Marius van den Beek mvdbeek

Request a fresh Pulsar job status

This script asks the running Pulsar service to publish its current status for each job again. It uses the AMQP settings from app.yml; RabbitMQ's management plugin is not required. Publishing a request is not confirmation that Galaxy has processed the response.

1. Copy the script to the Pulsar host

Download pulsar-status.py from this gist and copy it to the Pulsar host, for example as /tmp/pulsar-status.py.

Run it as the Pulsar service user, using the service's Python environment and working directory. Substitute your actual paths below:

galaxyproject/galaxy#24299 review screenshots

Taken on 2026-10-22 against PR head 5f224cb525855aa9a5e9b07485aafb6f53197c25, with a client built from that head.

test_zz_probe_pr24299.py is a throwaway Playwright-backend test. It subclasses TestWorkflowInvocationGraph, so it reuses that class's two-branch workflow. To run it, drop it into lib/galaxy_test/selenium/ and run:

PROBE_OUT=/some/dir GALAXY_TEST_DRIVER_BACKEND=playwright GALAXY_TEST_SELENIUM_HEADLESS=1 \
  pytest "lib/galaxy_test/selenium/test_zz_probe_pr24299.py::TestProbePr24299::test_probe"

The test writes each screenshot plus results.json, which records the duplicate ids, the popover counts and the pane heights for each shot.

apt hangs when the first mirror in a `mirror+file:` source is down

Reproduction of the 6-hour apt-get update hangs in galaxyproject/galaxy CI on 2026-10-07. The cause was an outage of azure.archive.ubuntu.com.

GitHub's ubuntu-24.04 runner image points every Ubuntu suite at mirror+file:/etc/apt/apt-mirrors.txt:

http://azure.archive.ubuntu.com/ubuntu/	priority:1
https://archive.ubuntu.com/ubuntu/	priority:2

Galaxy #22098: nested dynamic output collection reproduction

Reproduction for galaxyproject/galaxy#22098, using the existing collection_split_on_column framework tool and normal Galaxy API calls. No mocks or manually constructed model objects are used.

The tool is mapped over two tabular inputs. A dynamic destination rule sends the first job through directory metadata and the second through extended metadata. One local runner worker ensures that the first sibling has persisted its datasets before the second job is prepared.

Results

Historical commit 3a56ddfc8fa, before the March 17 fixes: reproduces both the collection-builder AssertionError and the host-side Failed to find HDA with id [3] in [{}], through the same nested HDCA import path as the issue.
Plain release_26.1 at 94e49b14448: 1 passed. Both jobs succeed; the test verifies the nested collection structure, element counts, dataset states, and all four outp

`.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

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.

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

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:

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).

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:

	"""Reproduction for GALAXY-MAIN-14RZ / galaxyproject/galaxy#23146.

	A libmagic cookie builds its description in a buffer it owns and returns a
	pointer into that buffer, so one cookie cannot serve two threads at once.

	`magic.detect_from_content()` / `magic.detect_from_filename()` are python-magic's
	deprecated compatibility shims. They route through `magic/compat.py`, which holds
	two process-wide cookies and takes no lock:

	# magic/compat.py