Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

nadove-ucsc · 2025-06-16T21:59:37Z

Connected issues: #7154, #7214

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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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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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Mirrored anvilbox
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Mirrored anvildev
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codecov · 2025-06-17T07:52:13Z

Codecov Report

❌ Patch coverage is 75.00000% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.86%. Comparing base (9b68251) to head (4695a1a).

Files with missing lines	Patch %	Lines
src/azul/plugins/repository/tdr_anvil/__init__.py	77.27%	5 Missing ⚠️
src/azul/indexer/mirror_file_service.py	0.00%	2 Missing ⚠️
test/integration_test.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7223      +/-   ##
===========================================
- Coverage    84.88%   84.86%   -0.02%     
===========================================
  Files          157      157              
  Lines        22796    22816      +20     
===========================================
+ Hits         19350    19363      +13     
- Misses        3446     3453       +7

☔ View full report in Codecov by Sentry.
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coveralls · 2025-06-17T09:29:02Z

coverage: 85.087% (-0.02%) from 85.104%
when pulling 4695a1a on issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding
into 9b68251 on develop.

dsotirho-ucsc

Approved.

hannes-ucsc

This will get conflicts once the backport I just approved land on develop.

It's not evident from the title of that commit that removes the snapshot what the defect is. Either add a ticket reference or describe the defect in the body of the commit message. Probably the former is warranted so that we can point our collaborators at it.

The base branch was changed.

hannes-ucsc

While the link in the message body of the middle commit is helpful, the body should be self-contained and include a description of the alleged defect.

dsotirho-ucsc

Approved.

hannes-ucsc · 2025-12-08T23:55:53Z

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

+        def missing_md5(row: BigQueryRow) -> bool:
+            missing = row['file_md5sum'] is None
+            if missing:
+                assert source.spec.name == 'ANVIL_1000G_2019_Dev_20230609_ANV5_202306121732', R(


Since this is a (hopefully) temporary workaround, there should be a FIXME conmment before it. The FIXME comment should also be in every environment.py where this specific source is mentioned.

hannes-ucsc · 2025-12-09T00:09:06Z

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

            return {'*'}
        else:
            columns = set(columns)
            columns.add('datarepo_row_id')


It seems a little inefficient that we're copying the entire set, and are making the same additions/replacements, for every call. Let's use a cached property that returns a dict from table name to set of column names. We would still need this method to handle the default, but that is cheap.

Unrelated, but it would be good to add a comment explaining when we expect the default to kick in. I assume it's for non-schema tables.

and document use case for default value

hannes-ucsc · 2025-12-10T16:34:08Z

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

+    @cached_property
+    def _columns_by_table(self) -> Mapping[str, AbstractSet[str]]:
+        # Include all columns for replicas of non-schema tables
+        columns_by_table = defaultdict(lambda: {'*'})


I don't like using defaultdict because read access can modify the dictionary, which contradicts the return type, or the intend behind it. I recently fixed a bug that was caused by exactly this misuse of defaultdict. As I wrote in my previous review, my preferred solution is to retain the _columns method.

If I remember correctly, this is now the second time in a short period were nuances in my review comments were (dis)missed. This is worries me a bit, given that we frequently only get to do one review per PR per day, and that this PR is for a high priority issue.

We would still need this method to handle the default, but that is cheap.

I misinterpreted "this method" to refer to the newly added cached property (which is technically a method, or at least implemented using one), not the original method. Hence my mistaken belief that the default ought to provided within the body of that property definition.

hannes-ucsc · 2025-12-10T16:41:59Z

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

-            columns.add('datarepo_row_id')
-            return columns
+    @cached_property
+    def _columns_by_table(self) -> Mapping[str, AbstractSet[str]]:


Suggested change

def _columns_by_table(self) -> Mapping[str, AbstractSet[str]]:

def __columns_by_table(self) -> Mapping[str, AbstractSet[str]]:

unless the resulting name mangling breaks the caching.

It does break the caching.

>>> from azul.azulclient import AzulClient >>> p = AzulClient().repository_plugin('anvil') '_Plugin__schema_columns_by_table'? >>> s1 = p._Plugin__schema_columns_by_table >>> s2 = p._Plugin__schema_columns_by_table >>> s1 == s2 True >>> s1 is s2 False

hannes-ucsc

The split commit doesn't follow our convention that all parts in a split have the same title, except for differences in the tags. Maybe you intended to remove the split designation altogether? Please also change "Workaround" to "Work around" in the commit title.

Previously disabled due to the issues with MD5 encoding

…7634)

nadove-ucsc added reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Jun 16, 2025

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nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch 3 times, most recently from 85448b8 to 1cb13db Compare June 17, 2025 07:28

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 1cb13db to 9dc69e5 Compare June 26, 2025 06:39

nadove-ucsc assigned dsotirho-ucsc Jun 26, 2025

nadove-ucsc requested a review from dsotirho-ucsc June 26, 2025 07:05

dsotirho-ucsc previously approved these changes Jun 26, 2025

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dsotirho-ucsc marked this pull request as ready for review June 26, 2025 18:14

dsotirho-ucsc requested a review from hannes-ucsc as a code owner June 26, 2025 18:14

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nadove-ucsc changed the base branch from develop to backports/36999c52 July 3, 2025 00:30

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 9dc69e5 to a0ad747 Compare July 3, 2025 00:30

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nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from a0ad747 to 8056e9e Compare July 9, 2025 06:56

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nadove-ucsc added 2 commits December 8, 2025 17:15

Refactor manifest tests

259849d

Refactor BigQuery column lookup in AnVIL plugin

124bce5

and document use case for default value

nadove-ucsc dismissed dsotirho-ucsc’s stale review via c9c334a December 9, 2025 01:15

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch 2 times, most recently from c9c334a to 259849d Compare December 10, 2025 00:51

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nadove-ucsc added 6 commits December 10, 2025 13:06

fixup! Refactor BigQuery column lookup in AnVIL plugin

968b242

Verify download size in mirror file service

b65d5bd

[r] Fix: AnVIL uses uncommon encoding for MD5 digests (#7154)

6201409

Enable mirror URI column in compact AnVIL manifests (#7151)

93f866f

Previously disabled due to the issues with MD5 encoding

[u] Enable mirroring in anvildev and anvilbox (#7214)

7db9003

[u] Work around unmirrorable files in 1000G snapshot and add FIXME (#…

4695a1a

…7634)

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 2969660 to 4695a1a Compare December 10, 2025 21:08

nadove-ucsc requested a review from hannes-ucsc December 10, 2025 21:43

nadove-ucsc assigned hannes-ucsc Dec 10, 2025

	def _columns_by_table(self) -> Mapping[str, AbstractSet[str]]:
	def __columns_by_table(self) -> Mapping[str, AbstractSet[str]]:

Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

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Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

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