Promotion 2024-10-15 prod (#6630)

[dsotirho-ucsc]

Connected issue: #6630

Checklist

Author

• Target branch is prod
• Name of PR branch matches promotions/yyyy-mm-dd-prod
• On ZenHub, PR is connected to the promotion issue it resolves
• PR description links to connected issue
• Title of connected issue matches Promotion yyyy-mm-dd
• PR title starts with title of connected issue followed by prod
• PR title references the connected issue

Author (reindex, API changes)

• This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
• This PR is labeled reindex:partial and its description documents the specific reindexing procedure for prod _{or requires a full reindex or is not labeledreindex:prod}

Author (upgrading deployments)

• This PR is labeled upgrade _{or does not require upgrading deployments}
• This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
• This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
• This PR is labeled deploy:runner _{or does not require deploying the runner image}

System administrator (after approval)

• Actually approved the PR
• Labeled PR as no sandbox
• Moved connected issue to Approved column
• PR is assigned to only the operator

Operator (before pushing merge the commit)

• Pushed PR branch to GitHub
• Ran _select prod.shared && CI_COMMIT_REF_NAME=prod make -C terraform/shared apply _{or this PR is not labeled deploy:shared}
• Made a backup of the GitLab data volume in prod (see operator manual for details) _{or this PR is not labeled backup:gitlab}
• Ran _select prod.gitlab && CI_COMMIT_REF_NAME=prod make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
• Checked the items in the next section _{or this PR is labeled deploy:gitlab}
• PR is assigned to only the system administrator _{or this PR is not labeled deploy:gitlab}

System administrator

• Background migrations for prod.gitlab are complete _{or this PR is not labeled deploy:gitlab}
• PR is assigned to only the operator

Operator (before pushing merge the commit)

• Ran _select prod.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
• The title of the merge commit starts with the title of this PR
• Added PR # reference to merge commit title
• Collected commit title tags in merge commit title _{but excluded any p tags}
• Pushed merge commit to GitHub

Operator (after pushing the merge commit)

• Pushed merge commit to GitLab prod
• Build passes on GitLab prod Fixed with hotfixes PR Hotfix prod: Optimistic lock contention on HCA replicas (#6648) #6650, PR Hotfix prod: Error indexing lm8 catalog (#6644) #6651, PR Hotfix prod: Optimistic lock contention on HCA replicas (#6648) #6654
• Reviewed build logs for anomalies on GitLab prod
• Deleted PR branch from GitHub
• Moved connected issue to Merged stable column on ZenHub
• Moved promoted issues from Merged lower to Merged stable column on ZenHub
• Moved promoted issues from Lower to Stable column on ZenHub

Operator (reindex)

• Deindexed all unreferenced catalogs in prod _{or this PR is neither labeled reindex:partial nor reindex:prod}
• Deindexed specific sources in prod _{or this PR is neither labeled reindex:partial nor reindex:prod}
• Indexed specific sources in prod _{or this PR is neither labeled reindex:partial nor reindex:prod}
• Started reindex in prod _{or this PR does not require reindexing prod}
• Checked for, triaged and possibly requeued messages in both fail queues in prod _{or this PR does not require reindexing prod}
• Emptied fail queues in prod _{or this PR does not require reindexing prod}

Operator

• PR is assigned to only the system administrator

System administrator

• Removed unused image tags from pycharm image on DockerHub _{or this promotion does not alter references to that image}
• Removed unused image tags from elasticsearch image on DockerHub _{or this promotion does not alter references to that image}
• Removed unused image tags from bigquery_emulator image on DockerHub _{or this promotion does not alter references to that image}
• PR is assigned to no one

Shorthand for review comments

• L line is too long
• W line wrapping is wrong
• Q bad quotes
• F other formatting problem

[codecov]

Codecov Report

Attention: Patch coverage is 91.32420% with 19 lines in your changes missing coverage. Please review.

Project coverage is 85.36%. Comparing base (e0a4ceb) to head (54e12dd).
Report is 36 commits behind head on prod.

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	10 Missing ⚠️
src/azul/plugins/metadata/anvil/bundle.py	89.65%	3 Missing ⚠️
src/azul/terraform.py	25.00%	3 Missing ⚠️
src/azul/chalice.py	83.33%	1 Missing ⚠️
src/azul/indexer/index_service.py	91.66%	1 Missing ⚠️
src/humancellatlas/data/metadata/api.py	83.33%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             prod    #6634      +/-   ##
==========================================
+ Coverage   84.18%   85.36%   +1.18%     
==========================================
  Files         155      155              
  Lines       22281    20770    -1511     
==========================================
- Hits        18757    17731    -1026     
+ Misses       3524     3039     -485     

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[coveralls]

coverage: 85.386% (-0.05%) from 85.431%
when pulling 54e12dd on promotions/2024-10-15-prod
into e0a4ceb on prod.

[nadove-ucsc]

pro-forma approval