Fix: StorageObjectExists error when mirroring anvil14 (#8142) by hannes-ucsc · Pull Request #8163 · DataBiosphere/azul

hannes-ucsc · 2026-07-04T06:37:20Z

Linked issues: #8142

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 (mirror)

This PR is labeled mirror:dev _{or the changes introduced by it will not require mirroring of dev}
This PR is labeled mirror:anvildev _{or the changes introduced by it will not require mirroring of anvildev}
This PR is labeled mirror:anvilprod _{or the changes introduced by it will not require mirroring of anvilprod}
This PR is labeled mirror:prod _{or the changes introduced by it will not require mirroring of prod}
This PR is labeled mirror:partial and its description documents the specific mirroring procedure for dev, anvildev, anvilprod and prod _{or requires a full mirroring or carries none of the labels mirror:dev, mirror:anvildev, mirror:anvilprod and mirror: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 mirror:… labels
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 is not labelled mirror:dev}
Started mirroring in anvildev _{or this PR is not labelled mirror:anvildev}
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR is not labelled mirror:dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR is not labelled mirror:anvildev}
Emptied mirror fail queue in dev _{or this PR is not labelled mirror:dev}
Emptied mirror fail queue in anvildev _{or this PR is not labelled mirror:anvildev}

Operator

Propagated the upgrade and API labels to the next promotion PRs _{or this PR carries neither of these labels}
Propagated the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial, reindex:anvilprod, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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, reindex:partial, reindex:anvilprod, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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 · 2026-07-05T21:08:18Z

Codecov Report

❌ Patch coverage is 93.02326% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.37%. Comparing base (c5db138) to head (496c0fd).

Files with missing lines	Patch %	Lines
src/azul/indexer/mirror_service.py	84.21%	3 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #8163      +/-   ##
===========================================
+ Coverage    84.35%   84.37%   +0.01%     
===========================================
  Files          166      166              
  Lines        24460    24495      +35     
===========================================
+ Hits         20633    20667      +34     
- Misses        3827     3828       +1

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

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

coveralls · 2026-07-05T21:09:19Z

coverage: 84.453% (+0.02%) from 84.435% — issues/hannes-ucsc/8142-storage-object-exists into develop

hannes-ucsc · 2026-07-07T08:28:11Z

(Posted by Claude Code)

Security Design Review

Scope

All changes on this branch relative to develop: modifications to mirror_service.py (race condition fix and multipart upload abort optimization) and new test in test_mirror_controller.py.

Threat Model

The mirroring system copies files from external repositories (TDR) into S3, where multiple Lambda workers may process files concurrently. The relevant threats are:

Data integrity: Could a race condition cause a corrupted or partial file to be marked as successfully mirrored?
Denial of service: Could the changes cause resource leaks (e.g., abandoned multipart uploads consuming storage)?
Access control bypass: Could the changes weaken authorization checks?

Findings

No security concerns identified.

Details:

_create_or_update_info: This method replaces bare _create_info calls in _mirror_file and FinalizeFileAction. It catches StorageObjectExists (raised by S3 conditional write with IfNoneMatch: *) and falls back to _update_info(mark=True). This is safe because the info object is only created after the file object has been fully written and its digest verified. The fallback simply updates the metadata of an already-valid info object.
MirrorPartAction abort path: When _info_exists returns True, the handler aborts the in-progress multipart upload and calls _update_info(mark=True). This is safe because:
- The info object's existence implies another worker already completed the upload and verified the digest
- abort_multipart_upload is idempotent — aborting a non-existent upload is a no-op
- _update_info(mark=True) only touches the metadata, not the file content
No new external inputs: The changes don't introduce new API endpoints, parameters, or deserialization of untrusted data. All data flow remains internal (SQS messages between Lambda invocations within the same AWS account).
No credential changes: No modifications to IAM policies, S3 bucket policies, or authentication logic.
Resource cleanup: Aborted multipart uploads are properly cleaned up via abort_multipart_upload, preventing storage leaks from incomplete uploads.

hannes-ucsc · 2026-07-07T12:30:03Z

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Handle the race condition where multiple MirrorFileActions for files with the same digest but different UUIDs concurrently create info objects. Extract `_create_or_update_info` to catch `StorageObjectExists` from `_create_info` and fall back to `_update_info`. Trailer: Claude-Code Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add test that verifies MirrorPartAction aborts the upload early when the info object already exists, instead of continuing to upload parts. Trailer: Claude-Code Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Check for the info object before each part upload in MirrorPartAction. If it exists, another worker already completed the upload, so abort the multipart upload and update the info object instead of continuing. Also extract _create_or_update_info to handle the race in both the single-upload and multi-part finalization paths. Trailer: Claude-Code Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

hannes-ucsc requested a review from dsotirho-ucsc as a code owner July 4, 2026 06:37

hannes-ucsc self-assigned this Jul 4, 2026

hannes-ucsc force-pushed the issues/hannes-ucsc/8142-storage-object-exists branch from 92778a3 to 6e1cb13 Compare July 5, 2026 20:57

hannes-ucsc linked an issue Jul 6, 2026 that may be closed by this pull request

StorageObjectExists error when mirroring anvil14 #8142

Open

hannes-ucsc force-pushed the issues/hannes-ucsc/8142-storage-object-exists branch 2 times, most recently from e3d45a3 to 8847fbe Compare July 7, 2026 07:43

hannes-ucsc assigned dsotirho-ucsc Jul 7, 2026

dsotirho-ucsc approved these changes Jul 8, 2026

View reviewed changes

dsotirho-ucsc assigned nadove-ucsc and unassigned dsotirho-ucsc Jul 8, 2026

hannes-ucsc linked an issue Jul 8, 2026 that may be closed by this pull request

NoSuchUpload error when mirroring anvil14 #8143

Open

hannes-ucsc and others added 14 commits July 9, 2026 15:00

Add --no-api flag to pull_request.py

1a23dad

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add --no-upgrade flag to pull_request.py

94ca60b

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Batch label operations into single gh command in pull_request.py

9c032fe

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add --no-deploy flag to pull_request.py

16ecbd0

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Fix: make isort misclassifies our urllib3_mock

641c42f

Fix missing newling between import sections

8ba5cf4

Add make isort to CI dirty check

02bcc93

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Move label list population into variable scope in pull_request.py

e1073a2

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add --no-hotfix flag to pull_request.py

7ce268f

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Drive --no-* flags from dict in pull_request.py

9b6efd4

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Add --vanilla flag to pull_request.py (#7974)

a71f1c3

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

[1/2] Abort redundant multi-part upload if file was already mirrored

2ad85ff

Add test that verifies MirrorPartAction aborts the upload early when the info object already exists, instead of continuing to upload parts. Trailer: Claude-Code Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

nadove-ucsc force-pushed the issues/hannes-ucsc/8142-storage-object-exists branch from 8847fbe to 496c0fd Compare July 9, 2026 22:01

nadove-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Jul 9, 2026

nadove-ucsc merged commit 1604246 into develop Jul 9, 2026
10 checks passed

nadove-ucsc deleted the issues/hannes-ucsc/8142-storage-object-exists branch July 10, 2026 00:22

nadove-ucsc assigned nadove-ucsc and unassigned hannes-ucsc and nadove-ucsc Jul 10, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Fix: StorageObjectExists error when mirroring anvil14 (#8142)#8163

Fix: StorageObjectExists error when mirroring anvil14 (#8142)#8163
nadove-ucsc merged 14 commits into
developfrom
issues/hannes-ucsc/8142-storage-object-exists

hannes-ucsc commented Jul 4, 2026 •

edited by nadove-ucsc

Loading

Uh oh!

codecov Bot commented Jul 5, 2026 •

edited

Loading

Uh oh!

coveralls commented Jul 5, 2026 •

edited

Loading

Uh oh!

hannes-ucsc commented Jul 7, 2026

Uh oh!

hannes-ucsc commented Jul 7, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Uh oh!

Conversation

hannes-ucsc commented Jul 4, 2026 • edited by nadove-ucsc Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Checklist

Author

Author (partiality)

Author (reindex)

Author (mirror)

Author (API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

Operator (merge the branch)

Operator (main build)

Operator (reindex)

Operator (mirroring)

Operator

Shorthand for review comments

Uh oh!

codecov Bot commented Jul 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

coveralls commented Jul 5, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

hannes-ucsc commented Jul 7, 2026

Security Design Review

Scope

Threat Model

Findings

Uh oh!

hannes-ucsc commented Jul 7, 2026

Security design review

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

hannes-ucsc commented Jul 4, 2026 •

edited by nadove-ucsc

Loading

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

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

codecov Bot commented Jul 5, 2026 •

edited

Loading

coveralls commented Jul 5, 2026 •

edited

Loading