Revision 79276af0
Added by Andreas Müller almost 5 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/app/pesi/PesiExportActivatorERMS.java | ||
|---|---|---|
| 57 | 57 |
boolean doInferredSynonyms = false; //only with doTaxa |
| 58 | 58 |
boolean doRelTaxa = false; |
| 59 | 59 |
boolean doAdditionalTaxonSource = false; |
| 60 |
boolean doDescriptions = false;
|
|
| 61 |
boolean doEcology = true;
|
|
| 60 |
boolean doDescriptions = true;
|
|
| 61 |
boolean doEcologyAndLink = doDescriptions;
|
|
| 62 | 62 |
|
| 63 | 63 |
static boolean doPureNames = false; //ERMS has no pure names |
| 64 | 64 |
|
| ... | ... | |
| 86 | 86 |
config.setDoRelTaxa(doRelTaxa); |
| 87 | 87 |
config.setDoAdditionalTaxonSource(doAdditionalTaxonSource); |
| 88 | 88 |
config.setDoDescription(doDescriptions); |
| 89 |
config.setDoEcology(doEcology);
|
|
| 89 |
config.setDoEcologyAndLink(doEcologyAndLink);
|
|
| 90 | 90 |
|
| 91 | 91 |
// config.setDoOccurrence(doOccurrence); |
| 92 | 92 |
// config.setDoOccurrenceSource(doOccurrenceSource); |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportState.java | ||
|---|---|---|
| 84 | 84 |
* @return |
| 85 | 85 |
* @throws RuntimeException |
| 86 | 86 |
**/ |
| 87 |
public Rank getRank (int rankId, int kingdomId){
|
|
| 87 |
public Rank getRank (int rankId, int kingdomId){
|
|
| 88 | 88 |
Rank result = null; |
| 89 | 89 |
if (this.rankMap == null){
|
| 90 | 90 |
throw new RuntimeException("rank map not initialized");
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumImportState.java | ||
|---|---|---|
| 26 | 26 |
/** |
| 27 | 27 |
* @author a.mueller |
| 28 | 28 |
* @since 11.05.2009 |
| 29 |
* @version 1.0 |
|
| 30 | 29 |
*/ |
| 31 | 30 |
public class IndexFungorumImportState extends DbImportStateBase<IndexFungorumImportConfigurator, IndexFungorumImportState>{
|
| 32 | 31 |
@SuppressWarnings("unused")
|
| 33 | 32 |
private static final Logger logger = Logger.getLogger(IndexFungorumImportState.class); |
| 34 | 33 |
|
| 35 |
Map<String, DefinedTermBase> dbCdmDefTermMap = new HashMap<String, DefinedTermBase>();
|
|
| 34 |
Map<String, DefinedTermBase> dbCdmDefTermMap = new HashMap<>(); |
|
| 36 | 35 |
|
| 37 |
Map<String, User> usernameMap = new HashMap<String, User>();
|
|
| 36 |
Map<String, User> usernameMap = new HashMap<>(); |
|
| 38 | 37 |
|
| 39 | 38 |
private Map<Integer, Map<Integer,Rank>> rankMap; |
| 40 | 39 |
|
| 41 | 40 |
private Map<String, TaxonBase> speciesMap; |
| 42 | 41 |
|
| 43 |
private List<UUID> infraspecificTaxaUUIDs = new ArrayList<UUID>();
|
|
| 42 |
private List<UUID> infraspecificTaxaUUIDs = new ArrayList<>(); |
|
| 44 | 43 |
|
| 45 | 44 |
|
| 46 | 45 |
|
| 47 |
|
|
| 48 |
public List<UUID> getInfraspecificTaxaUUIDs() {
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|
| 49 |
return infraspecificTaxaUUIDs; |
|
| 50 |
} |
|
| 51 |
|
|
| 52 |
|
|
| 53 |
public void setInfraspecificTaxaUUIDs(List<UUID> infraspecificTaxaUUIDs) {
|
|
| 54 |
this.infraspecificTaxaUUIDs = infraspecificTaxaUUIDs; |
|
| 55 |
} |
|
| 56 |
|
|
| 57 |
|
|
| 58 | 46 |
public IndexFungorumImportState(IndexFungorumImportConfigurator config) {
|
| 59 | 47 |
super(config); |
| 60 | 48 |
} |
| 61 | 49 |
|
| 62 |
|
|
| 63 |
/* (non-Javadoc) |
|
| 64 |
* @see eu.etaxonomy.cdm.io.common.IoStateBase#initialize(eu.etaxonomy.cdm.io.common.IoConfiguratorBase) |
|
| 65 |
*/ |
|
| 66 | 50 |
@Override |
| 67 | 51 |
public void initialize(IndexFungorumImportConfigurator config) {
|
| 68 | 52 |
// super(config); |
| 69 | 53 |
} |
| 70 | 54 |
|
| 55 |
public List<UUID> getInfraspecificTaxaUUIDs() {
|
|
| 56 |
return infraspecificTaxaUUIDs; |
|
| 57 |
} |
|
| 58 |
public void setInfraspecificTaxaUUIDs(List<UUID> infraspecificTaxaUUIDs) {
|
|
| 59 |
this.infraspecificTaxaUUIDs = infraspecificTaxaUUIDs; |
|
| 60 |
} |
|
| 71 | 61 |
|
| 72 | 62 |
public Map<String, DefinedTermBase> getDbCdmDefinedTermMap(){
|
| 73 | 63 |
return this.dbCdmDefTermMap; |
| 74 | 64 |
} |
| 75 |
|
|
| 76 | 65 |
public void putDefinedTermToMap(String tableName, String id, DefinedTermBase term){
|
| 77 | 66 |
this.dbCdmDefTermMap.put(tableName + "_" + id, term); |
| 78 | 67 |
} |
| 79 |
|
|
| 80 | 68 |
public void putDefinedTermToMap(String tableName, int id, DefinedTermBase term){
|
| 81 | 69 |
putDefinedTermToMap(tableName, String.valueOf(id), term); |
| 82 | 70 |
} |
| ... | ... | |
| 85 | 73 |
public User getUser(String username){
|
| 86 | 74 |
return usernameMap.get(username); |
| 87 | 75 |
} |
| 88 |
|
|
| 89 | 76 |
@Override |
| 90 | 77 |
public void putUser(String username, User user){
|
| 91 | 78 |
usernameMap.put(username, user); |
| 92 | 79 |
} |
| 93 |
/** |
|
| 94 |
* @return the speciesMap |
|
| 95 |
*/ |
|
| 80 |
|
|
| 96 | 81 |
public Map<String, TaxonBase> getSpeciesMap() {
|
| 97 | 82 |
return speciesMap; |
| 98 | 83 |
} |
| 99 |
|
|
| 100 |
|
|
| 101 |
/** |
|
| 102 |
* @param speciesMap the speciesMap to set |
|
| 103 |
*/ |
|
| 104 | 84 |
public void setSpeciesMap(Map<String, TaxonBase> speciesMap) {
|
| 105 | 85 |
this.speciesMap = speciesMap; |
| 106 | 86 |
} |
| 107 | 87 |
|
| 108 |
/** |
|
| 109 |
* @param rankMap the rankMap to set |
|
| 110 |
*/ |
|
| 111 | 88 |
public void setRankMap(Map<Integer, Map<Integer,Rank>> rankMap) {
|
| 112 | 89 |
this.rankMap = rankMap; |
| 113 | 90 |
} |
| 114 | 91 |
|
| 115 |
// /** |
|
| 116 |
// * @return the rankMap |
|
| 117 |
// */ |
|
| 118 |
// public Map<Integer, Map<Integer,Rank>> getRankMap() {
|
|
| 119 |
// return rankMap; |
|
| 120 |
// } |
|
| 121 |
|
|
| 122 |
|
|
| 123 |
/** |
|
| 124 |
* Returns the CDM rank depending on the ERMS rankId and the ERMS kingdomId. Returns <code> |
|
| 125 |
* null</code> if the rank does not exist. |
|
| 126 |
* Throws a RuntimeException if the rank map has not been initialized before. |
|
| 127 |
* @param rankId |
|
| 128 |
* @param kingdomId |
|
| 129 |
* @return |
|
| 130 |
* @throws RuntimeException |
|
| 131 |
**/ |
|
| 132 |
public Rank getRank (int rankId, int kingdomId){
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|
| 133 |
Rank result = null; |
|
| 134 |
if (this.rankMap == null){
|
|
| 135 |
throw new RuntimeException("rank map not initialized");
|
|
| 136 |
} |
|
| 137 |
if (kingdomId == 147415 && rankId == 10){
|
|
| 138 |
result = Rank.KINGDOM(); |
|
| 139 |
}else{
|
|
| 140 |
Map<Integer, Rank> kingdomMap = rankMap.get(rankId); |
|
| 141 |
if (kingdomMap != null){
|
|
| 142 |
result = kingdomMap.get(kingdomId); |
|
| 143 |
} |
|
| 144 |
} |
|
| 145 |
return result; |
|
| 146 |
} |
|
| 147 |
|
|
| 148 |
|
|
| 149 | 92 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/indexFungorum/IndexFungorumTransformer.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 15 | 15 |
import eu.etaxonomy.cdm.io.common.TdwgAreaProvider; |
| 16 | 16 |
import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase; |
| 17 | 17 |
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException; |
| 18 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
|
| 19 | 18 |
import eu.etaxonomy.cdm.model.location.Country; |
| 20 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
| 19 |
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
| 21 | 20 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 22 | 21 |
|
| 23 | 22 |
/** |
| 24 | 23 |
* @author a.mueller |
| 25 | 24 |
* @since 01.03.2010 |
| 26 |
* @version 1.0 |
|
| 27 | 25 |
*/ |
| 28 | 26 |
public final class IndexFungorumTransformer extends InputTransformerBase {
|
| 29 |
private static final Logger logger = Logger.getLogger(IndexFungorumTransformer.class); |
|
| 30 |
|
|
| 31 |
public static final String LSID_PREFIX = "urn:lsid:indexfungorum.org:names:"; |
|
| 32 | 27 |
|
| 33 |
public static NomenclaturalCode kingdomId2NomCode(Integer kingdomId){
|
|
| 34 |
switch (kingdomId){
|
|
| 35 |
case 1: return null; |
|
| 36 |
case 2: return NomenclaturalCode.ICZN; //Animalia |
|
| 37 |
case 3: return NomenclaturalCode.ICNAFP; //Plantae |
|
| 38 |
case 4: return NomenclaturalCode.ICNAFP; //Fungi |
|
| 39 |
case 5: return NomenclaturalCode.ICZN ; //Protozoa |
|
| 40 |
case 6: return NomenclaturalCode.ICNB ; //Bacteria |
|
| 41 |
case 7: return NomenclaturalCode.ICNAFP; //Chromista |
|
| 42 |
case 147415: return NomenclaturalCode.ICNB; //Monera |
|
| 43 |
default: return null; |
|
| 44 |
|
|
| 45 |
} |
|
| 46 |
} |
|
| 28 |
private static final long serialVersionUID = 7930365658820136180L; |
|
| 29 |
private static final Logger logger = Logger.getLogger(IndexFungorumTransformer.class); |
|
| 47 | 30 |
|
| 31 |
public static final String LSID_PREFIX = "urn:lsid:indexfungorum.org:names:"; |
|
| 48 | 32 |
|
| 49 | 33 |
|
| 50 | 34 |
@Override |
| ... | ... | |
| 66 | 50 |
logger.warn("Unhandled rank: " + rankFk);
|
| 67 | 51 |
return null; |
| 68 | 52 |
} |
| 69 |
|
|
| 70 | 53 |
} |
| 71 | 54 |
|
| 72 | 55 |
|
| 73 |
|
|
| 74 |
/* (non-Javadoc) |
|
| 75 |
* @see eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase#getNamedAreaByKey(java.lang.String) |
|
| 76 |
*/ |
|
| 77 | 56 |
@Override |
| 78 | 57 |
public NamedArea getNamedAreaByKey(String key) throws UndefinedTransformerMethodException {
|
| 79 | 58 |
if (StringUtils.isBlank(key)){
|
| ... | ... | |
| 101 | 80 |
}else if (key.equalsIgnoreCase("SE")){return TdwgAreaProvider.getAreaByTdwgAbbreviation("SWE-OO");
|
| 102 | 81 |
}else if (key.equalsIgnoreCase("AM")){return TdwgAreaProvider.getAreaByTdwgAbbreviation("TCS-AR");
|
| 103 | 82 |
}else if (key.equalsIgnoreCase("IL")){return TdwgAreaProvider.getAreaByTdwgAbbreviation("PAL-IS");
|
| 104 |
|
|
| 83 |
|
|
| 105 | 84 |
}else if (key.equalsIgnoreCase("UK")){return Country.UNITEDKINGDOMOFGREATBRITAINANDNORTHERNIRELAND();
|
| 106 | 85 |
}else if (key.equalsIgnoreCase("DK")){return Country.DENMARKKINGDOMOF();
|
| 107 | 86 |
}else if (key.equalsIgnoreCase("GR")){return Country.GREECEHELLENICREPUBLIC();
|
| ... | ... | |
| 111 | 90 |
}else if (key.equalsIgnoreCase("UA")){return Country.UKRAINE();
|
| 112 | 91 |
}else if (key.equalsIgnoreCase("GE")){return Country.GEORGIA();
|
| 113 | 92 |
}else if (key.equalsIgnoreCase("TR")){return Country.TURKEYREPUBLICOF();
|
| 114 |
|
|
| 115 |
|
|
| 93 |
|
|
| 116 | 94 |
} else {
|
| 117 | 95 |
logger.warn("Area not yet mapped: " + key);
|
| 118 | 96 |
return null; |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiAdditionalSourceExport.java | ||
|---|---|---|
| 90 | 90 |
} |
| 91 | 91 |
|
| 92 | 92 |
//PHASE 01: Sources |
| 93 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping) throws SQLException {
|
|
| 93 |
private boolean doPhase01(PesiExportState state, PesiExportMapping mapping) {
|
|
| 94 | 94 |
|
| 95 | 95 |
// System.out.println("PHASE 1 of description import");
|
| 96 | 96 |
logger.info("PHASE 1...");
|
| ... | ... | |
| 100 | 100 |
//int limit = state.getConfig().getLimitSave(); |
| 101 | 101 |
int limit = 1000; |
| 102 | 102 |
|
| 103 |
List<TaxonBase> taxonList = null; |
|
| 103 |
@SuppressWarnings("rawtypes")
|
|
| 104 |
List<TaxonBase> taxonList = null; |
|
| 104 | 105 |
|
| 105 | 106 |
TransactionStatus txStatus = startTransaction(true); |
| 106 | 107 |
|
| 107 | 108 |
if (logger.isDebugEnabled()){
|
| 108 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 109 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " (max: " + limit + ") ...");
|
|
| 109 | 110 |
logger.debug("Start snapshot, before starting loop");
|
| 110 | 111 |
ProfilerController.memorySnapshot(); |
| 111 | 112 |
} |
| ... | ... | |
| 115 | 116 |
while ((taxonList = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, propPath )) != null ) {
|
| 116 | 117 |
|
| 117 | 118 |
if (logger.isDebugEnabled()) {
|
| 118 |
logger.info("Fetched " + taxonList.size() + " " + pluralString + ". Exporting...");
|
|
| 119 |
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
| 119 | 120 |
} |
| 120 | 121 |
|
| 121 |
for (TaxonBase taxon : taxonList) {
|
|
| 122 |
for (TaxonBase<?> taxon : taxonList) {
|
|
| 122 | 123 |
countTaxa++; |
| 123 |
doCount(count++, modCount, pluralString); |
|
| 124 |
doCount(count++, modCount, parentPluralString);
|
|
| 124 | 125 |
state.setCurrentTaxon(taxon); |
| 125 | 126 |
if (!taxon.getSources().isEmpty()){
|
| 126 | 127 |
success &= handleSingleTaxon(taxon, mapping); |
| ... | ... | |
| 131 | 132 |
|
| 132 | 133 |
// Commit transaction |
| 133 | 134 |
commitTransaction(txStatus); |
| 134 |
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total taxa: " + count + ". Total sources " + countSources);
|
|
| 135 |
logger.info("Exported " + (count - pastCount) + " " + parentPluralString + ". Total taxa: " + count + ". Total sources " + countSources);
|
|
| 135 | 136 |
pastCount = count; |
| 136 | 137 |
if (logger.isDebugEnabled()) {
|
| 137 | 138 |
ProfilerController.memorySnapshot(); |
| ... | ... | |
| 139 | 140 |
// Start transaction |
| 140 | 141 |
txStatus = startTransaction(true); |
| 141 | 142 |
if(logger.isDebugEnabled()) {
|
| 142 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") for description import ...");
|
|
| 143 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " (max: " + limit + ") for description import ...");
|
|
| 143 | 144 |
} |
| 144 | 145 |
} |
| 145 | 146 |
|
| ... | ... | |
| 150 | 151 |
return success; |
| 151 | 152 |
} |
| 152 | 153 |
|
| 153 |
private boolean handleSingleTaxon(TaxonBase<?> taxon, PesiExportMapping mapping) throws SQLException {
|
|
| 154 |
private boolean handleSingleTaxon(TaxonBase<?> taxon, PesiExportMapping mapping) {
|
|
| 154 | 155 |
|
| 155 | 156 |
boolean success = true; |
| 156 | 157 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiDescriptionExport.java | ||
|---|---|---|
| 75 | 75 |
* <li>Phase 2: Export of TaxonName extensions <code>taxComment</code>, <code>fauComment</code> and <code>fauExtraCodes</code> as Notes.</ul> |
| 76 | 76 |
* @author e.-m.lee |
| 77 | 77 |
* @since 23.02.2010 |
| 78 |
* @author a.mueller |
|
| 78 | 79 |
*/ |
| 79 | 80 |
@Component |
| 80 | 81 |
public class PesiDescriptionExport extends PesiExportBase {
|
| ... | ... | |
| 90 | 91 |
private static final String dbVernacularTableName = "CommonName"; |
| 91 | 92 |
private static final String dbImageTableName = "Image"; |
| 92 | 93 |
private static final String dbAdditionalSourceTableName = "AdditionalTaxonSource"; |
| 93 |
private static final String pluralString = "attached infos";
|
|
| 94 |
private static final String pluralString = "descriptions";
|
|
| 94 | 95 |
private static final String parentPluralString = "Taxa"; |
| 95 | 96 |
|
| 96 | 97 |
//decide where to handle them best (configurator, transformer, single method, ...) |
| ... | ... | |
| 190 | 191 |
TransactionStatus txStatus = startTransaction(true); |
| 191 | 192 |
|
| 192 | 193 |
if (logger.isDebugEnabled()){
|
| 193 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
|
|
| 194 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " (max: " + limit + ") ...");
|
|
| 194 | 195 |
logger.debug("Start snapshot, before starting loop");
|
| 195 | 196 |
ProfilerController.memorySnapshot(); |
| 196 | 197 |
} |
| ... | ... | |
| 200 | 201 |
while ((taxonList = getNextTaxonPartition(Taxon.class, limit, partitionCount++, propPath )) != null ) {
|
| 201 | 202 |
|
| 202 | 203 |
if (logger.isDebugEnabled()) {
|
| 203 |
logger.info("Fetched " + taxonList.size() + " " + pluralString + ". Exporting...");
|
|
| 204 |
logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
|
|
| 204 | 205 |
} |
| 205 | 206 |
|
| 206 | 207 |
for (Taxon taxon : taxonList) {
|
| 207 | 208 |
countTaxa++; |
| 208 |
doCount(count++, modCount, pluralString); |
|
| 209 |
doCount(count++, modCount, parentPluralString);
|
|
| 209 | 210 |
state.setCurrentTaxon(taxon); |
| 210 | 211 |
if (!taxon.getDescriptions().isEmpty()){
|
| 211 | 212 |
success &= handleSingleTaxon(taxon, state, notesMapping, occurrenceMapping, addSourceSourceMapping, |
| ... | ... | |
| 217 | 218 |
|
| 218 | 219 |
// Commit transaction |
| 219 | 220 |
commitTransaction(txStatus); |
| 220 |
logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count + " (Phase 01)");
|
|
| 221 |
logger.info("Exported " + (count - pastCount) + " " + parentPluralString + ". Total: " + count + " (Phase 01)");
|
|
| 221 | 222 |
pastCount = count; |
| 222 | 223 |
ProfilerController.memorySnapshot(); |
| 223 | 224 |
// Start transaction |
| 224 | 225 |
txStatus = startTransaction(true); |
| 225 | 226 |
if(logger.isDebugEnabled()) {
|
| 226 |
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") for description import ...");
|
|
| 227 |
logger.info("Started new transaction. Fetching some " + parentPluralString + " (max: " + limit + ") for description import ...");
|
|
| 227 | 228 |
} |
| 228 | 229 |
} |
| 229 | 230 |
|
| 230 |
logger.info("No " + pluralString + " left to fetch.");
|
|
| 231 |
logger.info("No " + parentPluralString + " left to fetch.");
|
|
| 231 | 232 |
logger.info("Partition: " + partitionCount);
|
| 232 | 233 |
logger.info("Taxa: " + countTaxa);
|
| 233 | 234 |
logger.info("Desc: " + countDescriptions);
|
| ... | ... | |
| 304 | 305 |
logger.info("Started new transaction. Fetching some name descriptions (max: " + limit + ") for description import ...");
|
| 305 | 306 |
} |
| 306 | 307 |
|
| 307 |
logger.info("No " + pluralString + " left to fetch.");
|
|
| 308 |
logger.info("No " + parentPluralString + " left to fetch.");
|
|
| 308 | 309 |
logger.info("Partition: " + partitionCount);
|
| 309 | 310 |
logger.info("Taxa: " + countTaxa);
|
| 310 | 311 |
logger.info("Desc: " + countDescriptions);
|
| ... | ... | |
| 551 | 552 |
} |
| 552 | 553 |
} |
| 553 | 554 |
|
| 554 |
doCount(count++, modCount, pluralString); |
|
| 555 |
doCount(count++, modCount, parentPluralString);
|
|
| 555 | 556 |
} |
| 556 | 557 |
|
| 557 | 558 |
// Commit transaction |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiEcologyAndLinkExport.java | ||
|---|---|---|
| 340 | 340 |
|
| 341 | 341 |
@Override |
| 342 | 342 |
protected boolean isIgnore(PesiExportState state) {
|
| 343 |
return ! state.getConfig().isDoEcology(); |
|
| 343 |
return ! state.getConfig().isDoEcologyAndLink();
|
|
| 344 | 344 |
} |
| 345 | 345 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportConfigurator.java | ||
|---|---|---|
| 46 | 46 |
private boolean doInferredSynonyms = true; |
| 47 | 47 |
private boolean doPureNames = true; |
| 48 | 48 |
private boolean doDescription = true; |
| 49 |
private boolean doEcology = true; |
|
| 49 |
private boolean doEcologyAndLink = true;
|
|
| 50 | 50 |
|
| 51 | 51 |
private int nameIdStart = 10000000; |
| 52 | 52 |
|
| ... | ... | |
| 211 | 211 |
this.doParentAndBiota = doParentAndBiota; |
| 212 | 212 |
} |
| 213 | 213 |
|
| 214 |
public boolean isDoEcology() {
|
|
| 215 |
return doEcology; |
|
| 214 |
public boolean isDoEcologyAndLink() {
|
|
| 215 |
return doEcologyAndLink;
|
|
| 216 | 216 |
} |
| 217 |
public void setDoEcology(boolean doEcology) {
|
|
| 218 |
this.doEcology = doEcology;
|
|
| 217 |
public void setDoEcologyAndLink(boolean doEcologyAndLink) {
|
|
| 218 |
this.doEcologyAndLink = doEcologyAndLink;
|
|
| 219 | 219 |
} |
| 220 | 220 |
|
| 221 | 221 |
} |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 2456 | 2456 |
//experts |
| 2457 | 2457 |
ExtensionType extensionTypeSpeciesExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtSpeciesExpertName); |
| 2458 | 2458 |
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName")); |
| 2459 |
|
|
| 2459 | 2460 |
ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.uuidExtExpertName); |
| 2460 | 2461 |
mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName")); |
| 2461 | 2462 |
|
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
|---|---|---|
| 102 | 102 |
public static final UUID uuidExtTaxComment = UUID.fromString("8041a752-0479-4626-ab1b-b266b751f816");
|
| 103 | 103 |
public static final UUID uuidExtFauComment = UUID.fromString("054f773a-41c8-4ad5-83e3-981320c1c126");
|
| 104 | 104 |
public static final UUID uuidExtFauExtraCodes = UUID.fromString("b8c7e77d-9869-4787-bed6-b4b302dbc5f5");
|
| 105 |
|
|
| 105 |
|
|
| 106 | 106 |
// References |
| 107 | 107 |
public static int REF_ARTICLE_IN_PERIODICAL = 1; |
| 108 | 108 |
public static int REF_PART_OF_OTHER = 2; |
| ... | ... | |
| 912 | 912 |
return result; |
| 913 | 913 |
} |
| 914 | 914 |
|
| 915 |
|
|
| 916 | 915 |
/** |
| 917 | 916 |
* Returns the OccurrenceStatusId for a given PresenceAbsenceTerm. |
| 918 | 917 |
* @param term |
| ... | ... | |
| 959 | 958 |
return result; |
| 960 | 959 |
} |
| 961 | 960 |
|
| 962 |
|
|
| 963 | 961 |
@Override |
| 964 | 962 |
public String getCacheByPresenceAbsenceTerm(PresenceAbsenceTerm status) throws UndefinedTransformerMethodException {
|
| 965 | 963 |
if (status == null){
|
| ... | ... | |
| 974 | 972 |
return presenceAbsenceTerm2OccurrenceStatusId(status); |
| 975 | 973 |
} |
| 976 | 974 |
|
| 977 |
|
|
| 978 |
|
|
| 979 | 975 |
@Override |
| 980 | 976 |
public String getCacheByNamedArea(NamedArea namedArea) throws UndefinedTransformerMethodException {
|
| 981 | 977 |
NamedArea area = CdmBase.deproxy(namedArea, NamedArea.class); |
| ... | ... | |
| 986 | 982 |
} |
| 987 | 983 |
} |
| 988 | 984 |
|
| 989 |
|
|
| 990 | 985 |
@Override |
| 991 | 986 |
public Object getKeyByNamedArea(NamedArea area) throws UndefinedTransformerMethodException {
|
| 992 | 987 |
NamedArea namedArea = CdmBase.deproxy(area, NamedArea.class); |
| ... | ... | |
| 1572 | 1567 |
} else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureConservationStatus)){
|
| 1573 | 1568 |
return NoteCategory_Conservation_Status; |
| 1574 | 1569 |
|
| 1575 |
|
|
| 1576 | 1570 |
//E+M |
| 1577 | 1571 |
} else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureDistrEM)){
|
| 1578 | 1572 |
return NoteCategory_general_distribution_euromed; |
| ... | ... | |
| 1960 | 1954 |
logger.warn("Name Type Designation Status not yet supported in PESI: "+ nameTypeDesignationStatus.getLabel());
|
| 1961 | 1955 |
return null; |
| 1962 | 1956 |
} |
| 1963 |
|
|
| 1964 | 1957 |
} |
| 1965 | 1958 |
|
| 1966 | 1959 |
/** |
| ... | ... | |
| 2108 | 2101 |
} |
| 2109 | 2102 |
} |
| 2110 | 2103 |
|
| 2111 |
/** |
|
| 2112 |
* |
|
| 2113 |
* @param status |
|
| 2114 |
* @return |
|
| 2115 |
*/ |
|
| 2116 | 2104 |
@Override |
| 2117 | 2105 |
public String getCacheByNomStatus(NomenclaturalStatusType status) {
|
| 2118 | 2106 |
if (status == null){
|
| ... | ... | |
| 2294 | 2282 |
return null; |
| 2295 | 2283 |
} |
| 2296 | 2284 |
/** |
| 2285 |
* FIXME still needed? |
|
| 2297 | 2286 |
* Returns the RelTaxonQualifierFk for a TaxonRelation. |
| 2298 | 2287 |
* @param relation |
| 2299 | 2288 |
* @return |
Also available in: Unified diff
cleanup