Fix: Mirror URI in manifest /index/files response is set for MA files (#7687) #7693

nadove-ucsc · 2026-01-13T01:12:50Z

Linked issues: #7687

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¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

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Added p tag to titles of partial commits
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Started mirroring in dev _{or this PR does not require mirroring dev}
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Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR does not require mirroring dev}
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Shorthand for review comments

L line is too long
W line wrapping is wrong
Q bad quotes
F other formatting problem

src/azul/service/source_service.py

lambdas/indexer/vendor/resources/sources.json.template.py

lambdas/service/vendor/resources/sources.json.template.py

codecov · 2026-01-13T22:43:43Z

Codecov Report

❌ Patch coverage is 95.49550% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.86%. Comparing base (aaa40a3) to head (733a403).

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	3 Missing ⚠️
src/azul/plugins/__init__.py	50.00%	1 Missing ⚠️
src/azul/plugins/repository/tdr.py	85.71%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7693      +/-   ##
===========================================
+ Coverage    84.81%   84.86%   +0.04%     
===========================================
  Files          157      157              
  Lines        22984    23059      +75     
===========================================
+ Hits         19494    19569      +75     
  Misses        3490     3490

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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coveralls · 2026-01-13T22:43:55Z

coverage: 85.084% (+0.05%) from 85.036%
when pulling 733a403 on issues/nadove-ucsc/7687-mirror-uri-set-for-ma-files
into aaa40a3 on develop.

hannes-ucsc · 2026-01-20T17:45:42Z

src/azul/plugins/__init__.py

+        Implementations should raise PermissionError if the provided
+        authentication is insufficient to access the repository.


"Implementations" implies "implementations of this method". No authentication is provided to those implementations, so I don't understand this sentence.

hannes-ucsc · 2026-01-20T17:46:41Z

src/azul/service/source_service.py

+            all_sources = set()
+            public_sources = set()


We typically use tuple assignmets when they correlate like this.

hannes-ucsc · 2026-01-20T17:48:47Z

src/azul/service/source_service.py

        return int(time())
+
+    @cache
+    def _configured_sources(self) -> Mapping[str, AbstractSet[SourceRef]]:


The return type hint is a text-book case for a typed dict.

lambdas/indexer/vendor/resources/sources.json.template.py

hannes-ucsc

Also, please add unit test coverage for the the newly uncovered lines

https://app.codecov.io/gh/DataBiosphere/azul/pull/7693/blob/src/azul/service/source_service.py

nadove-ucsc · 2026-01-21T01:00:13Z

The bot is right, which raises the question as to why make pep8 didn't catch this.

It wasn't caught because $(project_root)/lambdas/{indexer,service}/vendor/ is not included in the paths passed to flake8. It also wasn't detected by PyCharm (not grayed out in the editor) because those directories are explicitly marked as ignored.

src/azul/service/source_service.py

    def _now(self) -> int:
        return int(time())
+
+    @cache


resources/sources.json.template.py

hannes-ucsc · 2026-01-22T00:31:49Z

src/azul/plugins/__init__.py

+        Overrides should raise PermissionError if the provided authentication is
+        insufficient to access the repository.


What is this "provided authentication"? There's no argument and the instance doesn't have any either.

Mistakenly copy-pasted from the previous method.

hannes-ucsc · 2026-01-22T00:44:42Z

test/service/test_source_service.py

@@ -1,3 +1,4 @@
+import json


Rename to test_source_service.py please.

hannes-ucsc · 2026-01-22T00:55:36Z

resources/sources.json.template.py

@@ -0,0 +1,8 @@
+from azul.service.source_service import (


Please ensure that these files are covered by make pep8

hannes-ucsc

Because this touches the Makefile, it needs r tag and reqs label and so on.

No fixups next time, please.

hannes-ucsc · 2026-01-22T06:47:52Z

Makefile

                                $(project_root)/environment.py \
                                $(project_root)/deployments/*/environment.py \
                                $(project_root)/.github/workflows/*.py \
+                                $(project_root)/lambdas/{indexer,service}/vendor/resources/*.py \


Suggested change

$(project_root)/lambdas/{indexer,service}/vendor/resources/*.py \

hannes-ucsc · 2026-01-22T06:48:32Z

Makefile

+                                $(project_root)/lambdas/{indexer,service}/vendor/resources/*.py \
                                $$(find $(project_root)/terraform{,/gitlab,/shared,/browser} \
                                        $(project_root)/lambdas/{indexer,service}{,/.chalice} \
                                        $(project_root)/.github \


Suggested change

$(project_root)/.github \

$(project_root)/resources \

$(project_root)/.github \

and consolidate redundant plugin instanciation

…#7687)

nadove-ucsc self-assigned this Jan 13, 2026

nadove-ucsc linked an issue Jan 13, 2026 that may be closed by this pull request

Fix: Mirror URI in manifest /index/files response is set for MA files #7687

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github-advanced-security bot found potential problems Jan 13, 2026

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src/azul/service/source_service.py Fixed Show fixed Hide fixed

lambdas/indexer/vendor/resources/sources.json.template.py Fixed Show fixed Hide fixed

lambdas/service/vendor/resources/sources.json.template.py Fixed Show fixed Hide fixed

nadove-ucsc force-pushed the issues/nadove-ucsc/7687-mirror-uri-set-for-ma-files branch 7 times, most recently from 52a4ca7 to d8627ae Compare January 13, 2026 22:28

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hannes-ucsc marked this pull request as ready for review January 16, 2026 18:55

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src/azul/service/source_service.py

def _now(self) -> int:

return int(time())

@cache

Check warning

Code scanning / CodeQL

Use of the return value of a procedure Warning

The result of

cache

Loading
is used even though it is always None.

nadove-ucsc force-pushed the issues/nadove-ucsc/7687-mirror-uri-set-for-ma-files branch from 7464fca to 73ab983 Compare January 21, 2026 02:23

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nadove-ucsc added 9 commits January 22, 2026 12:09

Fix conflation of absent/null properties in mirror documentation (#7637)

6a0b704

Rename source service test

263607e

Reorganize static resources

beae7e7

Deduplicate outsourced environ template file

5e9357d

[R] Cover resource templates with pep8

40c9fdf

Extract private method from list_sources

9f67473

Pull up MirrorService._source_service into superclass

1e1dd9e

and consolidate redundant plugin instanciation

Extract variable

4907282

Fix: Mirror URI in manifest /index/files response is set for MA files (…

733a403

…#7687)

nadove-ucsc force-pushed the issues/nadove-ucsc/7687-mirror-uri-set-for-ma-files branch from 05f3023 to 733a403 Compare January 22, 2026 20:56

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nadove-ucsc requested a review from hannes-ucsc January 22, 2026 21:22

nadove-ucsc assigned hannes-ucsc Jan 22, 2026

		Implementations should raise PermissionError if the provided
		authentication is insufficient to access the repository.

		Overrides should raise PermissionError if the provided authentication is
		insufficient to access the repository.

	$(project_root)/.github \
	$(project_root)/resources \
	$(project_root)/.github \

Fix: Mirror URI in manifest /index/files response is set for MA files (#7687) #7693

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Fix: Mirror URI in manifest /index/files response is set for MA files (#7687) #7693

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