Index Files Not Being Generated for Newly Imported BAM Files

[scottx611x]

• Specific code commit: 8434c17
• Version of the web browser and OS: Any
• Environment where the error occurred (Vagrant VM and site conf mode or AWS instance): https://test.stemcellcommons.org

Steps to reproduce

Please list all the actions and the input data used:

1. Run a workflow that produces a .bam file as output
2. Launch IGV with said bam as input

Observed behavior

• When zoomed in to the base-pair level there is a 404 when IGV tries to access the .bai file
  

Request URL: https://test.stemcellcommons.org/media/file_store/dd/6a/TopHat%20on%20data%203%3A%20accepted_hits_PWv0H1h.bam.bai
Request Method: GET
Status Code: 404 Not Found
Remote Address: 52.21.193.165:443
Referrer Policy: no-referrer-when-downgrade

Expected behavior

• For said .bai to be available, and to be able to zoom in all the way in IGV

Thoughts:

• Since IGV is now a self contained entity, would it make sense to create these index files on docker container startup instead of from Refinery's back-end or would other VisualizationTools need this information?

Related to: #2210 & #1378

[hackdna]

What do server logs say?

[scottx611x]

Repeatedly: Something went wrong while trying to generate the auxiliary file for /data/media/file_store/xx/xx/xxxx. 'FileExtension' object has no attribute 'lower'

Seems to be a side effect of the get_file_extension changes from #2634