Not exiting multi-case upload process when one gens upload fails

[Emil Bertilsson]

As mentioned in #3197, it'd be good to not exit the upload process entirely when singular Gens samples fail to upload to a duplicate key error.

I'm not entirely sure how to accomplish this in the best way. Would simply putting a try except CalledProcessError somewhere like here

cg/cg/apps/gens.py

Line 45 in 985acfb

 self.process.run_command(parameters=load_call_params, dry_run=self.dry_run) 

be enough?

[Isak Ohlsson Ångnell]

Hmm I think a try/except would be nice, but I would rather have it where the samples are being looped through. There could be benefits to having an error raised from GensAPI.load which is caught by the upload_to_gens method, say if you would want a method which uploads only a single sample. There it might make sense that an error is raised.

[Emil Bertilsson]

Hmmm, I might have misunderstood whoever originally noted this problem.
cg seems to already separate the cases here

cg/cg/cli/upload/base.py

Lines 116 to 121 in 985acfb

 try: 
     context.invoke(upload, case_id=case_id) 
 except Exception: 
     LOG.error(f"Case {case_id} upload failed") 
     LOG.error(traceback.format_exc()) 
     exit_code = 1 

The command still exits with an error code, but it continues to upload other cases after an exception is caught.
I've taken a look at chanjo and genotype, and they both simply print a warning when there's a duplicate. However, they respect the re_upload/restart/force flag.
For consistency's sake I guess it might be best to, as you say, have upload_to_gens catch an exception, but then just print a warning, and to have Gens respect the re_upload/restart flag?

[Henrik Stranneheim]

@raysloks Sounds good! Let's make it so.