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Pr 21935 Workflow Extraction Vue Conversion

Mako to Vue conversion of workflow extraction UI with new HID-keyed FastAPI extraction summary and extract workflow endpoints replacing legacy controller

draft research/prgalaxy/workflowsgalaxy/clientgalaxy/apigalaxy/models
Raw
Revised:
2026-05-16
Revision:
1
GitHub PR:
#21935
Sources:
https://github.com/galaxyproject/galaxy/pull/21935
Related Notes:
Issue 17506 - Convert Workflow Extraction Interface to Vue, PR 22706 - Workflow Extraction by IDs, Component - Workflow Extraction, Component - Workflow Extraction Models, Workflow Extraction Multiple Histories, Workflow Extraction Issues, Plan - Workflow Extraction Vue Conversion, Plan - Workflow Extraction Vue Conversion - API, Component - Workflow API, Component - Workflow Editor Terminals, Component - Collection Models, Component - Collection Tool Execution Semantics

PR #21935: Convert workflow extraction interface to Vue

Author: Ahmed Hamid Awan (@ahmedhamidawan) — implementation plan by @jmchilton Repo: galaxyproject/galaxy State: MERGED 2026-03-27 (merge ff944254b43c477e52455f71b099b65d5610c1d9) Created: 2026-02-25 Labels: area/UI-UX, kind/feature, highlight, release-testing-26.1

Fixes Issue 17506 - Convert Workflow Extraction Interface to Vue — the parent issue (“the last non-data-display Mako in Galaxy”). Direct follow-up is PR 22706 - Workflow Extraction by IDs (OPEN/unmerged), which “builds on this cycle’s #21935”: #21935 is the foundational HID-based Vue conversion; #22706 is the later ID/ICJ-native endpoint. #22706’s POST /api/workflows/extract is not part of this PR.

Summary

Deletes the Mako-based legacy history→workflow extraction UI (templates/build_from_current_history.mako, −178) and the legacy WorkflowController.build_from_current_history web-controller handler (controllers/workflow.py, −58, plus its now-dead imports). Replaces them with two new FastAPI endpoints on FastAPIHistories — GET /api/histories/{history_id}/extraction_summary (returns a Pydantic-typed WorkflowExtractionSummary of jobs/inputs) and POST /api/histories/{history_id}/extract_workflow (consumes the HID-keyed WorkflowExtractionPayload, returns WorkflowExtractionResult) — feeding a new SPA route /histories/{history_id}/extract_workflow rendered by WorkflowExtractionForm.vue plus WorkflowExtractionCard.vue / WorkflowExtractionMessages.vue. Introduces a reusable Common/RenameModal.vue that replaces the deleted Workflow/List/WorkflowRename.vue, rewrites History/Content/GenericItem.vue from Options API to <script setup> with useIntersectionObserver lazy provider rendering, and removes the legacy navigation plugin. Also a one-line, body-unmentioned bug fix in workflow/extract.py: dataset_collection_names was hard-coded None, silently dropping caller-supplied collection input names. The payload being HID-keyed and the endpoint history-scoped makes this design inherently single-history — the limitation PR 22706 - Workflow Extraction by IDs and Workflow Extraction Multiple Histories later address.

Changes

Line numbers verified at origin/dev SHA 78fc4a33 (the merge is an ancestor; nothing from this PR is superseded in dev — see below).

Backend

  • lib/galaxy/schema/workflows.py (+142): five new Pydantic models — WorkflowExtractionOutput (line 307), WorkflowExtractionJob (line 340; step_type: Literal["tool","input_dataset","input_collection"], checked, tool_version_warning), WorkflowExtractionSummary (line 383; history_id, warnings, jobs), WorkflowExtractionPayload (line 401; job_ids: list[DecodedDatabaseIdField], dataset_hids: list[int], dataset_collection_hids: list[int], names — no model validator), WorkflowExtractionResult (line 434; new workflow id).
  • lib/galaxy/webapps/galaxy/api/histories.py (+54): top-of-module from galaxy.workflow.extract import extract_workflow; extraction_summary @router.get("/api/histories/{history_id}/extraction_summary") (def line 862) → service.create_workflow_extraction_summary; extract_workflow_from_history @router.post("/api/histories/{history_id}/extract_workflow") (def line 879) maps payload.dataset_hids → extract_workflow(dataset_ids=...), returns WorkflowExtractionResult.
  • lib/galaxy/webapps/galaxy/services/histories.py (+103): HistoriesService.create_workflow_extraction_summary(history_id, trans) (def line 802) wraps summarize(trans, history); classifies fake jobs (is_fake) as input steps (id=None), real jobs via toolbox.get_tool, demotes not tool.is_workflow_compatible to input (line 852), sets tool_version_warning on version mismatch, checked = any(not data.deleted ...).
  • lib/galaxy/workflow/extract.py (+1/−1): inside extract_workflow(), the delegating call’s dataset_collection_names=None → dataset_collection_names=dataset_collection_names (dev line 74). A real bug fix — collection input names were being dropped; the PR body does not mention it.
  • lib/galaxy/webapps/galaxy/buildapp.py (+1): add_client_route("/histories/{history_id}/extract_workflow") (dev line 276) so SPA deep links resolve.
  • lib/galaxy/webapps/galaxy/controllers/workflow.py (−58): removes @web.expose build_from_current_history + dead Optional/GalaxyWebTransaction/extract_workflow/summarize imports.
  • lib/galaxy/selenium/navigates_galaxy.py (−1): drops switch_to_main_panel() in navigate_to_workflow_extraction() (Vue page renders in the SPA router, not the legacy main-panel iframe).
  • templates/build_from_current_history.mako (−178): the entire legacy server-rendered form, deleted.

New Vue extraction UI

  • client/src/components/History/WorkflowExtractionForm.vue (+329, new) — top-level History/, not the WorkflowExtraction/ subdir. <script setup lang="ts">, prop historyId; computeds selectedJobIds (dev line 86), selectedInputs, submissionDisabled; submitWorkflow() (dev line 210) builds the HID payload (dataset_hids at line 224) → submitWorkflowExtraction(historyId, payload). Selenium hooks data-description="workflow-extraction-form", data-step-type, data-job-id.
  • client/src/components/History/WorkflowExtraction/WorkflowExtractionCard.vue (+126, new): GCard with badges from STEP_TYPE_META, “View Job” / “Different Tool Version” badges, renders one GenericHistoryItem per output, emits rename/select.
  • client/src/components/History/WorkflowExtraction/WorkflowExtractionMessages.vue (+60, new): static guidance + warnings as a dismissible BAlert that demotes to a BPopover.
  • client/src/components/History/WorkflowExtraction/types.ts (+13, new): WorkflowExtractionInput (job + newName); isWorkflowExtractionInput = step_type.startsWith("input").
  • client/src/components/History/HistoryOptions.vue (+1/−3) and client/src/entry/analysis/router.js (+6): rewire the “Extract Workflow” option to the new SPA route histories/:historyId/extract_workflow.

Shared components

  • client/src/components/Common/RenameModal.vue (+85, new): generic rename modal — props name, itemType, renameAction; wraps GModal + GFormInput, success/error toasts. Replaces client/src/components/Workflow/List/WorkflowRename.vue (−63, deleted); WorkflowCardList.vue (+4/−2) re-imports the shared one with rename-action calling updateWorkflow.
  • client/src/components/Common/GCard.vue (+14): dimWhenUnselected prop (saturate/opacity dim). Common/GTable.vue (+8/−1): selectCheckboxTitle prop. BaseComponents/GModal.vue (+3): onMounted calls showModal() if show is already true.

Client API / selenium / plugins

  • client/src/api/histories.ts (+42): re-exports the four schema types; extractWorkflowFromHistory (dev line 309, GET .../extraction_summary) and submitWorkflowExtraction (dev line 323, POST .../extract_workflow).
  • client/src/api/datasets.ts (+3/−2): fetchDatasetDetails gains an optional AbortSignal to cancel per-output fetches when cards unmount.
  • client/src/api/schema/schema.ts (+279, autogenerated); client/src/utils/navigation/navigation.yml (+9/−17) + schema.ts (+12): swap Mako-era selectors for the Vue set (tool_card = [data-step-type="tool"], card_checkbox_by_job_id, etc.).
  • client/src/components/plugins/index.js (−5) + client/src/components/plugins/legacyNavigation.js (−42, deleted): remove the legacy navigation mixin.
  • client/src/components/History/Content/GenericItem.vue (+118/−129): Options→<script setup lang="ts"> rewrite adding useIntersectionObserver lazy provider rendering. Load-bearing — the extraction card list mounts a GenericHistoryItem per output, so deferred provider resolution is what keeps a many-job summary viable. JobParameters.test.ts (+13/−18) is collateral of this refactor (stub now generichistoryitem-stub with item-id/item-src).

Changes since merge

git log ff944254..origin/dev per file: nothing from this PR is superseded in dev.

  • WorkflowExtractionForm.vue, WorkflowExtractionCard.vue, WorkflowExtractionMessages.vue, WorkflowExtraction/types.ts, Common/RenameModal.vue — zero post-merge commits, byte-identical to merge. (Confirms PR 22706 - Workflow Extraction by IDs, which rewrites all of these, is OPEN/unmerged and absent from dev — dev navigation.yml lines 1066–1076 are exactly the #21935 selector set, no mapped_*/card_by_icj_id.)
  • extract.py — three follow-ups (b50938e3cf LDDA-leaf NoneType guard for #22359 in WorkflowSummary; 345efca3e5 mypy assert; cd4f4686a8 release merge), none touching extract_workflow()’s signature or the dataset_collection_names fix.
  • schema/workflows.py — unrelated invocation-param validation commits; the five WorkflowExtraction* models unchanged (lines 307/340/383/401/434).
  • services/histories.py — 11 follow-ups (history-graph endpoint, .model_dump(), manager shims); create_workflow_extraction_summary itself unchanged (moved to line 802 only by preceding insertions).
  • api/histories.py — 4 follow-ups, neither extraction endpoint touched (dev lines 862/879).
  • test_workflow_extraction.py — a7d122afd9 gxformat2 0.26.0 fixture syntax bump, not the new summary test class. api/histories.ts — cacef72a70 modernized an unrelated fn.

The HID-keyed WorkflowExtractionPayload and both endpoints still exist unchanged at dev. Per #22706’s body the legacy HID path is intentionally kept as the default for the history endpoint even after #22706 lands, so this PR’s contribution remains the production path.

File path migration

No migrations — all 31 non-deleted touched paths exist at their PR-era paths at dev SHA. Notably WorkflowExtractionForm.vue stays at top-level History/ (not the WorkflowExtraction/ subdir, which holds only Card/Messages/types). The 4 deletions (build_from_current_history.mako, Workflow/List/WorkflowRename.vue, plugins/legacyNavigation.js, the controllers/workflow.py method) are expected-absent, not migrations.

Cross-checks

  • Mako deletion (−178), legacy controller handler deletion (−58) — confirmed absent at dev.
  • Two distinct routes: GET .../extraction_summary and POST .../extract_workflow — confirmed (api/histories.py:862/879). The PR body is correct; an earlier framing of this as a single extract_workflow GET/POST route was inaccurate.
  • WorkflowExtractionPayload HID-keyed (dataset_hids/dataset_collection_hids: list[int]) — confirmed (schema lines 412/417).
  • extract.py +1/−1 is a substantive bug fix (dataset_collection_names=None → caller value), not cosmetic — body omits it (noted gap).
  • RenameModal.vue replacing WorkflowRename.vue, legacyNavigation.js removal, buildapp.py route (dev line 276) — all confirmed. No body↔diff contradictions.

Unresolved questions

  • HID/single-history limitation is by design here (dataset_hids: list[int], /api/histories/{id}/...) — no cross-history copied-dataset support. Deprecate the HID path once PR 22706 - Workflow Extraction by IDs lands, or keep as default indefinitely (its body says keep)?
  • No API test of POST .../extract_workflow in the +90 (only the GET summary is API-tested); POST correctness rides on the Selenium rewrite + pre-existing extract_workflow/summarize coverage — thin for mapped/implicit-collection steps.
  • Behavior change: the Vue form blocks empty-step submission (create disabled) whereas the old Mako form allowed an inputs-only workflow — confirm no downstream reliance on the old behavior.
  • GenericItem.vue rewrite is load-bearing (lazy providers), not cosmetic — changed test-facing stub shape.

Tests

  • lib/galaxy_test/api/test_workflow_extraction.py (+90): new TestWorkflowExtractionSummaryApi — test_extraction_summary_empty_history, _input_datasets_from_upload, _input_collection, _tool_step (@skip_without_tool("cat1")), _structure. Summary endpoint only.
  • client/src/components/History/WorkflowExtractionForm.test.ts (+267): loading, empty-history, with-jobs, submission-validation, input-renaming, submission suites (calls submitWorkflowExtraction).
  • client/src/components/Common/RenameModal.test.ts (+90) and Workflow/List/WorkflowCardList.test.ts (+71): rename-flow incl. a shared-modal name-bleed regression guard.
  • client/src/components/JobParameters/JobParameters.test.ts (+13/−18): adjusted to the GenericItem.vue refactor (collateral, not a feature test).
  • lib/galaxy_test/selenium/test_workflow_extraction.py (+52/−54): rewrites the suite from the Mako page to the Vue form; asserts no_workflow_message for empty history and the create button aria-disabled when no steps selected.

Notes

Incoming References (10)