| Metric | Before | After |
|---|---|---|
| Total Lines | 160 | ~110 |
| Duplicated Lines | ~70 (44%) | ~10 (9%) |
| Test Methods | 2 | 2 |
| Helper Methods | 0 | 3 |
John Chilton jmchilton
jmchilton
/ dedup-plan-test-job-cache.md
Created
January 7, 2026 21:01
Deduplication Plan: test/integration/test_job_cache.py
jmchilton
/ trs_test_review.md
Created
January 5, 2026 15:21
TRS ID Tests Review: Mocking/Patching Analysis and Refactoring Plan
Review of tests/test_trs_id.py from the TRS ID support branch (claude/add-trs-id-support-mefAv). The branch adds support for running workflows via TRS IDs like workflow/github.com/iwc-workflows/parallel-accession-download/main.
jmchilton
/ gist_implementation.diff
Created
December 19, 2025 16:35
Add tool_shed_url config for explicit hostname setting
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| commit fa276e6532ba34939ce7d796370f679526e986e9 | |
| Author: John Chilton <[email protected]> | |
| Date: Fri Dec 19 11:16:09 2025 -0500 | |
| Add tool_shed_url config for explicit hostname setting | |
| Allows admins to set a fixed base URL for clone URLs and repository | |
| hostnames, useful when behind proxies or needing a specific public URL. | |
| 🤖 Generated with [Claude Code](https://claude.com/claude-code) |
Overall this is a solid test suite that covers the core functionality well. The tests are mostly focused on behavior, have clear names, and are independent. Mutation testing confirmed backward() behavior is properly tested.
jmchilton
/ refactor.diff
Created
December 17, 2025 19:50
Deduplication analysis and refactoring of test_history_archiving.py
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| diff --git a/test/integration/test_history_archiving.py b/test/integration/test_history_archiving.py | |
| index 2bbcb91ccb..e12c193fdd 100644 | |
| --- a/test/integration/test_history_archiving.py | |
| +++ b/test/integration/test_history_archiving.py | |
| @@ -229,7 +229,7 @@ class TestHistoryArchivingWithExportRecord(PosixFileSourceSetup, IntegrationTest | |
| ) | |
| self.dataset_populator.export_history_to_uri_async(history_id, target_uri, model_store_format) | |
| export_records = self.dataset_populator.get_history_export_tasks(history_id) | |
| - assert len(export_records) == 1 | |
| + assert len(export_records) >= 1 |
jmchilton
/ HISTORY_MARKDOWN_PLAN.md
Last active
December 24, 2025 14:53
History Notebooks: Implementation Plan for Galaxy
This plan implements History Notebooks - markdown documents tied to Galaxy histories that use HID-relative references. The feature enables human-AI collaborative analysis documentation with paths to Pages and Workflow Reports.
Reference Documents:
THE_PROBLEM_AND_GOAL.md- Vision and motivationRESEARCH_FOR_PLANNING.md- Backend implementation researchRESEARCH_FOR_PLANNING_UX.md- Frontend/UX implementation research
jmchilton
/ lively-napping-fiddle.md
Created
December 4, 2025 19:08
IWC Workflow Integration Plan - Two Implementation Approaches
Add link to IWC (Intergalactic Workflow Commission) curated workflows at https://iwc.galaxyproject.org/ in Galaxy's workflow list interface. Implement BOTH a tab approach and a banner approach so you can decide which works better.
- IWC has 100+ vetted bioinformatics workflows
- Current WorkflowList has 3 tabs: My workflows, Shared with me, Public workflows
- No existing IWC integration in frontend
- Uses Vue 3 + Bootstrap Vue + TypeScript
jmchilton
/ omero_review.md
Created
November 30, 2025 21:19
OMERO File Source Plugin Architecture Review
I'm review a PR. It adds this file lib/galaxy/files/sources/omero.py - which is implementing a Galaxy File Source plugins. I'm worried about the size of the file - it seems large and it interwines plugin implementation logic and API communication a lot - would it make sense to extract the API interaction layer out and reduce the size of the plugin or does it make more sense as is?
Based on my analysis, here's my assessment:
jmchilton
/ WES_TASK_PAGINATION_PLAN.md
Created
November 20, 2025 15:44
WES Task Logs Pagination - Database-Level Implementation Plan
Current implementation in wes.py:
_build_task_logs()(lines 886-913): Loads ALL WorkflowInvocationSteps into memory, then all related Jobs- Used in 3 places:
get_run_tasks()(line 701) - loads all, slices in Pythonget_run_task()(line 742) - loads all to find one_invocation_to_run_log()(line 868) - populates deprecated field
jmchilton
/ gist:333de4a142a25efe1071f85e712c063d
Last active
August 30, 2025 21:49
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