Revision 3ef2e1bd
Added by Andreas Müller over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/palmae/PalmaePostImportUpdater.java | ||
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// $Id$ |
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/** |
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* Copyright (C) 2007 EDIT |
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* European Distributed Institute of Taxonomy
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* European Distributed Institute of Taxonomy |
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* http://www.e-taxonomy.eu |
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*
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* |
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* The contents of this file are subject to the Mozilla Public License Version 1.1 |
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* See LICENSE.TXT at the top of this package for the full license terms. |
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*/ |
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private static final Logger logger = Logger.getLogger(PalmaePostImportUpdater.class); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae(); |
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private String relationships = "relationships"; |
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private String taxonomicAccounts = "taxonomic accounts"; |
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private String fossilRecord = "fossil record"; |
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public boolean updateMissingFeatures(ICdmDataSource dataSource) {
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try{
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int count = 0; |
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UUID featureTreeUuid = PalmaeActivator.featureTreeUuid; |
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CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE); |
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TransactionStatus tx = cdmApp.startTransaction(); |
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FeatureTree tree = cdmApp.getFeatureTreeService().find(featureTreeUuid); |
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FeatureNode root = tree.getRoot(); |
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List<Feature> featureList = cdmApp.getTermService().list(Feature.class, null, null, null, null); |
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for (Feature feature : featureList){
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String label = feature.getLabel(); |
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logger.error("ERROR in feature tree update");
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return false; |
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} |
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} |
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public boolean updateNameUsage(ICdmDataSource dataSource) {
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try{
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boolean result = true; |
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int count = cdmApp.getTaxonService().count(Taxon.class); |
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List<TaxonBase> taxonList = cdmApp.getTaxonService().list(TaxonBase.class, 100000, page, null, null); |
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int i = 0; |
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IReference treatmentReference = (IReference) cdmApp.getCommonService().getSourcedObjectByIdInSource(Reference.class, "palm_pub_ed_999999", "PublicationCitation"); |
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if (treatmentReference == null){
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logger.error("Treatment reference could not be found");
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}else{
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for (TaxonBase nameUsage : taxonList){
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if ((i++ % 100) == 0){System.out.println(i);};
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try {
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//if not in treatment |
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if (! isInTreatment(nameUsage, treatmentReference, false)){
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logger.error("ERROR in name usage update");
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return false; |
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} |
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} |
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/** |
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* @param nameUsage
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* @param nameUsage |
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* @return |
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*/ |
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private Taxon getAcceptedTreatmentTaxon(TaxonBase nameUsage, IReference treatmentReference) {
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} |
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}else if (candidate instanceof Synonym){
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Synonym synonym = (Synonym)candidate; |
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Set<Taxon> accTaxa = synonym.getAcceptedTaxa();
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Taxon accTaxon = synonym.getAcceptedTaxon();
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if (isInTreatment(synonym, treatmentReference, true)){
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hasSynonymInTreatment = true; |
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} |
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for (Taxon accTaxon : accTaxa){
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if (accTaxon != null){
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if (isInTreatment(accTaxon, treatmentReference, false)){
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return accTaxon; |
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} |
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/** |
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* @param taxonBase |
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* @param treatmentReference
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* @param treatmentReference |
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* @return |
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*/ |
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private boolean isInTreatment(TaxonBase taxonBase, IReference treatmentReference, boolean silent) {
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}else if (taxonBase instanceof Synonym){
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Synonym synonym = (Synonym)taxonBase; |
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boolean hasAccTaxonInTreatment = false; |
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for (Taxon accTaxon : synonym.getAcceptedTaxa()){
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Taxon accTaxon = synonym.getAcceptedTaxon(); |
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if (accTaxon != null){
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hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false); |
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} |
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if (hasAccTaxonInTreatment == false){
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}else if (taxonBase instanceof Synonym){
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Synonym synonym = (Synonym)taxonBase; |
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boolean hasAccTaxonInTreatment = false; |
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for (Taxon accTaxon : synonym.getAcceptedTaxa()){
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Taxon accTaxon = synonym.getAcceptedTaxon(); |
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if (accTaxon != null){
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hasAccTaxonInTreatment |= isInTreatment(accTaxon, treatmentReference, false); |
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} |
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if (hasAccTaxonInTreatment == true){
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return false; |
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} |
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} |
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/** |
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* @param taxonCandidate |
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* @param taxon |
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myDescription.addElement(textData); |
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return true; |
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} |
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/** |
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* @param args |
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*/ |
Also available in: Unified diff
ref #5974 Remove synonym relationships (not finished yet)