Package 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
    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 Details

    • 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.