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Fix: Subgraph stitching query crashes BQ emulator (#5847) #5862

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merged 1 commit into from
Jan 24, 2024

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@hannes-ucsc hannes-ucsc commented Jan 17, 2024

Connected issues: #5847

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

Author (partiality)

  • Added p tag to titles of partial commits
  • Added partial label to PR or this PR completely resolves all connected issues
  • All connected issues are resolved partially or this PR does not have the partial label

1 when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (reindex, API changes)

  • Added r tag to commit title or this PR does not require reindexing
  • Added reindex label to PR or this PR does not require reindexing
  • PR and connected issue 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 (chains)

  • This PR is blocked by previous PR in the chain or this PR is not chained to another PR
  • Added base label to the blocking PR or this PR is not chained to another PR
  • Added chained label to this PR or this PR is not chained to another PR

Author (upgrading deployments)

  • 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
  • Added upgrade label to PR or this PR does not require upgrading deployments

Author (operator tasks)

  • Added checklist items for additional operator tasks or this PR does not require additional tasks

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 prod branch has no temporary hotfixes for any connected issues

Author (before every review)

  • Rebased PR branch on develop, squashed old fixups
  • Ran make requirements_update or this PR does not touch requirements*.txt, common.mk, Makefile and Dockerfile
  • Added R tag to commit title or this PR does not touch requirements*.txt
  • Added reqs label to PR or this PR does not touch requirements*.txt
  • make integration_test passes in personal deployment or this PR does not touch functionality that could break the IT

Peer reviewer (after requesting changes)

Uncheck the Author (before every review) checklists.

Peer reviewer (after approval)

  • PR is not a draft
  • Ticket is in Review requested column
  • Requested review from system administrator
  • PR is assigned to system administrator

System administrator (after requesting changes)

Uncheck the before every review checklists. Update the N reviews label.

System administrator (after approval)

  • Actually approved the PR
  • Labeled connected issues as demo or no demo
  • Commented on connected issues about demo expectations or all connected issues are labeled no demo
  • Decided if PR can be labeled no sandbox
  • PR title is appropriate as title of merge commit
  • N reviews label is accurate
  • Moved ticket to Approved column
  • PR is assigned to current operator

Operator (before pushing merge the commit)

  • Checked reindex label and r commit title tag
  • Checked that demo expectations are clear or all connected issues are labeled no demo
  • PR has checklist items for upgrading instructions or PR is not labeled upgrade
  • Squashed PR branch and rebased onto develop
  • Sanity-checked history
  • Selected dev.shared and ran CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused or this PR does not change any Docker image versions
  • Selected anvildev.shared and ran CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused or this PR does not change any Docker image versions
  • Selected anvilprod.shared and ran CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused or this PR does not change any Docker image versions
  • Pushed PR branch to GitHub
  • Added sandbox label or PR is labeled no sandbox
  • Pushed PR branch to GitLab dev or PR is labeled no sandbox
  • Pushed PR branch to GitLab anvildev or PR is labeled no sandbox
  • Pushed PR branch to GitLab anvilprod or PR is labeled no sandbox
  • Build passes in sandbox deployment or PR is labeled no sandbox
  • Build passes in anvilbox deployment or PR is labeled no sandbox
  • Build passes in hammerbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in sandbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in anvilbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in hammerbox deployment or PR is labeled no sandbox
  • Deleted unreferenced indices in sandbox or this PR does not remove catalogs or otherwise causes unreferenced indices in dev
  • Deleted unreferenced indices in anvilbox or this PR does not remove catalogs or otherwise causes unreferenced indices in anvildev
  • Deleted unreferenced indices in hammerbox or this PR does not remove catalogs or otherwise causes unreferenced indices in anvilprod
  • Started reindex in sandbox or this PR does not require reindexing dev
  • Started reindex in anvilbox or this PR does not require reindexing anvildev
  • Started reindex in hammerbox or this PR does not require reindexing anvilprod
  • Checked for failures in sandbox or this PR does not require reindexing dev
  • Checked for failures in anvilbox or this PR does not require reindexing anvildev
  • Checked for failures in hammerbox or this PR does not require reindexing anvilprod
  • Title of merge commit starts with title from this PR
  • Added PR reference to merge commit title
  • Collected commit title tags in merge commit title but only include p if the PR is labeled partial
  • Moved connected issues to Merged column in ZenHub
  • Pushed merge commit to GitHub

Operator (chain shortening)

  • Changed the target branch of the blocked PR to develop or this PR is not labeled base
  • Removed the chained label from the blocked PR or this PR is not labeled base
  • Removed the blocking relationship from the blocked PR or this PR is not labeled base
  • Removed the base label from this PR or this PR is not labeled base

Operator (after pushing the merge commit)

  • Pushed merge commit to GitLab dev or PR is labeled no sandbox
  • Pushed merge commit to GitLab anvildev or PR is labeled no sandbox
  • Pushed merge commit to GitLab anvilprod or PR is labeled no sandbox
  • Build passes on GitLab dev1
  • Reviewed build logs for anomalies on GitLab dev1
  • Build passes on GitLab anvildev1
  • Reviewed build logs for anomalies on GitLab anvildev1
  • Build passes on GitLab anvilprod1
  • Reviewed build logs for anomalies on GitLab anvilprod1
  • Selected dev.shared and ran make -C terraform/shared apply or this PR does not change any Docker image versions
  • Selected anvildev.shared and ran make -C terraform/shared apply or this PR does not change any Docker image versions
  • Selected anvilprod.shared and ran make -C terraform/shared apply or this PR does not change any Docker image versions
  • Deleted PR branch from GitHub
  • Deleted PR branch from GitLab dev
  • Deleted PR branch from GitLab anvildev
  • Deleted PR branch from GitLab anvilprod

1 When pushing the merge commit is skipped due to the PR being
labelled no sandbox, the next build triggered by a PR whose merge commit is
pushed determines this checklist item.

Operator (reindex)

  • Deleted unreferenced indices in dev or this PR does not remove catalogs or otherwise causes unreferenced indices in dev
  • Deleted unreferenced indices in anvildev or this PR does not remove catalogs or otherwise causes unreferenced indices in anvildev
  • Deleted unreferenced indices in anvilprod or this PR does not remove catalogs or otherwise causes unreferenced indices in anvilprod
  • Considered deindexing individual sources in dev or this PR does not merely remove sources from existing catalogs in dev
  • Considered deindexing individual sources in anvildev or this PR does not merely remove sources from existing catalogs in anvildev
  • Considered deindexing individual sources in anvilprod or this PR does not merely remove sources from existing catalogs in anvilprod
  • Considered indexing individual sources in dev or this PR does not merely add sources to existing catalogs in dev
  • Considered indexing individual sources in anvildev or this PR does not merely add sources to existing catalogs in anvildev
  • Considered indexing individual sources in anvilprod or this PR does not merely add sources to existing catalogs in anvilprod
  • Started reindex in dev or this PR does not require reindexing dev
  • Started reindex in anvildev or this PR does not require reindexing anvildev
  • Started reindex in anvilprod or this PR does not require reindexing anvilprod
  • Checked for and triaged indexing failures in dev or this PR does not require reindexing dev
  • Checked for and triaged indexing failures in anvildev or this PR does not require reindexing anvildev
  • Checked for and triaged indexing failures in anvilprod or this PR does not require reindexing anvilprod
  • Emptied fail queues in dev deployment or this PR does not require reindexing dev
  • Emptied fail queues in anvildev deployment or this PR does not require reindexing anvildev
  • Emptied fail queues in anvilprod deployment or this PR does not require reindexing anvilprod

Operator

  • Promotion PR contains CL items for two-phase deployment of shared.prod
  • 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

@github-actions github-actions bot added the orange [process] Done by the Azul team label Jan 17, 2024
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coveralls commented Jan 17, 2024

Coverage Status

coverage: 83.179% (+0.06%) from 83.121%
when pulling 1c61f88 on issues/hannes-ucsc/5847-bq-emulator-crash
into 2bc279d on develop.

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codecov bot commented Jan 17, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (2bc279d) 83.10% compared to head (1c61f88) 83.15%.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #5862      +/-   ##
===========================================
+ Coverage    83.10%   83.15%   +0.05%     
===========================================
  Files          154      154              
  Lines        19634    19636       +2     
===========================================
+ Hits         16316    16329      +13     
+ Misses        3318     3307      -11     

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

@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/5847-bq-emulator-crash branch from b57add0 to 0a5be74 Compare January 17, 2024 04:38
@hannes-ucsc hannes-ucsc added the upgrade [process] PR includes commit requiring manual upgrade label Jan 17, 2024
@hannes-ucsc hannes-ucsc force-pushed the issues/hannes-ucsc/5847-bq-emulator-crash branch from 0a5be74 to 31db973 Compare January 17, 2024 06:17
@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/hannes-ucsc/5847-bq-emulator-crash branch from 31db973 to 1c61f88 Compare January 23, 2024 23:46
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Pro forma approval

@dsotirho-ucsc dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Jan 24, 2024
@dsotirho-ucsc dsotirho-ucsc merged commit c0c1b6f into develop Jan 24, 2024
12 checks passed
@dsotirho-ucsc dsotirho-ucsc deleted the issues/hannes-ucsc/5847-bq-emulator-crash branch January 24, 2024 04:13
@dsotirho-ucsc dsotirho-ucsc removed their assignment Jan 27, 2024
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4 participants