Assert metadata schema location (#6516) #6747

dsotirho-ucsc · 2024-12-06T19:09:32Z

Connected issues: #6516

Notes for operator

Full reindex of dev
Reindex of LungMAP catalogs in prod

Checklist

Author

PR is a draft
Target branch is develop
Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
On ZenHub, PR is connected to all issues it (partially) resolves
PR description links to connected issues
PR title matches¹ that of a connected issue _{or comment in PR explains why they're different}
PR title references all connected issues
For each connected issue, there is at least one commit whose title references that issue

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
This PR is labeled partial _{or completely resolves all connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

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This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
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This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
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Updated REST API version number in app.py _{or this PR does not modify a REST API}

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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}
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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 connected issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR}

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Rebased PR branch on develop, squashed old fixups
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make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

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Actually approved the PR
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Operator (before pushing merge the commit)

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Operator (after pushing the merge commit)

Operator (reindex)

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

codecov · 2024-12-09T19:42:42Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.54%. Comparing base (1b8b65d) to head (60f6ab5).
Report is 7 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6747      +/-   ##
===========================================
+ Coverage    85.52%   85.54%   +0.02%     
===========================================
  Files          147      147              
  Lines        21196    21226      +30     
===========================================
+ Hits         18128    18158      +30     
  Misses        3068     3068

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

coveralls · 2024-12-09T19:44:02Z

coverage: 85.563% (+0.02%) from 85.543%
when pulling 60f6ab5 on issues/dsotirho-ucsc/6516-drs-uri-property
into 1b8b65d on develop.

dsotirho-ucsc · 2024-12-10T00:30:40Z

6747_IT_2024-12-09.txt

achave11-ucsc

IIRC, we prefer committing test coverage first, followed by source code changes in order to demonstrate effectiveness via build status checks. Consider inverting the order of your commits. Also, I'd keep the commits simple and straight forward, a commit tests the feature the other is the feature. And lastly, for my personal preference, the patches are a bit duplicative, consider writing a handler for patching, and to keep the call sites concise.

dsotirho-ucsc · 2024-12-12T19:07:14Z

6747_IT_2024-12-12.txt

achave11-ucsc

LGTM ✅

hannes-ucsc · 2024-12-13T21:35:46Z

src/humancellatlas/data/metadata/api.py

-        schema_name = described_by.rpartition('/')[2]
+        described_by = furl(content['describedBy'])
+        require(described_by.netloc in valid_schema_domains,
+                described_by.netloc)


Suggested change

described_by.netloc)

'Invalid schema domain', netloc, valid_schema_domains)

hannes-ucsc · 2024-12-13T21:43:59Z

test/hca_metadata_api/test.py

@@ -85,6 +95,7 @@ def _rename_keys(self, d, **kwargs):
                d[new_name] = d[old_name]
                del d[old_name]

+    @valid_schema_domains(['schema.dev.data.humancellatlas.org'])


This is a marginal aspect of our tests and I don't think I want to pollute this many test methods with a decorator invocation for the sake of each test having a minimal set of valid domains. We should provide this patch in a super class of our unit tests case classes and just allow the union of all observed domains there.

hannes-ucsc · 2024-12-13T21:45:18Z

test/hca_metadata_api/test.py

+        json_body = self.json_body(domain='schema.humancellatlas.org')
+        with self.assertRaises(RequirementError):
+            Protocol.from_json(json_body)
+


Since you are actively working on #6666, let's not have a FIXME and just add this case in that PR.

hannes-ucsc · 2024-12-13T21:47:38Z

test/hca_metadata_api/test.py

+
+    def test_valid_schema_domain(self):
+        json_body = self.json_body(domain='schema.humancellatlas.org')
+        file = Protocol.from_json(json_body)


Why is the variable called file when it's referring to an instance of Protocol?

The variable name was a oversight from an earlier version that was using a File schema

dsotirho-ucsc · 2025-02-05T20:47:05Z

6747_IT_2025-02-05.txt

hannes-ucsc · 2025-02-06T19:02:34Z

test/azul_test_case.py

+        from humancellatlas.data.metadata import (
+            api,
+        )


I've added a fixup commit to get rid of the local import.

Local import is still there.

dsotirho-ucsc · 2025-02-06T21:31:41Z

6747_IT_2025-02-06.txt

hannes-ucsc · 2025-02-06T22:16:10Z

Security design review

…ndle

These two snapshots contain sequence file descriptors that use the schema: https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/lungmap-phantom-files/json_schema/system/file_descriptor.json

This dcp3 snapshot contains project metadata that uses the schema: https://schema.dev.data.humancellatlas.org/type/project/14.0.0/project

Add tests

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hannes-ucsc added reindex:dev [process] PR requires reindexing dev reindex:prod [process] PR requires reindexing prod reindex:partial [process] PR allows for (de)indexing a specific source or catalog labels Feb 6, 2025

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hannes-ucsc force-pushed the develop branch from 33a7a95 to 118ade8 Compare February 7, 2025 02:20

dsotirho-ucsc added 6 commits February 7, 2025 08:58

Add dummy checksums and valid describedBy values to canned TDR HCA bu…

835e61b

…ndle

[u] Remove LungMAP snapshots from dev with invalid schema locations

e32d123

These two snapshots contain sequence file descriptors that use the schema: https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/lungmap-phantom-files/json_schema/system/file_descriptor.json

[u] Remove dcp3 snapshohts from dev with invalid schema locations

b08bf73

This dcp3 snapshot contains project metadata that uses the schema: https://schema.dev.data.humancellatlas.org/type/project/14.0.0/project

[1/2] Assert metadata schema location (#6516)

f774185

Add tests

[2/2] Assert metadata schema location (#6516)

0f92147

Add FIXME (#6299)

60f6ab5

achave11-ucsc force-pushed the issues/dsotirho-ucsc/6516-drs-uri-property branch from 9494ef8 to 60f6ab5 Compare February 7, 2025 16:59

achave11-ucsc added sandbox [process] Resolution is being verified in sandbox deployment upgrade [process] PR includes commit requiring manual upgrade labels Feb 7, 2025

achave11-ucsc merged commit 54a2200 into develop Feb 7, 2025
11 checks passed

achave11-ucsc deleted the issues/dsotirho-ucsc/6516-drs-uri-property branch February 8, 2025 00:13

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Assert metadata schema location (#6516) #6747

Assert metadata schema location (#6516) #6747

dsotirho-ucsc commented Dec 6, 2024 •

edited by achave11-ucsc

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hannes-ucsc commented Feb 6, 2025

	described_by.netloc)
	'Invalid schema domain', netloc, valid_schema_domains)

Assert metadata schema location (#6516) #6747

Assert metadata schema location (#6516) #6747

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dsotirho-ucsc commented Dec 6, 2024 • edited by achave11-ucsc Loading

Notes for operator

Checklist

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Operator (before pushing merge the commit)

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Security design review

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