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

Example 16 with TimePeriod

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

the class MarkupSpecimenImport method handleDates.

private TimePeriod handleDates(MarkupImportState state, XMLEventReader reader, XMLEvent parent) throws XMLStreamException {
    checkNoAttributes(parent);
    TimePeriod result = TimePeriod.NewInstance();
    String parseMessage = "%s can not be parsed: %s";
    boolean hasFullDate = false;
    boolean hasAtomised = false;
    boolean hasUnparsedAtomised = false;
    while (reader.hasNext()) {
        XMLEvent next = readNoWhitespace(reader);
        if (isMyEndingElement(next, parent)) {
            if (!isAlternative(hasFullDate, hasAtomised, hasUnparsedAtomised)) {
                String message = "Some problems exist when defining the date";
                fireWarningEvent(message, parent, 4);
            }
            return result;
        } else if (isStartingElement(next, FULL_DATE)) {
            String fullDate = getCData(state, reader, next, true);
            if (fullDate.endsWith(".")) {
                fullDate = fullDate.substring(0, fullDate.length() - 1);
            }
            result = TimePeriodParser.parseString(fullDate);
            if (result.getFreeText() != null) {
                fireWarningEvent(String.format(parseMessage, FULL_DATE, fullDate), parent, 1);
            }
            hasFullDate = true;
        } else if (isStartingElement(next, DAY)) {
            String day = getCData(state, reader, next, true).trim();
            day = normalizeDate(day);
            if (CdmUtils.isNumeric(day)) {
                result.setStartDay(Integer.valueOf(day));
                hasAtomised = true;
            } else {
                fireWarningEvent(String.format(parseMessage, "Day", day), parent, 2);
                hasUnparsedAtomised = true;
            }
        } else if (isStartingElement(next, MONTH)) {
            String month = getCData(state, reader, next, true).trim();
            month = normalizeDate(month);
            if (CdmUtils.isNumeric(month)) {
                result.setStartMonth(Integer.valueOf(month));
                hasAtomised = true;
            } else {
                fireWarningEvent(String.format(parseMessage, "Month", month), parent, 2);
                hasUnparsedAtomised = true;
            }
        } else if (isStartingElement(next, YEAR)) {
            String year = getCData(state, reader, next, true).trim();
            year = normalizeDate(year);
            if (CdmUtils.isNumeric(year)) {
                result.setStartYear(Integer.valueOf(year));
                hasAtomised = true;
            } else {
                fireWarningEvent(String.format(parseMessage, "Year", year), parent, 2);
                hasUnparsedAtomised = true;
            }
        } else {
            handleUnexpectedElement(next);
        }
    }
    throw new IllegalStateException("Dates has no closing tag.");
}

Example 17 with TimePeriod

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

the class ReferencingObjectFormatter method getCache.

private static String getCache(GatheringEvent gatheringEvent) {
    String ALTITUDE_PREFIX = "alt. ";
    final String METER = "m";
    String result = "";
    // collector
    AgentBase<?> collector = CdmBase.deproxy(gatheringEvent.getCollector());
    String collectorStr = collector == null ? null : collector.getTitleCache();
    result = CdmUtils.concat(", ", result, collectorStr);
    // gathering period
    TimePeriod gatheringPeriod = gatheringEvent.getTimeperiod();
    result = CdmUtils.concat(", ", result, (gatheringPeriod == null ? null : gatheringPeriod.toString()));
    // 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
    LanguageString locality = gatheringEvent.getLocality();
    if (locality != null) {
        result = CdmUtils.concat(", ", result, locality.getText());
    }
    // elevation
    String elevationStr;
    if (isNotBlank(gatheringEvent.getAbsoluteElevationText())) {
        elevationStr = gatheringEvent.getAbsoluteElevationText();
    } else {
        String text = gatheringEvent.getAbsoluteElevationText();
        Integer min = gatheringEvent.getAbsoluteElevation();
        Integer max = gatheringEvent.getAbsoluteElevationMax();
        elevationStr = DistanceStringFormatter.distanceString(min, max, text, METER);
    }
    if (isNotBlank(elevationStr)) {
        result = CdmUtils.concat(", ", result, ALTITUDE_PREFIX);
        result += elevationStr;
    }
    // exact locality
    if (gatheringEvent.getExactLocation() != null) {
        String exactLocation = gatheringEvent.getExactLocation().toSexagesimalString(false, false);
        result = CdmUtils.concat(", ", result, exactLocation);
    }
    return result;
}

Example 18 with TimePeriod

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

the class TaxonXExtractor method extractSpecimenOrObservation.

@SuppressWarnings({ "unused", "rawtypes" })
protected MySpecimenOrObservation extractSpecimenOrObservation(Node specimenObservationNode, DerivedUnit derivedUnitBase, SpecimenOrObservationType defaultAssociation, TaxonName typifiableName) {
    String country = null;
    String locality = null;
    String stateprov = null;
    String collector = null;
    String fieldNumber = null;
    Double latitude = null, longitude = null;
    TimePeriod tp = null;
    String day, month, year = "";
    String descr = "not available";
    String type = "";
    boolean asso = false;
    NodeList eventContent = null;
    // create facade
    DerivedUnitFacade derivedUnitFacade = null;
    UnitsGatheringEvent unitsGatheringEvent;
    UnitsGatheringArea unitsGatheringArea;
    DefinedTermBase areaCountry;
    MySpecimenOrObservation specimenOrObservation = new MySpecimenOrObservation();
    NodeList xmldata = specimenObservationNode.getChildNodes();
    for (int n = 0; n < xmldata.getLength(); n++) {
        eventContent = xmldata.item(n).getChildNodes();
        if (xmldata.item(n).getNodeName().equalsIgnoreCase("tax:xmldata")) {
            asso = true;
            country = null;
            locality = null;
            stateprov = null;
            collector = null;
            fieldNumber = null;
            latitude = null;
            longitude = null;
            day = "";
            month = "";
            year = "";
            type = "";
            for (int j = 0; j < eventContent.getLength(); j++) {
                if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:country")) {
                    country = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:locality")) {
                    locality = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:stateprovince")) {
                    stateprov = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:collector")) {
                    collector = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:yearcollected")) {
                    year = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:monthcollected")) {
                    month = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:daycollected")) {
                    day = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:decimallongitude")) {
                    String tmp = eventContent.item(j).getTextContent().trim();
                    try {
                        longitude = Double.valueOf(tmp);
                    } catch (Exception e) {
                        logger.warn("longitude is not a number");
                    }
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:decimallatitude")) {
                    String tmp = eventContent.item(j).getTextContent().trim();
                    try {
                        latitude = Double.valueOf(tmp);
                    } catch (Exception e) {
                        logger.warn("latitude is not a number");
                    }
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("dwc:TypeStatus")) {
                    type = eventContent.item(j).getTextContent().trim();
                } else if (eventContent.item(j).getNodeName().equalsIgnoreCase("#text") && StringUtils.isBlank(eventContent.item(j).getTextContent())) {
                // do nothing
                } else {
                    logger.info("UNEXTRACTED FIELD FOR SPECIMEN " + eventContent.item(j).getNodeName() + ", " + eventContent.item(j).getTextContent());
                }
            }
            if (!day.isEmpty() || !month.isEmpty() || !year.isEmpty()) {
                try {
                    if (!year.isEmpty()) {
                        tp = TimePeriod.NewInstance(Integer.parseInt(year));
                        if (!month.isEmpty()) {
                            tp.setStartMonth(Integer.parseInt(month));
                            if (!day.isEmpty()) {
                                tp.setStartDay(Integer.parseInt(day));
                            }
                        }
                    }
                } catch (Exception e) {
                    logger.warn("Collection date error " + e);
                }
            }
        }
        if (xmldata.item(n).getNodeName().equalsIgnoreCase("#text")) {
            descr = xmldata.item(n).getTextContent().replaceAll(";", "").trim();
            if (descr.length() > 1 && containsDistinctLetters(descr)) {
                specimenOrObservation.setDescr(descr);
                asso = true;
            }
        }
        if (xmldata.item(n).getNodeName().equalsIgnoreCase("tax:p")) {
            descr = xmldata.item(n).getTextContent().replaceAll(";", "").trim();
            if (descr.length() > 1 && containsDistinctLetters(descr)) {
                specimenOrObservation.setDescr(descr);
                asso = true;
            }
        }
    }
    // logger.info("DESCR: "+descr);
    if (!type.isEmpty()) {
        if (!containsDistinctLetters(type)) {
            type = "no description text";
        }
        derivedUnitFacade = getFacade(type.replaceAll(";", ""), defaultAssociation);
        SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
        if (typifiableName != null) {
            typifiableName.addTypeDesignation(designation, true);
        } else {
            logger.warn("No typifiable name available");
        }
        SpecimenTypeDesignationStatus stds = getSpecimenTypeDesignationStatusByKey(type);
        if (stds != null) {
            stds = (SpecimenTypeDesignationStatus) importer.getTermService().find(stds.getUuid());
        }
        designation.setTypeStatus(stds);
        derivedUnitFacade.innerDerivedUnit().addSpecimenTypeDesignation(designation);
        derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
    // System.out.println("derivedUnitBase: "+derivedUnitBase);
    // designation.setTypeSpecimen(derivedUnitBase);
    // TaxonName name = taxon.getName();
    // name.addTypeDesignation(designation, true);
    } else {
        if (!containsDistinctLetters(descr.replaceAll(";", ""))) {
            descr = "no description text";
        }
        derivedUnitFacade = getFacade(descr.replaceAll(";", ""), defaultAssociation);
        derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
    // System.out.println("derivedUnitBase2: "+derivedUnitBase);
    }
    unitsGatheringEvent = new UnitsGatheringEvent(importer.getTermService(), locality, collector, longitude, latitude, state2.getConfig(), importer.getAgentService());
    if (tp != null) {
        unitsGatheringEvent.setGatheringDate(tp);
    }
    // country
    unitsGatheringArea = new UnitsGatheringArea();
    unitsGatheringArea.setParams(null, country, state2.getConfig(), importer.getTermService(), importer.getVocabularyService());
    // TODO other areas
    if (StringUtils.isNotBlank(stateprov)) {
        Map<String, String> namedAreas = new HashMap<>();
        namedAreas.put(stateprov, null);
        unitsGatheringArea.setAreaNames(namedAreas, state2.getConfig(), importer.getTermService(), importer.getVocabularyService());
    }
    areaCountry = unitsGatheringArea.getCountry();
    // // other areas
    // unitsGatheringArea = new UnitsGatheringArea(namedAreaList,dataHolder.getTermService());
    // ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
    // for (DefinedTermBase namedArea : nas) {
    // unitsGatheringEvent.addArea(namedArea);
    // }
    // copy gathering event to facade
    GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
    derivedUnitFacade.setGatheringEvent(gatheringEvent);
    derivedUnitFacade.setLocality(gatheringEvent.getLocality());
    derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
    derivedUnitFacade.setCollector(gatheringEvent.getCollector());
    derivedUnitFacade.setCountry((NamedArea) areaCountry);
    for (DefinedTermBase<?> area : unitsGatheringArea.getAreas()) {
        derivedUnitFacade.addCollectingArea((NamedArea) area);
    }
    // add fieldNumber
    if (fieldNumber != null) {
        derivedUnitFacade.setFieldNumber(fieldNumber);
    }
    specimenOrObservation.setDerivedUnitBase(derivedUnitBase);
    // }
    return specimenOrObservation;
}

Example 19 with TimePeriod

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

the class ExcelImportBase method getTimePeriod.

/**
 * @param start
 * @param end
 * @return
 */
protected TimePeriod getTimePeriod(String start, String end) {
    String strPeriod = CdmUtils.concat(" - ", start, end);
    TimePeriod result = TimePeriodParser.parseString(strPeriod);
    return result;
}

Example 20 with TimePeriod

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

the class DwcaEmlExport method handleTermporalCoverage.

/**
 * @param writer
 * @param emlRecord
 * @throws XMLStreamException
 */
private void handleTermporalCoverage(XMLStreamWriter writer, DwcaEmlRecord emlRecord) throws XMLStreamException {
    TimePeriod timePeriod = emlRecord.getDate();
    if (timePeriod == null) {
        return;
    }
    writer.writeStartElement("termporalCoverage");
    if (!timePeriod.isPeriod()) {
        // singleDateTime
        writer.writeStartElement("singleDateTime");
        writeCalendarDate(writer, timePeriod.getStart());
        writer.writeEndElement();
    } else {
        // rangeOfDates
        writer.writeStartElement("rangeOfDates");
        writer.writeStartElement("beginDate");
        writeCalendarDate(writer, timePeriod.getStart());
        writer.writeEndElement();
        writer.writeStartElement("endDate");
        writeCalendarDate(writer, timePeriod.getStart());
        writer.writeEndElement();
        writer.writeEndElement();
    }
    // termporalCoverage
    writer.writeEndElement();
}