Revision 7115f486
Added by Andreas Müller almost 9 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/redlist/BfnXmlTestActivator.java | ||
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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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import java.util.Arrays; |
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import java.util.List; |
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import java.util.Scanner; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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|
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES; |
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import eu.etaxonomy.cdm.io.redlist.bfnXml.BfnXmlImportConfigurator; |
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
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/** |
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* @author a.oppermann |
| ... | ... | |
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public class BfnXmlTestActivator {
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private static final Logger logger = Logger.getLogger(BfnXmlTestActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation schemaValidation = DbSchemaValidation.CREATE; |
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_plant_localhost(); |
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_redlist_plant_localhost(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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private final String filename; |
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private String filename; |
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private static final String strSource = "/eu/etaxonomy/cdm/io/bfnXml/"; |
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static final boolean includeNormalExplicit = true; |
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//check - import |
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
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//authors |
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static final boolean doMetaData = true; |
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//references |
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static final DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
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//names |
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static final boolean doTaxonNames = true; |
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static final boolean doRelNames = false; |
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//taxa |
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static final boolean doTaxa = true; |
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static final boolean doRelTaxa = false; |
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//feature |
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static final boolean doFeature = true; |
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//feature |
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static final boolean doAdditionalTerms = true; |
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public BfnXmlTestActivator(String fileName){
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filename = fileName; |
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} |
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private void doImport(){
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System.out.println("Start import from BfnXML to "+ cdmDestination.getDatabase() + " ...");
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//make Source |
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URI source; |
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try {
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source = this.getClass().getResource(strSource+filename).toURI(); |
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ICdmDataSource destination = cdmDestination; |
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BfnXmlImportConfigurator bfnImportConfigurator = BfnXmlImportConfigurator.NewInstance(source, destination); |
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//if xmllist has two lists |
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bfnImportConfigurator.setHasSecondList(false); |
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bfnImportConfigurator.setNomenclaturalSig("Botanical");// "Zoological";//"Botanical"ICNAFP
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bfnImportConfigurator.setDoMetaData(doMetaData); |
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bfnImportConfigurator.setDoReferences(doReferences); |
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bfnImportConfigurator.setDoTaxonNames(doTaxonNames); |
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bfnImportConfigurator.setDoRelNames(doRelNames); |
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bfnImportConfigurator.setDoTaxa(doTaxa); |
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bfnImportConfigurator.setDoRelTaxa(doRelTaxa); |
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bfnImportConfigurator.setCheck(check); |
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bfnImportConfigurator.setDbSchemaValidation(schemaValidation); |
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// invoke import |
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CdmDefaultImport<BfnXmlImportConfigurator> bfnImport = new CdmDefaultImport<BfnXmlImportConfigurator>(); |
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bfnImport.invoke(bfnImportConfigurator); |
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logger.warn("End");
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System.out.println("End import from BfnXML ("+ source.toString() + ")...");
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} catch (URISyntaxException e) {
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e.printStackTrace(); |
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} |
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} |
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/** |
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* @param args |
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*/ |
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public static void main(String[] args) {
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List<String> fileNames = Arrays.asList( |
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// Plants |
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"rldb_print_v4_0_1_0_Flechten_korr_verantw_syn.xml" |
| ... | ... | |
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// |
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// Animals |
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// "rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml" |
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// "rldb_print_v4_0_1_0_artenarmeWeichtiergruppen_121127_verantw_syn.xml", |
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// "rldb_print_v4_0_1_0_Asilidae_GMH_Wolff_110314_HGxls_120413_DF_korrV_Verantw_syn.xml", |
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// "rldb_print_v4_0_1_0_Asseln_121128_verantw_syn.xml", |
| ... | ... | |
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// "rldb_print_v4_0_1_0_Blattoptera_140413_DF_syn.xml", |
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// "rldb_print_v4_0_1_0_Empidoidea_120413_DF.xml", |
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// "rldb_print_v4_0_1_0_Eulen_Korruebern_23-05-2012_KorrV_syn.xml", |
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//
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// |
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//// "rldb_print_v4_0_1_0_Eulenspinner_Spanner_13-06-2012_KorrV_syn.xml", |
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//
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// |
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// "rldb_print_v4_0_1_0_Flohkrebse_121128_verantw_syn.xml", |
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// "rldb_print_v4_0_1_0_Heuschrecken_syn.xml", |
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// "rldb_print_v4_0_1_0_Igelwuermer_120907_verantw.xml", |
| ... | ... | |
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// "rldb_print_v4_0_1_0_Vielborster_130206_verantw_syn.xml", |
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// "rldb_print_v4_0_1_0_Wenigborster_121128_verantw_syn.xml", |
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// "rldb_print_v4_0_1_0_Zehnfusskrebse_130104_verantw_syn.xml" |
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//
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// |
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//old list |
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// "rldb_print_v4_0_1_0_Amphibien.xml", |
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// "rldb_print_v4_0_1_0_Brutvoegel.xml", |
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// "rldb_print_v4_0_1_0_Fische.xml", |
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// "rldb_print_v4_0_1_0_Reptilien_1.xml" |
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//two lists in one |
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// "RoteListe_v4_0_6_0_BFN_Saeuger_korr.xml" |
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); |
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bfnXmlTestActivator.doImport(); |
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// pauseProg(); |
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} |
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//first run |
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//create DB,Metadata |
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// String fileName = "rldb_print_v4_0_1_0_Ameisen_110609_rev120113_syn.xml"; |
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// BfnXmlTestActivator bfnXmlTestActivator = new BfnXmlTestActivator(fileName); |
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// bfnXmlTestActivator.doImport(); |
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} |
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public static void pauseProg(){
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System.out.println("Press enter to continue...");
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Scanner keyboard = new Scanner(System.in); |
| app-import/src/main/java/eu/etaxonomy/cdm/app/redlist/RoteListeDbChecklistActivator.java | ||
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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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import eu.etaxonomy.cdm.database.DbSchemaValidation; |
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import eu.etaxonomy.cdm.database.ICdmDataSource; |
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK; |
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import eu.etaxonomy.cdm.io.common.Source; |
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import eu.etaxonomy.cdm.io.redlist.RoteListeDbImportConfigurator; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| ... | ... | |
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public class RoteListeDbChecklistActivator {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(RoteListeDbChecklistActivator.class); |
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//database validation status (create, update, validate ...) |
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static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
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static final Source mySource = CdmImportSources.ROTE_LISTE_DB(); |
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static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
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int recordsPerTransaction = 1000; |
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//feature tree uuid |
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public static final UUID featureTreeUuid = UUID.fromString("ebe558b5-d04d-41d5-83d9-b61c56e6e34a");
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public static final String sourceReference = "Flora of Central Africa - Checklist"; |
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private UUID uuidGenevaReference = UUID.fromString("cf3fd13d-6cad-430c-ab70-7ea841b7159f");
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private String genevaReferenceTitle = "Geneva Database"; |
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//classification |
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public static final UUID classificationUuid = UUID.fromString("ce1d035a-79a9-4a3a-95bf-26641ecb4fbe");
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//check - import |
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static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK; |
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//taxa |
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static final boolean doTaxa = true; |
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private void doImport(ICdmDataSource cdmDestination){
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//make Source |
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Source source = mySource; |
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RoteListeDbImportConfigurator config= RoteListeDbImportConfigurator.NewInstance(source, cdmDestination); |
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config.setClassificationUuid(classificationUuid); |
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config.setDoTaxa(doTaxa); |
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config.setCheck(check); |
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config.setDbSchemaValidation(hbm2dll); |
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config.setRecordsPerTransaction(recordsPerTransaction); |
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CdmDefaultImport<RoteListeDbImportConfigurator> myImport = new CdmDefaultImport<RoteListeDbImportConfigurator>(); |
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System.out.println("Start import from ("+ source.toString() + ") ...");
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config.setSourceReference(getSourceReference(sourceReference)); |
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myImport.invoke(config); |
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System.out.println("End import from ("+ source.toString() + ")...");
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// FeatureTree tree = makeFeatureNode(myImport.getCdmAppController().getTermService()); |
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// myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree); |
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} |
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private Reference getSourceReference(String string) {
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Reference result = ReferenceFactory.newGeneric(); |
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result.setTitleCache(string); |
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return result; |
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} |
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// private FeatureTree makeFeatureNode(ITermService service){
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// FloraMalesianaTransformer transformer = new FloraMalesianaTransformer(); |
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// |
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// FeatureTree result = FeatureTree.NewInstance(featureTreeUuid); |
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// result.setTitleCache("Flora Malesiana Presentation Feature Tree");
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// FeatureNode root = result.getRoot(); |
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// FeatureNode newNode; |
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// |
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// newNode = FeatureNode.NewInstance(Feature.CITATION()); |
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// root.addChild(newNode); |
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// |
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// newNode = FeatureNode.NewInstance(Feature.DESCRIPTION()); |
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// root.addChild(newNode); |
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// |
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// return result; |
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// } |
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/** |
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* @param args |
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RoteListeDbChecklistActivator me = new RoteListeDbChecklistActivator(); |
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me.doImport(cdmDestination); |
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} |
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} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportAddtionalTerms.java | ||
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import eu.etaxonomy.cdm.api.service.ITermService; |
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import eu.etaxonomy.cdm.api.service.IVocabularyService; |
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import eu.etaxonomy.cdm.io.common.ICdmIO; |
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import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
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import eu.etaxonomy.cdm.model.common.OrderedTermBase; |
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
| ... | ... | |
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* |
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*/ |
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@Component |
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public class BfnXmlImportAddtionalTerms extends BfnXmlImportBase implements ICdmIO<BfnXmlImportState> {
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public class BfnXmlImportAddtionalTerms extends BfnXmlImportBase {
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private static final Logger logger = Logger.getLogger(BfnXmlImportAddtionalTerms.class); |
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public BfnXmlImportAddtionalTerms(){
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super(); |
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} |
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@Override |
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public boolean doCheck(BfnXmlImportState state){
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boolean result = true; |
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//TODO needs to be implemented |
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return result; |
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} |
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public enum Vocabulary{
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GERMAN_FEDERAL_STATES("Bundesländer"),
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GERMAN_PRESENCE_TERMS("Vorkommensstatus"),
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} |
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} |
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private static final List<String> GERMAN_PRESENCE_ABSENCE_TERMS = Arrays.asList(new String[] {
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"a:abwesend", |
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"aa:abwesend - ausgestorben", |
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"af:abwesend - frühere Fehleingabe", |
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"v:vorkommend", |
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"v+:vorkommend - in Einbürgerung befindlich", |
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"ve:vorkommend - etabliert", |
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"vk:vorkommend - kultiviert, domestiziert", |
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"vu:vorkommend - unbeständig", |
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"vs:vorkommend - Vorkommen unsicher", |
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"s:vorkommend - unsicher" |
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}); |
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private static final List<String> GERMAN_ESTABLISHMENT_STATUS_TERMS = Arrays.asList(new String[] {
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"A:Archaeophyt", |
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"I:Indigen", |
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"K:Kulturpflanze / domestiziertes Tier", |
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"N:Neophyt", |
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"KF:Kultuflüchtling" |
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}); |
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private static final List<String> GERMAN_FEDERAL_STATES = Arrays.asList(new String[] {
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"DE:Deutschland", |
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"BW:Baden-Württemberg", |
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"BY:Bayern", |
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"BE:Berlin", |
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"BB:Brandenburg", |
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"HB:Bremen", |
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"HH:Hamburg", |
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"HE:Hessen", |
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"MV:Mecklenburg-Vorpommern", |
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"NI:Niedersachsen", |
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"NW:Nordrhein-Westfalen", |
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"RP:Rheinland-Pfalz", |
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"SL:Saarland", |
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"SN:Sachsen", |
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"ST:Sachsen-Anhalt", |
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"SH:Schleswig-Holstein", |
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"TH:Thüringen" |
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}); |
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/** Hibernate classification vocabulary initialisation strategy */ |
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private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
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"classification.$", |
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"classification.rootNodes", |
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"childNodes", |
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"childNodes.taxon", |
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"childNodes.taxon.name", |
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"taxonNodes", |
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"taxonNodes.taxon", |
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"synonymRelations", |
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"taxon.*", |
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"taxon.sec", |
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"taxon.name.*", |
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"taxon.synonymRelations", |
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"termVocabulary.*", |
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"terms", |
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"namedArea" |
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}); |
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public BfnXmlImportAddtionalTerms(){
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super(); |
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} |
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@Override |
| 74 |
@SuppressWarnings({ "unchecked", "rawtypes" })
|
|
| 75 | 132 |
public void doInvoke(BfnXmlImportState state){
|
| 76 | 133 |
logger.info("create german terms ...");
|
| 77 | 134 |
IVocabularyService vocabularyService = getVocabularyService(); |
| ... | ... | |
| 227 | 284 |
return termVocabulary; |
| 228 | 285 |
} |
| 229 | 286 |
|
| 230 |
|
|
| 231 |
/* (non-Javadoc) |
|
| 232 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 233 |
*/ |
|
| 234 | 287 |
@Override |
| 235 | 288 |
protected boolean isIgnore(BfnXmlImportState state){
|
| 236 |
return ! state.getConfig().isDoTaxonNames();
|
|
| 289 |
return ! state.getConfig().isDoAdditionalTerms();
|
|
| 237 | 290 |
} |
| 238 | 291 |
|
| 239 | 292 |
|
| 240 | 293 |
|
| 241 |
private static final List<String> GERMAN_PRESENCE_ABSENCE_TERMS = Arrays.asList(new String[] {
|
|
| 242 |
"a:abwesend", |
|
| 243 |
"aa:abwesend - ausgestorben", |
|
| 244 |
"af:abwesend - frühere Fehleingabe", |
|
| 245 |
"v:vorkommend", |
|
| 246 |
"v+:vorkommend - in Einbürgerung befindlich", |
|
| 247 |
"ve:vorkommend - etabliert", |
|
| 248 |
"vk:vorkommend - kultiviert, domestiziert", |
|
| 249 |
"vu:vorkommend - unbeständig", |
|
| 250 |
"vs:vorkommend - Vorkommen unsicher", |
|
| 251 |
"s:vorkommend - unsicher" |
|
| 252 |
|
|
| 253 |
}); |
|
| 254 | 294 |
|
| 255 |
private static final List<String> GERMAN_ESTABLISHMENT_STATUS_TERMS = Arrays.asList(new String[] {
|
|
| 256 |
"A:Archaeophyt", |
|
| 257 |
"I:Indigen", |
|
| 258 |
"K:Kulturpflanze / domestiziertes Tier", |
|
| 259 |
"N:Neophyt", |
|
| 260 |
"KF:Kultuflüchtling" |
|
| 261 |
}); |
|
| 262 |
|
|
| 263 |
private static final List<String> GERMAN_FEDERAL_STATES = Arrays.asList(new String[] {
|
|
| 264 |
"DE:Deutschland", |
|
| 265 |
"BW:Baden-Württemberg", |
|
| 266 |
"BY:Bayern", |
|
| 267 |
"BE:Berlin", |
|
| 268 |
"BB:Brandenburg", |
|
| 269 |
"HB:Bremen", |
|
| 270 |
"HH:Hamburg", |
|
| 271 |
"HE:Hessen", |
|
| 272 |
"MV:Mecklenburg-Vorpommern", |
|
| 273 |
"NI:Niedersachsen", |
|
| 274 |
"NW:Nordrhein-Westfalen", |
|
| 275 |
"RP:Rheinland-Pfalz", |
|
| 276 |
"SL:Saarland", |
|
| 277 |
"SN:Sachsen", |
|
| 278 |
"ST:Sachsen-Anhalt", |
|
| 279 |
"SH:Schleswig-Holstein", |
|
| 280 |
"TH:Thüringen" |
|
| 281 |
}); |
|
| 282 |
|
|
| 283 |
|
|
| 284 |
/** Hibernate classification vocabulary initialisation strategy */ |
|
| 285 |
private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
|
|
| 286 |
"classification.$", |
|
| 287 |
"classification.rootNodes", |
|
| 288 |
"childNodes", |
|
| 289 |
"childNodes.taxon", |
|
| 290 |
"childNodes.taxon.name", |
|
| 291 |
"taxonNodes", |
|
| 292 |
"taxonNodes.taxon", |
|
| 293 |
"synonymRelations", |
|
| 294 |
"taxon.*", |
|
| 295 |
"taxon.sec", |
|
| 296 |
"taxon.name.*", |
|
| 297 |
"taxon.synonymRelations", |
|
| 298 |
"termVocabulary.*", |
|
| 299 |
"terms", |
|
| 300 |
"namedArea" |
|
| 301 |
|
|
| 302 |
}); |
|
| 295 |
@Override |
|
| 296 |
public boolean doCheck(BfnXmlImportState state){
|
|
| 297 |
boolean result = true; |
|
| 298 |
//TODO needs to be implemented |
|
| 299 |
return result; |
|
| 300 |
} |
|
| 303 | 301 |
|
| 304 | 302 |
|
| 305 | 303 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportConfigurator.java | ||
|---|---|---|
| 5 | 5 |
* |
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 |
*/
|
|
| 8 |
*/ |
|
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.redlist.bfnXml; |
| 11 | 11 |
|
| ... | ... | |
| 15 | 15 |
* |
| 16 | 16 |
*/ |
| 17 | 17 |
import java.io.InputStream; |
| 18 |
import java.lang.reflect.Method; |
|
| 19 | 18 |
import java.net.MalformedURLException; |
| 20 | 19 |
import java.net.URI; |
| 21 | 20 |
import java.net.URL; |
| ... | ... | |
| 27 | 26 |
|
| 28 | 27 |
import eu.etaxonomy.cdm.common.XmlHelp; |
| 29 | 28 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 30 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
| 31 | 29 |
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase; |
| 32 | 30 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 33 |
import eu.etaxonomy.cdm.io.tcsxml.DefaultTcsXmlPlaceholders; |
|
| 34 |
import eu.etaxonomy.cdm.io.tcsxml.ITcsXmlPlaceholderClass; |
|
| 35 | 31 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 36 | 32 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 37 | 33 |
|
| 38 | 34 |
@Component |
| 39 |
public class BfnXmlImportConfigurator extends ImportConfiguratorBase<BfnXmlImportState, URI> implements IImportConfigurator {
|
|
| 35 |
public class BfnXmlImportConfigurator extends ImportConfiguratorBase<BfnXmlImportState, URI> {
|
|
| 40 | 36 |
private static final Logger logger = Logger.getLogger(BfnXmlImportConfigurator.class); |
| 41 |
|
|
| 37 |
|
|
| 42 | 38 |
//TODO |
| 43 | 39 |
private static IInputTransformer defaultTransformer = null; |
| 44 | 40 |
|
| 45 |
|
|
| 41 |
|
|
| 46 | 42 |
private boolean doMetaData = true; |
| 47 |
private boolean doSpecimen = true; |
|
| 48 |
private boolean doInformationImport = true; |
|
| 49 |
private boolean fillSecondList = false; |
|
| 50 |
private boolean hasSecondList = false; |
|
| 43 |
private boolean doTaxonNames = true; |
|
| 44 |
private boolean doFeature = true; |
|
| 45 |
private boolean doAdditionalTerms = true; |
|
| 46 |
|
|
| 47 |
private boolean doInformationImport = true; |
|
| 48 |
private boolean fillSecondList = false; |
|
| 49 |
private boolean hasSecondList = false; |
|
| 51 | 50 |
|
| 52 | 51 |
|
| 53 |
|
|
| 54 |
public boolean isFillSecondList() {
|
|
| 52 |
|
|
| 53 |
public boolean isFillSecondList() {
|
|
| 55 | 54 |
return fillSecondList; |
| 56 | 55 |
} |
| 57 | 56 |
|
| ... | ... | |
| 59 | 58 |
this.fillSecondList = fillSecondList; |
| 60 | 59 |
} |
| 61 | 60 |
|
| 62 |
// //references |
|
| 63 |
private DO_REFERENCES doReferences = DO_REFERENCES.ALL; |
|
| 64 |
// //names |
|
| 65 |
private boolean doTaxonNames = true; |
|
| 66 |
private boolean doRelNames = true; |
|
| 67 |
// //taxa |
|
| 68 |
private boolean doTaxa = true; |
|
| 69 |
private boolean doRelTaxa = true; |
|
| 70 |
|
|
| 71 |
|
|
| 72 |
|
|
| 73 |
private Method functionMetaDataDetailed = null; |
|
| 74 |
private ITcsXmlPlaceholderClass placeholderClass; |
|
| 75 |
|
|
| 61 |
|
|
| 76 | 62 |
// rdfNamespace |
| 77 | 63 |
Namespace bfnXmlNamespace; |
| 78 | 64 |
|
| 79 | 65 |
private String nomenclaturalCode = null; |
| 80 | 66 |
|
| 81 |
protected static Namespace nsTcsXml = Namespace.getNamespace("http://www.tdwg.org/schemas/tcs/1.01");
|
|
| 82 |
|
|
| 83 | 67 |
@SuppressWarnings("unchecked")
|
| 68 |
@Override |
|
| 84 | 69 |
protected void makeIoClassList(){
|
| 85 | 70 |
ioClassList = new Class[]{
|
| 86 | 71 |
BfnXmlImportAddtionalTerms.class, |
| ... | ... | |
| 89 | 74 |
BfnXmlImportTaxonName.class |
| 90 | 75 |
}; |
| 91 | 76 |
}; |
| 92 |
|
|
| 77 |
|
|
| 93 | 78 |
public static BfnXmlImportConfigurator NewInstance(URI uri, |
| 94 | 79 |
ICdmDataSource destination){
|
| 95 | 80 |
return new BfnXmlImportConfigurator(uri, destination); |
| 96 | 81 |
} |
| 97 |
|
|
| 82 |
|
|
| 98 | 83 |
/** |
| 99 | 84 |
* @param berlinModelSource |
| 100 | 85 |
* @param sourceReference |
| ... | ... | |
| 102 | 87 |
*/ |
| 103 | 88 |
private BfnXmlImportConfigurator() {
|
| 104 | 89 |
super(defaultTransformer); |
| 105 |
// setSource(url); |
|
| 106 |
// setDestination(destination); |
|
| 107 | 90 |
} |
| 108 |
|
|
| 91 |
|
|
| 109 | 92 |
/** |
| 110 | 93 |
* @param berlinModelSource |
| 111 | 94 |
* @param sourceReference |
| ... | ... | |
| 116 | 99 |
setSource(uri); |
| 117 | 100 |
setDestination(destination); |
| 118 | 101 |
} |
| 119 |
|
|
| 120 |
|
|
| 121 | 102 |
|
| 122 |
/* (non-Javadoc) |
|
| 123 |
* @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState() |
|
| 124 |
*/ |
|
| 103 |
|
|
| 104 |
@Override |
|
| 125 | 105 |
public BfnXmlImportState getNewState() {
|
| 126 | 106 |
return new BfnXmlImportState(this); |
| 127 | 107 |
} |
| 128 | 108 |
|
| 129 |
/* (non-Javadoc) |
|
| 130 |
* @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSource() |
|
| 131 |
*/ |
|
| 132 |
public URI getSource() {
|
|
| 133 |
return (URI)super.getSource(); |
|
| 134 |
} |
|
| 135 |
|
|
| 136 |
/** |
|
| 137 |
* @param file |
|
| 138 |
*/ |
|
| 139 |
public void setSource(URI uri) {
|
|
| 140 |
super.setSource(uri); |
|
| 141 |
} |
|
| 142 |
|
|
| 143 | 109 |
/** |
| 144 | 110 |
* @return |
| 145 | 111 |
*/ |
| ... | ... | |
| 161 | 127 |
} |
| 162 | 128 |
return null; |
| 163 | 129 |
} |
| 164 |
|
|
| 130 |
|
|
| 165 | 131 |
private boolean makeNamespaces(Element root){
|
| 166 | 132 |
bfnXmlNamespace = root.getNamespace(); |
| 167 |
if (bfnXmlNamespace == null
|
|
| 168 |
/**|| tcNamespace == null
|
|
| 169 |
* || tnNamespace == null
|
|
| 170 |
* || commonNamespace == null
|
|
| 171 |
* || geoNamespace == null
|
|
| 133 |
if (bfnXmlNamespace == null |
|
| 134 |
/**|| tcNamespace == null |
|
| 135 |
* || tnNamespace == null |
|
| 136 |
* || commonNamespace == null |
|
| 137 |
* || geoNamespace == null |
|
| 172 | 138 |
* || publicationNamespace == null*/){
|
| 173 | 139 |
logger.warn("At least one Namespace is NULL");
|
| 174 | 140 |
} |
| 175 | 141 |
return true; |
| 176 | 142 |
} |
| 177 | 143 |
|
| 178 |
|
|
| 179 |
/* (non-Javadoc) |
|
| 180 |
* @see eu.etaxonomy.cdm.io.common.ImportConfiguratorBase#getSourceReference() |
|
| 181 |
*/ |
|
| 182 | 144 |
@Override |
| 183 | 145 |
public Reference getSourceReference() {
|
| 184 | 146 |
//TODO |
| ... | ... | |
| 190 | 152 |
return sourceReference; |
| 191 | 153 |
} |
| 192 | 154 |
|
| 193 |
|
|
| 194 |
/* (non-Javadoc) |
|
| 195 |
* @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getSourceNameString() |
|
| 196 |
*/ |
|
| 197 |
public String getSourceNameString() {
|
|
| 155 |
@Override |
|
| 156 |
public String getSourceNameString() {
|
|
| 198 | 157 |
if (this.getSource() == null){
|
| 199 | 158 |
return null; |
| 200 | 159 |
}else{
|
| 201 | 160 |
return this.getSource().toString(); |
| 202 | 161 |
} |
| 203 | 162 |
} |
| 204 |
|
|
| 163 |
|
|
| 205 | 164 |
public Namespace getBfnXmlNamespace() {
|
| 206 | 165 |
return bfnXmlNamespace; |
| 207 | 166 |
} |
| ... | ... | |
| 210 | 169 |
this.bfnXmlNamespace = bfnXmlNamespace; |
| 211 | 170 |
} |
| 212 | 171 |
|
| 213 |
/** |
|
| 214 |
* @param funMetaDataDetailed the funMetaDataDetailed to set |
|
| 215 |
*/ |
|
| 216 |
public void setFunctionMetaDataDetailed(Method functionMetaDataDetailed) {
|
|
| 217 |
this.functionMetaDataDetailed = functionMetaDataDetailed; |
|
| 218 |
} |
|
| 219 |
|
|
| 220 |
public DO_REFERENCES getDoReferences() {
|
|
| 221 |
return doReferences; |
|
| 222 |
} |
|
| 223 |
public void setDoReferences(DO_REFERENCES doReferences) {
|
|
| 224 |
this.doReferences = doReferences; |
|
| 225 |
} |
|
| 226 |
|
|
| 227 | 172 |
public boolean isDoTaxonNames() {
|
| 228 | 173 |
return doTaxonNames; |
| 229 | 174 |
} |
| ... | ... | |
| 231 | 176 |
this.doTaxonNames = doTaxonNames; |
| 232 | 177 |
} |
| 233 | 178 |
|
| 234 |
public boolean isDoTaxa() {
|
|
| 235 |
return doTaxa; |
|
| 236 |
} |
|
| 237 |
public void setDoTaxa(boolean doTaxa) {
|
|
| 238 |
this.doTaxa = doTaxa; |
|
| 239 |
} |
|
| 240 |
|
|
| 241 |
public boolean isDoRelTaxa() {
|
|
| 242 |
return doRelTaxa; |
|
| 243 |
} |
|
| 244 |
public void setDoRelTaxa(boolean doRelTaxa) {
|
|
| 245 |
this.doRelTaxa = doRelTaxa; |
|
| 246 |
} |
|
| 247 |
|
|
| 248 |
/** |
|
| 249 |
* Import name relationships yes/no?. |
|
| 250 |
* @return |
|
| 251 |
*/ |
|
| 252 |
public boolean isDoRelNames() {
|
|
| 253 |
return doRelNames; |
|
| 254 |
} |
|
| 255 |
public void setDoRelNames(boolean doRelNames) {
|
|
| 256 |
this.doRelNames = doRelNames; |
|
| 257 |
} |
|
| 258 |
|
|
| 259 | 179 |
/** |
| 260 | 180 |
* @return the doMetaData |
| 261 | 181 |
*/ |
| ... | ... | |
| 271 | 191 |
} |
| 272 | 192 |
|
| 273 | 193 |
|
| 274 |
/** |
|
| 275 |
* @return the doSpecimen |
|
| 276 |
*/ |
|
| 277 |
public boolean isDoSpecimen() {
|
|
| 278 |
return doSpecimen; |
|
| 279 |
} |
|
| 280 |
|
|
| 281 |
/** |
|
| 282 |
* @param doSpecimen the doSpecimen to set |
|
| 283 |
*/ |
|
| 284 |
public void setDoSpecimen(boolean doSpecimen) {
|
|
| 285 |
this.doSpecimen = doSpecimen; |
|
| 286 |
} |
|
| 287 |
|
|
| 288 |
/** |
|
| 289 |
* @return the placeholderClass |
|
| 290 |
*/ |
|
| 291 |
public ITcsXmlPlaceholderClass getPlaceholderClass() {
|
|
| 292 |
if (placeholderClass == null){
|
|
| 293 |
placeholderClass = new DefaultTcsXmlPlaceholders(); |
|
| 294 |
} |
|
| 295 |
return placeholderClass; |
|
| 296 |
} |
|
| 297 |
|
|
| 298 |
/** |
|
| 299 |
* @param placeholderClass the placeholderClass to set |
|
| 300 |
*/ |
|
| 301 |
public void setPlaceholderClass(ITcsXmlPlaceholderClass placeholderClass) {
|
|
| 302 |
this.placeholderClass = placeholderClass; |
|
| 303 |
} |
|
| 304 |
|
|
| 305 | 194 |
public boolean isDoInformationImport() {
|
| 306 | 195 |
return doInformationImport; |
| 307 | 196 |
} |
| ... | ... | |
| 325 | 214 |
public String getNomenclaturalSig(){
|
| 326 | 215 |
return nomenclaturalCode; |
| 327 | 216 |
} |
| 217 |
|
|
| 218 |
/** |
|
| 219 |
* @return the doFeature |
|
| 220 |
*/ |
|
| 221 |
public boolean isDoFeature() {
|
|
| 222 |
return doFeature; |
|
| 223 |
} |
|
| 224 |
|
|
| 225 |
|
|
| 226 |
/** |
|
| 227 |
* @param doFeature the doFeature to set |
|
| 228 |
*/ |
|
| 229 |
public void setDoFeature(boolean doFeature) {
|
|
| 230 |
this.doFeature = doFeature; |
|
| 231 |
} |
|
| 232 |
|
|
| 233 |
/** |
|
| 234 |
* @return the doAdditionalTerms |
|
| 235 |
*/ |
|
| 236 |
public boolean isDoAdditionalTerms() {
|
|
| 237 |
return doAdditionalTerms; |
|
| 238 |
} |
|
| 239 |
|
|
| 240 |
/** |
|
| 241 |
* @param doAdditionalTerms the doAdditionalTerms to set |
|
| 242 |
*/ |
|
| 243 |
public void setDoAdditionalTerms(boolean doAdditionalTerms) {
|
|
| 244 |
this.doAdditionalTerms = doAdditionalTerms; |
|
| 245 |
} |
|
| 328 | 246 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportFeature.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 14 | 14 |
import java.util.List; |
| 15 | 15 |
import java.util.UUID; |
| 16 | 16 |
|
| 17 |
import javax.management.ObjectInstance; |
|
| 18 |
|
|
| 19 |
import org.apache.commons.lang.StringUtils; |
|
| 20 | 17 |
import org.apache.log4j.Logger; |
| 21 |
import org.hibernate.id.UUIDGenerator; |
|
| 22 | 18 |
import org.jdom.Element; |
| 23 | 19 |
import org.jdom.Namespace; |
| 24 | 20 |
import org.springframework.stereotype.Component; |
| 25 | 21 |
import org.springframework.transaction.TransactionStatus; |
| 26 | 22 |
|
| 27 |
import eu.etaxonomy.cdm.api.service.IClassificationService; |
|
| 28 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
|
| 29 |
import eu.etaxonomy.cdm.api.service.IFeatureNodeService; |
|
| 30 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
|
| 31 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 32 | 23 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
| 33 | 24 |
import eu.etaxonomy.cdm.common.ResultWrapper; |
| 34 | 25 |
import eu.etaxonomy.cdm.common.XmlHelp; |
| 35 | 26 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
| 36 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
|
| 37 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
| 38 | 27 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 39 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 40 | 28 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
| 41 | 29 |
import eu.etaxonomy.cdm.model.common.TermType; |
| 42 | 30 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
| 43 |
import eu.etaxonomy.cdm.model.common.VocabularyEnum; |
|
| 44 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
|
| 45 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
| 46 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
| 47 | 31 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 48 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 49 | 32 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
| 50 | 33 |
import eu.etaxonomy.cdm.model.description.State; |
| 51 |
import eu.etaxonomy.cdm.model.description.StateData; |
|
| 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 53 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 55 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 56 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
| 57 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 58 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
|
| 59 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 60 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 61 |
import eu.etaxonomy.cdm.persistence.dao.description.IFeatureDao; |
|
| 62 | 34 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
| 63 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 64 |
import eu.etaxonomy.cdm.strategy.parser.ParserProblem; |
|
| 65 | 35 |
/** |
| 66 |
*
|
|
| 36 |
* |
|
| 67 | 37 |
* @author a.oppermann |
| 68 | 38 |
* @date 04.07.2013 |
| 69 | 39 |
* |
| ... | ... | |
| 76 | 46 |
super(); |
| 77 | 47 |
} |
| 78 | 48 |
|
| 79 |
@Override |
|
| 80 |
public boolean doCheck(BfnXmlImportState state){
|
|
| 81 |
boolean result = true; |
|
| 82 |
//TODO needs to be implemented |
|
| 83 |
return result; |
|
| 84 |
} |
|
| 49 |
|
|
| 50 |
/** Hibernate classification vocabulary initialisation strategy */ |
|
| 51 |
private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
|
|
| 52 |
"classification.$", |
|
| 53 |
"classification.rootNodes", |
|
| 54 |
"childNodes", |
|
| 55 |
"childNodes.taxon", |
|
| 56 |
"childNodes.taxon.name", |
|
| 57 |
"taxonNodes", |
|
| 58 |
"taxonNodes.taxon", |
|
| 59 |
"synonymRelations", |
|
| 60 |
"taxon.*", |
|
| 61 |
"taxon.sec", |
|
| 62 |
"taxon.name.*", |
|
| 63 |
"taxon.synonymRelations", |
|
| 64 |
"termVocabulary.*", |
|
| 65 |
"terms" |
|
| 66 |
|
|
| 67 |
}); |
|
| 85 | 68 |
|
| 86 | 69 |
@Override |
| 87 | 70 |
@SuppressWarnings({ "unchecked", "rawtypes" })
|
| 88 | 71 |
public void doInvoke(BfnXmlImportState state){
|
| 89 | 72 |
|
| 90 | 73 |
IVocabularyService vocabularyService = getVocabularyService(); |
| 91 |
|
|
| 92 |
|
|
| 74 |
|
|
| 75 |
|
|
| 93 | 76 |
logger.warn("start create Features in CDM...");
|
| 94 | 77 |
ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
| 95 | 78 |
String childName; |
| ... | ... | |
| 97 | 80 |
BfnXmlImportConfigurator config = state.getConfig(); |
| 98 | 81 |
Element elDataSet = getDataSetElement(config); |
| 99 | 82 |
Namespace bfnNamespace = config.getBfnXmlNamespace(); |
| 100 |
|
|
| 83 |
|
|
| 101 | 84 |
List contentXML = elDataSet.getContent(); |
| 102 | 85 |
Element currentElement = null; |
| 103 | 86 |
for(Object object:contentXML){
|
| 104 |
|
|
| 87 |
|
|
| 105 | 88 |
if(object instanceof Element){
|
| 106 | 89 |
currentElement = (Element)object; |
| 107 | 90 |
|
| 108 | 91 |
if(currentElement.getName().equalsIgnoreCase("ROTELISTEDATEN")){
|
| 109 |
|
|
| 92 |
|
|
| 110 | 93 |
TransactionStatus tx = startTransaction(); |
| 111 | 94 |
|
| 112 | 95 |
childName = "EIGENSCHAFTEN"; |
| ... | ... | |
| 114 | 97 |
Element elFeatureNames = XmlHelp.getSingleChildElement(success, currentElement, childName, bfnNamespace, obligatory); |
| 115 | 98 |
|
| 116 | 99 |
String bfnElementName = "EIGENSCHAFT"; |
| 117 |
List<Element> elFeatureList = (List<Element>)elFeatureNames.getChildren(bfnElementName, bfnNamespace);
|
|
| 100 |
List<Element> elFeatureList = elFeatureNames.getChildren(bfnElementName, bfnNamespace); |
|
| 118 | 101 |
List<Feature> featureList = new ArrayList<Feature>(); |
| 119 | 102 |
//for each taxonName |
| 120 | 103 |
for (Element elFeature : elFeatureList){
|
| ... | ... | |
| 168 | 151 |
} |
| 169 | 152 |
createFeatureTree(featureList); |
| 170 | 153 |
commitTransaction(tx); |
| 171 |
|
|
| 154 |
|
|
| 172 | 155 |
logger.info("end create features ...");
|
| 173 |
|
|
| 156 |
|
|
| 174 | 157 |
if (!success.getValue()){
|
| 175 | 158 |
state.setUnsuccessfull(); |
| 176 | 159 |
} |
| ... | ... | |
| 193 | 176 |
} |
| 194 | 177 |
|
| 195 | 178 |
/** |
| 196 |
*
|
|
| 179 |
* |
|
| 197 | 180 |
* @param vocabularyService |
| 198 | 181 |
* @param featureList |
| 199 | 182 |
* @param success |
| ... | ... | |
| 241 | 224 |
if(termVocabulary == null){
|
| 242 | 225 |
termVocabulary = TermVocabulary.NewInstance(termType, strTermVocabulary, strTermVocabulary, strTermVocabulary, null); |
| 243 | 226 |
} |
| 244 |
termVocabulary.addTerm(term);
|
|
| 227 |
termVocabulary.addTerm(term); |
|
| 245 | 228 |
vocabularyService.saveOrUpdate(termVocabulary); |
| 246 |
|
|
| 229 |
|
|
| 247 | 230 |
return termVocabulary; |
| 248 | 231 |
} |
| 249 | 232 |
|
| ... | ... | |
| 253 | 236 |
* @param bfnNamespace |
| 254 | 237 |
* @param elListValues |
| 255 | 238 |
* @param childElementName |
| 256 |
* @param redListCat
|
|
| 239 |
* @param redListCat |
|
| 257 | 240 |
*/ |
| 258 |
|
|
| 241 |
|
|
| 259 | 242 |
@SuppressWarnings({ "unchecked", "rawtypes"})
|
| 260 |
private void createOrUpdateStates(Namespace bfnNamespace, Element elListValues, String childElementName,
|
|
| 243 |
private void createOrUpdateStates(Namespace bfnNamespace, Element elListValues, String childElementName, |
|
| 261 | 244 |
Feature redListCat, BfnXmlImportState state) {
|
| 262 | 245 |
|
| 263 |
List<Element> elListValueList = (List<Element>)elListValues.getChildren(childElementName, bfnNamespace);
|
|
| 246 |
List<Element> elListValueList = elListValues.getChildren(childElementName, bfnNamespace); |
|
| 264 | 247 |
// List<StateData> stateList = new ArrayList<StateData>(); |
| 265 |
|
|
| 248 |
|
|
| 266 | 249 |
OrderedTermVocabulary termVocabulary = null; |
| 267 | 250 |
for(Element elListValue:elListValueList){
|
| 268 | 251 |
String listValue = elListValue.getTextNormalize(); |
| ... | ... | |
| 280 | 263 |
} catch (UnknownCdmTypeException e) {
|
| 281 | 264 |
matchedListValue = listValue; |
| 282 | 265 |
logger.warn("no matched red list code nor UUID found. \n" + e);
|
| 283 |
|
|
| 266 |
|
|
| 284 | 267 |
} |
| 285 | 268 |
try {
|
| 286 | 269 |
stateTermUuid = BfnXmlTransformer.getRedlistStateTermUUID(matchedListValue, redListCat.getTitleCache()); |
| 287 | 270 |
} catch (UnknownCdmTypeException e) {
|
| 288 |
// stateTermUuid = UUID.randomUUID();
|
|
| 271 |
// stateTermUuid = UUID.randomUUID(); |
|
| 289 | 272 |
//TODO: needs to be fixed for "eindeutiger Code" |
| 290 | 273 |
logger.warn("could not finde state term uuid for " + matchedListValue + " and redlist category"+ redListCat.getTitleCache()+"\n"+e);
|
| 291 | 274 |
} |
| 292 | 275 |
String vocName = redListCat.toString()+" States"; |
| 293 |
termVocabulary = (OrderedTermVocabulary) getVocabulary(TermType.State, vocabularyStateUuid, vocName, vocName, vocName, null, true, null);
|
|
| 276 |
termVocabulary = (OrderedTermVocabulary) getVocabulary(TermType.State, vocabularyStateUuid, vocName, vocName, vocName, null, true, null); |
|
| 294 | 277 |
State stateTerm = getStateTerm(state, stateTermUuid, matchedListValue, matchedListValue, matchedListValue, termVocabulary); |
| 295 | 278 |
} |
| 296 | 279 |
if(termVocabulary != null){
|
| 297 | 280 |
redListCat.addSupportedCategoricalEnumeration(termVocabulary); |
| 298 | 281 |
getTermService().saveOrUpdate(redListCat); |
| 299 | 282 |
} |
| 300 |
|
|
| 283 |
|
|
| 301 | 284 |
} |
| 302 | 285 |
|
| 303 |
|
|
| 304 |
|
|
| 305 |
|
|
| 306 | 286 |
|
| 307 |
|
|
| 308 |
|
|
| 309 |
|
|
| 310 |
|
|
| 311 |
/* (non-Javadoc) |
|
| 312 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 313 |
*/ |
|
| 287 |
@Override |
|
| 288 |
public boolean doCheck(BfnXmlImportState state){
|
|
| 289 |
boolean result = true; |
|
| 290 |
//TODO needs to be implemented |
|
| 291 |
return result; |
|
| 292 |
} |
|
| 293 |
|
|
| 294 |
@Override |
|
| 314 | 295 |
protected boolean isIgnore(BfnXmlImportState state){
|
| 315 |
return ! state.getConfig().isDoTaxonNames();
|
|
| 296 |
return ! state.getConfig().isDoFeature();
|
|
| 316 | 297 |
} |
| 317 |
|
|
| 318 |
|
|
| 319 |
|
|
| 320 |
/** Hibernate classification vocabulary initialisation strategy */ |
|
| 321 |
private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
|
|
| 322 |
"classification.$", |
|
| 323 |
"classification.rootNodes", |
|
| 324 |
"childNodes", |
|
| 325 |
"childNodes.taxon", |
|
| 326 |
"childNodes.taxon.name", |
|
| 327 |
"taxonNodes", |
|
| 328 |
"taxonNodes.taxon", |
|
| 329 |
"synonymRelations", |
|
| 330 |
"taxon.*", |
|
| 331 |
"taxon.sec", |
|
| 332 |
"taxon.name.*", |
|
| 333 |
"taxon.synonymRelations", |
|
| 334 |
"termVocabulary.*", |
|
| 335 |
"terms" |
|
| 336 |
|
|
| 337 |
}); |
|
| 338 | 298 |
|
| 339 | 299 |
|
| 340 | 300 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportMetaData.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| 9 | 9 |
|
| 10 | 10 |
package eu.etaxonomy.cdm.io.redlist.bfnXml; |
| 11 | 11 |
|
| 12 |
import java.util.ArrayList; |
|
| 13 |
import java.util.Arrays; |
|
| 14 | 12 |
import java.util.List; |
| 15 |
import java.util.UUID; |
|
| 16 | 13 |
|
| 17 |
import javax.management.ObjectInstance; |
|
| 18 |
|
|
| 19 |
import org.apache.commons.lang.StringUtils; |
|
| 20 | 14 |
import org.apache.log4j.Logger; |
| 21 |
import org.hibernate.id.UUIDGenerator; |
|
| 22 | 15 |
import org.jdom.Element; |
| 23 | 16 |
import org.jdom.Namespace; |
| 24 | 17 |
import org.springframework.stereotype.Component; |
| 25 | 18 |
import org.springframework.transaction.TransactionStatus; |
| 26 | 19 |
|
| 27 |
import eu.etaxonomy.cdm.api.service.IClassificationService; |
|
| 28 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
|
| 29 |
import eu.etaxonomy.cdm.api.service.IFeatureNodeService; |
|
| 30 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
|
| 31 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
| 32 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
|
| 33 | 20 |
import eu.etaxonomy.cdm.common.ResultWrapper; |
| 34 |
import eu.etaxonomy.cdm.common.XmlHelp; |
|
| 35 | 21 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
| 36 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
|
| 37 |
import eu.etaxonomy.cdm.io.common.MapWrapper; |
|
| 38 |
import eu.etaxonomy.cdm.io.common.Source; |
|
| 39 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
|
| 40 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 41 |
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary; |
|
| 42 |
import eu.etaxonomy.cdm.model.common.TermType; |
|
| 43 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
|
| 44 | 22 |
import eu.etaxonomy.cdm.model.common.TimePeriod; |
| 45 |
import eu.etaxonomy.cdm.model.common.VocabularyEnum; |
|
| 46 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
|
| 47 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
| 48 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
| 49 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
| 50 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 51 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 52 |
import eu.etaxonomy.cdm.model.description.State; |
|
| 53 |
import eu.etaxonomy.cdm.model.description.StateData; |
|
| 54 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 55 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 56 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
| 57 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
| 58 | 23 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 59 | 24 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 60 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
| 61 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 62 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
|
| 63 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
| 64 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 65 |
import eu.etaxonomy.cdm.persistence.dao.description.IFeatureDao; |
|
| 66 |
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
|
| 67 |
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
|
| 68 |
import eu.etaxonomy.cdm.strategy.parser.ParserProblem; |
|
| 69 | 25 |
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser; |
| 70 | 26 |
/** |
| 71 |
*
|
|
| 27 |
* |
|
| 72 | 28 |
* @author a.oppermann |
| 73 | 29 |
* @date 04.07.2013 |
| 74 | 30 |
* |
| ... | ... | |
| 94 | 50 |
@Override |
| 95 | 51 |
public void doInvoke(BfnXmlImportState state){
|
| 96 | 52 |
logger.warn("start import MetaData...");
|
| 97 |
|
|
| 98 |
|
|
| 53 |
|
|
| 54 |
|
|
| 99 | 55 |
ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true); |
| 100 | 56 |
|
| 101 | 57 |
BfnXmlImportConfigurator config = state.getConfig(); |
| ... | ... | |
| 106 | 62 |
sourceFileName = elDataSet.getAttributeValue("source");
|
| 107 | 63 |
debVersion = elDataSet.getAttributeValue("debversion");
|
| 108 | 64 |
timeStamp = elDataSet.getAttributeValue("timestamp");
|
| 109 |
|
|
| 110 |
Reference sourceReference = ReferenceFactory.newGeneric(); |
|
| 65 |
|
|
| 66 |
Reference<?> sourceReference = ReferenceFactory.newGeneric();
|
|
| 111 | 67 |
sourceReference.setTitle(sourceFileName); |
| 112 | 68 |
TimePeriod parsedTimePeriod = TimePeriodParser.parseString(timeStamp); |
| 113 | 69 |
sourceReference.setDatePublished(parsedTimePeriod); |
| 114 | 70 |
state.setCompleteSourceRef(sourceReference); |
| 115 | 71 |
} |
| 116 |
|
|
| 117 |
List contentXML = elDataSet.getContent(); |
|
| 72 |
|
|
| 73 |
List<?> contentXML = elDataSet.getContent();
|
|
| 118 | 74 |
Element currentElement = null; |
| 119 | 75 |
for(Object object:contentXML){
|
| 120 |
|
|
| 121 |
|
|
| 76 |
|
|
| 77 |
|
|
| 122 | 78 |
if(object instanceof Element){
|
| 123 | 79 |
currentElement = (Element)object; |
| 124 | 80 |
|
| 125 | 81 |
if(currentElement.getName().equalsIgnoreCase("METADATEN")){
|
| 126 |
|
|
| 82 |
|
|
| 127 | 83 |
TransactionStatus tx = startTransaction(); |
| 128 | 84 |
|
| 129 | 85 |
String bfnElementName = "METADATEN"; |
| 130 |
List<Element> elMetaDataList = (List<Element>)currentElement.getChildren(); |
|
| 86 |
@SuppressWarnings("unchecked")
|
|
| 87 |
List<Element> elMetaDataList = currentElement.getChildren(); |
|
| 131 | 88 |
//for each taxonName |
| 132 | 89 |
for (Element elMetaData : elMetaDataList){
|
| 133 | 90 |
if( elMetaData.getAttributeValue("standardname").equalsIgnoreCase("KurzLit_A")){
|
| 134 |
List<Element> children = (List<Element>)elMetaData.getChildren(); |
|
| 91 |
@SuppressWarnings("unchecked")
|
|
| 92 |
List<Element> children = elMetaData.getChildren(); |
|
| 135 | 93 |
String kurzlitA = children.get(0).getTextNormalize(); |
| 136 |
Reference sourceReference = ReferenceFactory.newGeneric(); |
|
| 94 |
Reference<?> sourceReference = ReferenceFactory.newGeneric();
|
|
| 137 | 95 |
sourceReference.setTitle(kurzlitA); |
| 138 | 96 |
state.setFirstListSecRef(sourceReference); |
| 139 | 97 |
|
| 140 | 98 |
} |
| 141 | 99 |
else if( elMetaData.getAttributeValue("standardname").equalsIgnoreCase("Klassifikation_A")){
|
| 142 |
List<Element> children = (List<Element>)elMetaData.getChildren(); |
|
| 100 |
@SuppressWarnings("unchecked")
|
|
| 101 |
List<Element> children = elMetaData.getChildren(); |
|
| 143 | 102 |
String klassifikation_A = children.get(0).getTextNormalize(); |
| 144 | 103 |
state.setFirstClassificationName(klassifikation_A); |
| 145 | 104 |
|
| 146 |
}
|
|
| 105 |
} |
|
| 147 | 106 |
else if( elMetaData.getAttributeValue("standardname").equalsIgnoreCase("KurzLit_B")){
|
| 148 |
List<Element> children = (List<Element>)elMetaData.getChildren(); |
|
| 107 |
@SuppressWarnings("unchecked")
|
|
| 108 |
List<Element> children = elMetaData.getChildren(); |
|
| 149 | 109 |
String kurzlitB = children.get(0).getTextNormalize(); |
| 150 |
Reference sourceReference = ReferenceFactory.newGeneric(); |
|
| 110 |
Reference<?> sourceReference = ReferenceFactory.newGeneric();
|
|
| 151 | 111 |
sourceReference.setTitle(kurzlitB); |
| 152 | 112 |
state.setSecondListSecRef(sourceReference); |
| 153 | 113 |
} |
| 154 | 114 |
else if( elMetaData.getAttributeValue("standardname").equalsIgnoreCase("Klassifikation_B")){
|
| 155 |
List<Element> children = (List<Element>)elMetaData.getChildren(); |
|
| 115 |
@SuppressWarnings("unchecked")
|
|
| 116 |
List<Element> children = elMetaData.getChildren(); |
|
| 156 | 117 |
String klassifikation_B = children.get(0).getTextNormalize(); |
| 157 | 118 |
state.setSecondClassificationName(klassifikation_B); |
| 158 | 119 |
|
| 159 | 120 |
} |
| 160 | 121 |
|
| 161 | 122 |
} |
| 162 |
|
|
| 123 |
|
|
| 163 | 124 |
logger.warn("end import MetaData ...");
|
| 164 | 125 |
commitTransaction(tx); |
| 165 |
|
|
| 166 |
|
|
| 167 |
|
|
| 168 |
|
|
| 126 |
|
|
| 127 |
|
|
| 169 | 128 |
if (!success.getValue()){
|
| 170 | 129 |
state.setUnsuccessfull(); |
| 171 | 130 |
} |
| 172 | 131 |
//FIXME: Only take the first RoteListeData Features |
| 173 |
|
|
| 174 |
|
|
| 132 |
|
|
| 133 |
|
|
| 175 | 134 |
return; |
| 176 | 135 |
} |
| 177 | 136 |
} |
| ... | ... | |
| 182 | 141 |
|
| 183 | 142 |
@Override |
| 184 | 143 |
protected boolean isIgnore(BfnXmlImportState state) {
|
| 185 |
return ! state.getConfig().isDoTaxonNames();
|
|
| 144 |
return ! state.getConfig().isDoMetaData();
|
|
| 186 | 145 |
} |
| 187 | 146 |
|
| 188 | 147 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportState.java | ||
|---|---|---|
| 1 | 1 |
// $Id$ |
| 2 | 2 |
/** |
| 3 | 3 |
* Copyright (C) 2007 EDIT |
| 4 |
* European Distributed Institute of Taxonomy
|
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 | 5 |
* http://www.e-taxonomy.eu |
| 6 |
*
|
|
| 6 |
* |
|
| 7 | 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 8 | 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 9 | 9 |
*/ |
| ... | ... | |
| 24 | 24 |
* @version 1.0 |
| 25 | 25 |
*/ |
| 26 | 26 |
public class BfnXmlImportState extends ImportStateBase<BfnXmlImportConfigurator, BfnXmlImportBase>{
|
| 27 |
private Reference refA; |
|
| 28 |
private Reference refB; |
|
| 29 |
private Reference currentMicroRef; |
|
| 30 |
private Reference completeSourceRef; |
|
| 27 |
private Reference<?> refA;
|
|
| 28 |
private Reference<?> refB;
|
|
| 29 |
private Reference<?> currentMicroRef;
|
|
| 30 |
private Reference<?> completeSourceRef;
|
|
| 31 | 31 |
private String classificationA; |
| 32 | 32 |
private String classificationB; |
| 33 | 33 |
@SuppressWarnings("unused")
|
| ... | ... | |
| 35 | 35 |
|
| 36 | 36 |
//TODO make it better |
| 37 | 37 |
private Map<String, CommonTaxonName> commonNameMap = null; |
| 38 |
|
|
| 38 |
|
|
| 39 | 39 |
public BfnXmlImportState(BfnXmlImportConfigurator config) {
|
| 40 | 40 |
super(config); |
| 41 | 41 |
} |
| 42 |
|
|
| 42 |
|
|
| 43 | 43 |
public Map<String, CommonTaxonName> getCommonNameMap() {
|
| 44 | 44 |
return commonNameMap; |
| 45 | 45 |
} |
| 46 | 46 |
|
| 47 |
|
|
| 48 |
|
|
| 47 |
|
|
| 48 |
|
|
| 49 | 49 |
public void setCommonNameMap(Map<String, CommonTaxonName> commonNameMap) {
|
| 50 | 50 |
this.commonNameMap = commonNameMap; |
| 51 | 51 |
} |
| 52 | 52 |
|
| 53 |
public void setFirstListSecRef(Reference ref) {
|
|
| 53 |
public void setFirstListSecRef(Reference<?> ref) {
|
|
| 54 | 54 |
this.refA = ref; |
| 55 | 55 |
} |
| 56 |
|
|
| 57 |
public void setSecondListSecRef(Reference ref) {
|
|
| 56 |
|
|
| 57 |
public void setSecondListSecRef(Reference<?> ref) {
|
|
| 58 | 58 |
this.refB = ref; |
| 59 | 59 |
} |
| 60 | 60 |
|
| 61 |
public Reference getFirstListSecRef(){
|
|
| 61 |
public Reference<?> getFirstListSecRef(){
|
|
| 62 | 62 |
return refA; |
| 63 | 63 |
} |
| 64 |
|
|
| 65 |
public Reference getSecondListSecRef(){
|
|
| 64 |
|
|
| 65 |
public Reference<?> getSecondListSecRef(){
|
|
| 66 | 66 |
return refB; |
| 67 | 67 |
} |
| 68 | 68 |
|
| 69 |
public void setCurrentMicroRef(Reference currentRef) {
|
|
| 69 |
public void setCurrentMicroRef(Reference<?> currentRef) {
|
|
| 70 | 70 |
this.currentMicroRef = currentRef; |
| 71 | 71 |
} |
| 72 |
public Reference getCompleteSourceRef() {
|
|
| 72 |
public Reference<?> getCompleteSourceRef() {
|
|
| 73 | 73 |
return completeSourceRef; |
| 74 | 74 |
} |
| 75 | 75 |
|
| 76 |
public void setCompleteSourceRef(Reference completeSourceRef) {
|
|
| 76 |
public void setCompleteSourceRef(Reference<?> completeSourceRef) {
|
|
| 77 | 77 |
this.completeSourceRef = completeSourceRef; |
| 78 | 78 |
} |
| 79 | 79 |
|
| 80 |
public Reference getCurrentMicroRef(){
|
|
| 80 |
public Reference<?> getCurrentMicroRef(){
|
|
| 81 | 81 |
return currentMicroRef; |
| 82 | 82 |
} |
| 83 | 83 |
public void setFirstClassificationName(String classificationA) {
|
| 84 | 84 |
this.classificationA = classificationA; |
| 85 | 85 |
} |
| 86 |
|
|
| 86 |
|
|
| 87 | 87 |
public void setSecondClassificationName(String classificationB) {
|
| 88 | 88 |
this.classificationB = classificationB; |
| 89 | 89 |
} |
| 90 |
|
|
| 90 |
|
|
| 91 | 91 |
public String getFirstClassificationName() {
|
| 92 | 92 |
return classificationA; |
| 93 | 93 |
} |
| ... | ... | |
| 95 | 95 |
public String getSecondClassificationName() {
|
| 96 | 96 |
return classificationB; |
| 97 | 97 |
} |
| 98 |
|
|
| 98 |
|
|
| 99 | 99 |
// /* (non-Javadoc) |
| 100 | 100 |
// * @see eu.etaxonomy.cdm.io.common.IoStateBase#initialize(eu.etaxonomy.cdm.io.common.IoConfiguratorBase) |
| 101 | 101 |
// */ |
| 102 | 102 |
// @Override |
| 103 | 103 |
// public void initialize(TcsXmlImportConfigurator config) {
|
| 104 |
//
|
|
| 104 |
// |
|
| 105 | 105 |
// } |
| 106 | 106 |
|
| 107 | 107 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/BfnXmlImportTaxonName.java | ||
|---|---|---|
| 27 | 27 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
| 28 | 28 |
import eu.etaxonomy.cdm.common.ResultWrapper; |
| 29 | 29 |
import eu.etaxonomy.cdm.common.XmlHelp; |
| 30 |
import eu.etaxonomy.cdm.io.common.ICdmIO; |
|
| 31 | 30 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 32 | 31 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 33 | 32 |
import eu.etaxonomy.cdm.model.common.Language; |
| ... | ... | |
| 66 | 65 |
*/ |
| 67 | 66 |
//@Component("bfnXmlTaxonNameIO")
|
| 68 | 67 |
@Component |
| 69 |
public class BfnXmlImportTaxonName extends BfnXmlImportBase implements ICdmIO<BfnXmlImportState> {
|
|
| 68 |
public class BfnXmlImportTaxonName extends BfnXmlImportBase {
|
|
| 70 | 69 |
|
| 71 |
|
|
| 72 |
private static final Logger logger = Logger.getLogger(BfnXmlImportTaxonName.class); |
|
| 70 |
private static final Logger logger = Logger.getLogger(BfnXmlImportTaxonName.class); |
|
| 73 | 71 |
|
| 74 | 72 |
private static String strNomenclaturalCode = null;// "Zoological";//"Botanical"; |
| 75 | 73 |
private static int parsingProblemCounter = 0; |
| ... | ... | |
| 81 | 79 |
super(); |
| 82 | 80 |
} |
| 83 | 81 |
|
| 84 |
@Override |
|
| 85 |
public boolean doCheck(BfnXmlImportState state){
|
|
| 86 |
boolean result = true; |
|
| 87 |
return result; |
|
| 88 |
} |
|
| 89 | 82 |
|
| 90 | 83 |
@Override |
| 91 | 84 |
@SuppressWarnings({"rawtypes" })
|
| ... | ... | |
| 894 | 887 |
} |
| 895 | 888 |
|
| 896 | 889 |
|
| 890 |
@Override |
|
| 891 |
public boolean doCheck(BfnXmlImportState state){
|
|
Also available in: Unified diff
Cleanup BfnXmlImport