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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.ext.occurrence.gbif;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.net.MalformedURLException;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.nio.charset.Charset;
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import java.text.ParseException;
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import java.util.ArrayList;
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import java.util.Collection;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.HttpException;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.common.UriUtils;
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import eu.etaxonomy.cdm.common.media.CdmImageInfo;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.media.ImageFile;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import net.sf.json.JSONArray;
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import net.sf.json.JSONObject;
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/**
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* Utility class which provides the functionality to convert a JSON response
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* resulting from a GBIF query for occurrences to the corresponding CDM entities.
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* @author pplitzner
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* @since 22.05.2014
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*/
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public class GbifJsonOccurrenceParser {
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private static final Logger logger = Logger.getLogger(GbifJsonOccurrenceParser.class);
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private static final String DATASET_KEY = "datasetKey";
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private static final String DATASET_PROTOCOL = "protocol";
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private static final String KEY = "key";
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private static final String URL = "url";
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private static final String TYPE = "type";
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private static final String COUNTRY_CODE = "countryCode";
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private static final String LOCALITY = "locality";
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private static final String LONGITUDE = "decimalLongitude";
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private static final String LATITUDE = "decimalLatitude";
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private static final String GEOREFERENCE_PROTOCOL = "georeferenceProtocol";//reference system
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private static final String VERBATIM_ELEVATION = "verbatimElevation";
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private static final String YEAR = "year";
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private static final String MONTH = "month";
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private static final String DAY = "day";
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private static final String EVENT_DATE= "eventDate";
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private static final String RECORDED_BY= "recordedBy";//collector
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private static final String RECORD_NUMBER = "recordNumber";//collector number
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private static final String FIELD_NUMBER = "fieldNumber";//collector number
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private static final String EVENT_REMARKS = "eventRemarks";//gathering event description
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private static final String OCCURRENCE_REMARKS = "occurrenceRemarks";//ecology
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private static final String COLLECTION_CODE = "collectionCode";
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private static final String CATALOG_NUMBER = "catalogNumber";//accession number
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private static final String INSTITUTION_CODE = "institutionCode";
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protected static final String PUBLISHING_ORG_KEY = "publishingOrgKey";
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protected static final String PUBLISHING_COUNTRY = "publishingCountry";
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protected static final String EXTENSIONS = "extensions";
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protected static final String BASIS_OF_RECORD = "basisOfRecord";
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protected static final String INDIVIDUAL_COUNT = "individualCount";
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protected static final String TAXONKEY = "taxonKey";
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protected static final String KINGDOM_KEY = "kingdomKey";
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protected static final String PHYLUM_KEY = "phylumKey";
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protected static final String CLASS_KEY = "classKey";
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protected static final String ORDER_KEY = "orderKey";
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protected static final String FAMILY_KEY = "familyKey";
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protected static final String GENUS_KEY = "genusKey";
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protected static final String SPECIES_KEY = "speciesKey";
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protected static final String SCIENTIFIC_NAME = "scientificName";
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protected static final String KINGDOM = "kingdom";
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protected static final String PHYLUM = "phylum";
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protected static final String ORDER = "order";
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protected static final String FAMILY = "family";
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protected static final String GENUS = "genus";
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protected static final String SPECIES = "species";
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protected static final String GENERIC_NAME = "genericName";
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protected static final String SPECIFIC_EPITHET = "specificEpithet";
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protected static final String INFRASPECIFIC_EPITHET = "infraspecificEpithet";
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protected static final String TAXON_RANK = "taxonRank";
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protected static final String DATE_IDENTIFIED = "dateIdentified";
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protected static final String SCIENTIFIC_NAME_AUTHORSHIP = "scientificNameAuthorship";
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protected static final String ELEVATION = "elevation";
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protected static final String CONITNENT = "continent";
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protected static final String STATE_PROVINCE = "stateProvince";
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protected static final String ISSUES = "issues";
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protected static final String LAST_INTERPRETED = "lastInterpreted";
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protected static final String IDENTIFIERS = "identifiers";
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protected static final String FACTS = "facts";
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protected static final String RELATIONS = "relations";
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protected static final String GEODETICDATUM = "geodeticDatum";
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protected static final String CLASS = "class";
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protected static final String COUNTRY = "country";
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protected static final String NOMENCLATURAL_STATUS = "nomenclaturalStatus";
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protected static final String RIGHTSHOLDER = "rightsHolder";
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protected static final String IDEMTIFIER = "identifier";
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protected static final String NOMENCLATURALCODE = "nomenclaturalCode";
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protected static final String COUNTY = "county";
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protected static final String DATASET_NAME = "datasetName";
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protected static final String GBIF_ID = "gbifID";
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protected static final String OCCURENCE_ID = "occurrenceID";
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protected static final String TAXON_ID = "taxonID";
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protected static final String LICENCE = "license";
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protected static final String OWNER_INSTITUTION_CODE = "ownerInstitutionCode";
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protected static final String BIBLIOGRAPHIC_CITATION = "bibliographicCitation";
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protected static final String IDENTIFIED_BY = "identifiedBy";
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protected static final String COLLECTION_ID = "collectionID";
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private static final String PLANTAE = "Plantae";
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private static final String ANIMALIA = "Animalia";
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private static final String FUNGI = "Fungi";
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private static final String BACTERIA = "Bacteria";
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private static final String MULTIMEDIA = "media";
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/**
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* Parses the given {@link String} for occurrences.<br>
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* Note: The data structure of the GBIF response should not be changed.
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* @param jsonString JSON data as a String
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* @return the found occurrences as a collection of {@link GbifResponse}
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*/
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public static Collection<GbifResponse> parseJsonRecords(String jsonString) {
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return parseJsonRecords(JSONObject.fromObject(jsonString));
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}
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/**
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* Parses the given {@link InputStream} for occurrences.
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* @param jsonString JSON data as an InputStream
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* @return the found occurrences as a collection of {@link GbifResponse}
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*/
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public static Collection<GbifResponse> parseJsonRecords(InputStream inputStream) throws IOException{
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StringWriter stringWriter = new StringWriter();
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IOUtils.copy(inputStream, stringWriter, Charset.defaultCharset());
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return parseJsonRecords(stringWriter.toString());
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}
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/**
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* Parses the given {@link JSONObject} for occurrences.<br>
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* Note: The data structure of the GBIF response should not be changed.
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* @param jsonString JSON data as an JSONObject
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* @return the found occurrences as a collection of {@link GbifResponse}
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*/
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public static Collection<GbifResponse> parseJsonRecords(JSONObject jsonObject){
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return parseJsonRecords(jsonObject.getJSONArray("results"));
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}
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/**
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* Parses the given {@link JSONArray} for occurrences.
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* @param jsonString JSON data as an {@link JSONArray}
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* @return the found occurrences as a collection of {@link GbifResponse}
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*/
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private static Collection<GbifResponse> parseJsonRecords(JSONArray jsonArray) {
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Collection<GbifResponse> results = new ArrayList<>();
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String[] tripleId = new String[3];
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String string;
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for(Object o:jsonArray){
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//parse every record
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tripleId = new String[3];
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if(o instanceof JSONObject){
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String dataSetKey = null;
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GbifDataSetProtocol dataSetProtocol = null;
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DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
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TaxonName name = null;
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JSONObject record = (JSONObject)o;
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if(record.has(DATASET_PROTOCOL)){
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dataSetProtocol = GbifDataSetProtocol.parseProtocol(record.getString(DATASET_PROTOCOL));
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}
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if(record.has(DATASET_KEY)){
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dataSetKey = record.getString(DATASET_KEY);
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}
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if(record.has(COUNTRY_CODE)){
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string = record.getString(COUNTRY_CODE);
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Country country = Country.getCountryByIso3166A2(string);
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if(country!=null){
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derivedUnitFacade.setCountry(country);
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}
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}
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if(record.has(LOCALITY)){
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string = record.getString(LOCALITY);
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derivedUnitFacade.setLocality(string);
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}
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if (record.has("species")){
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Rank rank = null;
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if (record.has(TAXON_RANK)){
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string= record.getString(TAXON_RANK);
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try {
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rank = Rank.getRankByName(string);
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} catch (UnknownCdmTypeException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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}
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if (rank != null){
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if (record.has(NOMENCLATURALCODE)){
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string = record.getString(NOMENCLATURALCODE);
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if (string.equals(NomenclaturalCode.ICZN.getTitleCache())){
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name = TaxonNameFactory.NewZoologicalInstance(rank);
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} else if (string.equals(NomenclaturalCode.ICNAFP.getTitleCache())) {
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name = TaxonNameFactory.NewBotanicalInstance(rank);
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} else if (string.equals(NomenclaturalCode.ICNB.getTitleCache())){
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name = TaxonNameFactory.NewBacterialInstance(rank);
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} else if (string.equals(NomenclaturalCode.ICNCP.getTitleCache())){
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name = TaxonNameFactory.NewCultivarInstance(rank);
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} else if (string.equals(NomenclaturalCode.ICVCN.getTitleCache())){
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name = TaxonNameFactory.NewViralInstance(rank);
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} else if (string.equals("ICN")){
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name = TaxonNameFactory.NewBotanicalInstance(rank);
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}
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}else {
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if (record.has(KINGDOM)){
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if (record.getString(KINGDOM).equals(PLANTAE)){
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name = TaxonNameFactory.NewBotanicalInstance(rank);
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} else if (record.getString(KINGDOM).equals(ANIMALIA)){
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name = TaxonNameFactory.NewZoologicalInstance(rank);
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256
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} else if (record.getString(KINGDOM).equals(FUNGI)){
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257
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name = TaxonNameFactory.NewBotanicalInstance(rank);
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258
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} else if (record.getString(KINGDOM).equals(BACTERIA)){
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259
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name = TaxonNameFactory.NewBacterialInstance(rank);
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260
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} else{
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261
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name = TaxonNameFactory.NewNonViralInstance(rank);
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262
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}
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263
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} else{
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264
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name = TaxonNameFactory.NewNonViralInstance(rank);
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265
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}
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266
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}
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267
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if (name == null){
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268
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name = TaxonNameFactory.NewNonViralInstance(rank);
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269
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}
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270
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if (record.has(GENUS)){
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271
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name.setGenusOrUninomial(record.getString(GENUS));
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272
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}
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273
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if (record.has(SPECIFIC_EPITHET)){
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274
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name.setSpecificEpithet(record.getString(SPECIFIC_EPITHET));
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275
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}
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276
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if (record.has(INFRASPECIFIC_EPITHET)){
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277
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name.setInfraSpecificEpithet(record.getString(INFRASPECIFIC_EPITHET));
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278
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}
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279
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if (record.has(SCIENTIFIC_NAME)){
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280
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name.setTitleCache(record.getString(SCIENTIFIC_NAME), true);
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281
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}
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282
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}
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283
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DeterminationEvent detEvent = DeterminationEvent.NewInstance();
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284
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285
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if (record.has(IDENTIFIED_BY)){
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286
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Person determiner = Person.NewTitledInstance(record.getString(IDENTIFIED_BY));
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287
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detEvent.setDeterminer(determiner);
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288
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}
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289
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detEvent.setTaxonName(name);
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290
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detEvent.setPreferredFlag(true);
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291
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derivedUnitFacade.addDetermination(detEvent);
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292
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}
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293
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294
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// GPS location
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295
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Point location = Point.NewInstance();
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296
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derivedUnitFacade.setExactLocation(location);
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297
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try {
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298
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if(record.has(LATITUDE)){
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299
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String lat = record.getString(LATITUDE);
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300
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location.setLatitudeByParsing(lat);
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301
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}
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302
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if(record.has(LONGITUDE)){
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303
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String lon = record.getString(LONGITUDE);
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304
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location.setLongitudeByParsing(lon);
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305
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}
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306
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} catch (ParseException e) {
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307
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logger.error("Could not parse GPS coordinates", e);
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308
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}
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309
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if(record.has(GEOREFERENCE_PROTOCOL)){
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310
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String geo = record.getString(GEOREFERENCE_PROTOCOL);
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311
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ReferenceSystem referenceSystem = null;
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312
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//TODO: Is there another way than string comparison
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313
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//to check which reference system is used?
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314
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if(ReferenceSystem.WGS84().getLabel().contains(geo)){
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315
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referenceSystem = ReferenceSystem.WGS84();
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316
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}
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317
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else if(ReferenceSystem.GOOGLE_EARTH().getLabel().contains(geo)){
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318
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referenceSystem = ReferenceSystem.GOOGLE_EARTH();
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319
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}
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320
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else if(ReferenceSystem.GAZETTEER().getLabel().contains(geo)){
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321
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referenceSystem = ReferenceSystem.GAZETTEER();
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322
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}
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323
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location.setReferenceSystem(referenceSystem);
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324
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}
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325
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326
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if(record.has(ELEVATION)){
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327
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try {
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328
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//parse integer and strip of unit
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329
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string = record.getString(ELEVATION);
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330
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int length = string.length();
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331
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StringBuilder builder = new StringBuilder();
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332
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for(int i=0;i<length;i++){
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333
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if(Character.isDigit(string.charAt(i))){
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334
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builder.append(string.charAt(i));
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|
335
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}
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336
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else{
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337
|
break;
|
|
338
|
}
|
|
339
|
}
|
|
340
|
derivedUnitFacade.setAbsoluteElevation(Integer.parseInt(builder.toString()));
|
|
341
|
} catch (NumberFormatException e) {
|
|
342
|
logger.warn("Could not parse elevation", e);
|
|
343
|
}
|
|
344
|
}
|
|
345
|
|
|
346
|
//Date (Gathering Period)
|
|
347
|
TimePeriod timePeriod = TimePeriod.NewInstance();
|
|
348
|
derivedUnitFacade.setGatheringPeriod(timePeriod);
|
|
349
|
//TODO what happens with eventDate??
|
|
350
|
if(record.has(YEAR)){
|
|
351
|
timePeriod.setStartYear(record.getInt(YEAR));
|
|
352
|
}
|
|
353
|
if(record.has(MONTH)){
|
|
354
|
timePeriod.setStartMonth(record.getInt(MONTH));
|
|
355
|
}
|
|
356
|
if(record.has(DAY)){
|
|
357
|
timePeriod.setStartDay(record.getInt(DAY));
|
|
358
|
}
|
|
359
|
if(record.has(RECORDED_BY)){
|
|
360
|
Person person = Person.NewTitledInstance(record.getString(RECORDED_BY));
|
|
361
|
//FIXME check data base if collector already present
|
|
362
|
derivedUnitFacade.setCollector(person);
|
|
363
|
}
|
|
364
|
|
|
365
|
//collector number (fieldNumber OR recordNumber)
|
|
366
|
if(record.has(FIELD_NUMBER)){
|
|
367
|
derivedUnitFacade.setFieldNumber(record.getString(FIELD_NUMBER));
|
|
368
|
}
|
|
369
|
//collector number (fieldNumber OR recordNumber)
|
|
370
|
if(record.has(RECORD_NUMBER)){
|
|
371
|
derivedUnitFacade.setFieldNumber(record.getString(RECORD_NUMBER));
|
|
372
|
}
|
|
373
|
|
|
374
|
if(record.has(EVENT_REMARKS)){
|
|
375
|
derivedUnitFacade.setGatheringEventDescription(record.getString(EVENT_REMARKS));
|
|
376
|
}
|
|
377
|
if(record.has(OCCURRENCE_REMARKS)){
|
|
378
|
derivedUnitFacade.setEcology(record.getString(OCCURRENCE_REMARKS));
|
|
379
|
}
|
|
380
|
if(record.has(COLLECTION_CODE)){
|
|
381
|
String collectionCode = record.getString(COLLECTION_CODE);
|
|
382
|
tripleId[2] = collectionCode;
|
|
383
|
//FIXME: check data base for existing collections
|
|
384
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = eu.etaxonomy.cdm.model.occurrence.Collection.NewInstance();
|
|
385
|
collection.setCode(collectionCode);
|
|
386
|
if(record.has(INSTITUTION_CODE)){
|
|
387
|
Institution institution = Institution.NewNamedInstance(record.getString(INSTITUTION_CODE));
|
|
388
|
institution.setCode(record.getString(INSTITUTION_CODE));
|
|
389
|
collection.setInstitute(institution);
|
|
390
|
}
|
|
391
|
derivedUnitFacade.setCollection(collection);
|
|
392
|
}
|
|
393
|
if(record.has(CATALOG_NUMBER)){
|
|
394
|
derivedUnitFacade.setCatalogNumber(record.getString(CATALOG_NUMBER));
|
|
395
|
derivedUnitFacade.setAccessionNumber(record.getString(CATALOG_NUMBER));
|
|
396
|
tripleId[0]= record.getString(CATALOG_NUMBER);
|
|
397
|
}
|
|
398
|
if(record.has(INSTITUTION_CODE)){
|
|
399
|
derivedUnitFacade.setAccessionNumber(record.getString(INSTITUTION_CODE));
|
|
400
|
tripleId[1]= record.getString(INSTITUTION_CODE);
|
|
401
|
}
|
|
402
|
|
|
403
|
if (record.has(OCCURENCE_ID)){
|
|
404
|
IdentifiableSource source = IdentifiableSource.NewDataImportInstance((record.getString(OCCURENCE_ID)));
|
|
405
|
derivedUnitFacade.addSource(source);
|
|
406
|
}
|
|
407
|
|
|
408
|
if (record.has(MULTIMEDIA)){
|
|
409
|
//http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
|
|
410
|
JSONArray multimediaArray = record.getJSONArray(MULTIMEDIA);
|
|
411
|
JSONObject mediaRecord;
|
|
412
|
Media media;
|
|
413
|
URI uri = null;
|
|
414
|
CdmImageInfo imageInf = null;
|
|
415
|
MediaRepresentation representation = null;
|
|
416
|
SpecimenOrObservationType type = null;
|
|
417
|
for(Object object:multimediaArray){
|
|
418
|
//parse every record
|
|
419
|
media = Media.NewInstance();
|
|
420
|
uri = null;
|
|
421
|
imageInf = null;
|
|
422
|
|
|
423
|
if(object instanceof JSONObject){
|
|
424
|
mediaRecord = (JSONObject) object;
|
|
425
|
|
|
426
|
if (mediaRecord.has("identifier")){
|
|
427
|
try {
|
|
428
|
uri = new URI(mediaRecord.getString("identifier"));
|
|
429
|
imageInf = CdmImageInfo.NewInstance(uri, 0);
|
|
430
|
} catch (URISyntaxException |IOException | HttpException e) {
|
|
431
|
e.printStackTrace();
|
|
432
|
}
|
|
433
|
// media.addIdentifier(mediaRecord.getString("identifier"), null);
|
|
434
|
}
|
|
435
|
if (mediaRecord.has("references")){
|
|
436
|
|
|
437
|
|
|
438
|
}
|
|
439
|
if (mediaRecord.has("format")){
|
|
440
|
|
|
441
|
}
|
|
442
|
if (mediaRecord.has("type")){
|
|
443
|
if (mediaRecord.get("type").equals("StillImage")){
|
|
444
|
type = SpecimenOrObservationType.StillImage;
|
|
445
|
}
|
|
446
|
}
|
|
447
|
}
|
|
448
|
ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInf);
|
|
449
|
representation = MediaRepresentation.NewInstance();
|
|
450
|
|
|
451
|
representation.addRepresentationPart(imageFile);
|
|
452
|
media.addRepresentation(representation);
|
|
453
|
|
|
454
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
455
|
}
|
|
456
|
//identifier=http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
|
|
457
|
//references=http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=136628
|
|
458
|
//format=image/jpeg
|
|
459
|
//type=StillImage
|
|
460
|
}
|
|
461
|
|
|
462
|
// create dataset URL
|
|
463
|
URI uri = null;
|
|
464
|
try {
|
|
465
|
uri = UriUtils.createUri(new URL(GbifQueryServiceWrapper.BASE_URL), "/v1/dataset/"+dataSetKey+"/endpoint", null, null);
|
|
466
|
} catch (MalformedURLException e) {
|
|
467
|
logger.error("Endpoint URI could not be created!", e);
|
|
468
|
} catch (URISyntaxException e) {
|
|
469
|
logger.error("Endpoint URI could not be created!", e);
|
|
470
|
}
|
|
471
|
results.add(new GbifResponse(derivedUnitFacade, uri, dataSetProtocol, tripleId, name));
|
|
472
|
}
|
|
473
|
}
|
|
474
|
return results;
|
|
475
|
}
|
|
476
|
|
|
477
|
public static DataSetResponse parseOriginalDataSetUri(InputStream inputStream) throws IOException {
|
|
478
|
StringWriter stringWriter = new StringWriter();
|
|
479
|
IOUtils.copy(inputStream, stringWriter, Charset.defaultCharset());
|
|
480
|
return parseOriginalDataSetUri(stringWriter.toString());
|
|
481
|
}
|
|
482
|
|
|
483
|
public static DataSetResponse parseOriginalDataSetUri(String jsonString) {
|
|
484
|
DataSetResponse response = new DataSetResponse();
|
|
485
|
JSONArray jsonArray = JSONArray.fromObject(jsonString);
|
|
486
|
Object next = jsonArray.iterator().next();
|
|
487
|
if(next instanceof JSONObject){
|
|
488
|
JSONObject jsonObject = (JSONObject)next;
|
|
489
|
if(jsonObject.has(URL)){
|
|
490
|
response.setEndpoint(URI.create(jsonObject.getString(URL)));
|
|
491
|
}
|
|
492
|
if(jsonObject.has(TYPE)){
|
|
493
|
response.setProtocol(GbifDataSetProtocol.parseProtocol(jsonObject.getString(TYPE)));
|
|
494
|
}
|
|
495
|
}
|
|
496
|
return response;
|
|
497
|
}
|
|
498
|
}
|