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

Example 6 with Specimen

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

Example 7 with Specimen

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

the class StudyImporterForSPIRE method createSpecimen.

private Specimen createSpecimen(String taxonName, Study study) throws NodeFactoryException {
    taxonName = taxonName.replaceAll("_", " ");
    Specimen specimen = nodeFactory.createSpecimen(study, new TaxonImpl(taxonName, null));
    if (taxonName.contains("adult")) {
        addLifeStage(specimen, "adult");
    } else if (taxonName.contains("juvenile")) {
        addLifeStage(specimen, "juvenile");
    } else if (taxonName.contains(" egg")) {
        addLifeStage(specimen, "egg");
    } else if (taxonName.contains("larvae")) {
        addLifeStage(specimen, "larvae");
    } else if (taxonName.contains("immature")) {
        addLifeStage(specimen, "immature");
    } else if (taxonName.contains("nymphs")) {
        addLifeStage(specimen, "nymphs");
    }
    return specimen;
}

Example 8 with Specimen

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

the class StudyImporterForSPIRE method importValidLink.

private void importValidLink(Map<String, String> properties) throws NodeFactoryException {
    Study study = nodeFactory.getOrCreateStudy(new StudyImpl(properties.get(StudyConstant.TITLE), SOURCE_SPIRE, null, properties.get(StudyConstant.DESCRIPTION)));
    try {
        Specimen predator = createSpecimen(properties.get(PREDATOR_NAME), study);
        String locality = properties.get(LOCALITY_ORIGINAL);
        LatLng latLng = getGeoNamesService().findLatLng(locality);
        if (latLng == null) {
            getLogger().warn(study, "failed to find location for county [" + locality + "]");
        } else {
            Location location = nodeFactory.getOrCreateLocation(new LocationImpl(latLng.getLat(), latLng.getLng(), null, null));
            predator.caughtIn(location);
            String habitat = properties.get(OF_HABITAT);
            if (StringUtils.isNotBlank(habitat)) {
                addEnvironment(location, "SPIRE:" + habitat, habitat);
            }
        }
        Specimen prey = createSpecimen(properties.get(PREY_NAME), study);
        predator.ate(prey);
    } catch (NodeFactoryException e) {
        getLogger().warn(study, "failed to import trophic link with properties [" + properties + "]: " + e.getMessage());
    } catch (IOException e) {
        getLogger().warn(study, "failed to import trophic link with properties [" + properties + "]: " + e.getMessage());
    }
}

Example 9 with Specimen

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

the class StudyImporterForWrast method addPredatorSpecimen.

private Specimen addPredatorSpecimen(LabeledCSVParser csvParser, Study study, LengthParser lengthParser, String seasonName, Location sampleLocation, String speciesName, String predatorId, Map<String, Specimen> predatorMap) throws StudyImporterException {
    Specimen predator = createAndClassifySpecimen(speciesName, study);
    predatorMap.put(predatorId, predator);
    predator.setLengthInMm(lengthParser.parseLengthInMm(csvParser));
    if (null != sampleLocation) {
        predator.caughtIn(sampleLocation);
    }
    predator.caughtDuring(getOrCreateSeason(seasonName));
    return predator;
}

Example 10 with Specimen

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

the class LinkerTrustyNanoPubs method generateOrganisms.

public static void generateOrganisms(StringBuilder builder, InteractionNode interaction) {
    Collection<Specimen> participants = interaction.getParticipants();
    Map<Long, Integer> nodeIdParticipantMap = new TreeMap<>();
    int participantNumber = 0;
    for (Specimen participant : participants) {
        builder.append(String.format("\n    obo:RO_0000057 :Organism_%d ", participantNumber));
        builder.append(participants.size() - 1 == participantNumber ? "." : ";");
        nodeIdParticipantMap.put(((NodeBacked) participant).getNodeID(), participantNumber);
        participantNumber++;
    }
    participantNumber = 0;
    for (Specimen participant : participants) {
        Iterable<Relationship> classification = NodeUtil.getClassifications(participant);
        if (classification != null && classification.iterator().hasNext()) {
            TaxonNode taxonNode = new TaxonNode(classification.iterator().next().getEndNode());
            String ncbiTaxonId = resolveNCBITaxonId(taxonNode);
            if (StringUtils.isNotBlank(ncbiTaxonId)) {
                builder.append(String.format("\n  :Organism_%d a NCBITaxon:%s ", participantNumber, ncbiTaxonId));
                Iterable<Relationship> interactRel = ((NodeBacked) participant).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.values()));
                for (Relationship relationship : interactRel) {
                    if (!relationship.hasProperty(PropertyAndValueDictionary.INVERTED)) {
                        if (relationship.hasProperty(PropertyAndValueDictionary.IRI)) {
                            String interactIRI = relationship.getProperty(PropertyAndValueDictionary.IRI).toString();
                            if (StringUtils.isNotBlank(interactIRI)) {
                                builder.append(";\n");
                                builder.append(String.format("    <%s> :Organism_%d ", interactIRI, nodeIdParticipantMap.get(relationship.getEndNode().getId())));
                            }
                        }
                    }
                }
                builder.append(".");
                participantNumber++;
            }
        }
    }
}