Assert metadata schema location (#6516) #6747

dsotirho-ucsc · 2024-12-06T19:09:32Z

Connected issues: #6516

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codecov · 2024-12-09T19:42:42Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.64%. Comparing base (fb360ea) to head (4f2a63c).
Report is 15 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6747      +/-   ##
===========================================
+ Coverage    85.62%   85.64%   +0.02%     
===========================================
  Files          149      149              
  Lines        20944    20974      +30     
===========================================
+ Hits         17934    17964      +30     
  Misses        3010     3010

☔ View full report in Codecov by Sentry.
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coveralls · 2024-12-09T19:44:02Z

coverage: 85.666% (+0.02%) from 85.645%
when pulling 4f2a63c on issues/dsotirho-ucsc/6516-drs-uri-property
into fb360ea 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

hannes-ucsc

There are two more places where we would expect the describedBy property: links and the descriptor. links is passed to the Bundle constructor. And I believe the descriptor is available via ManifestEntry.json but I could be wrong. Please confirm and request a PL slot. We may want to place the schema validation into the repository plugin or finally get rid of the ManifestEntry class and replace it with Descriptor so that the API matches what TDR gives us, instead of what the DSS used to give us, years ago.

Note that the ticket mentions the descriptor and what you've implemented here does not check the descriptor schema, AFAICT. We've both lost sight of that aspect.

dsotirho-ucsc · 2025-01-13T18:12:34Z

6747_IT_2025-01-13.txt

hannes-ucsc

I'd like @nadove-ucsc's eyes on this, too. Please request a thorough peer review from them.

nadove-ucsc

Code changes look good, but I'm confused regarding the PR's context. This doesn't appear to have anything to do with the drs_uri property, so the PR title makes no sense to me. Is the PR partial? Has the scope of the issue changed?

Consider whether it would be more appropriate to rename the PR to match the commit title and add a comment explaining why the PR title differs from the issue title.

nadove-ucsc · 2025-01-14T23:01:50Z

src/azul/plugins/repository/tdr_hca/__init__.py

@@ -189,6 +189,10 @@ def add_entity(self,
            self.stitched.add(entity.entity_id)
        if entity.entity_type.endswith('_file'):
            descriptor = json.loads(row['descriptor'])
+            # FIXME Move validation of descriptor to the metadata API
+            #       https://github.com/DataBiosphere/azul/issues/6299
+            from humancellatlas.data.metadata.api import Entity  # noqa AZL131


Why is noqa used here instead of just properly formatting the import statement?

I originally thought the local import looked cleaner using one line rather than three.

Add tests

dsotirho-ucsc · 2025-01-15T17:11:07Z

PR HumanCellAtlas/metadata-schema#1575 added the drs_uri property to the file descriptor schema.
This PR (#6747) makes it so that all HCA schema URLs are required to use netloc schema.humancellatlas.org as requested in comment.

dsotirho-ucsc · 2025-01-15T17:26:35Z

6747_IT_2025-01-15.txt

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dsotirho-ucsc added 3 commits January 15, 2025 08:55

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

78ffe27

Add tests

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

fd2ac65

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

4f2a63c

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dsotirho-ucsc changed the title ~~Fix: HCA schemas for descriptor lacks drs_uri property (#6516)~~ Assert metadata schema location (#6516) Jan 15, 2025

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Assert metadata schema location (#6516) #6747

Assert metadata schema location (#6516) #6747

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dsotirho-ucsc commented Jan 15, 2025

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

Assert metadata schema location (#6516) #6747

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Assert metadata schema location (#6516) #6747

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

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