Revision f261b330
Added by Andreas Kohlbecker over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTExcelImport.java | ||
|---|---|---|
| 17 | 17 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 18 | 18 |
import eu.etaxonomy.cdm.model.taxon.*; |
| 19 | 19 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 20 |
import org.apache.commons.lang.ArrayUtils; |
|
| 20 | 21 |
import org.apache.commons.lang.StringEscapeUtils; |
| 21 | 22 |
import org.apache.commons.lang.StringUtils; |
| 22 | 23 |
import org.apache.log4j.Level; |
| ... | ... | |
| 66 | 67 |
private static final Pattern nomRefTokenizeP = Pattern.compile("^(.*):\\s([^\\.:]+)\\.(.*)$");
|
| 67 | 68 |
private static final Pattern nomRefPubYearExtractP = Pattern.compile("(.*?)(1[7,8,9][0-9]{2}).*$|^.*?[0-9]{1,2}([\\./])[0-1]?[0-9]\\3([0-9]{2})\\.$"); // 1700 - 1999
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| 68 | 69 |
|
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private MarkerType markerTypeFossil = null; |
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|
|
| 69 | 72 |
private Taxon makeTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state, |
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TaxonNode higherTaxonNode, boolean isSynonym) {
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TaxonNode higherTaxonNode, boolean isSynonym, boolean isFossil) {
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| 71 | 74 |
|
| 72 | 75 |
String line = state.getCurrentLine() + ": "; |
| 73 | 76 |
|
| ... | ... | |
| 75 | 78 |
String nameStr = getValue(record, NAMESTRING, true); |
| 76 | 79 |
String authorStr = getValue(record, AUTHORSTRING, true); |
| 77 | 80 |
String nomRefStr = getValue(record, LITSTRING, true); |
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String authorsSpelling = getValue(record, AUTHORSSPELLING, true); |
|
| 78 | 82 |
|
| 79 | 83 |
String nomRefTitle = null; |
| 80 | 84 |
String nomRefDetail = null; |
| ... | ... | |
| 94 | 98 |
Matcher m2 = nomRefPubYearExtractP.matcher(nomRefPupDate); |
| 95 | 99 |
if(m2.matches()){
|
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nomRefPupYear = m2.group(2); |
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if(nomRefPupYear == null){
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nomRefPupYear = m2.group(4); |
|
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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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} |
|
| 97 | 107 |
if(nomRefPupYear.length() == 2 ){
|
| 98 | 108 |
// it is an abbreviated year from the 19** years |
| 99 | 109 |
nomRefPupYear = "19" + nomRefPupYear; |
| ... | ... | |
| 108 | 118 |
} |
| 109 | 119 |
} |
| 110 | 120 |
|
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|
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BotanicalName taxonName; |
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// cache field for the taxonName.titleCache |
|
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String taxonNameTitleCache = null; |
|
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Map<String, AnnotationType> nameAnnotations = new HashMap<>(); |
| 114 | 125 |
|
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if(titleCacheStr.endsWith(ANNOTATION_MARKER_STRING) && authorStr.endsWith(ANNOTATION_MARKER_STRING)){
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// TitleCache preprocessing |
|
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if(titleCacheStr.endsWith(ANNOTATION_MARKER_STRING) || authorStr.endsWith(ANNOTATION_MARKER_STRING)){
|
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nameAnnotations.put("Author abbreviation not checked.", AnnotationType.EDITORIAL());
|
| 117 | 129 |
titleCacheStr = titleCacheStr.replace(ANNOTATION_MARKER_STRING, "").trim(); |
| 118 | 130 |
authorStr = authorStr.replace(ANNOTATION_MARKER_STRING, "").trim(); |
| 119 | 131 |
} |
| 120 | 132 |
|
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// parse the full taxon name |
|
| 121 | 134 |
if(!StringUtils.isEmpty(nomRefTitle)){
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| 122 | 135 |
String referenceSeparator = nomRefTitle.startsWith("in ") ? " " : ", ";
|
| 123 | 136 |
String taxonFullNameStr = titleCacheStr + referenceSeparator + nomRefTitle; |
| ... | ... | |
| 127 | 140 |
taxonName = (BotanicalName) nameParser.parseFullName(titleCacheStr, NomenclaturalCode.ICNAFP, null); |
| 128 | 141 |
} |
| 129 | 142 |
|
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taxonNameTitleCache = taxonName.getTitleCache().trim(); |
|
| 130 | 144 |
if (taxonName.isProtectedTitleCache()) {
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logger.warn(line + "Name could not be parsed: " + titleCacheStr); |
| 132 | 146 |
} else {
|
| 133 | 147 |
|
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boolean doRestoreTitleCacheStr = false; |
| 135 | 149 |
// Check titleCache |
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String generatedTitleCache = taxonName.getTitleCache(); |
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if (!generatedTitleCache.trim().equals(titleCacheStr)) {
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logger.warn(line + "The generated titleCache differs from the imported string : " + generatedTitleCache + " <> " + titleCacheStr + " will restore original titleCacheStr"); |
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if (!taxonNameTitleCache.equals(titleCacheStr)) {
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logger.warn(line + "The generated titleCache differs from the imported string : " + taxonNameTitleCache + " <> " + titleCacheStr + " will restore original titleCacheStr"); |
|
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doRestoreTitleCacheStr = true; |
| 140 | 153 |
} |
| 141 | 154 |
// Check Name |
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if (!taxonName.getNameCache().trim().equals(nameStr)) {
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logger.warn(line + "parsed nameCache differs from " + NAMESTRING + " : " + taxonName.getNameCache() + " <> " + nameStr); |
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String nameCache = taxonName.getNameCache(); |
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if (!nameCache.trim().equals(nameStr)) {
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logger.warn(line + "parsed nameCache differs from " + NAMESTRING + " : " + nameCache + " <> " + nameStr); |
|
| 144 | 158 |
} |
| 145 | 159 |
|
| 146 | 160 |
// Author |
| ... | ... | |
| 156 | 170 |
|
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// deduplicate |
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replaceAuthorNamesAndNomRef(state, taxonName); |
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} |
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|
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// Annotations |
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if(!nameAnnotations.isEmpty()){
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for(String text : nameAnnotations.keySet()){
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taxonName.addAnnotation(Annotation.NewInstance(text, nameAnnotations.get(text), Language.DEFAULT())); |
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} |
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getNameService().save(taxonName); |
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} |
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|
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// Namerelations |
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if(!StringUtils.isEmpty(authorsSpelling)){
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authorsSpelling = authorsSpelling.replaceFirst("Author's spelling:", "").replaceAll("\"", "").trim();
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|
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// Annotations |
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if(!nameAnnotations.isEmpty()){
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for(String text : nameAnnotations.keySet()){
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taxonName.addAnnotation(Annotation.NewInstance(text, nameAnnotations.get(text), Language.DEFAULT())); |
|
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String[] authorSpellingTokens = StringUtils.split(authorsSpelling, " "); |
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String[] nameStrTokens = StringUtils.split(nameStr, " "); |
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ArrayUtils.reverse(authorSpellingTokens); |
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ArrayUtils.reverse(nameStrTokens); |
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for (int i = 0; i < nameStrTokens.length; i++){
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if(i < authorSpellingTokens.length){
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nameStrTokens[i] = authorSpellingTokens[i]; |
|
| 164 | 196 |
} |
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getNameService().save(taxonName); |
|
| 166 | 197 |
} |
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ArrayUtils.reverse(nameStrTokens); |
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|
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String misspelledNameStr = StringUtils.join (nameStrTokens, ' '); |
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// build the fullnameString of the misspelled name |
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misspelledNameStr = taxonNameTitleCache.replace(nameStr, misspelledNameStr); |
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|
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TaxonNameBase misspelledName = (BotanicalName) nameParser.parseReferencedName(misspelledNameStr, NomenclaturalCode.ICNAFP, null); |
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misspelledName.addRelationshipToName(taxonName, NameRelationshipType.MISSPELLING(), null); |
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getNameService().save(misspelledName); |
|
| 167 | 207 |
} |
| 168 | 208 |
|
| 169 | 209 |
Reference sec = state.getConfig().getSecReference(); |
| 170 | 210 |
Taxon taxon = Taxon.NewInstance(taxonName, sec); |
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|
|
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// Markers |
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if(isFossil){
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taxon.addMarker(Marker.NewInstance(markerTypeFossil(), true)); |
|
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} |
|
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|
|
| 171 | 217 |
getTaxonService().save(taxon); |
| 172 | 218 |
if(higherTaxonNode != null){
|
| 173 | 219 |
higherTaxonNode.addChildTaxon(taxon, null, null); |
| ... | ... | |
| 260 | 306 |
} |
| 261 | 307 |
|
| 262 | 308 |
String reg_id = record.get(REGISTRATIONNO_PK); |
| 309 |
|
|
| 263 | 310 |
//higherTaxon |
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TaxonNode higherTaxon = getHigherTaxon(record, (IAPTImportState)state); |
|
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String higherTaxaString = record.get(HIGHERTAXON); |
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boolean isFossil = false; |
|
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if(higherTaxaString.startsWith("FOSSIL ")){
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higherTaxaString = higherTaxaString.replace("FOSSIL ", "");
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isFossil = true; |
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} |
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TaxonNode higherTaxon = getHigherTaxon(higherTaxaString, (IAPTImportState)state); |
|
| 265 | 318 |
|
| 266 | 319 |
//Taxon |
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Taxon taxon = makeTaxon(record, state, higherTaxon, isSynonymOnly); |
|
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Taxon taxon = makeTaxon(record, state, higherTaxon, isSynonymOnly, isFossil);
|
|
| 268 | 321 |
if (taxon == null && ! isSynonymOnly){
|
| 269 | 322 |
logger.warn(line + "taxon could not be created and is null"); |
| 270 | 323 |
return; |
| ... | ... | |
| 281 | 334 |
return; |
| 282 | 335 |
} |
| 283 | 336 |
|
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private TaxonNode getHigherTaxon(HashMap<String, String> record, IAPTImportState state) {
|
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String higherTaxaString = record.get(HIGHERTAXON); |
|
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private TaxonNode getHigherTaxon(String higherTaxaString, IAPTImportState state) {
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|
|
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// higherTaxaString is like |
| 287 | 340 |
// - DICOTYLEDONES: LEGUMINOSAE: MIMOSOIDEAE |
| 288 | 341 |
// - FOSSIL DICOTYLEDONES: PROTEACEAE |
| ... | ... | |
| 376 | 429 |
return ref; |
| 377 | 430 |
} |
| 378 | 431 |
|
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private MarkerType markerTypeFossil(){
|
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if(this.markerTypeFossil == null){
|
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markerTypeFossil = MarkerType.NewInstance("isFossilTaxon", "isFossil", null);
|
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getTermService().save(this.markerTypeFossil); |
|
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} |
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return markerTypeFossil; |
|
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} |
|
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|
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| 379 | 440 |
|
| 380 | 441 |
|
| 381 | 442 |
} |
Also available in: Unified diff
ref #6026 multiple improvements