Fix: curl manifest futilely includes external LungMAP files (#8027) by nadove-ucsc · Pull Request #8030 · DataBiosphere/azul

nadove-ucsc · 2026-05-15T22:13:54Z

Linked issues: #8027

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coveralls · 2026-05-15T23:15:53Z

coverage: 84.95% (+0.02%) from 84.931% — issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files into develop

codecov · 2026-05-18T01:29:45Z

Codecov Report

❌ Patch coverage is 97.91667% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 84.87%. Comparing base (204945e) to head (5fd6082).

Files with missing lines	Patch %	Lines
src/azul/service/manifest_service.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #8030      +/-   ##
===========================================
+ Coverage    84.85%   84.87%   +0.01%     
===========================================
  Files          165      165              
  Lines        24177    24207      +30     
===========================================
+ Hits         20515    20545      +30     
  Misses        3662     3662

☔ View full report in Codecov by Sentry.
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achave11-ucsc

To confirm, these changes do not require re-indexing?

Also, consider adding a (unit/integration) test that covers the new elif branch.

achave11-ucsc · 2026-05-18T23:54:52Z



-@attr.s(auto_attribs=True, kw_only=True, frozen=True)
+@attrs.frozen(auto_attribs=True, frozen=True)


It seems frozen is redundant and kw_only was dropped.

Suggested change

@attrs.frozen(auto_attribs=True, frozen=True)

@attrs.frozen(auto_attribs=True, kw_only=True)

achave11-ucsc · 2026-05-18T23:55:32Z

+            config.catalogs[catalog].atlas == 'lungmap'
+            and drs_uri.startswith('drs://dg.4503:')
+        ):
+            # Lungmap contains external files hosted on BioDataCatalyst.


Suggested change

# Lungmap contains external files hosted on BioDataCatalyst.

# LungMAP contains external files hosted on BioDataCatalyst.

achave11-ucsc · 2026-05-19T00:02:04Z

-    @cache
-    def mirror_service(self, catalog: CatalogName) -> MirrorService:
-        return MirrorService(catalog=catalog)
+@attrs.frozen(kw_only=True)


Like the sibling class definitions in query_service.py?

Suggested change

@attrs.frozen(kw_only=True)

@attrs.frozen(auto_attribs=True, kw_only=True)

nadove-ucsc · 2026-05-19T00:35:05Z

To confirm, these changes do not require re-indexing?

Confirmed. The affected fields in the response are synthesized by the service and are not present in the index.

achave11-ucsc

Approved ✅

hannes-ucsc

Please remove the FileUrlService refactoring and only fix the issue at hand, plus the test. Leave the attrs conversion, but make sure it is done correctly (see comment below).

Please clear these types of refactorings with me before embarking on them. Feel free to create an issue for the refactoring and motivate the refactoring in the description of that issue.

hannes-ucsc · 2026-05-19T14:36:10Z

-    @cache
-    def mirror_service(self, catalog: CatalogName) -> MirrorService:
-        return MirrorService(catalog=catalog)
+@attrs.frozen(auto_attribs=True, kw_only=True)


Suggested change

@attrs.frozen(auto_attribs=True, kw_only=True)

@attrs.frozen(kw_only=True)

The new API infers it automatically.

hannes-ucsc · 2026-05-21T22:28:38Z

            return None
+        elif (
+            config.catalogs[self.catalog].atlas == 'lungmap'
+            and drs_uri.startswith('drs://dg.4503:')


Hard-coding the prefix is too brittle. The issue description states

any file with a compact DRS URI is external.

Is there a reason we can't exploit that here?

hannes-ucsc · 2026-05-22T14:46:31Z

        elif (
            config.catalogs[self.catalog].atlas == 'lungmap'
-            and drs_uri.startswith('drs://dg.4503:')
+            and CompactDRSURI.regex.match(drs_uri)


Use DRSURI.parse followed by instanceof. This is how we perform DRS URI type detection everywhere else.

hannes-ucsc

The new test is a bit lazy. It indexes two bundles, even though only one file in one bundle is patched. The same bundles were indexed already in a different test. The need for extracting a superclass stems from the fact that these test cases index their bundles during class setup, so the patching needs to be done at class setup, and therefore a new class is needed.

We'd get more bang for the buck if actually canned two LungMAP bundles, one from a project with compact DRS UIRs, and one from a project with host-based DRS URIS. We wouldn't extend the test duration but we would get more meaningful coverage.

Also, I'd like to the main commit to be split and pushed individually so that I can see the test fail.

hannes-ucsc · 2026-05-23T02:57:07Z

+        }
+
+    external_file_uuid = '27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6'
+    # Compact identifier for BioDataCatalyst


Suggested change

# Compact identifier for BioDataCatalyst

The need for extracting a superclass stems from the fact that these test cases...

The need for extracting a superclass stems from the fact that the new test uses a different catalog configuration due to requiring the Config.Catalog.atlas property to be set to 'lungmap' instead of 'hca', regardless of how/which bundles are indexed.

This bundle naturally contains a mixture of host-based and compact DRS URIs, so I just canned that one.

)

nadove-ucsc self-assigned this May 15, 2026

nadove-ucsc linked an issue May 15, 2026 that may be closed by this pull request

curl manifest futilely includes external LungMAP files #8027

Open

nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch from a70d2de to 9e2cb1f Compare May 15, 2026 22:18

github-advanced-security AI found potential problems May 15, 2026

View reviewed changes

Comment thread src/azul/service/index_service.py Fixed

nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch 3 times, most recently from 3194880 to e012e86 Compare May 15, 2026 23:04

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nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch from 40836f1 to 71ca313 Compare May 21, 2026 06:31

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nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch from bd29c06 to 26cfd2d Compare May 22, 2026 18:35

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nadove-ucsc added 4 commits May 27, 2026 19:38

Switch query service to new attrs API

be1ff25

Add FIXMEs (#8042)

408835b

Extract test superclass

e220015

Extract private method

9c17be7

nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch from 26cfd2d to be1ff25 Compare May 28, 2026 04:10

nadove-ucsc added 2 commits May 27, 2026 22:03

[1/2] Fix: curl manifest futilely includes external LungMAP files (#8027

0699599

)

[2/2] Fix: curl manifest futilely includes external LungMAP files (#8027

5fd6082

)

nadove-ucsc force-pushed the issues/nadove-ucsc/8027-curl-manifest-includes-external-lungmap-files branch from f9c1dee to 0699599 Compare May 28, 2026 05:05

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nadove-ucsc assigned hannes-ucsc May 28, 2026



		@attr.s(auto_attribs=True, kw_only=True, frozen=True)
		@attrs.frozen(auto_attribs=True, frozen=True)

	@attrs.frozen(auto_attribs=True, frozen=True)
	@attrs.frozen(auto_attribs=True, kw_only=True)

	# Lungmap contains external files hosted on BioDataCatalyst.
	# LungMAP contains external files hosted on BioDataCatalyst.

	@attrs.frozen(kw_only=True)
	@attrs.frozen(auto_attribs=True, kw_only=True)

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nadove-ucsc commented May 15, 2026 •

edited by achave11-ucsc

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