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Promotion 2024-09-10 anvilprod (#6555) #6561

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merged 31 commits into from
Sep 12, 2024

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@achave11-ucsc achave11-ucsc commented Sep 11, 2024

Connected issue: #6555

Checklist

Author

  • Target branch is anvilprod
  • Name of PR branch matches promotions/yyyy-mm-dd-anvilprod
  • 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 anvilprod
  • PR title references the connected issue

Author (reindex, API changes)

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

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
  • Decided if PR can be labeled 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 anvilprod.shared && CI_COMMIT_REF_NAME=anvilprod make -C terraform/shared apply_keep_unused or this PR is not labeled deploy:shared
  • Made a backup of the GitLab data volume in anvilprod (see operator manual for details) or this PR is not labeled backup:gitlab
  • Ran _select anvilprod.gitlab && CI_COMMIT_REF_NAME=anvilprod 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 anvilprod.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 anvilprod.gitlab && make -C terraform/gitlab/runner or this PR is not labeled deploy:runner
  • Added sandbox label or PR is labeled no sandbox
  • Pushed PR branch to GitLab anvilprod or PR is labeled no sandbox
  • Build passes in hammerbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in hammerbox deployment or PR is labeled no sandbox
  • 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 anvilprod
  • Build passes on GitLab anvilprod
  • Reviewed build logs for anomalies on GitLab anvilprod
  • Ran _select anvilprod.shared && make -C terraform/shared apply or this PR is not labeled deploy:shared
  • Deleted PR branch from GitHub
  • Deleted PR branch from GitLab anvilprod
  • 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 anvilprod or this PR is neither labeled reindex:partial nor reindex:anvilprod
  • Deindexed specific sources in anvilprod or this PR is neither labeled reindex:partial nor reindex:anvilprod
  • Indexed specific sources in anvilprod or this PR is neither labeled reindex:partial nor reindex:anvilprod
  • Started reindex in anvilprod or this PR does not require reindexing anvilprod
  • Checked for, triaged and possibly requeued messages in both fail queues in anvilprod or this PR does not require reindexing anvilprod
  • Emptied fail queues in anvilprod or this PR does not require reindexing anvilprod

Operator

  • PR is assigned to only the system administrator

System administrator

Shorthand for review comments

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

dsotirho-ucsc and others added 30 commits August 28, 2024 17:21
Some canned table rows contain conflicting values for the entities' UUIDs: the
primary keys do not match the document IDs in the `content` column. We suspect
this is the result of a bug in the recently-retired `recan_bundle_tdr` script.
Soon, we will replace file names in HCA bundles with entity references, at
which point these inconsistent UUIDs would break the build.
There are no metadata documents associated with these entries. Soon we will
convert the manifest to a dictionary using entity references as keys, at which
point it will become impossible for bundles to include such dangling entries.
Removing them preemptively proves that they have no effect on any of our tests.
… when PR lands on `develop`
@github-actions github-actions bot added the orange [process] Done by the Azul team label Sep 11, 2024
@@ -140,7 +140,7 @@
def fetch_bundle(self, bundle_fqid: DSSBundleFQID) -> DSSBundle:
assert False, 'DSS is EOL'
# noinspection PyUnreachableCode
return DSSBundle(fqid=bundle_fqid, manifest=[], metadata_files={})
return DSSBundle(fqid=bundle_fqid, manifest={}, metadata={}, links={})

Check warning

Code scanning / CodeQL

Unreachable code Warning

This statement is unreachable.
@achave11-ucsc achave11-ucsc added the upgrade [process] PR includes commit requiring manual upgrade label Sep 11, 2024
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codecov bot commented Sep 11, 2024

Codecov Report

Attention: Patch coverage is 99.42529% with 1 line in your changes missing coverage. Please review.

Project coverage is 85.38%. Comparing base (ec4e3b1) to head (f42a38e).
Report is 36 commits behind head on anvilprod.

Files with missing lines Patch % Lines
src/azul/plugins/repository/canned/__init__.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           anvilprod    #6561   +/-   ##
==========================================
  Coverage      85.38%   85.38%           
==========================================
  Files            156      155    -1     
  Lines          20767    20735   -32     
==========================================
- Hits           17731    17704   -27     
+ Misses          3036     3031    -5     

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

@hannes-ucsc hannes-ucsc added no sandbox [process] PR will not be tested in the sandbox and removed no sandbox [process] PR will not be tested in the sandbox labels Sep 11, 2024
@achave11-ucsc achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Sep 11, 2024
@achave11-ucsc achave11-ucsc merged commit 7238f73 into anvilprod Sep 12, 2024
516 checks passed
@achave11-ucsc achave11-ucsc deleted the promotions/2024-09-10-anvilprod branch September 12, 2024 17:00
@hannes-ucsc hannes-ucsc removed their assignment Sep 16, 2024
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4 participants