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@hannes-ucsc hannes-ucsc commented Jan 4, 2026

Linked issues: #7673

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  • PR is assigned to the author
  • Status of PR is In progress
  • PR is a draft
  • Target branch is develop
  • Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
  • PR is linked to all issues it (partially) resolves
  • Status of linked issues is In progress
  • PR description links to linked issues
  • PR title matches1 that of a linked issue or comment in PR explains why they're different
  • PR title references all linked issues
  • For each linked 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 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
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  • 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

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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
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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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  • 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
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  • N reviews label is accurate
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  • Checked reindex:… labels and r commit title tag
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  • Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused or this PR is not labeled deploy:shared
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  • Started reindex in sandbox or this PR is not labeled reindex:dev
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  • All status checks passed and the PR is mergeable
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  • Pushed merge commit to GitLab dev
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  • Ran _select dev.shared && make -C terraform/shared apply or this PR is not labeled deploy:shared
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  • Deindexed all unreferenced catalogs in dev or this PR is neither labeled reindex:partial nor reindex:dev
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  • Deindexed specific sources in dev or this PR is neither labeled reindex:partial nor reindex:dev
  • Deindexed specific sources in anvildev or this PR is neither labeled reindex:partial nor reindex:anvildev
  • Indexed specific sources in dev or this PR is neither labeled reindex:partial nor reindex:dev
  • Indexed specific sources in anvildev or this PR is neither labeled reindex:partial nor reindex:anvildev
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  • Emptied fail queues in anvildev or this PR does not require reindexing anvildev
  • Restarted the Data Browser pipeline for the ucsc/hca/dev branch on GitLab in dev or this PR does not require reindexing dev
  • Restarted the Data Browser pipeline for the ucsc/lungmap/dev branch on GitLab in dev or this PR does not require reindexing dev
  • Restarted deploy_browser job in the GitLab pipeline for this PR in dev or this PR does not require reindexing dev
  • Restarted the Data Browser pipeline for the ucsc/anvil/anvildev branch on GitLab in anvildev or this PR does not require reindexing anvildev
  • Restarted deploy_browser job in the GitLab pipeline for this PR in anvildev or this PR does not require reindexing anvildev

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
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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

Yes, generators are iterators and therefore iterables. However, I consider the fact that iterators are iterables a flaw in Python. The type system should express whether something can be consumed more than once or not.
@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/7673 branch from 9069c2a to ee3e462 Compare January 4, 2026 08:13
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codecov bot commented Jan 4, 2026

Codecov Report

❌ Patch coverage is 89.02439% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.84%. Comparing base (158e524) to head (7c8217e).

Files with missing lines Patch % Lines
src/azul/indexer/mirror_service.py 83.92% 9 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #7676      +/-   ##
===========================================
+ Coverage    84.82%   84.84%   +0.01%     
===========================================
  Files          156      156              
  Lines        22862    22896      +34     
===========================================
+ Hits         19393    19425      +32     
- Misses        3469     3471       +2     

☔ View full report in Codecov by Sentry.
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coveralls commented Jan 4, 2026

Coverage Status

coverage: 85.061% (+0.01%) from 85.047%
when pulling 7c8217e on issues/hannes-ucsc/7673
into 158e524 on develop.

@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/7673 branch from ee3e462 to 8369ac5 Compare January 5, 2026 07:25
@achave11-ucsc achave11-ucsc linked an issue Jan 5, 2026 that may be closed by this pull request
@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/7673 branch from 8369ac5 to c8ad383 Compare January 6, 2026 01:52
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Security design review

  • Security design review completed; this PR does not
    • … affect authentication; for example:
      • OAuth 2.0 with the application (API or Swagger UI)
      • Authentication of developers with Google Cloud APIs
      • Authentication of developers with AWS APIs
      • Authentication with a GitLab instance in the system
      • Password and 2FA authentication with GitHub
      • API access token authentication with GitHub
      • Authentication with Terra
    • … affect the permissions of internal users like access to
      • Cloud resources on AWS and GCP
      • GitLab repositories, projects and groups, administration
      • an EC2 instance via SSH
      • GitHub issues, pull requests, commits, commit statuses, wikis, repositories, organizations
    • … affect the permissions of external users like access to
      • TDR snapshots
    • … affect permissions of service or bot accounts
      • Cloud resources on AWS and GCP
    • … affect audit logging in the system, like
      • adding, removing or changing a log message that represents an auditable event
      • changing the routing of log messages through the system
    • … affect monitoring of the system
    • … introduce a new software dependency like
      • Python packages on PYPI
      • Command-line utilities
      • Docker images
      • Terraform providers
    • … add an interface that exposes sensitive or confidential data at the security boundary
    • … affect the encryption of data at rest
    • … require persistence of sensitive or confidential data that might require encryption at rest
    • … require unencrypted transmission of data within the security boundary
    • … affect the network security layer; for example by
      • modifying, adding or removing firewall rules
      • modifying, adding or removing security groups
      • changing or adding a port a service, proxy or load balancer listens on
  • Documentation on any unchecked boxes is provided in comments below

@achave11-ucsc achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Jan 6, 2026
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PR failed sandbox IT due to #7660, but also the failed (mirroring) queues weren't empty.

======================================================================
FAIL: test_indexing (integration_test.IndexingIntegrationTest.test_indexing) [mirror_sources_and_files]
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/builds/ucsc/azul/test/integration_test.py", line 385, in subTest
    yield
  File "/builds/ucsc/azul/test/integration_test.py", line 1789, in _test_mirroring
    self._assert_queues_empty([config.mirror_queue.to_fail.name])
    ~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/builds/ucsc/azul/test/integration_test.py", line 1410, in _assert_queues_empty
    self.assertTrue(self.azul_client.is_queue_empty(queue_name))
    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError: False is not true
----------------------------------------------------------------------

Failing section seems to have been introduced in this PR.

CloudWatch Logs Insights
region: us-east-1
log-group-names: /aws/lambda/azul-indexer-sandbox-mirror
data-sources:
facets:
start-time: 2026-01-06T07:30:05.112Z
end-time: 2026-01-06T07:31:51.882Z
query-string:

fields @timestamp, @message
| filter @message like /ERROR/
| sort @timestamp desc
| limit 10000

@timestamp @message
2026-01-06 07:31:05.051 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:31:00.479 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:57.004 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:56.909 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:51.435 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:51.336 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:47.889 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)
2026-01-06 07:30:40.944 [ERROR] AssertionError Traceback (most recent call last):   File "/var/task/azul/chalice.py", line 194, in patched_event_source_handler     return old_handler(self_, event, context)   File "/var/task/chalice/app.py", line 1761, in call     return self.handler(event_obj)   File "/var/task/azul/indexer/mirror_controller.py", line 65, in mirror     self.mirror(event)   File "/var/task/azul/indexer/mirror_controller.py", line 75, in mirror     self._handle_events(event, message_handler)   File "/var/task/azul/indexer/action_controller.py", line 50, in _handle_events     message_handler(action)   File "/var/task/azul/indexer/mirror_controller.py", line 73, in message_handler     self.service(action.catalog).mirror(action)   File "/var/task/azul/indexer/mirror_service.py", line 539, in mirror     self._queue_actions(self._mirror(action))   File "/var/task/azul/indexer/mirror_service.py", line 408, in _queue_actions     return self._queues.send_messages(self._mirror_queue(),   File "/var/task/azul/queues.py", line 208, in send_messages     for batch in chunked(messages, self.batch_size):   File "/opt/python/more_itertools/recipes.py", line 133, in take     return list(islice(iterable, n))   File "/var/task/azul/indexer/mirror_service.py", line 663, in _     yield devolve(FinalizeFileAction, a, upload=upload)   File "/var/task/azul/attrs.py", line 951, in devolve     assert issubclass(subcls, cls)

@achave11-ucsc achave11-ucsc removed their assignment Jan 6, 2026
@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/7673 branch from c8ad383 to 7c8217e Compare January 7, 2026 05:28
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NoSuchUpload exception when finalizing mirrored file

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