mvdbeek

.lint_skip Changes — Last 294 Commits (fix_testcase_validation branch)

Full Change Table

Tool	Action	Rule(s)	Commit
abricate	Removed	TestsCaseValidation	3a6544ef
artic	Added	OutputsFormatSourceReference	5b142410
b2btools	Removed	TestsCaseValidation	c6d48ef7
b2btools	Added	TestsCaseValidation	cce027b6

mvdbeek

Upstreaming plan: galaxy-tool-refactor → planemo

Date: 2026-06-13

This document records the analysis, decisions, and phased plan for moving galaxy-tool-refactor's auto-fix capabilities upstream into planemo (and its underlying galaxy.tool_util library). It is the output of a cross-codebase redundancy audit; the raw findings live in planemo_linter_parity.md.

mvdbeek

Harden API Parameter Validation — 10 Sentry Issues

Context

The last 10 GitHub issues filed on galaxyproject/galaxy (#22341–#22350) are all caused by malformed or malicious API inputs that bypass validation and crash deep inside application code, producing 500 errors logged to Sentry. Every one of these should be caught at the API frontier and returned as a 4xx response.

---

Fix 1 — #22350: ValueError parsing date b'file' in history controller

mvdbeek

Root Cause Analysis: Flaky test_swift_objectstore.py::test_tools[composite_output]

Issue: galaxyproject/galaxy#21226
Test: test/integration/objectstore/test_swift_objectstore.py::test_tools[composite_output]

Symptoms

The test transiently fails in two ways:

1. IncompleteRead: IncompleteRead(5242880 bytes read, 24576 more expected) — the server sets Content-Length for the full file but the connection closes after exactly 5 MB (80 × 64 KB chunks).

mvdbeek

Investigation: Flaky test_search_delete_hdca_output (Issue #21230)

Summary

func.array_agg(column, order_by=column) in SQLAlchemy silently drops the order_by keyword argument, generating array_agg(path_sig) instead of array_agg(path_sig ORDER BY path_sig). This means the HDCA signature arrays used for job search equivalence checking are unordered, causing non-deterministic comparison results on PostgreSQL.

Root Cause

In lib/galaxy/managers/jobs.py, the agg_expression method:

mvdbeek

"""Demonstrate the N+1 fix for workflow download (GALAXY-MAIN-14JQ).

Creates a workflow with many steps and connections, then measures
the number of SQL statements emitted when accessing input_connections
with and without the selectinload fix.
"""

import logging
import threading
import time

mvdbeek

"""Benchmark for UrlBuilder.url_path_for caching.

Demonstrates the performance difference when serializing N history items,
each requiring up to 2 url_path_for calls. Without caching, each call
does a linear scan through all registered routes. With caching, only the
first call per route name scans; subsequent calls go directly to the
matching route.
"""

import sys

mvdbeek

PostgreSQL Query Planner Catastrophe: dataset_collection_element Self-Joins

Summary

Nested dataset collection queries in Galaxy degrade from ~8ms to 843 seconds when PostgreSQL's planner chooses hash/merge joins for dataset_collection_element self-joins. The fix: replace DCE-to-DCE joins with nested ARRAY(subquery) expressions.

Root Cause

mvdbeek

{
    "$defs": {
        "BatchDataInstance": {
            "additionalProperties": false,
            "properties": {
                "src": {
                    "enum": [
                        "hda",
                        "ldda",
                        "hdca"

mvdbeek

Plan: Fix Interrupted Celery set_meta Causes Stuck Non-Terminal Jobs (#20186)

Problem Analysis

When metadata_strategy: directory_celery (or celery_extended) is configured, if the Celery process is interrupted (OOM killed, process restart, etc.) while executing a set_job_metadata task, jobs become permanently stuck in a non-terminal state (running) with no recovery mechanism.

Root Cause

The handler blocks forever on .get() when a worker dies.