Add support for HCA tissue atlas (#7128) by dsotirho-ucsc · Pull Request #7877 · DataBiosphere/azul

dsotirho-ucsc · 2026-03-17T17:30:40Z

Linked issues: #7128

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L line is too long
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codecov · 2026-03-17T18:33:52Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.92%. Comparing base (604ff11) to head (5b5526f).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7877      +/-   ##
===========================================
+ Coverage    84.88%   84.92%   +0.03%     
===========================================
  Files          164      164              
  Lines        23511    23578      +67     
===========================================
+ Hits         19958    20024      +66     
- Misses        3553     3554       +1

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coveralls · 2026-03-17T18:34:59Z

coverage: 85.006% (+0.04%) from 84.968% — issues/dsotirho-ucsc/7128-tissue-atlas into develop

dsotirho-ucsc · 2026-03-31T16:20:19Z

7877_IT_2026-03-30.txt

achave11-ucsc

Looking good,

Consider adding the testing infra in an initial (maybe split) commit, it gives a stronger signal. As well a test case for None namespace in Nested.to_index/from_index round-trip.

achave11-ucsc · 2026-04-01T15:51:56Z

+            path = dotted(facet_path, 'keyword')
+            nested_agg.bucket(name='myTerms',
+                              agg_type='terms',
+                              field=path,
+                              size=config.terms_aggregation_size)
+            nested_agg.bucket('untagged', 'missing', field=path)


Since this is the same type of invocation as the one below, isn't a FIXME in order?

Additionally, you should consider not duplicating the section and just having the one FIXME, as it is now.

The FIXME is for a closed/invalid isseue (#3413). Removed.

achave11-ucsc · 2026-04-01T16:16:19Z

                        bucket['key'] = field_type.from_index(bucket['key'])
                        translate(k, bucket)
                try:
+                    # From a MultiTerms aggregation


Consider elaborating on this comment (and perhaps also the one in L423) as to why the MultiTerms aggregation isn't recursive.

Lastly, this comment is misplaced. It should be part of the commit which introduced the change.

achave11-ucsc · 2026-04-01T16:19:55Z

+                try:
+                    paths = v['meta']['paths']
+                except KeyError:
+                    pass
+                else:
+                    for i, path in enumerate(paths):
+                        field_type = self.service.field_type(self.catalog, tuple(path))
+                        for bucket in buckets:
+                            bucket['key'][i] = field_type.from_index(bucket['key'][i])


I don't think this is semantically neutral. Consider adding this as a subsequent commit or squashing it with the main changes.

Also, consider elaborating on the "Refactor method" commit message by adding some context, if you do decide to keep it.

This section should have been in the main commit, not the refactoring commit. Moved.

dsotirho-ucsc · 2026-04-01T23:28:47Z

As well a test case for None namespace in Nested.to_index/from_index round-trip.

The bundle 2c7d06b8 used in the new test cases contains both {'atlas': 'Lung', 'version': None} and {'atlas': None, 'version': None} tissue atlas values, which are confirmed to be translated with ~null in the test added to test_indexer.py, and translated back to None in the test added to test_response.py.

dsotirho-ucsc · 2026-04-02T01:18:29Z

7877_IT_2026-04-01.txt

achave11-ucsc

Approved ✅

hannes-ucsc

As agreed in PL, try to feed the field types to the make_terms code which post-processes the OpenSearch aggregation results. Avoid duplicating hard-coded aggregation names (e.g. reverseNested). Use the field type to decide how to processes the agg results, not the presence of an aggregation name. Try to eliminate the need for an reverse_nested aggregation by removing the duplicate entries in the index.

            # does not undergo translation
        )

+    @cache


dsotirho-ucsc · 2026-04-21T18:44:51Z

7877_IT_2026-04-21.txt

hannes-ucsc · 2026-04-30T15:21:18Z

+    def to_index(self, value: JSON) -> JSON:
+        return {
+            field: field_type.to_index(value[field])
+            for field, field_type in self.properties.items()
+        }
+
+    def from_index(self, value: JSON) -> JSON:
+        return {
+            field: field_type.from_index(value[field])
+            for field, field_type in self.properties.items()
+        }


This comment was generated by Claude Code.

With these two overrides, does it still make sense for Nested to inherit PassThrough?

The defining characteristic of PassThrough is that to_index and from_index are identity operations. After this change, Nested overrides both with non-trivial logic that delegates to per-property field types — the values are no longer "passed through" unchanged.

What Nested still gets from PassThrough:

The es_type property (trivial — stores and returns _es_type)

allow_sorting_by_empty_lists = False

The __init__ convenience of setting both native_form and index_form to the same type (JSON)

All three are easy to replicate by inheriting FieldType[JSON, JSON] directly.

hannes-ucsc · 2026-04-30T15:23:24Z

                    field_type = self.service.field_type(self.catalog, tuple(path))
                    for bucket in buckets:
                        bucket['key'] = field_type.from_index(bucket['key'])
-                        translate(k, bucket)


PL to explain why

I was mistaken in thinking that this is no longer needed. We still have occurrences of nested agg buckets such as in the HCA agg project.

Please don't ignore my PL request.

Decided in PL to refactor the changes to the translation of aggregates (_translate_response_aggs()) in order to remove duplication. This will be done by using the existing meta field path when annotating both kinds of aggregates (MultiTerms and not MultiTerms), instead of adding a new meta field paths specifically for MultiTerms aggregates.

hannes-ucsc · 2026-04-30T15:26:25Z

                     type='terms')

    def make_facets(self, aggs: JSON) -> dict[str, Terms]:
+        field_types = self.service.field_types_by_name(self.catalog)


Please familiarize yourself with what the "Pull up method" refactoring does. This change is not that.

Add tests

Implement support for aggregation of a nested field

dsotirho-ucsc · 2026-05-01T00:22:47Z

7877_IT_2026-04-30.txt

hannes-ucsc

#7877 (comment)

dsotirho-ucsc self-assigned this Mar 17, 2026

dsotirho-ucsc linked an issue Mar 17, 2026 that may be closed by this pull request

Add support for HCA tissue atlas #7128

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Comment thread src/azul/indexer/document_service.py

# does not undergo translation

)

@cache

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dsotirho-ucsc added 7 commits April 30, 2026 10:19

Remove obsolete FIXME (#3413)

1065984

Change test data to use a valid HCA facet name

68d8af0

Refactor method

a3f15bb

Refactor functionality from QueryController into DocumentService

8b17022

[1/2] Add support for HCA tissue atlas (#7128)

aabb30f

Add tests

[r 2/2] Add support for HCA tissue atlas (#7128)

8b5b645

Implement support for aggregation of a nested field

fixup! [r 2/2] Add support for HCA tissue atlas (#7128)

5b5526f

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dsotirho-ucsc commented Mar 17, 2026 •

edited by achave11-ucsc

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