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import org.apache.log4j.Logger;
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import org.joda.time.DateTimeFieldType;
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import org.joda.time.Partial;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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import org.springframework.stereotype.Component;
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import java.util.*;
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| ... | ... | |
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Pattern.compile("^(?<monthName>\\p{L}+\\.?),?\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // April 99 or April, 1999 or Apr. 12
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Pattern.compile("^(?<day>[0-9]{1,2})([\\.\\-/])(?<month>[0-1]?[0-9])\\2(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like 12.04.1969 or 12/04/1969 or 12-04-1969
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Pattern.compile("^(?<month>[0-1]?[0-9])([\\.\\-/])(?<year>(?:1[7,8,9])?[0-9]{2})$"), // partial date like 04.1969 or 04/1969 or 04-1969
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Pattern.compile("^(?<year>(?:1[7,8,9])?[0-9]{2})([\\.\\-/])(?<month>[0-1]?[0-9])$"),// partial date like 1999-04
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Pattern.compile("^(?<day>[0-9]{1,2})(?:[\\./]|th|rd)?\\s(?<monthName>\\p{L}+\\.?),?\\s(?<year>(?:1[7,8,9])?[0-9]{2})$"), // full date like 12. April 1969 or april 1999 or 22 Dec.1999
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};
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private static final Pattern typeSplitPattern = Pattern.compile("^(?:\"*[Tt]ype: (?<type>.*?))(?:[Hh]olotype:(?<holotype>.*?))?(?:[Ii]sotype[^:]*:(?<isotype>.*))?$");
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| ... | ... | |
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monthFromNameMap.put("Februari", 2);
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}
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DateTimeFormatter formatterYear = DateTimeFormat.forPattern("yyyy");
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enum TypesName {
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type, holotype, isotype;
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| ... | ... | |
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String line = state.getCurrentLine() + ": ";
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String regNumber = getValue(record, REGISTRATIONNO_PK, false);
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String regStr = getValue(record, REGISTRATION, true);
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String titleCacheStr = getValue(record, FULLNAME, true);
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String nameStr = getValue(record, NAMESTRING, true);
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String authorStr = getValue(record, AUTHORSTRING, true);
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| ... | ... | |
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String synSubstStr = getValue(record, SYNSUBSTSTR, true);
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String typeStr = getValue(record, TYPE, true);
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String nomRefTitle = null;
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String nomRefDetail = null;
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String nomRefDetail;
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String nomRefPupDate = null;
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String nomRefPupDay = null;
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String nomRefPupMonth = null;
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String nomRefPupMonthName = null;
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String nomRefPupYear = null;
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Partial pupDate = null;
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// preprocess nomRef: separate citation, reference detail, publishing date
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if(!StringUtils.isEmpty(nomRefStr)){
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| ... | ... | |
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nomRefDetail = m.group(2);
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nomRefPupDate = m.group(3).trim();
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// nomRefDetail.replaceAll("[\\:\\.\\s]", ""); // TODO integrate into nomRefTokenizeP
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for(Pattern p : nomRefPubDatePs){
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Matcher m2 = p.matcher(nomRefPupDate);
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if(m2.matches()){
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try {
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nomRefPupYear = m2.group("year");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonth = m2.group("month");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonthName = m2.group("monthName");
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nomRefPupMonth = monthFromName(nomRefPupMonthName, regNumber);
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupDay = m2.group("day");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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if(nomRefPupYear == null){
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logger.error("nomRefPupYear in " + nomRefStr + " is NULL" );
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}
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if(nomRefPupYear.length() == 2 ){
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// it is an abbreviated year from the 19** years
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nomRefPupYear = "19" + nomRefPupYear;
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}
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nomRefTitle = nomRefTitle + ": " + nomRefDetail + ". " + nomRefPupYear + ".";
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break;
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}
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}
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if(nomRefPupYear == null){
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logger.warn("Pub date not found in [" + regNumber + "]: " + nomRefPupDate + " from " + nomRefStr );
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}
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List<DateTimeFieldType> types = new ArrayList<>();
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List<Integer> values = new ArrayList<>();
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if(nomRefPupYear != null){
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types.add(DateTimeFieldType.year());
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values.add(Integer.parseInt(nomRefPupYear));
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}
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if(nomRefPupMonth != null){
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types.add(DateTimeFieldType.monthOfYear());
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values.add(Integer.parseInt(nomRefPupMonth));
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pupDate = parsePubDate(regNumber, nomRefStr, nomRefPupDate);
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if (pupDate != null) {
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nomRefTitle = nomRefTitle + ": " + nomRefDetail + ". " + pupDate.toString(formatterYear) + ".";
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}
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if(nomRefPupDay != null){
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types.add(DateTimeFieldType.dayOfMonth());
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values.add(Integer.parseInt(nomRefPupDay));
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}
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Partial pupDate = new Partial(types.toArray(new DateTimeFieldType[types.size()]), ArrayUtils.toPrimitive(values.toArray(new Integer[values.size()])));
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} else {
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nomRefTitle = nomRefStr;
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}
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| ... | ... | |
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BotanicalName taxonName = makeBotanicalName(state, titleCacheStr, nameStr, authorStr, nomRefTitle);
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// always add the original strings of parsed data as annotation
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taxonName.addAnnotation(Annotation.NewInstance("imported and parsed data strings:" +
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"\n - '" + LITSTRING + "': "+ nomRefStr +
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"\n - '" + TYPE + "': " + typeStr +
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"\n - '" + REGISTRATION + "': " + regStr
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, AnnotationType.TECHNICAL(), Language.DEFAULT()));
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if(pupDate != null) {
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taxonName.getNomenclaturalReference().setDatePublished(TimePeriod.NewInstance(pupDate));
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}
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| 232 |
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if(!StringUtils.isEmpty(notesTxt)){
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notesTxt = notesTxt.replace("Notes: ", "").trim();
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taxonName.addAnnotation(Annotation.NewInstance(notesTxt, AnnotationType.EDITORIAL(), Language.DEFAULT()));
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| ... | ... | |
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280 |
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}
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| 319 |
282 |
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283 |
private Partial parsePubDate(String regNumber, String nomRefStr, String nomRefPupDate) {
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285 |
Partial pupDate = null;
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boolean parseError = false;
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String nomRefPupDay = null;
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String nomRefPupMonth = null;
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String nomRefPupMonthName = null;
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String nomRefPupYear = null;
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292 |
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293 |
// nomRefDetail.replaceAll("[\\:\\.\\s]", ""); // TODO integrate into nomRefTokenizeP
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for(Pattern p : nomRefPubDatePs){
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Matcher m2 = p.matcher(nomRefPupDate);
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if(m2.matches()){
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try {
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nomRefPupYear = m2.group("year");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonth = m2.group("month");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupMonthName = m2.group("monthName");
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nomRefPupMonth = monthFromName(nomRefPupMonthName, regNumber);
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if(nomRefPupMonth == null){
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parseError = true;
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}
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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try {
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nomRefPupDay = m2.group("day");
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} catch (IllegalArgumentException e){
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// named capture group not found
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}
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321 |
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if(nomRefPupYear == null){
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logger.error("nomRefPupYear in " + nomRefStr + " is NULL" );
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parseError = true;
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}
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if(nomRefPupYear.length() == 2 ){
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327 |
// it is an abbreviated year from the 19** years
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328 |
nomRefPupYear = "19" + nomRefPupYear;
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}
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330 |
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331 |
break;
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}
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}
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if(nomRefPupYear == null){
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logger.warn("Pub date not found in [" + regNumber + "]: " + nomRefPupDate + " from " + nomRefStr );
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parseError = true;
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}
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List<DateTimeFieldType> types = new ArrayList<>();
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339 |
List<Integer> values = new ArrayList<>();
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340 |
if(!parseError) {
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341 |
types.add(DateTimeFieldType.year());
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values.add(Integer.parseInt(nomRefPupYear));
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if (nomRefPupMonth != null) {
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types.add(DateTimeFieldType.monthOfYear());
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values.add(Integer.parseInt(nomRefPupMonth));
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}
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if (nomRefPupDay != null) {
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348 |
types.add(DateTimeFieldType.dayOfMonth());
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349 |
values.add(Integer.parseInt(nomRefPupDay));
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350 |
}
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351 |
pupDate = new Partial(types.toArray(new DateTimeFieldType[types.size()]), ArrayUtils.toPrimitive(values.toArray(new Integer[values.size()])));
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352 |
}
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353 |
return pupDate;
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354 |
}
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355 |
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| 320 |
356 |
private String monthFromName(String monthName, String regNumber) {
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| 321 |
357 |
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| 322 |
358 |
Integer month = monthFromNameMap.get(monthName.toLowerCase());
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ref #6026 publication date parsing completed