Ann Loraine added a comment - 07/Sep/21 5:20 PM Reply from UCSC regarding unavailable file question in preceding comment: Brian Lee <brianlee@soe.ucsc.edu> to: "Liu, Jing" <Jing.Liu@med.usc.edu> cc: "genome@soe.ucsc.edu" <genome@soe.ucsc.edu> date: Sep 7, 2021, 3:54 PM subject: [EXTERNAL] Re: [genome] RE: trouble viewing bam files mailing list: genome@soe.ucsc.edu Filter messages from this mailing list mailed-by: soe.ucsc.edu Dear Jing, Thank you for using the UCSC Genome Browser and your question about having trouble viewing bam files. It looks like at this moment the CyVerse site is having maintenance: https: //cyverse.org/maintenance They have started a cycle of using the first Tuesday of every month from 7 am - 7 pm Pacific Time to perform work. These dates will be impacted: September 7, 2021 October 5, 2021 November 2, 2021 December 7, 2021 However, just in case after they are back online you are still having the issue, be sure that you have made the files for both the file.bam and the file.bam.bai public on the CyVerse site. In the past, I believe CyVerse had automatic software to make any file.bam and its related file.bam.bai public , and I believe it may be different now where you may have to select both files and mark them as public manually. You can see some illustrated steps of their updated system here, http: //genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting, where you may also want to read about inquiring with your institution about hosting data. Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum. If your question includes sensitive data, you may send it instead to genome-www@soe.ucsc.edu. All the best,

Ann Loraine added a comment - 07/Sep/21 5:25 PM - edited We need to notice these problems immediately - before users do, anyway. Possible solutions: Write an app that notifies site administrators when an error occurs Configure Apache to report an error to the user when there's an internal server error, detected as text " [wsgi:error] " appearing in the log, first making sure that this error message only appears in blocker situations

Ann Loraine added a comment - 08/Sep/21 2:15 PM Describe how to test any changes made to the code. Come up with a strategy that will let the testers simulate CyVerse API failing.

Karthik Raveendran added a comment - 09/Sep/21 10:01 AM - edited As discussed yesterday during the meeting, the issue was caused because the Cyverse server was down and the errors were improperly handled, specifically in ResponseParser.py in the terrain_model folder. Possible Solution: Custom error handling classes built for API calls made in the application. How the error classes should be designed and placed in the code base is yet to be determined. The error handling should avoid code smells, useful information should be sent to the UI, and should be class-specific for easier debugging. Also, a testing protocol should be designed as well for checking all the errors before deployment.

Ann Loraine added a comment - 14/Sep/21 10:49 AM Loraine: Needs to create a ticket describing the next phase of making the site more robust to back end CyVerse errors.