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pathogen-repo-build improvements #101

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merged 3 commits into from
Jun 21, 2024
Merged

pathogen-repo-build improvements #101

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4fc42a5
pathogen-repo-build: Include `AWS_DEFAULT_REGION` in envdir
joverlee521 Jun 18, 2024
d8640df
pathogen-repo-build: Add output `aws-batch-job-id`
joverlee521 Jun 18, 2024
e5d5d4f
CI: Verify pathogen-repo-build's aws-batch-job-id output
joverlee521 Jun 21, 2024
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11 changes: 11 additions & 0 deletions .github/workflows/pathogen-repo-build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,16 @@ on:
This is not supported for builds on AWS Batch because the workflow detaches from the build. Please use the `nextstrain build` command locally to reattach to AWS Batch builds to download outputs.
type: string
required: false
outputs:
aws-batch-job-id:
description: >-
AWS Batch job id of the build if it was run with the `aws-batch` runtime. This can be used to re-attach to the AWS Batch job with:


nextstrain build --aws-batch --attach <aws-batch-job-id>

This can be useful to download results from the build and use them in subsequent jobs.
value: ${{ jobs.run-build.outputs.AWS_BATCH_JOB_ID }}
workflow_dispatch:
inputs:
runtime:
Expand Down Expand Up @@ -287,6 +297,7 @@ jobs:
"$NEXTSTRAIN_GITHUB_DIR"/bin/write-envdir "$NEXTSTRAIN_RUNTIME_ENVDIR" \
AWS_ACCESS_KEY_ID \
AWS_SECRET_ACCESS_KEY \
AWS_DEFAULT_REGION \
${AWS_SESSION_TOKEN:+AWS_SESSION_TOKEN}
# This will overwrite the runtime AWS credential envvars configured above
# so if the build is using the aws-batch runtime, the Nextstrain CLI will
Expand Down
14 changes: 14 additions & 0 deletions .github/workflows/pathogen-repo-build.yaml.in
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Expand Up @@ -162,6 +162,19 @@ on:
type: string
required: false

outputs:
aws-batch-job-id:
description: >-
AWS Batch job id of the build if it was run with the `aws-batch` runtime.
This can be used to re-attach to the AWS Batch job with:

nextstrain build --aws-batch --attach <aws-batch-job-id>

This can be useful to download results from the build and use them
in subsequent jobs.

value: ${{ jobs.run-build.outputs.AWS_BATCH_JOB_ID }}

workflow_dispatch:
inputs:
<<: *inputs
Expand Down Expand Up @@ -256,6 +269,7 @@ jobs:
"$NEXTSTRAIN_GITHUB_DIR"/bin/write-envdir "$NEXTSTRAIN_RUNTIME_ENVDIR" \
AWS_ACCESS_KEY_ID \
AWS_SECRET_ACCESS_KEY \
AWS_DEFAULT_REGION \
${AWS_SESSION_TOKEN:+AWS_SESSION_TOKEN}

# This will overwrite the runtime AWS credential envvars configured above
Expand Down