Revision 2fedea5a
Added by Andreas Müller 8 months ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/SileneaeImportActivator.java | ||
|---|---|---|
| 38 | 38 |
private static final URI source = sileneae(); |
| 39 | 39 |
|
| 40 | 40 |
private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp(); |
| 41 |
//private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp(); |
|
| 41 |
// private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp1(); |
|
| 42 |
// private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp(); |
|
| 42 | 43 |
|
| 43 | 44 |
private static final UUID acceptedUuid = UUID.fromString("8ac4a182-1281-4473-b6a1-c4f681f7dea3");
|
| 44 | 45 |
private static final UUID unresolvedUuid = UUID.fromString("99ab0e67-4214-4bc7-884d-6af8c2e60c38");
|
| app-import/src/main/java/eu/etaxonomy/cdm/app/common/CdmDestinations.java | ||
|---|---|---|
| 611 | 611 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 612 | 612 |
} |
| 613 | 613 |
|
| 614 |
public static ICdmDataSource cdm_local_caryo_spp2(){
|
|
| 614 |
public static ICdmDataSource cdm_local_caryo_spp1(){
|
|
| 615 | 615 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
| 616 | 616 |
String cdmServer = "127.0.0.1"; |
| 617 |
String cdmDB = "cdm_caryo_spp2";
|
|
| 617 |
String cdmDB = "cdm_local_caryophyllales_spp1";
|
|
| 618 | 618 |
String cdmUserName = "edit"; |
| 619 | 619 |
return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null); |
| 620 | 620 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportBase.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.caryo; |
| 10 | 10 |
|
| 11 |
import java.util.HashMap; |
|
| 12 |
import java.util.HashSet; |
|
| 13 |
import java.util.Map; |
|
| 14 |
import java.util.Set; |
|
| 15 |
|
|
| 16 |
import eu.etaxonomy.cdm.common.DoubleResult; |
|
| 11 | 17 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 12 | 18 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 13 | 19 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| ... | ... | |
| 24 | 30 |
|
| 25 | 31 |
private Reference secRef = null; |
| 26 | 32 |
|
| 27 |
protected Taxon getTaxon(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state, Integer taxonLinkId) {
|
|
| 28 |
// TODO Auto-generated method stub |
|
| 29 |
return null; |
|
| 33 |
protected static Map<Integer,TaxonName> nameMap = new HashMap<>(); |
|
| 34 |
|
|
| 35 |
private static Map<Integer,Taxon> taxonMap = new HashMap<>(); |
|
| 36 |
|
|
| 37 |
protected static Map<Integer,TaxonName> origNameMap = new HashMap<>(); |
|
| 38 |
protected static Map<Integer,TaxonName> orphanedNameMap = new HashMap<>(); |
|
| 39 |
protected static Set<TaxonName> origSpellingNames = new HashSet<>(); |
|
| 40 |
|
|
| 41 |
protected static Map<Integer, Integer> accIdMap = new HashMap<>(); |
|
| 42 |
|
|
| 43 |
protected static Map<Integer,DoubleResult<String,String>> origPublicationMap = new HashMap<>(); |
|
| 44 |
|
|
| 45 |
|
|
| 46 |
|
|
| 47 |
protected Taxon getTaxon(Integer taxonLinkId) {
|
|
| 48 |
return taxonMap.get(taxonLinkId); |
|
| 30 | 49 |
} |
| 31 | 50 |
|
| 32 |
protected TaxonName getName(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state, Integer nameLinkID) {
|
|
| 33 |
// TODO Auto-generated method stub |
|
| 34 |
return null; |
|
| 51 |
protected TaxonName getName(Integer nameLinkId) {
|
|
| 52 |
return nameMap.get(nameLinkId); |
|
| 53 |
} |
|
| 54 |
|
|
| 55 |
protected void putToNameMap(Integer id, TaxonName name) {
|
|
| 56 |
nameMap.put(id, name); |
|
| 57 |
origNameMap.put(id, name); |
|
| 58 |
orphanedNameMap.put(id, name); |
|
| 59 |
} |
|
| 60 |
protected void putToTaxonMap(Integer id, Taxon taxon) {
|
|
| 61 |
taxonMap.put(id, taxon); |
|
| 35 | 62 |
} |
| 36 | 63 |
|
| 37 | 64 |
protected Reference getSecRef(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeImportConfigurator.java | ||
|---|---|---|
| 31 | 31 |
private UUID acceptedNodeUuid; |
| 32 | 32 |
private UUID unresolvedNodeUuid; |
| 33 | 33 |
|
| 34 |
private static IInputTransformer defaultTransformer = new CaryoAizoaceaeTransformer();
|
|
| 34 |
private static IInputTransformer defaultTransformer = new CaryoSileneaeTransformer();
|
|
| 35 | 35 |
|
| 36 | 36 |
public static CaryoSileneaeImportConfigurator NewInstance(URI source, ICdmDataSource destination) {
|
| 37 | 37 |
return new CaryoSileneaeImportConfigurator(source, destination); |
| ... | ... | |
| 54 | 54 |
@Override |
| 55 | 55 |
protected void makeIoClassList() {
|
| 56 | 56 |
ioClassList = new Class[]{
|
| 57 |
CaryoSileneaeNameImport.class |
|
| 57 |
CaryoSileneaeNameImport.class, |
|
| 58 |
CaryoSileneaeNomRefImport.class, |
|
| 59 |
CaryoSileneaeTaxonImport.class, |
|
| 60 |
CaryoSileneaeSynonymImport.class |
|
| 58 | 61 |
}; |
| 59 | 62 |
} |
| 60 | 63 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeNameImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.caryo; |
| 10 | 10 |
|
| 11 |
import java.util.HashMap; |
|
| 12 |
import java.util.List; |
|
| 13 | 11 |
import java.util.Map; |
| 14 | 12 |
import java.util.UUID; |
| 15 | 13 |
|
| ... | ... | |
| 17 | 15 |
import org.apache.logging.log4j.Logger; |
| 18 | 16 |
import org.springframework.stereotype.Component; |
| 19 | 17 |
|
| 20 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
|
| 21 | 18 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 19 |
import eu.etaxonomy.cdm.common.DoubleResult; |
|
| 20 |
import eu.etaxonomy.cdm.facade.DerivedUnitFacade; |
|
| 22 | 21 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 23 | 22 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 24 | 23 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| ... | ... | |
| 32 | 31 |
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType; |
| 33 | 32 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 34 | 33 |
import eu.etaxonomy.cdm.model.term.DefinedTerm; |
| 35 |
import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException; |
|
| 36 | 34 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 37 | 35 |
|
| 38 | 36 |
/** |
| ... | ... | |
| 45 | 43 |
private static final long serialVersionUID = 8931253645038029899L; |
| 46 | 44 |
private static final Logger logger = LogManager.getLogger(); |
| 47 | 45 |
|
| 48 |
private static final String NOMEN_ID = "nomen_id"; |
|
| 49 |
private static final String RANK = "rank"; |
|
| 46 |
private static final UUID uuidSileneaeInfoNameIdType = UUID.fromString("95ecbf6d-521d-447f-bae5-d82585ff3617");
|
|
| 47 |
|
|
| 48 |
private static final String NOMEN_ID = "nomen_ID"; |
|
| 49 |
private static final String RANK = "Rank"; |
|
| 50 | 50 |
private static final String GENUS = "Genus"; |
| 51 | 51 |
private static final String INFRAGEN_NAME = "Infragen_name"; |
| 52 | 52 |
private static final String SPECIES = "Species"; |
| ... | ... | |
| 72 | 72 |
@SuppressWarnings("unused")
|
| 73 | 73 |
private static final String SynonymyReference_link = "SynonymyReference_link"; |
| 74 | 74 |
|
| 75 |
private Map<Integer, UUID> nameMapping = new HashMap<>(); |
|
| 76 |
|
|
| 77 |
private SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state; |
|
| 75 |
@Override |
|
| 76 |
protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
|
|
| 77 |
return "Names"; |
|
| 78 |
} |
|
| 78 | 79 |
|
| 79 | 80 |
@Override |
| 80 | 81 |
protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| 81 | 82 |
int line = state.getCurrentLine(); |
| 82 |
if ((line % 500) == 0){
|
|
| 83 |
newTransaction(state); |
|
| 84 |
System.out.println(line); |
|
| 85 |
} |
|
| 83 |
// if ((line % 500) == 0){
|
|
| 84 |
// newTransaction(state);
|
|
| 85 |
// System.out.println(line);
|
|
| 86 |
// }
|
|
| 86 | 87 |
|
| 87 |
this.state = state; |
|
| 88 | 88 |
Map<String, String> record = state.getOriginalRecord(); |
| 89 | 89 |
|
| 90 | 90 |
Integer nomenId = Integer.valueOf(getValue(record, NOMEN_ID)); |
| ... | ... | |
| 93 | 93 |
String infragenStr = getValue(record, INFRAGEN_NAME); |
| 94 | 94 |
String speciesStr = getValue(record, SPECIES); |
| 95 | 95 |
String infraspStr = getValue(record, INFRASP_EPITHET); |
| 96 |
String publicationStr = getValue(record, PUBLICATION); |
|
| 97 |
String publDateStr = getValue(record, PUBL_DATE); |
|
| 96 | 98 |
String authorsStr = getValue(record, AUTHORS); |
| 97 | 99 |
String ipniId = getValue(record, IPNI_ID); |
| 98 | 100 |
String notes = getValue(record, NOTES); |
| ... | ... | |
| 104 | 106 |
try {
|
| 105 | 107 |
//create name |
| 106 | 108 |
Rank rank = state.getTransformer().getRankByKey(rankStr); |
| 109 |
if (rank == null) {
|
|
| 110 |
logger.warn(row + "rank not recognized: " + rankStr); |
|
| 111 |
} |
|
| 107 | 112 |
TaxonName name = TaxonNameFactory.NewBotanicalInstance(rank); |
| 108 | 113 |
|
| 109 | 114 |
//fill simple |
| 110 | 115 |
name.setGenusOrUninomial(Ne(genusStr)); |
| 111 | 116 |
name.setInfraGenericEpithet(Ne(infragenStr)); |
| 117 |
if (speciesStr != null && speciesStr.startsWith("×")) {
|
|
| 118 |
name.setBinomHybrid(true); |
|
| 119 |
speciesStr = speciesStr.replace("×", "").trim();
|
|
| 120 |
} |
|
| 112 | 121 |
name.setSpecificEpithet(Ne(speciesStr)); |
| 113 | 122 |
name.setInfraSpecificEpithet(Ne(infraspStr)); |
| 114 |
NonViralNameParserImpl.NewInstance().parseAuthors(name, authorsStr); |
|
| 123 |
try {
|
|
| 124 |
NonViralNameParserImpl.NewInstance().parseAuthors(name, authorsStr); |
|
| 125 |
} catch (Exception e) {
|
|
| 126 |
name.setAuthorshipCache(authorsStr, true); |
|
| 127 |
logger.warn(row + "authorship not parsable: " + authorsStr); |
|
| 128 |
} |
|
| 115 | 129 |
|
| 116 |
//TODO ??publication + PublDate |
|
| 130 |
//publication |
|
| 131 |
publicationStr = normalizePublication(publicationStr); |
|
| 132 |
if (isNotBlank(publicationStr) || isNotBlank(publDateStr)) {
|
|
| 133 |
DoubleResult<String, String> publ = new DoubleResult<>(publicationStr, publDateStr); |
|
| 134 |
origPublicationMap.put(nomenId, publ); |
|
| 135 |
} |
|
| 117 | 136 |
|
| 118 | 137 |
//ipni ID |
| 119 | 138 |
if (isNotBlank(ipniId)) {
|
| 120 | 139 |
name.addIdentifier(ipniId, DefinedTerm.IDENTIFIER_NAME_IPNI()); |
| 121 | 140 |
} |
| 122 | 141 |
|
| 142 |
//add ID |
|
| 143 |
DefinedTerm sileneaeInfoNameIdType = getIdentiferType(state, |
|
| 144 |
uuidSileneaeInfoNameIdType, null, null, null, null); |
|
| 145 |
name.addIdentifier(nomenId.toString(), sileneaeInfoNameIdType); |
|
| 146 |
|
|
| 123 | 147 |
//notes |
| 124 | 148 |
if (isNotBlank(notes)) {
|
| 125 |
Annotation annotation = Annotation.NewDefaultLanguageInstance(notes); |
|
| 126 |
annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
|
| 127 |
name.addAnnotation(annotation); |
|
| 149 |
handleNotes(name, notes, row); |
|
| 128 | 150 |
} |
| 129 | 151 |
|
| 130 |
//nominval flag |
|
| 152 |
//nom.inval flag
|
|
| 131 | 153 |
if (nomInvalFlag != null && nomInvalFlag.trim().equalsIgnoreCase("yes")) {
|
| 132 | 154 |
Reference ref = null; |
| 133 | 155 |
name.addStatus(NomenclaturalStatusType.INVALID(), ref, null); |
| ... | ... | |
| 137 | 159 |
if (isNotBlank(typeSpecimenStr)) {
|
| 138 | 160 |
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(SpecimenOrObservationType.PreservedSpecimen); |
| 139 | 161 |
facade.setCollector(null); //just to create field unit and gathering event |
| 162 |
facade.innerFieldUnit().setTitleCache("Field Unit for: " + typeSpecimenStr, true);
|
|
| 140 | 163 |
facade.innerDerivedUnit().setTitleCache(typeSpecimenStr, true); |
| 141 |
SpecimenTypeDesignationStatus status = null; //TODO
|
|
| 164 |
SpecimenTypeDesignationStatus status = SpecimenTypeDesignationStatus.UNSPECIFIC();
|
|
| 142 | 165 |
Reference ref = null; |
| 143 | 166 |
String originalInfo = null; |
| 144 | 167 |
name.addSpecimenTypeDesignation(facade.innerDerivedUnit(), status, ref, null, originalInfo, false, false); |
| 145 | 168 |
// save ?? |
| 146 | 169 |
} |
| 147 | 170 |
|
| 171 |
Reference sourceRef = getSourceReference(state); |
|
| 172 |
name.addImportSource(nomenId.toString(), "Names.nomen_ID", sourceRef, "row " + String.valueOf(line)); |
|
| 173 |
|
|
| 174 |
putToNameMap(nomenId, name); |
|
| 148 | 175 |
|
| 149 |
} catch (UndefinedTransformerMethodException | StringNotParsableException e) {
|
|
| 176 |
} catch (UndefinedTransformerMethodException e) {
|
|
| 150 | 177 |
e.printStackTrace(); |
| 151 | 178 |
} |
| 152 | 179 |
} |
| 153 | 180 |
|
| 154 |
private String Ne(String genusStr) {
|
|
| 155 |
return CdmUtils.Ne(genusStr); |
|
| 156 |
} |
|
| 157 |
|
|
| 158 |
private TaxonName dedupliateNameParts(TaxonName name) {
|
|
| 159 |
if (state.getConfig().isDoDeduplicate()){
|
|
| 160 |
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(name); |
|
| 181 |
private String normalizePublication(String publicationStr) {
|
|
| 182 |
if (isBlank(publicationStr)) {
|
|
| 183 |
return null; |
|
| 161 | 184 |
} |
| 162 |
return name; |
|
| 163 |
} |
|
| 164 |
|
|
| 165 |
private String getOtherAuthors(List<TaxonName> otherNames) {
|
|
| 166 |
String result = ""; |
|
| 167 |
for (TaxonName name : otherNames){
|
|
| 168 |
result = CdmUtils.concat(";", result, name.getAuthorshipCache());
|
|
| 185 |
if ("-".equalsIgnoreCase(publicationStr)) {
|
|
| 186 |
return null; |
|
| 187 |
} |
|
| 188 |
if ("?".equalsIgnoreCase(publicationStr)) {
|
|
| 189 |
return null; |
|
| 169 | 190 |
} |
| 170 |
return result; |
|
| 191 |
if ("??".equalsIgnoreCase(publicationStr)) {
|
|
| 192 |
return null; |
|
| 193 |
} |
|
| 194 |
if ("none".equalsIgnoreCase(publicationStr)) {
|
|
| 195 |
return null; |
|
| 196 |
} |
|
| 197 |
return publicationStr; |
|
| 171 | 198 |
} |
| 172 | 199 |
|
| 200 |
private String Ne(String genusStr) {
|
|
| 201 |
return CdmUtils.Ne(genusStr); |
|
| 202 |
} |
|
| 173 | 203 |
|
| 174 |
private void handleNomenclRemarkAndNameStatus(String nomenclaturalRemarks, String row, boolean isNewName, TaxonName name, |
|
| 175 |
List<NomenclaturalStatusType> statusTypes) {
|
|
| 204 |
private String handleNotes(TaxonName name, String notes, String row) {
|
|
| 176 | 205 |
|
| 177 | 206 |
NomenclaturalStatusType remarkType = null; |
| 178 |
NomenclaturalStatusType statusType = statusTypes.isEmpty()? null: statusTypes.iterator().next(); |
|
| 179 |
if (nomenclaturalRemarks == null){
|
|
| 207 |
if (notes == null){
|
|
| 180 | 208 |
//nothing to do |
| 181 |
}else if (", nom. illeg.".equals(nomenclaturalRemarks)){
|
|
| 182 |
remarkType = NomenclaturalStatusType.ILLEGITIMATE(); |
|
| 183 |
}else if (", nom. cons.".equals(nomenclaturalRemarks)){
|
|
| 184 |
remarkType = NomenclaturalStatusType.CONSERVED(); |
|
| 185 |
}else if (", nom. nud.".equals(nomenclaturalRemarks)){
|
|
| 209 |
}else if ("ined".equals(notes)){
|
|
| 210 |
remarkType = NomenclaturalStatusType.INED(); |
|
| 211 |
notes = null; |
|
| 212 |
}else if ("nom. utique rej.".equals(notes)){
|
|
| 213 |
remarkType = NomenclaturalStatusType.UTIQUE_REJECTED(); |
|
| 214 |
notes = null; |
|
| 215 |
}else if ("nomen nudum".equalsIgnoreCase(notes)){
|
|
| 216 |
remarkType = NomenclaturalStatusType.NUDUM(); |
|
| 217 |
notes = null; |
|
| 218 |
}else if (notes.startsWith("nomen nudum") || notes.startsWith("Nomen nudum") ){
|
|
| 186 | 219 |
remarkType = NomenclaturalStatusType.NUDUM(); |
| 187 |
}else if (", nom. provis.".equals(nomenclaturalRemarks)){
|
|
| 188 |
remarkType = NomenclaturalStatusType.PROVISIONAL(); |
|
| 189 |
}else if (", nom. rej.".equals(nomenclaturalRemarks)){
|
|
| 220 |
}else if (notes.startsWith("nom. illeg.")){
|
|
| 221 |
remarkType = NomenclaturalStatusType.ILLEGITIMATE(); |
|
| 222 |
}else if (notes.startsWith("nom. inval")){
|
|
| 223 |
remarkType = NomenclaturalStatusType.INVALID(); |
|
| 224 |
}else if ("Nom. rej.".equals(notes)){
|
|
| 190 | 225 |
remarkType = NomenclaturalStatusType.REJECTED(); |
| 191 |
}else if (", nom. subnud.".equals(nomenclaturalRemarks)){
|
|
| 192 |
remarkType = NomenclaturalStatusType.SUBNUDUM(); |
|
| 193 |
}else if (", nom. superfl.".equals(nomenclaturalRemarks)){
|
|
| 194 |
remarkType = NomenclaturalStatusType.SUPERFLUOUS(); |
|
| 195 |
}else if (", not validly publ.".equals(nomenclaturalRemarks)){
|
|
| 196 |
statusTypes.add(NomenclaturalStatusType.INVALID()); |
|
| 197 |
}else if (", opus utique oppr.".equals(nomenclaturalRemarks)){
|
|
| 198 |
statusTypes.add(NomenclaturalStatusType.OPUS_UTIQUE_OPPR()); |
|
| 199 |
}else {
|
|
| 200 |
logger.warn(row + "Unhandled nomenclatural remark: " + nomenclaturalRemarks); |
|
| 226 |
notes = null; |
|
| 201 | 227 |
} |
| 202 | 228 |
|
| 203 |
NomenclaturalStatusType kewType = remarkType != null? remarkType : statusType; |
|
| 204 |
if (isNewName){
|
|
| 205 |
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
| 206 |
logger.warn(row + "Kew suggests 2 different nom. status. types for new name. The status from nomenclatural_remarks was taken."); |
|
| 207 |
} |
|
| 208 |
if (kewType != null){
|
|
| 209 |
name.addStatus(kewType, getSecRef(state), null); |
|
| 210 |
} |
|
| 211 |
}else{
|
|
| 212 |
NomenclaturalStatusType existingType = null; |
|
| 213 |
if (!name.getStatus().isEmpty()){
|
|
| 214 |
existingType = name.getStatus().iterator().next().getType(); |
|
| 215 |
} |
|
| 216 |
if (existingType != null && kewType != null){
|
|
| 217 |
if (!existingType.equals(kewType)){
|
|
| 218 |
logger.warn(row + "Existing name status "+existingType.getTitleCache()+" differs from Kew status " + kewType.getTitleCache() + ". Key status ignored"); |
|
| 219 |
} |
|
| 220 |
}else if (existingType != null && kewType == null){
|
|
| 221 |
logger.warn(row + "Info: Existing name has a name status "+existingType.getTitleCache()+" but Kew name has no status. Existing status kept."); |
|
| 222 |
}else if (existingType == null && kewType != null){
|
|
| 223 |
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
| 224 |
logger.warn(row + "Existing name has no status while Kew name suggests a status (but 2 different status form status and nomenclatural_remarks field)."); |
|
| 225 |
}else{
|
|
| 226 |
logger.warn(row + "Existing name has no status while Kew name suggests a status ("+kewType.getTitleCache()+"). Kew status ignored.");
|
|
| 229 |
//annotation |
|
| 230 |
if (isNotBlank(notes)) {
|
|
| 231 |
Annotation annotation = Annotation.NewDefaultLanguageInstance(notes); |
|
| 232 |
annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
|
| 233 |
name.addAnnotation(annotation); |
|
| 234 |
} |
|
| 235 |
|
|
| 236 |
//nom. status. |
|
| 237 |
if (remarkType != null) {
|
|
| 238 |
if (!name.hasStatus(remarkType)) {
|
|
| 239 |
|
|
| 240 |
Reference ref = null; |
|
| 241 |
name.addStatus(remarkType, ref, null); |
|
| 242 |
if (name.getStatus().size() > 1) {
|
|
| 243 |
logger.warn(row + "name has >1 status: " + name.getFullTitleCache()); |
|
| 227 | 244 |
} |
| 228 | 245 |
} |
| 229 | 246 |
} |
| 247 |
|
|
| 248 |
return notes; |
|
| 230 | 249 |
} |
| 231 | 250 |
|
| 232 | 251 |
@Override |
| ... | ... | |
| 239 | 258 |
Integer typeSpeciesId = getInt(getValue(record, TYPE_SPECIES_LINK)); |
| 240 | 259 |
|
| 241 | 260 |
String row = String.valueOf(line) + "("+nomenId+"): ";
|
| 242 |
if ((line % 500) == 0){
|
|
| 243 |
newTransaction(state); |
|
| 244 |
System.out.println(line); |
|
| 245 |
} |
|
| 261 |
// if ((line % 500) == 0){
|
|
| 262 |
// newTransaction(state);
|
|
| 263 |
// System.out.println(line);
|
|
| 264 |
// }
|
|
| 246 | 265 |
|
| 247 |
TaxonName name = getName(state, nomenId);
|
|
| 266 |
TaxonName name = getName(nomenId); |
|
| 248 | 267 |
if (name == null) {
|
| 249 | 268 |
logger.warn(row + "Name does not exist"); |
| 250 | 269 |
return; |
| 251 | 270 |
} |
| 252 | 271 |
|
| 253 | 272 |
//basionym |
| 254 |
if (basionymId != null) {
|
|
| 255 |
TaxonName basionym = getName(state, basionymId);
|
|
| 273 |
if (basionymId != null && !basionymId.equals(nomenId)) {
|
|
| 274 |
TaxonName basionym = getName(basionymId); |
|
| 256 | 275 |
if (basionym == null) {
|
| 257 | 276 |
logger.warn(row + "basionym does not exist"); |
| 258 | 277 |
}else {
|
| ... | ... | |
| 262 | 281 |
|
| 263 | 282 |
//type name |
| 264 | 283 |
if (typeSpeciesId != null) {
|
| 265 |
TaxonName typeSpecies = getName(state, typeSpeciesId);
|
|
| 284 |
TaxonName typeSpecies = getName(typeSpeciesId); |
|
| 266 | 285 |
if (typeSpecies == null) {
|
| 267 | 286 |
logger.warn(row + "typeSpecies does not exist"); |
| 268 | 287 |
}else {
|
| 269 | 288 |
Reference ref = null; |
| 270 |
NameTypeDesignationStatus status = null; //TODO
|
|
| 289 |
NameTypeDesignationStatus status = null; // NameTypeDesignationStatus.NOT_APPLICABLE(); //TODO minor NameTypeDesignationStatus
|
|
| 271 | 290 |
name.addNameTypeDesignation(typeSpecies, ref, null, null, status, false); |
| 272 | 291 |
} |
| 273 | 292 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeNomRefImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.caryo; |
| 10 | 10 |
|
| 11 |
import java.util.HashMap; |
|
| 12 | 11 |
import java.util.HashSet; |
| 13 |
import java.util.List; |
|
| 14 | 12 |
import java.util.Map; |
| 15 | 13 |
import java.util.Set; |
| 16 |
import java.util.UUID; |
|
| 17 | 14 |
|
| 18 | 15 |
import org.apache.logging.log4j.LogManager; |
| 19 | 16 |
import org.apache.logging.log4j.Logger; |
| 20 | 17 |
import org.springframework.stereotype.Component; |
| 21 | 18 |
|
| 22 | 19 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 23 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
|
|
| 20 |
import eu.etaxonomy.cdm.common.DoubleResult;
|
|
| 24 | 21 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 25 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
| 26 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
| 22 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 27 | 23 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 28 | 24 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| 29 | 25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 26 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
| 30 | 27 |
import eu.etaxonomy.cdm.model.reference.ReferenceType; |
| 31 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 32 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 33 | 28 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
| 29 |
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser; |
|
| 34 | 30 |
|
| 35 | 31 |
/** |
| 36 | 32 |
* @author a.mueller |
| ... | ... | |
| 42 | 38 |
private static final long serialVersionUID = 7227226331297614469L; |
| 43 | 39 |
private static final Logger logger = LogManager.getLogger(); |
| 44 | 40 |
|
| 45 |
private static final String NOMEN_ID = "nomen_id";
|
|
| 41 |
private static final String NOMEN_ID = "nomen_ID";
|
|
| 46 | 42 |
private static final String NAME = "name"; |
| 47 | 43 |
private static final String PUBLICATION = "Publication"; |
| 48 | 44 |
private static final String PUB_TYPE_ED = "PubTypeEd"; |
| ... | ... | |
| 52 | 48 |
private static final String ORIG_SPELLING = "Original spelling"; |
| 53 | 49 |
private static final String NOM_STATUS = "Nom. Status"; |
| 54 | 50 |
|
| 51 |
@SuppressWarnings("unused")
|
|
| 55 | 52 |
private static final String SECOND_PUBLICATION = "SecondPublication"; |
| 53 |
@SuppressWarnings("unused")
|
|
| 56 | 54 |
private static final String IMPORT = "import"; |
| 55 |
@SuppressWarnings("unused")
|
|
| 57 | 56 |
private static final String DUPL = "dupl"; |
| 58 | 57 |
|
| 59 |
|
|
| 60 |
private Map<Integer, Reference> nameMapping = new HashMap<>(); |
|
| 61 |
private Set<String> neglectedRecords = new HashSet<>(); |
|
| 62 |
private Set<UUID> createdNames = new HashSet<>(); |
|
| 63 |
|
|
| 64 | 58 |
private static final NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 65 | 59 |
|
| 66 | 60 |
private SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state; |
| 67 | 61 |
|
| 62 |
@Override |
|
| 63 |
protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
|
|
| 64 |
return "NomRef"; |
|
| 65 |
} |
|
| 66 |
|
|
| 68 | 67 |
@Override |
| 69 | 68 |
protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| 70 | 69 |
int line = state.getCurrentLine(); |
| 71 |
if ((line % 500) == 0){
|
|
| 72 |
newTransaction(state); |
|
| 73 |
System.out.println(line); |
|
| 74 |
} |
|
| 70 |
// if ((line % 500) == 0){
|
|
| 71 |
// newTransaction(state);
|
|
| 72 |
// System.out.println(line);
|
|
| 73 |
// }
|
|
| 75 | 74 |
|
| 76 | 75 |
this.state = state; |
| 77 | 76 |
Map<String, String> record = state.getOriginalRecord(); |
| ... | ... | |
| 85 | 84 |
|
| 86 | 85 |
String nimmKew = getValue(record, NIMM_KEW); |
| 87 | 86 |
String origSpelling = getValue(record, ORIG_SPELLING); |
| 88 |
//TODO erstmal nicht importieren laut NaK |
|
| 87 |
|
|
| 89 | 88 |
@SuppressWarnings("unused")
|
| 90 | 89 |
String nomStatus = getValue(record, NOM_STATUS); |
| 91 | 90 |
|
| 92 |
String row = String.valueOf(line) + "("+nameStr+"): ";
|
|
| 91 |
String row = String.valueOf(line) + "("+nomenId+"): ";
|
|
| 93 | 92 |
|
| 94 |
TaxonName name = getName(state, nomenId); |
|
| 93 |
origNameMap.remove(nomenId); |
|
| 94 |
TaxonName name = getName(nomenId); |
|
| 95 | 95 |
if (name == null) {
|
| 96 | 96 |
return; //record did not exist |
| 97 |
//TODO check if it is really a duplicate |
|
| 97 |
//TODO minor check if it is really a duplicate
|
|
| 98 | 98 |
} |
| 99 | 99 |
|
| 100 | 100 |
boolean isKew = isNotBlank(nimmKew) && "x".equals(nimmKew); |
| 101 | 101 |
|
| 102 | 102 |
String publication = isKew ? pubKew : origPublication; |
| 103 |
String pubType = isKew ? pubTypeEd : pubTypeKew; |
|
| 103 |
String pubType = isKew ? pubTypeKew : pubTypeEd; |
|
| 104 |
|
|
| 105 |
DoubleResult<String, String> origPubl = origPublicationMap.get(nomenId); |
|
| 106 |
boolean useOrigPubl = false; |
|
| 107 |
if (isBlank(publication) && origPubl != null) {
|
|
| 108 |
publication = origPubl.getFirstResult(); |
|
| 109 |
useOrigPubl = true; |
|
| 110 |
logger.warn(row + "use original (Nomen.xlsx) publication and/or year"); |
|
| 111 |
} |
|
| 112 |
|
|
| 113 |
if ("ined.".equals(publication)) {
|
|
| 114 |
publication = null; |
|
| 115 |
NomenclaturalStatusType type = NomenclaturalStatusType.INED(); |
|
| 116 |
if (name.hasStatus(type)) {
|
|
| 117 |
name.addStatus(type, null, null); |
|
| 118 |
} |
|
| 119 |
} |
|
| 104 | 120 |
|
| 105 | 121 |
ReferenceType refType = getRefType(pubType); |
| 106 |
if (refType == null) {
|
|
| 107 |
logger.warn(row + "reference type not found"); |
|
| 122 |
if (refType == null && isNotBlank(publication)) {
|
|
| 123 |
logger.warn(row + "reference type not found for: " + publication); |
|
| 124 |
}else if (publication == null) {
|
|
| 125 |
if (!name.isAutonym()) {
|
|
| 126 |
logger.warn(row + "no publication"); |
|
| 127 |
} |
|
| 108 | 128 |
}else if (refType == ReferenceType.Article) {
|
| 109 |
publication = "in " + publication; |
|
| 129 |
if (!publication.startsWith("in ")) {
|
|
| 130 |
publication = " in " + publication; |
|
| 131 |
}else {
|
|
| 132 |
publication = " " + publication; |
|
| 133 |
} |
|
| 110 | 134 |
}else if (refType == ReferenceType.Book) {
|
| 111 |
// |
|
| 135 |
if (publication.startsWith("in ")) {
|
|
| 136 |
publication = " " + publication; |
|
| 137 |
}else if (publication.contains(",")) {
|
|
| 138 |
// logger.warn(row + "book with ',': " + publication); |
|
| 139 |
String[] split = publication.split(",");
|
|
| 140 |
String potentialAuthor = split[0]; |
|
| 141 |
if (potentialAuthor.split(" ").length <= 2) {
|
|
| 142 |
boolean noAbbrev = true; |
|
| 143 |
for(String str : potentialAuthor.split(" ")) {
|
|
| 144 |
if (str.endsWith(".")) {
|
|
| 145 |
noAbbrev = false; |
|
| 146 |
break; |
|
| 147 |
} |
|
| 148 |
} |
|
| 149 |
if (noAbbrev) {
|
|
| 150 |
refType = ReferenceType.BookSection; |
|
| 151 |
publication = " in " + publication; |
|
| 152 |
}else {
|
|
| 153 |
// logger.warn(row + "probably only abbrev title"); |
|
| 154 |
publication = ", " + publication; |
|
| 155 |
} |
|
| 156 |
} else {
|
|
| 157 |
// logger.warn(row + "probably not booksection"); |
|
| 158 |
publication = ", " + publication; |
|
| 159 |
} |
|
| 160 |
}else {
|
|
| 161 |
publication = ", " + publication; |
|
| 162 |
} |
|
| 112 | 163 |
}else {
|
| 113 | 164 |
logger.warn(row + "reference type not handled: " + refType); |
| 165 |
publication = ", " + publication; |
|
| 114 | 166 |
} |
| 115 |
String referenceName = name.getTitleCache()+ " " + publication;
|
|
| 116 |
TaxonName parsedName = parser.parseReferencedName(referenceName); |
|
| 167 |
String referenceName = CdmUtils.concat("", name.getTitleCache(), publication);
|
|
| 168 |
TaxonName parsedName = parser.parseReferencedName(referenceName, NomenclaturalCode.ICNAFP, null);
|
|
| 117 | 169 |
if (parsedName.isProtectedFullTitleCache() || parsedName.isProtectedTitleCache() ) {
|
| 118 |
logger.warn(row + "name could not be parsed");
|
|
| 170 |
logger.warn(row + "name could not be parsed: " + referenceName);
|
|
| 119 | 171 |
}else {
|
| 120 | 172 |
Reference ref = parsedName.getNomenclaturalReference(); |
| 173 |
if (useOrigPubl && origPubl != null && origPubl.getSecondResult() != null) {
|
|
| 174 |
if (ref != null) {
|
|
| 175 |
ref.setDatePublished(TimePeriodParser.parseStringVerbatim(origPubl.getSecondResult())); |
|
| 176 |
}else {
|
|
| 177 |
ref = ReferenceFactory.newGeneric(); |
|
| 178 |
ref.setDatePublished(TimePeriodParser.parseStringVerbatim(origPubl.getSecondResult())); |
|
| 179 |
} |
|
| 180 |
logger.warn(row + "set original (Nomen.xlsx) year"); |
|
| 181 |
} |
|
| 121 | 182 |
name.setNomenclaturalReference(ref); |
| 122 | 183 |
String microRef = parsedName.getNomenclaturalMicroReference(); |
| 123 | 184 |
name.setNomenclaturalMicroReference(microRef); |
| ... | ... | |
| 125 | 186 |
|
| 126 | 187 |
//validateName (name); |
| 127 | 188 |
validateName(name, nameStr, row); |
| 189 |
|
|
| 128 | 190 |
//deduplicate |
| 129 | 191 |
dedupliateNameParts(name); |
| 130 | 192 |
|
| ... | ... | |
| 134 | 196 |
if (origName.isProtectedTitleCache()) {
|
| 135 | 197 |
logger.warn(row + "orig name could not be parsed"); |
| 136 | 198 |
} |
| 137 |
name.getNomenclaturalSource().setNameUsedInSource(origName); |
|
| 199 |
if (name.getNomenclaturalSource() == null) {
|
|
| 200 |
logger.warn(row + "no nomsource yet"); |
|
| 201 |
} |
|
| 202 |
name.getNomenclaturalSource(true).setNameUsedInSource(origName); |
|
| 203 |
origSpellingNames.add(origName); |
|
| 138 | 204 |
} |
| 139 | 205 |
} |
| 140 | 206 |
|
| 141 |
private void validateName(TaxonName name, String nameStr, String row) {
|
|
| 142 |
if (name.getTitleCache().equals(nameStr)) {
|
|
| 143 |
logger.warn(row+ "name titleCache does not match"); |
|
| 207 |
private void validateName(TaxonName name, String nomRefStr, String row) {
|
|
| 208 |
nomRefStr = nomRefStr.replace("× ", "×");
|
|
| 209 |
nomRefStr = nomRefStr.replace(" unranked ", " [unranked] ");
|
|
| 210 |
nomRefStr = nomRefStr.replace(" [infrasp.unranked] ", " [infraspec.] ");
|
|
| 211 |
|
|
| 212 |
if (!name.getTitleCache().equals(nomRefStr)) {
|
|
| 213 |
TaxonName nomRefName = (TaxonName)parser.parseFullName(nomRefStr, NomenclaturalCode.ICNAFP, null); |
|
| 214 |
if (!nomRefName.getNameCache().equals(name.getNameCache())) {
|
|
| 215 |
logger.warn(row+ "nameCache does not match: " + name.getNameCache() + "<->" + nomRefName.getNameCache()); |
|
| 216 |
if (!CdmUtils.Nz(name.getAuthorshipCache()).equals(nomRefName.getAuthorshipCache())) {
|
|
| 217 |
logger.warn(row+ "also authorship differs: " + name.getAuthorshipCache() + "<->" + nomRefName.getAuthorshipCache()); |
|
| 218 |
} |
|
| 219 |
}else {
|
|
| 220 |
logger.warn(row+ "authors/titleCache do not match: " + name.getTitleCache() + "<->" + nomRefStr); |
|
| 221 |
} |
|
| 222 |
if (!CdmUtils.Nz(name.getAuthorshipCache()).equals(nomRefName.getAuthorshipCache())) {
|
|
| 223 |
if (isBlank(nomRefName.getAuthorshipCache())) {
|
|
| 224 |
logger.warn(row + "'NomRef' authorship is empty but differs. Kept 'Nomen' authorship"); |
|
| 225 |
}else {
|
|
| 226 |
name.setCombinationAuthorship(nomRefName.getCombinationAuthorship()); |
|
| 227 |
name.setExCombinationAuthorship(nomRefName.getExCombinationAuthorship()); |
|
| 228 |
name.setBasionymAuthorship(nomRefName.getBasionymAuthorship()); |
|
| 229 |
name.setExBasionymAuthorship(nomRefName.getExBasionymAuthorship()); |
|
| 230 |
} |
|
| 231 |
} |
|
| 144 | 232 |
} |
| 145 | 233 |
} |
| 146 | 234 |
|
| ... | ... | |
| 160 | 248 |
return name; |
| 161 | 249 |
} |
| 162 | 250 |
|
| 163 |
private void makeStatus(String status, String sourceId, |
|
| 164 |
String accId, String row, List<NomenclaturalStatusType> statusTypes) {
|
|
| 165 | 251 |
|
| 166 |
Class<? extends CdmBase> clazz; |
|
| 167 |
if ("Accepted".equals(status) || "Unplaced".equals(status) || "Artificial Hybrid".equals(status) ){
|
|
| 168 |
clazz = Taxon.class; |
|
| 169 |
}else if ("Synonym".equals(status) || "Orthographic".equals(status)){
|
|
| 170 |
clazz = (accId == null)? Taxon.class : Synonym.class; |
|
| 171 |
if("Orthographic".equals(status)){
|
|
| 172 |
statusTypes.add(NomenclaturalStatusType.SUPERFLUOUS()); |
|
| 173 |
} |
|
| 174 |
}else if("Illegitimate".equals(status)){
|
|
| 175 |
statusTypes.add(NomenclaturalStatusType.ILLEGITIMATE()); |
|
| 176 |
}else if ("Invalid".equals(status)){
|
|
| 177 |
statusTypes.add(NomenclaturalStatusType.INVALID()); |
|
| 178 |
}else{
|
|
| 179 |
logger.warn(row + "Unhandled status: " + status); |
|
| 180 |
} |
|
| 181 |
return; |
|
| 182 |
} |
|
| 183 |
|
|
| 184 |
private void handleNomenclRemarkAndNameStatus(String nomenclaturalRemarks, String row, boolean isNewName, TaxonName name, |
|
| 185 |
List<NomenclaturalStatusType> statusTypes) {
|
|
| 186 |
|
|
| 187 |
NomenclaturalStatusType remarkType = null; |
|
| 188 |
NomenclaturalStatusType statusType = statusTypes.isEmpty()? null: statusTypes.iterator().next(); |
|
| 189 |
if (nomenclaturalRemarks == null){
|
|
| 190 |
//nothing to do |
|
| 191 |
}else if (", nom. illeg.".equals(nomenclaturalRemarks)){
|
|
| 192 |
remarkType = NomenclaturalStatusType.ILLEGITIMATE(); |
|
| 193 |
}else if (", nom. cons.".equals(nomenclaturalRemarks)){
|
|
| 194 |
remarkType = NomenclaturalStatusType.CONSERVED(); |
|
| 195 |
}else if (", nom. nud.".equals(nomenclaturalRemarks)){
|
|
| 196 |
remarkType = NomenclaturalStatusType.NUDUM(); |
|
| 197 |
}else if (", nom. provis.".equals(nomenclaturalRemarks)){
|
|
| 198 |
remarkType = NomenclaturalStatusType.PROVISIONAL(); |
|
| 199 |
}else if (", nom. rej.".equals(nomenclaturalRemarks)){
|
|
| 200 |
remarkType = NomenclaturalStatusType.REJECTED(); |
|
| 201 |
}else if (", nom. subnud.".equals(nomenclaturalRemarks)){
|
|
| 202 |
remarkType = NomenclaturalStatusType.SUBNUDUM(); |
|
| 203 |
}else if (", nom. superfl.".equals(nomenclaturalRemarks)){
|
|
| 204 |
remarkType = NomenclaturalStatusType.SUPERFLUOUS(); |
|
| 205 |
}else if (", not validly publ.".equals(nomenclaturalRemarks)){
|
|
| 206 |
statusTypes.add(NomenclaturalStatusType.INVALID()); |
|
| 207 |
}else if (", opus utique oppr.".equals(nomenclaturalRemarks)){
|
|
| 208 |
statusTypes.add(NomenclaturalStatusType.OPUS_UTIQUE_OPPR()); |
|
| 209 |
}else {
|
|
| 210 |
logger.warn(row + "Unhandled nomenclatural remark: " + nomenclaturalRemarks); |
|
| 211 |
} |
|
| 252 |
private boolean first = true; |
|
| 253 |
@Override |
|
| 254 |
protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
|
| 212 | 255 |
|
| 213 |
NomenclaturalStatusType kewType = remarkType != null? remarkType : statusType; |
|
| 214 |
if (isNewName){
|
|
| 215 |
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
| 216 |
logger.warn(row + "Kew suggests 2 different nom. status. types for new name. The status from nomenclatural_remarks was taken."); |
|
| 217 |
} |
|
| 218 |
if (kewType != null){
|
|
| 219 |
name.addStatus(kewType, getSecRef(state), null); |
|
| 220 |
} |
|
| 221 |
}else{
|
|
| 222 |
NomenclaturalStatusType existingType = null; |
|
| 223 |
if (!name.getStatus().isEmpty()){
|
|
| 224 |
existingType = name.getStatus().iterator().next().getType(); |
|
| 225 |
} |
|
| 226 |
if (existingType != null && kewType != null){
|
|
| 227 |
if (!existingType.equals(kewType)){
|
|
| 228 |
logger.warn(row + "Existing name status "+existingType.getTitleCache()+" differs from Kew status " + kewType.getTitleCache() + ". Key status ignored"); |
|
| 229 |
} |
|
| 230 |
}else if (existingType != null && kewType == null){
|
|
| 231 |
logger.warn(row + "Info: Existing name has a name status "+existingType.getTitleCache()+" but Kew name has no status. Existing status kept."); |
|
| 232 |
}else if (existingType == null && kewType != null){
|
|
| 233 |
if(remarkType != null && statusType != null && !remarkType.equals(statusType)){
|
|
| 234 |
logger.warn(row + "Existing name has no status while Kew name suggests a status (but 2 different status form status and nomenclatural_remarks field)."); |
|
| 235 |
}else{
|
|
| 236 |
logger.warn(row + "Existing name has no status while Kew name suggests a status ("+kewType.getTitleCache()+"). Kew status ignored.");
|
|
| 256 |
if (first) {
|
|
| 257 |
if (origNameMap.size() > 0) {
|
|
| 258 |
logger.warn("There are " + origNameMap.size() + " unhandled names");
|
|
| 259 |
for (Integer key : origNameMap.keySet()) {
|
|
| 260 |
System.out.println(key + ": " + origNameMap.get(key).getTitleCache()); |
|
| 237 | 261 |
} |
| 238 | 262 |
} |
| 239 |
} |
|
| 240 |
} |
|
| 241 |
|
|
| 242 |
private void testParsedName(SimpleExcelTaxonImportState<CaryoAizoaceaeExcelImportConfigurator> state, TaxonName name, |
|
| 243 |
String row, String fullCitation) throws UndefinedTransformerMethodException {
|
|
| 244 |
Map<String, String> record = state.getOriginalRecord(); |
|
| 245 |
|
|
| 246 |
String nameCache = getValue(record, NAME); |
|
| 247 |
String pubType = getValue(record, "PubType"); |
|
| 248 |
String place_of_publication = getValue(record, "place_of_publication"); |
|
| 249 |
String volume_and_page = getValue(record, "volume_and_page"); |
|
| 250 |
|
|
| 251 |
// if (!CdmUtils.nullSafeEqual(name.getNameCache(), nameCache)){
|
|
| 252 |
// logger.warn(row + "Unexpected nameCache: " + nameCache); |
|
| 253 |
// } |
|
| 254 |
// if (!CdmUtils.nullSafeEqual(name.getTitleCache(), fullName)){
|
|
| 255 |
// logger.warn(row + "Unexpected titleCache: <->" + name.getTitleCache()); |
|
| 256 |
// } |
|
| 257 |
// if (isBlank(genusHybrid) == name.isMonomHybrid()){
|
|
| 258 |
// logger.warn(row + "Unexpected genus hybrid: " + genusHybrid); |
|
| 259 |
// } |
|
| 260 |
// if (!CdmUtils.nullSafeEqual(name.getGenusOrUninomial(),genus)){
|
|
| 261 |
// logger.warn(row + "Unexpected genus: " + genus); |
|
| 262 |
// }if (isBlank(speciesHybrid) == name.isBinomHybrid()){
|
|
| 263 |
// logger.warn(row + "Unexpected species hybrid: " + speciesHybrid); |
|
| 264 |
// } |
|
| 265 |
// if (!CdmUtils.nullSafeEqual(name.getSpecificEpithet(),species)){
|
|
| 266 |
// logger.warn(row + "Unexpected species epithet: " + name.getSpecificEpithet() +"<->"+ species); |
|
| 267 |
// } |
|
| 268 |
// if (!CdmUtils.nullSafeEqual(name.getInfraSpecificEpithet(), infraspecies)){
|
|
| 269 |
// logger.warn(row + "Unexpected infraspecific epithet: " + name.getInfraSpecificEpithet() +"<->"+ infraspecies); |
|
| 270 |
// } |
|
| 271 |
// if (!CdmUtils.nullSafeEqual(name.getAuthorshipCache(),authors)){
|
|
| 272 |
// logger.warn(row + "Unexpected authors: " + name.getAuthorshipCache() +"<->"+ authors); |
|
| 273 |
// } |
|
| 274 |
// String combinationAndExAuthor = authorTitle(name.getCombinationAuthorship(), name.getExCombinationAuthorship()); |
|
| 275 |
// if (!CdmUtils.nullSafeEqual(combinationAndExAuthor, combinationAuthor)){
|
|
| 276 |
// logger.warn(row + "Unexpected combination author: " + combinationAndExAuthor +"<->"+ combinationAuthor); |
|
| 277 |
// } |
|
| 278 |
// String basionymAndExAuthor = authorTitle(name.getBasionymAuthorship(), name.getExBasionymAuthorship()); |
|
| 279 |
// if (!CdmUtils.nullSafeEqual(basionymAndExAuthor, basionymAuthor)){
|
|
| 280 |
// logger.warn(row + "Unexpected basionym author: " + basionymAndExAuthor +"<->"+ basionymAuthor); |
|
| 281 |
// } |
|
| 282 |
// Rank rank = state.getTransformer().getRankByKey(rankStr); |
|
| 283 |
// if (!rank.equals(name.getRank())){
|
|
| 284 |
// logger.warn(row + "Unexpected rank: " + rankStr); |
|
| 285 |
// } |
|
| 286 |
// |
|
| 287 |
// Reference nomRef = name.getNomenclaturalReference(); |
|
| 288 |
// if (nomRef == null){
|
|
| 289 |
// if (fullCitation != null){
|
|
| 290 |
// NonViralNameParserImpl parser = new NonViralNameParserImpl(); |
|
| 291 |
// TaxonName parsedName = parser.parseReferencedName(fullCitation, NomenclaturalCode.ICNAFP, rank); |
|
| 292 |
// if (parsedName.getNomenclaturalReference() != null){
|
|
| 293 |
// name.setNomenclaturalReference(parsedName.getNomenclaturalReference()); |
|
| 294 |
// logger.warn(row + "Nom.ref. was missing. Taken from Kew"); |
|
| 295 |
// }else{
|
|
| 296 |
// logger.warn(row + "Nom. ref. is missing or can not be parsed"); |
|
| 297 |
// } |
|
| 298 |
// }else{
|
|
| 299 |
// logger.warn(row + "NomRef is missing."); |
|
| 300 |
// } |
|
| 301 |
// }else{
|
|
| 302 |
// if ("A".equals(pubType) && nomRef.getType() != ReferenceType.Article){
|
|
| 303 |
// logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString()); |
|
| 304 |
// } |
|
| 305 |
// if ("B".equals(pubType) && nomRef.getType() != ReferenceType.Book){
|
|
| 306 |
// logger.warn(row + "Unexpected nomref type: " + pubType + "<->" + nomRef.getType().toString()); |
|
| 307 |
// } |
|
| 308 |
// year = normalizeYear(year); |
|
| 309 |
// if (!CdmUtils.nullSafeEqual(year, nomRef.getDatePublishedString())){
|
|
| 310 |
// logger.warn(row + "Unexpected year: " + year + "<->" + nomRef.getDatePublishedString()); |
|
| 311 |
// } |
|
| 312 |
// if (volume_and_page != null && !name.getFullTitleCache().contains(volume_and_page)){
|
|
| 313 |
// logger.warn(row + "volume_and_page not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ volume_and_page); |
|
| 314 |
// } |
|
| 315 |
// if (place_of_publication != null && !name.getFullTitleCache().contains(place_of_publication)){
|
|
| 316 |
// logger.warn(row + "place_of_publication not found in fullTitleCache: " + name.getFullTitleCache() +"<->"+ place_of_publication); |
|
| 317 |
// } |
|
| 318 |
// } |
|
| 319 |
// if ("subsp.".equals(infraSpecRank) && !rank.equals(Rank.SUBSPECIES())){
|
|
| 320 |
// logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank); |
|
| 321 |
// }else if ("var.".equals(infraSpecRank) && !rank.equals(Rank.VARIETY())){
|
|
| 322 |
// logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank); |
|
| 323 |
// }else if ("f.".equals(infraSpecRank) && !rank.equals(Rank.FORM())){
|
|
| 324 |
// logger.warn(row + "Unexpected infraspec marker: " + infraSpecRank); |
|
| 325 |
// } |
|
| 326 |
} |
|
| 327 |
|
|
| 328 |
private String authorTitle(TeamOrPersonBase<?> author, TeamOrPersonBase<?> exAuthor) {
|
|
| 329 |
String authorStr = author == null? null: author.getNomenclaturalTitleCache(); |
|
| 330 |
String exAuthorStr = exAuthor == null? null: exAuthor.getNomenclaturalTitleCache(); |
|
| 331 |
return CdmUtils.concat(" ex ", exAuthorStr, authorStr);
|
|
| 332 |
} |
|
| 333 | 263 |
|
| 334 |
private String normalizeYear(String year) {
|
|
| 335 |
if (year == null){
|
|
| 336 |
return null; |
|
| 337 |
}else if (year.contains("\" [")){
|
|
| 338 |
String[] split = year.split("\" \\[");
|
|
| 339 |
year = split[1].replace("]","") + " [" + split[0]+"\"]";
|
|
| 340 |
}else if ("?".equals(year)){
|
|
| 341 |
return null; |
|
| 264 |
Set<TaxonName> commonSet = new HashSet<>(nameMap.values()); |
|
| 265 |
commonSet.addAll(origNameMap.values()); |
|
| 266 |
commonSet.addAll(origSpellingNames); |
|
| 267 |
try {
|
|
| 268 |
getNameService().saveOrUpdate(commonSet); |
|
| 269 |
} catch (Exception e) {
|
|
| 270 |
e.printStackTrace(); |
|
| 271 |
} |
|
| 272 |
first = false; |
|
| 342 | 273 |
} |
| 343 |
return year; |
|
| 344 |
} |
|
| 345 |
|
|
| 346 |
@Override |
|
| 347 |
protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
|
| 348 |
// Map<String, String> record = state.getOriginalRecord(); |
|
| 349 |
// int line = state.getCurrentLine(); |
|
| 350 |
// String accName = getValue(record, "AcceptedName"); |
|
| 351 |
// String basionymId = getValue(record, "basionym_plant_name_id"); |
|
| 352 |
// String homotypicSynonym = getValue(record, "homotypic_synonym"); |
|
| 353 |
// |
|
| 354 |
// String row = String.valueOf(line) + "("+fullName+"): ";
|
|
| 355 |
// |
|
| 356 |
// if ((line % 500) == 0){
|
|
| 357 |
// newTransaction(state); |
|
| 358 |
// System.out.println(line); |
|
| 359 |
// } |
|
| 360 | 274 |
} |
| 361 | 275 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeSynonymImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.caryo; |
| 10 | 10 |
|
| 11 |
import java.util.HashSet; |
|
| 12 | 11 |
import java.util.Map; |
| 13 |
import java.util.Set; |
|
| 14 | 12 |
|
| 15 | 13 |
import org.apache.logging.log4j.LogManager; |
| 16 | 14 |
import org.apache.logging.log4j.Logger; |
| 17 | 15 |
import org.springframework.stereotype.Component; |
| 18 | 16 |
|
| 19 | 17 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 20 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
| 21 | 18 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| 22 | 19 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| 23 | 20 |
import eu.etaxonomy.cdm.model.taxon.SynonymType; |
| 24 | 21 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 25 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
| 22 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
|
| 26 | 23 |
|
| 27 | 24 |
/** |
| 28 | 25 |
* @author a.mueller |
| ... | ... | |
| 38 | 35 |
private static final String NOMEN_LINK = "Nomen_link"; |
| 39 | 36 |
private static final String TAXON_LINK = "Taxon_link"; |
| 40 | 37 |
|
| 41 |
private Set<String> neglectedRecords = new HashSet<>(); |
|
| 42 |
|
|
| 43 |
private SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state; |
|
| 38 |
@Override |
|
| 39 |
protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
|
|
| 40 |
return "Synonyms"; |
|
| 41 |
} |
|
| 44 | 42 |
|
| 45 | 43 |
@Override |
| 46 | 44 |
protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| ... | ... | |
| 50 | 48 |
System.out.println(line); |
| 51 | 49 |
} |
| 52 | 50 |
|
| 53 |
this.state = state; |
|
| 54 | 51 |
Map<String, String> record = state.getOriginalRecord(); |
| 55 | 52 |
|
| 56 | 53 |
Integer nomTaxId = Integer.valueOf(getValue(record, NOMTAX_ID)); |
| ... | ... | |
| 60 | 57 |
|
| 61 | 58 |
String row = String.valueOf(line) + "("+nomTaxId+"): ";
|
| 62 | 59 |
|
| 63 |
TaxonName name = getName(state, nameLinkID);
|
|
| 60 |
TaxonName name = getName(nameLinkID); |
|
| 64 | 61 |
|
| 65 | 62 |
if (name == null) {
|
| 66 | 63 |
logger.warn(row + "Name does not exist"); |
| ... | ... | |
| 69 | 66 |
|
| 70 | 67 |
Synonym synonym = Synonym.NewInstance(name, getSecRef(state)); |
| 71 | 68 |
|
| 72 |
Taxon taxon = getTaxon(state, taxonLinkId);
|
|
| 69 |
Taxon taxon = getTaxon(taxonLinkId); |
|
| 73 | 70 |
if (taxon == null) {
|
| 74 | 71 |
logger.warn(row + "Taxon does not exist"); |
| 75 | 72 |
return; |
| 76 | 73 |
} |
| 74 |
|
|
| 77 | 75 |
//TODO type (compute homotypics) |
| 76 |
|
|
| 78 | 77 |
taxon.addSynonym(synonym, SynonymType.SYNONYM_OF); |
| 78 |
orphanedNameMap.remove(nameLinkID); |
|
| 79 |
getTaxonService().saveOrUpdate(taxon); //TODO does with work with session handling? I forgot it for the final import |
|
| 79 | 80 |
} |
| 80 | 81 |
|
| 82 |
boolean first = true; |
|
| 81 | 83 |
@Override |
| 82 | 84 |
protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| 85 |
if (first) {
|
|
| 86 |
for (TaxonName taxonName : orphanedNameMap.values()) {
|
|
| 87 |
Taxon taxon = Taxon.NewInstance(taxonName, getSecRef(state)); |
|
| 88 |
TaxonNode node = getUnresolvedNode(state).addChildTaxon(taxon, null); |
|
| 89 |
getTaxonNodeService().saveOrUpdate(node); |
|
| 90 |
} |
|
| 91 |
first = false; |
|
| 92 |
} |
|
| 83 | 93 |
} |
| 84 | 94 |
|
| 85 |
private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
|
|
| 86 |
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
| 87 |
taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon(); |
|
| 95 |
private TaxonNode unresolvedNode; |
|
| 96 |
private TaxonNode getUnresolvedNode(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
|
| 97 |
if (unresolvedNode == null) {
|
|
| 98 |
unresolvedNode = getTaxonNodeService().find(state.getConfig().getUnresolvedNodeUuid()); |
|
| 88 | 99 |
} |
| 89 |
if (basionymTaxon.isInstanceOf(Synonym.class)){
|
|
| 90 |
basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon(); |
|
| 91 |
} |
|
| 92 |
return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon); |
|
| 100 |
return unresolvedNode; |
|
| 93 | 101 |
} |
| 102 |
|
|
| 94 | 103 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeTaxonImport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.caryo; |
| 10 | 10 |
|
| 11 |
import java.util.HashMap; |
|
| 12 |
import java.util.HashSet; |
|
| 13 | 11 |
import java.util.Map; |
| 14 |
import java.util.Set; |
|
| 15 |
import java.util.UUID; |
|
| 16 | 12 |
|
| 17 | 13 |
import org.apache.logging.log4j.LogManager; |
| 18 | 14 |
import org.apache.logging.log4j.Logger; |
| 19 | 15 |
import org.springframework.stereotype.Component; |
| 20 | 16 |
|
| 21 | 17 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| 22 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
| 23 | 18 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
| 24 | 19 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 25 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 26 | 20 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 27 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 28 | 21 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 29 | 22 |
|
| 30 | 23 |
/** |
| ... | ... | |
| 41 | 34 |
private static final String NOMEN_LINK = "nomen_link"; |
| 42 | 35 |
private static final String PARENT = "parent"; |
| 43 | 36 |
|
| 44 |
private Map<String, UUID> taxonMapping = new HashMap<>();
|
|
| 45 |
private Set<String> neglectedRecords = new HashSet<>();
|
|
| 46 |
|
|
| 47 |
private SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state;
|
|
| 37 |
@Override
|
|
| 38 |
protected String getWorksheetName(CaryoSileneaeImportConfigurator config) {
|
|
| 39 |
return "Taxa"; |
|
| 40 |
}
|
|
| 48 | 41 |
|
| 49 | 42 |
@Override |
| 50 | 43 |
protected void firstPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| 51 |
int line = state.getCurrentLine(); |
|
| 52 |
if ((line % 500) == 0){
|
|
| 53 |
newTransaction(state); |
|
| 54 |
System.out.println(line); |
|
| 55 |
} |
|
| 56 |
|
|
| 57 |
this.state = state; |
|
| 58 |
Map<String, String> record = state.getOriginalRecord(); |
|
| 44 |
try {
|
|
| 45 |
int line = state.getCurrentLine(); |
|
| 46 |
// if ((line % 500) == 0){
|
|
| 47 |
// newTransaction(state); |
|
| 48 |
// System.out.println(line); |
|
| 49 |
// } |
|
| 59 | 50 |
|
| 60 |
Integer accTaxonId = Integer.valueOf(getValue(record, ACCEPTED_TAXON_ID)); |
|
| 61 |
Integer nameLinkID = Integer.valueOf(getValue(record, NOMEN_LINK)); |
|
| 51 |
Map<String, String> record = state.getOriginalRecord(); |
|
| 62 | 52 |
|
| 63 |
String row = String.valueOf(line) + "("+accTaxonId+"): ";
|
|
| 53 |
Integer accTaxonId = Integer.valueOf(getValue(record, ACCEPTED_TAXON_ID)); |
|
| 54 |
Integer nameLinkID = Integer.valueOf(getValue(record, NOMEN_LINK)); |
|
| 64 | 55 |
|
| 65 |
TaxonName name = getName(state, nameLinkID);
|
|
| 56 |
String row = String.valueOf(line) + "("+accTaxonId+"): ";
|
|
| 66 | 57 |
|
| 67 |
if (name == null) {
|
|
| 68 |
logger.warn(row + "Name does not exist"); |
|
| 69 |
return; |
|
| 70 |
} |
|
| 58 |
TaxonName name = getName(nameLinkID); |
|
| 59 |
if (name == null) {
|
|
| 60 |
logger.warn(row + "Name does not exist"); |
|
| 61 |
return; |
|
| 62 |
} |
|
| 71 | 63 |
|
| 72 |
Taxon taxon = Taxon.NewInstance(name, getSecRef(state)); |
|
| 64 |
orphanedNameMap.remove(nameLinkID); |
|
| 65 |
Taxon taxon = Taxon.NewInstance(name, getSecRef(state)); |
|
| 73 | 66 |
|
| 74 |
getTaxonService().saveOrUpdate(taxon); |
|
| 67 |
putToTaxonMap(accTaxonId, taxon); |
|
| 68 |
getTaxonService().saveOrUpdate(taxon); |
|
| 69 |
} catch (Exception e) {
|
|
| 70 |
e.printStackTrace(); |
|
| 71 |
} |
|
| 75 | 72 |
} |
| 76 | 73 |
|
| 77 | 74 |
@Override |
| 78 | 75 |
protected void secondPass(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
| 79 |
int line = state.getCurrentLine(); |
|
| 80 |
if ((line % 500) == 0){
|
|
| 81 |
newTransaction(state); |
|
| 82 |
System.out.println(line); |
|
| 83 |
} |
|
| 84 |
|
|
| 85 |
this.state = state; |
|
| 86 |
Map<String, String> record = state.getOriginalRecord(); |
|
| 87 |
|
|
| 88 |
Integer accTaxonId = Integer.valueOf(getValue(record, ACCEPTED_TAXON_ID)); |
|
| 89 |
Integer parentId = Integer.valueOf(getValue(record, PARENT)); |
|
| 90 |
|
|
| 91 |
String row = String.valueOf(line) + "("+accTaxonId+"): ";
|
|
| 92 |
|
|
| 93 |
Taxon taxon = getTaxon(state, accTaxonId); |
|
| 94 |
if (taxon == null) {
|
|
| 95 |
logger.warn(row + "Taxon does not exist"); |
|
| 96 |
return; |
|
| 76 |
try {
|
|
| 77 |
int line = state.getCurrentLine(); |
|
| 78 |
// if ((line % 500) == 0){
|
|
| 79 |
// newTransaction(state); |
|
| 80 |
// System.out.println(line); |
|
| 81 |
// } |
|
| 82 |
|
|
| 83 |
Map<String, String> record = state.getOriginalRecord(); |
|
| 84 |
|
|
| 85 |
Integer accTaxonId = Integer.valueOf(getValue(record, ACCEPTED_TAXON_ID)); |
|
| 86 |
Integer parentId = getInt(getValue(record, PARENT)); |
|
| 87 |
|
|
| 88 |
String row = String.valueOf(line) + "("+accTaxonId+"): ";
|
|
| 89 |
|
|
| 90 |
Taxon taxon = getTaxon(accTaxonId); |
|
| 91 |
if (taxon == null) {
|
|
| 92 |
logger.warn(row + "Taxon does not exist"); |
|
| 93 |
return; |
|
| 94 |
} |
|
| 95 |
|
|
| 96 |
Taxon parent; |
|
| 97 |
if (parentId == null) {
|
|
| 98 |
TaxonNode rootNode = getRootNode(state); |
|
| 99 |
parent = rootNode.getTaxon(); |
|
| 100 |
}else {
|
|
| 101 |
parent = getTaxon(parentId); |
|
| 102 |
|
|
| 103 |
} |
|
| 104 |
if (parent == null) {
|
|
| 105 |
logger.warn(row + "Taxon does not exist"); |
|
| 106 |
return; |
|
| 107 |
} |
|
| 108 |
Classification classification = getClassification(state); |
|
| 109 |
|
|
| 110 |
TaxonNode node = classification.addParentChild(parent, taxon, null, null); |
|
| 111 |
|
|
| 112 |
getTaxonNodeService().saveOrUpdate(node); |
|
| 113 |
} catch (Exception e) {
|
|
| 114 |
e.printStackTrace(); |
|
| 97 | 115 |
} |
| 98 |
|
|
| 99 |
Taxon parent = getTaxon(state, parentId); |
|
| 100 |
if (parent == null) {
|
|
| 101 |
logger.warn(row + "Taxon does not exist"); |
|
| 102 |
return; |
|
| 103 |
} |
|
| 104 |
|
|
| 105 |
Classification classification = getClassification(state); |
|
| 106 |
|
|
| 107 |
//TODO ref needed? |
|
| 108 |
TaxonNode node = classification.addParentChild(parent, taxon, null, null); |
|
| 109 |
|
|
| 110 |
getTaxonNodeService().saveOrUpdate(node); |
|
| 111 |
} |
|
| 112 |
|
|
| 113 |
private Classification getClassification(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state2) {
|
|
| 114 |
// TODO Auto-generated method stub |
|
| 115 |
return null; |
|
| 116 | 116 |
} |
| 117 | 117 |
|
| 118 |
private boolean hasSameAcceptedTaxon(TaxonBase<?> taxonBase, TaxonBase<?> basionymTaxon) {
|
|
| 119 |
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
| 120 |
taxonBase = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon(); |
|
| 121 |
} |
|
| 122 |
if (basionymTaxon.isInstanceOf(Synonym.class)){
|
|
| 123 |
basionymTaxon = CdmBase.deproxy(basionymTaxon, Synonym.class).getAcceptedTaxon(); |
|
| 118 |
private TaxonNode rootNode; |
|
| 119 |
private TaxonNode getRootNode(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
|
| 120 |
if (rootNode == null) {
|
|
| 121 |
rootNode = getTaxonNodeService().find(state.getConfig().getAcceptedNodeUuid()); |
|
| 124 | 122 |
} |
| 125 |
return taxonBase != null && basionymTaxon != null && taxonBase.equals(basionymTaxon); |
|
| 126 |
} |
|
| 127 |
|
|
| 128 |
private TaxonNode getFamily(){
|
|
| 129 |
UUID uuid = UUID.fromString("0334809a-aa20-447d-add9-138194f80f56");
|
|
| 130 |
TaxonNode aizoaceae = getTaxonNodeService().find(uuid); |
|
| 131 |
return aizoaceae; |
|
| 123 |
return rootNode; |
|
| 132 | 124 |
} |
| 133 | 125 |
|
| 134 |
private TaxonNode hybridParent(){
|
|
| 135 |
UUID uuid = UUID.fromString("2fae0fa1-758a-4fcb-bb6c-a2bd11f40641");
|
|
| 136 |
TaxonNode hybridParent = getTaxonNodeService().find(uuid); |
|
| 137 |
return hybridParent; |
|
| 138 |
} |
|
| 139 |
private TaxonNode unresolvedParent(){
|
|
| 140 |
UUID uuid = UUID.fromString("accb1ff6-5748-4b18-b529-9368c331a38d");
|
|
| 141 |
TaxonNode unresolvedParent = getTaxonNodeService().find(uuid); |
|
| 142 |
return unresolvedParent; |
|
| 126 |
private Classification classification; |
|
| 127 |
private Classification getClassification(SimpleExcelTaxonImportState<CaryoSileneaeImportConfigurator> state) {
|
|
| 128 |
if (classification == null) {
|
|
| 129 |
classification = getClassificationService().find(state.getConfig().getClassificationUuid()); |
|
| 130 |
} |
|
| 131 |
return classification; |
|
| 143 | 132 |
} |
| 144 | 133 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/CaryoSileneaeTransformer.java | ||
|---|---|---|
| 1 |
/** |
|
| 2 |
* Copyright (C) 2016 EDIT |
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 |
* http://www.e-taxonomy.eu |
|
| 5 |
* |
|
| 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 8 |
*/ |
|
| 9 |
package eu.etaxonomy.cdm.io.caryo; |
|
| 10 |
|
|
| 11 |
import org.apache.commons.lang3.StringUtils; |
|
| 12 |
import org.apache.logging.log4j.LogManager; |
|
| 13 |
import org.apache.logging.log4j.Logger; |
|
| 14 |
|
|
| 15 |
import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase; |
|
| 16 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
|
| 17 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 18 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 19 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
|
| 20 |
|
|
| 21 |
/** |
|
| 22 |
* @author a.mueller |
|
| 23 |
* @since 16.06.2016 |
|
| 24 |
*/ |
|
| 25 |
public class CaryoSileneaeTransformer extends InputTransformerBase{
|
|
| 26 |
|
|
| 27 |
private static final long serialVersionUID = 4635704148993246218L; |
|
| 28 |
|
|
| 29 |
private static final Logger logger = LogManager.getLogger(); |
|
| 30 |
|
|
| 31 |
@Override |
|
| 32 |
public Rank getRankByKey(String key) throws UndefinedTransformerMethodException {
|
|
| 33 |
if (StringUtils.isBlank(key)){
|
|
| 34 |
return null; |
|
| 35 |
} |
|
| 36 |
try {
|
|
| 37 |
Rank rank = Rank.getRankByIdInVoc(key, NomenclaturalCode.ICNAFP); |
|
| 38 |
return rank; |
|
| 39 |
} catch (UnknownCdmTypeException e) {
|
|
| 40 |
if (key.equals("gen.")) {return Rank.GENUS();
|
|
| 41 |
} else if (key.equals("spec.")) {return Rank.SPECIES();
|
|
| 42 |
} else if (key.equals("unranked")) {return Rank.UNRANKED_INFRAGENERIC();
|
|
| 43 |
} else if (key.equals("[infrasp.unranked]")) {return Rank.UNRANKED_INFRASPECIFIC();
|
|
| 44 |
} else{
|
|
| 45 |
logger.warn("Rank not defined: " + key);
|
|
| 46 |
return null; |
|
| 47 |
} |
|
| 48 |
} |
|
| 49 |
|
|
| 50 |
} |
|
| 51 |
} |
|
Also available in: Unified diff
ref #10242 final version of Sileneae import (before synonym cleanup=