Revision 50818ab7
Added by Katja Luther over 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.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 |
*/ |
| ... | ... | |
| 25 | 25 |
import eu.etaxonomy.cdm.app.common.CdmDestinations; |
| 26 | 26 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 27 | 27 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 28 |
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
| 28 |
import eu.etaxonomy.cdm.io.common.ImportResult;
|
|
| 29 | 29 |
import eu.etaxonomy.cdm.model.common.Language; |
| 30 | 30 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
| 31 | 31 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
| ... | ... | |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 40 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 41 | 40 |
|
| 42 | 41 |
/** |
| 43 | 42 |
* @author a.mueller |
| ... | ... | |
| 48 | 47 |
private static final Logger logger = Logger.getLogger(DipteraPostImportUpdater.class); |
| 49 | 48 |
|
| 50 | 49 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae(); |
| 51 |
|
|
| 50 |
|
|
| 52 | 51 |
/** |
| 53 |
* This method updateds the citation text by deleting <code>OriginalName</code> tags and
|
|
| 52 |
* This method updateds the citation text by deleting <code>OriginalName</code> tags and |
|
| 54 | 53 |
* adding the original name to the source either as a link to an existing taxon name |
| 55 | 54 |
* or as a string. The later becomes true if there is not exactly one matching name |
| 56 | 55 |
* @param dataSource |
| 57 | 56 |
* @return |
| 58 | 57 |
*/ |
| 59 |
public boolean updateCitations(ICdmDataSource dataSource) {
|
|
| 60 |
try{
|
|
| 58 |
public ImportResult updateCitations(ICdmDataSource dataSource) {
|
|
| 59 |
|
|
| 61 | 60 |
logger.warn("start updating citations");
|
| 62 |
boolean result = true; |
|
| 61 |
ImportResult result = new ImportResult(); |
|
| 62 |
try{
|
|
| 63 | 63 |
CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE); |
| 64 | 64 |
Set<DescriptionElementBase> citationsToSave = new HashSet<DescriptionElementBase>(); |
| 65 | 65 |
TransactionStatus tx = cdmApp.startTransaction(); |
| ... | ... | |
| 73 | 73 |
Map<String, TaxonNameBase> nameMap = new HashMap<String, TaxonNameBase>(); |
| 74 | 74 |
Map<String, TaxonNameBase> nameDuplicateMap = new HashMap<String, TaxonNameBase>(); |
| 75 | 75 |
fillNameMaps(nameList, nameMap, nameDuplicateMap); |
| 76 |
|
|
| 76 |
|
|
| 77 | 77 |
int i = 0; |
| 78 |
|
|
| 78 |
|
|
| 79 | 79 |
for (Taxon taxon : taxonList){
|
| 80 | 80 |
if ((i++ % modCount) == 0){ logger.warn("taxa handled: " + (i-1));}
|
| 81 |
|
|
| 81 |
|
|
| 82 | 82 |
Set<TextData> citations = getCitations(taxon); |
| 83 | 83 |
for (TextData citation : citations){
|
| 84 | 84 |
Language language = Language.DEFAULT(); |
| ... | ... | |
| 88 | 88 |
citation.removeText(language); |
| 89 | 89 |
citation.putText(language, newText); |
| 90 | 90 |
TaxonNameBase<?,?> scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap); |
| 91 |
|
|
| 91 |
|
|
| 92 | 92 |
Set<DescriptionElementSource> sources = citation.getSources(); |
| 93 | 93 |
if (sources.size() > 1){
|
| 94 | 94 |
logger.warn("There are more then 1 sources for a description");
|
| ... | ... | |
| 104 | 104 |
source.setOriginalNameString(originalNameString); |
| 105 | 105 |
} |
| 106 | 106 |
} |
| 107 |
|
|
| 107 |
|
|
| 108 | 108 |
citationsToSave.add(citation); |
| 109 | 109 |
} |
| 110 | 110 |
} |
| 111 |
|
|
| 111 |
|
|
| 112 | 112 |
cdmApp.getDescriptionService().saveDescriptionElement(citationsToSave); |
| 113 | 113 |
//commit |
| 114 | 114 |
cdmApp.commitTransaction(tx); |
| 115 | 115 |
logger.warn("Citations updated!");
|
| 116 |
result.setSuccess(true); |
|
| 116 | 117 |
return result; |
| 117 | 118 |
} catch (Exception e) {
|
| 118 | 119 |
e.printStackTrace(); |
| 119 | 120 |
logger.error("ERROR in citation update");
|
| 120 |
return false; |
|
| 121 |
result.setSuccess(false); |
|
| 122 |
result.addReport(e.getMessage().getBytes()); |
|
| 123 |
return result; |
|
| 121 | 124 |
} |
| 122 |
|
|
| 125 |
|
|
| 123 | 126 |
} |
| 124 |
|
|
| 125 |
public boolean updateCollections(ICdmDataSource dataSource){
|
|
| 127 |
|
|
| 128 |
public ImportResult updateCollections(ICdmDataSource dataSource){
|
|
| 126 | 129 |
DipteraCollectionImport collectionImport = new DipteraCollectionImport(); |
| 127 | 130 |
return collectionImport.invoke(dataSource); |
| 128 | 131 |
} |
| ... | ... | |
| 139 | 142 |
} |
| 140 | 143 |
} |
| 141 | 144 |
} |
| 142 |
|
|
| 143 |
|
|
| 145 |
|
|
| 146 |
|
|
| 144 | 147 |
private TaxonNameBase getScientificName(String originalNameString, Map<String, TaxonNameBase> nameMap, Map<String, TaxonNameBase> nameDuplicateMap) {
|
| 145 | 148 |
originalNameString = originalNameString.trim(); |
| 146 | 149 |
TaxonNameBase result = nameMap.get(originalNameString); |
| ... | ... | |
| 203 | 206 |
|
| 204 | 207 |
|
| 205 | 208 |
|
| 206 |
|
|
| 209 |
|
|
| 207 | 210 |
/** |
| 208 | 211 |
* @param args |
| 209 | 212 |
*/ |
Also available in: Unified diff
adapt the import classes to the new return type ImportResult