Revision a124222b
Added by Katja Luther over 9 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java | ||
|---|---|---|
| 1 | 1 |
// $Id$ |
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/** |
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* Copyright (C) 2009 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 |
| 8 | 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 9 | 9 |
*/ |
| ... | ... | |
| 37 | 37 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.description.PresenceTerm; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
|
| 41 | 40 |
import eu.etaxonomy.cdm.model.location.Country; |
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import eu.etaxonomy.cdm.model.location.NamedArea; |
|
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus; |
| ... | ... | |
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private static final Logger logger = Logger.getLogger(PesiTransformer.class); |
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|
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public static final String AUCT_STRING = "auct."; |
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|
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//source identifiers |
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public static final int SOURCE_EM = 1; |
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public static final int SOURCE_FE = 2; |
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public static final int SOURCE_IF = 3; |
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public static final int SOURCE_ERMS = 4; |
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|
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//sourceRefUUIDs |
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public static final UUID uuidSourceRefFaunaEuropaea = UUID.fromString("6786d863-75d4-4796-b916-c1c3dff4cb70");
|
| 80 | 80 |
public static final UUID uuidSourceRefErms = UUID.fromString("7744bc26-f914-42c4-b54a-dd2a030a8bb7");
|
| 81 | 81 |
public static final UUID uuidSourceRefIndexFungorum = UUID.fromString("8de25d27-7d40-47f4-af3b-59d64935a843");
|
| 82 | 82 |
public static final UUID uuidSourceRefAuct = UUID.fromString("5f79f96c-c100-4cd8-b78e-2b2dacf09a23");
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public static final String SOURCE_STR_EM = "E+M"; |
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public static final String SOURCE_STR_FE = "FaEu"; |
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public static final String SOURCE_STR_IF = "IF"; |
| ... | ... | |
| 91 | 91 |
public static int QUALITY_STATUS_ADD_BY_DBMT= 2; |
| 92 | 92 |
public static int QUALITY_STATUS_CHECKED_EDITOR = 3; |
| 93 | 93 |
public static int QUALITY_STATUS_EDITED_BY_DBMT = 4; |
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// marker type |
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public static final UUID uuidMarkerGuidIsMissing = UUID.fromString("24e70843-05e2-44db-954b-84df0d23ea20");
|
| 97 | 97 |
public static final UUID uuidMarkerTypeHasNoLastAction = UUID.fromString("99652d5a-bc92-4251-b57d-0fec4d258ab7");
|
| 98 | 98 |
// public static final UUID uuidMarkerFossil = UUID.fromString("761ce108-031a-4e07-b444-f8d757070312");
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//extension type uuids |
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public static final UUID cacheCitationUuid = UUID.fromString("29656168-32d6-4301-9067-d57c63be5c67");
|
| 103 | 103 |
//public static final UUID expertUserIdUuid = UUID.fromString("e25813d3-c67c-4585-9aa0-970fafde50b4");
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| 104 | 104 |
//public static final UUID speciesExpertUserIdUuid = UUID.fromString("6d42abd8-8894-4980-ae07-e918affd4172");
|
| 105 | 105 |
public static final UUID expertNameUuid = BerlinModelTransformer.uuidExpertName; |
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public static final UUID speciesExpertNameUuid = BerlinModelTransformer.uuidSpeciesExpertName;
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public static final UUID speciesExpertNameUuid = BerlinModelTransformer.uuidSpeciesExpertName; |
|
| 107 | 107 |
public static final UUID lastActionDateUuid = UUID.fromString("8d0a7d81-bb83-4576-84c3-8c906ef039b2");
|
| 108 | 108 |
public static final UUID lastActionUuid = UUID.fromString("bc20d5bc-6161-4279-9499-89ea26ce5f6a");
|
| 109 | 109 |
public static final UUID taxCommentUuid = UUID.fromString("8041a752-0479-4626-ab1b-b266b751f816");
|
| ... | ... | |
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public static int REF_UNRESOLVED = 10; |
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public static int REF_PUBLICATION = 11; |
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public static String REF_STR_UNRESOLVED = "unresolved"; |
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// NameStatus |
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public static int NAME_ST_NOM_INVAL = 1; |
| 129 | 129 |
public static int NAME_ST_NOM_ILLEG = 2; |
| ... | ... | |
| 163 | 163 |
public static int T_STATUS_ORPHANED = 6; |
| 164 | 164 |
public static int T_STATUS_UNACCEPTED = 7; |
| 165 | 165 |
public static int T_STATUS_NOT_ACCEPTED = 8; |
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// TypeDesginationStatus // -> not a table anymore |
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public static int TYPE_BY_ORIGINAL_DESIGNATION = 1; |
| 169 | 169 |
public static int TYPE_BY_SUBSEQUENT_DESIGNATION = 2; |
| ... | ... | |
| 171 | 171 |
public static String TYPE_STR_BY_ORIGINAL_DESIGNATION = "Type by original designation"; |
| 172 | 172 |
public static String TYPE_STR_BY_SUBSEQUENT_DESIGNATION = "Type by subsequent designation"; |
| 173 | 173 |
public static String TYPE_STR_BY_MONOTYPY = "Type by monotypy"; |
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// RelTaxonQualifier |
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public static int IS_BASIONYM_FOR = 1; |
| 177 | 177 |
public static int IS_LATER_HOMONYM_OF = 2; |
| ... | ... | |
| 208 | 208 |
public static int IS_INFERRED_GENUS_FOR = 302; |
| 209 | 209 |
public static int IS_POTENTIAL_COMBINATION_FOR = 303; |
| 210 | 210 |
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|
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//namespaces |
| 213 | 213 |
public static String STR_NAMESPACE_NOMINAL_TAXON = "Nominal taxon from TAX_ID:"; |
| 214 | 214 |
public static String STR_NAMESPACE_INFERRED_EPITHET = "Inferred epithet from TAX_ID:"; |
| ... | ... | |
| 225 | 225 |
public static int KINGDOM_BACTERIA = 6; |
| 226 | 226 |
public static int KINGDOM_CHROMISTA = 7; |
| 227 | 227 |
|
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// Kingdoms |
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public static Map<String, Integer> pesiKingdomMap = new HashMap<String, Integer>(); |
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public static String KINGDOM_PLANTAE_STRING = "Plantae"; |
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public static String KINGDOM_FUNGI_STRING = "Fungi"; |
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public static String KINGDOM_PROTOZOA_STRING = "Protozoa"; |
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public static String kINGDOM_BACTERIA_STRING = "Bacteria"; |
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public static String KINGDOM_CHROMISTA_STRING = "Chromista"; |
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|
|
| 228 | 238 |
// Animalia Ranks |
| 229 | 239 |
public static int Animalia_Kingdom = 10; |
| 230 | 240 |
public static int Animalia_Subkingdom = 20; |
| ... | ... | |
| 293 | 303 |
public static int Plantae_Forma_spec = 275; |
| 294 | 304 |
public static int Plantae_Taxa_infragen = 280; |
| 295 | 305 |
public static int Plantae_Taxa_infraspec = 285; |
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|
|
| 297 | 307 |
// Fungi Ranks |
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public static int Fungi_Kingdom = 10; |
| 299 | 309 |
public static int Fungi_Subkingdom = 20; |
| ... | ... | |
| 317 | 327 |
public static int Fungi_Subvariety = 250; |
| 318 | 328 |
public static int Fungi_Forma = 260; |
| 319 | 329 |
public static int Fungi_Subforma = 270; |
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public static int Fungi_Forma_spec = 275; |
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|
|
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//Protozoa Ranks |
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public static int Protozoa_Kingdom = 10; |
| 323 | 334 |
public static int Protozoa_Subkingdom = 20; |
| ... | ... | |
| 342 | 353 |
public static int Protozoa_Subspecies = 230; |
| 343 | 354 |
public static int Protozoa_Variety = 240; |
| 344 | 355 |
public static int Protozoa_Forma = 260; |
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|
| 346 | 357 |
// Bacteria Ranks |
| 347 | 358 |
public static int Bacteria_Kingdom = 10; |
| 348 | 359 |
public static int Bacteria_Subkingdom = 20; |
| ... | ... | |
| 396 | 407 |
public static int Chromista_Variety = 240; |
| 397 | 408 |
public static int Chromista_Subvariety = 250; |
| 398 | 409 |
public static int Chromista_Forma = 260; |
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// NoteCategory |
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public static int NoteCategory_description = 1; |
| 402 | 413 |
public static int NoteCategory_ecology = 4; |
| ... | ... | |
| 451 | 462 |
public static int NoteCategory_Use = 302; |
| 452 | 463 |
public static int NoteCategory_Comments = 303; |
| 453 | 464 |
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| 455 | 466 |
// Language |
| 456 | 467 |
public static int Language_Albanian = 1; |
| 457 | 468 |
public static int Language_Arabic = 2; |
| ... | ... | |
| 520 | 531 |
public static int FOSSILSTATUS_FOSSIL_ONLY = 2; |
| 521 | 532 |
public static int FOSSILSTATUS_RECENT_FOSSIL = 3; |
| 522 | 533 |
public static String STR_FOSSIL_ONLY = "fossil only"; //still used for Index Fungorum |
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|
| 524 | 535 |
// SourceUse |
| 525 | 536 |
public static int ORIGINAL_DESCRIPTION = 1; |
| 526 | 537 |
public static int BASIS_OF_RECORD = 2; |
| ... | ... | |
| 732 | 743 |
public static int AREA_TURKISH_EXCLUSIVE_ECONOMIC_ZONE = 197; |
| 733 | 744 |
public static int AREA_DANISH_EXCLUSIVE_ECONOMIC_ZONE = 198; |
| 734 | 745 |
public static int AREA_TRANSCAUCASUS = 199; |
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|
| 736 | 747 |
public static int AREA_GEORGIA_G = 200; |
| 737 | 748 |
public static int AREA_ABKHAZIA = 201; |
| 738 | 749 |
public static int AREA_ADZARIA = 202; |
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public static int AREA_UNITED_KINGDOM = 203; |
| 741 | 752 |
public static int AREA_DENMARK_COUNTRY = 204; |
| 742 | 753 |
public static int AREA_TURKEY_COUNTRY = 205; |
| ... | ... | |
| 754 | 765 |
public static int STATUS_MANAGED = 7; |
| 755 | 766 |
public static int STATUS_DOUBTFUL = 8; |
| 756 | 767 |
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private Map<String, Integer> tdwgKeyMap = new HashMap<String, Integer>(); |
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private Map<Integer, String> areaCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> languageCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> featureCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> nameStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> qualityStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> taxonStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> taxRelQualifierCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> taxRelZooQualifierCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> sourceUseCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> fossilStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> typeDesigStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> sourceCategoryCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, String> occurrenceStatusCacheMap = new HashMap<Integer, String>(); |
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private Map<Integer, Map<Integer, String>> rankCacheMap = new HashMap<Integer, Map<Integer, String>>(); |
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private Map<Integer, Map<Integer, String>> rankAbbrevCacheMap = new HashMap<Integer, Map<Integer, String>>(); |
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private Source destination; |
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private final Map<String, Integer> tdwgKeyMap = new HashMap<String, Integer>();
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private final Map<Integer, String> areaCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> languageCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> featureCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> nameStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> qualityStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> taxonStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> taxRelQualifierCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> taxRelZooQualifierCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> sourceUseCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> fossilStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> typeDesigStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> sourceCategoryCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, String> occurrenceStatusCacheMap = new HashMap<Integer, String>();
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private final Map<Integer, Map<Integer, String>> rankCacheMap = new HashMap<Integer, Map<Integer, String>>();
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private final Map<Integer, Map<Integer, String>> rankAbbrevCacheMap = new HashMap<Integer, Map<Integer, String>>();
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private final Source destination;
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public PesiTransformer(Source destination) {
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| 778 | 789 |
super(); |
| 779 | 790 |
this.destination = destination; |
| ... | ... | |
| 789 | 800 |
String tdwg = rs.getString("AreaTdwgCode");
|
| 790 | 801 |
Integer id = rs.getInt("AreaId");
|
| 791 | 802 |
String label = rs.getString("AreaName");
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|
| 803 |
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|
| 793 | 804 |
if (StringUtils.isNotBlank(tdwg)){
|
| 794 | 805 |
this.tdwgKeyMap.put(tdwg, id); |
| 795 | 806 |
} |
| 796 | 807 |
this.areaCacheMap.put(id, label); |
| 797 | 808 |
} |
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|
| 799 | 810 |
//rankCache |
| 800 |
sql = " SELECT KingdomId, RankId, Rank, RankAbbrev FROM Rank"; |
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| 811 |
sql = " SELECT KingdomId, RankId, Rank, RankAbbrev, Kingdom FROM Rank";
|
|
| 801 | 812 |
rs = destination.getResultSet(sql); |
| 802 | 813 |
while (rs.next()){
|
| 803 | 814 |
String rank = rs.getString("Rank");
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| 804 | 815 |
String abbrev = rs.getString("RankAbbrev");
|
| 805 | 816 |
Integer rankId = rs.getInt("RankId");
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| 806 | 817 |
Integer kingdomId = rs.getInt("KingdomId");
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| 807 |
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String kingdom = rs.getString("Kingdom");
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|
| 808 | 820 |
//rank str |
| 809 | 821 |
Map<Integer, String> kingdomMap = rankCacheMap.get(kingdomId); |
| 810 | 822 |
if (kingdomMap == null){
|
| ... | ... | |
| 812 | 824 |
rankCacheMap.put(kingdomId, kingdomMap); |
| 813 | 825 |
} |
| 814 | 826 |
kingdomMap.put(rankId, rank); |
| 815 |
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| 828 |
if (rank.equals("Kingdom")){
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| 829 |
pesiKingdomMap.put(kingdom, kingdomId); |
|
| 830 |
} |
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| 831 |
|
|
| 816 | 832 |
//rank abbrev |
| 817 | 833 |
Map<Integer, String> kingdomAbbrevMap = rankAbbrevCacheMap.get(kingdomId); |
| 818 | 834 |
if (kingdomAbbrevMap == null){
|
| ... | ... | |
| 822 | 838 |
if (StringUtils.isNotBlank(abbrev)){
|
| 823 | 839 |
kingdomAbbrevMap.put(rankId, abbrev); |
| 824 | 840 |
} |
| 825 |
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|
| 841 |
|
|
| 826 | 842 |
} |
| 827 |
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| 843 |
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| 844 |
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| 845 |
|
|
| 846 |
|
|
| 828 | 847 |
//languageCache |
| 829 | 848 |
fillSingleMap(languageCacheMap,"Language"); |
| 830 | 849 |
|
| 831 | 850 |
//feature / note category |
| 832 | 851 |
fillSingleMap(featureCacheMap,"NoteCategory"); |
| 833 |
|
|
| 852 |
|
|
| 834 | 853 |
//nameStatusCache |
| 835 | 854 |
fillSingleMap(nameStatusCacheMap,"NameStatus", "NomStatus"); |
| 836 | 855 |
|
| ... | ... | |
| 839 | 858 |
|
| 840 | 859 |
//taxonStatusCache |
| 841 | 860 |
fillSingleMap(taxonStatusCacheMap,"TaxonStatus", "Status"); |
| 842 |
|
|
| 861 |
|
|
| 843 | 862 |
//sourceUse |
| 844 | 863 |
fillSingleMap(sourceUseCacheMap,"SourceUse"); |
| 845 | 864 |
|
| 846 | 865 |
//fossil status |
| 847 | 866 |
fillSingleMap(fossilStatusCacheMap,"FossilStatus"); |
| 848 |
|
|
| 867 |
|
|
| 849 | 868 |
//fossil status |
| 850 | 869 |
fillSingleMap(typeDesigStatusCacheMap,"FossilStatus"); |
| 851 | 870 |
|
| 852 | 871 |
//fossil status |
| 853 | 872 |
fillSingleMap(occurrenceStatusCacheMap,"OccurrenceStatus"); |
| 854 |
|
|
| 873 |
|
|
| 855 | 874 |
//source category |
| 856 | 875 |
fillSingleMap(sourceCategoryCacheMap,"SourceCategory", "Category", "SourceCategoryId"); |
| 857 |
|
|
| 876 |
|
|
| 858 | 877 |
//RelTaxonQualifier |
| 859 | 878 |
sql = " SELECT QualifierId, Qualifier, ZoologQualifier FROM RelTaxonQualifier "; |
| 860 | 879 |
rs = destination.getResultSet(sql); |
| ... | ... | |
| 869 | 888 |
this.taxRelZooQualifierCacheMap.put(key, zoologCache); |
| 870 | 889 |
} |
| 871 | 890 |
} |
| 872 |
rs = null;
|
|
| 891 |
rs = null; |
|
| 873 | 892 |
} catch (SQLException e) {
|
| 874 | 893 |
logger.error("SQLException when trying to read area map", e);
|
| 875 | 894 |
e.printStackTrace(); |
| 876 | 895 |
} |
| 877 |
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|
| 896 |
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|
| 878 | 897 |
} |
| 879 | 898 |
|
| 880 | 899 |
private void fillSingleMap(Map<Integer, String> map, String tableName) throws SQLException {
|
| 881 | 900 |
fillSingleMap(map, tableName, tableName, tableName + "Id"); |
| 882 | 901 |
} |
| 883 |
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|
| 902 |
|
|
| 884 | 903 |
private void fillSingleMap(Map<Integer, String> map, String tableName, String attr) throws SQLException {
|
| 885 | 904 |
fillSingleMap(map, tableName, attr, attr + "Id"); |
| 886 | 905 |
} |
| 887 |
|
|
| 906 |
|
|
| 888 | 907 |
private void fillSingleMap(Map<Integer, String> map, String tableName, String attr, String idAttr) throws SQLException {
|
| 889 | 908 |
String sql; |
| 890 | 909 |
ResultSet rs; |
| ... | ... | |
| 896 | 915 |
String cache = rs.getString(attr); |
| 897 | 916 |
if (StringUtils.isNotBlank(cache)){
|
| 898 | 917 |
map.put(key, cache); |
| 899 |
}
|
|
| 918 |
} |
|
| 900 | 919 |
} |
| 901 | 920 |
} |
| 902 | 921 |
|
| ... | ... | |
| 914 | 933 |
return result; |
| 915 | 934 |
} |
| 916 | 935 |
|
| 917 |
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|
| 936 |
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|
| 918 | 937 |
/** |
| 919 | 938 |
* Returns the OccurrenceStatusId for a given PresenceAbsenceTerm. |
| 920 | 939 |
* @param term |
| 921 | 940 |
* @return |
| 922 |
* @throws UnknownCdmTypeException
|
|
| 941 |
* @throws UnknownCdmTypeException |
|
| 923 | 942 |
*/ |
| 924 | 943 |
public static Integer presenceAbsenceTerm2OccurrenceStatusId(PresenceAbsenceTermBase<?> term) {
|
| 925 | 944 |
Integer result = null; |
| ... | ... | |
| 928 | 947 |
//present |
| 929 | 948 |
}else if (term.isInstanceOf(PresenceTerm.class)) {
|
| 930 | 949 |
PresenceTerm presenceTerm = CdmBase.deproxy(term, PresenceTerm.class); |
| 931 |
if (presenceTerm.equals(PresenceTerm.PRESENT()) ||
|
|
| 932 |
presenceTerm.equals(PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED()) ||
|
|
| 950 |
if (presenceTerm.equals(PresenceTerm.PRESENT()) || |
|
| 951 |
presenceTerm.equals(PresenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED()) || |
|
| 933 | 952 |
presenceTerm.equals(PresenceTerm.NATIVE_DOUBTFULLY_NATIVE())) {
|
| 934 | 953 |
result = STATUS_PRESENT; |
| 935 | 954 |
} else if (presenceTerm.equals(PresenceTerm.NATIVE())) {
|
| 936 | 955 |
result = STATUS_NATIVE; |
| 937 |
} else if (presenceTerm.equals(PresenceTerm.INTRODUCED()) ||
|
|
| 956 |
} else if (presenceTerm.equals(PresenceTerm.INTRODUCED()) || |
|
| 938 | 957 |
presenceTerm.equals(PresenceTerm.INTRODUCED_ADVENTITIOUS()) || |
| 939 | 958 |
presenceTerm.equals(PresenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION())) {
|
| 940 | 959 |
result = STATUS_INTRODUCED; |
| 941 |
} else if (presenceTerm.equals(PresenceTerm.NATURALISED())
|
|
| 960 |
} else if (presenceTerm.equals(PresenceTerm.NATURALISED()) |
|
| 942 | 961 |
|| presenceTerm.equals(PresenceTerm.INTRODUCED_NATURALIZED())) {
|
| 943 | 962 |
result = STATUS_NATURALISED; |
| 944 | 963 |
} else if (presenceTerm.equals(PresenceTerm.INVASIVE())) {
|
| ... | ... | |
| 952 | 971 |
} else {
|
| 953 | 972 |
logger.error("PresenceTerm could not be translated to datawarehouse occurrence status id: " + presenceTerm.getLabel());
|
| 954 | 973 |
} |
| 955 |
//absent
|
|
| 974 |
//absent |
|
| 956 | 975 |
} else if (term.isInstanceOf(AbsenceTerm.class)) {
|
| 957 | 976 |
AbsenceTerm absenceTerm = CdmBase.deproxy(term, AbsenceTerm.class); |
| 958 | 977 |
if (absenceTerm.equals(AbsenceTerm.ABSENT()) || absenceTerm.equals(AbsenceTerm.NATIVE_FORMERLY_NATIVE()) || |
| ... | ... | |
| 965 | 984 |
} |
| 966 | 985 |
return result; |
| 967 | 986 |
} |
| 968 |
|
|
| 987 |
|
|
| 969 | 988 |
|
| 970 | 989 |
@Override |
| 971 | 990 |
public String getCacheByPresenceAbsenceTerm(PresenceAbsenceTermBase status) throws UndefinedTransformerMethodException {
|
| 972 | 991 |
if (status == null){
|
| 973 | 992 |
return null; |
| 974 | 993 |
}else{
|
| 975 |
return this.occurrenceStatusCacheMap.get(getKeyByPresenceAbsenceTerm(status));
|
|
| 994 |
return this.occurrenceStatusCacheMap.get(getKeyByPresenceAbsenceTerm(status)); |
|
| 976 | 995 |
} |
| 977 | 996 |
} |
| 978 |
|
|
| 997 |
|
|
| 979 | 998 |
@Override |
| 980 | 999 |
public Object getKeyByPresenceAbsenceTerm(PresenceAbsenceTermBase status) throws UndefinedTransformerMethodException {
|
| 981 | 1000 |
return presenceAbsenceTerm2OccurrenceStatusId(status); |
| 982 | 1001 |
} |
| 983 |
|
|
| 984 |
|
|
| 985 |
|
|
| 1002 |
|
|
| 1003 |
|
|
| 1004 |
|
|
| 986 | 1005 |
@Override |
| 987 | 1006 |
public String getCacheByNamedArea(NamedArea namedArea) throws UndefinedTransformerMethodException {
|
| 988 | 1007 |
NamedArea area = CdmBase.deproxy(namedArea, NamedArea.class); |
| 989 | 1008 |
if (area == null){
|
| 990 | 1009 |
return null; |
| 991 | 1010 |
}else{
|
| 992 |
return this.areaCacheMap.get(getKeyByNamedArea(area));
|
|
| 1011 |
return this.areaCacheMap.get(getKeyByNamedArea(area)); |
|
| 993 | 1012 |
} |
| 994 | 1013 |
} |
| 995 |
|
|
| 996 |
|
|
| 1014 |
|
|
| 1015 |
|
|
| 997 | 1016 |
@Override |
| 998 | 1017 |
public Object getKeyByNamedArea(NamedArea area) throws UndefinedTransformerMethodException {
|
| 999 | 1018 |
NamedArea namedArea = CdmBase.deproxy(area, NamedArea.class); |
| ... | ... | |
| 1044 | 1063 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidIbizaWithFormentera)) { return AREA_IBIZA_WITH_FORMENTERA; }
|
| 1045 | 1064 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMallorca)) { return AREA_MALLORCA; }
|
| 1046 | 1065 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidMenorca)) { return AREA_MENORCA; }
|
| 1047 |
//
|
|
| 1066 |
// |
|
| 1048 | 1067 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUssr)) { return AREA_FORMER_USSR; }
|
| 1049 | 1068 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRussiaBaltic)) { return AREA_RUSSIA_BALTIC; }
|
| 1050 | 1069 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRussiaSouthEast)) { return AREA_RUSSIA_SOUTHEAST; }
|
| 1051 | 1070 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRussiaSouthWest)) { return AREA_RUSSIA_SOUTHWEST; }
|
| 1052 | 1071 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRussiaCentral)) { return AREA_RUSSIA_CENTRAL; }
|
| 1053 | 1072 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidRussiaNorthern)) { return AREA_RUSSIA_NORTHERN; }
|
| 1054 |
//
|
|
| 1073 |
// |
|
| 1055 | 1074 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTurkey)) { return AREA_TURKEY; }
|
| 1056 | 1075 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEastAegeanIslands)) { return AREA_EAST_AEGEAN_ISLANDS; }
|
| 1057 | 1076 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidTurkishEastAegeanIslands)) { return AREA_TURKISH_EAST_AEGEAN_ISLANDS; }
|
| ... | ... | |
| 1060 | 1079 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidCaucasia)) { return AREA_CAUCASUS_REGION; }
|
| 1061 | 1080 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUkraineAndCrimea)) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
|
| 1062 | 1081 |
// else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidAzerbaijanNakhichevan)) { return AREA_AZERBAIJAN_INCLUDING_NAKHICHEVAN; }
|
| 1063 |
|
|
| 1064 |
if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEM)) {
|
|
| 1065 |
// logger.warn("E+M area not available in PESI");
|
|
| 1082 |
|
|
| 1083 |
if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEM)) {
|
|
| 1084 |
// logger.warn("E+M area not available in PESI");
|
|
| 1066 | 1085 |
return null; |
| 1067 | 1086 |
} |
| 1068 | 1087 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidEUR)) { logger.warn("EUR area not available in PESI"); return null; }
|
| ... | ... | |
| 1125 | 1144 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_C)) { return AREA_CHANNEL_ISLANDS; }
|
| 1126 | 1145 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_F)) { return AREA_FRENCH_MAINLAND; }
|
| 1127 | 1146 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGa_M)) { return AREA_MONACO; }
|
| 1128 |
|
|
| 1147 |
|
|
| 1129 | 1148 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGe)) { return AREA_GERMANY; }
|
| 1130 | 1149 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg)) { return AREA_GEORGIA; }
|
| 1131 |
|
|
| 1150 |
|
|
| 1132 | 1151 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_G)) { return AREA_GEORGIA_G; }
|
| 1133 | 1152 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_A)) { return AREA_ABKHAZIA; }
|
| 1134 | 1153 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGg_D)) { return AREA_ADZARIA; }
|
| 1135 |
|
|
| 1154 |
|
|
| 1136 | 1155 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidGr)) { return AREA_GREECE_WITH_CYCLADES_AND_MORE_ISLANDS; }
|
| 1137 | 1156 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHb)) { return AREA_IRELAND; }
|
| 1138 | 1157 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidHb_E)) { return AREA_REPUBLIC_OF_IRELAND; }
|
| ... | ... | |
| 1205 | 1224 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk)) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
|
| 1206 | 1225 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk_K)) { return AREA_CRIMEA; }
|
| 1207 | 1226 |
else if (namedArea.getUuid().equals(BerlinModelTransformer.uuidUk_U)) { return AREA_UKRAINE; }
|
| 1208 |
|
|
| 1209 |
|
|
| 1210 |
|
|
| 1227 |
|
|
| 1228 |
|
|
| 1229 |
|
|
| 1211 | 1230 |
//FE |
| 1212 | 1231 |
else if (namedArea.getUuid().equals(FaunaEuropaeaTransformer.uuidAreaAFR)) { return AREA_AFRO_TROPICAL_REGION; }
|
| 1213 | 1232 |
else if (namedArea.getUuid().equals(FaunaEuropaeaTransformer.uuidAreaAUS)) { return AREA_AUSTRALIAN_REGION; }
|
| ... | ... | |
| 1225 | 1244 |
else if (namedArea.getUuid().equals(FaunaEuropaeaTransformer.uuidAreaUA)) { return AREA_UKRAINE_INCLUDING_CRIMEA; }
|
| 1226 | 1245 |
else if (namedArea.getUuid().equals(FaunaEuropaeaTransformer.uuidAreaRU_FJL)) { return AREA_FRANZ_JOSEF_LAND; }
|
| 1227 | 1246 |
else if (namedArea.getUuid().equals(FaunaEuropaeaTransformer.uuidAreaRU_NOZ)) { return AREA_NOVAYA_ZEMLYA; }
|
| 1228 |
|
|
| 1247 |
|
|
| 1229 | 1248 |
|
| 1230 | 1249 |
//ERMS |
| 1231 | 1250 |
else if (namedArea.getUuid().equals(ErmsTransformer.uuidEuropeanMarineWaters)) { return AREA_EUROPEAN_MARINE_WATERS; }
|
| ... | ... | |
| 1281 | 1300 |
else if (namedArea.getUuid().equals(ErmsTransformer.uuidBalearSea)) { return AREA_BALEAR_SEA; }
|
| 1282 | 1301 |
else if (namedArea.getUuid().equals(ErmsTransformer.uuidTurkishExclusiveEconomicZone)) { return AREA_TURKISH_EXCLUSIVE_ECONOMIC_ZONE; }
|
| 1283 | 1302 |
else if (namedArea.getUuid().equals(ErmsTransformer.uuidDanishExclusiveEconomicZone)) { return AREA_DANISH_EXCLUSIVE_ECONOMIC_ZONE; }
|
| 1284 |
|
|
| 1285 | 1303 |
else {
|
| 1286 | 1304 |
logger.warn("Unknown NamedArea Area: " + area.getTitleCache());
|
| 1287 | 1305 |
} |
| ... | ... | |
| 1289 | 1307 |
} |
| 1290 | 1308 |
return null; |
| 1291 | 1309 |
} |
| 1292 |
|
|
| 1310 |
|
|
| 1293 | 1311 |
|
| 1294 | 1312 |
/** |
| 1295 | 1313 |
* Returns the PESI SourceUseId for a given CDM sourceUseId. |
| ... | ... | |
| 1307 | 1325 |
return result; |
| 1308 | 1326 |
} |
| 1309 | 1327 |
|
| 1310 |
|
|
| 1328 |
|
|
| 1311 | 1329 |
/** |
| 1312 | 1330 |
* Returns the FossilStatusCache to a given Fossil. |
| 1313 | 1331 |
* @param fossil |
| ... | ... | |
| 1327 | 1345 |
Integer result = null; |
| 1328 | 1346 |
return result; |
| 1329 | 1347 |
} |
| 1330 |
|
|
| 1331 |
|
|
| 1332 |
|
|
| 1348 |
|
|
| 1349 |
|
|
| 1350 |
|
|
| 1333 | 1351 |
@Override |
| 1334 | 1352 |
public Object getKeyByLanguage(Language language) throws UndefinedTransformerMethodException {
|
| 1335 | 1353 |
return language2LanguageId(language); |
| ... | ... | |
| 1340 | 1358 |
if (language == null){
|
| 1341 | 1359 |
return null; |
| 1342 | 1360 |
}else{
|
| 1343 |
return this.languageCacheMap.get(getKeyByLanguage(language));
|
|
| 1361 |
return this.languageCacheMap.get(getKeyByLanguage(language)); |
|
| 1344 | 1362 |
} |
| 1345 | 1363 |
} |
| 1346 | 1364 |
|
| 1347 |
|
|
| 1365 |
|
|
| 1348 | 1366 |
/** |
| 1349 | 1367 |
* Returns the identifier of the given Language. |
| 1350 | 1368 |
* @param language |
| ... | ... | |
| 1481 | 1499 |
return null; |
| 1482 | 1500 |
} |
| 1483 | 1501 |
} |
| 1484 |
|
|
| 1502 |
|
|
| 1485 | 1503 |
/** |
| 1486 | 1504 |
* Returns the NodeCategoryCache for a given TextData. |
| 1487 | 1505 |
* @param feature |
| 1488 | 1506 |
* @return |
| 1489 | 1507 |
*/ |
| 1490 |
public String getCacheByFeature(Feature feature) {
|
|
| 1508 |
@Override |
|
| 1509 |
public String getCacheByFeature(Feature feature) {
|
|
| 1491 | 1510 |
if (feature == null){
|
| 1492 | 1511 |
return null; |
| 1493 | 1512 |
}else{
|
| 1494 |
return this.featureCacheMap.get(feature2NoteCategoryFk(feature));
|
|
| 1513 |
return this.featureCacheMap.get(feature2NoteCategoryFk(feature)); |
|
| 1495 | 1514 |
} |
| 1496 | 1515 |
} |
| 1497 | 1516 |
|
| ... | ... | |
| 1577 | 1596 |
return NoteCategory_Comments; |
| 1578 | 1597 |
} else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureConservationStatus)){
|
| 1579 | 1598 |
return NoteCategory_Conservation_Status; |
| 1580 |
|
|
| 1599 |
|
|
| 1581 | 1600 |
//E+M |
| 1582 | 1601 |
} else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureDistrEM)){
|
| 1583 | 1602 |
return NoteCategory_general_distribution_euromed; |
| ... | ... | |
| 1591 | 1610 |
return NoteCategory_Inedited; |
| 1592 | 1611 |
} else if (feature.getUuid().equals(BerlinModelTransformer.uuidFeatureCommentsEditing)){
|
| 1593 | 1612 |
return NoteCategory_Comments_on_editing_process; |
| 1594 |
|
|
| 1595 |
|
|
| 1613 |
|
|
| 1614 |
|
|
| 1596 | 1615 |
// TODO: Unknown NoteCategories |
| 1597 | 1616 |
// NoteCategory_Common_names = 12; |
| 1598 | 1617 |
// NoteCategory_Maps =14; |
| ... | ... | |
| 1625 | 1644 |
if (rank == null){
|
| 1626 | 1645 |
return null; |
| 1627 | 1646 |
}else{
|
| 1628 |
return this.rankCacheMap.get(pesiKingdomId).get(rank2RankId(rank, pesiKingdomId));
|
|
| 1647 |
return this.rankCacheMap.get(pesiKingdomId).get(rank2RankId(rank, pesiKingdomId)); |
|
| 1629 | 1648 |
} |
| 1630 | 1649 |
} |
| 1631 |
|
|
| 1650 |
|
|
| 1632 | 1651 |
/** |
| 1633 | 1652 |
* Returns the abbreviation for a given rank. |
| 1634 | 1653 |
* Currently unused. |
| ... | ... | |
| 1640 | 1659 |
if (rank == null){
|
| 1641 | 1660 |
return null; |
| 1642 | 1661 |
}else{
|
| 1643 |
return this.rankAbbrevCacheMap.get(pesiKingdomId).get(rank2RankId(rank, pesiKingdomId));
|
|
| 1662 |
return this.rankAbbrevCacheMap.get(pesiKingdomId).get(rank2RankId(rank, pesiKingdomId)); |
|
| 1644 | 1663 |
} |
| 1645 | 1664 |
} |
| 1646 | 1665 |
|
| ... | ... | |
| 1659 | 1678 |
} else if (nomenclaturalCode.equals(NomenclaturalCode.ICNB)) {
|
| 1660 | 1679 |
result = KINGDOM_BACTERIA; |
| 1661 | 1680 |
// } else if (nomenclaturalCode.equals(NomenclaturalCode.)) { // Biota
|
| 1662 |
// result =
|
|
| 1681 |
// result = |
|
| 1663 | 1682 |
} else {
|
| 1664 | 1683 |
logger.error("NomenclaturalCode not yet considered: " + nomenclaturalCode.getUuid() + " (" + nomenclaturalCode.getTitleCache() + ")");
|
| 1665 | 1684 |
} |
| 1666 | 1685 |
return result; |
| 1667 | 1686 |
} |
| 1668 |
|
|
| 1687 |
|
|
| 1669 | 1688 |
/** |
| 1670 | 1689 |
* Returns the RankId for a Rank. |
| 1671 | 1690 |
* @param rank |
| ... | ... | |
| 1676 | 1695 |
if (rank == null) {
|
| 1677 | 1696 |
return null; |
| 1678 | 1697 |
} |
| 1679 |
|
|
| 1698 |
|
|
| 1680 | 1699 |
// We differentiate between Animalia and Plantae only for now. |
| 1681 | 1700 |
if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_ANIMALIA) {
|
| 1682 | 1701 |
if (rank.equals(Rank.KINGDOM())) {
|
| ... | ... | |
| 1790 | 1809 |
} else if (rank.equals(Rank.SPECIESGROUP())) {
|
| 1791 | 1810 |
logger.warn("Rank Species Group not yet implemented");
|
| 1792 | 1811 |
result = null; |
| 1793 |
} else if (rank.getUuid().equals(BerlinModelTransformer.uuidRankCollSpecies)) {
|
|
| 1812 |
} else if (rank.getUuid().equals(BerlinModelTransformer.uuidRankCollSpecies)) {
|
|
| 1794 | 1813 |
result = Plantae_Coll_Species; |
| 1795 | 1814 |
} else if (rank.equals(Rank.SPECIES())) {
|
| 1796 | 1815 |
result = Plantae_Species; |
| ... | ... | |
| 1814 | 1833 |
result = Plantae_Subforma; |
| 1815 | 1834 |
// } else if (rank.equals(Rank.)) { // not yet specified
|
| 1816 | 1835 |
// result = Plantae_Forma_spec; |
| 1817 |
} else if (rank.equals(Rank.INFRAGENERICTAXON())) {
|
|
| 1836 |
} else if (rank.equals(Rank.INFRAGENERICTAXON())) {
|
|
| 1818 | 1837 |
result = Plantae_Taxa_infragen; |
| 1819 |
} else if (rank.equals(Rank.INFRASPECIFICTAXON())) {
|
|
| 1838 |
} else if (rank.equals(Rank.INFRASPECIFICTAXON())) {
|
|
| 1820 | 1839 |
result = Plantae_Taxa_infraspec; |
| 1821 | 1840 |
} else {
|
| 1822 | 1841 |
//TODO Exception |
| ... | ... | |
| 1847 | 1866 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Bacteria_Subspecies; }
|
| 1848 | 1867 |
else if (rank.equals(Rank.VARIETY())) { result = Bacteria_Variety; }
|
| 1849 | 1868 |
else if (rank.equals(Rank.FORM())) { result = Bacteria_Forma; }
|
| 1850 |
} else {
|
|
| 1869 |
} else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_FUNGI) {
|
|
| 1870 |
if (rank.equals(Rank.KINGDOM())) { result = Fungi_Kingdom; }
|
|
| 1871 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Fungi_Subkingdom; }
|
|
| 1872 |
else if (rank.equals(Rank.DIVISION())) { result = Fungi_Division;}
|
|
| 1873 |
else if (rank.equals(Rank.SUBDIVISION())) { result = Fungi_Subdivision;}
|
|
| 1874 |
else if (rank.equals(Rank.CLASS())) { result = Fungi_Class; }
|
|
| 1875 |
else if (rank.equals(Rank.SUBCLASS())) { result = Fungi_Subclass; }
|
|
| 1876 |
else if (rank.equals(Rank.ORDER())) { result = Fungi_Order; }
|
|
| 1877 |
else if (rank.equals(Rank.SUBORDER())) { result = Fungi_Suborder; }
|
|
| 1878 |
|
|
| 1879 |
else if (rank.equals(Rank.FAMILY())) { result = Fungi_Family; }
|
|
| 1880 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Fungi_Subfamily; }
|
|
| 1881 |
else if (rank.equals(Rank.TRIBE())) { result = Fungi_Tribe; }
|
|
| 1882 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Fungi_Subtribe; }
|
|
| 1883 |
else if (rank.equals(Rank.GENUS())) { result = Fungi_Genus; }
|
|
| 1884 |
else if (rank.equals(Rank.SUBGENUS())) { result = Fungi_Subgenus; }
|
|
| 1885 |
else if (rank.equals(Rank.SECTION_BOTANY())) { result = Fungi_Section;}
|
|
| 1886 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Fungi_Subsection;}
|
|
| 1887 |
else if (rank.equals(Rank.SPECIES())) { result = Fungi_Species; }
|
|
| 1888 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Fungi_Subspecies; }
|
|
| 1889 |
else if (rank.equals(Rank.VARIETY())) { result = Fungi_Variety; }
|
|
| 1890 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Fungi_Subvariety; }
|
|
| 1891 |
else if (rank.equals(Rank.FORM())) { result = Fungi_Forma; }
|
|
| 1892 |
else if (rank.equals(Rank.SUBFORM())) { result = Fungi_Subforma;}
|
|
| 1893 |
}else if (pesiKingdomId != null && pesiKingdomId.intValue() == KINGDOM_CHROMISTA) {
|
|
| 1894 |
if (rank.equals(Rank.KINGDOM())) { result = Chromista_Kingdom; }
|
|
| 1895 |
else if (rank.equals(Rank.SUBKINGDOM())) { result = Chromista_Subkingdom; }
|
|
| 1896 |
|
|
| 1897 |
else if (rank.equals(Rank.CLASS())) { result = Chromista_Class; }
|
|
| 1898 |
else if (rank.equals(Rank.SUBCLASS())) { result = Chromista_Subclass; }
|
|
| 1899 |
else if (rank.equals(Rank.ORDER())) { result = Chromista_Order; }
|
|
| 1900 |
else if (rank.equals(Rank.SUBORDER())) { result = Chromista_Suborder; }
|
|
| 1901 |
else if (rank.equals(Rank.INFRAORDER())) { result = Chromista_Infraorder; }
|
|
| 1902 |
else if (rank.equals(Rank.SUPERFAMILY())) { result = Chromista_Superfamily; }
|
|
| 1903 |
else if (rank.equals(Rank.FAMILY())) { result = Chromista_Family; }
|
|
| 1904 |
else if (rank.equals(Rank.SUBFAMILY())) { result = Chromista_Subfamily; }
|
|
| 1905 |
else if (rank.equals(Rank.TRIBE())) { result = Chromista_Tribe; }
|
|
| 1906 |
else if (rank.equals(Rank.SUBTRIBE())) { result = Chromista_Subtribe; }
|
|
| 1907 |
else if (rank.equals(Rank.GENUS())) { result = Chromista_Genus; }
|
|
| 1908 |
else if (rank.equals(Rank.SUBGENUS())) { result = Chromista_Subgenus; }
|
|
| 1909 |
else if (rank.equals(Rank.SECTION_BOTANY())) { result = Chromista_Section;}
|
|
| 1910 |
else if (rank.equals(Rank.SUBSECTION_BOTANY())) { result = Chromista_Subsection;}
|
|
| 1911 |
else if (rank.equals(Rank.SPECIES())) { result = Chromista_Species; }
|
|
| 1912 |
else if (rank.equals(Rank.SUBSPECIES())) { result = Chromista_Subspecies; }
|
|
| 1913 |
else if (rank.equals(Rank.VARIETY())) { result = Chromista_Variety; }
|
|
| 1914 |
else if (rank.equals(Rank.SUBVARIETY())) { result = Chromista_Subvariety; }
|
|
| 1915 |
else if (rank.equals(Rank.FORM())) { result = Chromista_Forma; }
|
|
| 1916 |
|
|
| 1917 |
|
|
| 1918 |
|
|
| 1919 |
}else{
|
|
| 1851 | 1920 |
//TODO Exception |
| 1852 | 1921 |
logger.warn("Kingdom not yet supported in CDM: "+ pesiKingdomId);
|
| 1853 | 1922 |
return null; |
| 1854 | 1923 |
} |
| 1855 | 1924 |
return result; |
| 1925 |
|
|
| 1856 | 1926 |
} |
| 1857 | 1927 |
|
| 1858 | 1928 |
/** |
| 1859 |
*
|
|
| 1929 |
* |
|
| 1860 | 1930 |
* @param nameTypeDesignationStatus |
| 1861 | 1931 |
* @return |
| 1862 | 1932 |
*/ |
| ... | ... | |
| 1879 | 1949 |
} |
| 1880 | 1950 |
|
| 1881 | 1951 |
/** |
| 1882 |
*
|
|
| 1952 |
* |
|
| 1883 | 1953 |
* @param nameTypeDesignationStatus |
| 1884 | 1954 |
* @return |
| 1885 | 1955 |
*/ |
| ... | ... | |
| 1909 | 1979 |
public static Integer taxonBase2statusFk (TaxonBase<?> taxonBase){
|
| 1910 | 1980 |
if (taxonBase == null){
|
| 1911 | 1981 |
return null; |
| 1912 |
}
|
|
| 1982 |
} |
|
| 1913 | 1983 |
if (taxonBase.isInstanceOf(Taxon.class)){
|
| 1914 | 1984 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
| 1915 | 1985 |
if (taxon.getTaxonNodes().size() == 0){
|
| ... | ... | |
| 1923 | 1993 |
logger.warn("Unknown ");
|
| 1924 | 1994 |
return T_STATUS_UNRESOLVED; |
| 1925 | 1995 |
} |
| 1926 |
//TODO
|
|
| 1996 |
//TODO |
|
| 1927 | 1997 |
// public static int T_STATUS_PARTIAL_SYN = 3; |
| 1928 | 1998 |
// public static int T_STATUS_PRO_PARTE_SYN = 4; |
| 1929 | 1999 |
// public static int T_STATUS_UNRESOLVED = 5; |
| ... | ... | |
| 1931 | 2001 |
} |
| 1932 | 2002 |
|
| 1933 | 2003 |
// /** |
| 1934 |
// *
|
|
| 2004 |
// * |
|
| 1935 | 2005 |
// * @param taxonBase |
| 1936 | 2006 |
// * @return |
| 1937 | 2007 |
// */ |
| ... | ... | |
| 1950 | 2020 |
// logger.warn("Unknown ");
|
| 1951 | 2021 |
// return T_STATUS_STR_UNRESOLVED; |
| 1952 | 2022 |
// } |
| 1953 |
// //TODO
|
|
| 2023 |
// //TODO |
|
| 1954 | 2024 |
// public static int T_STATUS_STR_PARTIAL_SYN = 3; |
| 1955 | 2025 |
// public static int T_STATUS_STR_PRO_PARTE_SYN = 4; |
| 1956 | 2026 |
// public static int T_STATUS_STR_UNRESOLVED = 5; |
| 1957 | 2027 |
// public static int T_STATUS_STR_ORPHANED = 6; |
| 1958 | 2028 |
// } |
| 1959 |
|
|
| 2029 |
|
|
| 1960 | 2030 |
/** |
| 1961 | 2031 |
* Returns the {@link SourceCategory SourceCategory} representation of the given {@link ReferenceType ReferenceType} in PESI.
|
| 1962 | 2032 |
* @param reference The {@link Reference Reference}.
|
| ... | ... | |
| 2000 | 2070 |
return null; |
| 2001 | 2071 |
} |
| 2002 | 2072 |
} |
| 2003 |
|
|
| 2073 |
|
|
| 2004 | 2074 |
/** |
| 2005 | 2075 |
* Returns the {@link SourceCategoryCache SourceCategoryCache}.
|
| 2006 | 2076 |
* @param reference The {@link Reference Reference}.
|
| ... | ... | |
| 2010 | 2080 |
if (reference == null){
|
| 2011 | 2081 |
return null; |
| 2012 | 2082 |
}else{
|
| 2013 |
return this.sourceCategoryCacheMap.get(reference2SourceCategoryFK(reference));
|
|
| 2083 |
return this.sourceCategoryCacheMap.get(reference2SourceCategoryFK(reference)); |
|
| 2014 | 2084 |
} |
| 2015 | 2085 |
} |
| 2016 | 2086 |
|
| 2017 | 2087 |
/** |
| 2018 |
*
|
|
| 2088 |
* |
|
| 2019 | 2089 |
* @param status |
| 2020 | 2090 |
* @return |
| 2021 | 2091 |
*/ |
| 2022 |
public String getCacheByNomStatus(NomenclaturalStatusType status) {
|
|
| 2092 |
@Override |
|
| 2093 |
public String getCacheByNomStatus(NomenclaturalStatusType status) {
|
|
| 2023 | 2094 |
if (status == null){
|
| 2024 | 2095 |
return null; |
| 2025 | 2096 |
}else{
|
| 2026 |
return this.nameStatusCacheMap.get(nomStatus2nomStatusFk(status));
|
|
| 2097 |
return this.nameStatusCacheMap.get(nomStatus2nomStatusFk(status)); |
|
| 2027 | 2098 |
} |
| 2028 | 2099 |
} |
| 2029 |
|
|
| 2100 |
|
|
| 2030 | 2101 |
/** |
| 2031 |
*
|
|
| 2102 |
* |
|
| 2032 | 2103 |
* @param status |
| 2033 | 2104 |
* @return |
| 2034 | 2105 |
*/ |
| ... | ... | |
| 2044 | 2115 |
}else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED())) {return NAME_ST_NOM_UTIQUE_REJ;
|
| 2045 | 2116 |
}else if (status.equals(NomenclaturalStatusType.UTIQUE_REJECTED_PROP())) {return NAME_ST_NOM_UTIQUE_REJ_PROP;
|
| 2046 | 2117 |
}else if (status.equals(NomenclaturalStatusType.CONSERVED())) {return NAME_ST_NOM_CONS;
|
| 2047 |
|
|
| 2118 |
|
|
| 2048 | 2119 |
}else if (status.equals(NomenclaturalStatusType.CONSERVED_PROP())) {return NAME_ST_NOM_CONS_PROP;
|
| 2049 | 2120 |
}else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED())) {return NAME_ST_ORTH_CONS;
|
| 2050 | 2121 |
}else if (status.equals(NomenclaturalStatusType.ORTHOGRAPHY_CONSERVED_PROP())) {return NAME_ST_ORTH_CONS_PROP;
|
| ... | ... | |
| 2053 | 2124 |
}else if (status.equals(NomenclaturalStatusType.PROVISIONAL())) {return NAME_ST_NOM_PROVIS;
|
| 2054 | 2125 |
}else if (status.equals(NomenclaturalStatusType.DOUBTFUL())) {return NAME_ST_NOM_DUB;
|
| 2055 | 2126 |
}else if (status.equals(NomenclaturalStatusType.NOVUM())) {return NAME_ST_NOM_NOV;
|
| 2056 |
|
|
| 2127 |
|
|
| 2057 | 2128 |
}else if (status.equals(NomenclaturalStatusType.CONFUSUM())) {return NAME_ST_NOM_CONFUS;
|
| 2058 | 2129 |
}else if (status.equals(NomenclaturalStatusType.ALTERNATIVE())) {return NAME_ST_NOM_ALTERN;
|
| 2059 | 2130 |
}else if (status.equals(NomenclaturalStatusType.COMBINATION_INVALID())) {return NAME_ST_COMB_INVAL;
|
| 2060 | 2131 |
}else if (status.equals(NomenclaturalStatusType.LEGITIMATE())) {return NAME_ST_LEGITIMATE;
|
| 2061 |
|
|
| 2132 |
|
|
| 2062 | 2133 |
}else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusCombIned)) {return NAME_ST_COMB_INED;
|
| 2063 | 2134 |
}else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusNomOrthCons)) {return NAME_ST_NOM_AND_ORTH_CONS;
|
| 2064 | 2135 |
}else if (status.getUuid().equals(BerlinModelTransformer.uuidNomStatusSpNovIned)) {return NAME_ST_SP_NOV_INED;
|
| 2065 |
|
|
| 2066 |
|
|
| 2136 |
|
|
| 2137 |
|
|
| 2067 | 2138 |
// The following are non-existent in CDM |
| 2068 | 2139 |
// }else if (status.equals(NomenclaturalStatusType.)) {return NAME_ST_COMB_AND_STAT_INED;
|
| 2069 | 2140 |
// }else if (status.equals(NomenclaturalStatusType.)) {return NAME_ST_NOM_NOV_INED;
|
| ... | ... | |
| 2078 | 2149 |
return null; |
| 2079 | 2150 |
} |
| 2080 | 2151 |
} |
| 2081 |
|
|
| 2152 |
|
|
| 2082 | 2153 |
/** |
| 2083 | 2154 |
* Returns the RelTaxonQualifierCache for a given taxonRelation. |
| 2084 | 2155 |
* @param relation |
| ... | ... | |
| 2088 | 2159 |
if (relation == null){
|
| 2089 | 2160 |
return null; |
| 2090 | 2161 |
}else{
|
| 2091 |
String result;
|
|
| 2162 |
String result; |
|
| 2092 | 2163 |
Integer key = taxonRelation2RelTaxonQualifierFk(relation); |
| 2093 | 2164 |
if (code.equals(NomenclaturalCode.ICZN)){
|
| 2094 | 2165 |
result = this.taxRelZooQualifierCacheMap.get(key); |
| 2095 | 2166 |
if (result == null){
|
| 2096 |
this.taxRelQualifierCacheMap.get(key);
|
|
| 2167 |
this.taxRelQualifierCacheMap.get(key); |
|
| 2097 | 2168 |
} |
| 2098 | 2169 |
}else{
|
| 2099 |
result = this.taxRelQualifierCacheMap.get(key);
|
|
| 2170 |
result = this.taxRelQualifierCacheMap.get(key); |
|
| 2100 | 2171 |
} |
| 2101 | 2172 |
return result; |
| 2102 | 2173 |
} |
| 2103 | 2174 |
} |
| 2104 |
|
|
| 2175 |
|
|
| 2105 | 2176 |
/** |
| 2106 | 2177 |
* Returns the RelTaxonQualifierFk for a TaxonRelation. |
| 2107 | 2178 |
* @param relation |
| ... | ... | |
| 2191 | 2262 |
|
| 2192 | 2263 |
return null; |
| 2193 | 2264 |
} |
| 2194 |
|
|
| 2265 |
|
|
| 2195 | 2266 |
/** |
| 2196 | 2267 |
* Returns the StatusFk for a given StatusCache. |
| 2197 | 2268 |
* @param StatusCache |
| ... | ... | |
| 2210 | 2281 |
} else {
|
| 2211 | 2282 |
logger.error("StatusFk could not be determined. StatusCache unknown: " + StatusCache);
|
| 2212 | 2283 |
} |
| 2213 |
|
|
| 2284 |
|
|
| 2214 | 2285 |
return result; |
| 2215 | 2286 |
} |
| 2216 |
|
|
| 2287 |
|
|
| 2217 | 2288 |
/** |
| 2218 | 2289 |
* Returns the FossilStatusFk for a given FossilStatusCache. |
| 2219 | 2290 |
* @param fossilStatusCache |
| ... | ... | |
| 2230 | 2301 |
} else {
|
| 2231 | 2302 |
logger.error("FossilStatusFk could not be determined. FossilStatusCache unknown: " + fossilStatusCache);
|
| 2232 | 2303 |
} |
| 2233 |
|
|
| 2304 |
|
|
| 2234 | 2305 |
return result; |
| 2235 | 2306 |
} |
| 2236 | 2307 |
|
| ... | ... | |
| 2250 | 2321 |
} |
| 2251 | 2322 |
return result; |
| 2252 | 2323 |
} |
| 2253 |
|
|
| 2324 |
|
|
| 2254 | 2325 |
/** |
| 2255 | 2326 |
* Returns the NoteCategoryCache for a given UUID representing an ExtensionType. |
| 2256 | 2327 |
* @param uuid |
| ... | ... | |
| 2289 | 2360 |
return null; |
| 2290 | 2361 |
} |
| 2291 | 2362 |
}else{
|
| 2292 |
return null; // TODO needs to be implemented for others
|
|
| 2363 |
return null; // TODO needs to be implemented for others |
|
| 2293 | 2364 |
} |
| 2294 | 2365 |
} |
| 2295 | 2366 |
|
| 2296 |
|
|
| 2367 |
|
|
| 2297 | 2368 |
private static Set<String> getAllQualityStatus(TaxonNameBase<?, ?> taxonName) {
|
| 2298 | 2369 |
Set<String> result = new HashSet<String>(); |
| 2299 | 2370 |
for (TaxonBase<?> taxonBase : taxonName.getTaxonBases()){
|
| ... | ... | |
| 2307 | 2378 |
if (qualityStatusId == null){
|
| 2308 | 2379 |
return null; |
| 2309 | 2380 |
}else{
|
| 2310 |
return this.qualityStatusCacheMap.get(qualityStatusId);
|
|
| 2381 |
return this.qualityStatusCacheMap.get(qualityStatusId); |
|
| 2311 | 2382 |
} |
| 2312 | 2383 |
} |
| 2313 |
|
|
| 2384 |
|
|
| 2314 | 2385 |
|
| 2315 | 2386 |
public Object getSourceUseCacheByKey(Integer sourceUseFk) {
|
| 2316 | 2387 |
if (sourceUseFk == null){
|
| 2317 | 2388 |
return null; |
| 2318 | 2389 |
}else{
|
| 2319 |
return this.sourceUseCacheMap.get(sourceUseFk);
|
|
| 2390 |
return this.sourceUseCacheMap.get(sourceUseFk); |
|
| 2320 | 2391 |
} |
| 2321 | 2392 |
} |
| 2322 |
|
|
| 2393 |
|
|
| 2323 | 2394 |
@Override |
| 2324 | 2395 |
public String getTaxonStatusCacheByKey(Integer taxonStatusId) throws UndefinedTransformerMethodException {
|
| 2325 | 2396 |
if (taxonStatusId == null){
|
| 2326 | 2397 |
return null; |
| 2327 | 2398 |
}else{
|
| 2328 |
return this.taxonStatusCacheMap.get(taxonStatusId);
|
|
| 2399 |
return this.taxonStatusCacheMap.get(taxonStatusId); |
|
| 2329 | 2400 |
} |
| 2330 | 2401 |
} |
| 2331 | 2402 |
|
| ... | ... | |
| 2343 | 2414 |
if (sources.get(SOURCE_ERMS)){
|
| 2344 | 2415 |
result = CdmUtils.concat(",", result, SOURCE_STR_ERMS);
|
| 2345 | 2416 |
} |
| 2346 |
|
|
| 2417 |
|
|
| 2347 | 2418 |
return result; |
| 2348 | 2419 |
} |
| 2349 | 2420 |
|
| 2421 |
/** |
|
| 2422 |
* @param titleCache |
|
| 2423 |
*/ |
|
| 2424 |
public static Integer pesiKingdomId(String titleCache) {
|
|
| 2425 |
return pesiKingdomMap.get(titleCache); |
|
| 2426 |
|
|
| 2427 |
} |
|
| 2428 |
|
|
| 2429 |
|
|
| 2350 | 2430 |
|
| 2351 |
|
|
| 2352 | 2431 |
} |
Also available in: Unified diff