Skip to content

Update process results workflow for new website #919

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
wants to merge 57 commits into
base: main
Choose a base branch
from
Open

Update process results workflow for new website #919

wants to merge 57 commits into from

Conversation

lazappi
Copy link
Member

@lazappi lazappi commented Feb 3, 2025 •
edited
Loading

Describe your changes

  • Add a new component to combine results output
  • Update the results processing workflow to output combined results
  • Update results format to new JSON schemas

TODO:

  • Output metric execution info from get_results
  • Update generate_qc to new schema
  • Update combine_output to new schema
  • Add schema validation to components
    • Add "additionalProperties": false to schemas
    • Add schemas to input info
  • Add roles to author schema
  • Add report
  • Update workflow to new components
  • Update container image versions
  • Strip quotes from descriptions
  • Add QC check for missing controls
  • Add a script for creating results v4 test resources
  • Update the main repository reference
  • Add a QC check for missing links
  • Test reprocesssing existing results

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
    • Documentation

  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@lazappi
Copy link
Member Author

lazappi commented Feb 3, 2025

This should produce a combined tasks.json file in the format required by the new website. However, parts of that file (datasets etc.) will be in the v2 format which the website may not expect.

@lazappi lazappi marked this pull request as draft February 10, 2025 09:29
lazappi and others added 18 commits July 17, 2025 08:40
@lazappi
Add metric resources to results component/schema
d318832
@lazappi
Update generate_qc to match new schema
d5d1b8f 
Add some new QC checks
@lazappi
Update combine_output to new schema
11d6d9d
@lazappi
Update viash version and reference
6a91673
@lazappi
Update process_results workflow to new components
5f70ab9
@lazappi
Add render_report component
99a4a50
@lazappi
Add render_report to process results workflow
264790e
@lazappi
Handle missing values in generate_qc()
272bba8 
This can happen when a method is disabled/skipped so there are no
results to check
@lazappi
Handle missing controls in results report
8ab4f60 
Skip scaling/results when there are no controls or give a warning when
some controls failed
@rcannood
update common submodule
d8fdfd9
@rcannood
Merge remote-tracking branch 'origin/main' into feature/no-ref/update…
15a2d18 
…-process-results
@lazappi
Merge remote-tracking branch 'origin' into feature/no-ref/update-proc…
e9e3ef1 
…ess-results

* origin:
  Rename items (#932)
  Rename dataset loader and add compression argument to more components (#930)
  Added op3 loader (#926)
  Patch: Update image version for openproblems/base_* images (#928)
  bump viash version (#925)
  Add email address to CoC (#923)
@lazappi
Merge branch 'feature/no-ref/update-process-results' of github.com:op…
cbf0e50 
…enproblems-bio/openproblems into feature/no-ref/update-process-results

* 'feature/no-ref/update-process-results' of github.com:openproblems-bio/openproblems:
  update common submodule
@lazappi
Strip quotes from descriptions/summaries
c1198e5
@lazappi
Add roles to author details
a7b9c6d
@lazappi
Add QC check for number of successful controls
19ecc9d
@lazappi
Handle missing exit codes in report
dc75604
@lazappi
Add schema validation to process_results workflow
382a35d
@lazappi lazappi marked this pull request as ready for review July 30, 2025 13:31
@lazappi lazappi requested a review from rcannood July 30, 2025 13:32
@lazappi lazappi mentioned this pull request Aug 4, 2025
Open
@rcannood rcannood force-pushed the feature/no-ref/update-process-results branch from cd92905 to 01acc49 Compare August 5, 2025 08:58
rcannood
rcannood requested changes Aug 5, 2025
View reviewed changes
Copy link
Member

@rcannood rcannood left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@lazappi Could you add scripts/create_resources/task_results_v4.sh?

rcannood
rcannood reviewed Aug 5, 2025
View reviewed changes
@lazappi lazappi requested a review from rcannood August 6, 2025 08:43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@rcannood rcannood Awaiting requested review from rcannood

Requested changes must be addressed to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@lazappi @rcannood