Fix: Accumulator overflow during aggregation (#6793) #7641

dsotirho-ucsc · 2025-12-12T19:27:47Z

Linked issues: #6793

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 · 2025-12-16T18:20:26Z

Codecov Report

❌ Patch coverage is 99.02913% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 84.88%. Comparing base (4ef3ad2) to head (c90ae5c).
⚠️ Report is 11 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/azul/plugins/metadata/hca/indexer/aggregate.py	98.36%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7641      +/-   ##
===========================================
+ Coverage    84.82%   84.88%   +0.06%     
===========================================
  Files          156      156              
  Lines        22862    22969     +107     
===========================================
+ Hits         19393    19498     +105     
- Misses        3469     3471       +2

☔ View full report in Codecov by Sentry.
📢 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 · 2025-12-16T18:21:31Z

coverage: 85.106% (+0.06%) from 85.047%
when pulling c90ae5c on issues/dsotirho-ucsc/6793-accumulator-overflow
into 4ef3ad2 on develop.

…#6793)

…6793)

)

…6793)

dsotirho-ucsc · 2026-01-08T16:28:23Z

7641_IT_2026-01-07.txt

nadove-ucsc

Checklist was incomplete, although the relevant actions had all been taken

Don't need to see each commit pushed separately going forward

nadove-ucsc · 2026-01-08T22:44:23Z

src/azul/plugins/metadata/anvil/indexer/aggregate.py

-    pass
+
+    def _accumulator(self, field: str) -> Accumulator | None:
+        # dataset.document_id aggregation is required for creating of manifests


Either "creating manifests" or "creation of manifests", not "creating of"

Also it would be useful to record why the field is required, i.e., what the symptom of failure would be if it were to be removed.

nadove-ucsc · 2026-01-08T22:52:10Z

src/azul/plugins/metadata/anvil/indexer/aggregate.py

+        if field in ('activity_id', 'document_id', 'source_datarepo_row_ids'):
+            # Added to the files aggregate in order to be included in manifests
+            if self.outer_entity_type == 'files':
+                return super()._accumulator(field)
+            else:
+                return None
+        else:
+            return super()._accumulator(field)


Nitpick: each of these could be rewritten as:

Suggested change

if field in ('activity_id', 'document_id', 'source_datarepo_row_ids'):

# Added to the files aggregate in order to be included in manifests

if self.outer_entity_type == 'files':

return super()._accumulator(field)

else:

return None

else:

return super()._accumulator(field)

# Added to the files aggregate in order to be included in manifests

if field in ('activity_id', 'document_id', 'source_datarepo_row_ids') and self.outer_entity_type != 'files':

return None

else:

return super()._accumulator(field)

Which I personally think is cleaner since it reduces the number of return pathways and keeps a consistent, flat level of nesting. But it does cause issues with line length, and there's also an argument to be made that keeping the return statements separate is the more resilient approach.

nadove-ucsc · 2026-01-08T22:57:32Z

src/azul/plugins/metadata/anvil/indexer/aggregate.py

+
+    def _accumulator(self, field: str) -> Accumulator | None:
+        if field in ('document_id', 'donor_id', 'source_datarepo_row_ids'):
+            # Added to the files aggregate in order to be included in manifests


Grammar nit

Suggested change

# Added to the files aggregate in order to be included in manifests

# Add to the files aggregate so that it can be included in manifests

nadove-ucsc · 2026-01-08T22:58:41Z

src/azul/plugins/metadata/hca/indexer/aggregate.py

+            return SetAccumulator(max_size=200)
+        elif field == 'organism_age_range':
+            return SetAccumulator(max_size=200)
+        elif field == 'organism_age':


Was it intentional to keep these separate?

nadove-ucsc · 2026-01-08T23:03:09Z

src/azul/plugins/metadata/hca/indexer/aggregate.py

-    pass
+
+    def _accumulator(self, field) -> Accumulator | None:
+        return super()._accumulator(field)


What's the point of adding these here? Surely the diff on subsequent commits would be cleaner if they were removed?

nadove-ucsc · 2026-01-08T23:03:35Z

src/azul/plugins/metadata/anvil/indexer/aggregate.py

 class ActivityAggregator(SimpleAggregator):
-    pass
+
+    def _accumulator(self, field: str) -> Accumulator | None:


Again, don't see the point of this

dsotirho-ucsc self-assigned this Dec 12, 2025

dsotirho-ucsc linked an issue Dec 12, 2025 that may be closed by this pull request

Accumulator overflow during aggregation #6793

Open

3 tasks

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6793-accumulator-overflow branch 3 times, most recently from d47920c to 8248dae Compare December 16, 2025 18:06

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6793-accumulator-overflow branch 3 times, most recently from be95d6d to 061cc73 Compare December 19, 2025 18:57

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6793-accumulator-overflow branch 6 times, most recently from 2c1ed6b to 8733d33 Compare January 7, 2026 17:46

dsotirho-ucsc requested a review from nadove-ucsc January 7, 2026 23:30

dsotirho-ucsc assigned nadove-ucsc Jan 7, 2026

dsotirho-ucsc added reindex:dev [process] PR requires reindexing dev reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod reindex:prod [process] PR requires reindexing prod labels Jan 7, 2026

dsotirho-ucsc removed the request for review from nadove-ucsc January 7, 2026 23:32

dsotirho-ucsc unassigned nadove-ucsc Jan 7, 2026

dsotirho-ucsc added the API API change affecting callers label Jan 7, 2026

dsotirho-ucsc added 5 commits January 7, 2026 15:36

Remove files.version from HCA response (#6793)

b4de0da

[A] Remove sort & filter key sampleId from HCA (#6793)

d220c03

Refactor HCA aggregators

4ba906f

[r] Remove aggregation of cell_suspensions.document_id in HCA (#6793)

0306ca3

[r] Remove aggregation of cell_suspensions.biomaterial_id in HCA (#6793)

4b2588e

dsotirho-ucsc added 24 commits January 7, 2026 15:41

[r] Remove aggregation of activities.document_id in AnVIL (#6793)

18a3dc8

[r] Remove aggregation of activities.source_datarepo_row_ids in AnVIL (…

a53f8a3

…#6793)

[r] Remove aggregation of biosamples.biosample_id in AnVIL (#6793)

17e9939

[r] Remove aggregation of biosamples.document_id in AnVIL (#6793)

a08f757

[r] Remove aggregation of biosamples.source_datarepo_row_ids in AnVIL (…

346dfa7

…#6793)

[r] Remove aggregation of datasets.source_datarepo_row_ids in AnVIL (#…

bf334f8

…6793)

[r] Remove aggregation of diagnoses.diagnosis_id in AnVIL (#6793)

c13cbab

[r] Remove aggregation of diagnoses.document_id in AnVIL (#6793)

926df11

[r] Remove aggregation of diagnoses.source_datarepo_row_ids in AnVIL (#…

acac60e

…6793)

[r] Remove aggregation of donors.document_id in AnVIL (#6793)

f7368bd

[r] Remove aggregation of donors.donor_id in AnVIL (#6793)

4077d82

[r] Remove aggregation of donors.source_datarepo_row_ids in AnVIL (#6793

06690ab

)

[r] Remove aggregation of files.document_id in AnVIL (#6793)

4fde1d3

[r] Remove aggregation of files.drs_uri in AnVIL (#6793)

11c58fa

[r] Remove aggregation of files.file_id in AnVIL (#6793)

38a6058

[r] Remove aggregation of files.file_md5sum in AnVIL (#6793)

fb233bf

[r] Remove aggregation of files.file_name in AnVIL (#6793)

b1116ea

[r] Remove aggregation of files.source_datarepo_row_ids in AnVIL (#6793)

5d58065

[r] Remove aggregation of files.version in AnVIL (#6793)

6e39e8b

[r] Increase accumulator limit for donors.development_stage in HCA (#…

26bce55

…6793)

[r] Increase accumulator limit for donors.organism_age_range in HCA (#…

a2bac0f

…6793)

[r] Increase accumulator limit for donors.organism_age in HCA (#6793)

936def6

[r] Increase accumulator limit for matrices.file in HCA (#6793)

be80b78

[r] Increase accumulator limit for diagnoses.disease in AnVIL (#6793)

c90ae5c

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6793-accumulator-overflow branch from 8403e69 to b4de0da Compare January 7, 2026 23:42

dsotirho-ucsc requested a review from nadove-ucsc January 8, 2026 16:28

dsotirho-ucsc assigned nadove-ucsc Jan 8, 2026

nadove-ucsc requested changes Jan 8, 2026

View reviewed changes

nadove-ucsc removed their assignment Jan 8, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Fix: Accumulator overflow during aggregation (#6793) #7641

Fix: Accumulator overflow during aggregation (#6793) #7641

Uh oh!

dsotirho-ucsc commented Dec 12, 2025 •

edited

Loading

Uh oh!

codecov bot commented Dec 16, 2025 •

edited

Loading

Uh oh!

coveralls commented Dec 16, 2025 •

edited

Loading

Uh oh!

dsotirho-ucsc commented Jan 8, 2026

Uh oh!

nadove-ucsc left a comment

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

nadove-ucsc Jan 8, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

	# Added to the files aggregate in order to be included in manifests
	# Add to the files aggregate so that it can be included in manifests

Fix: Accumulator overflow during aggregation (#6793) #7641

Are you sure you want to change the base?

Fix: Accumulator overflow during aggregation (#6793) #7641

Uh oh!

Conversation

dsotirho-ucsc commented Dec 12, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Checklist

Author

Author (partiality)

Author (reindex)

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 Dec 16, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

coveralls commented Dec 16, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

dsotirho-ucsc commented Jan 8, 2026

Uh oh!

nadove-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

nadove-ucsc Jan 8, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

dsotirho-ucsc commented Dec 12, 2025 •

edited

Loading

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

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

codecov bot commented Dec 16, 2025 •

edited

Loading

coveralls commented Dec 16, 2025 •

edited

Loading