Fix: Accumulator overflow during aggregation (#6793) by dsotirho-ucsc · Pull Request #7641 · DataBiosphere/azul

dsotirho-ucsc · 2025-12-12T19:27:47Z

Linked issues: #6793

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codecov · 2025-12-16T18:20:26Z

Codecov Report

❌ Patch coverage is 97.59036% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.85%. Comparing base (8d9eb5c) to head (1ee87e7).

Files with missing lines	Patch %	Lines
src/azul/indexer/aggregate.py	0.00%	1 Missing ⚠️
src/azul/plugins/metadata/hca/indexer/aggregate.py	98.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7641      +/-   ##
===========================================
+ Coverage    84.82%   84.85%   +0.02%     
===========================================
  Files          157      157              
  Lines        23060    23117      +57     
===========================================
+ Hits         19561    19616      +55     
- Misses        3499     3501       +2

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

coverage: 85.074% (+0.03%) from 85.046%
when pulling 1ee87e7 on issues/dsotirho-ucsc/6793-accumulator-overflow
into 8d9eb5c on develop.

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

Adding fixup commits for this would have nearly doubled the count of commits, so I've squashed this change into the existing commits.

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?

No. I've combined them in the fixup commit.

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?

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

…d document_id in HCA (#6793)

…6793)

…t_id in HCA (#6793)

…nd document_id in HCA (#6793)

…n HCA (#6793)

…ent_id in HCA (#6793)

)

dsotirho-ucsc · 2026-02-03T16:48:14Z

7641_IT_2026-02-02-anvil.txt
7641_IT_2026-02-02-hca.txt

hannes-ucsc

Until further notice, please push commits individually. Ask on Slack for advice on how to automate that.

hannes-ucsc · 2026-02-04T17:34:20Z

src/azul/plugins/metadata/hca/service/response.py

            'size': file.get('size'),
            'fileSource': file.get('file_source'),
            self.plugin.special_fields.file_uuid.name_in_hit: file.get('uuid'),
-            'version': file.get('version'),


Why are we removing the version?

hannes-ucsc · 2026-02-04T18:07:37Z

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

+            'document_id',
+            'source_datarepo_row_ids'
+        } and self.outer_entity_type != 'files':
+            # These fields are removed from all aggregations, except file


In the context of indexing, aggregation is a process, and aggregate is the output of that process. Make sure you don't conflate these two anywhere.

Suggested change

# These fields are removed from all aggregations, except file

# These fields are only aggregated for files, where they are needed for manifests

PL: Which manifests

hannes-ucsc · 2026-02-04T18:10:15Z

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

+            # If any dataset IDs are missing from the aggregate, those datasets
+            # will be omitted during the verbatim handover. Datasets are a "hot"
+            # entity type, and we can't track their hubs in replica documents,
+            # so we rely on the inner entity IDs instead. We also need to
+            # aggregate document_id to allow filtering by the value on
+            # non-dataset endpoints.


PL: hypothetical; datasets don't have hubs, replicas do, "the value"

@hannes-ucsc: "I think I'm wrong about one thing: If replicas have hubs, then replicas of datasets have hubs, therefor datasets have hubs."

Also find a a good place to include this ascii chart

┏━━━━━━━━━━━━━━━━━━┓ ┃ Project replica ┃ ┃ ┃ ┣━━━━━━━━━━━━━━━━━━┫ ┏━━━━━━━━━━━━━━━━━━┓ ┃ entity_id ┃◀─┐ ┃ File replica ┃ ┣━━━━━━━━━━━━━━━━━━┫ │ ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ ┃ ┃ hub_ids ┃ │ ┃ File aggregate ┃ ┣━━━━━━━━━━━━━━━━━━┫ ┗━━━━━━━━━━━━━━━━━━┛ │ ┃ ┃ ┌─▶┃ entity_id ┃ │ ┣━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫ │ ┣━━━━━━━━━━━━━━━━━━┫ ┏━━━━━━━━━━━━━━━━━━┓ │ ┃ entity_id ┃──┼─▶┃ hub_ids ┃ ┃ Donor replica ┃ │ ┣━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫ │ ┗━━━━━━━━━━━━━━━━━━┛ ┃ ┃ └──┃ contents.projects.document_id ┃ │ ┣━━━━━━━━━━━━━━━━━━┫ ┣━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫ │ ┏━━━━━━━━━━━━━━━━━━┓ ┃ entity_id ┃◀────┃ contents.donors.document_id ┃ │ ┃ Specimen replica ┃ ┣━━━━━━━━━━━━━━━━━━┫ ┣━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫ │ ┃ ┃ ┃ hub_ids ┃ ┌──┃ contents.protocols.document_id ┃ │ ┣━━━━━━━━━━━━━━━━━━┫ ┗━━━━━━━━━━━━━━━━━━┛ │ ┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛ │ ┃ entity_id ┃ │ │ ┣━━━━━━━━━━━━━━━━━━┫ ┏━━━━━━━━━━━━━━━━━━┓ │ └─▶┃ hub_ids ┃ ┃ Protocol replica ┃ │ ┗━━━━━━━━━━━━━━━━━━┛ ┃ ┃ │ ┣━━━━━━━━━━━━━━━━━━┫ │ ┃ entity_id ┃◀─┘ ┣━━━━━━━━━━━━━━━━━━┫ ┃ hub_ids ┃ ┗━━━━━━━━━━━━━━━━━━┛

hannes-ucsc · 2026-02-04T18:11:12Z

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

                                        key=compose_keys(none_safe_tuple_key(none_last=True),
                                                         itemgetter('lte', 'gte')))
+        elif field == 'disease':
+            return SetAccumulator(max_size=17700)


hannes-ucsc · 2026-02-04T18:12:21Z

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


    def _accumulator(self, field: str) -> Accumulator | None:
-        if field in ('count', 'file_size'):
+        if field in {


hannes-ucsc · 2026-02-04T18:15:15Z

src/azul/service/manifest_service.py

            document_ids = [
                document_id
                for entity_type in self.hot_entity_types
+                # Some "hot" entity types may be missing from hit['contents']


PL: What's an empty inner entity, why is it "empty" and which types can be "empty"?

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

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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 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

dsotirho-ucsc added 17 commits February 2, 2026 16:56

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

b0d8a0a

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

6ee504c

[r] Increase accumulator limit for cell_suspensions.biomaterial_id an…

55359fc

…d document_id in HCA (#6793)

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

5c1e7e0

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

93974aa

…6793)

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

8612d2b

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

0a98c07

…6793)

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

bc3b3ec

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

f4289b1

[r] Increase accumulator limit for samples.biomaterial_id and documen…

c623fe3

…t_id in HCA (#6793)

[r] Increase accumulator limit for sequencing_inputs.biomaterial_id a…

b5fa97e

…nd document_id in HCA (#6793)

[r] Increase accumulator limit for sequencing_processes.document_id i…

743ecdb

…n HCA (#6793)

[r] Increase accumulator limit for specimens.biomaterial_id and docum…

6581ea7

…ent_id in HCA (#6793)

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

5da25a1

Raise exception if aggregation drops values, remove FIXMEs (#6793)

0bc0223

fixup! Raise exception if aggregation drops values, remove FIXMEs (#6793

581e0d9

)

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1ee87e7

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6793-accumulator-overflow branch from abca22d to 1ee87e7 Compare February 3, 2026 04:46

dsotirho-ucsc requested a review from nadove-ucsc February 3, 2026 16:48

dsotirho-ucsc assigned nadove-ucsc Feb 3, 2026

nadove-ucsc approved these changes Feb 3, 2026

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nadove-ucsc removed their assignment Feb 3, 2026

nadove-ucsc marked this pull request as ready for review February 3, 2026 20:34

nadove-ucsc requested a review from hannes-ucsc as a code owner February 3, 2026 20:34

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hannes-ucsc requested changes Feb 4, 2026

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hannes-ucsc assigned dsotirho-ucsc and unassigned dsotirho-ucsc and hannes-ucsc Feb 4, 2026

	# 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

	# These fields are removed from all aggregations, except file
	# These fields are only aggregated for files, where they are needed for manifests

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dsotirho-ucsc commented Dec 12, 2025 •

edited by nadove-ucsc

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