Fix: Left-overs from orphan-related PRs (#6691) #6705

nadove-ucsc · 2024-11-13T04:20:06Z

Connected issues: #6691

Checklist

Author

PR is a draft
Target branch is develop
Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
On ZenHub, PR is connected to all issues it (partially) resolves
PR description links to connected issues
PR title matches¹ that of a connected issue _{or comment in PR explains why they're different}
PR title references all connected issues
For each connected issue, there is at least one commit whose title references that issue

¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

Author (chains)

This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
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 dev, anvildev, anvilprod and prod _{or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod}
This PR and its connected issues are labeled API _{or this PR does not modify a REST API}
Added a (A) tag to commit title for backwards (in)compatible changes _{or this PR does not modify a REST API}
Updated REST API version number in app.py _{or this PR does not modify a REST API}

Author (upgrading deployments)

Ran make docker_images.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require 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}

Author (hotfixes)

Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
Reverted the temporary hotfixes for any connected issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR}

Author (before every review)

Rebased PR branch on develop, 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}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

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PR is not a draft
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PR is assigned to only the system administrator

System administrator (after approval)

Actually approved the PR
Labeled connected issues as demo or no demo
Commented on connected issues about demo expectations _{or all connected issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Moved connected issues to Approved column
PR is assigned to only the operator

Operator (before pushing merge the commit)

System administrator

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

Operator (before pushing merge the commit)

Operator (chain shortening)

Changed the target branch of the blocked PR to develop _{or this PR is not labeled base}
Removed the chained label from the blocked PR _{or this PR is not labeled base}
Removed the blocking relationship from the blocked PR _{or this PR is not labeled base}
Removed the base label from this PR _{or this PR is not labeled base}

Operator (after pushing the merge commit)

Operator (reindex)

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
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 · 2024-11-13T04:40:31Z

Codecov Report

Attention: Patch coverage is 66.66667% with 13 lines in your changes missing coverage. Please review.

Project coverage is 85.58%. Comparing base (efe016f) to head (56c9ed8).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	8 Missing ⚠️
src/azul/plugins/repository/canned/__init__.py	0.00%	4 Missing ⚠️
src/azul/plugins/metadata/anvil/bundle.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6705      +/-   ##
===========================================
- Coverage    85.59%   85.58%   -0.02%     
===========================================
  Files          155      155              
  Lines        20903    20916      +13     
===========================================
+ Hits         17892    17901       +9     
- Misses        3011     3015       +4

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

coveralls · 2024-11-13T04:41:41Z

coverage: 85.602% (-0.01%) from 85.613%
when pulling 56c9ed8 on issues/nadove-ucsc/6691-leftovers-orphan-prs
into efe016f on develop.

achave11-ucsc

Approved ✅

hannes-ucsc · 2024-11-15T00:04:40Z

test/integration_test.py

+        :param public: If none (as by default), allow the source to be either
+        public or non-public. If true, choose a public source, or raise an


Suggested change

:param public: If none (as by default), allow the source to be either

public or non-public. If true, choose a public source, or raise an

:param public: If none (as by default), allow the source to be either

public or non-public. If true, choose a public source, or raise an

hannes-ucsc · 2024-11-15T00:54:01Z

test/service/test_manifest.py

@@ -2122,7 +2122,9 @@ def hash_entities(entities: dict[EntityReference, JSON]) -> dict[str, JSON]:
        return all_entities_by_hash.values(), linked_entities_by_hash.values()

    def test_verbatim_pfb_manifest(self):
-        response = self._get_manifest(ManifestFormat.verbatim_pfb, filters={})
+        response = self._get_manifest(ManifestFormat.verbatim_pfb, filters={


We should have two cases, one unfiltered, the other one with this filter. In the unfiltered case, we should dynamically edit out the parts of the canned PFB that aren't expected in that case.

github-actions bot added the orange [process] Done by the Azul team label Nov 13, 2024

nadove-ucsc force-pushed the issues/nadove-ucsc/6691-leftovers-orphan-prs branch 3 times, most recently from aeeaceb to cb4455e Compare November 14, 2024 05:53

nadove-ucsc requested a review from achave11-ucsc November 14, 2024 06:23

nadove-ucsc assigned achave11-ucsc Nov 14, 2024

achave11-ucsc previously approved these changes Nov 14, 2024

View reviewed changes

achave11-ucsc marked this pull request as ready for review November 14, 2024 18:43

achave11-ucsc requested a review from hannes-ucsc as a code owner November 14, 2024 18:43

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Nov 14, 2024

nadove-ucsc added the base [process] Another PR needs to be rebased before merging this one label Nov 14, 2024

hannes-ucsc requested changes Nov 15, 2024

View reviewed changes

hannes-ucsc removed their assignment Nov 15, 2024

hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Nov 15, 2024

nadove-ucsc added 13 commits November 14, 2024 18:15

Add FIXME (#6704)

f01ef0f

Fix missing log statement (#6691)

d546094

Rename local functions (#6691)

55c0669

Extract variables and fix wrapping (#6691)

adaf157

Extract variable and rename method (#6691)

0416d44

Tweak assertion message (#6691)

0c62047

Refactor bundle counting in Canned plugin (#6691)

0658666

Refactor and document short-circuit for empty tallies (#6691)

b472e63

Fix type warnings in BundleType (#6691)

a78e906

Improve internal documentation (#6691)

9fcda5b

fixup! Improve internal documentation (#6691)

c9a1a5e

Cover orphans in AnVIL verbatim PFB unit test (#6691)

0eec790

fixup! Cover orphans in AnVIL verbatim PFB unit test (#6691)

56c9ed8

nadove-ucsc dismissed achave11-ucsc’s stale review via 56c9ed8 November 15, 2024 02:42

nadove-ucsc force-pushed the issues/nadove-ucsc/6691-leftovers-orphan-prs branch from cb4455e to 56c9ed8 Compare November 15, 2024 02:42

nadove-ucsc requested a review from hannes-ucsc November 15, 2024 05:52

nadove-ucsc assigned hannes-ucsc Nov 15, 2024

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Fix: Left-overs from orphan-related PRs (#6691) #6705

Fix: Left-overs from orphan-related PRs (#6691) #6705

nadove-ucsc commented Nov 13, 2024 •

edited by achave11-ucsc

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hannes-ucsc Nov 15, 2024

hannes-ucsc Nov 15, 2024

		:param public: If none (as by default), allow the source to be either
		public or non-public. If true, choose a public source, or raise an

Fix: Left-overs from orphan-related PRs (#6691) #6705

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Fix: Left-overs from orphan-related PRs (#6691) #6705

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nadove-ucsc commented Nov 13, 2024 • edited by achave11-ucsc Loading

Checklist

Author

Author (partiality)

Author (chains)

Author (reindex, API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator (before pushing merge the commit)

System administrator

Operator (before pushing merge the commit)

Operator (chain shortening)

Operator (after pushing the merge commit)

Operator (reindex)

Operator

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nadove-ucsc commented Nov 13, 2024 •

edited by achave11-ucsc

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