Validate info object schemas during unit and integration tests (#7752) by nadove-ucsc · Pull Request #7770 · DataBiosphere/azul

nadove-ucsc · 2026-02-11T04:32:42Z

Linked issues: #7752

Checklist

Author

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

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all linked issues}
This PR partially resolves each of the linked issues _{or does not have the partial label}

Author (reindex)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
This PR is labeled reindex:partial and its description documents the specific reindexing procedure for dev, anvildev, anvilprod and prod _{or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod}

Author (API changes)

This PR and its linked issues are labeled API _{or this PR does not modify a REST API}
Added a (A) tag to commit title for backwards (in)compatible changes _{or this PR does not modify a REST API}
Updated REST API version number in app.py _{or this PR does not modify a REST API}

Author (upgrading deployments)

Ran make docker_images.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require upgrading deployments}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
This PR is labeled deploy:runner _{or does not require deploying the runner image}

Author (hotfixes)

Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
Reverted the temporary hotfixes for any linked issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues linked to this PR}

Author (before every review)

Rebased PR branch on develop, squashed fixups from prior reviews
Ran make requirements_update _{or this PR does not modify Dockerfile, environment, requirements*.txt, common.mk, Makefile or environment.boot}
Added R tag to commit title _{or this PR does not modify requirements*.txt}
This PR is labeled reqs _{or does not modify requirements*.txt}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}
PR is awaiting requested review from a peer
Status of PR is Review requested
PR is assigned to only the peer and the author

Peer reviewer (after approval)

Note that after requesting changes, the PR must be assigned to only the author.

Actually approved the PR
PR is not a draft
PR is awaiting requested review from system administrator
Status of PR is Review requested
PR is assigned to only the system administrator and the author

System administrator (after approval)

Actually approved the PR
Labeled linked issues as demo or no demo
Commented on linked issues about demo expectations _{or all linked issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Status of PR is Approved
PR is assigned to only the operator and the author

Operator

Checked reindex:… labels and r commit title tag
Checked that demo expectations are clear _{or all linked issues are labeled no demo}
Squashed PR branch and rebased onto develop
Sanity-checked history
Pushed PR branch to GitHub

Operator (deploy `.shared` and `.gitlab` components)

Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Checked the items in the next section _{or this PR is labeled deploy:gitlab}
PR is assigned to only the system administrator and the author _{or this PR is not labeled deploy:gitlab}

System administrator (post-deploy of `.gitlab` component)

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator and the author

Operator (deploy runner image)

Ran _select dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
Ran _select anvildev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

Operator (merge the branch)

All status checks passed and the PR is mergeable
The title of the merge commit starts with the title of this PR
Added PR # reference to merge commit title
Collected commit title tags in merge commit title _{but only included p if the PR is also labeled partial}
Pushed merge commit to GitHub
Status of PR is Merged lower
Status of blocked issues is Triage _{or no issues are blocked on the linked issues}

Operator (main build)

Operator (reindex)

Operator (mirroring)

Started mirroring in dev _{or this PR does not require mirroring dev}
Started mirroring in anvildev _{or this PR does not require mirroring anvildev}
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR does not require mirroring dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}
Emptied mirror fail queue in dev _{or this PR does not require mirroring dev}
Emptied mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
PR is assigned to no one

Shorthand for review comments

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

coveralls · 2026-02-11T04:47:17Z

coverage: 85.264% (-0.02%) from 85.286%
when pulling 4715698 on issues/nadove-ucsc/7752-validate-info-object-schemas
into b584b7d on develop.

dsotirho-ucsc

Approved.

hannes-ucsc

#7752 (comment)

hannes-ucsc · 2026-02-12T18:43:29Z

src/azul/indexer/mirror_service.py

                                               file_name=file.name,
                                               content_type=file.content_type)

+    def get_info(self, file: File) -> MutableJSON:


Suggested change

def get_info(self, file: File) -> MutableJSON:

def info(self, file: File) -> MutableJSON:

test/integration_test.py

codecov · 2026-02-14T08:05:31Z

Codecov Report

❌ Patch coverage is 77.58621% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.05%. Comparing base (b584b7d) to head (4715698).
⚠️ Report is 9 commits behind head on develop.

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	11 Missing ⚠️
src/azul/indexer/mirror_service.py	75.00%	1 Missing ⚠️
src/azul/schemas.py	95.23%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7770      +/-   ##
===========================================
- Coverage    85.07%   85.05%   -0.03%     
===========================================
  Files          157      157              
  Lines        23293    23340      +47     
===========================================
+ Hits         19816    19851      +35     
- Misses        3477     3489      +12

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

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
📦 JS Bundle Analysis: Save yourself from yourself by tracking and limiting bundle sizes in JS merges.

hannes-ucsc · 2026-02-17T17:06:13Z

test/indexer/test_mirror_controller.py

+    @cached_property
+    def _info_schema(self) -> JSON:
+        basename = f'v{self.service.info_schema_version}.json'
+        schema_path = f'{config.project_root}/resources/static/schemas/mirror/info/'
+        with open(schema_path + basename) as f:
+            return json.load(f)


It would be OK to use the app's resource loading mechanism instead of duplicating it here.

test/integration_test.py

hannes-ucsc · 2026-02-18T22:49:28Z

test/integration_test.py

+                        info_object = service.info(repository_file)
+                        schema_url = info_object['$schema']
+                        self.assertTrue(schema_url.endswith(f'/v{service.info_schema_version}.json'))
+                        schema_response = self._get_url_json('GET', furl(schema_url))


Since we know that the schema URL is going to be the same for every info object, we shouldn't need to download it for every file.

hannes-ucsc · 2026-02-20T00:23:13Z

test/integration_test.py

-    def _get_url_json(self, method: str, url: furl) -> JSON:
+    def _get_url_json(self, method: str, url: furl) -> MutableJSON:


Doesn't need to be mutable anymore.

test/indexer/test_mirror_controller.py

src/azul/indexer/mirror_service.py

hannes-ucsc · 2026-02-23T16:43:12Z

- Fix version regex to disallow leading zeros - Improve usability of Swagger UI by providing parameter and response examples - Avoid duplicating schema loading in test - Validate schema against known instance in test - Eliminate the need to pop $id during tests

nadove-ucsc mentioned this pull request Feb 11, 2026

Validate info object schemas during unit and integration tests (#7752) #7769

Closed

nadove-ucsc self-assigned this Feb 11, 2026

nadove-ucsc linked an issue Feb 11, 2026 that may be closed by this pull request

Validate info object schemas during unit and integration tests #7752

Open

nadove-ucsc assigned dsotirho-ucsc Feb 11, 2026

nadove-ucsc requested a review from dsotirho-ucsc February 11, 2026 04:34

dsotirho-ucsc previously approved these changes Feb 11, 2026

View reviewed changes

dsotirho-ucsc marked this pull request as ready for review February 11, 2026 17:50

dsotirho-ucsc requested a review from hannes-ucsc as a code owner February 11, 2026 17:50

dsotirho-ucsc assigned hannes-ucsc and unassigned nadove-ucsc Feb 11, 2026

nadove-ucsc assigned nadove-ucsc and unassigned dsotirho-ucsc Feb 11, 2026

hannes-ucsc requested changes Feb 12, 2026

View reviewed changes

hannes-ucsc removed their assignment Feb 12, 2026

nadove-ucsc dismissed dsotirho-ucsc’s stale review via 848417f February 14, 2026 07:52

nadove-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from 346ac5d to 848417f Compare February 14, 2026 07:52

nadove-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch 3 times, most recently from c3cd339 to 43a6ce8 Compare February 14, 2026 09:02

nadove-ucsc requested a review from hannes-ucsc February 14, 2026 18:57

nadove-ucsc assigned hannes-ucsc Feb 14, 2026

hannes-ucsc requested changes Feb 17, 2026

View reviewed changes

hannes-ucsc removed their assignment Feb 17, 2026

hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Feb 17, 2026

nadove-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from 43a6ce8 to effb415 Compare February 18, 2026 05:39

nadove-ucsc requested a review from hannes-ucsc February 18, 2026 06:37

nadove-ucsc assigned hannes-ucsc Feb 18, 2026

hannes-ucsc requested changes Feb 18, 2026

View reviewed changes

nadove-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from 3b07317 to c13993b Compare February 19, 2026 22:17

nadove-ucsc requested a review from hannes-ucsc February 19, 2026 22:35

nadove-ucsc assigned hannes-ucsc Feb 19, 2026

hannes-ucsc requested changes Feb 20, 2026

View reviewed changes

hannes-ucsc removed their assignment Feb 20, 2026

nadove-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from c13993b to 8d0603e Compare February 20, 2026 20:30

nadove-ucsc requested a review from hannes-ucsc February 20, 2026 21:08

nadove-ucsc assigned hannes-ucsc Feb 20, 2026

hannes-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from 8d0603e to ece33cc Compare February 23, 2026 06:36

github-advanced-security bot found potential problems Feb 23, 2026

View reviewed changes

src/azul/indexer/mirror_service.py Dismissed Show dismissed Hide dismissed

hannes-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from ece33cc to b820994 Compare February 23, 2026 06:49

hannes-ucsc approved these changes Feb 23, 2026

View reviewed changes

hannes-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Feb 23, 2026

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Feb 23, 2026

nadove-ucsc and others added 8 commits February 23, 2026 09:47

Rename test

bf78314

Extract class attribute for info schema version

4ccdc87

Extract variable

680c95d

Improve validation of info schemas during unit tests (#7752)

d5247fa

Validate info object schemas during integration tests (#7752)

71e39a1

Rename method argument

a7bc0b2

Fix mock of base_url property in OpenAPI document generation

2303bf8

dsotirho-ucsc force-pushed the issues/nadove-ucsc/7752-validate-info-object-schemas branch from b820994 to 4715698 Compare February 23, 2026 17:47

dsotirho-ucsc assigned achave11-ucsc and unassigned dsotirho-ucsc Feb 23, 2026

achave11-ucsc merged commit c935581 into develop Feb 23, 2026
10 checks passed

achave11-ucsc unassigned nadove-ucsc and achave11-ucsc Feb 23, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Validate info object schemas during unit and integration tests (#7752)#7770

Validate info object schemas during unit and integration tests (#7752)#7770
achave11-ucsc merged 8 commits intodevelopfrom
issues/nadove-ucsc/7752-validate-info-object-schemas

nadove-ucsc commented Feb 11, 2026 •

edited by achave11-ucsc

Loading

Uh oh!

coveralls commented Feb 11, 2026 •

edited

Loading

Uh oh!

dsotirho-ucsc left a comment

Uh oh!

hannes-ucsc left a comment

Uh oh!

hannes-ucsc Feb 12, 2026

Uh oh!

Uh oh!

codecov bot commented Feb 14, 2026 •

edited

Loading

Uh oh!

hannes-ucsc Feb 17, 2026

Uh oh!

Uh oh!

hannes-ucsc Feb 18, 2026

Uh oh!

hannes-ucsc Feb 20, 2026

Uh oh!

Uh oh!

Uh oh!

Uh oh!

hannes-ucsc commented Feb 23, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

	def get_info(self, file: File) -> MutableJSON:
	def info(self, file: File) -> MutableJSON:

		def _get_url_json(self, method: str, url: furl) -> JSON:
		def _get_url_json(self, method: str, url: furl) -> MutableJSON:

Conversation

nadove-ucsc commented Feb 11, 2026 • edited by achave11-ucsc Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Checklist

Author

Author (partiality)

Author (reindex)

Author (API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

Operator (merge the branch)

Operator (main build)

Operator (reindex)

Operator (mirroring)

Operator

Shorthand for review comments

Uh oh!

coveralls commented Feb 11, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

dsotirho-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

hannes-ucsc left a comment

Choose a reason for hiding this comment

Uh oh!

hannes-ucsc Feb 12, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

codecov bot commented Feb 14, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

hannes-ucsc Feb 17, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

hannes-ucsc Feb 18, 2026

Choose a reason for hiding this comment

Uh oh!

hannes-ucsc Feb 20, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

hannes-ucsc commented Feb 23, 2026

Security design review

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

nadove-ucsc commented Feb 11, 2026 •

edited by achave11-ucsc

Loading

Operator (deploy `.shared` and `.gitlab` components)

System administrator (post-deploy of `.gitlab` component)

coveralls commented Feb 11, 2026 •

edited

Loading

codecov bot commented Feb 14, 2026 •

edited

Loading