName, "F.", "Ficus");
                    if (areNamesAvailable(parasiteName, hostName)) {
                        Specimen parasite = nodeFactory.createSpecimen(study, new TaxonImpl(parasiteName, null));
                        Specimen host = nodeFactory.createSpecimen(study, new TaxonImpl(hostName, null));
                        parasite.interactsWith(host, InteractType.PARASITE_OF);
                        String samplingLocation = StringUtils.trim(dataParser.getValueByLabel("Sampling location"));
                        if (getGeoNamesService().hasTermForLocale(samplingLocation)) {
                            LatLng pointForLocality = getGeoNamesService().findLatLng(samplingLocation);
                            if (pointForLocality == null) {
                                LOG.warn("no location associated with locality [" + samplingLocation + "]");
                            } else {
                                Location location = nodeFactory.getOrCreateLocation(new LocationImpl(pointForLocality.getLat(), pointForLocality.getLng(), null, null));
                                parasite.caughtIn(location);
                                host.caughtIn(location);
                            }
                        } else {
                            LOG.warn("no location associated with locality [" + samplingLocation + "]");
                        }
                    }
                } catch (NodeFactoryException | NumberFormatException e) {
                    throw new StudyImporterException("failed to import line [" + (dataParser.lastLineNumber() + 1) + "]", e);
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem importing [" + RESOURCE_PATH + "]", e);
    }
}

Example 87 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 88 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl 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 TaxonImpl

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

the class StudyImporterForHechinger method addLink.

private void addLink(Study study, Map<Integer, Term> stageForNode, Map<Integer, String> taxonForNode, LabeledCSVParser links, Location location) throws StudyImporterException, NodeFactoryException {
    Integer consumerNodeID = Integer.parseInt(links.getValueByLabel("ConsumerNodeID"));
    Integer resourceNodeID = Integer.parseInt(links.getValueByLabel("ResourceNodeID"));
    String linkType = links.getValueByLabel("LinkType");
    InteractType interactType = interactionMapping.get(StringUtils.trim(StringUtils.lowerCase(linkType)));
    if (interactType == null) {
        throw new StudyImporterException("failed to map interaction type [" + linkType + "] in line [" + links.lastLineNumber() + "]");
    }
    Specimen consumer = nodeFactory.createSpecimen(study, new TaxonImpl(taxonForNode.get(consumerNodeID), null));
    consumer.setLifeStage(stageForNode.get(consumerNodeID));
    consumer.setExternalId(getNamespace() + ":NodeID:" + consumerNodeID);
    consumer.caughtIn(location);
    String resourceName = taxonForNode.get(resourceNodeID);
    Specimen resource = nodeFactory.createSpecimen(study, new TaxonImpl(resourceName, null));
    resource.setLifeStage(stageForNode.get(resourceNodeID));
    resource.setExternalId(getNamespace() + ":NodeID:" + resourceNodeID);
    resource.caughtIn(location);
    consumer.interactsWith(resource, interactType);
}

Example 90 with TaxonImpl

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

the class StudyImporterForICES method addPredator.

private Specimen addPredator(LabeledCSVParser parser, Study study) throws StudyImporterException {
    Specimen predatorSpecimen;
    predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl(parser.getValueByLabel("Predator"), null));
    predatorSpecimen.setLengthInMm(parseDoubleField(parser, "Predator (mean) Lengh"));
    return predatorSpecimen;
}