Add updated snapshot for project 6135382f to `lm8` (#6689) #6701

achave11-ucsc · 2024-11-12T18:24:42Z

Connected issues: #6689

Notes

Manually index lm8's snapshot 6135382f

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

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 connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

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This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
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Author (reindex, API changes)

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}
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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}
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This PR and its connected 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 connected issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR}

Author (before every review)

Rebased PR branch on develop, squashed old fixups
Ran make requirements_update _{or this PR does not modify requirements*.txt, common.mk, Makefile and Dockerfile}
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}

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Actually approved the PR
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N reviews label is accurate
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Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
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Changed the target branch of the blocked PR to develop _{or this PR is not labeled base}
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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

codecov · 2024-11-12T18:45:09Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.59%. Comparing base (2bfc8ca) to head (19ba5d9).
Report is 2 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #6701   +/-   ##
========================================
  Coverage    85.59%   85.59%           
========================================
  Files          155      155           
  Lines        20903    20903           
========================================
  Hits         17892    17892           
  Misses        3011     3011

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

coveralls · 2024-11-12T18:46:17Z

coverage: 85.613%. remained the same
when pulling 19ba5d9 on issues/achave11-ucsc/6689-index-6135382f-lm8
into 2bfc8ca on develop.

hannes-ucsc · 2024-11-13T20:26:34Z

deployments/prod/environment.py

@@ -1181,6 +1181,7 @@ def mkdict(previous_catalog: dict[str, str],
    mksrc('bigquery', 'datarepo-c9158593', 'lungmap_prod_20037472ea1d4ddb9cd356a11a6f0f76__20220307_20241002_lm8'),
    mksrc('bigquery', 'datarepo-35a6d7ca', 'lungmap_prod_3a02d15f9c6a4ef7852b4ddec733b70b__20241001_20241002_lm8'),
    mksrc('bigquery', 'datarepo-131a1234', 'lungmap_prod_4ae8c5c91520437198276935661f6c84__20231004_20241002_lm8'),
+    mksrc('bigquery', 'datarepo-936db385', 'lungmap_prod_6135382f487d4adb9cf84d6634125b68__20230207_20241106_lm8'),


I think this requires bumping the count.

Negative, this is actually an update to https://github.com/DataBiosphere/azul/pull/6701/files/56c53c1a7fa0865c798600f5dcd8985bb885b0a2#diff-8f9d00d944593bab5e94f965b9d6dc374cbc696434623ed155ddf59ebf8edad2R1166.

Bumping the count causes issues:

❯ . environment envhook.py: Currently disabled because the ENVHOOK environment variable is set to 0. export_environment.py: Loading environment from deployments/prod/environment.local.py export_environment.py: Loading environment from environment.local.py export_environment.py: Loading environment from deployments/prod/environment.py Traceback (most recent call last): File "/Users/achave11/Pycharm/Azul/azul.stable/scripts/export_environment.py", line 434, in <module> main() File "/Users/achave11/Pycharm/Azul/azul.stable/scripts/export_environment.py", line 418, in main env, warning = load_env() ^^^^^^^^^^ File "/Users/achave11/Pycharm/Azul/azul.stable/scripts/export_environment.py", line 159, in load_env active_deployment_dir and _load(active_deployment_dir), ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/achave11/Pycharm/Azul/azul.stable/scripts/export_environment.py", line 148, in _load spec.loader.exec_module(module) File "<frozen importlib._bootstrap_external>", line 940, in exec_module File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed File "/Users/achave11/Pycharm/Azul/azul.stable/deployments/prod/environment.py", line 1179, in <module> lm8_sources = mkdict(lm7_sources, 13, mkdelta([ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/achave11/Pycharm/Azul/azul.stable/deployments/prod/environment.py", line 53, in mkdict assert num_expected == num_actual, (num_expected, num_actual) ^^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: (13, 12)

hannes-ucsc · 2024-11-13T21:01:28Z

Security design review

github-actions bot added the orange [process] Done by the Azul team label Nov 12, 2024

achave11-ucsc added reindex:prod [process] PR requires reindexing prod reindex:partial [process] PR allows for (de)indexing a specific source or catalog labels Nov 12, 2024

achave11-ucsc requested a review from dsotirho-ucsc November 12, 2024 18:57

achave11-ucsc assigned dsotirho-ucsc Nov 12, 2024

dsotirho-ucsc assigned hannes-ucsc and unassigned dsotirho-ucsc Nov 13, 2024

dsotirho-ucsc removed their request for review November 13, 2024 19:34

dsotirho-ucsc marked this pull request as ready for review November 13, 2024 19:34

dsotirho-ucsc requested a review from hannes-ucsc as a code owner November 13, 2024 19:34

hannes-ucsc requested changes Nov 13, 2024

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hannes-ucsc assigned achave11-ucsc and unassigned hannes-ucsc and achave11-ucsc Nov 13, 2024

hannes-ucsc added the 1 review [process] Lead requested changes once label Nov 13, 2024

achave11-ucsc requested a review from hannes-ucsc November 13, 2024 20:32

achave11-ucsc assigned hannes-ucsc Nov 13, 2024

hannes-ucsc added 0 reviews [process] Lead didn't request any changes and removed 1 review [process] Lead requested changes once labels Nov 13, 2024

hannes-ucsc approved these changes Nov 13, 2024

View reviewed changes

hannes-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Nov 13, 2024

[r] Add updated snapshot for project 6135382f to lm8 (#6689)

19ba5d9

dsotirho-ucsc force-pushed the issues/achave11-ucsc/6689-index-6135382f-lm8 branch from 56c53c1 to 19ba5d9 Compare November 14, 2024 20:15

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Nov 14, 2024

dsotirho-ucsc merged commit fba2e1b into develop Nov 14, 2024
11 checks passed

dsotirho-ucsc deleted the issues/achave11-ucsc/6689-index-6135382f-lm8 branch November 14, 2024 22:28

dsotirho-ucsc removed their assignment Nov 15, 2024

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Add updated snapshot for project 6135382f to `lm8` (#6689) #6701

Add updated snapshot for project 6135382f to `lm8` (#6689) #6701

achave11-ucsc commented Nov 12, 2024 •

edited by dsotirho-ucsc

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hannes-ucsc commented Nov 13, 2024

Add updated snapshot for project 6135382f to lm8 (#6689) #6701

Add updated snapshot for project 6135382f to lm8 (#6689) #6701

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achave11-ucsc commented Nov 12, 2024 • edited by dsotirho-ucsc Loading

Notes

Checklist

Author

Author (partiality)

Author (chains)

Author (reindex, API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator (before pushing merge the commit)

System administrator

Operator (before pushing merge the commit)

Operator (chain shortening)

Operator (after pushing the merge commit)

Operator (reindex)

Operator

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hannes-ucsc commented Nov 13, 2024

Security design review

Add updated snapshot for project 6135382f to `lm8` (#6689) #6701

Add updated snapshot for project 6135382f to `lm8` (#6689) #6701

achave11-ucsc commented Nov 12, 2024 •

edited by dsotirho-ucsc

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coveralls commented Nov 12, 2024 •

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achave11-ucsc Nov 13, 2024 •

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