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feat: Added option to pass custom WES Adapter environment variables #420

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@kankou-aliaksei kankou-aliaksei commented Apr 29, 2022

Issue #: #396

Description of Changes

[//]: # This adds option to pass custom environment variables into WES Adapter
[//]: # This adds option to pass custom environment variables into Workflow Job

Description of how you validated changes

[//]: # Add configuration for context

contexts:
  miniContext:
    customWesEnvVars:
      - key: k1
        value: v1
      - key: CUSTOM_WORKFLOW_JOB_ENV_VARS
        value: "[{ \"key\": \"MINIWDL__AWS__BOTO3_RETRIES\", \"value\": { \"max_attempts\": 15, \"mode\": \"standard\" } }, { \"key\": \"MINIWDL__AWS__DESCRIBE_PERIOD\", \"value\": 10 }, { \"key\": \"MINIWDL__AWS__SUBMIT_PERIOD\", \"value\": 10 }]"
    engines:
      - type: wdl
        engine: miniwdl

[//]: # Deploy context agc context deploy --context miniContext
[//]: # After context deploying a WES Adapter Lambda must have k1 and CUSTOM_WORKFLOW_JOB_ENV_VARS env vars
[//]: # After agc workflow run hello --context miniContext go to Batch Workflow Job Logs and find MINIWDL__AWS__BOTO3_RETRIES, MINIWDL__AWS__DESCRIBE_PERIOD, MINIWDL__AWS__SUBMIT_PERIOD vars under === ENVIRONMENT === section

Checklist

  • If this change would make any existing documentation invalid, I have included those updates within this PR
  • I have added unit tests that prove my fix is effective or that my feature works
  • I have linted my code before raising the PR
  • Title of this Pull Request follows Conventional Commits standard: https://www.conventionalcommits.org/en/v1.0.0/

By submitting this pull request, I confirm that my contribution is made under the terms of the Apache-2.0 license

markjschreiber
markjschreiber previously approved these changes Apr 29, 2022
markjschreiber
markjschreiber previously approved these changes Apr 29, 2022
markjschreiber
markjschreiber previously approved these changes May 10, 2022
@nh13
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nh13 commented Jul 14, 2022

Looking forward to this so I can set config options as per chanzuckerberg/miniwdl#570

@wleepang wleepang removed the request for review from IllyaYalovyy July 29, 2022 23:44
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4 participants