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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¹ when the issue title describes a problem, the corresponding PR
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Shorthand for review comments

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 84.97%. Comparing base (e9b8597) to head (ae153ae).
⚠️ Report is 16 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7877      +/-   ##
===========================================
+ Coverage    84.93%   84.97%   +0.03%     
===========================================
  Files          161      161              
  Lines        23130    23189      +59     
===========================================
+ Hits         19646    19704      +58     
- Misses        3484     3485       +1

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coveralls · 2026-03-17T18:34:59Z

coverage: 85.113% (+0.03%) from 85.08%
when pulling ae153ae on issues/dsotirho-ucsc/7128-tissue-atlas
into e9b8597 on 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

src/azul/service/query_service.py

+            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

src/azul/service/query_service.py

                        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

src/azul/service/query_service.py

+                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.

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

Add tests

Implement support for aggregation of a nested field

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.

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

Open

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7128-tissue-atlas branch from a5fa3db to 3fb45f1 Compare March 17, 2026 17:44

dsotirho-ucsc added reindex:dev [process] PR requires reindexing dev reindex:prod [process] PR requires reindexing prod labels Mar 17, 2026

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7128-tissue-atlas branch from 3fb45f1 to 95a800d Compare March 17, 2026 18:22

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7128-tissue-atlas branch 3 times, most recently from 080a58a to da4787e Compare March 23, 2026 23:49

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7128-tissue-atlas branch 5 times, most recently from 1798785 to c0b9465 Compare March 30, 2026 23:29

dsotirho-ucsc requested a review from achave11-ucsc March 31, 2026 16:21

dsotirho-ucsc assigned achave11-ucsc Mar 31, 2026

achave11-ucsc requested changes Apr 1, 2026

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achave11-ucsc assigned dsotirho-ucsc and unassigned dsotirho-ucsc and achave11-ucsc Apr 1, 2026

dsotirho-ucsc added 6 commits April 1, 2026 13:55

Remove obsolete FIXME (#3413)

d67c292

Remove unneeded recursion call

84aeae0

Refactor method

7802005

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

07ad541

Add tests

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

c0da817

Implement support for aggregation of a nested field

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

ae153ae

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/7128-tissue-atlas branch from c0b9465 to d67c292 Compare April 1, 2026 23:29

dsotirho-ucsc requested a review from achave11-ucsc April 2, 2026 01:18

dsotirho-ucsc assigned achave11-ucsc Apr 2, 2026

achave11-ucsc approved these changes Apr 6, 2026

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achave11-ucsc marked this pull request as ready for review April 6, 2026 18:18

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc Apr 6, 2026

achave11-ucsc requested a review from hannes-ucsc April 6, 2026 18:18

hannes-ucsc requested changes Apr 10, 2026

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hannes-ucsc added the 1 review [process] Lead requested changes once label Apr 10, 2026

hannes-ucsc removed their assignment Apr 10, 2026

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dsotirho-ucsc commented Mar 17, 2026 •

edited by achave11-ucsc

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