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aws / amazon-genomics-cli

https://aws.github.io/amazon-genomics-cli/
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`agc logs workflow` output does not use the configured formatter #409

Open wleepang opened 2 years ago

wleepang commented 2 years ago

Describe the Bug

The output from the agc logs workflow command does not use the configured formatter and instead always outputs a mixture of text + table format that looks like the following:

RunId: 20ceffe1-9664-4f41-a5e9-66ab5eaf57ac
State: COMPLETE
Tasks: 
    Name                        JobId                   StartTime               StopTime                ExitCode
    HaplotypeCallerGvcf_GATK4.MergeGVCFs        12d27ad2-df4e-44f7-90ba-6140bde14cf0    2022-03-24 17:50:06.575 +0000 UTC   2022-03-24 18:00:34.439 +0000 UTC   0
    HaplotypeCallerGvcf_GATK4.HaplotypeCaller   39e61999-079a-4671-9625-9a1fada62c6b    2022-03-24 17:29:12.955 +0000 UTC   2022-03-24 17:48:22.475 +0000 UTC   0
    HaplotypeCallerGvcf_GATK4.HaplotypeCaller   ce9a6f75-9c9d-4e55-b4f9-1f46c516a3b5    2022-03-24 17:29:12.961 +0000 UTC   2022-03-24 17:47:25.444 +0000 UTC   0

In most cases this format is fine. However, when task names are long, the separator between the task name and the job-id is omitted (shown below) making it difficult to parse the output consistently.

# ok line
    PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment    7e244b7b-e02d-4bb9-bee7-9005204382f3    2022-03-24 10:17:20.673 +0000 UTC   2022-03-24 10:23:00.67 +0000 UTC    0

# bad line
    PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV85c5a61b-867e-49ed-a11d-951910444c03    2022-03-24 10:05:53.583 +0000 UTC   2022-03-24 10:11:55.023 +0000 UTC   0

Steps to Reproduce

Relevant Logs

Expected Behavior

All agc commands produce output per the configured formatter

Actual Behavior

The agc logs workflow command output has its own special format

Screenshots

Additional Context

Operating System: macOS, Linux AGC Version: 1.3.0 Was AGC setup with a custom bucket: No Was AGC setup with a custom VPC: No

github-actions[bot] commented 1 year ago

Greetings! Sorry to say but this is a very old issue that is probably not getting as much attention as it deserves. We encourage you to check if this is still an issue in the latest release and if you find that this is still a problem, please feel free to open a new one.