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

Example 1 with StudyImpl

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

the class StudyImporterForJSONLD method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    Model model;
    try {
        model = buildModel();
    } catch (IOException e) {
        throw new StudyImporterException("failed to import [" + getResourceURI() + "]", e);
    }
    Query query;
    try {
        query = QueryFactory.create(IOUtils.toString(new DatasetLocal().getResource("find-jsonld-interactions.rq"), CharsetConstant.UTF8));
    } catch (IOException e) {
        throw new StudyImporterException("failed to find sparql query", e);
    }
    QueryExecution exec = QueryExecutionFactory.create(query, model);
    try {
        ResultSet results = exec.execSelect();
        while (results.hasNext()) {
            QuerySolution solution = results.nextSolution();
            String subj = solution.get("subj").asResource().getURI();
            String creationDate = solution.get("creationDate").asLiteral().getString();
            String authorURI = solution.get("author").toString();
            String author;
            try {
                author = nodeFactory.getAuthorResolver().findFullName(authorURI);
            } catch (IOException e) {
                throw new StudyImporterException("failed to resolve author URI [" + authorURI + "]");
            }
            final String source1 = author + ". " + new DateTime(parseDate(creationDate)).getYear() + ". " + CitationUtil.createLastAccessedString(getResourceURI().toString());
            Study study = nodeFactory.getOrCreateStudy(new StudyImpl(getResourceURI() + subj, source1, null, subj));
            study.setExternalId(subj);
            Specimen source = createSpecimen(solution, study, "subjTaxon");
            Specimen target = createSpecimen(solution, study, "targetTaxon");
            String interactType = solution.get("p").asResource().getLocalName();
            InteractType interactType1 = InteractType.typeOf(StringUtils.replace(interactType, "RO_", "RO:"));
            if (interactType1 == null) {
                throw new StudyImporterException("failed to map interaction type [" + interactType + "]");
            }
            String collTime = solution.get("collTime").asLiteral().getString();
            Date date = parseDate(collTime);
            nodeFactory.setUnixEpochProperty(source, date);
            nodeFactory.setUnixEpochProperty(target, date);
            Location loc = nodeFactory.getOrCreateLocation(new LocationImpl(solution.get("collLat").asLiteral().getDouble(), solution.get("collLng").asLiteral().getDouble(), null, null));
            target.caughtIn(loc);
            source.caughtIn(loc);
            source.interactsWith(target, interactType1);
        }
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to import jsonld data in [" + getResourceURI() + "]", e);
    } finally {
        exec.close();
    }
}

Example 2 with StudyImpl

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

the class StudyImporterForINaturalist method importInteraction.

private void importInteraction(Taxon targetTaxon, long observationId, String interactionDataType, InteractType interactionTypeId, JsonNode observation, Taxon sourceTaxon, String interactionTypeName) throws StudyImporterException, NodeFactoryException {
    Date observationDate = getObservationDate(observation);
    StringBuilder citation = buildCitation(observation, interactionTypeName, targetTaxon.getName(), sourceTaxon.getName(), observationDate);
    String url = ExternalIdUtil.urlForExternalId(TaxonomyProvider.ID_PREFIX_INATURALIST + observationId);
    citation.append(CitationUtil.createLastAccessedString(url));
    StudyImpl study1 = new StudyImpl(TaxonomyProvider.ID_PREFIX_INATURALIST + observationId, getSourceString(), null, citation.toString());
    study1.setExternalId(url);
    Study study = nodeFactory.getOrCreateStudy(study1);
    createAssociation(observationId, interactionDataType, interactionTypeId, observation, targetTaxon, sourceTaxon, study, observationDate);
}

Example 3 with StudyImpl

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

the class StudyImporterForRobledo method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String description = "García-Robledo C, Erickson DL, Staines CL, Erwin TL, Kress WJ. Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes Heil M, editor. PLoS ONE [Internet]. 2013 January 8;8(1):e52967. Available from: http://dx.doi.org/10.1371/journal.pone.0052967";
    String doi = "http://dx.doi.org/10.1371/journal.pone.0052967";
    Study study1 = new StudyImpl("García-Robledo et al 2013", description, doi, description);
    Study study = nodeFactory.getOrCreateStudy(study1);
    Map<String, String> abrLookup = buildPlantLookup();
    // spatial location from: http://www.ots.ac.cr/index.php?option=com_content&task=view&id=163&Itemid=348
    Double latitude = LocationUtil.parseDegrees("10°26'N");
    Double longitude = LocationUtil.parseDegrees("83°59'W");
    Location location;
    try {
        location = nodeFactory.getOrCreateLocation(new LocationImpl(latitude, longitude, 35.0, null));
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("failed to create location", e);
    }
    // TODO: need to map date range of collections
    String studyResource = "robledo/table_s1_extract.csv";
    try {
        LabeledCSVParser parser = parserFactory.createParser(studyResource, CharsetConstant.UTF8);
        while (parser.getLine() != null) {
            String beetleName = parser.getValueByLabel("Herbivore species");
            String beetleScientificName = completeBeetleName(beetleName);
            Specimen predator = nodeFactory.createSpecimen(study, new TaxonImpl(beetleScientificName, null));
            predator.caughtIn(location);
            for (String plantAbbreviation : abrLookup.keySet()) {
                String plantScientificName = abrLookup.get(plantAbbreviation);
                String valueByLabel = parser.getValueByLabel(plantAbbreviation);
                try {
                    int interactionCode = Integer.parseInt(valueByLabel);
                    if (interactionCode > 0) {
                        Specimen plant = nodeFactory.createSpecimen(study, new TaxonImpl(plantScientificName, null));
                        plant.caughtIn(location);
                        predator.ate(plant);
                    }
                } catch (NumberFormatException ex) {
                    getLogger().warn(study, "malformed or no value [" + valueByLabel + "] found for [" + plantScientificName + "(" + plantAbbreviation + ")" + "] and beetle [" + beetleScientificName + "] could be found in [" + studyResource + ":" + parser.lastLineNumber() + "]");
                }
            }
        }
    } catch (IOException e) {
        throw new StudyImporterException("problem reading [" + studyResource + "]", e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException("cannot create specimens from [" + studyResource + "]", e);
    }
}

Example 4 with StudyImpl

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

the class StudyImporterForWebOfLife method importNetworks.

public void importNetworks(String archiveURL, String sourceCitation) throws StudyImporterException {
    try {
        InputStream inputStream = getDataset().getResource(archiveURL);
        ZipInputStream zipInputStream = new ZipInputStream(inputStream);
        ZipEntry entry;
        File referencesTempFile = null;
        Map<String, File> networkTempFileMap = new HashMap<String, File>();
        while ((entry = zipInputStream.getNextEntry()) != null) {
            if (entry.getName().matches("(^|(.*/))references\\.csv$")) {
                referencesTempFile = FileUtils.saveToTmpFile(zipInputStream, entry);
            } else if (entry.getName().matches(".*\\.csv$")) {
                networkTempFileMap.put(entry.getName().replace(".csv", ""), FileUtils.saveToTmpFile(zipInputStream, entry));
            } else {
                IOUtils.copy(zipInputStream, new NullOutputStream());
            }
        }
        IOUtils.closeQuietly(zipInputStream);
        if (referencesTempFile == null) {
            throw new StudyImporterException("failed to find expected [references.csv] resource in [" + archiveURL + "]");
        }
        if (networkTempFileMap.size() == 0) {
            throw new StudyImporterException("failed to find expected network csv files");
        }
        BufferedReader assocReader = FileUtils.getUncompressedBufferedReader(new FileInputStream(referencesTempFile), CharsetConstant.UTF8);
        LabeledCSVParser parser = CSVTSVUtil.createLabeledCSVParser(assocReader);
        while (parser.getLine() != null) {
            final String citation = parser.getValueByLabel("Reference");
            if (StringUtils.isBlank(citation)) {
                throw new StudyImporterException("found missing reference");
            }
            final String networkId = parser.getValueByLabel("ID");
            if (!networkTempFileMap.containsKey(networkId)) {
                throw new StudyImporterException("found network id [" + networkId + "], but no associated data.");
            }
            final Study study = nodeFactory.getOrCreateStudy(new StudyImpl("bascompte:" + citation, sourceCitation, null, citation));
            importNetwork(parseInteractionType(parser), parseLocation(parser), study, networkTempFileMap.get(networkId));
        }
    } catch (IOException e) {
        throw new StudyImporterException(e);
    } catch (NodeFactoryException e) {
        throw new StudyImporterException(e);
    }
}

Example 5 with StudyImpl

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

the class StudyImporterForRoopnarine method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    String suffix = ".csv";
    String prefix = "roopnarine/857470.item.";
    String trophicGuildLookup = prefix + 4 + suffix;
    final Map<Integer, List<String>> trophicGuildNumberToSpeciesMap = buildGuildLookup(trophicGuildLookup);
    Map<String, LatLng> resourceLocation = resourceLocationMap(suffix, prefix);
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl("Roopnarine et al 2013", "Roopnarine, P.D. & Hertog, R., 2013. Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica. DatasetImpl Papers in Ecology, 2013, pp.1–9. Available at: http://dx.doi.org/10.7167/2013/857470.", "http://dx.doi.org/10.7167/2013/857470", null));
    for (Map.Entry<String, LatLng> resourceLatLngEntry : resourceLocation.entrySet()) {
        LatLng latLng = resourceLatLngEntry.getValue();
        Location location;
        try {
            location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), 0.0, null));
        } catch (NodeFactoryException e) {
            throw new StudyImporterException("failed to create location", e);
        }
        String studyResource = resourceLatLngEntry.getKey();
        getLogger().info(study, "import of [" + studyResource + "] started...");
        List<Specimen> predatorSpecimen = importTrophicInteractions(trophicGuildLookup, trophicGuildNumberToSpeciesMap, studyResource, study, location);
        getLogger().info(study, "import of [" + studyResource + "] done.");
    }
}