org.molgenis.data.vcf.importer

Class VcfImporterService

java.lang.Object

org.molgenis.data.vcf.importer.VcfImporterService

All Implemented Interfaces:

ImportService, org.springframework.core.Ordered

@Service
public class VcfImporterService
extends Object
implements ImportService

Field Summary

Fields inherited from interface org.springframework.core.Ordered

HIGHEST_PRECEDENCE, LOWEST_PRECEDENCE

Constructor Summary

Constructors

Constructor and Description
VcfImporterService(FileRepositoryCollectionFactory fileRepositoryCollectionFactory, DataService dataService, SearchService searchService, RepositoryDecoratorFactory repositoryDecoratorFactory, PermissionSystemService permissionSystemService)

Method Summary

Modifier and Type	Method and Description
boolean	canImport(File file, RepositoryCollection source)
EntityImportReport	doImport(RepositoryCollection source, DatabaseAction databaseAction)
boolean	getMustChangeEntityName()
int	getOrder()
List<DatabaseAction>	getSupportedDatabaseActions()
void	importVcf(File vcfFile)
EntityImportReport	importVcf(Repository inRepository, int batchSize, List<EntityMetaData> addedEntities)
EntitiesValidationReport	validateImport(File file, RepositoryCollection source)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VcfImporterService

@Autowired
public VcfImporterService(FileRepositoryCollectionFactory fileRepositoryCollectionFactory,
                                     DataService dataService,
                                     SearchService searchService,
                                     RepositoryDecoratorFactory repositoryDecoratorFactory,
                                     PermissionSystemService permissionSystemService)

Method Detail

doImport

public EntityImportReport doImport(RepositoryCollection source,
                                   DatabaseAction databaseAction)

Specified by:

doImport in interface ImportService

validateImport

public EntitiesValidationReport validateImport(File file,
                                               RepositoryCollection source)

Specified by:

validateImport in interface ImportService

canImport

public boolean canImport(File file,
                         RepositoryCollection source)

Specified by:

canImport in interface ImportService

importVcf

public void importVcf(File vcfFile)
               throws IOException

Throws:

IOException

importVcf

public EntityImportReport importVcf(Repository inRepository,
                                    int batchSize,
                                    List<EntityMetaData> addedEntities)
                             throws IOException

Throws:

IOException

getOrder

public int getOrder()

Specified by:

getOrder in interface org.springframework.core.Ordered

getSupportedDatabaseActions

public List<DatabaseAction> getSupportedDatabaseActions()

Specified by:

getSupportedDatabaseActions in interface ImportService

getMustChangeEntityName

public boolean getMustChangeEntityName()

Specified by:

getMustChangeEntityName in interface ImportService