Examples with TimePeriod eu.etaxonomy.cdm.model.common.TimePeriod used on opensource projects

Example 11 with TimePeriod

use of eu.etaxonomy.cdm.model.common.TimePeriod in project cdmlib by cybertaxonomy.

the class TimePeriodParserTest method testSlashPattern.

@Test
public void testSlashPattern() {
    String strSlashDate = "31/12/2015 - 2/1/2016";
    TimePeriod tp = TimePeriodParser.parseString(strSlashDate);
    assertNotNull(tp);
    Assert.assertEquals("31 Dec 2015" + SEP + "2 Jan 2016", tp.toString());
    Assert.assertEquals("2015" + SEP + "2016", tp.getYear());
    Assert.assertEquals(Integer.valueOf(2015), tp.getStartYear());
    Assert.assertEquals(Integer.valueOf(12), tp.getStartMonth());
    Assert.assertEquals(Integer.valueOf(31), tp.getStartDay());
    Assert.assertEquals(Integer.valueOf(2016), tp.getEndYear());
    Assert.assertEquals(Integer.valueOf(1), tp.getEndMonth());
    Assert.assertEquals(Integer.valueOf(2), tp.getEndDay());
    strSlashDate = "1/12/2015 - 2/1/2016";
    tp = TimePeriodParser.parseString(strSlashDate);
    assertNotNull(tp);
    Assert.assertEquals("1 Dec 2015" + SEP + "2 Jan 2016", tp.toString());
    Assert.assertEquals("2015" + SEP + "2016", tp.getYear());
    Assert.assertEquals(Integer.valueOf(2015), tp.getStartYear());
    Assert.assertEquals(Integer.valueOf(12), tp.getStartMonth());
    Assert.assertEquals(Integer.valueOf(1), tp.getStartDay());
    Assert.assertEquals(Integer.valueOf(2016), tp.getEndYear());
    Assert.assertEquals(Integer.valueOf(1), tp.getEndMonth());
    Assert.assertEquals(Integer.valueOf(2), tp.getEndDay());
}

Example 12 with TimePeriod

use of eu.etaxonomy.cdm.model.common.TimePeriod in project cdmlib by cybertaxonomy.

the class IpniService method getNameFromLine.

private IBotanicalName getNameFromLine(String line, Map<Integer, String> parameterMap, ICdmRepository repository, IpniServiceNamesConfigurator config) {
    // Id%Version%Standard form%Default author forename%Default author surname%Taxon groups%Dates%Alternative names
    String[] splits = line.split("%");
    Map<String, String> valueMap = fillValueMap(parameterMap, splits);
    IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(null);
    // epithets
    name.setGenusOrUninomial(valueMap.get(GENUS));
    name.setInfraGenericEpithet(valueMap.get(INFRA_GENUS));
    name.setSpecificEpithet(valueMap.get(SPECIES));
    name.setInfraSpecificEpithet(valueMap.get(INFRA_SPECIFIC));
    // rank
    try {
        String rankStr = nomalizeRank(valueMap.get(RANK));
        Rank rank = Rank.getRankByLatinNameOrIdInVoc(rankStr, NomenclaturalCode.ICNAFP, true);
        name.setRank(rank);
    } catch (UnknownCdmTypeException e) {
        logger.warn("Rank was unknown");
    }
    // caches
    String pureName = valueMap.get(FULL_NAME_WITHOUT_FAMILY_AND_AUTHORS);
    String nameCache = name.getNameCache();
    if (!Nz(pureName).equals(nameCache)) {
        nvnParser.parseSimpleName(name, valueMap.get(FULL_NAME_WITHOUT_FAMILY_AND_AUTHORS), name.getRank(), true);
    // name.setNameCache(valueMap.get(FULL_NAME_WITHOUT_FAMILY_AND_AUTHORS), true);
    }
    String authors = "";
    // authors
    if (valueMap.get(BASIONYM_AUTHOR) != null) {
        authors = valueMap.get(BASIONYM_AUTHOR);
    // name.setBasionymAuthorship(Team.NewTitledInstance(valueMap.get(BASIONYM_AUTHOR), valueMap.get(BASIONYM_AUTHOR)));
    }
    if (valueMap.get(PUBLISHING_AUTHOR) != null) {
        authors += valueMap.get(PUBLISHING_AUTHOR);
    // name.setCombinationAuthorship(Team.NewTitledInstance(valueMap.get(PUBLISHING_AUTHOR), valueMap.get(PUBLISHING_AUTHOR)));
    }
    try {
        nvnParser.parseAuthors(name, authors);
    } catch (StringNotParsableException e1) {
    // 
    }
    if (!Nz(valueMap.get(AUTHORS)).equals(name.getAuthorshipCache())) {
        name.setAuthorshipCache(valueMap.get(AUTHORS), true);
    }
    if ("Y".equals(valueMap.get(HYBRID))) {
        if (!name.isHybrid()) {
            // Is there a concrete way to include the hybrid flag info? As it does not say which type of hybrid it seems
            // to be best to handle hybrids via parsing. But there might be a better errror handling possible.
            logger.warn("Name is flagged as hybrid at IPNI but CDM name has no hybrid flag set: " + name.getTitleCache());
        }
    }
    // publication
    if (valueMap.get(PUBLICATION) != null || valueMap.get(COLLATION) != null || valueMap.get(PUBLICATION_YEAR_FULL) != null) {
        Reference ref = ReferenceFactory.newGeneric();
        // TODO probably we can do better parsing here
        String pub = CdmUtils.concat(" ", valueMap.get(PUBLICATION), valueMap.get(COLLATION));
        if (isNotBlank(pub)) {
            String nomRefTitle = pub;
            String[] split = nomRefTitle.split(":");
            if (split.length > 1) {
                String detail = split[split.length - 1];
                name.setNomenclaturalMicroReference(detail.trim());
                nomRefTitle = nomRefTitle.substring(0, nomRefTitle.length() - detail.length() - 1).trim();
            }
            ref.setAbbrevTitle(nomRefTitle);
        }
        VerbatimTimePeriod datePublished = parsePublicationFullYear(valueMap.get(PUBLICATION_YEAR_FULL));
        ref.setDatePublished(datePublished);
        name.setNomenclaturalReference(ref);
    }
    // name status
    NomenclaturalStatusType statusType = null;
    String statusString = valueMap.get(NAME_STATUS);
    if (isNotBlank(statusString)) {
        try {
            statusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusString, name);
            NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(statusType);
            name.addStatus(nomStatus);
        } catch (UnknownCdmTypeException e) {
            logger.warn("Name status not recognized: " + statusString);
            Annotation annotation = Annotation.NewInstance("Name status: " + statusString, AnnotationType.EDITORIAL(), Language.ENGLISH());
            name.addAnnotation(annotation);
        }
    }
    // remarks
    String remarks = valueMap.get(REMARKS);
    if (remarks != null) {
        Annotation annotation = Annotation.NewInstance(remarks, AnnotationType.EDITORIAL(), Language.ENGLISH());
        name.addAnnotation(annotation);
    }
    // basionym
    if (config.isDoBasionyms() && valueMap.get(BASIONYM) != null) {
        TaxonName basionym = TaxonNameFactory.NewBotanicalInstance(null);
        basionym.setTitleCache(valueMap.get(BASIONYM), true);
        name.addBasionym(basionym);
    }
    // replaced synonym
    if (config.isDoBasionyms() && valueMap.get(REPLACED_SYNONYM) != null) {
        TaxonName replacedSynoynm = TaxonNameFactory.NewBotanicalInstance(null);
        replacedSynoynm.setTitleCache(valueMap.get(REPLACED_SYNONYM), true);
        name.addReplacedSynonym(replacedSynoynm, null, null, null, null);
    }
    // type information
    if (config.isDoType() && valueMap.get(COLLECTION_DATE_AS_TEXT) != null || valueMap.get(COLLECTION_NUMBER) != null || valueMap.get(COLLECTION_DAY1) != null || valueMap.get(COLLECTION_DAY2) != null || valueMap.get(COLLECTION_MONTH1) != null || valueMap.get(COLLECTION_MONTH2) != null || valueMap.get(COLLECTION_YEAR1) != null || valueMap.get(COLLECTION_YEAR2) != null || valueMap.get(COLLECTOR_TEAM_AS_TEXT) != null || valueMap.get(LOCALITY) != null || valueMap.get(LATITUDE_DEGREES) != null || valueMap.get(LATITUDE_MINUTES) != null || valueMap.get(LATITUDE_SECONDS) != null || valueMap.get(NORTH_OR_SOUTH) != null || valueMap.get(COLLECTION_YEAR1) != null || valueMap.get(COLLECTION_YEAR2) != null) // TODO TBC
    {
        DerivedUnitFacade specimen = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
        // gathering period
        String collectionDateAsText = valueMap.get(COLLECTION_DATE_AS_TEXT);
        TimePeriod gatheringPeriod = TimePeriodParser.parseString(collectionDateAsText);
        try {
            gatheringPeriod.setStartDay(getIntegerDateValueOrNull(valueMap, COLLECTION_DAY1));
            gatheringPeriod.setStartMonth(getIntegerDateValueOrNull(valueMap, COLLECTION_MONTH1));
            gatheringPeriod.setStartYear(getIntegerDateValueOrNull(valueMap, COLLECTION_YEAR1));
            gatheringPeriod.setEndDay(getIntegerDateValueOrNull(valueMap, COLLECTION_DAY2));
            gatheringPeriod.setEndMonth(getIntegerDateValueOrNull(valueMap, COLLECTION_MONTH2));
            gatheringPeriod.setEndYear(getIntegerDateValueOrNull(valueMap, COLLECTION_YEAR2));
        } catch (IndexOutOfBoundsException e) {
            logger.info("Exception occurred when trying to fill gathering period");
        }
        specimen.setGatheringPeriod(gatheringPeriod);
        specimen.setFieldNumber(valueMap.get(COLLECTION_NUMBER));
        // collector team
        String team = valueMap.get(COLLECTOR_TEAM_AS_TEXT);
        if (team != null) {
            Team collectorTeam = Team.NewTitledInstance(team, team);
            specimen.setCollector(collectorTeam);
        }
        specimen.setLocality(valueMap.get(LOCALITY));
        try {
            String latDegrees = CdmUtils.Nz(valueMap.get(LATITUDE_DEGREES));
            String latMinutes = CdmUtils.Nz(valueMap.get(LATITUDE_MINUTES));
            String latSeconds = CdmUtils.Nz(valueMap.get(LATITUDE_SECONDS));
            String direction = CdmUtils.Nz(valueMap.get(NORTH_OR_SOUTH));
            String latitude = latDegrees + "°" + latMinutes + "'" + latSeconds + "\"" + direction;
            String lonDegrees = CdmUtils.Nz(valueMap.get(LONGITUDE_DEGREES));
            String lonMinutes = CdmUtils.Nz(valueMap.get(LONGITUDE_MINUTES));
            String lonSeconds = CdmUtils.Nz(valueMap.get(LONGITUDE_SECONDS));
            direction = CdmUtils.Nz(valueMap.get(EAST_OR_WEST));
            String longitude = lonDegrees + "°" + lonMinutes + "'" + lonSeconds + "\"" + direction;
            specimen.setExactLocationByParsing(longitude, latitude, null, null);
        } catch (ParseException e) {
            logger.info("Parsing exception occurred when trying to parse type exact location." + e.getMessage());
        } catch (Exception e) {
            logger.info("Exception occurred when trying to read type exact location." + e.getMessage());
        }
        // type annotation
        if (valueMap.get(TYPE_REMARKS) != null) {
            Annotation typeAnnotation = Annotation.NewInstance(valueMap.get(TYPE_REMARKS), AnnotationType.EDITORIAL(), Language.DEFAULT());
            specimen.addAnnotation(typeAnnotation);
        }
    }
    // TODO  Type name
    // TODO "Type locations"  , eg. holotype   CAT  ,isotype   CAT  ,isotype   FI
    // TODO Geographic unit as text
    // source
    Reference citation = getIpniCitation(repository);
    name.addSource(OriginalSourceType.Lineage, valueMap.get(ID), "Name", citation, valueMap.get(VERSION));
    /*		EXTENDED
 *      Species author,
 *       Standardised basionym author flag,
 *       Standardised publishing author flag
	      Full name
	      Full name without family
	      Full name without authors

	      Reference
	      Standardised publication flag
	      Publication year
	      publication year note
	      Publication year text
	      Volume
	      Start page
	      End page
	      Primary pagination
	      Secondary pagination
	      Reference remarks
	      Hybrid parents
	      Replaced synonym Author team
	      Other links
	      Same citation as
	      Bibliographic reference
	      Bibliographic type info

	      Original taxon name
	      Original taxon name author team
	      Original replaced synonym
	      Original replaced synonym author team
	      Original basionym
	      Original basionym author team
	      Original parent citation taxon name author team
	      Original taxon distribution
	      Original hybrid parentage
	      Original cited type
	      Original remarks

		*/
    return name;
}

Example 13 with TimePeriod

use of eu.etaxonomy.cdm.model.common.TimePeriod in project cdmlib by cybertaxonomy.

the class GbifJsonOccurrenceParser method parseJsonRecords.

/**
 * Parses the given {@link JSONArray} for occurrences.
 * @param jsonString JSON data as an {@link JSONArray}
 * @return the found occurrences as a collection of {@link GbifResponse}
 */
private static Collection<GbifResponse> parseJsonRecords(JSONArray jsonArray) {
    Collection<GbifResponse> results = new ArrayList<>();
    String[] tripleId = new String[3];
    String string;
    for (Object o : jsonArray) {
        // parse every record
        tripleId = new String[3];
        if (o instanceof JSONObject) {
            String dataSetKey = null;
            GbifDataSetProtocol dataSetProtocol = null;
            DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
            TaxonName name = null;
            JSONObject record = (JSONObject) o;
            if (record.has(DATASET_PROTOCOL)) {
                dataSetProtocol = GbifDataSetProtocol.parseProtocol(record.getString(DATASET_PROTOCOL));
            }
            if (record.has(DATASET_KEY)) {
                dataSetKey = record.getString(DATASET_KEY);
            }
            if (record.has(COUNTRY_CODE)) {
                string = record.getString(COUNTRY_CODE);
                Country country = Country.getCountryByIso3166A2(string);
                if (country != null) {
                    derivedUnitFacade.setCountry(country);
                }
            }
            if (record.has(LOCALITY)) {
                string = record.getString(LOCALITY);
                derivedUnitFacade.setLocality(string);
            }
            if (record.has("species")) {
                Rank rank = null;
                if (record.has(TAXON_RANK)) {
                    string = record.getString(TAXON_RANK);
                    try {
                        rank = Rank.getRankByLatinName(string);
                    } catch (UnknownCdmTypeException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    }
                }
                if (rank != null) {
                    if (record.has(NOMENCLATURALCODE)) {
                        string = record.getString(NOMENCLATURALCODE);
                        if (string.equals(NomenclaturalCode.ICZN.getTitleCache())) {
                            name = TaxonNameFactory.NewZoologicalInstance(rank);
                        } else if (string.equals(NomenclaturalCode.ICNAFP.getTitleCache())) {
                            name = TaxonNameFactory.NewBotanicalInstance(rank);
                        } else if (string.equals(NomenclaturalCode.ICNP.getTitleCache())) {
                            name = TaxonNameFactory.NewBacterialInstance(rank);
                        } else if (string.equals(NomenclaturalCode.ICNCP.getTitleCache())) {
                            name = TaxonNameFactory.NewCultivarInstance(rank);
                        } else if (string.equals(NomenclaturalCode.ICVCN.getTitleCache())) {
                            name = TaxonNameFactory.NewViralInstance(rank);
                        } else if (string.equals("ICN")) {
                            name = TaxonNameFactory.NewBotanicalInstance(rank);
                        }
                    } else {
                        if (record.has(KINGDOM)) {
                            if (record.getString(KINGDOM).equals(PLANTAE)) {
                                name = TaxonNameFactory.NewBotanicalInstance(rank);
                            } else if (record.getString(KINGDOM).equals(ANIMALIA)) {
                                name = TaxonNameFactory.NewZoologicalInstance(rank);
                            } else if (record.getString(KINGDOM).equals(FUNGI)) {
                                name = TaxonNameFactory.NewBotanicalInstance(rank);
                            } else if (record.getString(KINGDOM).equals(BACTERIA)) {
                                name = TaxonNameFactory.NewBacterialInstance(rank);
                            } else {
                                name = TaxonNameFactory.NewNonViralInstance(rank);
                            }
                        } else {
                            name = TaxonNameFactory.NewNonViralInstance(rank);
                        }
                    }
                    if (name == null) {
                        name = TaxonNameFactory.NewNonViralInstance(rank);
                    }
                    if (record.has(GENUS)) {
                        name.setGenusOrUninomial(record.getString(GENUS));
                    }
                    if (record.has(SPECIFIC_EPITHET)) {
                        name.setSpecificEpithet(record.getString(SPECIFIC_EPITHET));
                    }
                    if (record.has(INFRASPECIFIC_EPITHET)) {
                        name.setInfraSpecificEpithet(record.getString(INFRASPECIFIC_EPITHET));
                    }
                    if (record.has(SCIENTIFIC_NAME)) {
                        name.setTitleCache(record.getString(SCIENTIFIC_NAME), true);
                    }
                }
                DeterminationEvent detEvent = DeterminationEvent.NewInstance();
                if (record.has(IDENTIFIED_BY)) {
                    Person determiner = Person.NewTitledInstance(record.getString(IDENTIFIED_BY));
                    detEvent.setDeterminer(determiner);
                }
                detEvent.setTaxonName(name);
                detEvent.setPreferredFlag(true);
                derivedUnitFacade.addDetermination(detEvent);
            }
            // GPS location
            Point location = Point.NewInstance();
            derivedUnitFacade.setExactLocation(location);
            try {
                if (record.has(LATITUDE)) {
                    String lat = record.getString(LATITUDE);
                    location.setLatitudeByParsing(lat);
                }
                if (record.has(LONGITUDE)) {
                    String lon = record.getString(LONGITUDE);
                    location.setLongitudeByParsing(lon);
                }
            } catch (ParseException e) {
                logger.error("Could not parse GPS coordinates", e);
            }
            if (record.has(GEOREFERENCE_PROTOCOL)) {
                String geo = record.getString(GEOREFERENCE_PROTOCOL);
                ReferenceSystem referenceSystem = null;
                // to check which reference system is used?
                if (ReferenceSystem.WGS84().getLabel().contains(geo)) {
                    referenceSystem = ReferenceSystem.WGS84();
                } else if (ReferenceSystem.GOOGLE_EARTH().getLabel().contains(geo)) {
                    referenceSystem = ReferenceSystem.GOOGLE_EARTH();
                } else if (ReferenceSystem.GAZETTEER().getLabel().contains(geo)) {
                    referenceSystem = ReferenceSystem.GAZETTEER();
                }
                location.setReferenceSystem(referenceSystem);
            }
            if (record.has(ELEVATION)) {
                try {
                    // parse integer and strip of unit
                    string = record.getString(ELEVATION);
                    int length = string.length();
                    StringBuilder builder = new StringBuilder();
                    for (int i = 0; i < length; i++) {
                        if (Character.isDigit(string.charAt(i))) {
                            builder.append(string.charAt(i));
                        } else {
                            break;
                        }
                    }
                    derivedUnitFacade.setAbsoluteElevation(Integer.parseInt(builder.toString()));
                } catch (NumberFormatException e) {
                    logger.warn("Could not parse elevation", e);
                }
            }
            // Date (Gathering Period)
            TimePeriod timePeriod = TimePeriod.NewInstance();
            derivedUnitFacade.setGatheringPeriod(timePeriod);
            // TODO what happens with eventDate??
            if (record.has(YEAR)) {
                timePeriod.setStartYear(record.getInt(YEAR));
            }
            if (record.has(MONTH)) {
                timePeriod.setStartMonth(record.getInt(MONTH));
            }
            if (record.has(DAY)) {
                timePeriod.setStartDay(record.getInt(DAY));
            }
            if (record.has(RECORDED_BY)) {
                Person person = Person.NewTitledInstance(record.getString(RECORDED_BY));
                // FIXME check data base if collector already present
                derivedUnitFacade.setCollector(person);
            }
            // collector number (fieldNumber OR recordNumber)
            if (record.has(FIELD_NUMBER)) {
                derivedUnitFacade.setFieldNumber(record.getString(FIELD_NUMBER));
            }
            // collector number (fieldNumber OR recordNumber)
            if (record.has(RECORD_NUMBER)) {
                derivedUnitFacade.setFieldNumber(record.getString(RECORD_NUMBER));
            }
            if (record.has(EVENT_REMARKS)) {
                derivedUnitFacade.setGatheringEventDescription(record.getString(EVENT_REMARKS));
            }
            if (record.has(OCCURRENCE_REMARKS)) {
                derivedUnitFacade.setEcology(record.getString(OCCURRENCE_REMARKS));
            }
            if (record.has(COLLECTION_CODE)) {
                String collectionCode = record.getString(COLLECTION_CODE);
                tripleId[2] = collectionCode;
                // FIXME: check data base for existing collections
                eu.etaxonomy.cdm.model.occurrence.Collection collection = eu.etaxonomy.cdm.model.occurrence.Collection.NewInstance();
                collection.setCode(collectionCode);
                if (record.has(INSTITUTION_CODE)) {
                    Institution institution = Institution.NewNamedInstance(record.getString(INSTITUTION_CODE));
                    institution.setCode(record.getString(INSTITUTION_CODE));
                    collection.setInstitute(institution);
                }
                derivedUnitFacade.setCollection(collection);
            }
            if (record.has(CATALOG_NUMBER)) {
                derivedUnitFacade.setCatalogNumber(record.getString(CATALOG_NUMBER));
                derivedUnitFacade.setAccessionNumber(record.getString(CATALOG_NUMBER));
                tripleId[0] = record.getString(CATALOG_NUMBER);
            }
            if (record.has(INSTITUTION_CODE)) {
                derivedUnitFacade.setAccessionNumber(record.getString(INSTITUTION_CODE));
                tripleId[1] = record.getString(INSTITUTION_CODE);
            }
            if (record.has(OCCURENCE_ID)) {
                IdentifiableSource source = IdentifiableSource.NewDataImportInstance((record.getString(OCCURENCE_ID)));
                derivedUnitFacade.addSource(source);
            }
            if (record.has(MULTIMEDIA)) {
                // http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
                JSONArray multimediaArray = record.getJSONArray(MULTIMEDIA);
                JSONObject mediaRecord;
                SpecimenOrObservationType type = null;
                for (Object object : multimediaArray) {
                    // parse every record
                    Media media = Media.NewInstance();
                    URI uri = null;
                    CdmImageInfo imageInf = null;
                    if (object instanceof JSONObject) {
                        mediaRecord = (JSONObject) object;
                        if (mediaRecord.has("identifier")) {
                            try {
                                uri = new URI(mediaRecord.getString("identifier"));
                                imageInf = MediaInfoFileReader.legacyFactoryMethod(uri).readBaseInfo().getCdmImageInfo();
                            } catch (URISyntaxException | IOException | HttpException e) {
                                e.printStackTrace();
                            }
                        // media.addIdentifier(mediaRecord.getString("identifier"), null);
                        }
                        if (mediaRecord.has("references")) {
                        }
                        if (mediaRecord.has("format")) {
                        }
                        if (mediaRecord.has("type")) {
                            if (mediaRecord.get("type").equals("StillImage")) {
                                type = SpecimenOrObservationType.StillImage;
                            }
                        }
                    }
                    ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInf);
                    MediaRepresentation representation = MediaRepresentation.NewInstance();
                    representation.addRepresentationPart(imageFile);
                    media.addRepresentation(representation);
                    derivedUnitFacade.addDerivedUnitMedia(media);
                }
            // identifier=http://ww2.bgbm.org/herbarium/images/B/-W/08/53/B_-W_08537%20-00%201__3.jpg
            // references=http://ww2.bgbm.org/herbarium/view_biocase.cfm?SpecimenPK=136628
            // format=image/jpeg
            // type=StillImage
            }
            // create dataset URL
            URI uri = null;
            try {
                uri = UriUtils.createUri(new URL(GbifQueryServiceWrapper.BASE_URL), "/v1/dataset/" + dataSetKey + "/endpoint", null, null);
            } catch (MalformedURLException e) {
                logger.error("Endpoint URI could not be created!", e);
            } catch (URISyntaxException e) {
                logger.error("Endpoint URI could not be created!", e);
            }
            results.add(new GbifResponse(derivedUnitFacade, uri, dataSetProtocol, tripleId, name));
        }
    }
    return results;
}

Example 14 with TimePeriod

use of eu.etaxonomy.cdm.model.common.TimePeriod in project cdmlib by cybertaxonomy.

the class IpniService method getAuthorFromLine.

private Person getAuthorFromLine(String line, Map<Integer, String> categoryMap, ICdmRepository repository, IpniServiceAuthorConfigurator config) {
    // Id%Version%Standard form%Default author forename%Default author surname%Taxon groups%Dates%Alternative names
    String[] splits = line.split("%");
    Map<String, String> valueMap = fillValueMap(categoryMap, splits);
    Person person = Person.NewInstance();
    person.setNomenclaturalTitle(valueMap.get(STANDARD_FORM));
    person.setGivenName(valueMap.get(DEFAULT_AUTHOR_FORENAME));
    person.setFamilyName(valueMap.get(DEFAULT_AUTHOR_SURNAME));
    Reference citation = getIpniCitation(repository);
    // id, version
    person.addSource(OriginalSourceType.Lineage, valueMap.get(ID), "Author", citation, valueMap.get(VERSION));
    // dates
    TimePeriod lifespan = TimePeriodParser.parseString(valueMap.get(DATES));
    person.setLifespan(lifespan);
    // alternative_names
    String alternativeNames = valueMap.get(ALTERNATIVE_NAMES);
    if (isNotBlank(alternativeNames)) {
        String[] alternativeNameSplits = alternativeNames.split("%");
        for (String alternativeName : alternativeNameSplits) {
            if (alternativeName.startsWith(">")) {
                alternativeName = alternativeName.substring(1);
            }
            Extension.NewInstance(person, alternativeName, ExtensionType.INFORMAL_CATEGORY());
        }
    }
    return person;
}

Example 15 with TimePeriod

use of eu.etaxonomy.cdm.model.common.TimePeriod in project cdmlib by cybertaxonomy.

the class FieldUnitDefaultCacheStrategy method getFieldData.

private String getFieldData(FieldUnit fieldUnit) {
    if (fieldUnit.isProtectedTitleCache()) {
        return fieldUnit.getTitleCache();
    }
    String ALTITUDE_PREFIX = "alt. ";
    // String ALTITUDE_POSTFIX = " m";
    String result = "";
    if (hasGatheringEvent(fieldUnit)) {
        GatheringEvent gatheringEvent = CdmBase.deproxy(fieldUnit.getGatheringEvent());
        // country
        String strCountry = null;
        NamedArea country = gatheringEvent.getCountry();
        Representation repCountry = country == null ? null : country.getRepresentation(Language.DEFAULT());
        strCountry = repCountry == null ? null : repCountry.getLabel();
        result = CdmUtils.concat(", ", result, strCountry);
        // locality
        result = CdmUtils.concat(", ", result, getLocalityText(gatheringEvent));
        // elevation
        if (isNotBlank(absoluteElevationToString(gatheringEvent))) {
            result = CdmUtils.concat(", ", result, ALTITUDE_PREFIX);
            result += absoluteElevationToString(gatheringEvent);
        }
        // exact locality
        if (gatheringEvent.getExactLocation() != null) {
            String exactLocation = gatheringEvent.getExactLocation().toSexagesimalString(this.includeEmptySeconds, this.includeReferenceSystem);
            result = CdmUtils.concat(", ", result, exactLocation);
        }
    }
    // ecology
    result = CdmUtils.concat(", ", result, getEcology(fieldUnit));
    // gathering period
    // TODO period.toString ??
    TimePeriod gatheringPeriod = hasGatheringEvent(fieldUnit) ? fieldUnit.getGatheringEvent().getTimeperiod() : null;
    result = CdmUtils.concat(", ", result, (gatheringPeriod == null ? null : gatheringPeriod.toString()));
    // collector (team) and field number
    String collectorAndFieldNumber = getCollectorAndFieldNumber(fieldUnit);
    result = CdmUtils.concat(", ", result, collectorAndFieldNumber);
    return result;
}