ubic.gemma.core.loader.genome.gene

Interface ExternalFileGeneLoaderService

All Known Implementing Classes:

ExternalFileGeneLoaderServiceImpl

public interface ExternalFileGeneLoaderService

Author:

paul, Louise

Method Summary

Modifier and Type	Method and Description
int	load(InputStream geneInputStream, String taxonName)
int	load(String geneFile, String taxonName) Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma.

Method Detail

load

int load(String geneFile,
         String taxonName)
  throws Exception

Work flow is: The file is first checked to see if readable, and the taxon checked to see it is in Gemma. If validation passes the file is read line by line. Each line equates to a gene and its gene product, which is created from the file details. The gene is then persisted. If successfully loaded taxon flag isGenesLoaded is set to true to indicate that there are genes loaded for this taxon.

Parameters:

geneFile - Full path to file containing genes details

taxonName - taxonName to be associated to this gene, does not have to be a species.

Returns:

number of genes loaded

Throws:

Exception - Thrown with a file format error or problem in persisting gene to database.

load

int load(InputStream geneInputStream,
         String taxonName)
  throws Exception

Parameters:

geneInputStream - gene input stream

taxonName - taxon name

Returns:

number of genes loaded

Throws:

Exception - Thrown with a file format error or problem in persisting gene to database.