Revision 96533ef2
Added by Andreas Müller about 12 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java | ||
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase; |
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import eu.etaxonomy.cdm.model.name.HybridRelationship; |
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import eu.etaxonomy.cdm.model.name.NameRelationship; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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import eu.etaxonomy.cdm.model.name.Rank; |
| ... | ... | |
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private static final String dbTableName = "RelTaxon"; |
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private static final String pluralString = "Relationships"; |
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private static PreparedStatement synonymsStmt; |
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private HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>(); |
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private List<Rank> rankList = new ArrayList<Rank>(); |
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private PesiExportMapping mapping; |
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private int count = 0; |
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private static NomenclaturalCode nomenclaturalCode2; |
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public PesiRelTaxonExport() {
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super(); |
| ... | ... | |
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return result; |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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@Override |
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protected void doInvoke(PesiExportState state) {
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try {
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logger.info("*** Started Making " + pluralString + " ...");
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Connection connection = state.getConfig().getDestination().getConnection(); |
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String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?"; |
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synonymsStmt = connection.prepareStatement(synonymsSql); |
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// Stores whether this invoke was successful or not. |
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boolean success = true; |
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// PESI: Clear the database table RelTaxon. |
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doDelete(state); |
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// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon |
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mapping = getMapping(); |
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// Initialize the db mapper |
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mapping.initialize(state); |
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//Export Taxa.. |
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// success &= doPhase01(state, mapping); |
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// 2nd Round: Add ParentTaxonFk, TreeIndex to each Taxon |
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success &= doPhase02(state, mapping); |
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} catch (SQLException e) {
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e.printStackTrace(); |
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logger.error(e.getMessage()); |
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state.setUnsuccessfull(); |
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return; |
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} |
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} |
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private boolean doPhase01(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
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logger.info("PHASE 1: Relationships ...");
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boolean success = true; |
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int limit = state.getConfig().getLimitSave(); |
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// Start transaction |
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TransactionStatus txStatus = startTransaction(true); |
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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List<RelationshipBase> list; |
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//taxon relations |
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int partitionCount = 0; |
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while ((list = getNextTaxonRelationshipPartition(null, limit, partitionCount++, null)).size() > 0 ) {
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for (RelationshipBase rel : list){
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try {
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mapping.invoke(rel); |
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} catch (Exception e) {
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logger.error(e.getMessage() + ". Relationship: " + rel.getUuid()); |
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e.printStackTrace(); |
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} |
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} |
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} |
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return success; |
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} |
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private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) throws SQLException {
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logger.info("PHASE 1: Relationships ...");
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boolean success = true; |
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int limit = state.getConfig().getLimitSave(); |
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// Start transaction |
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TransactionStatus txStatus = startTransaction(true); |
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");
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List<RelationshipBase> list; |
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//name relations |
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int partitionCount = 0; |
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while ((list = getNextNameRelationshipPartition(null, limit, partitionCount++, null)).size() > 0 ) {
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for (RelationshipBase rel : list){
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try {
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TaxonNameBase<?,?> name1; |
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TaxonNameBase<?,?> name2; |
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if (rel.isInstanceOf(HybridRelationship.class)){
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HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class); |
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name1 = hybridRel.getParentName(); |
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name2 = hybridRel.getHybridName(); |
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}else if (rel.isInstanceOf(NameRelationship.class)){
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NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class); |
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name1 = nameRel.getFromName(); |
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name2 = nameRel.getToName(); |
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}else{
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logger.warn ("Only hybrid- and name-relationships alowed here");
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continue; |
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} |
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List<IdentifiableEntity> fromList = new ArrayList<IdentifiableEntity>(); |
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List<IdentifiableEntity> toList = new ArrayList<IdentifiableEntity>(); |
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makeList(name1, fromList); |
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makeList(name2, toList); |
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for (IdentifiableEntity fromEntity : fromList){
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for (IdentifiableEntity toEntity : toList){
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//TODO set entities to state |
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state.setCurrentFromObject(fromEntity); |
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state.setCurrentToObject(toEntity); |
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mapping.invoke(rel); |
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} |
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} |
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} catch (Exception e) {
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logger.error(e.getMessage() + ". Relationship: " + rel.getUuid()); |
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e.printStackTrace(); |
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} |
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} |
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} |
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return success; |
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} |
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private void makeList(TaxonNameBase<?, ?> name, List<IdentifiableEntity> list) {
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if (! hasPesiTaxon(name)){
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list.add(name); |
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}else{
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for (TaxonBase taxon: getPesiTaxa(name)){
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list.add(taxon); |
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} |
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} |
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} |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase) |
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*/ |
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protected void doInvoke_Old(PesiExportState state) {
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try {
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logger.info("*** Started Making " + pluralString + " ...");
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|
| ... | ... | |
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* @see MethodMapper |
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*/ |
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@SuppressWarnings("unused")
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private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship) {
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private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {
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String result = null; |
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NomenclaturalCode code = null; |
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if (relationship.isInstanceOf(TaxonRelationship.class)){
|
| ... | ... | |
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code = CdmBase.deproxy(relationship, NameRelationship.class).getFromName().getNomenclaturalCode(); |
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} |
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if (code != null) {
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result = PesiTransformer.taxonRelation2RelTaxonQualifierCache(relationship, code);
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result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);
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} else {
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logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());
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} |
| ... | ... | |
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} else if (relationship.isInstanceOf(SynonymRelationship.class)) {
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SynonymRelationship sr = (SynonymRelationship)relationship; |
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taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon(); |
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} else if (relationship.isInstanceOf(NameRelationship.class)) {
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} else if (relationship.isInstanceOf(NameRelationship.class) || relationship.isInstanceOf(HybridRelationship.class)) {
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if (isFrom){
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return state.getDbId(state.getCurrentFromObject()); |
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}else{
|
| ... | ... | |
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", standardMethodParameter, PesiExportState.class));
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", standardMethodParameter, PesiExportState.class));
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mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this));
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mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this));
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mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));
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mapping.addMapper(MethodMapper.NewInstance("Notes", this));
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| 599 | 733 |
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return mapping; |
Also available in: Unified diff
getAllRelationships reimplemented to match only relevant relationship classes,
Export generics include Transformer type