import java.sql.PreparedStatement;\r
import java.sql.ResultSet;\r
import java.sql.SQLException;\r
+import java.sql.Types;\r
import java.util.ArrayList;\r
+import java.util.BitSet;\r
import java.util.HashMap;\r
import java.util.HashSet;\r
import java.util.List;\r
import org.springframework.transaction.TransactionStatus;\r
\r
import eu.etaxonomy.cdm.api.service.TaxonServiceImpl;\r
-import eu.etaxonomy.cdm.app.pesi.ErmsActivator;\r
-import eu.etaxonomy.cdm.app.pesi.EuroMedActivator;\r
-import eu.etaxonomy.cdm.app.pesi.FaunaEuropaeaActivator;\r
import eu.etaxonomy.cdm.common.CdmUtils;\r
import eu.etaxonomy.cdm.io.common.Source;\r
+import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;\r
+import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper;\r
import eu.etaxonomy.cdm.io.common.mapping.out.DbExtensionMapper;\r
+import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;\r
import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;\r
import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper;\r
import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper;\r
import eu.etaxonomy.cdm.model.name.Rank;\r
import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
import eu.etaxonomy.cdm.model.name.ZoologicalName;\r
+import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;\r
import eu.etaxonomy.cdm.model.reference.Reference;\r
import eu.etaxonomy.cdm.model.taxon.Classification;\r
import eu.etaxonomy.cdm.model.taxon.Synonym;\r
import eu.etaxonomy.cdm.model.taxon.TaxonNode;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;\r
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
-import eu.etaxonomy.cdm.persistence.query.MatchMode;\r
import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;\r
import eu.etaxonomy.cdm.strategy.cache.TagEnum;\r
-import eu.etaxonomy.cdm.strategy.cache.TaggedText;\r
import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;\r
import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;\r
import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;\r
-import eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy;\r
import eu.etaxonomy.cdm.strategy.cache.name.ZooNameNoMarkerCacheStrategy;\r
\r
/**\r
private static ExtensionType expertNameExtensionType;\r
private static ExtensionType speciesExpertNameExtensionType;\r
private static ExtensionType cacheCitationExtensionType;\r
- private static ExtensionType expertUserIdExtensionType;\r
- private static ExtensionType speciesExpertUserIdExtensionType;\r
- private static NonViralNameDefaultCacheStrategy zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();\r
- private static NonViralNameDefaultCacheStrategy botanicalNameStrategy = BotanicNameDefaultCacheStrategy.NewInstance();\r
+ private static NonViralNameDefaultCacheStrategy<?> zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();\r
+ private static NonViralNameDefaultCacheStrategy<?> botanicalNameStrategy = BotanicNameDefaultCacheStrategy.NewInstance();\r
\r
\r
/**\r
expertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.expertNameUuid);\r
speciesExpertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertNameUuid);\r
cacheCitationExtensionType = (ExtensionType)getTermService().find(PesiTransformer.cacheCitationUuid);\r
- expertUserIdExtensionType = (ExtensionType)getTermService().find(PesiTransformer.expertUserIdUuid);\r
- speciesExpertUserIdExtensionType = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertUserIdUuid);\r
-\r
-\r
\r
//Export Taxa..\r
success &= doPhase01(state, mapping);\r
\r
// 2nd Round: Add ParentTaxonFk, TreeIndex to each Taxon\r
success &= doPhase02(state);\r
-\r
- //PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...\r
+ \r
+ //PHASE 3: Add Rank data, KingdomFk, TypeNameFk ...\r
success &= doPhase03(state);\r
\r
+ \r
//"PHASE 4: Creating Inferred Synonyms...\r
success &= doPhase04(state, mapping);\r
\r
+ //updates to TaxonStatus and others\r
+ success &= doPhaseUpdates(state);\r
+\r
\r
logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success));\r
\r
}\r
}\r
\r
+ //TODO check if this can all be done by getTaxonStatus\r
+ private boolean doPhaseUpdates(PesiExportState state) {\r
+ \r
+ \r
+ String oldStatusFilter = "= 7 "; //"= '" + PesiTransformer.T_STATUS_STR_UNACCEPTED + "' ";\r
+ String emStr = PesiTransformer.SOURCE_STR_EM;\r
+ String feStr = PesiTransformer.SOURCE_STR_FE;\r
+ String ifStr = PesiTransformer.SOURCE_STR_IF;\r
+ \r
+ //NOT ACCEPTED names\r
+ String updateNotAccepted = " UPDATE Taxon SET TaxonStatusFk = %d, TaxonStatusCache = '%s' " +\r
+ " WHERE OriginalDB = '%s' AND taxonstatusfk = 1 AND ParentTaxonFk %s AND RankFk > 180 ";\r
+ updateNotAccepted = String.format(updateNotAccepted, 8, "NOT ACCEPTED: TAXONOMICALLY VALUELESS LOCAL OR SINGULAR BIOTYPE", emStr, oldStatusFilter);\r
+ int updated = state.getConfig().getDestination().update(updateNotAccepted);\r
+ \r
+ //alternative names\r
+ String updateAlternativeName = "UPDATE Taxon SET TaxonStatusFk = 1, TaxonStatusCache = 'accepted' " + \r
+ " FROM RelTaxon RIGHT OUTER JOIN Taxon ON RelTaxon.TaxonFk1 = Taxon.TaxonId " +\r
+ " WHERE (RelTaxon.RelTaxonQualifierFk = 17) AND (Taxon.TaxonStatusFk %s) ";\r
+ updateAlternativeName = String.format(updateAlternativeName, oldStatusFilter);\r
+ updated = state.getConfig().getDestination().update(updateAlternativeName);\r
+ \r
+ String updateSynonyms = " UPDATE Taxon SET TaxonStatusFk = 2, TaxonStatusCache = 'synonym' " + \r
+ " FROM RelTaxon RIGHT OUTER JOIN Taxon ON RelTaxon.TaxonFk1 = Taxon.TaxonId " + \r
+ " WHERE (RelTaxon.RelTaxonQualifierFk in (1, 3)) AND (Taxon.TaxonStatusFk %S)";\r
+ updateSynonyms = String.format(updateSynonyms, oldStatusFilter);\r
+ updated = state.getConfig().getDestination().update(updateSynonyms);\r
+ \r
+ // cache citation - check if this can't be done in getCacheCitation\r
+ // cache citation - FE\r
+// String updateCacheCitationFE = " UPDATE Taxon " +\r
+// " SET CacheCitation = IsNull(SpeciesExpertName + '. ', '') + WebShowName + '. Accessed through: Fauna Europaea at http://www.faunaeur.org/full_results.php?id=' + cast(TempFE_Id as varchar) " +\r
+// " WHERE OriginalDb = '%s'";\r
+// updateCacheCitationFE = String.format(updateCacheCitationFE, feStr);\r
+// updated = state.getConfig().getDestination().update(updateCacheCitationFE);\r
+ \r
+ // cache citation - EM\r
+ String updateCacheCitationEM = " UPDATE Taxon " +\r
+ " SET CacheCitation = SpeciesExpertName + ' ' + WebShowName + '. Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=' + GUID " +\r
+ " WHERE OriginalDb = '%s'";\r
+ updateCacheCitationEM = String.format(updateCacheCitationEM, emStr);\r
+ updated = state.getConfig().getDestination().update(updateCacheCitationEM);\r
+ \r
+ // cache citation - IF\r
+// String updateCacheCitationIF = " UPDATE Taxon " +\r
+// " SET CacheCitation = IsNull(SpeciesExpertName + ' ', '') + WebShowName + '. Accessed through: Index Fungorum at http://www.indexfungorum.org/names/NamesRecord.asp?RecordID=' + cast(TempIF_Id as varchar) " +\r
+// " WHERE OriginalDb = '%s'";\r
+// updateCacheCitationIF = String.format(updateCacheCitationIF, ifStr);\r
+// updated = state.getConfig().getDestination().update(updateCacheCitationIF);\r
+ \r
+ return true;\r
+ }\r
+\r
private void initPreparedStatements(PesiExportState state) throws SQLException {\r
initTreeIndexStatement(state);\r
initRankExpertsUpdateStmt(state);\r
\r
\r
int partitionCount = 0;\r
- while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)).size() > 0 ) {\r
+ while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)) != null ) {\r
\r
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");\r
for (TaxonBase<?> taxon : list) {\r
txStatus = startTransaction(true);\r
logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
}\r
- if (list.size() == 0) {\r
+ if (list == null ) {\r
logger.info("No " + pluralString + " left to fetch.");\r
}\r
// Commit transaction\r
ancestorLevel = 1;\r
}\r
if (ancestorLevel > 0) {\r
- if (ancestorOfSpecificRank(taxon, ancestorLevel, Rank.SUBGENUS())) {\r
+ if (validateAncestorOfSpecificRank(taxon, ancestorLevel, Rank.SUBGENUS())) {\r
// The child (species or subspecies) of this parent (subgenus) has to have an infraGenericEpithet\r
if (infraGenericEpithet == null) {\r
logger.warn("InfraGenericEpithet does not exist even though it should for: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");\r
\r
\r
\r
- commitTransaction(txStatus);\r
- logger.debug("Committed transaction.");\r
+ try {\r
+ commitTransaction(txStatus);\r
+ logger.debug("Committed transaction.");\r
+ } catch (Exception e) {\r
+ logger.error(e.getMessage());\r
+ e.printStackTrace();\r
+ }\r
\r
}\r
}\r
TransactionStatus txStatus = startTransaction(true);\r
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
int partitionCount = 0;\r
- while ((list = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, null)).size() > 0) {\r
+ while ((list = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, null)) != null) {\r
\r
logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");\r
for (TaxonBase<?> taxon : list) {\r
TaxonNameBase<?,?> taxonName = taxon.getName();\r
// Determine expertFk\r
- Integer expertFk = makeExpertFk(state, taxonName);\r
-\r
- // Determine speciesExpertFk\r
- Integer speciesExpertFk = makeSpeciesExpertFk(state, taxonName);\r
+// Integer expertFk = makeExpertFk(state, taxonName);\r
+//\r
+// // Determine speciesExpertFk\r
+// Integer speciesExpertFk = makeSpeciesExpertFk(state, taxonName);\r
\r
doCount(count++, modCount, pluralString);\r
Integer typeNameFk = getTypeNameFk(taxonName, state);\r
//TODO why are expertFks needed? (Andreas M.)\r
// if (expertFk != null || speciesExpertFk != null) {\r
invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomenclaturalCode, state.getDbId(taxon), \r
- typeNameFk, kingdomFk, expertFk, speciesExpertFk);\r
+ typeNameFk, kingdomFk);\r
// }\r
}\r
\r
txStatus = startTransaction(true);\r
logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
}\r
- if (list.size() == 0) {\r
+ if (list == null) {\r
logger.info("No " + pluralString + " left to fetch.");\r
}\r
// Commit transaction\r
logger.debug("Committed transaction.");\r
return success;\r
}\r
-\r
- private Integer makeSpeciesExpertFk(PesiExportState state, TaxonNameBase<?, ?> taxonName) {\r
- List<Reference> referenceList;\r
- Integer speciesExpertFk = null;\r
- String speciesExpertUserId = getSpeciesExpertUserId(taxonName);\r
- if (speciesExpertUserId != null) {\r
- \r
- // The speciesExpertUserId was stored in the field 'title' of the corresponding Reference during FaEu import\r
- referenceList = getReferenceService().listByReferenceTitle(null, speciesExpertUserId, MatchMode.EXACT, null, null, null, null, null);\r
- if (referenceList.size() == 1) {\r
- speciesExpertFk = getSpeciesExpertFk(referenceList.iterator().next(), state);\r
- } else if (referenceList.size() > 1) {\r
- logger.error("Found more than one match using listByTitle() searching for a Reference with this speciesExpertUserId as title: " + speciesExpertUserId);\r
- } else if (referenceList.size() == 0) {\r
- logger.error("Found no match using listByReferenceTitle() searching for a Reference with this speciesExpertUserId as title: " + speciesExpertUserId);\r
- }\r
- } else {\r
- logger.debug("SpeciesExpertName is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
- }\r
- return speciesExpertFk;\r
- }\r
-\r
- private Integer makeExpertFk(PesiExportState state,\r
- TaxonNameBase<?, ?> taxonName) {\r
- List<Reference> referenceList;\r
- Integer expertFk = null;\r
- String expertUserId = getExpertUserId(taxonName);\r
- if (expertUserId != null) {\r
-\r
- // The expertUserId was stored in the field 'title' of the corresponding Reference during FaEu import\r
- referenceList = getReferenceService().listByReferenceTitle(null, expertUserId, MatchMode.EXACT, null, null, null, null, null);\r
- if (referenceList.size() == 1) {\r
- expertFk = getExpertFk(referenceList.iterator().next(), state);\r
- } else if (referenceList.size() > 1) {\r
- logger.error("Found more than one match using listByReferenceTitle() searching for a Reference with this expertUserId as title: " + expertUserId);\r
- } else if (referenceList.size() == 0) {\r
- logger.error("Found no match using listByReferenceTitle() searching for a Reference with this expertUserId as title: " + expertUserId);\r
- }\r
- } else {\r
- logger.debug("ExpertName is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
- }\r
- return expertFk;\r
- }\r
\r
// "PHASE 4: Creating Inferred Synonyms..."\r
private boolean doPhase04(PesiExportState state, PesiExportMapping mapping) throws SQLException {\r
}\r
\r
try {\r
- PesiExportMapping mapping = getNameMapping();\r
+ PesiExportMapping mapping = getPureNameMapping();\r
mapping.initialize(state);\r
int count = 0;\r
int pastCount = 0;\r
while ((list = getNextPureNamePartition(null, limit, partitionCount++)) != null ) {\r
\r
logger.info("Fetched " + list.size() + " names without taxa. Exporting...");\r
- for (NonViralName<?> taxonName : list) {\r
+ for (TaxonNameBase taxonName : list) {\r
doCount(count++, modCount, pluralString);\r
success &= mapping.invoke(taxonName);\r
}\r
}\r
return result;\r
}\r
-\r
- /**\r
- * Returns the userId of the expert associated with the given TaxonName.\r
- * @param taxonName A {@link TaxonNameBase TaxonName}.\r
- * @return The userId.\r
- */\r
- private String getExpertUserId(TaxonNameBase<?,?> taxonName) {\r
- String result = null;\r
- try {\r
- Set<Extension> extensions = taxonName.getExtensions();\r
- for (Extension extension : extensions) {\r
- if (extension.getType().equals(expertUserIdExtensionType)) {\r
- result = extension.getValue();\r
- }\r
- }\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- return result;\r
- }\r
-\r
- /**\r
- * Returns the userId of the speciesExpert associated with the given TaxonName.\r
- * @param taxonName A {@link TaxonNameBase TaxonName}.\r
- * @return The userId.\r
- */\r
- private String getSpeciesExpertUserId(TaxonNameBase<?,?> taxonName) {\r
- String result = null;\r
- try {\r
- Set<Extension> extensions = taxonName.getExtensions();\r
- for (Extension extension : extensions) {\r
- if (extension.getType().equals(speciesExpertUserIdExtensionType)) {\r
- result = extension.getValue();\r
- }\r
- }\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- return result;\r
- }\r
\r
/**\r
* Checks whether a parent at specific level has a specific Rank.\r
* @param ancestorRank The ancestor rank.\r
* @return Whether a parent at a specific level has a specific Rank.\r
*/\r
- private boolean ancestorOfSpecificRank(TaxonBase<?> taxonBase, int level, Rank ancestorRank) {\r
+ private boolean validateAncestorOfSpecificRank(TaxonBase<?> taxonBase, int level, Rank ancestorRank) {\r
boolean result = false;\r
TaxonNode parentNode = null;\r
if (taxonBase.isInstanceOf(Taxon.class)){\r
* @return Whether save was successful or not.\r
*/\r
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode, \r
- Integer taxonFk, Integer typeNameFk, Integer kingdomFk,\r
- Integer expertFk, Integer speciesExpertFk) {\r
+ Integer taxonFk, Integer typeNameFk, Integer kingdomFkk) {\r
try {\r
int index = 1;\r
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);\r
return ! state.getConfig().isDoTaxa();\r
}\r
\r
+ \r
+ /**\r
+ * Creates the kingdom fk.\r
+ * @param taxonName\r
+ * @return\r
+ */\r
+ @SuppressWarnings("unused") //used by mapper\r
+ private static Integer getKingdomFk(TaxonNameBase taxonName){\r
+ return PesiTransformer.nomenClaturalCode2Kingdom(taxonName.getNomenclaturalCode());\r
+ }\r
+ \r
+ /**\r
+ * Creates the parent fk.\r
+ * @param taxonName\r
+ * @return\r
+ */\r
+ @SuppressWarnings("unused") //used by mapper\r
+ private static Integer getParentTaxonFk(TaxonBase<?> taxonBase, PesiExportState state){\r
+ if (taxonBase.isInstanceOf(Taxon.class)){\r
+ Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);\r
+ if (! isMisappliedName(taxon)){\r
+ Set<TaxonNode> nodes = taxon.getTaxonNodes();\r
+ if (nodes.size() == 0){\r
+ if (taxon.getName().getRank().isLower(Rank.KINGDOM())){\r
+ logger.warn("Accepted taxon has no parent. " + taxon.getTitleCache() + ", " + taxon.getUuid());\r
+ }\r
+ }else if (nodes.size() > 1){\r
+ logger.warn("Taxon has more than 1 node attached. This is not supported by PESI export." + taxon.getTitleCache() + ", " + taxon.getUuid());\r
+ }else{\r
+ Taxon parent =nodes.iterator().next().getParent().getTaxon();\r
+ return state.getDbId(parent);\r
+ }\r
+ }\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Returns the rankFk for the taxon name based on the names nomenclatural code.\r
+ * You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.\r
+ * @param taxonName\r
+ * @return\r
+ */\r
+ @SuppressWarnings("unused") //used by mapper\r
+ private static Integer getRankFk(TaxonNameBase<?,?> taxonName) {\r
+ return getRankFk(taxonName, taxonName.getNomenclaturalCode());\r
+ }\r
+ \r
+ \r
/**\r
* Returns the <code>RankFk</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
private static Integer getRankFk(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode) {\r
Integer result = null;\r
try {\r
- if (nomenclaturalCode != null) {\r
- if (taxonName != null) {\r
- if (taxonName.getRank() == null) {\r
- logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
- } else {\r
- result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));\r
- }\r
- if (result == null) {\r
- logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ if (nomenclaturalCode != null) {\r
+ if (taxonName != null) {\r
+ if (taxonName.getRank() == null) {\r
+ logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ } else {\r
+ result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));\r
+ }\r
+ if (result == null) {\r
+ logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
}\r
}\r
- }\r
} catch (Exception e) {\r
e.printStackTrace();\r
}\r
return result;\r
}\r
\r
+ /**\r
+ * Returns the rank cache for the taxon name based on the names nomenclatural code.\r
+ * You may not use this method for kingdoms other then Animalia, Plantae and Bacteria.\r
+ * @param taxonName\r
+ * @return\r
+ */\r
+ @SuppressWarnings("unused") //used by mapper\r
+ private static String getRankCache(TaxonNameBase<?,?> taxonName) {\r
+ return getRankCache(taxonName, taxonName.getNomenclaturalCode());\r
+ }\r
+\r
+ \r
/**\r
* Returns the <code>RankCache</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
private static String getRankCache(TaxonNameBase<?,?> taxonName, NomenclaturalCode nomenclaturalCode) {\r
String result = null;\r
try {\r
- if (nomenclaturalCode != null) {\r
- result = PesiTransformer.rank2RankCache(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));\r
- }\r
+ if (nomenclaturalCode != null) {\r
+ result = PesiTransformer.rank2RankCache(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));\r
+ }\r
} catch (Exception e) {\r
e.printStackTrace();\r
}\r
}\r
\r
\r
+ /**\r
+ * Returns the <code>DisplayName</code> attribute.\r
+ * @param taxon The {@link TaxonBase Taxon}.\r
+ * @return The <code>DisplayName</code> attribute.\r
+ * @see MethodMapper\r
+ */\r
+ @SuppressWarnings("unused") //used by Mapper\r
+ private static String getDisplayName(TaxonBase<?> taxon) {\r
+ TaxonNameBase<?,?> taxonName = taxon.getName();\r
+ String result = getDisplayName(taxonName);\r
+ if (isMisappliedName(taxon)){\r
+ result = result + " " + getAuthorString(taxon);\r
+ }\r
+ return result;\r
+ }\r
+ \r
+ \r
+ /**\r
+ * Returns the <code>DisplayName</code> attribute.\r
+ * @param taxonName The {@link TaxonNameBase TaxonName}.\r
+ * @return The <code>DisplayName</code> attribute.\r
+ * @see MethodMapper\r
+ */\r
+ @SuppressWarnings("unused") //used by Mapper\r
+ private static String getDisplayName(TaxonNameBase<?,?> taxonName) {\r
+ // TODO: extension?\r
+ if (taxonName == null) {\r
+ return null;\r
+ }else{\r
+ INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);\r
+ HTMLTagRules tagRules = new HTMLTagRules().\r
+ addRule(TagEnum.name, "i").\r
+ addRule(TagEnum.nomStatus, "@status@");\r
+ \r
+ NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);\r
+ String result = cacheStrategy.getFullTitleCache(nvn, tagRules);\r
+ return result.replaceAll("\\<@status@\\>.*\\</@status@\\>", "");\r
+ }\r
+ }\r
+ \r
+\r
+ /**\r
+ * Returns the <code>WebShowName</code> attribute for a taxon.\r
+ * @param taxonName The {@link TaxonNameBase TaxonName}.\r
+ * @return The <code>WebShowName</code> attribute.\r
+ * @see MethodMapper\r
+ */\r
+ @SuppressWarnings("unused")\r
+ private static String getWebShowName(TaxonBase<?> taxon) {\r
+ TaxonNameBase<?,?> taxonName = taxon.getName();\r
+ String result = getWebShowName(taxonName);\r
+ if (isMisappliedName(taxon)){\r
+ result = result + " " + getAuthorString(taxon);\r
+ }\r
+ return result;\r
+ }\r
+ \r
/**\r
* Returns the <code>WebShowName</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
* @return The <code>WebShowName</code> attribute.\r
* @see MethodMapper\r
*/\r
- @SuppressWarnings("unused")\r
private static String getWebShowName(TaxonNameBase<?,?> taxonName) {\r
//TODO extensions?\r
if (taxonName == null) {\r
}\r
}\r
\r
+ \r
/**\r
* Returns the <code>WebSearchName</code> attribute.\r
* @param taxonName The {@link NonViralName NonViralName}.\r
}\r
\r
\r
+ /**\r
+ * Returns the nomenclatural reference which is the reference\r
+ * including the detail (microreference).\r
+ * @param taxonName The {@link TaxonNameBase TaxonName}.\r
+ * @return The <code>AuthorString</code> attribute.\r
+ * @see MethodMapper\r
+ */\r
+ @SuppressWarnings("unused")\r
+ private static String getNomRefString(TaxonNameBase<?,?> taxonName) {\r
+ INomenclaturalReference ref = taxonName.getNomenclaturalReference();\r
+ return ref == null ? null : ref.getNomenclaturalCitation(taxonName.getNomenclaturalMicroReference());\r
+ }\r
+ \r
+ \r
/**\r
* Returns the <code>AuthorString</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
*/\r
@SuppressWarnings("unused")\r
private static String getAuthorString(TaxonBase<?> taxon) {\r
- String result = null;\r
try {\r
+ String result = null;\r
boolean isNonViralName = false;\r
String authorshipCache = null;\r
TaxonNameBase<?,?> taxonName = taxon.getName();\r
authorshipCache = CdmBase.deproxy(taxonName, NonViralName.class).getAuthorshipCache();\r
isNonViralName = true;\r
}\r
- // For a misapplied name without an authorshipCache the authorString should be set to "auct."\r
- if (isMisappliedName(taxon) && authorshipCache == null) {\r
- // Set authorshipCache to "auct."\r
- result = PesiTransformer.AUCT_STRING;\r
- }else{\r
- result = authorshipCache;\r
+ result = authorshipCache;\r
+ \r
+ // For a misapplied names there are special rules\r
+ if (isMisappliedName(taxon)){\r
+ if (taxon.getSec() != null){\r
+ String secTitle = taxon.getSec().getTitleCache();\r
+ if (! secTitle.startsWith("auct")){\r
+ secTitle = "sensu " + secTitle;\r
+ }else if (secTitle.equals("auct")){ //may be removed once the title cache is generated correctly for references with title auct. #\r
+ secTitle = "auct.";\r
+ }\r
+ return secTitle;\r
+ }else if (StringUtils.isBlank(authorshipCache)) {\r
+ // Set authorshipCache to "auct."\r
+ result = PesiTransformer.AUCT_STRING;\r
+ }else{\r
+ result = PesiTransformer.AUCT_STRING;\r
+// result = authorshipCache;\r
+ }\r
}\r
+ \r
if (taxonName == null){\r
logger.warn("TaxonName does not exist for taxon: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");\r
}else if (! isNonViralName){\r
logger.warn("TaxonName is not of instance NonViralName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
}\r
\r
+ if (StringUtils.isBlank(result)) {\r
+ return null;\r
+ } else {\r
+ return result;\r
+ }\r
} catch (Exception e) {\r
e.printStackTrace();\r
- }\r
- \r
- if (StringUtils.isBlank(result)) {\r
return null;\r
- } else {\r
- return result;\r
}\r
+ \r
}\r
\r
- \r
+ \r
/**\r
- * Checks whether a given TaxonName is a misapplied name.\r
- * @param taxonName The {@link TaxonNameBase TaxonName}.\r
+ * Checks whether a given taxon is a misapplied name.\r
+ * @param taxon The {@link TaxonBase Taxon}.\r
* @return Whether the given TaxonName is a misapplied name or not.\r
- */ \r
- private static boolean isMisappliedName(TaxonNameBase taxonName) {\r
- boolean result = false;\r
- Set<Taxon> taxa = taxonName.getTaxa();\r
- if (taxa.size() == 1){\r
- return isMisappliedName(taxa.iterator().next());\r
- }else if (taxa.size() > 1){\r
- logger.warn("TaxonNameBase has " + taxa.size() + " taxa attached. Can't define if it is a misapplied name.");\r
- }\r
- return result;\r
- }\r
+ */\r
+ private static boolean isMisappliedName(TaxonBase<?> taxon) {\r
+ return getAcceptedTaxonForMisappliedName(taxon) != null;\r
\r
- \r
+ }\r
\r
\r
/**\r
- * Checks whether a given Taxon is a misapplied name.\r
- * @param taxonName The {@link TaxonNameBase TaxonName}.\r
- * @return Whether the given TaxonName is a misapplied name or not.\r
+ * Returns the first accepted taxon for this misapplied name.\r
+ * If this misapplied name is not a misapplied name, <code>null</code> is returned. \r
+ * @param taxon The {@link TaxonBase Taxon}.\r
*/\r
- private static boolean isMisappliedName(TaxonBase<?> taxon) {\r
- boolean result = false;\r
- \r
+ private static Taxon getAcceptedTaxonForMisappliedName(TaxonBase<?> taxon) {\r
if (! taxon.isInstanceOf(Taxon.class)){\r
- return false;\r
+ return null;\r
}\r
Set<TaxonRelationship> taxonRelations = CdmBase.deproxy(taxon, Taxon.class).getRelationsFromThisTaxon();\r
for (TaxonRelationship taxonRelationship : taxonRelations) {\r
TaxonRelationshipType taxonRelationshipType = taxonRelationship.getType();\r
if (taxonRelationshipType.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {\r
- result = true;\r
+ return taxonRelationship.getToTaxon();\r
}\r
}\r
- return result;\r
+ return null;\r
}\r
\r
- \r
- /**\r
- * Returns the <code>DisplayName</code> attribute.\r
- * @param taxonName The {@link TaxonNameBase TaxonName}.\r
- * @return The <code>DisplayName</code> attribute.\r
- * @see MethodMapper\r
- */\r
- @SuppressWarnings("unused")\r
- private static String getDisplayName(TaxonNameBase<?,?> taxonName) {\r
- // TODO: extension?\r
- if (taxonName == null) {\r
- return null;\r
- }else{\r
- \r
- INonViralNameCacheStrategy cacheStrategy = getCacheStrategy(taxonName);\r
- \r
- HTMLTagRules tagRules = new HTMLTagRules().addRule(TagEnum.name, "i");\r
- NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);\r
- return cacheStrategy.getFullTitleCache(nvn, tagRules);\r
- }\r
- }\r
+\r
\r
\r
/**\r
* Returns the <code>NameStatusCache</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
* @return The <code>NameStatusCache</code> attribute.\r
+ * @throws UndefinedTransformerMethodException \r
* @see MethodMapper\r
*/\r
@SuppressWarnings("unused")\r
- private static String getNameStatusCache(TaxonNameBase<?,?> taxonName) {\r
+ private static String getNameStatusCache(TaxonNameBase taxonName, PesiExportState state) throws UndefinedTransformerMethodException {\r
String result = null;\r
- NomenclaturalStatus state = getNameStatus(taxonName);\r
- if (state != null) {\r
- result = PesiTransformer.nomStatus2NomStatusCache(state.getType());\r
+ NomenclaturalStatus status = getNameStatus(taxonName);\r
+ if (status != null) {\r
+ result = state.getTransformer().getCacheByNomStatus(status.getType());\r
}\r
return result;\r
}\r
NonViralName<?> nonViralName = CdmBase.deproxy(taxonName, NonViralName.class);\r
Set<NomenclaturalStatus> states = nonViralName.getStatus();\r
if (states.size() == 1) {\r
- NomenclaturalStatus state = states.iterator().next();\r
- return state;\r
+ NomenclaturalStatus status = states.iterator().next();\r
+ return status;\r
} else if (states.size() > 1) {\r
logger.error("This TaxonName has more than one Nomenclatural Status: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
}\r
}\r
return result;\r
}\r
+\r
\r
/**\r
* Returns the <code>QualityStatusFk</code> attribute.\r
* @return The <code>QualityStatusFk</code> attribute.\r
* @see MethodMapper\r
*/\r
- @SuppressWarnings("unused")\r
- private static Integer getQualityStatusFk(TaxonBase<?> taxonName) {\r
- // TODO: Not represented in CDM right now. Depends on import.\r
- Integer result = null;\r
- return result;\r
+ private static Integer getQualityStatusFk(TaxonNameBase taxonName) {\r
+ BitSet sources = getSources(taxonName);\r
+ return PesiTransformer.getQualityStatusKeyBySource(sources);\r
}\r
+\r
\r
/**\r
* Returns the <code>QualityStatusCache</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
* @return The <code>QualityStatusCache</code> attribute.\r
+ * @throws UndefinedTransformerMethodException \r
* @see MethodMapper\r
*/\r
@SuppressWarnings("unused")\r
- private static String getQualityStatusCache(TaxonBase<?> taxonName) {\r
- // TODO: Not represented in CDM right now. Depends on import.\r
- String result = null;\r
- return result;\r
+ private static String getQualityStatusCache(TaxonNameBase taxonName, PesiExportState state) throws UndefinedTransformerMethodException {\r
+ return state.getTransformer().getQualityStatusCacheByKey(getQualityStatusFk(taxonName));\r
}\r
\r
/**\r
try {\r
Set<IdentifiableSource> sources = getPesiSources(taxonName);\r
for (IdentifiableSource source : sources) {\r
- Reference ref = source.getCitation();\r
+ Reference<?> ref = source.getCitation();\r
UUID refUuid = ref.getUuid();\r
if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed)){\r
result = "NameId: " + source.getIdInSource();\r
result = "Inferred genus from TAX_ID: " + source.getIdInSource();\r
} else if (sourceIdNameSpace.equals(TaxonServiceImpl.POTENTIAL_COMBINATION_NAMESPACE)) {\r
result = "Potential combination from TAX_ID: " + source.getIdInSource();\r
- } else {\r
-// result = "TAX_ID: " + source.getIdInSource();\r
- result = sourceIdNameSpace + source.getIdInSource();\r
- }\r
+ } \r
}\r
}\r
} catch (Exception e) {\r
* @see MethodMapper\r
*/\r
@SuppressWarnings("unused")\r
- private static String getCacheCitation(TaxonBase<?> taxon) {\r
+ private static String getCacheCitation(TaxonBase taxon) {\r
+ // !!! See also doPhaseUpdates\r
+ \r
+ TaxonNameBase<?,?> taxonName = taxon.getName();\r
String result = "";\r
//TODO implement anew for taxa\r
-// try {\r
-// String originalDb = getOriginalDB(taxon);\r
-// if (originalDb == null) {\r
-//// logger.error("OriginalDB is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// } else if (originalDb.equals("ERMS")) {\r
-// // TODO: 19.08.2010: An import of CacheCitation does not exist in the ERMS import yet or it will be imported in a different way...\r
-// // So the following code is some kind of harmless assumption.\r
-// Set<Extension> extensions = taxon.getExtensions();\r
-// for (Extension extension : extensions) {\r
-// if (extension.getType().equals(cacheCitationExtensionType)) {\r
-// result = extension.getValue();\r
-// }\r
-// }\r
-// } else {\r
-// String expertName = getExpertName(taxon);\r
-// String webShowName = getWebShowName(taxon);\r
-// \r
-// // idInSource only\r
-// String idInSource = getIdInSourceOnly(taxo);\r
-// \r
-// // build the cacheCitation\r
-// if (expertName != null) {\r
-// result += expertName + ". ";\r
-// } else {\r
-// // logger.error("ExpertName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// if (webShowName != null) {\r
-// result += webShowName + ". ";\r
-// } else {\r
-// // logger.error("WebShowName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// \r
-// if (getOriginalDB(taxonName).equals("FaEu")) {\r
-// result += "Accessed through: Fauna Europaea at http://faunaeur.org/full_results.php?id=";\r
-// } else if (getOriginalDB(taxonName).equals("EM")) {\r
-// result += "Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=";\r
-// }\r
-// \r
-// if (idInSource != null) {\r
-// result += idInSource;\r
-// } else {\r
-// // logger.error("IdInSource could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// }\r
-// } catch (Exception e) {\r
-// e.printStackTrace();\r
-// }\r
-// \r
-// if ("".equals(result)) {\r
-// return null;\r
-// } else {\r
-// return result;\r
-// }\r
- return result;\r
- }\r
- \r
- /**\r
- * Returns the <code>OriginalDB</code> attribute.\r
- * @param taxonName The {@link TaxonNameBase TaxonName}.\r
- * @return The <code>OriginalDB</code> attribute.\r
- * @see MethodMapper\r
- */\r
- private static String getOriginalDB(IdentifiableEntity identEntity) {\r
- String result = "";\r
try {\r
-\r
- // Sources from TaxonName\r
-// Set<IdentifiableSource> sources = taxonName.getSources();\r
- Set<IdentifiableSource> sources = identEntity.getSources();\r
- \r
-// IdentifiableEntity<?> taxonBase = null;\r
-// if (sources != null && sources.isEmpty()) {\r
-// // Sources from Taxa or Synonyms\r
-// Set<Taxon> taxa = taxonName.getTaxa();\r
-// if (taxa.size() == 1) {\r
-// taxonBase = taxa.iterator().next();\r
-// sources = taxonBase.getSources();\r
-// } else if (taxa.size() > 1) {\r
-// logger.warn("This TaxonName has " + taxa.size() + " Taxa: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");\r
-// }\r
-// Set<Synonym> synonyms = taxonName.getSynonyms();\r
-// if (synonyms.size() == 1) {\r
-// taxonBase = synonyms.iterator().next();\r
-// sources = taxonBase.getSources();\r
-// } else if (synonyms.size() > 1) {\r
-// logger.warn("This TaxonName has " + synonyms.size() + " Synonyms: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() +")");\r
-// }\r
-// }\r
-\r
- if (sources != null && ! sources.isEmpty()) {\r
- if (sources.size() == 1) {\r
- IdentifiableSource source = sources.iterator().next();\r
- if (source != null) {\r
- Reference<?> citation = source.getCitation();\r
- if (citation != null) {\r
- result = PesiTransformer.databaseString2Abbreviation(citation.getTitleCache());\r
- }\r
- }\r
- } else if (sources.size() > 1) {\r
- int count = 1;\r
- for (IdentifiableSource source : sources) {\r
- Reference<?> citation = source.getCitation();\r
- if (citation != null) {\r
- if (count > 1) {\r
- result += "; ";\r
- }\r
- result += PesiTransformer.databaseString2Abbreviation(citation.getTitleCache());\r
- count++;\r
+ BitSet sources = getSources(taxonName);\r
+ if (sources.isEmpty()) {\r
+// logger.error("OriginalDB is NULL for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ } else if (sources.get(PesiTransformer.SOURCE_ERMS)) {\r
+ // TODO: 19.08.2010: An import of CacheCitation does not exist in the ERMS import yet or it will be imported in a different way...\r
+ // So the following code is some kind of harmless assumption.\r
+ Set<Extension> extensions = taxonName.getExtensions();\r
+ for (Extension extension : extensions) {\r
+ if (extension.getType().equals(cacheCitationExtensionType)) {\r
+ result = extension.getValue();\r
}\r
}\r
} else {\r
- result = null;\r
+ String expertName = getExpertName(taxon);\r
+ String webShowName = getWebShowName(taxonName);\r
+ \r
+ // idInSource only\r
+ String idInSource = getIdInSourceOnly(taxonName);\r
+ \r
+ // build the cacheCitation\r
+ if (expertName != null) {\r
+ result += expertName + ". ";\r
+ } else {\r
+ if (logger.isDebugEnabled()){logger.debug("ExpertName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");}\r
+ }\r
+ if (webShowName != null) {\r
+ result += webShowName + ". ";\r
+ } else {\r
+ logger.warn("WebShowName could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ \r
+ if (getOriginalDB(taxonName).equals("FaEu")) {\r
+ result += "Accessed through: Fauna Europaea at http://faunaeur.org/full_results.php?id=";\r
+ } else if (getOriginalDB(taxonName).equals("EM")) {\r
+ result += "Accessed through: Euro+Med PlantBase at http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=";\r
+ }\r
+ \r
+ if (idInSource != null) {\r
+ result += idInSource;\r
+ } else {\r
+ logger.warn("IdInSource could not be determined for this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
}\r
- }\r
-\r
} catch (Exception e) {\r
e.printStackTrace();\r
}\r
- if ("".equals(result)) {\r
+ \r
+ if (StringUtils.isBlank(result)) {\r
return null;\r
} else {\r
return result;\r
}\r
}\r
\r
+ /**\r
+ * Returns the <code>OriginalDB</code> attribute.\r
+ * @param taxonName The {@link TaxonNameBase TaxonName}.\r
+ * @return The <code>OriginalDB</code> attribute.\r
+ * @see MethodMapper\r
+ */\r
+ private static String getOriginalDB(IdentifiableEntity identEntity) {\r
+ // Sources from TaxonName\r
+ BitSet sources = getSources(identEntity);\r
+ return PesiTransformer.getOriginalDbBySources(sources);\r
+ }\r
+ \r
/**\r
* Returns the <code>LastAction</code> attribute.\r
* @param taxonName The {@link TaxonNameBase TaxonName}.\r
}\r
\r
\r
+ /**\r
+ * Returns the source (E+M, Fauna Europaea, Index Fungorum, ERMS) of a given\r
+ * Identifiable Entity as a BitSet\r
+ * @param identEntity\r
+ * @return\r
+ */\r
+ private static BitSet getSources(IdentifiableEntity<?> identEntity){\r
+ BitSet bitSet = new BitSet();\r
+ Set<IdentifiableSource> sources = getPesiSources(identEntity);\r
+ for (IdentifiableSource source : sources) {\r
+ Reference<?> ref = source.getCitation();\r
+ UUID refUuid = ref.getUuid();\r
+ if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed)){\r
+ bitSet.set(PesiTransformer.SOURCE_EM);\r
+ }else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){\r
+ bitSet.set(PesiTransformer.SOURCE_FE);\r
+ }else if (refUuid.equals(PesiTransformer.uuidSourceRefErms)){\r
+ bitSet.set(PesiTransformer.SOURCE_ERMS);\r
+ }else if (refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum)){\r
+ bitSet.set(PesiTransformer.SOURCE_IF);\r
+ }else{\r
+ if (logger.isDebugEnabled()){logger.debug("Not a PESI source");};\r
+ }\r
+ }\r
+ return bitSet;\r
+ \r
+ }\r
+ \r
private static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {\r
NonViralNameDefaultCacheStrategy cacheStrategy;\r
if (taxonName.isInstanceOf(ZoologicalName.class)){\r
*/\r
private PesiExportMapping getMapping() {\r
PesiExportMapping mapping = new PesiExportMapping(dbTableName);\r
- ExtensionType extensionType = null;\r
\r
mapping.addMapper(IdMapper.NewInstance("TaxonId"));\r
mapping.addMapper(DbObjectMapper.NewInstance("sec", "sourceFk")); //OLD:mapping.addMapper(MethodMapper.NewInstance("SourceFK", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));\r
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));\r
mapping.addMapper(MethodMapper.NewInstance("TaxonStatusCache", this.getClass(), "getTaxonStatusCache", standardMethodParameter, PesiExportState.class));\r
+ \r
// QualityStatus (Fk, Cache)\r
- extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidQualityStatus);\r
- if (extensionType != null) {\r
- mapping.addMapper(DbExtensionMapper.NewInstance(extensionType, "QualityStatusCache"));\r
- } else {\r
- mapping.addMapper(MethodMapper.NewInstance("QualityStatusCache", this));\r
- }\r
- mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this)); // PesiTransformer.QualityStatusCache2QualityStatusFk?\r
+// extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidQualityStatus);\r
+// if (extensionType != null) {\r
+// mapping.addMapper(DbExtensionMapper.NewInstance(extensionType, "QualityStatusCache"));\r
+// } else {\r
+// mapping.addMapper(MethodMapper.NewInstance("QualityStatusCache", this));\r
+// }\r
+// mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this)); // PesiTransformer.QualityStatusCache2QualityStatusFk?\r
\r
mapping.addMapper(MethodMapper.NewInstance("GUID", this));\r
\r
mapping.addMapper(MethodMapper.NewInstance("DerivedFromGuid", this));\r
mapping.addMapper(MethodMapper.NewInstance("CacheCitation", this));\r
- mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this.getClass(), "getOriginalDB", IdentifiableEntity.class) );\r
+ mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misallied Names are handled differently\r
+ mapping.addMapper(MethodMapper.NewInstance("WebShowName", this));\r
\r
- //handled by name mapping\r
-// mapping.addMapper(MethodMapper.NewInstance("LastAction", this.getClass(), "getLastAction", IdentifiableEntity.class));\r
-// mapping.addMapper(MethodMapper.NewInstance("LastActionDate", this.getClass(), "getLastActionDate", IdentifiableEntity.class));\r
-// mapping.addMapper(MethodMapper.NewInstance("SpeciesExpertName", this));\r
-\r
+ // DisplayName\r
+ ExtensionType extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidDisplayName); \r
+ if (extensionType != null) {\r
+ mapping.addMapper(DbExtensionMapper.NewInstance(extensionType, "DisplayName"));\r
+ } else {\r
+ mapping.addMapper(MethodMapper.NewInstance("DisplayName", this));\r
+ }\r
\r
- mapping.addMapper(MethodMapper.NewInstance("ExpertName", this));\r
-\r
- mapping.addMapper(MethodMapper.NewInstance("AuthorString", this)); //For Taxon because Misallied Names are handled differently\r
+ //handled by name mapping\r
+ mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));\r
+ mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));\r
\r
+ ExtensionType extensionTypeSpeciesExpertName = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertNameUuid);\r
+ mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeSpeciesExpertName, "SpeciesExpertName"));\r
+ ExtensionType extensionTypeExpertName = (ExtensionType)getTermService().find(PesiTransformer.expertNameUuid);\r
+ mapping.addMapper(DbExtensionMapper.NewInstance(extensionTypeExpertName, "ExpertName"));\r
\r
+// mapping.addMapper(MethodMapper.NewInstance("ParentTaxonFk", this, TaxonBase.class, PesiExportState.class)); //doesn't work, FK exceptioni\r
mapping.addMapper(ObjectChangeMapper.NewInstance(TaxonBase.class, TaxonNameBase.class, "Name"));\r
\r
addNameMappers(mapping);\r
* Returns the CDM to PESI specific export mappings.\r
* @return The {@link PesiExportMapping PesiExportMapping}.\r
*/\r
- private PesiExportMapping getNameMapping() {\r
+ private PesiExportMapping getPureNameMapping() {\r
PesiExportMapping mapping = new PesiExportMapping(dbTableName);\r
\r
mapping.addMapper(IdMapper.NewInstance("TaxonId"));\r
\r
// mapping.addMapper(MethodMapper.NewInstance("TaxonStatusFk", this.getClass(), "getTaxonStatusFk", standardMethodParameter, PesiExportState.class));\r
\r
-// mapping.addMapper(MethodMapper.NewInstance("LastAction", this.getClass(), "getLastAction", IdentifiableEntity.class));\r
-// mapping.addMapper(MethodMapper.NewInstance("LastActionDate", this.getClass(), "getLastAction", IdentifiableEntity.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("KingdomFk", this, TaxonNameBase.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("RankFk", this, TaxonNameBase.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("RankCache", this, TaxonNameBase.class));\r
+ mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusFk", Types.INTEGER , PesiTransformer.T_STATUS_UNACCEPTED));\r
+ mapping.addMapper(DbConstantMapper.NewInstance("TaxonStatusCache", Types.VARCHAR , PesiTransformer.T_STATUS_STR_UNACCEPTED));\r
+ mapping.addMapper(DbStringMapper.NewInstance("AuthorshipCache", "AuthorString").setBlankToNull(true)); \r
+ mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonNameBase.class));\r
\r
- mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this.getClass(), "getOriginalDB", IdentifiableEntity.class) );\r
+ // DisplayName\r
+ ExtensionType extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidDisplayName); \r
+ if (extensionType != null) {\r
+ mapping.addMapper(DbExtensionMapper.NewInstance(extensionType, "DisplayName"));\r
+ } else {\r
+ mapping.addMapper(MethodMapper.NewInstance("DisplayName", this, TaxonNameBase.class));\r
+ }\r
\r
- addNameMappers(mapping);\r
+ mapping.addMapper(DbLastActionMapper.NewInstance("LastActionDate", false));\r
+ mapping.addMapper(DbLastActionMapper.NewInstance("LastAction", true));\r
\r
- //TODO add author mapper, taxonStatusFk, TaxonStatusCache, TypeNameFk\r
-\r
-// immer 2 für E+M ? mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this)); // PesiTransformer.QualityStatusCache2QualityStatusFk?\r
-// mapping.addMapper(MethodMapper.NewInstance("TaxonStatusCache", this.getClass(), "getTaxonStatusCache", standardMethodParameter, PesiExportState.class));\r
+ addNameMappers(mapping);\r
+ //TODO add author mapper, TypeNameFk\r
\r
return mapping;\r
}\r
mapping.addMapper(MethodMapper.NewInstance("FullName", this, TaxonNameBase.class));\r
\r
\r
- //TODO FIXME incorrect mapping -> should be ref + microref but is only microref\r
- mapping.addMapper(DbStringMapper.NewInstance("NomenclaturalMicroReference", "NomRefString"));\r
- mapping.addMapper(MethodMapper.NewInstance("WebShowName", this, TaxonNameBase.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("NomRefString", this, TaxonNameBase.class));\r
\r
- // DisplayName\r
- extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidDisplayName); \r
- if (extensionType != null) {\r
- mapping.addMapper(DbExtensionMapper.NewInstance(extensionType, "DisplayName"));\r
- } else {\r
- mapping.addMapper(MethodMapper.NewInstance("DisplayName", this, TaxonNameBase.class));\r
- }\r
+\r
\r
mapping.addMapper(MethodMapper.NewInstance("NameStatusFk", this, TaxonNameBase.class));\r
- mapping.addMapper(MethodMapper.NewInstance("NameStatusCache", this, TaxonNameBase.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("NameStatusCache", this, TaxonNameBase.class, PesiExportState.class));\r
mapping.addMapper(MethodMapper.NewInstance("TypeFullnameCache", this, TaxonNameBase.class));\r
//TODO TypeNameFk\r
+ mapping.addMapper(MethodMapper.NewInstance("QualityStatusFk", this, TaxonNameBase.class));\r
+ mapping.addMapper(MethodMapper.NewInstance("QualityStatusCache", this, TaxonNameBase.class, PesiExportState.class));\r
+ \r
\r
// FossilStatus (Fk, Cache)\r
extensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidFossilStatus);\r
mapping.addMapper(MethodMapper.NewInstance("FossilStatusFk", this, TaxonNameBase.class)); // PesiTransformer.FossilStatusCache2FossilStatusFk?\r
\r
mapping.addMapper(MethodMapper.NewInstance("IdInSource", this, IdentifiableEntity.class));\r
- mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());\r
+ mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this, IdentifiableEntity.class) );\r
+\r
+ //mapping.addMapper(ExpertsAndLastActionMapper.NewInstance());\r
\r
}\r
\r
BGBM BDI Projects / cdmlib-apps.git / blobdiff