org.molgenis.omx.xgap.db

Class VariantEntityImporter

java.lang.Object

org.molgenis.omx.xgap.db.VariantEntityImporter

All Implemented Interfaces:

EntityImporter

public class VariantEntityImporter
extends Object
implements EntityImporter

Reads Variant from a delimited (csv) file, resolving xrefs to ids where needed, that is the tricky bit ;-)

Constructor Summary

Constructors

Constructor and Description
VariantEntityImporter()

Method Summary

Methods

Modifier and Type	Method and Description
int	importEntity(Repository<? extends Entity> repository, Database db, Database.DatabaseAction dbAction) Imports Variant from tab/comma delimited File

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantEntityImporter

public VariantEntityImporter()

Method Detail

importEntity

public int importEntity(Repository<? extends Entity> repository,
               Database db,
               Database.DatabaseAction dbAction)
                 throws IOException,
                        DatabaseException

Imports Variant from tab/comma delimited File

Specified by:

importEntity in interface EntityImporter

Parameters:

db - database to import into

reader - csv reader to load data from

defaults - to set default values for each row

dbAction - indicating wether to add,update,remove etc

missingValues - indicating what value in the csv is treated as 'null' (e.g. "" or "NA")

Returns:

number of elements imported

Throws:

IOException

DatabaseException