Rename files.url to files.azul_file_url for AnVIL (#6549) #7247

dsotirho-ucsc · 2025-06-27T00:50:15Z

Connected issues: #6549

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test/service/test_response_anvil.py

codecov · 2025-06-27T18:52:22Z

Codecov Report

Attention: Patch coverage is 63.63636% with 8 lines in your changes missing coverage. Please review.

Project coverage is 85.06%. Comparing base (e993592) to head (ffd09c2).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	8 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7247      +/-   ##
===========================================
- Coverage    85.08%   85.06%   -0.02%     
===========================================
  Files          155      155              
  Lines        22369    22389      +20     
===========================================
+ Hits         19033    19046      +13     
- Misses        3336     3343       +7

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coveralls · 2025-06-27T18:53:38Z

coverage: 85.246% (-0.02%) from 85.263%
when pulling ffd09c2 on issues/dsotirho-ucsc/6549-rename-anvil-fields
into e993592 on develop.

dsotirho-ucsc · 2025-07-01T17:32:04Z

7247_IT_2025-07-01.txt

nadove-ucsc · 2025-07-03T00:36:09Z

src/azul/plugins/metadata/hca/__init__.py

@@ -297,6 +298,9 @@ def special_fields(self) -> SpecialFields:
                             bundle_version='bundleVersion',
                             root_entity_id='projectId')

+    def modify_hits(self, hits: MutableJSONs) -> None:
+        return None


Suggested change

return None

pass

Since the return value is not meant to be used

nadove-ucsc · 2025-07-03T00:45:50Z

src/azul/service/repository_service.py

@@ -175,6 +177,8 @@ def inject_file_urls(node: AnyMutableJSON, *path: str) -> None:
        inject_file_urls(response['hits'], 'projects', 'matrices')
        inject_file_urls(response['hits'], 'files')

+        self.metadata_plugin(catalog).modify_hits(response['hits'])
+


The injection of the file URLs on the preceding lines is also a plugin-specification modification of the hits, since it references HCA-specific entity types (projects, matrices, etc). I think we should try to integrate those calls into this method.

Perhaps the injection of the accessible field could go into the method body in the superclass.

nadove-ucsc · 2025-07-03T00:51:37Z

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

-                    ]
-                    if self.entity_type == 'donors' else
-                    []
-                )


The aggregations for these fields may be very large in dataset inner entities. Are we sure we want to include them?

nadove-ucsc · 2025-07-03T00:55:00Z

src/azul/plugins/metadata/anvil/__init__.py

+        for hit in hits:
+            for file in hit['files']:
+                # The fields `uuid` and `version` are included in the response
+                # so they can be used to inject file URLs (see


I think that injection should be done in a call to super().modify_hits() here. This would require changing inject_file_urls from a local function to a (private) method in MetadataPlugin.

Side note/nitpick: consider changing the signature to modify_hit(self, hit: MutableJSON) -> None and move the loop to the call site.

github-actions bot added the orange [process] Done by the Azul team label Jun 27, 2025

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6549-rename-anvil-fields branch from 29ffab0 to a98a2e7 Compare June 27, 2025 18:12

github-advanced-security bot found potential problems Jun 27, 2025

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test/service/test_response_anvil.py Fixed Show fixed Hide fixed

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dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6549-rename-anvil-fields branch 2 times, most recently from 9697963 to d0e6b0d Compare June 27, 2025 18:28

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6549-rename-anvil-fields branch from d0e6b0d to c5aa9b9 Compare June 27, 2025 21:50

dsotirho-ucsc added partial [process] PR is does not completely resolve associated ticket reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Jun 27, 2025

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6549-rename-anvil-fields branch 2 times, most recently from ac252e3 to 2616ad0 Compare June 30, 2025 23:48

dsotirho-ucsc added 12 commits July 1, 2025 09:05

Add biosamples.apriori_cell_type to AnVIL response (#6549)

281c673

Add datasets.consent_group to AnVIL response (#6549)

f402c07

Add datasets.data_modality to AnVIL response (#6549)

08babd0

Add datasets.data_use_permission to AnVIL response (#6549)

9107761

Add datasets.owner to AnVIL response (#6549)

ca8acf5

Add datasets.principal_investigator to AnVIL response (#6549)

869af23

Add datasets.registered_identifier to AnVIL response (#6549)

60e5b22

Add diagnosis.diagnosis_age & onset_age to AnVIL response (#6549)

42d4aa0

[r] Remove files.name and size from AnVIL response (#6549)

4d31670

Remove files.uuid & version from AnVIL response (#6549)

668f6f3

[p] Rename files.url to files.azul_file_url for AnVIL (#6549)

602aaa2

Add FIXME (#6549)

ffd09c2

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6549-rename-anvil-fields branch from 2616ad0 to ffd09c2 Compare July 1, 2025 16:06

dsotirho-ucsc requested a review from nadove-ucsc July 1, 2025 17:32

dsotirho-ucsc assigned nadove-ucsc Jul 1, 2025

nadove-ucsc requested changes Jul 3, 2025

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nadove-ucsc removed their assignment Jul 3, 2025

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Rename files.url to files.azul_file_url for AnVIL (#6549) #7247

Rename files.url to files.azul_file_url for AnVIL (#6549) #7247

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Rename files.url to files.azul_file_url for AnVIL (#6549) #7247

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