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.

mvdbeek

Issue #21642: Fetching data from repositories does not seem to respect storage quota

State: OPEN Author: martenson Labels: area/backend, area/jobs, kind/bug Assignees: mvdbeek Comments: 1

Description

mvdbeek

diff --git a/lib/galaxy/model/migrations/alembic/env.py b/lib/galaxy/model/migrations/alembic/env.py
index 98091912b80..c9db41cc84d 100644
--- a/lib/galaxy/model/migrations/alembic/env.py
+++ b/lib/galaxy/model/migrations/alembic/env.py
@@ -1,7 +1,7 @@
 import logging
 import re
+from collections.abc import Callable
 from typing import (
-    Callable,

mvdbeek

Test Results (powered by Planemo)

Test Summary

mvdbeek

Plan: Migrate data_input Forms to Client-Side

Context

Galaxy's workflow engine currently defines input forms server-side for data_input steps, requiring server round-trips and complex translation code (step_state_to_tool_state, _parse_state_into_dict). PR #19313 successfully migrated data_collection_input to client-side rendering. This plan extends that pattern to data_input, which is simpler since it manages only three parameters: optional, format, and tag.

Implementation

1. Server: Empty get_inputs() for InputDataModule

mvdbeek

#!/usr/bin/env python3
"""
Fetch 100 random small (<500MB) SRR/ERR accessions from ENA and write their FTP links to a file.
"""

import csv
import io
import random
import sys
import urllib.request

mvdbeek

rnaseq_de:
  workflow_id: 8cd7bdc8d3cf35cd
  workflow_target_type: stored_workflow
  request_state:
    Sample sheet of sequencing reads:
      class: Collection
      collection_type: sample_sheet:paired
      name: RNA-Seq DE sample sheet
      elements:
        - class: Collection

mvdbeek

Aspera ascp File Source Implementation Plan

Overview

This document outlines the implementation plan for creating a Galaxy file source plugin that uses Aspera ascp for high-speed file downloads. The implementation will be a configured plugin (not stock) with download-only functionality, using a custom fsspec filesystem.

Requirements Summary

• Plugin Type: Configured plugin only (requires explicit configuration)
• Features: Download-only (no upload or browsing)

mvdbeek

{
  "@context": "http://schema.org",
  "@type": "LearningResource",
  "http://purl.org/dc/terms/conformsTo": {
    "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE",
    "@type": "CreativeWork"
  },
  "audience": {
    "@type": "EducationalAudience",
    "educationalRole": "Students"