Revision 74d84f79
Added by Andreas Kohlbecker over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/iapt/IAPTActivator.java | ||
|---|---|---|
| 35 | 35 |
public class IAPTActivator {
|
| 36 | 36 |
private static final Logger logger = Logger.getLogger(IAPTActivator.class); |
| 37 | 37 |
|
| 38 |
public static final String DATA_FILE_0_100 = "iapt-100.xls"; |
|
| 39 | 38 |
public static final String DATA_FILE_FULL = "Registration_DB_from_BGBM17.xls"; |
| 39 |
public static final String DATA_FILE_0_100 = "iapt-100.xls"; |
|
| 40 | 40 |
public static final String DATA_ENCODING_PROBLEMS = "encoding-problems.xls"; |
| 41 | 41 |
public static final String DATA_IAPT_TYPES_100 = "iapt-types-100.xls"; |
| 42 | 42 |
public static final String DATA_TYPE_LEG_100 = "iapt-type-leg-100.xls"; |
| 43 | 43 |
public static final String DATA_NAME_TYPES = "iapt-name-types.xls"; |
| 44 | 44 |
public static final String DATA_SINGLE = "single.xls"; |
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public static final String DATA_FILE = DATA_SINGLE;
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public static final String DATA_FILE = DATA_FILE_FULL;
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|
| 46 | 46 |
|
| 47 | 47 |
//database validation status (create, update, validate ...) |
| 48 | 48 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTExcelImport.java | ||
|---|---|---|
| 10 | 10 |
package eu.etaxonomy.cdm.io.iapt; |
| 11 | 11 |
|
| 12 | 12 |
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade; |
| 13 |
import eu.etaxonomy.cdm.api.service.pager.Pager; |
|
| 13 | 14 |
import eu.etaxonomy.cdm.common.CdmUtils; |
| 14 | 15 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport; |
| 15 | 16 |
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState; |
| ... | ... | |
| 340 | 341 |
} |
| 341 | 342 |
|
| 342 | 343 |
getTaxonService().save(taxon); |
| 344 |
|
|
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if(taxonName.getRank().equals(Rank.SPECIES()) || taxonName.getRank().isLower(Rank.SPECIES())){
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|
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// try to find the genus, it should have been imported already, Genera are coming first in the import file |
|
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Taxon genus = ((IAPTImportState)state).getGenusTaxonMap().get(taxonName.getGenusOrUninomial()); |
|
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if(genus != null){
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higherTaxonNode = genus.getTaxonNodes().iterator().next(); |
|
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} else {
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logger.info(csvReportLine(regNumber, "Parent genus not found for", nameStr)); |
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} |
|
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} |
|
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|
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| 343 | 355 |
if(higherTaxonNode != null){
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| 344 | 356 |
higherTaxonNode.addChildTaxon(taxon, null, null); |
| 345 | 357 |
getTaxonNodeService().save(higherTaxonNode); |
| 346 | 358 |
} |
| 347 | 359 |
|
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if(taxonName.getRank().isGenus()){
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((IAPTImportState)state).getGenusTaxonMap().put(taxonName.getGenusOrUninomial(), taxon); |
|
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} |
|
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|
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| 348 | 364 |
return taxon; |
| 349 | 365 |
} |
| 350 | 366 |
|
| ... | ... | |
| 1054 | 1070 |
((IAPTImportState)state).setCurrentTaxon(taxon); |
| 1055 | 1071 |
|
| 1056 | 1072 |
|
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logger.info("#of imported Genera: " + ((IAPTImportState) state).getGenusTaxonMap().size());
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|
| 1057 | 1074 |
return; |
| 1058 | 1075 |
} |
| 1059 | 1076 |
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| app-import/src/main/java/eu/etaxonomy/cdm/io/iapt/IAPTImportState.java | ||
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| 38 | 38 |
|
| 39 | 39 |
private final Map<String, UUID> higherTaxonUuidMap = new HashMap<String, UUID>(); |
| 40 | 40 |
|
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private final Map<String, Taxon> genusTaxonMap = new HashMap<String, Taxon>(); |
|
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|
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| 41 | 43 |
private final Map<String, BotanicalName> familyNameMap = new HashMap<String, BotanicalName>(); |
| 42 | 44 |
|
| 43 | 45 |
//classification |
| ... | ... | |
| 96 | 98 |
return higherTaxonUuidMap.containsKey(higherName); |
| 97 | 99 |
} |
| 98 | 100 |
|
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//family names |
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public BotanicalName getFamilyName(String familyStr) {
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return familyNameMap.get(familyStr); |
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} |
|
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public void putFamilyName(String familyStr, BotanicalName name) {
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familyNameMap.put(familyStr, name); |
|
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public Map<String, Taxon> getGenusTaxonMap() {
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return genusTaxonMap; |
|
| 105 | 103 |
} |
| 106 | 104 |
|
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| 108 | 105 |
Map<UUID, Reference> refMap = new HashMap<UUID, Reference>(); |
| 109 | 106 |
//reference |
| 110 | 107 |
public Reference getReference(UUID uuidRef) {
|
Also available in: Unified diff
ref #6026 using genera as higher taxon for species