Revision 86ea4f4a
Added by Andreas Müller over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/app/berlinModelImport/SalvadorActivator.java | ||
|---|---|---|
| 47 | 47 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE; |
| 48 | 48 |
static final Source berlinModelSource = BerlinModelSources.El_Salvador(); |
| 49 | 49 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
| 50 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_salvador_preview(); |
|
| 51 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_salvador_production();
|
|
| 50 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_salvador_preview();
|
|
| 51 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_salvador_production(); |
|
| 52 | 52 |
static final UUID treeUuid = UUID.fromString("b010c84d-6049-45f4-9f13-c065101eaa26");
|
| 53 | 53 |
static final UUID secUuid = UUID.fromString("d03ef02a-f226-4cb1-bdb4-f6c154f08a34");
|
| 54 | 54 |
static final int sourceSecId = 7331; |
| 55 | 55 |
|
| 56 | 56 |
static final UUID featureTreeUuid = UUID.fromString("9d0e5628-2eda-43ed-bc59-138a7e39ce56");
|
| 57 |
static final Object[] featureKeyList = new Integer[]{302, 303, 306, 307, 309, 310, 311, 312, 350, 1500, 1800, 1900, 1950, 1980, 2000, 10299};
|
|
| 57 |
static final Object[] featureKeyList = new Integer[]{302, 303, 306, 307, 309, 310, 311, 312, 350, 1500, 1800, 1900, 1950, 1980, 2000};
|
|
| 58 | 58 |
static boolean isIgnore0AuthorTeam = true; //special case for Salvador. |
| 59 | 59 |
static boolean doExport = false; |
| 60 | 60 |
static boolean useClassification = true; |
| ... | ... | |
| 96 | 96 |
static final boolean doUser = true; |
| 97 | 97 |
|
| 98 | 98 |
|
| 99 |
static String factFilter = " factCategoryFk NOT IN (1980, 1500, 1950, 1700) "; |
|
| 99 |
static String factFilter = " factCategoryFk NOT IN ("
|
|
| 100 |
// + "302, 303, 306, 307, 309, 311, 310, " |
|
| 101 |
+ "1980, 1500, 1950, 1700) "; |
|
| 100 | 102 |
|
| 101 | 103 |
|
| 102 | 104 |
// ************************ NONE **************************************** // |
| ... | ... | |
| 154 | 156 |
config.setDoMarker(doMarker); |
| 155 | 157 |
config.setDoUser(doUser); |
| 156 | 158 |
|
| 159 |
config.setTaxonNoteAsFeature(true); |
|
| 160 |
|
|
| 157 | 161 |
config.setDbSchemaValidation(hbm2dll); |
| 158 | 162 |
|
| 159 | 163 |
config.setCheck(check); |
| ... | ... | |
| 166 | 170 |
config.setSalvador(isSalvador); |
| 167 | 171 |
config.setFactFilter(factFilter); |
| 168 | 172 |
|
| 173 |
config.setFeatureTreeUuid(featureTreeUuid); |
|
| 174 |
config.setFeatureTreeTitle("Salvador Portal Feature Tree");
|
|
| 175 |
|
|
| 169 | 176 |
// invoke import |
| 170 | 177 |
CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>(); |
| 171 | 178 |
ImportResult result = bmImport.invoke(config); |
| ... | ... | |
| 178 | 185 |
|
| 179 | 186 |
//create feature tree |
| 180 | 187 |
private void createFeatureTree(BerlinModelImportConfigurator config, |
| 181 |
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) |
|
| 182 |
{
|
|
| 188 |
CdmDefaultImport<BerlinModelImportConfigurator> bmImport){
|
|
| 183 | 189 |
if (config.isDoFacts() && (config.getCheck().isImport() ) ){
|
| 184 | 190 |
try {
|
| 185 | 191 |
ICdmApplicationConfiguration app = bmImport.getCdmAppController(); |
| 186 |
TransactionStatus tx = app.startTransaction(); |
|
| 192 |
TransactionStatus tx = app.startTransaction(false);
|
|
| 187 | 193 |
|
| 188 | 194 |
//make feature tree |
| 189 | 195 |
FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelFactsImport.java | ||
|---|---|---|
| 58 | 58 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
| 59 | 59 |
import eu.etaxonomy.cdm.model.description.Distribution; |
| 60 | 60 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 61 |
import eu.etaxonomy.cdm.model.description.FeatureNode; |
|
| 62 |
import eu.etaxonomy.cdm.model.description.FeatureTree; |
|
| 61 | 63 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm; |
| 62 | 64 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 63 | 65 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 64 |
import eu.etaxonomy.cdm.model.location.Country; |
|
| 65 | 66 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 66 | 67 |
import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
| 67 | 68 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| ... | ... | |
| 124 | 125 |
|
| 125 | 126 |
Map<Integer, Feature> result = state.getConfig().getFeatureMap(); |
| 126 | 127 |
Source source = state.getConfig().getSource(); |
| 128 |
boolean createFeatureTree = state.getConfig().isSalvador(); //for some reason feature tree creation does not work for salavdor |
|
| 127 | 129 |
|
| 128 |
try {
|
|
| 130 |
FeatureTree featureTree = (!createFeatureTree) ? null : FeatureTree.NewInstance(state.getConfig().getFeatureTreeUuid()); |
|
| 131 |
if (createFeatureTree){
|
|
| 132 |
featureTree.setTitleCache(state.getConfig().getFeatureTreeTitle(), true); |
|
| 133 |
} |
|
| 134 |
|
|
| 135 |
try {
|
|
| 129 | 136 |
//get data from database |
| 130 | 137 |
String strQuery = |
| 131 | 138 |
" SELECT FactCategory.* " + |
| ... | ... | |
| 173 | 180 |
} |
| 174 | 181 |
|
| 175 | 182 |
result.put(factCategoryId, feature); |
| 183 |
if (createFeatureTree){
|
|
| 184 |
featureTree.getRoot().addChild(FeatureNode.NewInstance(feature)); |
|
| 185 |
} |
|
| 186 |
} |
|
| 187 |
if (createFeatureTree){
|
|
| 188 |
getFeatureTreeService().save(featureTree); |
|
| 176 | 189 |
} |
| 177 | 190 |
return result; |
| 178 | 191 |
} catch (SQLException e) {
|
| ... | ... | |
| 388 | 401 |
|
| 389 | 402 |
if (state.getConfig().isSalvador()){
|
| 390 | 403 |
if (categoryFkInt == 306){
|
| 391 |
deb = CommonTaxonName.NewInstance(fact, Language.SPANISH_CASTILIAN(), Country.ELSALVADORREPUBLICOF()); |
|
| 404 |
NamedArea area = null; // for now we do not set an area as it can not be disabled in dataportals via css yet |
|
| 405 |
deb = CommonTaxonName.NewInstance(fact, Language.SPANISH_CASTILIAN(), area); |
|
| 392 | 406 |
}else if (categoryFkInt == 307){
|
| 393 | 407 |
Distribution salvadorDistribution = salvadorDistributionFromMuestrasDeHerbar((Taxon)taxonBase, fact); |
| 394 | 408 |
if (salvadorDistribution != null){
|
| ... | ... | |
| 914 | 928 |
vol2.setInSeries(englera); |
| 915 | 929 |
vol3.setInSeries(englera); |
| 916 | 930 |
|
| 917 |
vol1.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 1: Angiospermae - Familias A-L");
|
|
| 918 |
vol2.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 2: Angiospermae - Familias M-P y Pteridophyta");
|
|
| 919 |
vol3.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 3: Angiospermae - Familias R-Z y Gymnospermae");
|
|
| 931 |
vol1.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 1: Angiospermae - Familias A a L");
|
|
| 932 |
vol2.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 2: Angiospermae - Familias M a P y Pteridophyta");
|
|
| 933 |
vol3.setTitle("Nova Silva Cuscatlanica, Árboles nativos e introducidos de El Salvador - Parte 3: Angiospermae - Familias R a Z y Gymnospermae");
|
|
| 920 | 934 |
|
| 921 | 935 |
vol1.setVolume("29(1)");
|
| 922 | 936 |
vol2.setVolume("29(2)");
|
| ... | ... | |
| 926 | 940 |
vol2.setVolume("1-300");
|
| 927 | 941 |
vol3.setVolume("1-356");
|
| 928 | 942 |
|
| 943 |
String placePublished = "Berlin: Botanic Garden and Botanical Museum Berlin; Antiguo Cuscatlán: Asociación Jardín Botánico La Laguna, El Salvador"; |
|
| 944 |
vol1.setPlacePublished(placePublished); |
|
| 945 |
vol2.setPlacePublished(placePublished); |
|
| 946 |
vol3.setPlacePublished(placePublished); |
|
| 947 |
|
|
| 929 | 948 |
salvadorRef1Id = getReferenceService().save(vol1).getId(); |
| 930 | 949 |
salvadorRef2Id = getReferenceService().find(getReferenceService().saveOrUpdate(vol2)).getId(); |
| 931 | 950 |
salvadorRef3Id = getReferenceService().find(getReferenceService().saveOrUpdate(vol3)).getId(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelImportConfigurator.java | ||
|---|---|---|
| 13 | 13 |
import java.lang.reflect.Method; |
| 14 | 14 |
import java.net.MalformedURLException; |
| 15 | 15 |
import java.net.URL; |
| 16 |
import java.util.UUID; |
|
| 16 | 17 |
|
| 17 | 18 |
import org.apache.log4j.Logger; |
| 18 | 19 |
|
| ... | ... | |
| 20 | 21 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser; |
| 21 | 22 |
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelGeneralImportValidator; |
| 22 | 23 |
import eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase; |
| 23 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
| 24 | 24 |
import eu.etaxonomy.cdm.io.common.Source; |
| 25 | 25 |
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer; |
| 26 | 26 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| ... | ... | |
| 29 | 29 |
* @author a.mueller |
| 30 | 30 |
* @created 20.03.2008 |
| 31 | 31 |
*/ |
| 32 |
public class BerlinModelImportConfigurator extends DbImportConfiguratorBase<BerlinModelImportState> implements IImportConfigurator{
|
|
| 32 |
public class BerlinModelImportConfigurator extends DbImportConfiguratorBase<BerlinModelImportState>{
|
|
| 33 | 33 |
private static final long serialVersionUID = 70300913255425256L; |
| 34 | 34 |
|
| 35 | 35 |
private static Logger logger = Logger.getLogger(BerlinModelImportConfigurator.class); |
| ... | ... | |
| 110 | 110 |
//specific functions |
| 111 | 111 |
private Method makeUrlForTaxon = null; |
| 112 | 112 |
|
| 113 |
@Override |
|
| 113 |
private UUID featureTreeUuid; |
|
| 114 |
private String featureTreeTitle; |
|
| 115 |
|
|
| 116 |
private boolean isTaxonNoteAsFeature = false; |
|
| 117 |
|
|
| 118 |
|
|
| 119 |
public boolean isTaxonNoteAsFeature() {return isTaxonNoteAsFeature;}
|
|
| 120 |
public void setTaxonNoteAsFeature(boolean isTaxonNoteAsFeature) {this.isTaxonNoteAsFeature = isTaxonNoteAsFeature;}
|
|
| 121 |
|
|
| 122 |
@Override |
|
| 114 | 123 |
protected void makeIoClassList(){
|
| 115 | 124 |
ioClassList = new Class[]{
|
| 116 | 125 |
BerlinModelGeneralImportValidator.class |
| ... | ... | |
| 632 | 641 |
public boolean isSalvador() {return isSalvador;}
|
| 633 | 642 |
public void setSalvador(boolean isSalvador) {this.isSalvador = isSalvador;}
|
| 634 | 643 |
|
| 644 |
public UUID getFeatureTreeUuid() {
|
|
| 645 |
return featureTreeUuid; |
|
| 646 |
} |
|
| 647 |
public void setFeatureTreeUuid(UUID featureTreeUuid) {
|
|
| 648 |
this.featureTreeUuid = featureTreeUuid; |
|
| 649 |
} |
|
| 650 |
|
|
| 651 |
public String getFeatureTreeTitle() {
|
|
| 652 |
return featureTreeTitle; |
|
| 653 |
} |
|
| 654 |
public void setFeatureTreeTitle(String featureTreeTitle) {
|
|
| 655 |
this.featureTreeTitle = featureTreeTitle; |
|
| 656 |
} |
|
| 657 |
|
|
| 658 |
|
|
| 659 |
|
|
| 660 |
|
|
| 635 | 661 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelReferenceImport.java | ||
|---|---|---|
| 76 | 76 |
*/ |
| 77 | 77 |
@Component |
| 78 | 78 |
public class BerlinModelReferenceImport extends BerlinModelImportBase {
|
| 79 |
private static final Logger logger = Logger.getLogger(BerlinModelReferenceImport.class); |
|
| 79 |
private static final long serialVersionUID = -3667566958769967591L; |
|
| 80 |
|
|
| 81 |
private static final Logger logger = Logger.getLogger(BerlinModelReferenceImport.class); |
|
| 80 | 82 |
|
| 81 | 83 |
public static final String REFERENCE_NAMESPACE = "Reference"; |
| 84 |
private static final String REF_AUTHOR_NAMESPACE = "Reference.refAuthorString"; |
|
| 85 |
|
|
| 82 | 86 |
|
| 83 | 87 |
public static final UUID REF_DEPOSITED_AT_UUID = UUID.fromString("23ca88c7-ce73-41b2-8ca3-2cb22f013beb");
|
| 84 | 88 |
public static final UUID REF_SOURCE_UUID = UUID.fromString("d6432582-2216-4b08-b0db-76f6c1013141");
|
| ... | ... | |
| 239 | 243 |
|
| 240 | 244 |
Map<Integer, Reference> refToSave = new HashMap<Integer, Reference>(); |
| 241 | 245 |
|
| 242 |
Map<String, Reference> relatedReferences = partitioner.getObjectMap(REFERENCE_NAMESPACE); |
|
| 246 |
@SuppressWarnings("unchecked")
|
|
| 247 |
Map<String, Reference> relatedReferences = partitioner.getObjectMap(REFERENCE_NAMESPACE); |
|
| 243 | 248 |
|
| 244 | 249 |
BerlinModelImportConfigurator config = state.getConfig(); |
| 245 | 250 |
|
| ... | ... | |
| 350 | 355 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 351 | 356 |
|
| 352 | 357 |
try{
|
| 353 |
Set<String> teamIdSet = new HashSet<String>(); |
|
| 354 |
Set<String> referenceIdSet = new HashSet<String>(); |
|
| 358 |
Set<String> teamIdSet = new HashSet<>(); |
|
| 359 |
Set<String> referenceIdSet = new HashSet<>(); |
|
| 360 |
Set<String> teamStringSet = new HashSet<>(); |
|
| 355 | 361 |
|
| 356 | 362 |
while (rs.next()){
|
| 357 | 363 |
handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk"); |
| 358 | 364 |
handleForeignKey(rs, referenceIdSet, "InRefFk"); |
| 365 |
handleForeignKey(rs, teamStringSet, "refAuthorString"); |
|
| 359 | 366 |
//TODO only needed in second path but state not available here to check if state is second path |
| 360 | 367 |
handleForeignKey(rs, referenceIdSet, "refId"); |
| 361 | 368 |
} |
| 362 | 369 |
|
| 370 |
Set<String> teamStringSet2 = new HashSet<>(); |
|
| 371 |
for (String teamString : teamStringSet){
|
|
| 372 |
teamStringSet2.add(teamString.replace("'", "´"));
|
|
| 373 |
} |
|
| 374 |
|
|
| 363 | 375 |
//team map |
| 364 | 376 |
nameSpace = BerlinModelAuthorTeamImport.NAMESPACE; |
| 365 | 377 |
cdmClass = Team.class; |
| 366 | 378 |
idSet = teamIdSet; |
| 367 |
Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 379 |
@SuppressWarnings("unchecked")
|
|
| 380 |
Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 368 | 381 |
result.put(nameSpace, teamMap); |
| 369 | 382 |
|
| 383 |
//refAuthor map |
|
| 384 |
nameSpace = REF_AUTHOR_NAMESPACE; |
|
| 385 |
cdmClass = Team.class; |
|
| 386 |
idSet = teamStringSet2; |
|
| 387 |
@SuppressWarnings("unchecked")
|
|
| 388 |
Map<String, Team> refAuthorMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 389 |
result.put(nameSpace, refAuthorMap); |
|
| 390 |
|
|
| 370 | 391 |
//reference map |
| 371 | 392 |
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE; |
| 372 | 393 |
cdmClass = Reference.class; |
| ... | ... | |
| 399 | 420 |
Map<Integer, Reference> refToSave, |
| 400 | 421 |
Map<String, Reference> relatedReferences, |
| 401 | 422 |
RefCounter refCounter){
|
| 402 |
boolean success = true; |
|
| 423 |
|
|
| 424 |
boolean success = true; |
|
| 403 | 425 |
|
| 404 | 426 |
Integer refId = null; |
| 405 | 427 |
try {
|
| ... | ... | |
| 494 | 516 |
Map<Integer, Reference> refToSave |
| 495 | 517 |
) throws SQLException{
|
| 496 | 518 |
|
| 497 |
Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE); |
|
| 519 |
@SuppressWarnings("unchecked")
|
|
| 520 |
Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE); |
|
| 498 | 521 |
|
| 499 | 522 |
String refCache = rs.getString("refCache");
|
| 500 | 523 |
String nomRefCache = rs.getString("nomRefCache");
|
| ... | ... | |
| 523 | 546 |
} |
| 524 | 547 |
|
| 525 | 548 |
//author |
| 526 |
TeamOrPersonBase<?> author = getAuthorship(refAuthorString , nomAuthor); |
|
| 549 |
TeamOrPersonBase<?> author = getAuthorship(state, refAuthorString , nomAuthor);
|
|
| 527 | 550 |
ref.setAuthorship(author); |
| 528 | 551 |
|
| 529 | 552 |
//save |
| ... | ... | |
| 694 | 717 |
|
| 695 | 718 |
//Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};
|
| 696 | 719 |
|
| 697 |
Set<String> omitAttributes = new HashSet<String>();
|
|
| 720 |
Set<String> omitAttributes = new HashSet<>(); |
|
| 698 | 721 |
String attrSeries = "series"; |
| 699 | 722 |
// omitAttributes.add(attrSeries); |
| 700 | 723 |
|
| ... | ... | |
| 844 | 867 |
} |
| 845 | 868 |
|
| 846 | 869 |
|
| 847 |
private static TeamOrPersonBase<?> getAuthorship(String authorString, TeamOrPersonBase<?> nomAuthor){
|
|
| 848 |
TeamOrPersonBase<?> result; |
|
| 870 |
private static TeamOrPersonBase<?> getAuthorship(BerlinModelImportState state, String authorString, TeamOrPersonBase<?> nomAuthor){
|
|
| 871 |
|
|
| 872 |
TeamOrPersonBase<?> result; |
|
| 849 | 873 |
if (nomAuthor != null){
|
| 850 | 874 |
result = nomAuthor; |
| 851 | 875 |
} else if (StringUtils.isNotBlank(authorString)){
|
| 852 |
//FIXME check for existing team / persons |
|
| 853 |
TeamOrPersonBase<?> team = Team.NewInstance(); |
|
| 854 |
team.setNomenclaturalTitle(authorString); |
|
| 855 |
team.setTitleCache(authorString, true); |
|
| 856 |
team.setNomenclaturalTitle(authorString); |
|
| 876 |
//TODO match with existing Persons/Teams |
|
| 877 |
Team team = state.getRelatedObject(REF_AUTHOR_NAMESPACE, authorString, Team.class); |
|
| 878 |
if (team == null){
|
|
| 879 |
team = Team.NewInstance(); |
|
| 880 |
team.setNomenclaturalTitle(authorString); |
|
| 881 |
team.setTitleCache(authorString, true); |
|
| 882 |
state.addRelatedObject(REF_AUTHOR_NAMESPACE, authorString, team); |
|
| 883 |
team.addImportSource(authorString, REF_AUTHOR_NAMESPACE, state.getConfig().getSourceReference(), null); |
|
| 884 |
} |
|
| 857 | 885 |
result = team; |
| 858 | 886 |
}else{
|
| 859 | 887 |
result = null; |
| ... | ... | |
| 869 | 897 |
* @return |
| 870 | 898 |
*/ |
| 871 | 899 |
public Set<String> getObligatoryAttributes(boolean lowerCase, BerlinModelImportConfigurator config){
|
| 872 |
Set<String> result = new HashSet<String>();
|
|
| 900 |
Set<String> result = new HashSet<>(); |
|
| 873 | 901 |
Class<ICdmImport>[] ioClassList = config.getIoClassList(); |
| 874 | 902 |
logger.warn("getObligatoryAttributes has been commented because it still needs to be adapted to the new package structure");
|
| 875 | 903 |
result.addAll(Arrays.asList(unclearMappers)); |
| ... | ... | |
| 881 | 909 |
} |
| 882 | 910 |
result.addAll(mapping.getSourceAttributes()); |
| 883 | 911 |
if (lowerCase){
|
| 884 |
Set<String> lowerCaseResult = new HashSet<String>();
|
|
| 912 |
Set<String> lowerCaseResult = new HashSet<>(); |
|
| 885 | 913 |
for (String str : result){
|
| 886 | 914 |
if (str != null){lowerCaseResult.add(str.toLowerCase());}
|
| 887 | 915 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonImport.java | ||
|---|---|---|
| 37 | 37 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.common.Extension; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.common.ExtensionType; |
| 40 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 41 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
| 42 |
import eu.etaxonomy.cdm.model.description.TextData; |
|
| 40 | 43 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 41 | 44 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 42 | 45 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 47 | 50 |
/** |
| 48 | 51 |
* @author a.mueller |
| 49 | 52 |
* @created 20.03.2008 |
| 50 |
* @version 1.0 |
|
| 51 | 53 |
*/ |
| 52 | 54 |
@Component |
| 53 | 55 |
public class BerlinModelTaxonImport extends BerlinModelImportBase {
|
| 54 |
private static final Logger logger = Logger.getLogger(BerlinModelTaxonImport.class); |
|
| 56 |
private static final long serialVersionUID = -1186364983750790695L; |
|
| 57 |
|
|
| 58 |
private static final Logger logger = Logger.getLogger(BerlinModelTaxonImport.class); |
|
| 55 | 59 |
|
| 56 | 60 |
public static final String NAMESPACE = "Taxon"; |
| 57 | 61 |
|
| ... | ... | |
| 255 | 259 |
} |
| 256 | 260 |
|
| 257 | 261 |
//Notes |
| 258 |
doIdCreatedUpdatedNotes(state, taxonBase, rs, taxonId, NAMESPACE); |
|
| 262 |
boolean excludeNotes = state.getConfig().isTaxonNoteAsFeature() && taxonBase.isInstanceOf(Taxon.class); |
|
| 263 |
doIdCreatedUpdatedNotes(state, taxonBase, rs, taxonId, NAMESPACE, false, excludeNotes); |
|
| 264 |
if (excludeNotes){
|
|
| 265 |
makeTaxonomicNote(state, CdmBase.deproxy(taxonBase, Taxon.class), rs.getString("Notes"));
|
|
| 266 |
} |
|
| 259 | 267 |
|
| 260 | 268 |
//external url |
| 261 | 269 |
if (config.getMakeUrlForTaxon() != null){
|
| ... | ... | |
| 284 | 292 |
return success; |
| 285 | 293 |
} |
| 286 | 294 |
|
| 287 |
@Override |
|
| 295 |
/** |
|
| 296 |
* @param state |
|
| 297 |
* @param taxonBase |
|
| 298 |
* @param notes |
|
| 299 |
*/ |
|
| 300 |
private void makeTaxonomicNote(BerlinModelImportState state, Taxon taxon, String notes) {
|
|
| 301 |
TaxonDescription desc = getTaxonDescription(taxon, false, true); |
|
| 302 |
desc.addElement(TextData.NewInstance(notes, Language.SPANISH_CASTILIAN(), null)); |
|
| 303 |
} |
|
| 304 |
|
|
| 305 |
@Override |
|
| 288 | 306 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 289 | 307 |
String nameSpace; |
| 290 | 308 |
Class<?> cdmClass; |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
|---|---|---|
| 300 | 300 |
} |
| 301 | 301 |
handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk); |
| 302 | 302 |
Synonym synonym = (Synonym)taxon1; |
| 303 |
if (synonym.getAcceptedTaxon()!= null){
|
|
| 304 |
logger.warn("Synonym already has an accepted taxon. Create clone.");
|
|
| 305 |
synonym = (Synonym)synonym.clone(); |
|
| 306 |
} |
|
| 303 | 307 |
makeSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation); |
| 304 | 308 |
if (isNotBlank(notes)){
|
| 305 | 309 |
logger.warn("Notes for synonym relationship or unknown taxon relationship not handled");
|
Also available in: Unified diff
ref #3934 latest changes to Salvador import