Modifier and Type | Class and Description |
---|---|
class |
CdmApplicationController |
class |
CdmRepository
This class actually is the central access point to all cdm api services and thus to all the
entities stored in the cdm.
|
Modifier and Type | Field and Description |
---|---|
protected ICdmRepository |
CdmApplicationController.configuration |
Modifier and Type | Method and Description |
---|---|
protected ICdmRepository |
DescriptionAggregationBase.getRepository() |
Modifier and Type | Method and Description |
---|---|
UpdateResult |
DescriptionAggregationBase.invoke(CONFIG config,
ICdmRepository repository) |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
BatchValidator.getAppController()
Get the application context that will provide the services that will, on
their turn, provide the entities to be validated.
|
Modifier and Type | Method and Description |
---|---|
void |
BatchValidator.setAppController(ICdmRepository context)
Set the application context.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Collection> |
IBciServiceWrapper.getCollectionsByCode(java.lang.String code,
ICdmRepository appConfig)
Returns a list of collections collection code.
|
java.util.List<Collection> |
BciServiceWrapper.getCollectionsByCode(java.lang.String code,
ICdmRepository appConfig) |
Modifier and Type | Method and Description |
---|---|
java.util.List<Person> |
IpniService.getAuthors(java.lang.String abbreviation,
java.lang.String surname,
java.lang.String forename,
java.lang.String isoCountry,
ICdmRepository services,
IpniServiceAuthorConfigurator config) |
java.util.List<Person> |
IIpniService.getAuthors(java.lang.String abbreviation,
java.lang.String surname,
java.lang.String forename,
java.lang.String isoCountry,
ICdmRepository appConfig,
IpniServiceAuthorConfigurator config)
Returns a list of persons (authors) defined by their abbreviation, surname, forename and/or isoCountry.
|
java.util.List<IBotanicalName> |
IpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
IpniService.IpniRank rankToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository services) |
java.util.List<IBotanicalName> |
IIpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
IpniService.IpniRank ipniRankToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository repository)
Returns a list of names matching the relevant parameters according to the IPNI full search function.
|
java.util.List<IBotanicalName> |
IpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
Rank rankInRangeToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository services) |
java.util.List<IBotanicalName> |
IIpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
Rank rankRangeToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository repository)
As
#getNamesAdvanced(String, String, String, String, String, String, String, Boolean, Boolean, String, Boolean, Boolean, Boolean, IpniRank, Boolean, IpniServiceNamesConfigurator, ICdmRepository)
but using CDM Rank instead of IpniRank. |
java.util.List<IBotanicalName> |
IpniService.getNamesSimple(java.lang.String wholeName,
ICdmRepository repository,
IpniServiceNamesConfigurator config) |
java.util.List<IBotanicalName> |
IIpniService.getNamesSimple(java.lang.String wholeName,
ICdmRepository services,
IpniServiceNamesConfigurator config)
Returns a list of names matching the wholeName parameter according to the IPNI Quick search function.
|
java.util.List<Reference> |
IpniService.getPublications(java.lang.String title,
java.lang.String abbreviation,
ICdmRepository services,
IpniServicePublicationConfigurator config) |
java.util.List<Reference> |
IIpniService.getPublications(java.lang.String title,
java.lang.String abbreviation,
ICdmRepository services,
IpniServicePublicationConfigurator config)
Returns a list of publications matching the title and/or the abbreviation parameter according to the IPNI Publication search function.
|
Modifier and Type | Class and Description |
---|---|
class |
CdmIoApplicationController |
Modifier and Type | Class and Description |
---|---|
class |
Cdm2CdmDescriptionImport |
class |
Cdm2CdmImportBase
Base class for migrating data from one CDM instance to another.
|
class |
Cdm2CdmTaxonNodeImport |
class |
CdmCdmTermImport |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
Cdm2CdmImportState.getSourceRepository() |
protected ICdmRepository |
Cdm2CdmImportBase.sourceRepo(Cdm2CdmImportState state) |
Modifier and Type | Method and Description |
---|---|
void |
Cdm2CdmImportState.setSourceRepository(ICdmRepository sourceRepository) |
Modifier and Type | Class and Description |
---|---|
class |
CdmLightClassificationExport |
Modifier and Type | Class and Description |
---|---|
class |
CdmExportBase<CONFIG extends ExportConfiguratorBase<STATE,TRANSFORM,DEST>,STATE extends ExportStateBase,TRANSFORM extends IExportTransformer,DEST> |
class |
CdmImportBase<CONFIG extends IImportConfigurator,STATE extends ImportStateBase> |
class |
CdmIoBase<STATE extends IoStateBase,RESULT extends IoResultBase> |
class |
DbExportBase<CONFIG extends DbExportConfiguratorBase<STATE,TRANSFORM,Source>,STATE extends DbExportStateBase<CONFIG,TRANSFORM>,TRANSFORM extends IExportTransformer> |
class |
DbImportBase<STATE extends DbImportStateBase<CONFIG,STATE>,CONFIG extends DbImportConfiguratorBase<STATE>> |
class |
SimpleImport<CONFIG extends ImportConfiguratorBase,SOURCE> |
class |
XmlImportBase<CONFIG extends XmlImportConfiguratorBase<STATE>,STATE extends XmlImportState<CONFIG,?>>
Base class for XML imports
|
Modifier and Type | Field and Description |
---|---|
protected ICdmRepository |
CdmDefaultIOBase.cdmApp |
protected ICdmRepository |
IoConfiguratorBase.cdmApp |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
CdmDefaultIOBase.getCdmAppController()
Returns the
CdmApplicationController . |
ICdmRepository |
IoConfiguratorBase.getCdmAppController() |
ICdmRepository |
IIoConfigurator.getCdmAppController()
Returns the CdmApplicationController
|
ICdmRepository |
ExportConfiguratorBase.getCdmAppController(boolean createNew)
Returns a
CdmApplicationController created by the values of this configuration. |
ICdmRepository |
ExportConfiguratorBase.getCdmAppController(boolean createNew,
boolean omitTermLoading)
Returns a
CdmApplicationController created by the values of this configuration. |
ICdmRepository |
ExportConfiguratorBase.getNewCdmAppController()
Returns a new instance of
CdmApplicationController created by the values of this configuration. |
Modifier and Type | Method and Description |
---|---|
static <ST extends IoStateBase> |
TaxonNodeOutStreamPartitioner.NewInstance(ICdmRepository repository,
ST state,
TaxonNodeFilter filter,
java.lang.Integer partitionSize,
IProgressMonitor parentMonitor,
java.lang.Integer parentTicks) |
static <ST extends IoStateBase> |
TaxonNodeOutStreamPartitioner.NewInstance(ICdmRepository repository,
ST state,
TaxonNodeFilter filter,
java.lang.Integer partitionSize,
IProgressMonitor parentMonitor,
java.lang.Integer parentTicks,
java.util.List<java.lang.String> propertyPath) |
void |
CdmDefaultIOBase.setCdmAppController(ICdmRepository cdmApp) |
void |
IoConfiguratorBase.setCdmAppController(ICdmRepository cdmApp) |
void |
IIoConfigurator.setCdmAppController(ICdmRepository cdmApp)
Sets the CdmApplicationController
|
Modifier and Type | Method and Description |
---|---|
static ImportDeduplicationHelper<?> |
ImportDeduplicationHelper.NewInstance(ICdmRepository repository) |
static <STATE extends ImportStateBase<?,?>> |
ImportDeduplicationHelper.NewInstance(ICdmRepository repository,
STATE state) |
void |
ImportDeduplicationHelper.restartSession(ICdmRepository repository,
ImportResult importResult) |
Constructor and Description |
---|
ImportDeduplicationHelper(ICdmRepository repository) |
Modifier and Type | Class and Description |
---|---|
class |
CsvNameExport |
class |
CsvNameExportBase |
Modifier and Type | Class and Description |
---|---|
class |
CsvImportBase<CONFIG extends CsvImportConfiguratorBase,STATE extends CsvImportState<CONFIG>,T>
A base class for simple CSV imports.
|
Modifier and Type | Class and Description |
---|---|
class |
CsvDemoBase |
class |
CsvDemoExport |
Modifier and Type | Class and Description |
---|---|
class |
CsvExportBaseRedlist |
class |
CsvTaxExportRedlist |
Modifier and Type | Class and Description |
---|---|
class |
CharacterOwlImport |
class |
StructureTreeOwlImport |
class |
TermVocabularyOwlImport |
Modifier and Type | Class and Description |
---|---|
class |
StructureTreeOwlExport |
class |
TermVocabularyOwlExport |
Modifier and Type | Class and Description |
---|---|
class |
WordExport |
Modifier and Type | Class and Description |
---|---|
class |
ExcelDistributionUpdate
This Import class updates existing distributions with the new state
described in the Excel file.
|
Modifier and Type | Class and Description |
---|---|
class |
DwcaDataImportBase<CONFIG extends DwcaDataImportConfiguratorBase<STATE>,STATE extends DwcaDataImportStateBase<CONFIG>> |
class |
DwcaImport |
Modifier and Type | Class and Description |
---|---|
class |
DwcaDataExportBase |
class |
DwcaDescriptionExport |
class |
DwcaDistributionExport |
class |
DwcaEmlExport |
class |
DwcaExportBase |
class |
DwcaImageExport |
class |
DwcaMetaDataExport |
class |
DwcaReferenceExport |
class |
DwcaResourceRelationExport
Mapps taxon concept relationships, taxon name relationships and taxon interactions
|
class |
DwcaResultWriter
Final result processor for Darwin Core Archive exports.
|
class |
DwcaTaxExport |
class |
DwcaTaxonExport |
class |
DwcaTypesExport |
class |
DwcaVernacularExport |
Modifier and Type | Class and Description |
---|---|
class |
ExcelImportBase<STATE extends ExcelImportState<CONFIG,ROW>,CONFIG extends ExcelImportConfiguratorBase,ROW extends ExcelRowBase> |
class |
ExcelTaxonOrSpecimenImportBase<STATE extends ExcelImportState<CONFIG,ROW>,CONFIG extends ExcelImportConfiguratorBase,ROW extends ExcelRowBase> |
Modifier and Type | Class and Description |
---|---|
class |
DistributionImport |
Modifier and Type | Class and Description |
---|---|
class |
NormalExplicitImport |
class |
TaxonExcelImportBase |
class |
TaxonListImport |
Modifier and Type | Class and Description |
---|---|
class |
IdentifierImport
Imports identifiers for a certain
IdentifiableEntity class from a csv
file. |
Modifier and Type | Class and Description |
---|---|
class |
JaxbExport |
class |
JaxbImport |
Modifier and Type | Class and Description |
---|---|
class |
MarkupDocumentImport |
Modifier and Type | Method and Description |
---|---|
ImportDeduplicationHelper<MarkupImportState> |
MarkupImportState.getDeduplicationHelper(ICdmRepository repository) |
Modifier and Type | Class and Description |
---|---|
class |
MediaExcelImport |
Modifier and Type | Class and Description |
---|---|
class |
DeleteNonReferencedReferencesUpdater |
Modifier and Type | Class and Description |
---|---|
class |
PilotOutputDescriptionExporter |
class |
PilotOutputExporter |
Modifier and Type | Class and Description |
---|---|
class |
EndNoteImportBase |
class |
EndnoteRecordsImport |
Modifier and Type | Class and Description |
---|---|
class |
RisReferenceImport |
Modifier and Type | Class and Description |
---|---|
class |
SDDIoBase |
Modifier and Type | Class and Description |
---|---|
class |
IkeyPlusImport |
Modifier and Type | Class and Description |
---|---|
class |
SDDImport |
Modifier and Type | Class and Description |
---|---|
class |
SDDCdmExporter |
Modifier and Type | Class and Description |
---|---|
class |
SpecimenImportBase<CONFIG extends IImportConfigurator,STATE extends SpecimenImportStateBase> |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
SpecimenImportStateBase.getCdmRepository() |
Modifier and Type | Method and Description |
---|---|
void |
SpecimenImportStateBase.setCdmRepository(ICdmRepository cdmRepository) |
Modifier and Type | Class and Description |
---|---|
class |
Abcd206Import |
Modifier and Type | Method and Description |
---|---|
static Reference |
AbcdParseUtility.parseFirstReference(org.w3c.dom.NodeList referenceNodeList,
ICdmRepository cdmAppController) |
Constructor and Description |
---|
AbcdPersonParser(java.lang.String prefix,
SpecimenImportReport report,
ICdmRepository cdmAppController) |
UnitAssociationParser(java.lang.String prefix,
SpecimenImportReport report,
ICdmRepository cdmAppController) |
Constructor and Description |
---|
AbcdDnaParser(java.lang.String prefix,
SpecimenImportReport report,
ICdmRepository cdmAppController) |
AbcdGgbnParser(SpecimenImportReport report,
ICdmRepository cdmAppController) |
Modifier and Type | Class and Description |
---|---|
class |
ExtensionTypeExcelImport |
class |
NamedAreaLevelExcelImport |
class |
SpecimenCdmExcelImport |
class |
SpecimenSythesysExcelImport |
Modifier and Type | Class and Description |
---|---|
class |
GbifImport |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
GbifImportState.getCdmRepository() |
Modifier and Type | Method and Description |
---|---|
void |
GbifImportState.setCdmRepository(ICdmRepository cdmRepository) |
Modifier and Type | Class and Description |
---|---|
class |
StreamImportBase<CONFIG extends StreamImportConfiguratorBase,STATE extends StreamImportStateBase<CONFIG,StreamImportBase>> |
Modifier and Type | Class and Description |
---|---|
class |
ExcelStreamImport |
Modifier and Type | Class and Description |
---|---|
class |
TaxonXDescriptionImport |
class |
TaxonXModsImport |
class |
TaxonXNomenclatureImport |
Modifier and Type | Class and Description |
---|---|
class |
TaxonXImport |
Modifier and Type | Class and Description |
---|---|
class |
TcsRdfImportBase |
class |
TcsRdfReferenceImport |
class |
TcsRdfTaxonImport |
class |
TcsRdfTaxonNameImport |
class |
TcsRdfTaxonNameRelationsImport |
class |
TcsRdfTaxonRelationsImport |
Modifier and Type | Class and Description |
---|---|
class |
TcsXmlImportBase |
class |
TcsXmlMetaDataImport |
class |
TcsXmlPublicationsImport |
class |
TcsXmlSpecimensImport |
class |
TcsXmlTaxonImport |
class |
TcsXmlTaxonNameImport |
class |
TcsXmlTaxonNameRelationsImport |
class |
TcsXmlTaxonRelationsImport |
Modifier and Type | Class and Description |
---|---|
class |
TcsXmlExportBase<T extends CdmBase> |
Modifier and Type | Class and Description |
---|---|
class |
RepresentationCsvImport
Imports term representations from a csv file following the format:
1. |
Modifier and Type | Class and Description |
---|---|
class |
TropicosNameImport<STATE extends TropicosNameImportState> |
Modifier and Type | Class and Description |
---|---|
class |
WfoAccessClassificationImport<STATE extends WfoAccessImportState> |
class |
WfoAccessTaxonImport<STATE extends WfoAccessImportState> |
Modifier and Type | Method and Description |
---|---|
ICdmRepository |
PublishConfigurator.getApplicationConfiguration()
The application controller
associated with this instance
|
Modifier and Type | Method and Description |
---|---|
static PublishConfigurator |
PublishConfigurator.NewLocalInstance(ICdmRepository applicationConfiguration)
Creates a new instance connected to the given application controller.
|
Constructor and Description |
---|
LocalXMLEntityFactory(ICdmRepository applicationConfiguration,
IProgressMonitor monitor) |
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