*/\r
package eu.etaxonomy.cdm.io.pesi.out;\r
\r
-import java.sql.Connection;\r
-import java.sql.PreparedStatement;\r
-import java.sql.SQLException;\r
-import java.sql.Statement;\r
import java.util.ArrayList;\r
import java.util.List;\r
\r
*/\r
public class PesiExportState extends DbExportStateBase<PesiExportConfigurator>{\r
private static final Logger logger = Logger.getLogger(PesiExportState.class);\r
- private static List<Integer> processedTaxonNameList = new ArrayList<Integer>();\r
private static List<Integer> processedSourceList = new ArrayList<Integer>();\r
- private List<Integer> treeIndexList = new ArrayList<Integer>();\r
- private static final String state_db_table = "tmp_state";\r
- private static final String processed_taxonname_db_table = "tmp_processed_taxonname";\r
- private static final String processed_source_db_table = "tmp_processed_source";\r
- private static final String processed_treeindex_and_kingdomfk_db_table = "tmp_processed_treeindex_kingdomfk";\r
- private Connection connection;\r
- private PreparedStatement select_KingdomId_TreeIndex_NomenclaturalCode_Stmt;\r
- private PreparedStatement insert_KingdomId_TreeIndex_NomenclaturalCode_Stmt;\r
- private PreparedStatement insert_state_Stmt;\r
- private PreparedStatement select_state_Stmt;\r
- \r
+\r
/**\r
* @param config\r
*/\r
public PesiExportState(PesiExportConfigurator config) {\r
super(config);\r
- \r
- try {\r
- connection = getConfig().getDestination().getConnection();\r
-\r
- // Retrieve treeIndex, kingdomId and nomenclaturalCode from database\r
-// String sql = "SELECT kingdom_id, tree_index, nomenclatural_code FROM " + processed_treeindex_and_kingdomfk_db_table + " WHERE tree_index like ?";\r
-// select_KingdomId_TreeIndex_NomenclaturalCode_Stmt = connection.prepareStatement(sql);\r
- \r
- // Add TreeIndex, KingdomFk and nomenclaturalCode to database\r
-// sql = "INSERT INTO " + processed_treeindex_and_kingdomfk_db_table + " VALUES (?, ?, ?)";\r
-// insert_KingdomId_TreeIndex_NomenclaturalCode_Stmt = connection.prepareStatement(sql);\r
- \r
- // Add cdmId/pesiId pair to database \r
- String sql = "INSERT INTO " + state_db_table + " VALUES ( ?, ?)";\r
- insert_state_Stmt = connection.prepareStatement(sql);\r
- \r
- sql = "SELECT pesi_id FROM " + state_db_table + " WHERE cdm_id = ?";\r
- select_state_Stmt = connection.prepareStatement(sql);\r
-\r
- } catch (SQLException e) {\r
- // TODO Auto-generated catch block\r
- e.printStackTrace();\r
- }\r
-\r
- createStateTables();\r
}\r
\r
- /**\r
- * Create the database table that hosts state information.\r
- */\r
- public boolean createStateTables() {\r
- \r
- String query;\r
- Statement stmt;\r
- \r
- if (deleteStateTables()) {\r
-/* try {\r
- query="CREATE TABLE " + state_db_table + " (cdm_id varchar(100), pesi_id int)";\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- } catch (Exception e) {\r
- logger.error("Couldn't create database table for state information.");\r
- e.printStackTrace();\r
- throw new RuntimeException("Couldn't create database table for state information.");\r
- }\r
- \r
- try {\r
- query="CREATE TABLE " + processed_taxonname_db_table + " (cdm_id varchar(100))";\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't create database table for processed taxonnames.");\r
- e.printStackTrace();\r
- throw new RuntimeException("Couldn't create database table for processed taxonnames.");\r
- }\r
- \r
- try {\r
- query="CREATE TABLE " + processed_source_db_table + " (cdm_id int)";\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't create database table for processed sources.");\r
- e.printStackTrace();\r
- throw new RuntimeException("Couldn't create database table for processed sources.");\r
- }\r
-\r
- try {\r
- query="CREATE TABLE " + processed_treeindex_and_kingdomfk_db_table + " (kingdom_id int, tree_index varchar(200), nomenclatural_code varchar(100))";\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't create database table for processed treeindex and kingdomfk.");\r
- e.printStackTrace();\r
- throw new RuntimeException("Couldn't create database table for processed treeindex and kingdomfk.");\r
- }*/\r
- }\r
-\r
- return true;\r
- }\r
-\r
- /**\r
- * Deletes existing state tables.\r
- */\r
- public boolean deleteStateTables() {\r
- boolean result = true;\r
- \r
- String query;\r
- Statement stmt;\r
- \r
-/* try {\r
- query="DROP TABLE " + state_db_table;\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't drop database table for state information.");\r
-// result = false;\r
- }\r
-\r
- try {\r
- query="DROP TABLE " + processed_taxonname_db_table;\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't drop database table for processed taxonnames.");\r
-// result = false;\r
- }\r
\r
- try {\r
- query="DROP TABLE " + processed_source_db_table;\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't drop database table for processed sources.");\r
-// result = false;\r
- }\r
-\r
- try {\r
- query="DROP TABLE " + processed_treeindex_and_kingdomfk_db_table;\r
- stmt = connection.createStatement();\r
- stmt.executeUpdate(query);\r
- stmt.close();\r
- } catch (Exception e) {\r
- logger.error("Couldn't drop database table for treeindex and kingdomfk.");\r
-// result = false;\r
- }*/\r
-\r
- return result;\r
- }\r
- \r
/**\r
- * Put datawarehouse database identifier into table for state information.\r
+ * Stores the Datawarehouse.id to a specific CDM object originally.\r
+ * Does nothing now since we do not want to store Cdm.id/Datawarehouse.id pairs. This saves precious memory.\r
* @param cdmBase\r
* @param dbId\r
*/\r
@Override\r
public void putDbId(CdmBase cdmBase, int dbId) {\r
-// try {\r
-// insert_state_Stmt.setInt(1, cdmBase.getId());\r
-// insert_state_Stmt.setInt(2, dbId);\r
-// insert_state_Stmt.executeUpdate();\r
-// } catch (SQLException e) {\r
-// logger.error("Could not store state information into database: " + e.getMessage());\r
-// e.printStackTrace();\r
-// }\r
+ // Do nothing\r
}\r
\r
/**\r
- * Get datawarehouse database identifier from table for state information.\r
+ * Gets the Datawarehouse.id to a specific CDM object originally.\r
+ * Here it just returns the CDM object's id.\r
* @param cdmBase\r
* @return\r
*/\r
@Override\r
public Integer getDbId(CdmBase cdmBase) {\r
- return cdmBase.getId();\r
- \r
-// ResultSet resultSet = null;\r
-// try {\r
-// select_state_Stmt.setInt(1, cdmBase.getId());\r
-// resultSet = select_state_Stmt.executeQuery();\r
-// } catch (SQLException e) {\r
-// logger.error("Could not determine datawarehouse database identifier: " + e.getMessage());\r
-// e.printStackTrace();\r
-// }\r
-//\r
-// Integer pesiDbKey = 0;\r
-// try {\r
-// if (resultSet != null) {\r
-// while (resultSet.next()) {\r
-// pesiDbKey = resultSet.getInt("pesi_id");\r
-// }\r
-// }\r
-// } catch (SQLException e) {\r
-// logger.error("Could not determine pesiId for cdmId.");\r
-// throw new RuntimeException("Could not determine pesiId for cdmId.");\r
-// }\r
-// if (pesiDbKey == 0) {\r
-// logger.warn("A datawarehouse database identifier could not be determined for this cdmBase entity: " + cdmBase.getId());\r
-// pesiDbKey = null;\r
-// }\r
-// return pesiDbKey;\r
+ // We use the Cdm.id for Datawarehouse.id\r
+ if (cdmBase == null) {\r
+ return null;\r
+ } else {\r
+ return cdmBase.getId();\r
+ }\r
}\r
\r
-\r
-// @Override\r
-// public Integer getDbId(CdmBase cdmBase) {\r
-// if (cdmBase != null) {\r
-// IdType type = getConfig().getIdType();\r
-// if (type == IdType.CDM_ID) {\r
-// return cdmBase.getId();\r
-// } else {\r
-// return dbIdMap.get(cdmBase.getUuid());\r
-// }\r
-// } else {\r
-// logger.warn("CdmBase was (null). No entries in dbIdMap available");\r
-// return null;\r
-// }\r
-// }\r
-\r
- /**\r
- * Removes a {@link CdmBase CdmBase} entry from this state's {@link java.util.Map Map}.\r
- * @param cdmBase The {@link CdmBase CdmBase} to be deleted.\r
- * @return Whether deletion was successful or not.\r
- */\r
-// public boolean removeDbId(CdmBase cdmBase) {\r
-// if (cdmBase != null) {\r
-// IdType type = getConfig().getIdType();\r
-// if (type != IdType.CDM_ID) {\r
-// dbIdMap.remove(cdmBase.getUuid());\r
-// return true;\r
-// } else {\r
-// return false;\r
-// }\r
-// } else {\r
-// logger.warn("CdmBase was (null). No entries in dbIdMap available");\r
-// return false;\r
-// }\r
-// }\r
-\r
/**\r
- * Returns whether the given object was processed before or not.\r
+ * Returns whether the given Source object was processed before or not.\r
* @param\r
* @return\r
*/\r
import java.sql.PreparedStatement;\r
import java.sql.SQLException;\r
import java.util.ArrayList;\r
+import java.util.HashMap;\r
import java.util.List;\r
import java.util.Set;\r
+import java.util.UUID;\r
import java.util.regex.Matcher;\r
import java.util.regex.Pattern;\r
\r
import eu.etaxonomy.cdm.io.berlinModel.out.mapper.IdMapper;\r
import eu.etaxonomy.cdm.io.berlinModel.out.mapper.MethodMapper;\r
import eu.etaxonomy.cdm.io.common.Source;\r
+import eu.etaxonomy.cdm.model.common.Annotation;\r
+import eu.etaxonomy.cdm.model.common.AnnotationType;\r
import eu.etaxonomy.cdm.model.common.CdmBase;\r
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;\r
import eu.etaxonomy.cdm.model.common.IdentifiableSource;\r
+import eu.etaxonomy.cdm.model.common.Language;\r
import eu.etaxonomy.cdm.model.common.VersionableEntity;\r
import eu.etaxonomy.cdm.model.name.NameTypeDesignation;\r
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;\r
private static final String pluralString = "Taxa";\r
private PreparedStatement parentTaxonFk_TreeIndex_KingdomFkStmt;\r
private PreparedStatement synonymsStmt;\r
+ private NomenclaturalCode nomenclaturalCode;\r
+ private Integer kingdomFk;\r
+ private HashMap<Rank, Rank> rankMap = new HashMap<Rank, Rank>();\r
+ private List<Rank> rankList = new ArrayList<Rank>();\r
\r
enum NamePosition {\r
beginning,\r
/* (non-Javadoc)\r
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)\r
*/\r
- @SuppressWarnings("deprecation")\r
@Override\r
protected boolean doInvoke(PesiExportState state) {\r
try {\r
\r
String synonymsSql = "UPDATE Taxon SET ParentTaxonFk = ?, KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?"; \r
synonymsStmt = con.prepareStatement(synonymsSql);\r
-\r
+ \r
// Get the limit for objects to save within a single transaction.\r
int limit = state.getConfig().getLimitSave();\r
\r
List<TaxonNameBase> list = null;\r
\r
// 1st Round: Make Taxa\r
-/* logger.error("PHASE 1...");\r
+ logger.error("PHASE 1...");\r
// Start transaction\r
txStatus = startTransaction(true);\r
logger.error("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
success &= mapping.invoke(taxonName);\r
\r
// Check whether some rules are violated\r
-// if (rank == null) {\r
-// logger.error("Rank was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// } else {\r
-// if (infraSpecificEpithet == null && rank.intValue() == 190) {\r
-// logger.error("InfraSpecificEpithet was not determined although it should exist for rank 190: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// if (specificEpithet != null && rank.intValue() < 220) {\r
-// logger.error("SpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 220: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// if (infraSpecificEpithet != null && rank.intValue() < 230) {\r
-// logger.error("InfraSpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 230: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// }\r
-// if (infraSpecificEpithet != null && specificEpithet == null) {\r
-// logger.error("An infraSpecificEpithet was determined, but a specificEpithet was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// if (genusOrUninomial == null) {\r
-// logger.error("GenusOrUninomial was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
-// }\r
-// \r
-// rank = null;\r
-// infraSpecificEpithet = null;\r
-// genusOrUninomial = null;\r
-// specificEpithet = null;\r
-\r
+ nomenclaturalCode = taxonName.getNomenclaturalCode();\r
+ String genusOrUninomial = getGenusOrUninomial(taxonName);\r
+ String specificEpithet = getSpecificEpithet(taxonName);\r
+ String infraSpecificEpithet = getInfraSpecificEpithet(taxonName);\r
+ Integer rank = getRankFk(taxonName, nomenclaturalCode);\r
+ \r
+ if (rank == null) {\r
+ logger.error("Rank was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ } else {\r
+ if (infraSpecificEpithet == null && rank.intValue() == 190) {\r
+ logger.error("InfraSpecificEpithet was not determined although it should exist for rank 190: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ if (specificEpithet != null && rank.intValue() < 220) {\r
+ logger.error("SpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 220: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ if (infraSpecificEpithet != null && rank.intValue() < 230) {\r
+ logger.error("InfraSpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 230: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ }\r
+ if (infraSpecificEpithet != null && specificEpithet == null) {\r
+ logger.error("An infraSpecificEpithet was determined, but a specificEpithet was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ if (genusOrUninomial == null) {\r
+ logger.error("GenusOrUninomial was not determined: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
+ }\r
+ \r
}\r
\r
// Commit transaction\r
}\r
// Commit transaction\r
commitTransaction(txStatus);\r
- logger.error("Committed transaction.");*/\r
+ logger.error("Committed transaction.");\r
\r
count = 0;\r
pastCount = 0;\r
List<TaxonomicTree> taxonomicTreeList = null;\r
- // 2nd Round: Add ParentTaxonFk to each Taxon\r
+ // 2nd Round: Add ParentTaxonFk, TreeIndex, Rank and KingdomFk to each Taxon\r
logger.error("PHASE 2...");\r
- // Start transaction\r
- txStatus = startTransaction(true);\r
- logger.error("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
- Integer taxonomicTreeLimit = 1;\r
- Integer taxonomicTreeStart = 0;\r
+ \r
+ // Specify starting ranks for tree traversing\r
+ rankList.add(Rank.KINGDOM());\r
+ rankList.add(Rank.GENUS());\r
+\r
+ // Specify where to stop traversing (value) when starting at a specific Rank (key)\r
+ rankMap.put(Rank.GENUS(), null); // Since NULL does not match an existing Rank, traverse all the way down to the leafs\r
+ rankMap.put(Rank.KINGDOM(), Rank.GENUS()); // excludes rank genus\r
+ \r
StringBuffer treeIndex = new StringBuffer();\r
- while ((taxonomicTreeList = getTaxonTreeService().listTaxonomicTrees(taxonomicTreeLimit, taxonomicTreeStart, null, null)).size() > 0) {\r
- logger.error("Fetched " + taxonomicTreeList.size() + " Taxonomic Tree.");\r
+ \r
+ // Retrieve list of Taxonomic Trees\r
+ txStatus = startTransaction(true);\r
+ logger.error("Started transaction. Fetching all Taxonomic Trees...");\r
+ taxonomicTreeList = getTaxonTreeService().listTaxonomicTrees(null, 0, null, null);\r
+ commitTransaction(txStatus);\r
+ logger.error("Committed transaction.");\r
+\r
+ logger.error("Fetched " + taxonomicTreeList.size() + " Taxonomic Tree.");\r
\r
- for (TaxonomicTree taxonomicTree : taxonomicTreeList) {\r
- logger.error("Number of Root Nodes for this Taxonomic Tree: " + taxonomicTree.getRootNodes().size());\r
+ for (TaxonomicTree taxonomicTree : taxonomicTreeList) {\r
+ for (Rank rank : rankList) {\r
\r
- for (TaxonNode rootNode : taxonomicTree.getRootNodes()) {\r
- logger.error("Number of Child Nodes for this Root Node: " + rootNode.getChildNodes().size() + ". Traversing branches...");\r
+ txStatus = startTransaction(true);\r
+ logger.error("Started transaction for Tree Pass starting from Rank " + rank.getLabel() + " ...");\r
+ \r
+ logger.error("Fetching RootNodes for Rank " + rank.getLabel());\r
+ List<TaxonNode> rankSpecificRootNodes = getTaxonTreeService().loadRankSpecificRootNodes(taxonomicTree, rank, null);\r
+ logger.error("Fetched " + rankSpecificRootNodes.size() + " RootNodes for Rank " + rank.getLabel());\r
+\r
+ commitTransaction(txStatus);\r
+ logger.error("Committed transaction.");\r
+\r
+ int elementCount = 0;\r
+ int halfCount = rankSpecificRootNodes.size() / 2;\r
+\r
+ logger.error("Working through nodes...");\r
+ for (TaxonNode rootNode : rankSpecificRootNodes) {\r
+ txStatus = startTransaction(false);\r
+ \r
+ rootNode = getTaxonNodeService().load(rootNode.getUuid());\r
\r
- for (TaxonNode rootChild : rootNode.getChildNodes()) {\r
- // Traverse all branches from this rootChild\r
+// logger.error("Traversing childNodes of Node " + rootNode.getUuid());\r
+\r
+ TaxonNode parentNode = rootNode.getParent();\r
+ if (rank.equals(Rank.KINGDOM())) {\r
+ treeIndex = new StringBuffer();\r
treeIndex.append("#");\r
- traverseTree(rootChild, rootNode, treeIndex, rootChild.getTaxon().getName().getRank(), state);\r
+ } else {\r
+ // Get treeIndex from parentNode\r
+ if (parentNode != null) {\r
+ boolean annotationFound = false;\r
+ Set<Annotation> annotations = parentNode.getAnnotations();\r
+ for (Annotation annotation : annotations) {\r
+ AnnotationType annotationType = annotation.getAnnotationType();\r
+ if (annotationType != null && annotationType.equals(AnnotationType.TREEINDEX())) {\r
+ // It is assumed that there is only one annotation using AnnotationType TREEINDEX. If there are more only the first is noticed.\r
+ treeIndex = new StringBuffer(annotation.getText());\r
+ annotationFound = true;\r
+ logger.error("treeIndex: " + treeIndex);\r
+ break;\r
+ }\r
+ }\r
+ if (!annotationFound) {\r
+ // This should not happen usually since it means that the treeIndex was not set correctly as an annotation to parentNode\r
+// logger.error("TreeIndex could not be read from annotation of this TaxonNode: " + parentNode.getUuid());\r
+ treeIndex = new StringBuffer();\r
+ treeIndex.append("#");\r
+ }\r
+ } else {\r
+ // TreeIndex could not be determined, but it's unclear how to proceed to generate a correct treeIndex if the parentNode is NULL\r
+ logger.error("ParentNode for RootNode is NULL. TreeIndex could not be determined: " + rootNode.getUuid());\r
+ treeIndex = new StringBuffer(); // This just prevents growing of the treeIndex in a wrong manner\r
+ treeIndex.append("#");\r
+ }\r
}\r
- }\r
- }\r
+ \r
+ nomenclaturalCode = rootNode.getTaxon().getName().getNomenclaturalCode();\r
+ kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);\r
+ traverseTree(rootNode, parentNode, treeIndex, rankMap.get(rank), state);\r
+ \r
+ commitTransaction(txStatus);\r
\r
- // Commit transaction\r
- commitTransaction(txStatus);\r
- logger.error("Committed transaction.");\r
+ elementCount++;\r
+ if (elementCount == halfCount) {\r
+ logger.error("50% of " + rank.getLabel() + " RootNodes processed...");\r
+ }\r
+ }\r
\r
- // Start transaction\r
- txStatus = startTransaction(true);\r
- logger.error("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");\r
- \r
- // Pick next Taxonomic Tree\r
- taxonomicTreeStart++;\r
- }\r
- if (taxonomicTreeList.size() == 0) {\r
- logger.error("No " + pluralString + " left to fetch.");\r
+ }\r
}\r
- // Commit transaction\r
- commitTransaction(txStatus);\r
- logger.error("Committed transaction.");\r
\r
logger.error("*** Finished Making " + pluralString + " ..." + getSuccessString(success));\r
\r
}\r
\r
/**\r
- * Traverse the TaxonTree and store determined values for every Taxon.\r
- * @param rootChild\r
+ * Traverse the TaxonTree recursively and store determined values for every Taxon.\r
+ * @param childNode\r
+ * @param parentNode\r
+ * @param treeIndex\r
+ * @param fetchLevel\r
+ * @param state\r
*/\r
- private void traverseTree(TaxonNode childNode, TaxonNode parentNode, StringBuffer treeIndex, Rank kingdomRank, PesiExportState state) {\r
+ private void traverseTree(TaxonNode childNode, TaxonNode parentNode, StringBuffer treeIndex, Rank fetchLevel, PesiExportState state) {\r
+ // Traverse all branches from this childNode until specified fetchLevel is reached.\r
if (childNode.getTaxon() != null) {\r
- if (state.getDbId(childNode.getTaxon().getName()) != null) {\r
- treeIndex.append(state.getDbId(childNode.getTaxon().getName()));\r
- treeIndex.append("#");\r
+ TaxonNameBase taxonName = childNode.getTaxon().getName();\r
+ Integer taxonNameId = state.getDbId(taxonName);\r
+ if (taxonNameId != null) {\r
+ Rank childTaxonNameRank = taxonName.getRank();\r
+ if (childTaxonNameRank != null) {\r
+ if (! childTaxonNameRank.equals(fetchLevel)) {\r
\r
- saveData(childNode, parentNode, treeIndex, state, state.getDbId(childNode.getTaxon().getName()));\r
+ treeIndex.append(taxonNameId);\r
+ treeIndex.append("#");\r
\r
- for (TaxonNode newNode : childNode.getChildNodes()) {\r
- traverseTree(newNode, childNode, treeIndex, kingdomRank, state);\r
+ saveData(childNode, parentNode, treeIndex, state, taxonNameId);\r
+ \r
+ // Store treeIndex as annotation for further use\r
+ Set<Annotation> annotations = childNode.getAnnotations();\r
+ boolean found = false;\r
+ for (Annotation annotation : annotations) {\r
+ AnnotationType annotationType = annotation.getAnnotationType();\r
+ if (annotationType != null && annotationType.equals(AnnotationType.TREEINDEX())) {\r
+ annotation.setText(treeIndex.toString());\r
+ found = true;\r
+ break;\r
+ }\r
+ }\r
+ if (!found) {\r
+ childNode.addAnnotation(Annotation.NewInstance(treeIndex.toString(), AnnotationType.TREEINDEX(), Language.DEFAULT()));\r
+ }\r
+\r
+ for (TaxonNode newNode : childNode.getChildNodes()) {\r
+ traverseTree(newNode, childNode, treeIndex, fetchLevel, state);\r
+ }\r
+ \r
+ } else {\r
+// logger.error("Target Rank " + fetchLevel.getLabel() + " reached");\r
+ return;\r
+ }\r
+ } else {\r
+ logger.error("Rank is NULL. FetchLevel can not be checked: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
}\r
} else {\r
- logger.error("TaxonName can not be found in State: " + childNode.getTaxon().getName().getUuid() + " (" + childNode.getTaxon().getName().getTitleCache());\r
+ logger.error("TaxonName can not be found in State: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");\r
}\r
+\r
} else {\r
logger.error("Taxon is NULL for TaxonNode: " + childNode.getUuid());\r
}\r
private void saveData(TaxonNode childNode, TaxonNode parentNode, StringBuffer treeIndex, PesiExportState state, Integer currentTaxonFk) {\r
// We are differentiating kingdoms by the nomenclatural code for now.\r
// This needs to be handled in a better way as soon as we know how to differentiate between more kingdoms.\r
- if (childNode.getTaxon() != null && childNode.getTaxon().getName() != null) {\r
- if (parentNode.getTaxon() != null && parentNode.getTaxon().getName() != null) {\r
- invokeParentTaxonFkAndTreeIndexAndKindomFk(childNode.getTaxon().getName(), \r
- childNode.getTaxon().getName().getNomenclaturalCode(), \r
- PesiTransformer.nomenClaturalCode2Kingdom(childNode.getTaxon().getName().getNomenclaturalCode()), \r
- state.getDbId(parentNode.getTaxon().getName()), \r
- currentTaxonFk, \r
- treeIndex);\r
+ Taxon childNodeTaxon = childNode.getTaxon();\r
+ TaxonNameBase childNodeTaxonName = childNode.getTaxon().getName();\r
+ if (childNodeTaxon != null && childNodeTaxonName != null) {\r
+ TaxonNameBase parentNodeTaxonName = null;\r
+ if (parentNode != null) {\r
+ Taxon parentNodeTaxon = parentNode.getTaxon();\r
+ if (parentNodeTaxon != null) {\r
+ parentNodeTaxonName = parentNodeTaxon.getName();\r
+ }\r
}\r
+\r
+ invokeParentTaxonFkAndTreeIndexAndKingdomFk(childNodeTaxonName, \r
+ nomenclaturalCode, \r
+ kingdomFk, \r
+ state.getDbId(parentNodeTaxonName), \r
+ currentTaxonFk, \r
+ treeIndex);\r
}\r
\r
+ // TODO: Move to RelTaxon export\r
// Synonyms of the current Taxon: Don't store treeIndex for Synonyms\r
- for (Synonym synonym : childNode.getTaxon().getSynonyms()) {\r
- invokeSynonyms(synonym.getName(), \r
- childNode.getTaxon().getName().getNomenclaturalCode(), \r
- PesiTransformer.nomenClaturalCode2Kingdom(childNode.getTaxon().getName().getNomenclaturalCode()), \r
- currentTaxonFk, \r
- state.getDbId(synonym.getName()));\r
- }\r
+// for (Synonym synonym : childNodeTaxon.getSynonyms()) {\r
+// TaxonNameBase synonymTaxonName = synonym.getName();\r
+// invokeSynonyms(synonymTaxonName, \r
+// nomenclaturalCode, \r
+// kingdomFk, \r
+// currentTaxonFk, \r
+// state.getDbId(synonymTaxonName));\r
+// }\r
}\r
\r
/**\r
* @param stmt\r
* @return\r
*/\r
- protected boolean invokeParentTaxonFkAndTreeIndexAndKindomFk(TaxonNameBase taxonName, NomenclaturalCode nomenclaturalCode, Integer kingdomFk, Integer parentTaxonFk, Integer currentTaxonFk, StringBuffer treeIndex) {\r
+ protected boolean invokeParentTaxonFkAndTreeIndexAndKingdomFk(TaxonNameBase taxonName, NomenclaturalCode nomenclaturalCode, Integer kingdomFk, Integer parentTaxonFk, Integer currentTaxonFk, StringBuffer treeIndex) {\r
try {\r
- parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(1, parentTaxonFk);\r
+ if (parentTaxonFk != null) {\r
+ parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(1, parentTaxonFk);\r
+ } else {\r
+ parentTaxonFk_TreeIndex_KingdomFkStmt.setObject(1, parentTaxonFk);\r
+ }\r
parentTaxonFk_TreeIndex_KingdomFkStmt.setString(2, treeIndex.toString());\r
parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(3, kingdomFk);\r
parentTaxonFk_TreeIndex_KingdomFkStmt.setInt(4, getRankFk(taxonName, nomenclaturalCode));\r
return true;\r
} catch (SQLException e) {\r
logger.error("SQLException during treeIndex invoke for taxonName - " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + "): " + e.getMessage());\r
- e.printStackTrace();\r
+ logger.error("parentTaxonFk: " + parentTaxonFk);\r
+ logger.error("treeIndex: " + treeIndex);\r
+ logger.error("kingdomFk: " + kingdomFk);\r
+ logger.error("rankFk: " + getRankFk(taxonName, nomenclaturalCode));\r
+ logger.error("rankCache: " + getRankCache(taxonName, nomenclaturalCode));\r
+ logger.error("taxonFk: " + currentTaxonFk);\r
+// e.printStackTrace();\r
return false;\r
}\r
}\r
BGBM BDI Projects / cdmlib.git / commitdiff