Fix: Redundant file fields for AnVIL are no longer needed (#7005) #7597

dsotirho-ucsc · 2025-11-26T18:42:26Z

Linked issues: #7005

Notes

In order to minimize the time frame during which the service returns 500 responses, cancel the deploy stage and then be present when starting it manually, cancel the integration_test stage and immediately trigger the early_reindex when the deploy_browser stage finishes

Checklist

Author

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 linked issues}
This PR partially resolves each of the linked issues _{or does not have the partial label}

Author (reindex)

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}

Author (API changes)

This PR and its linked 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 linked issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues linked to this PR}

Author (before every review)

Rebased PR branch on develop, squashed fixups from prior reviews
Ran make requirements_update _{or this PR does not modify Dockerfile, environment, requirements*.txt, common.mk, Makefile or environment.boot}
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}
PR is awaiting requested review from a peer
Status of PR is Review requested
PR is assigned to only the peer and the author

Peer reviewer (after approval)

Note that after requesting changes, the PR must be assigned to only the author.

Actually approved the PR
PR is not a draft
PR is awaiting requested review from system administrator
Status of PR is Review requested
PR is assigned to only the system administrator and the author

System administrator (after approval)

Actually approved the PR
Labeled linked issues as demo or no demo
Commented on linked issues about demo expectations _{or all linked 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
Status of PR is Approved
PR is assigned to only the operator and the author

Operator

Checked reindex:… labels and r commit title tag
Checked that demo expectations are clear _{or all linked issues are labeled no demo}
Squashed PR branch and rebased onto develop
Sanity-checked history
Pushed PR branch to GitHub

Operator (deploy `.shared` and `.gitlab` components)

Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop 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 and the author _{or this PR is not labeled deploy:gitlab}

System administrator (post-deploy of `.gitlab` component)

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 and the author

Operator (deploy runner image)

Ran _select dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
Ran _select anvildev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

Operator (merge the branch)

All status checks passed and the PR is mergeable
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 only included p if the PR is also labeled partial}
Pushed merge commit to GitHub
Status of PR is Merged lower
Status of blocked issues is Triage _{or no issues are blocked on the linked issues}

Operator (main build)

Operator (reindex)

Operator (mirroring)

Started mirroring in dev _{or this PR does not require mirroring dev}
Started mirroring in anvildev _{or this PR does not require mirroring anvildev}
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR does not require mirroring dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}
Emptied mirror fail queue in dev _{or this PR does not require mirroring dev}
Emptied mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}

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 · 2025-11-26T19:34:41Z

Codecov Report

❌ Patch coverage is 82.40741% with 19 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.84%. Comparing base (c533871) to head (51a2447).
⚠️ Report is 21 commits behind head on develop.

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	11 Missing ⚠️
src/azul/plugins/__init__.py	76.00%	6 Missing ⚠️
src/azul/service/repository_service.py	83.33%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7597      +/-   ##
===========================================
- Coverage    84.85%   84.84%   -0.02%     
===========================================
  Files          157      157              
  Lines        22833    22871      +38     
===========================================
+ Hits         19376    19405      +29     
- Misses        3457     3466       +9

☔ View full report in Codecov by Sentry.
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coveralls · 2025-11-26T19:39:12Z

coverage: 85.066% (-0.01%) from 85.08%
when pulling 51a2447 on issues/dsotirho-ucsc/7005-redundant-anvil-field
into c533871 on develop.

dsotirho-ucsc · 2025-12-02T17:32:34Z

7597_IT_2025-12-02.txt

nadove-ucsc

Looks good, just a naming recommendation 👍

nadove-ucsc · 2025-12-02T20:57:32Z

src/azul/plugins/__init__.py

+    file_uuid_facet: FieldName
+    file_uuid_field: FieldName


Suggested change

file_uuid_facet: FieldName

file_uuid_field: FieldName

file_id: FieldName

file_id_facet: FieldName

None of the other entries here have a "_field" suffix, so I think this can be made more terse.

Given the disclaimers in this class's docstring, I suspect a more in-depth refactoring is needed here to resolve the tension between these two new fields. But I'm not going to speculate on what that refactoring should look like without @hannes-ucsc 's input.

dsotirho-ucsc · 2025-12-03T18:56:18Z

7597_IT_2025-12-03.txt

hannes-ucsc · 2025-12-04T17:47:34Z

src/azul/plugins/metadata/anvil/__init__.py

+                             file_id='files.document_id',
+                             file_id_facet='document_id',


One of these is misplaced. Instances of this class encapsulate the names of special fields, and fields are the names of properties in index documents. So based on that they can't both be fields. PL with Noa and you, please.

…, i.e., special fields whose name in service response hits differs from the name used in facets, filters and the sort parameter of service requests

dsotirho-ucsc self-assigned this Nov 26, 2025

dsotirho-ucsc linked an issue Nov 26, 2025 that may be closed by this pull request

Redundant file fields for AnVIL are no longer needed #7005

Open

dsotirho-ucsc added reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Nov 26, 2025

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7005-redundant-anvil-field branch 2 times, most recently from fa14053 to c7a36fd Compare November 26, 2025 19:20

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7005-redundant-anvil-field branch 5 times, most recently from bf508d1 to 49df8df Compare December 2, 2025 03:51

dsotirho-ucsc requested a review from nadove-ucsc December 2, 2025 17:32

dsotirho-ucsc assigned nadove-ucsc Dec 2, 2025

nadove-ucsc requested changes Dec 2, 2025

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nadove-ucsc removed their assignment Dec 2, 2025

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7005-redundant-anvil-field branch from 49df8df to 8d9a65d Compare December 3, 2025 18:12

dsotirho-ucsc assigned nadove-ucsc Dec 3, 2025

dsotirho-ucsc requested a review from nadove-ucsc December 3, 2025 18:57

nadove-ucsc previously approved these changes Dec 3, 2025

View reviewed changes

nadove-ucsc assigned hannes-ucsc and unassigned nadove-ucsc Dec 3, 2025

nadove-ucsc marked this pull request as ready for review December 3, 2025 19:33

nadove-ucsc requested a review from hannes-ucsc as a code owner December 3, 2025 19:33

hannes-ucsc requested changes Dec 4, 2025

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hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Dec 4, 2025

hannes-ucsc removed their assignment Dec 4, 2025

hannes-ucsc removed their assignment Dec 14, 2025

dsotirho-ucsc assigned achave11-ucsc and dsotirho-ucsc and unassigned dsotirho-ucsc Dec 15, 2025

dsotirho-ucsc and others added 20 commits December 15, 2025 15:38

Remove unused special field root_entity_id

07f8792

[r] Remove files.sha256 from AnVIL (#7005)

1057512

[r] Remove files.crc32c from AnVIL (#7005)

30469ff

[r] Remove files.uuid from AnVIL (#7005)

b29e13e

Promote type for inverse field mapping to top level

629efc7

Fix typing of method, add docstring

75c6974

Rename method

5dd2149

Add missing reference to special field

e4b6c28

Implement abstract property with class attribute instead of property

f49a36f

Remove obvious comment

7f9769e

Remove redundant property override

0a0910d

Reorder methods

fee78ff

Add documentation to field-related types

e152cd5

Rename method

4e902fb

Extract properties for app and plugin used by tests

9a1a4d5

Protect test class attribute

75f3f86

Fix facet vs field misnomer

babb304

Allow for asymmetrically named special fields

eba91ac

…, i.e., special fields whose name in service response hits differs from the name used in facets, filters and the sort parameter of service requests

Remove redundant ABCMeta declaration

304a1d7

Push down DCP/1-specific method into DCP/1-specific subclass

51a2447

achave11-ucsc force-pushed the issues/dsotirho-ucsc/7005-redundant-anvil-field branch from 9103ba7 to 51a2447 Compare December 15, 2025 23:39

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Dec 15, 2025

achave11-ucsc merged commit ca6fa2d into develop Dec 16, 2025
10 checks passed

achave11-ucsc deleted the issues/dsotirho-ucsc/7005-redundant-anvil-field branch December 16, 2025 18:17

achave11-ucsc unassigned dsotirho-ucsc Dec 16, 2025

achave11-ucsc removed their assignment Jan 7, 2026

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Fix: Redundant file fields for AnVIL are no longer needed (#7005) #7597

Fix: Redundant file fields for AnVIL are no longer needed (#7005) #7597

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dsotirho-ucsc commented Nov 26, 2025 •

edited by achave11-ucsc

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Fix: Redundant file fields for AnVIL are no longer needed (#7005) #7597

Fix: Redundant file fields for AnVIL are no longer needed (#7005) #7597

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Checklist

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