Fix: Manifest content hash computation times out (#6123) #7258

dsotirho-ucsc · 2025-07-08T00:18:44Z

Linked issues: #6123

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codecov · 2025-07-08T01:11:28Z

Codecov Report

❌ Patch coverage is 85.07463% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.84%. Comparing base (ca6fa2d) to head (faf6036).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	6 Missing ⚠️
src/azul/azulclient.py	0.00%	3 Missing ⚠️
src/azul/__init__.py	66.66%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7258      +/-   ##
===========================================
- Coverage    84.84%   84.84%   -0.01%     
===========================================
  Files          157      157              
  Lines        22871    22899      +28     
===========================================
+ Hits         19405    19428      +23     
- Misses        3466     3471       +5

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coveralls · 2025-07-08T01:12:04Z

coverage: 85.042% (-0.005%) from 85.047%
when pulling e0f2625 on issues/dsotirho-ucsc/6123-manifest-content-hash
into 158e524 on develop.

dsotirho-ucsc · 2025-07-10T18:04:29Z

7258_IT_2025-07-10.txt

achave11-ucsc

LGTM ✅

environment.py

hannes-ucsc · 2025-07-14T23:35:34Z

src/azul/service/manifest_service.py

+        """
+        return self._manifest_hash('bundles')
+
+    def _manifest_hash(self, base: str) -> int:


PL (modal parameter smell, literal string)

scripts/reindex.py

hannes-ucsc · 2025-12-15T17:40:09Z

test/service/test_manifest.py

            for format in [ManifestFormat.compact]:
-                cases = [
+                source_hash = '4bc67e84-4873-591f-b524-a5fe4ec215eb'
+                for filters, name_with_notif_enabled, name_with_notif_disabled in [


It is not immediately apparent to me what a notif is and what it means for it to be enabled or disabled. Can you come up with a better name?

hannes-ucsc · 2025-12-15T17:41:27Z

test/azul_test_case.py

+        # FIXME: Remove patch once bundle notifications are enabled again
+        #        https://github.com/DataBiosphere/azul/issues/7183


Move to definition of method. If you remove the method, the call site breaks. If you remove the callsite, the definition may be accidentally left in place.

hannes-ucsc · 2025-12-15T17:42:09Z

test/integration_test.py

-                          self.azul_client.index,
-                          first(config.integration_test_catalogs),
-                          notifications)
+        with self.assertRaises(AzulClientNotificationError) as cm:


I have the feeling that there is some other if False-like construct in the IT that disables sending bundle notifications. They should all be backed by the config variable.

dsotirho-ucsc · 2025-12-17T19:06:53Z

7258_IT_2025-12-17.txt

hannes-ucsc

No fixups next time, please. Please prove that every commit passes unit tests by pushing them individually. Please prove that IT passes in personal deployment with bundle notification enabled and disabled.

hannes-ucsc · 2026-01-06T16:23:06Z

test/service/test_manifest.py

                self.assertEqual([1, 1], list(map(len, map(set, file_names.values()))))

-    def test_hash_validity(self):
+    def test_hash_validity_with_notifications_enabled(self) -> None:


This still makes no sense in the refactor commit. At that point in the history, notifications can't be enabled or disabled.

hannes-ucsc · 2026-01-06T16:44:13Z

test/service/test_manifest.py

                        self.assertFalse(manifest.was_cached)
                        self.assertEqual(1, num_partitions)
                        url = furl(self._service.get_manifest_url(manifest))
+                        if config.enable_bundle_notifications:


Bools are ints:

['a', 'b'][True] >>> 'b'

But I think we should push the conditional into the cases literal above.

hannes-ucsc · 2026-01-06T16:46:49Z

test/azul_test_case.py

+        cls.addClassPatch(patch.object(target=type(config),
+                                       attribute='enable_bundle_notifications',
+                                       new_callable=PropertyMock,
+                                       return_value=True))


Is this what's described in the issue? If so, please push a drop commit that

Suggested change

return_value=True))

return_value=False))

This was mentioned in the issue here:

+ # PATCH: Implement this property and the backing environment variable + # defaulting to 0. Patch the variable to 1 for unittests.

hannes-ucsc

I meant to request changes in my previous review.

dsotirho-ucsc · 2026-01-07T19:37:51Z

Please prove that IT passes in personal deployment with bundle notification enabled and disabled.

Note that IT was run prior to the drop commit.

With bundle notifications disabled (default configuration):
7258_IT_2026-01-07-disabled.txt

With bundle notifications enabled (set in environment.py):
7258_IT_2026-01-07-enabled.txt

hannes-ucsc

The unit tests break on the drop commit. Please address that, and leave the drop commit in place.

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hannes-ucsc linked an issue Sep 11, 2025 that may be closed by this pull request

Manifest content hash computation times out #6123

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dsotirho-ucsc added 4 commits January 7, 2026 09:26

Refactor test_hash_validity()

3984df1

[A] Workaround: Manifest content hash computation times out (#6123)

ccb4a97

Add FIXME (#7183)

ff31dc3

drop! Disable bundle notifications in tests

e0f2625

dsotirho-ucsc force-pushed the issues/dsotirho-ucsc/6123-manifest-content-hash branch from faf6036 to 3984df1 Compare January 7, 2026 17:38

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		# FIXME: Remove patch once bundle notifications are enabled again
		# https://github.com/DataBiosphere/azul/issues/7183

Fix: Manifest content hash computation times out (#6123) #7258

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Fix: Manifest content hash computation times out (#6123) #7258

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