Examples with SpecimenOrObservationType eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType used on opensource projects

Example 6 with SpecimenOrObservationType

use of eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType in project cdmlib by cybertaxonomy.

the class ExternalGeoController method doGetOccurrenceXMapUriParams.

/**
 * Assembles and returns URI parameter Strings for the EDIT Map Service. The distribution areas for the
 * {@link Taxon} instance identified by the <code>{taxon-uuid}</code> are found and are translated into
 * an valid URI parameter String. Higher level distribution areas are expanded in order to include all
 * nested sub-areas.
 * <p>
 * URI: <b>&#x002F;{datasource-name}&#x002F;geo&#x002F;map&#x002F;distribution&#x002F;{taxon-uuid}</b>
 *
 * @param request
 * @param response
 * @return URI parameter Strings for the EDIT Map Service
 * @throws IOException TODO write controller method documentation
 */
@RequestMapping(value = { "taxonOccurrencesForX" }, method = RequestMethod.GET)
public ModelAndView doGetOccurrenceXMapUriParams(@RequestParam(value = "fieldUnitUuidList", required = false) UuidList fieldUnitUuids, HttpServletRequest request, HttpServletResponse response) throws IOException {
    Map<SpecimenOrObservationType, Color> specimenOrObservationTypeColors = null;
    logger.info("doGetOccurrenceMapUriParams() " + requestPathAndQuery(request));
    ModelAndView mv = new ModelAndView();
    List<Point> fieldUnitPoints = occurrenceService.findPointsForFieldUnitList(fieldUnitUuids);
    OccurrenceServiceRequestParameterDto dto = EditGeoServiceUtilities.getOccurrenceServiceRequestParameterString(fieldUnitPoints, null, specimenOrObservationTypeColors);
    mv.addObject(dto);
    return mv;
}

Example 7 with SpecimenOrObservationType

use of eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType in project cdmlib by cybertaxonomy.

the class KmlController method doGetTypeDesignationsKml.

/**
 * Assembles and returns URI parameter Strings for the EDIT Map Service. The distribution areas for the
 * {@link Taxon} instance identified by the <code>{taxon-uuid}</code> are found and are translated into
 * an valid URI parameter String. Higher level distribution areas are expanded in order to include all
 * nested sub-areas.
 * <p>
 * URI: <b>&#x002F;{datasource-name}&#x002F;geo&#x002F;map&#x002F;distribution&#x002F;{taxon-uuid}</b>
 *
 * @param request
 * @param response
 * @return URI parameter Strings for the EDIT Map Service
 * @throws IOException TODO write controller method documentation
 */
@RequestMapping(value = { "typeDesignations/{uuid-list}" }, method = RequestMethod.GET)
public Kml doGetTypeDesignationsKml(@PathVariable("uuid-list") UuidList uuidList, HttpServletRequest request, HttpServletResponse response) throws IOException {
    logger.info("doGetTypeDesignationsKml() " + requestPathAndQuery(request));
    Map<SpecimenOrObservationType, Color> specimenOrObservationTypeColors = null;
    List<TypeDesignationBase<?>> typeDesignations = nameService.loadTypeDesignations(uuidList, Arrays.asList("typeSpecimen"));
    List<SpecimenOrObservationBase> specimensOrObersvations = typeDesignations.stream().filter(td -> td != null && td instanceof SpecimenTypeDesignation).map(SpecimenTypeDesignation.class::cast).map(SpecimenTypeDesignation::getTypeSpecimen).filter(s -> s != null).collect(Collectors.toList());
    Kml kml = geoservice.occurrencesToKML(specimensOrObersvations, specimenOrObservationTypeColors);
    return kml;
}

Example 8 with SpecimenOrObservationType

use of eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType in project cdmlib by cybertaxonomy.

the class KmlController method doGetTaxonOccurrenceKml.

/**
 * Assembles and returns URI parameter Strings for the EDIT Map Service. The distribution areas for the
 * {@link Taxon} instance identified by the <code>{taxon-uuid}</code> are found and are translated into
 * an valid URI parameter String. Higher level distribution areas are expanded in order to include all
 * nested sub-areas.
 * <p>
 * URI: <b>&#x002F;{datasource-name}&#x002F;geo&#x002F;map&#x002F;distribution&#x002F;{taxon-uuid}</b>
 *
 * @param request
 * @param response
 * @return URI parameter Strings for the EDIT Map Service
 * @throws IOException TODO write controller method documentation
 */
@RequestMapping(value = { "taxonOccurrencesFor/{uuid}" }, method = RequestMethod.GET)
public Kml doGetTaxonOccurrenceKml(@PathVariable("uuid") UUID uuid, @RequestParam(value = "relationships", required = false) UuidList relationshipUuids, @RequestParam(value = "relationshipsInvers", required = false) UuidList relationshipInversUuids, @RequestParam(value = "maxDepth", required = false) Integer maxDepth, HttpServletRequest request, HttpServletResponse response) throws IOException {
    logger.info("doGetTaxonOccurrenceKml() " + requestPathAndQuery(request));
    Map<SpecimenOrObservationType, Color> specimenOrObservationTypeColors = null;
    List<SpecimenOrObservationBase> specimensOrObersvations = occurencesForTaxon(uuid, relationshipUuids, relationshipInversUuids, maxDepth, response);
    Kml kml = geoservice.occurrencesToKML(specimensOrObersvations, specimenOrObservationTypeColors);
    return kml;
}

Example 9 with SpecimenOrObservationType

use of eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType in project cdmlib by cybertaxonomy.

the class OccurrenceServiceImpl method assembleFieldUnitDTO.

@Override
public FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit) {
    if (!getSession().contains(fieldUnit)) {
        fieldUnit = (FieldUnit) load(fieldUnit.getUuid());
    }
    // FIXME the filter for SpecimenOrObservationType.PreservedSpecimen has been preserved from the former implementation (see commit 07e3f63c7d  and older)
    // it is questionable if this filter makes sense for all use cases or if it is only a sensible default for the
    // compressed specimen table in the cdm-dataportal (see #6816, #6870)
    EnumSet<SpecimenOrObservationType> typeIncludeFilter = EnumSet.of(SpecimenOrObservationType.PreservedSpecimen);
    FieldUnitDTO fieldUnitDTO = FieldUnitDTO.fromEntity(fieldUnit, null, typeIncludeFilter);
    return fieldUnitDTO;
}

Example 10 with SpecimenOrObservationType

use of eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType in project cdmlib by cybertaxonomy.

the class OccurrenceServiceImpl method moveDerivate.

@Override
@Transactional(readOnly = false)
public UpdateResult moveDerivate(UUID specimenFromUuid, UUID specimenToUuid, UUID derivateUuid) {
    // reload specimens to avoid session conflicts
    SpecimenOrObservationBase<?> from = null;
    if (specimenFromUuid != null) {
        from = load(specimenFromUuid);
    }
    SpecimenOrObservationBase<?> to = load(specimenToUuid);
    DerivedUnit derivate = (DerivedUnit) load(derivateUuid);
    if ((specimenFromUuid != null && from == null) || to == null || derivate == null) {
        throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" + "Operation was move " + derivate + " from " + from + " to " + to);
    }
    UpdateResult result = new UpdateResult();
    SpecimenOrObservationType derivateType = derivate.getRecordBasis();
    SpecimenOrObservationType toType = to.getRecordBasis();
    // check if type is a sub derivate type
    if (// moving to FieldUnit always works
    toType == SpecimenOrObservationType.FieldUnit || // moving media always works
    derivateType == SpecimenOrObservationType.Media || (derivateType.isKindOf(toType) && toType != derivateType)) {
        // moving only to parent derivate type
        if (from != null) {
            // remove derivation event from parent specimen of dragged object
            DerivationEvent eventToRemove = null;
            for (DerivationEvent event : from.getDerivationEvents()) {
                if (event.getDerivatives().contains(derivate)) {
                    eventToRemove = event;
                    break;
                }
            }
            from.removeDerivationEvent(eventToRemove);
            if (eventToRemove != null) {
                // add new derivation event to target and copy the event parameters of the old one
                DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
                derivedFromNewOriginalEvent.setActor(eventToRemove.getActor());
                derivedFromNewOriginalEvent.setDescription(eventToRemove.getDescription());
                derivedFromNewOriginalEvent.setInstitution(eventToRemove.getInstitution());
                derivedFromNewOriginalEvent.setTimeperiod(eventToRemove.getTimeperiod());
                derivedFromNewOriginalEvent.setType(eventToRemove.getType());
                to.addDerivationEvent(derivedFromNewOriginalEvent);
                derivate.setDerivedFrom(derivedFromNewOriginalEvent);
            }
        } else {
            // derivative had no parent before so we use empty derivation event
            DerivationEvent derivedFromNewOriginalEvent = DerivationEvent.NewSimpleInstance(to, derivate, null);
            to.addDerivationEvent(derivedFromNewOriginalEvent);
            derivate.setDerivedFrom(derivedFromNewOriginalEvent);
        }
        if (from != null) {
            saveOrUpdate(from);
        }
        saveOrUpdate(to);
        result.setStatus(Status.OK);
        result.addUpdatedObject(from);
        result.addUpdatedObject(to);
    } else {
        result.setStatus(Status.ERROR);
    }
    return result;
}