Revision 5f0f426e
Added by Andreas Müller about 10 years ago
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/app/eflora/CentralAfricaEricaceaeActivator.java | ||
|---|---|---|
| 59 | 59 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE; |
| 60 | 60 |
static final URI source = EfloraSources.ericacea_local(); |
| 61 | 61 |
|
| 62 |
static final URI specimenSource = EfloraSources.ericacea_specimen_local();
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| 62 |
static final URI specimenSource = EfloraSources.vittaria_specimen_pesiimport3();
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|
| 63 | 63 |
|
| 64 | 64 |
|
| 65 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_andreasM3(); |
|
| 66 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
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| 65 |
static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_preview(); |
|
| 67 | 66 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_flora_central_africa_production(); |
| 68 |
static final ICdmDataSource cdmDestination = CdmDestinations.localH2(); |
|
| 67 |
// static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
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|
| 69 | 68 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_postgres_CdmTest(); |
| 70 | 69 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql(); |
| 71 | 70 |
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_jaxb(); |
| ... | ... | |
| 86 | 85 |
static boolean doPrintKeys = false; |
| 87 | 86 |
|
| 88 | 87 |
//taxa |
| 89 |
private boolean includeEricaceae = true;
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| 90 |
static final boolean doTaxa = true;
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| 88 |
private boolean includeEricaceae = false;
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| 89 |
static final boolean doTaxa = false;
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| 91 | 90 |
static final boolean doDeduplicate = false; |
| 92 | 91 |
|
| 93 | 92 |
|
| 94 | 93 |
private boolean doNewNamedAreas = false; |
| 95 | 94 |
private boolean doFeatureTree = false; |
| 96 | 95 |
|
| 97 |
private boolean doSpecimen = false;
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| 96 |
private boolean doSpecimen = true;
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|
| 98 | 97 |
private TermMatchMode specimenAreaMatchMode = TermMatchMode.UUID_ABBREVLABEL; |
| 99 | 98 |
|
| 100 | 99 |
|
| 101 | 100 |
private void doImport(ICdmDataSource cdmDestination){
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| 102 | 101 |
|
| 103 |
CdmUpdater su = CdmUpdater.NewInstance(); |
|
| 104 |
IProgressMonitor monitor = DefaultProgressMonitor.NewInstance(); |
|
| 102 |
// CdmUpdater su = CdmUpdater.NewInstance();
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| 103 |
// IProgressMonitor monitor = DefaultProgressMonitor.NewInstance();
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| 105 | 104 |
// |
| 106 | 105 |
// try {
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| 107 | 106 |
// su.updateToCurrentVersion(cdmDestination, monitor); |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistReferenceImport.java | ||
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| 80 | 80 |
return strRecordQuery; |
| 81 | 81 |
} |
| 82 | 82 |
|
| 83 |
/* (non-Javadoc) |
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| 84 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
|
| 85 |
*/ |
|
| 86 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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| 83 |
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@Override |
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| 85 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaChecklistImportState state) {
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| 87 | 86 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 88 | 87 |
return result; |
| 89 | 88 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistSynonymImport.java | ||
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| 39 | 39 |
/** |
| 40 | 40 |
* @author a.mueller |
| 41 | 41 |
* @created 20.02.2010 |
| 42 |
* @version 1.0 |
|
| 43 | 42 |
*/ |
| 44 | 43 |
@Component |
| 45 | 44 |
public class CentralAfricaChecklistSynonymImport extends CentralAfricaChecklistImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaChecklistImportState>{
|
| ... | ... | |
| 48 | 47 |
private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
| 49 | 48 |
|
| 50 | 49 |
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| 51 |
private DbImportMapping mapping; |
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| 50 |
private DbImportMapping<?, ?> mapping;
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| 52 | 51 |
|
| 53 | 52 |
//second path is not used anymore, there is now an ErmsTaxonRelationImport class instead |
| 54 |
private boolean isSecondPath = false; |
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| 53 |
// private boolean isSecondPath = false;
|
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| 55 | 54 |
|
| 56 |
private int modCount = 10000; |
|
| 55 |
// private int modCount = 10000;
|
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| 57 | 56 |
private static final String pluralString = "synonyms"; |
| 58 | 57 |
private static final String dbTableName = "synonyms"; |
| 59 |
private static final Class cdmTargetClass = TaxonBase.class; |
|
| 58 |
private static final Class<?> cdmTargetClass = TaxonBase.class;
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| 60 | 59 |
private static final String strOrderBy = ""; |
| 61 | 60 |
|
| 62 | 61 |
public CentralAfricaChecklistSynonymImport(){
|
| ... | ... | |
| 101 | 100 |
return strRecordQuery; |
| 102 | 101 |
} |
| 103 | 102 |
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| 104 |
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| 105 |
/* (non-Javadoc) |
|
| 106 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
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| 107 |
*/ |
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| 108 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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| 103 |
@Override |
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| 104 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaChecklistImportState state) {
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| 109 | 105 |
String nameSpace; |
| 110 |
Class cdmClass; |
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Class<?> cdmClass;
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| 111 | 107 |
Set<String> idSet; |
| 112 | 108 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 113 | 109 |
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/checklist/CentralAfricaChecklistTaxonImport.java | ||
|---|---|---|
| 139 | 139 |
} |
| 140 | 140 |
|
| 141 | 141 |
|
| 142 |
/* (non-Javadoc) |
|
| 143 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
|
| 144 |
*/ |
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| 145 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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| 142 |
@Override |
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| 143 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaChecklistImportState state) {
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| 146 | 144 |
String nameSpace; |
| 147 |
Class cdmClass; |
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| 145 |
Class<?> cdmClass;
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| 148 | 146 |
Set<String> idSet; |
| 149 | 147 |
Set<String> referenceIdSet = new HashSet<String>(); |
| 150 | 148 |
|
| ... | ... | |
| 168 | 166 |
return result; |
| 169 | 167 |
} |
| 170 | 168 |
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| 171 |
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| 172 |
/* (non-Javadoc) |
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| 173 |
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet) |
|
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*/ |
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| 169 |
@Override |
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| 175 | 170 |
public TaxonBase<?> createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {
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| 176 | 171 |
BotanicalName speciesName = BotanicalName.NewInstance(Rank.SPECIES()); |
| 177 | 172 |
|
| ... | ... | |
| 321 | 316 |
// } |
| 322 | 317 |
|
| 323 | 318 |
//TODO use Mapper |
| 324 |
private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
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| 319 |
private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference<?> citation, String microCitation){
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| 325 | 320 |
String treeKey; |
| 326 | 321 |
UUID treeUuid; |
| 327 | 322 |
if (treeRefFk == null){
|
| ... | ... | |
| 351 | 346 |
} |
| 352 | 347 |
|
| 353 | 348 |
|
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private Reference makeGenevaReference(CentralAfricaChecklistImportState state) {
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| 355 |
Reference result = ReferenceFactory.newDatabase(); |
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private Reference<?> makeGenevaReference(CentralAfricaChecklistImportState state) {
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Reference<?> result = ReferenceFactory.newDatabase();
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| 356 | 351 |
result.setTitleCache(state.getConfig().getGenevaReferenceTitle(), true); |
| 357 | 352 |
result.setUuid(state.getConfig().getUuidGenevaReference()); |
| 358 | 353 |
return result; |
| 359 | 354 |
} |
| 360 | 355 |
|
| 361 |
/* (non-Javadoc) |
|
| 362 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 363 |
*/ |
|
| 364 | 356 |
@Override |
| 365 | 357 |
protected boolean doCheck(CentralAfricaChecklistImportState state){
|
| 366 | 358 |
IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator(); |
| 367 | 359 |
return validator.validate(state); |
| 368 | 360 |
} |
| 369 | 361 |
|
| 370 |
|
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| 371 |
/* (non-Javadoc) |
|
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 373 |
*/ |
|
| 362 |
@Override |
|
| 374 | 363 |
protected boolean isIgnore(CentralAfricaChecklistImportState state){
|
| 375 | 364 |
return ! state.getConfig().isDoTaxa(); |
| 376 | 365 |
} |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsReferenceImport.java | ||
|---|---|---|
| 33 | 33 |
/** |
| 34 | 34 |
* @author a.mueller |
| 35 | 35 |
* @created 20.02.2010 |
| 36 |
* @version 1.0 |
|
| 37 | 36 |
*/ |
| 38 | 37 |
@Component |
| 39 | 38 |
public class CentralAfricaFernsReferenceImport extends CentralAfricaFernsImportBase<Reference> implements IMappingImport<Reference, CentralAfricaFernsImportState>{
|
| 40 | 39 |
private static final Logger logger = Logger.getLogger(CentralAfricaFernsReferenceImport.class); |
| 41 | 40 |
|
| 42 |
private DbImportMapping mapping; |
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private DbImportMapping<?,?> mapping;
|
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| 43 | 42 |
|
| 44 | 43 |
|
| 45 |
private int modCount = 10000; |
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| 44 |
// private int modCount = 10000;
|
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| 46 | 45 |
private static final String pluralString = "references"; |
| 47 | 46 |
private static final String dbTableName = "literature"; |
| 48 |
private static final Class cdmTargetClass = Reference.class; |
|
| 47 |
private static final Class<?> cdmTargetClass = Reference.class;
|
|
| 49 | 48 |
|
| 50 | 49 |
public CentralAfricaFernsReferenceImport(){
|
| 51 | 50 |
super(pluralString, dbTableName, cdmTargetClass); |
| ... | ... | |
| 154 | 153 |
return ref; |
| 155 | 154 |
} |
| 156 | 155 |
|
| 157 |
/* (non-Javadoc) |
|
| 158 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
|
| 159 |
*/ |
|
| 160 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
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| 156 |
|
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| 157 |
@Override |
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| 158 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaFernsImportState state) {
|
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| 161 | 159 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 162 | 160 |
return result; //not needed |
| 163 | 161 |
} |
| 164 | 162 |
|
| 165 |
/* (non-Javadoc) |
|
| 166 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 167 |
*/ |
|
| 168 | 163 |
@Override |
| 169 | 164 |
protected boolean doCheck(CentralAfricaFernsImportState state){
|
| 170 | 165 |
IOValidator<CentralAfricaFernsImportState> validator = new CentralAfricaFernsReferenceImportValidator(); |
| 171 | 166 |
return validator.validate(state); |
| 172 | 167 |
} |
| 173 | 168 |
|
| 174 |
|
|
| 175 |
/* (non-Javadoc) |
|
| 176 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 177 |
*/ |
|
| 169 |
@Override |
|
| 178 | 170 |
protected boolean isIgnore(CentralAfricaFernsImportState state){
|
| 179 | 171 |
//TODO |
| 180 | 172 |
return state.getConfig().getDoReferences() != IImportConfigurator.DO_REFERENCES.ALL; |
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonImport.java | ||
|---|---|---|
| 70 | 70 |
/** |
| 71 | 71 |
* @author a.mueller |
| 72 | 72 |
* @created 20.02.2010 |
| 73 |
* @version 1.0 |
|
| 74 | 73 |
*/ |
| 75 | 74 |
@Component |
| 76 | 75 |
public class CentralAfricaFernsTaxonImport extends CentralAfricaFernsImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaFernsImportState>{
|
| ... | ... | |
| 79 | 78 |
public static final UUID TNS_EXT_UUID = UUID.fromString("41cb0450-ac84-4d73-905e-9c7773c23b05");
|
| 80 | 79 |
|
| 81 | 80 |
|
| 82 |
private DbImportMapping mapping; |
|
| 81 |
private DbImportMapping<?,?> mapping;
|
|
| 83 | 82 |
|
| 84 | 83 |
//second path is not used anymore, there is now an ErmsTaxonRelationImport class instead |
| 85 |
private boolean isSecondPath = false; |
|
| 84 |
// private boolean isSecondPath = false;
|
|
| 86 | 85 |
|
| 87 | 86 |
private static final String pluralString = "taxa"; |
| 88 | 87 |
private static final String dbTableName = "[African pteridophytes]"; |
| 89 |
private static final Class cdmTargetClass = TaxonBase.class; |
|
| 88 |
private static final Class<?> cdmTargetClass = TaxonBase.class;
|
|
| 90 | 89 |
|
| 91 | 90 |
public CentralAfricaFernsTaxonImport(){
|
| 92 | 91 |
super(pluralString, dbTableName, cdmTargetClass); |
| 93 | 92 |
} |
| 94 | 93 |
|
| 95 |
|
|
| 96 | 94 |
|
| 97 |
/* (non-Javadoc) |
|
| 98 |
* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getIdQuery() |
|
| 99 |
*/ |
|
| 100 |
@Override |
|
| 101 | 95 |
protected String getIdQuery() {
|
| 102 | 96 |
String strQuery = " SELECT [Taxon number] FROM " + dbTableName ; |
| 103 | 97 |
return strQuery; |
| 104 | 98 |
} |
| 105 | 99 |
|
| 106 |
|
|
| 107 |
/* (non-Javadoc) |
|
| 108 |
* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getMapping() |
|
| 109 |
*/ |
|
| 110 |
protected DbImportMapping getMapping() {
|
|
| 100 |
@Override |
|
| 101 |
protected DbImportMapping<?,?> getMapping() {
|
|
| 111 | 102 |
if (mapping == null){
|
| 112 | 103 |
mapping = new DbImportMapping(); |
| 113 | 104 |
|
| ... | ... | |
| 167 | 158 |
} |
| 168 | 159 |
|
| 169 | 160 |
|
| 170 |
/* (non-Javadoc) |
|
| 171 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
|
| 172 |
*/ |
|
| 173 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
|
| 174 |
String nameSpace; |
|
| 175 |
Class cdmClass; |
|
| 176 |
Set<String> idSet; |
|
| 161 |
@Override |
|
| 162 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaFernsImportState state) {
|
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| 163 |
// String nameSpace; |
|
| 164 |
// Class<?> cdmClass; |
|
| 165 |
// Set<String> idSet; |
|
| 177 | 166 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 178 | 167 |
|
| 179 | 168 |
try{
|
| cdm-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsTaxonRelationImport.java | ||
|---|---|---|
| 44 | 44 |
import eu.etaxonomy.cdm.model.description.PresenceTerm; |
| 45 | 45 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 46 | 46 |
import eu.etaxonomy.cdm.model.description.TextData; |
| 47 |
import eu.etaxonomy.cdm.model.location.Country; |
|
| 47 | 48 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
| 48 | 49 |
import eu.etaxonomy.cdm.model.location.NamedAreaLevel; |
| 49 | 50 |
import eu.etaxonomy.cdm.model.location.NamedAreaType; |
| 50 |
import eu.etaxonomy.cdm.model.location.Country; |
|
| 51 | 51 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.Rank; |
| ... | ... | |
| 86 | 86 |
public CentralAfricaFernsTaxonRelationImport(){
|
| 87 | 87 |
super(pluralString, dbTableName, cdmTargetClass); |
| 88 | 88 |
} |
| 89 |
|
|
| 90 |
|
|
| 91 | 89 |
|
| 92 |
/* (non-Javadoc) |
|
| 93 |
* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery() |
|
| 94 |
*/ |
|
| 90 |
|
|
| 95 | 91 |
@Override |
| 96 | 92 |
protected String getIdQuery() {
|
| 97 | 93 |
String strQuery = " SELECT [Taxon number] FROM " + dbTableName;; |
| 98 | 94 |
return strQuery; |
| 99 | 95 |
} |
| 100 | 96 |
|
| 101 |
|
|
| 102 |
/* (non-Javadoc) |
|
| 103 |
* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getMapping() |
|
| 104 |
*/ |
|
| 105 | 97 |
@Override |
| 106 | 98 |
protected DbImportMapping<?,?> getMapping() {
|
| 107 | 99 |
if (mapping == null){
|
| ... | ... | |
| 161 | 153 |
} |
| 162 | 154 |
} |
| 163 | 155 |
|
| 164 |
/* (non-Javadoc) |
|
| 165 |
* @see eu.etaxonomy.cdm.io.common.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet) |
|
| 166 |
*/ |
|
| 167 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
|
| 156 |
|
|
| 157 |
@Override |
|
| 158 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaFernsImportState state) {
|
|
| 168 | 159 |
String nameSpace; |
| 169 | 160 |
Class<?> cdmClass; |
| 170 | 161 |
Set<String> idSet; |
Also available in: Unified diff
Change signature for IPartionedIO.setRelatedObjects in cdm-eflora