State: OPEN Author: martenson Labels: area/backend, area/jobs, kind/bug Assignees: mvdbeek Comments: 1
Marius van den Beek mvdbeek
mvdbeek
/ ISSUE_21642.md
Created
February 26, 2026 12:58
Triage artifacts for Galaxy issue #21642 - Remote data fetch not respecting quota
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| 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
/ merged_test_output.md
Created
February 24, 2026 10:15
IWC Workflow Test Results - Run 22339836776
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.
mvdbeek
/ fetch_small_accessions.py
Created
February 13, 2026 19:40
ENA/Galaxy stress test: fetch random small accessions, upload via ascp, run cat1
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| #!/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 |
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| 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
/ ASCP_IMPLEMENTATION_PLAN.md
Created
November 24, 2025 15:18
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.
- Plugin Type: Configured plugin only (requires explicit configuration)
- Features: Download-only (no upload or browsing)
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| { | |
| "@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" |
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| ========================================= | |
| Galaxy API Rate Limiting Test (Parallel) | |
| ========================================= | |
| Target: https://test.galaxyproject.org | |
| Endpoint: https://test.galaxyproject.org/api/version | |
| Temp dir: /var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp.9BmqdrrwVf | |
| === Test 1: Burst Capacity Test === | |
| Testing burst capacity with 0c918d2fbb... |
Job failed on first run, rerun with "replace dataset collection elements" selected. Discovered output dataset collection elements were added to original collection, while new output dataset collection is not populated. This probably makes the job ineligible for the job cache / job search.
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