Index anvil14 in anvilprod (#7983) by dsotirho-ucsc · Pull Request #7989 · DataBiosphere/azul

dsotirho-ucsc · 2026-05-04T23:09:56Z

Linked issues: #7983

Notes

Perform a targeted reindex of the anvil14 catalog in anvilprod & hammerbox
No mirroring is to be performed for this PR. A separate issue Mirror anvil14 #7988 will cover that.

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 (mirror)

This PR is labeled mirror:dev _{or the changes introduced by it will not require mirroring of dev}
This PR is labeled mirror:anvildev _{or the changes introduced by it will not require mirroring of anvildev}
This PR is labeled mirror:anvilprod _{or the changes introduced by it will not require mirroring of anvilprod}
This PR is labeled mirror:prod _{or the changes introduced by it will not require mirroring of prod}
This PR is labeled mirror:partial and its description documents the specific mirroring procedure for dev, anvildev, anvilprod and prod _{or requires a full mirroring or carries none of the labels mirror:dev, mirror:anvildev, mirror:anvilprod and mirror: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 mirror:… labels
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 is not labelled mirror:dev}
Started mirroring in anvildev _{or this PR is not labelled mirror:anvildev}
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR is not labelled mirror:dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR is not labelled mirror:anvildev}
Emptied mirror fail queue in dev _{or this PR is not labelled mirror:dev}
Emptied mirror fail queue in anvildev _{or this PR is not labelled mirror:anvildev}

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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 · 2026-05-04T23:23:13Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.88%. Comparing base (655237d) to head (7e8cd52).
⚠️ Report is 9 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #7989   +/-   ##
========================================
  Coverage    84.88%   84.88%           
========================================
  Files          164      164           
  Lines        23511    23511           
========================================
  Hits         19958    19958           
  Misses        3553     3553

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coveralls · 2026-05-04T23:23:52Z

coverage: 84.968%. remained the same — issues/dsotirho-ucsc/7983-add-anvil14 into develop

dsotirho-ucsc · 2026-05-05T01:20:12Z

7128_IT_2026-05-04.txt

achave11-ucsc

Approved ✅

achave11-ucsc · 2026-05-05T16:11:54Z

Consider adding a CL to propagate the crossing out of mirroring instructions in the promotion PRs.

dsotirho-ucsc · 2026-05-05T19:45:21Z

+    source('5e75a098', 'eMERGE_eMERGEseq_HMB_NPU_20260403_ANV5_202604220434', no_ma_mirror),
+    source('c57b8824', 'nhp_dGTEx_V1_20260416_ANV5_202604170018'),


Use SourceService._public_sources() to verify the public snapshots in this catalog are identified as public by TDR.

Verified.

envhook.py: Setting AWS_PROFILE to 'anvilprod' ... >>> from azul.service.source_service import SourceService >>> public = SourceService()._public_sources >>> set1 = {str(source.ref.spec) for source in public['anvil14']} >>> from azul import config >>> catalog = config.catalogs['anvil14'] >>> set2 = {str(source) for source, prop in catalog.sources.items() if prop['mirror'] == True} >>> set1 == set2 True >>> for source in sorted(set1): ... print(source) tdr:bigquery:gcp:datarepo-04778e89:ANVIL_MAGE_20250925_ANV5_202509251453 tdr:bigquery:gcp:datarepo-0677c238:ANVIL_IGVF_Mouse_R1_20260416_ANV5_202604162312 tdr:bigquery:gcp:datarepo-0a4ee218:ANVIL_HPRC_20260121_ANV5_202601222125 tdr:bigquery:gcp:datarepo-12211c34:ANVIL_T2T_20230714_ANV5_202510101315 tdr:bigquery:gcp:datarepo-13858a9f:ANVIL_1000G_high_coverage_2019_20230517_ANV5_202409231755 tdr:bigquery:gcp:datarepo-25d953fe:ANVIL_GTEx_public_data_20240117_ANV5_202510101251 tdr:bigquery:gcp:datarepo-5dff1da7:ANVIL_NIA_CARD_Coriell_Cell_Lines_Open_20230727_ANV5_202410021438 tdr:bigquery:gcp:datarepo-a20ffbf1:ANVIL_T2T_CHRY_20240301_ANV5_202409252300 tdr:bigquery:gcp:datarepo-a443c0bd:ANVIL_ENCORE_RS293_20251123_ANV5_202511232027 tdr:bigquery:gcp:datarepo-b555b2f5:ANVIL_1000G_PRIMED_data_model_20240410_ANV5_202502211647 tdr:bigquery:gcp:datarepo-c4d45673:ANVIL_HPRC_R2_20260428_ANV5_202604281434 tdr:bigquery:gcp:datarepo-c57b8824:ANVIL_nhp_dGTEx_V1_20260416_ANV5_202604170018 tdr:bigquery:gcp:datarepo-f5dfb465:ANVIL_ENCORE_293T_20251123_ANV5_202511232035

There are only three public snapshots added in this PR for anvil14:

ANVIL_HPRC_R2_20260428_ANV5_202604281434 ANVIL_IGVF_Mouse_R1_20260416_ANV5_202604162312 ANVIL_nhp_dGTEx_V1_20260416_ANV5_202604170018

hannes-ucsc · 2026-05-06T05:02:42Z

[r] Index anvil14 in anvilprod (#7983)

7e8cd52

dsotirho-ucsc self-assigned this May 4, 2026

dsotirho-ucsc linked an issue May 4, 2026 that may be closed by this pull request

Index anvil14 in anvilprod #7983

Open

dsotirho-ucsc added reindex:anvilprod [process] PR requires reindexing anvilprod reindex:partial [process] PR allows for (de)indexing a specific source or catalog labels May 4, 2026

dsotirho-ucsc assigned achave11-ucsc May 5, 2026

dsotirho-ucsc requested a review from achave11-ucsc May 5, 2026 01:20

achave11-ucsc approved these changes May 5, 2026

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achave11-ucsc marked this pull request as ready for review May 5, 2026 16:10

achave11-ucsc requested a review from hannes-ucsc as a code owner May 5, 2026 16:10

achave11-ucsc assigned hannes-ucsc and unassigned achave11-ucsc May 5, 2026

dsotirho-ucsc commented May 5, 2026

View reviewed changes

dsotirho-ucsc assigned hannes-ucsc and unassigned hannes-ucsc May 5, 2026

hannes-ucsc approved these changes May 6, 2026

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hannes-ucsc removed their assignment May 6, 2026

hannes-ucsc added no sandbox [process] PR will not be tested in the sandbox 0 reviews [process] Lead didn't request any changes labels May 6, 2026

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Index anvil14 in anvilprod (#7983)#7989

Index anvil14 in anvilprod (#7983)#7989
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issues/dsotirho-ucsc/7983-add-anvil14

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edited by hannes-ucsc

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		source('5e75a098', 'eMERGE_eMERGEseq_HMB_NPU_20260403_ANV5_202604220434', no_ma_mirror),
		source('c57b8824', 'nhp_dGTEx_V1_20260416_ANV5_202604170018'),

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Notes

Checklist

Author

Author (partiality)

Author (reindex)

Author (mirror)

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

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hannes-ucsc commented May 6, 2026

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dsotirho-ucsc commented May 4, 2026 •

edited by hannes-ucsc

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