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Update gen3-deployment documentation to include the updated helm based changes#99

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paulineribeyre merged 19 commits intomasterfrom
chore/add_helm_deployment_doc
Feb 19, 2026
Merged

Update gen3-deployment documentation to include the updated helm based changes#99
paulineribeyre merged 19 commits intomasterfrom
chore/add_helm_deployment_doc

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@nss10 nss10 commented Jan 29, 2026

Link to JIRA ticket if there is one:

New Features

Breaking Changes

Bug Fixes

Improvements

Dependency updates

Deployment changes

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The style in this PR agrees with black. ✔️

This formatting comment was generated automatically by a script in uc-cdis/wool.

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coveralls commented Jan 29, 2026

Pull Request Test Coverage Report for Build 22193529696

Details

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • 24 unchanged lines in 2 files lost coverage.
  • Overall coverage increased (+0.08%) to 88.873%

Files with Coverage Reduction New Missed Lines %
routes/s3.py 3 89.23%
routes/ga4gh_tes.py 21 85.19%
Totals Coverage Status
Change from base Build 21915478148: 0.08%
Covered Lines: 639
Relevant Lines: 719

💛 - Coveralls

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@paulineribeyre paulineribeyre marked this pull request as ready for review February 11, 2026 22:29
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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

Please find the detailed integration test report here

Please find the Github Action logs here

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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

Please find the detailed integration test report here

Please find the Github Action logs here

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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

Please find the detailed integration test report here

Please find the Github Action logs here

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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

Please find the detailed integration test report here

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Minor suggestions

```
* If **Crossplane is not enabled**, you can create them manually using [this Helm template](https://github.com/uc-cdis/gen3-helm/blob/master/helm/gen3-workflow/templates/crossplane.yaml) as reference.

> In CTDS environments, the recommendation is to use Crossplane for Dev and QA environments and Terraform/Terragrunt for Production environments. Check out [this internal link](https://github.com/uc-cdis/gen3-terragrunt/pull/251/changes) for an example of creating this role with Terragrunt.
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In CTDS environments, the recommendation is to use Crossplane for Dev/QA and Terraform/Terragrunt for Production environments. Check out this internal link for an example of creating this role with Terragrunt.

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...Dev and QA environments and Terraform/Terragrunt... this part seemed a little confusing to me.


- S3 mountpoint

We need to make sure the S3 mountpoint is configured correctly, and ideally we should have per-pod identity so that the workflows can use per-user buckets. See [this](https://github.com/awslabs/mountpoint-s3-csi-driver/issues/334#issuecomment-2613552946). More context [here](https://cdis.slack.com/archives/CLZJVC38B/p1738882570732499?thread_ts=1738880648.216489&cid=CLZJVC38B).
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Why are we removing them from docs? There could be newer clusters where we might want to deploy Gen3Workflow, and these docs would be helpful, right?

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We didn't need to do any of these manual steps when we deployed it to a new cluster this time, so this may have been resolved by deploying through helm charts. We can revert if later it turns out we need it

# Update each whitelisted image to a regex with updated {username} value with an actual username
# and `*` with `.*` to match any sequence of characters, storing the resulting patterns in a set
whitelisted_images_regex = {
def _image_to_regex(image: str) -> str:
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This is nice, I wanted to work on this once I get a chance. You beat me to it :D But this is great.

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filepath passed SUBTOTAL
tests/test_gen3_workflow.py 13 13
TOTAL 13 13

Please find the detailed integration test report here

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@paulineribeyre paulineribeyre merged commit b7981cd into master Feb 19, 2026
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@paulineribeyre paulineribeyre deleted the chore/add_helm_deployment_doc branch February 19, 2026 22:34
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3 participants