jmchilton

Filled Defaults in job_internal — Notes

The Question

Does job_internal have CWL defaults filled in?

Current State (post-discriminator fix, 94f61bc)

CWL param models already store default_value: Optional[Any] = None alongside has_default: bool (e.g. CwlStringParameterModel, CwlIntegerParameterModel, etc.). These are populated during tool parsing.

jmchilton

History Notebooks Phase 10: Agent Integration

The Problem

History Notebooks capture narrative alongside computation — but right now, only humans write. The notebook is a passive document: the user opens the editor, types markdown, inserts dataset references via toolbox or drag-and-drop, and saves. The AI agent framework (PR #21434, merged Dec 2025) gives Galaxy a multi-agent system with structured output, tool calling, and multi-turn conversation — but it has no surface for writing or editing documents tied to histories. These two systems sit side-by-side with no connection.

The original vision (from THE_PROBLEM_AND_GOAL.md):

History Notebooks are living documents that grow alongside your analysis. As analysis progresses — whether driven by human clicks, agent actions, or conversation between the two — the narrative builds up iteratively.

jmchilton

Problem

Galaxy's CWL integration (branch cwl-1.0 at common-workflow-lab/galaxy) translates CWL's schema-based parameter model into Galaxy's opinionated tool parameter model (basic.py). This round-trip — CWL schema to Galaxy widgets to user input to Galaxy param_dict to CWL job JSON — is the root of the problem. It requires:

• Every CWL type mapped to a Galaxy widget type (TYPE_REPRESENTATIONS)
• Union types encoded as Galaxy conditionals with synthetic _cwl__type_/_cwl__value_ keys
• A catch-all FieldTypeToolParameter added to basic.py
• Reverse-engineering Galaxy DatasetWrappers back into CWL File objects (to_cwl_job(), galactic_flavored_to_cwl_job() in representation.py)

This adaption layer is hack after hack and deeply entangles CWL with Galaxy's core parameter infrastructure.

jmchilton

CWL 1.0 Rebase Info

Rebasing cwl-1.0 onto db43f2dbc4 (dev, post release_26.0 merge).

Commit: e84401b665 — "Implement subset of the Common Workflow Language tool and workflow formats."

5 files conflicted. Resolutions below.

1. lib/galaxy/managers/workflows.py

jmchilton

Workflow Extraction - Known Issues

Summary of open GitHub issues related to workflow extraction limitations in Galaxy.

UI/UX Modernization

#17506 - Convert workflow extraction interface to Vue

Status: Open | Labels: enhancement, UI-UX, refactoring, backend

The build_from_current_history Mako template is the last non-data display Mako in Galaxy. Needs conversion to FastAPI + Vue.

jmchilton

Workflow Extraction: HID to ID Migration Plan

Executive Summary

Galaxy's workflow extraction API uses HIDs (History ID numbers) to identify datasets for workflow input selection. This creates limitations for cross-history workflows and handling copied datasets:

1. Cross-history restrictions: HID-based identification requires a single history context
2. Copied dataset issues: Datasets copied between histories lose proper job chain tracing

This plan details migrating from HID-based to ID-based dataset identification, enabling:

jmchilton

Workflow Extraction Vue Conversion Plan

Overview

Convert the legacy Mako-based workflow extraction UI (build_from_current_history.mako) to a modern Vue.js component with FastAPI backend. This is the last non-data-display Mako template in Galaxy.

Related Issue: #17506

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jmchilton

Issue #21604: How can I publish a dataset?

Author: Simon Bray (@simonbray) Created: 2026-01-16 URL: galaxyproject/galaxy#21604 Version: 25.1 (EU)

Problem Description

User has a published history containing 1 already published dataset. After uploading a second dataset, they cannot publish it to make it publicly available.

jmchilton

Issue #21602: Workflow: No propagation of possible options for a workflow input (with Attempt restriction based on connections) if connected to several subworkflows

Author: Bérénice Batut (@bebatut) State: OPEN Created: 2026-01-16T15:35:13Z Labels: None Milestone: None

Description

jmchilton

Feature Request #21591: Batch export of histories, workflow invocations, and datasets

URL: galaxyproject/galaxy#21591 Author: M Bernt (@bernt-matthias) Created: 2026-01-15 Labels: feature-request Reactions: 1 thumbs up

Description