Fix: Invalid columns in compact manifest for AnVIL (#6110) #6111

hannes-ucsc · 2024-04-01T01:12:59Z

Connected issues: #6110, #4135

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
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}

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

Author (chains)

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}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or this PR does not require reindexing}
This PR is labeled reindex:dev _{or does not require reindexing dev}
This PR is labeled reindex:anvildev _{or does not require reindexing anvildev}
This PR is labeled reindex:anvilprod _{or does not require reindexing anvilprod}
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}
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)

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}
Ran make image_manifests.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}
This PR is labeled upgrade _{or does not require upgrading deployments}
This PR is labeled deploy:shared _{or does not modify image_manifests.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 (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 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}

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 only the 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
A comment to this PR details the completed security design review _{or this PR is a promotion or a backport}
PR title is appropriate as title of merge commit
N reviews label is accurate
Moved ticket to Approved column
PR is assigned to only the operator

Operator (before pushing merge the commit)

System administrator

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}
Background migrations for anvilprod.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator

Operator (before pushing merge the commit)

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)

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)

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial and reindex:prod labels to the next promotion PR _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial and reindex:prod labels from the description of this PR to that of the next promotion PR _{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 · 2024-04-01T01:35:28Z

Codecov Report

Attention: Patch coverage is 91.92547% with 13 lines in your changes are missing coverage. Please review.

Project coverage is 85.37%. Comparing base (a74ed8f) to head (251945f).

Files	Patch %	Lines
test/integration_test.py	0.00%	12 Missing ⚠️
src/azul/plugins/metadata/anvil/__init__.py	95.45%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #6111      +/-   ##
===========================================
+ Coverage    85.35%   85.37%   +0.01%     
===========================================
  Files          154      154              
  Lines        20063    20110      +47     
===========================================
+ Hits         17125    17168      +43     
- Misses        2938     2942       +4

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

coveralls · 2024-04-01T01:35:31Z

coverage: 85.388% (+0.01%) from 85.374%
when pulling 251945f on issues/hannes-ucsc/6110-compact-anvil-manifest
into a74ed8f on develop.

hannes-ucsc · 2024-04-03T05:08:24Z

Security design review

Dissolve SearchResponseFactory

Dissolve SummaryResponseFactory

Introduce SpecialFields class

Add source_spec to SpecialFields

Add bundle_uuid and bundle_version to SpecialFields

This is the main part, it does break the IT.

Name special fields in camel case on AnVIL. This repairs the IT.

… sort of hierarchically

dsotirho-ucsc

Pro forma approval

github-actions bot added the orange [process] Done by the Azul team label Apr 1, 2024

hannes-ucsc changed the title ~~Issues/hannes ucsc/6110 compact anvil manifest~~ Fix: Invalid columns in compact manifest for AnVIL (#6110) Apr 1, 2024

hannes-ucsc force-pushed the issues/hannes-ucsc/6110-compact-anvil-manifest branch from c545379 to 31e70c9 Compare April 2, 2024 23:56

hannes-ucsc added the API API change affecting callers label Apr 3, 2024

hannes-ucsc force-pushed the issues/hannes-ucsc/6110-compact-anvil-manifest branch 3 times, most recently from 705ce2c to 363b91b Compare April 3, 2024 02:45

hannes-ucsc assigned dsotirho-ucsc Apr 3, 2024

hannes-ucsc added 12 commits April 2, 2024 23:36

[1/2] Dissolve response factories into response stages (#4135)

faa7eec

Dissolve SearchResponseFactory

[2/2] Dissolve response factories into response stages (#4135)

973443b

Dissolve SummaryResponseFactory

Collect stray source ID field references

3ba2a51

[1/3] Plugin-ify more special field names

ae692d3

Introduce SpecialFields class

[2/3] Plugin-ify more special field names

e7d3487

Add source_spec to SpecialFields

[3/3] Plugin-ify more special field names

5449a29

Add bundle_uuid and bundle_version to SpecialFields

Refactor manifest tests and DRY up URI/URL literals

6a99345

Add test for AnVIL manifest

7981575

[A 1/2] Derive manifest config for AnVIL from field mapping (#6110)

f16f103

This is the main part, it does break the IT.

[A 2/2] Derive manifest config for AnVIL from field mapping (#6110)

7ee9827

Name special fields in camel case on AnVIL. This repairs the IT.

[A] Suppress columns solely used for URL injection

7b318aa

[a] Reorder entries in manifest and /index endpoint response

251945f

… sort of hierarchically

dsotirho-ucsc force-pushed the issues/hannes-ucsc/6110-compact-anvil-manifest branch from cb3dc32 to 251945f Compare April 3, 2024 06:36

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Apr 3, 2024

dsotirho-ucsc reviewed Apr 3, 2024

View reviewed changes

dsotirho-ucsc approved these changes Apr 3, 2024

View reviewed changes

dsotirho-ucsc merged commit 3ddf36e into develop Apr 3, 2024
12 checks passed

dsotirho-ucsc deleted the issues/hannes-ucsc/6110-compact-anvil-manifest branch April 3, 2024 18:03

dsotirho-ucsc removed their assignment Apr 3, 2024

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Fix: Invalid columns in compact manifest for AnVIL (#6110) #6111

Fix: Invalid columns in compact manifest for AnVIL (#6110) #6111

hannes-ucsc commented Apr 1, 2024 •

edited by dsotirho-ucsc

Loading

codecov bot commented Apr 1, 2024 •

edited

Loading

coveralls commented Apr 1, 2024 •

edited

Loading

hannes-ucsc commented Apr 3, 2024

dsotirho-ucsc left a comment

Fix: Invalid columns in compact manifest for AnVIL (#6110) #6111

Fix: Invalid columns in compact manifest for AnVIL (#6110) #6111

Conversation

hannes-ucsc commented Apr 1, 2024 • edited by dsotirho-ucsc Loading

Checklist

Author

Author (partiality)

Author (chains)

Author (reindex, API changes)

Author (upgrading deployments)

Author (operator tasks)

Author (hotfixes)

Author (before every review)

Peer reviewer (after requesting changes)

Peer reviewer (after approval)

System administrator (after requesting changes)

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

Shorthand for review comments

codecov bot commented Apr 1, 2024 • edited Loading

Codecov Report

coveralls commented Apr 1, 2024 • edited Loading

hannes-ucsc commented Apr 3, 2024

Security design review

dsotirho-ucsc left a comment

Choose a reason for hiding this comment

hannes-ucsc commented Apr 1, 2024 •

edited by dsotirho-ucsc

Loading

codecov bot commented Apr 1, 2024 •

edited

Loading

coveralls commented Apr 1, 2024 •

edited

Loading