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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Python API issue #118

Closed haochenz96 closed 2 years ago

haochenz96 commented 2 years ago

Hi Rick,

I have been running lots of samples through the Python API and it has been working quite well. Thanks again for providing this amazing tool.

I recently ran into 2 issues while submitting jobs through the Python API:

  1. sometimes the output I get (with response = session.get( 'https://run.opencravat.org/submit/jobs/' + job_id + '/status')) contains different numbers of variants than what I put in. I have been searching around on my end but could not locate any bug. What could be the cause of this?

  2. My very recent jobs all show as "submitted" status without any response after a long time. When I attempt to click to see the log it says the log file does not exist.

Let me know what you think of these! Happy to DM any information you need if more convenient.

Best, Haochen

mryaninsilico commented 2 years ago

Hi Haochen,

Thanks for reporting the issue. We will take a look at the issue with python API submission and number of variants returned.

The run.opencravat.org server was restarted this morning to correct the issue with submitted jobs not getting processed. You may need to resubmit the jobs that did not run.

Michael Ryan, PhD

Kiromic

From: Haochen Zhang @.> Sent: Monday, July 11, 2022 12:43 AM To: KarchinLab/open-cravat @.> Cc: Subscribed @.***> Subject: [KarchinLab/open-cravat] Python API issue (Issue #118)

Hi Rick,

I have been running lots of samples through the Python API and it has been working quite well. Thanks again for providing this amazing tool.

I recently ran into 2 issues while submitting jobs through the Python API:

  1. sometimes the output I get (with response = session.get( 'https://run.opencravat.org/submit/jobs/' + job_id + '/status')) contains different numbers of variants than what I put in. I have been searching around on my end but could not locate any bug. What could be the cause of this?
  2. My very recent jobs all show as "submitted" status without any response after a long time. When I attempt to click to see the log it says the log file does not exist.

Let me know what you think of these! Happy to DM any information you need if more convenient.

Best, Haochen

— Reply to this email directly, view it on GitHub https://github.com/KarchinLab/open-cravat/issues/118 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ADC6Q63GYGTNOXJQDJROFF3VTOQ7BANCNFSM53GGFKRQ . You are receiving this because you are subscribed to this thread. https://github.com/notifications/beacon/ADC6Q6YVGWTBMQHE3CYLXD3VTOQ7BA5CNFSM53GGFKR2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4TL7OYZQ.gif Message ID: @. @.> >

haochenz96 commented 2 years ago

Thank you Michael!

Just to give you more information regarding the difference between input & output issue: I tried to rerun the job a couple of times and it worked, so I assumed it is not specific to my input variant list.

For future reference, will an issue like server restart be posted somewhere to notify users?

kmoad commented 2 years ago

For a multi-allelic vcf, the num_unique_var key in the status response is the number of variants that oc finds. The num_input_var key is not reliable for files that can contain more than one variant per line. We'll probably deprecate it in the future.

We schedule server restarts for when no jobs are being processed. Restarts don't take long, so it's there's usually a window. In the rare case we need to restart while a job is running, we resubmit jobs once the server is up.