Fix: Cannot generate unfiltered JSONL manifest in AnVIL (#7190) #7225

nadove-ucsc · 2025-06-17T07:22:50Z

Connected issues: #7190

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 fixups from prior reviews
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}

Peer reviewer (after approval)

Actually approved the PR
PR is not a draft
Ticket is in Review requested column
PR is awaiting requested review from system administrator
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 · 2025-06-17T07:46:44Z

Codecov Report

Attention: Patch coverage is 97.50000% with 2 lines in your changes missing coverage. Please review.

Please upload report for BASE (develop@a5515a3). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
src/azul/service/manifest_service.py	98.73%	1 Missing ⚠️
src/azul/service/storage_service.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             develop    #7225   +/-   ##
==========================================
  Coverage           ?   85.03%           
==========================================
  Files              ?      156           
  Lines              ?    22452           
  Branches           ?        0           
==========================================
  Hits               ?    19091           
  Misses             ?     3361           
  Partials           ?        0

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coveralls · 2025-06-17T09:28:57Z

coverage: 85.207% (+0.01%) from 85.196%
when pulling f3be2d1 on issues/nadove-ucsc/7190-cannot-generate-unfiltered-jsonl-manifest
into a5515a3 on develop.

dsotirho-ucsc

Approved.

hannes-ucsc · 2025-07-09T01:17:53Z

src/azul/service/storage_service.py

@@ -329,7 +329,7 @@ def _handle_overwrite(self,
                          object_key: str
                          ):
        error = exception.response['Error']
-        code, condition = error['Code'], error['Condition']
+        code, condition = error['Code'], error.get('Condition')


PL, commit title misleading

Added comment to explain when the KeyError occurs. Agreed at PL that this is sufficient.

hannes-ucsc · 2025-07-09T01:21:50Z