Figure capture manifest
Source object IDs for each PNG in this directory. Reference server: local Galaxy 26.2.dev0 (worktree history_pages). Captured via Playwright MCP against the dev client (http://localhost:5173), light theme, 1600×1000 window. Workflow graphs captured from the Workflow Editor canvas (.workflow-canvas), cropped to the node bounding box.
Previously captured (unchanged)
| File | Source object |
|---|---|
uc1_notebook_full.png | UC1 notebook page eafb646da3b7aac5, captured with history 48916fac0de9a85d (“MRSA mobile AMR context across isolates (clean)”) set as the active history — the right panel now shows the populated UC history (re-captured to fix the earlier empty “Unnamed history”) |
uc1_fig1_heatmap.png | UC1 heatmap dataset 29e36fb8642bf5ed (first mobile-resistome matrix), 2000×2000 downscaled to 463×464 |
uc2_notebook_full.png/uc3_notebook_full.pngwere generated earlier but are not currently infigures/— regenerate alongside the quality re-capture (UC2 page42a2c611109e5ed3/ history96d9e11f37f34b29; UC3 pagea7e42332dab8f5db/ history241d84796a24640a).
Newly captured (this pass)
| File | Source object | Notes |
|---|---|---|
uc1_fig1_workflow_graph.png | extracted workflow 33b43b4e7093c91f (14 steps) | Fig 1 graph half; pairs with uc1_notebook_full.png |
uc1_fig1_heatmap2.png | dataset 579ae69ccbd17e45 (“heatmap2”, second mobile-resistome matrix), 2000×2000 → 463×464 | matches uc1_fig1_heatmap.png style |
uc1_fig1_heatmap2_full.png | same dataset, full 2000×2000 | high-res source for layout |
uc3_fig3a_workflow_degenerate.png | workflow 4b187121143038ff (2 inputs, 0 tools) | Fig 3a “before”; extracted from off-graph page 36ddb788a0f14eb3, whose only references are two re-uploaded PNG datasets (64ed206b5444cf1a DESeq2 PCA, e1a34e8a9807a4ae Volcano). Same default zoom as the “after” panel. |
uc3_fig3a_workflow_5step.png | extracted workflow 0a248a1f62a0cc04 (5 steps) | Fig 3a “after”; same zoom as degenerate panel |
uc2_fig3b_caller_5step.png | extracted workflow 3f5830403180d620 (5 steps) | Fig 3b map-over peak caller |
uc2_fig3b_comparator_29step.png | extracted workflow e85a3be143d5905b (29 steps) | Fig 3b pairwise comparator |
uc2_single_condition-pinned_34step.png | extracted workflow 03501d7626bd192f (34 steps) | Fig 3b optional reference (single condition-pinned extract) |
uc1_revision_panel.png | page b887d74393f85b6d revision history (5 revisions) | evidence layer 4 / agent authorship. Badges: (AI) = edit_source="agent", (Unknown) = pre-feature/initial revision. See report caveat. |
UC3 rebuild — differential-accessibility application (Fig 3a, current)
Vignette 3 was rewritten from a before/after “display gates extraction” demo into a positive application (count matrix → ranked, re-runnable workflow). Notebook page d071e794759ab192, history be8c8ac3dbd1dd54, extracted 13-step workflow ba751ee0539fff04. Figures are on-graph image outputs: the DESeq2 PCA and volcano PDFs are converted to PNG in-graph (graphicsmagick_image_convert → __EXTRACT_DATASET__) and referenced with history_dataset_as_image. Captured against the dev client (:5173); chrome cropped to the document column.
| File | Source object | Notes |
|---|---|---|
uc3_notebook_source.png | page d071e794759ab192 editor (markdown source) | Fig 3a — history_dataset_as_image / history_dataset_as_table directives over on-graph outputs |
uc3_notebook_rendered_pca.png | extracted PCA image “Sample PCA plot” fbb70e50318ce3f7, rendered inline | Fig 3a — PC1 ≈ 98% variance |
uc3_notebook_rendered_volcano.png | extracted volcano image “Volcano plot” db724f789d20d73e, rendered inline | Fig 3a — Down/Not-Sig/Up |
uc3_notebook_rendered_tables.png | DESeq2 result + significant + top-50 ranked tables | Fig 3a — on-graph tabular outputs |
uc3_workflow_13step.png | extracted workflow ba751ee0539fff04 (13 steps) | Fig 3a — counts collection + sheet → DESeq2 → NA-filter → volcano ∥ sig-filter → sort → top-gained/-lost, plus two image-output branches (convert → extract) for the PCA and volcano figures |
Removed (no longer referenced by the manuscript): the old before/after
uc3_fig3a_workflow_degenerate.png/uc3_fig3a_workflow_5step.png, the PDF-renderer comparison shotsuc3_{pca,volcano}_embed.png/uc3_{pca,volcano}_as_pdf_directive.png, anduc3_workflow_9step.png.
Clean / extractable page + history IDs (for any further captures)
| UC | page | history |
|---|---|---|
| UC1 MRSA | eafb646da3b7aac5 | 48916fac0de9a85d |
| UC2 TAL1 | 42a2c611109e5ed3 | 96d9e11f37f34b29 |
| UC3 ATAC (rebuild) | d071e794759ab192 | be8c8ac3dbd1dd54 |