feat(scripts): add operator script for bulk score-set pipeline reruns - #841
Merged
bencap merged 1 commit intoAug 12, 2026
Merged
Conversation
bencap
force-pushed
the
feature/bencap/796/pipeline-operator-script
branch
from
August 12, 2026 01:15
cb809b7 to
b62685a
Compare
Coverage Report for CI Build 31553002891Warning No base build found for commit Coverage: 88.221%Details
Uncovered Changes
Coverage RegressionsRequires a base build to compare against. How to fix this → Coverage Stats
💛 - Coveralls |
bencap
force-pushed
the
chore/bencap/797/export-hardening
branch
from
August 12, 2026 18:27
585868e to
50c3137
Compare
bencap
changed the base branch from
chore/bencap/797/export-hardening
to
release-2026.2.7.1
August 12, 2026 19:15
Add run_score_set_pipelines.py to bulk-drive map/annotate pipelines across a cohort of score sets, replacing the one-score-set-per-invocation run_pipeline.py for large campaigns. It resolves a cohort by collection, publication state, taxonomy, or explicit URNs, orders it to exploit ClinGen's 24h cache, bounds concurrency against a campaign-wide in-flight window, skips already-current work, and reports per-score-set outcomes. - Extend PipelineFactory.create_pipeline with a custom_pipeline param (mutually exclusive with pipeline_name) so a caller can run an ad-hoc job subset under its own tracked name, enabling --phase presets (caid, fast-annotate, vep) that isolate slow VEP annotation from the fast jobs that unblock everything else. - Normalize finished_at to UTC before date comparison in is_current, since DB-returned timestamps can be in the server/session timezone and shift the day near midnight. - Filter out the start_pipeline JobRun's empty job_params in pipeline/ score-set queries, which could otherwise nondeterministically report score_set_id as None and let plan_enqueue miss an already in-flight pipeline for a score set. - Add tests/scripts/ package with local fixtures and factories, plus new PipelineFactory unit tests for the custom_pipeline contract.
bencap
force-pushed
the
feature/bencap/796/pipeline-operator-script
branch
from
August 12, 2026 19:19
b62685a to
c08d0c6
Compare
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Add run_score_set_pipelines.py to bulk-drive map/annotate pipelines across a cohort of score sets, replacing the one-score-set-per-invocation run_pipeline.py for large campaigns. It resolves a cohort by collection, publication state, taxonomy, or explicit URNs, orders it to exploit ClinGen's 24h cache, bounds concurrency against a campaign-wide in-flight window, skips already-current work, and reports per-score-set outcomes.