Schedule and monitor genomic data export jobs

Currently, jobs are scheduled only for Genomic Data Export. To schedule a job, navigate to the Genomic Data Export screen in the Cohort Viewer tab.

Note:

Any job executed prior to applying Oracle Healthcare Translational Research 3.1 will have its status changed back to 'Scheduled'.

1. Select the patient IDs source from one of these options:
   • active query
   • library query
   • list
   • ad-hoc
   • Omics query
2. Select the DNA reference version.
3. Select the location for the gene:
   • Ad-hoc List
   • Pathway
   • Gene Set
4. Select one of the following file formats to export:
   • Mutation-VCF
   • Copy Number Variation-SEG
   • Microarray Expression-RES
   • Microarray Expression Dual Channel-GCT
5. Select the Schedule export option.
6. Click Submit.

To view job information and progress, go to the Home page, and click the Jobs tab, along the top. All the jobs created by the Oracle Healthcare Translational Research UI are displayed. All users who created jobs can see job lists.

For more information, see:

• Manage jobs
  
• View job inputs
  
• View and download job outputs
  

Manage jobs

To search for a job:

1. On the Home page, along the top, click Jobs.
2. Scroll down, after the table, and either enter part of the job's name or slick the search icon ().
3. In the Search User Job window, select the appropriate conditions and enter part of a User Job Run ID or a User Job Name.
4. Click Search.
5. Select the job you want to include in the list.
6. Click Submit.

   To run that job, on the Jobs tab, click Submit again.

To view details of a particular job:

On the Jobs tab, in the first table column, click a job's name to get the details of the job.

Fo return to the Jobs tab, click the Jobs breadcrumb link.

Figure 6-2 Location of the Jobs link

To get back to the initial list of jobs, click Reset.

View job inputs

• To view details on the parameters provided when scheduling a job, in the Details page, click the Inputs button on the left.
• To load the job details in the Genomic Data Export page, click the Load input parameter values into Genomic Data Export page link.

  Note:

  You can only load these input parameters, when the job context matches the application's context.

View and download job outputs

This section shows the result files of a job. The following files are generated:

• Error log file contains the log file of the application if any exception or error occurred while running the job.
• User log file contains the log file, which shows the error occurred while generating the export files.
• Administrator log file is for the DB administrator.

To download any of these files, click the file link under the Files column.

You can download error and user log files, but cannot download the admin log file.

Note:

When you try to export a file that does not have any patients or subjects linked to the specimen, an empty file is generated in Schedule mode.