Hotfix prod: Optimistic lock contention on HCA replicas (#6648)

[dsotirho-ucsc]

Connected issue: #6648

Notes:

• Requires a reindex of lm7 and lm8.

Checklist

Author

• Target branch is prod
• Name of PR branch matches hotfixes/<GitHub handle of author>/<issue#>-<slug>-prod
• On ZenHub, PR is connected to the issue it hotfixes
• PR description links to connected issue
• PR title is Hotfix prod: followed by title of connected issue
• PR title references the connected issue

Author (hotfixes)

• Added h tag to commit title _{or this PR does not include a temporary hotfix}
• Added H tag to commit title _{or this PR does not include a permanent hotfix}
• Added hotfix label to PR
• This PR is labeled partial _{or represents a permanent hotfix}

Author (before every review)

• Rebased PR branch on prod, squashed old fixups
• Ran make requirements_update _{or this PR does not modify requirements*.txt, common.mk, Makefile and Dockerfile}
• Added R tag to commit title _{or this PR does not modify requirements*.txt}
• This PR is labeled reqs _{or does not modify requirements*.txt}

System administrator (after approval)

• Actually approved the PR
• Labeled PR as no sandbox
• A comment to this PR details the completed security design review
• PR title is appropriate as title of merge commit
• Moved connected issue to Approved column
• PR is assigned to only the operator

Operator (before pushing merge the commit)

• Squashed PR branch and rebased onto prod
• Sanity-checked history
• Pushed PR branch to GitHub
• 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}
• Moved connected issue to Merged stable column in ZenHub
• Pushed merge commit to GitHub

Operator (after pushing the merge commit)

• Pushed merge commit to GitLab prod To be pushed with PR Hotfix prod: Error indexing lm8 catalog (#6644) #6651
• Build passes on GitLab prod
• Reviewed build logs for anomalies on GitLab prod
• Deleted PR branch from GitHub

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 neither this PR nor a failed, prior promotion requires it}
• Checked for, triaged and possibly requeued messages in both fail queues in prod _{or neither this PR nor a failed, prior promotion requires it}
• Emptied fail queues in prod _{or neither this PR nor a failed, prior promotion requires it}
• Created backport PR and linked to it in a comment on this PR

Operator

• 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

All modified and coverable lines are covered by tests ✅

Project coverage is 85.36%. Comparing base (0f4f04c) to head (73f5837).
Report is 2 commits behind head on prod.

Additional details and impacted files

@@           Coverage Diff           @@
##             prod    #6650   +/-   ##
=======================================
  Coverage   85.36%   85.36%           
=======================================
  Files         155      155           
  Lines       20770    20770           
=======================================
  Hits        17731    17731           
  Misses       3039     3039           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[coveralls]

coverage: 85.386%. remained the same
when pulling 73f5837 on hotfixes/dsotirho-ucsc/6648-replicas
into 0f4f04c on prod.

[hannes-ucsc]

Security design review

• Security design review completed; this PR does not …
  • … affect authentication; for example:
    • OAuth 2.0 with the application (API or Swagger UI)
    • Authentication of developers with Google Cloud APIs
    • Authentication of developers with AWS APIs
    • Authentication with a GitLab instance in the system
    • Password and 2FA authentication with GitHub
    • API access token authentication with GitHub
    • Authentication with Terra
  • … affect the permissions of internal users like access to
    • Cloud resources on AWS and GCP
    • GitLab repositories, projects and groups, administration
    • an EC2 instance via SSH
    • GitHub issues, pull requests, commits, commit statuses, wikis, repositories, organizations
  • … affect the permissions of external users like access to
    • TDR snapshots
  • … affect permissions of service or bot accounts
    • Cloud resources on AWS and GCP
  • … affect audit logging in the system, like
    • adding, removing or changing a log message that represents an auditable event
    • changing the routing of log messages through the system
  • … affect monitoring of the system
  • … introduce a new software dependency like
    • Python packages on PYPI
    • Command-line utilities
    • Docker images
    • Terraform providers
  • … add an interface that exposes sensitive or confidential data at the security boundary
  • … affect the encryption of data at rest
  • … require persistence of sensitive or confidential data that might require encryption at rest
  • … require unencrypted transmission of data within the security boundary
  • … affect the network security layer; for example by
    • modifying, adding or removing firewall rules
    • modifying, adding or removing security groups
    • changing or adding a port a service, proxy or load balancer listens on
• Documentation on any unchecked boxes is provided in comments below

[hannes-ucsc]

Assignee to merge this one first, before PR #6651, and not push to GitLab.