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

Example 1 with Annotation

use of eu.etaxonomy.cdm.model.common.Annotation 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 2 with Annotation

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

the class GeoServiceAreaAnnotatedMapping method clear.

@Override
public void clear(NamedArea area) {
    Set<Annotation> removeCandidates = new HashSet<>();
    for (Annotation annotation : area.getAnnotations()) {
        if (AnnotationType.TECHNICAL().equals(annotation.getAnnotationType())) {
            if (GeoServiceArea.isAreaMapping(annotation.getText())) {
                removeCandidates.add(annotation);
            }
        }
    }
    for (Annotation remove : removeCandidates) {
        area.removeAnnotation(remove);
    }
    termService.saveOrUpdate(area);
}

Example 3 with Annotation

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

the class DescriptionPortalController method getAnnotations.

// mapped as absolute path, see CdmAntPathMatcher
@RequestMapping(value = "//portal/descriptionElement/{descriptionelement_uuid}/annotation", method = RequestMethod.GET)
public Pager<Annotation> getAnnotations(@PathVariable("descriptionelement_uuid") UUID uuid, HttpServletRequest request, HttpServletResponse response) {
    logger.info("getAnnotations() - " + requestPathAndQuery(request));
    DescriptionElementBase annotatableEntity = descriptionElementService.find(uuid);
    Pager<Annotation> annotations = descriptionElementService.getAnnotations(annotatableEntity, null, null, 0, null, getInitializationStrategy());
    return annotations;
}

Example 4 with Annotation

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

the class SDDDocumentBuilder method buildRepresentation.

/**
 * Builds a Representation element using a Reference
 */
public void buildRepresentation(ElementImpl element, IDatabase reference) throws ParseException {
    // create <Representation> element
    ElementImpl representation = new ElementImpl(document, REPRESENTATION);
    element.appendChild(representation);
    buildLabel(representation, reference.getTitleCache());
    Set<Annotation> annotations = ((Reference) reference).getAnnotations();
    Iterator<Annotation> iterator = annotations.iterator();
    String detailText = null;
    if (iterator.hasNext()) {
        Annotation annotation = iterator.next();
        detailText = annotation.getText();
    }
    if (detailText != null && !detailText.equals("")) {
        ElementImpl detail = new ElementImpl(document, DETAIL);
        detail.appendChild(document.createTextNode(detailText));
        representation.appendChild(detail);
    }
    Set<Media> rm = ((Reference) reference).getMedia();
    if (rm != null && rm.size() > 0) {
        ElementImpl mediaObject;
        for (int i = 0; i < rm.size(); i++) {
            mediaObject = new ElementImpl(document, MEDIA_OBJECT);
            mediasCount = buildReference((Media) rm.toArray()[i], medias, REF, mediaObject, "m", mediasCount);
            representation.appendChild(mediaObject);
        }
    }
}

Example 5 with Annotation

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

the class SDDDocumentBuilder method buildScope.

/**
 * Builds Scope associated with a CodedDescription
 */
public void buildScope(ElementImpl element, TaxonDescription taxonDescription) throws ParseException {
    // <Scope>
    // <TaxonName ref="t1"/>
    // <Citation ref="p1" location="p. 30"/>
    // </Scope>
    ElementImpl scope = new ElementImpl(document, SCOPE);
    Taxon taxon = taxonDescription.getTaxon();
    if (taxon != null) {
        TaxonName taxonName = taxon.getName();
        if (taxonName != null) {
            String ref = taxonNames.get(taxonName);
            if (!ref.equals("")) {
                ElementImpl taxonNameEl = new ElementImpl(document, TAXON_NAME);
                taxonNameEl.setAttribute(REF, ref);
                scope.appendChild(taxonNameEl);
            }
        }
    }
    Set<Reference> descriptionSources = new HashSet<Reference>();
    for (IdentifiableSource source : taxonDescription.getSources()) {
        descriptionSources.add(source.getCitation());
    }
    for (Iterator<Reference> rb = descriptionSources.iterator(); rb.hasNext(); ) {
        Reference descriptionSource = rb.next();
        if (descriptionSource.getType().equals(ReferenceType.Article)) {
            ElementImpl citation = new ElementImpl(document, CITATION);
            articlesCount = buildReference(descriptionSource, articles, REF, citation, "p", articlesCount);
            Set<Annotation> annotations = descriptionSource.getAnnotations();
            for (Iterator<Annotation> a = annotations.iterator(); a.hasNext(); ) {
                Annotation annotation = a.next();
                AnnotationType annotationType = annotation.getAnnotationType();
                if (annotationType != null) {
                    String type = annotationType.getLabel();
                    if (type.equals("location")) {
                        citation.setAttribute("location", annotation.getText());
                    }
                }
            }
            scope.appendChild(citation);
        }
    }
    element.appendChild(scope);
}