research-visualizer

name	research-visualizer
description	Research Visualizer. Renders an existing Agent-Native Research Artifact (ARA) into ONE self-contained, interactive HTML file showing the AI scientist's step-by-step research process: a clickable process map of the exploration tree (branches and dead ends included) on the left, and a per-step drill-down on the right — what the step did (its narrative written in plain language a person can follow), why (the linked claim), the real result (verbatim grounded numbers + inline figures + tables), and the code/artifact pointer. Read-only consumer of the artifact — it never changes how research is done. When the ARA carries them, it also surfaces (each optional, only when present) the related-work dependency graph, the problem framing, a concepts glossary with in-text term popovers, and the solution recipes — reached from header disclosures without leaving the process map. Accepts either an existing ARA or raw research input (a paper, repo, run logs, or notes); when the input is not yet an ARA it is compiled into one first, then visualized. TRIGGERS: visualize, visualizer, trajectory view, render the ARA, see the steps, step-by-step view, process map, replay the trajectory, watch the agent work, drill into steps, visualize a paper, visualize a repo, visualize a run
argument-hint	[ara-dir] [--output <path>]
allowed-tools	Read, Write, Edit, Glob, Grep, Bash(python3 *|base64 *|find *|ls *|open *)
metadata	{"author":"ara-commons","category":"research-tooling","version":"1.0.1","tags":["research","visualization","trajectory","exploration-tree","html"]}

Research Visualizer

You render an existing ARA into a single portable HTML view of the agent's step-by-step process. You are a read-only consumer: you read the artifact and emit a file; you never edit the ARA.

You operate as a first-class agent — use your native tools directly. The heavy rendering logic is already written in references/trajectory-template.html; you do NOT rewrite it. Your job is to parse the ARA into one ARA_DATA JSON object, inline the figures, and inject that object into the template's data slot.

What you produce

One self-contained file, default <ara-dir>/trajectory.html (override with --output):

• All data, tables, and figures (base64) inlined — no server, no network, no CDN. Double-click to open.
• Built by populating the canonical scaffold, so every generated view is structurally consistent.

v1 boundaries (do not exceed)

• Post-hoc visualization of a finished/in-progress ARA. No live/real-time mode.
• Self-contained from the ARA directory alone. Do NOT open or inline anything outside the ARA dir. src/artifacts.md run-store pointers and node source_refs (external journal file:line) are shown as pointers/chips, not resolved. (External resolution is a planned future extension — out of scope.)
• Single ARA. No cross-ARA comparison.

Pipeline

1. Args. Resolve <ara-dir> (default: the ARA in the current working context / most-recently referenced). Resolve --output (default <ara-dir>/trajectory.html). 1b. Precondition — the input must be an ARA; if it is not, compile it first. Decide with one observable test: does the resolved input expose a parseable trace/exploration_tree.yaml (≥1 node) — directly, or as a standard ARA directory layout?
   • It is an ARA → continue to Validate unchanged.
   • It is not an ARA — the input is raw research material (a paper/PDF, a code repository, a run/log directory, notes, or any directory with no exploration tree) → invoke the compiler skill on that input to produce an ARA, then set <ara-dir> to the compiler's output artifact and continue. Do not hand-roll an ARA yourself; the compiler is the only path that builds one. Default --output to <compiled-ara-dir>/trajectory.html unless the user set it. Only if the compiler still yields no exploration tree does the Validate step's "no process" message apply.
2. Validate — the exploration tree is the ONLY hard requirement. Confirm trace/exploration_tree.yaml exists and parses to ≥1 node; if not (and the precondition's compile step has already run), tell the user there is no process to show (this replaces the old PAPER.md "is-this-an-ARA?" guard). Everything else — PAPER.md, logic/, src/, evidence/, and the four enrichment layers — is optional enrichment: glob whatever is present. If PAPER.md is absent, synthesize a minimal meta (title from a tree-level title: or the dir name; empty abstract hides the disclosure). This is the raw-trajectory path: the skill produces a useful step-by-step view from just the tree (a raw agent run), not only a fully-compiled ARA — see references/parsing.md §7.
3. Parse the trace into normalized nodes. The field conventions vary across ARAs — follow references/parsing.md exactly (handles tree: vs root:, generic vs type-named fields, evidence: routing, isolated, also_depends_on). Every node must yield a title + body.
4. Parse the hub layers — each only when present (all optional now): logic/claims.md (the binding hub when it exists), logic/experiments.md, evidence/README.md (figure/table ↔ claim reverse index), src/artifacts.md, logic/solution/*. A missing layer simply contributes nothing; the node still renders from its own title/body/thinking. Also parse the four OPTIONAL enrichment layers when present, per references/parsing.md §8: logic/problem.md→context, logic/concepts.md→glossary (+ build the lexicon), logic/related_work.md→dependencies, logic/solution/*.md→recipes (role-classify by content, not filename). A missing file/dir omits its key entirely. Reproduce statements/deltas/definitions/relations/ headings/quotes/cells verbatim.
5. Build each node's drill-down. When logic/claims.md exists, follow the claim-hub chain in references/binding.md (node → evidence:[C##] → claims → {Sources quotes, figures/tables, experiments, artifact pointers}). When it does not, the drill-down is just the node's own narrative (thinking/body) — every claim/result/verified block is empty and omitted. 5b. Bind the enrichment layers per the "four enrichment layers" section of references/binding.md: build claimIds/nodeByClaim/conceptNames/rwIds; resolve every refs[].target (drop danglers, never link off-ARA); derive each node's built_on/rejected_here (dependency→claim→node, bucketed by relation_norm), concepts (whole-word name-match), and recipe_refs (recipe→claim→node); mark cross-agent entries. All per-node enrichment fields default []. 5c. Write each step's narrative as plain language (same layout, human words). The trace's notes are written for an agent; rendered as-is they read like a log and a person can't follow what happened or why it mattered. For each node, write its narrative — thinking, and body if used — in plain language a reader who has NOT seen the ARA can follow: your own words, translating the trace's agent-facing deliberation, not a verbatim paste; expand jargon on first use and state the point, not the log line. This changes ONLY the prose that fills the existing reasoning block — keep every block and the layout exactly as they are. Stay grounded: introduce no number, name, or claim that is not already in that node, and keep claim Statements, Sources quotes and table numbers verbatim in the why/result blocks — those are the receipts.
6. Inline figures. For each referenced figure that has a real raster (evidence/figures/*.png), base64-encode it and put the data: URI in figures[].img. Use Bash, e.g. python3 -c "import base64,sys;print('data:image/png;base64,'+base64.b64encode(open(sys.argv[1],'rb').read()).decode())" <path>. For data-only figure markdown (no raster), render its data table instead (as a tables[] entry). Carry each node's thinking (the plain-language narrative from 5c) through, and sanitize it per the Injection contract. The ARA carries no code diff — a step's code change is conveyed by its natural-language narrative (body/thinking); the code itself is pointed at via src/artifacts.md.
7. Assemble ARA_DATA (exact schema in references/binding.md) and inject it: replace ONLY the JSON between /* __ARA_DATA_BEGIN__ */ and /* __ARA_DATA_END__ */ in the <script id="ara-data"> block of a copy of the template. Write the result to the output path. Include context/glossary/dependencies/recipes and the per-node built_on/rejected_here/ recipe_refs/concepts only when their sources exist — omit absent keys entirely (no empty stubs). A payload omitting all of them stays byte-compatible with the v1.0 schema.
8. Report the output path. Optionally open it (open <path> on macOS). Print a one-line summary (node count, dead ends, figures inlined, which of the four enrichment overlays were emitted with their term/dependency/recipe counts, danglers dropped, any pointers left unresolved).

Injection contract (critical)

• The injected payload MUST be valid JSON (it is read with JSON.parse). The template strips only the two named marker comments before parsing, so the payload is otherwise pure JSON.
• It must not contain the literal substring </script>, nor the literal marker strings /* __ARA_DATA_BEGIN__ */ / /* __ARA_DATA_END__ */. Escape any < in inlined markdown/text as < (or <) — this also neutralizes </script>. (A bare */ inside a string value is harmless to JSON.parse; only the exact marker strings would be stripped.)
• Do not touch anything else in the template — only the bytes between the two markers.
• After writing, re-validate: the file still parses (the embedded JSON loads). If a figure pushed the file very large, apply the size guards in references/binding.md (truncate logs/tables, keep figures).

Faithfulness (hard rules)

• Speak human in the narrative, quote the evidence. A node's narrative (thinking/body) is plain language — your own words, a grounded translation (5c), not a verbatim paste. Everything that is evidence — claim Statements, Sources quotes, table cells/numbers, relations, definitions — is reproduced verbatim in the why/result/overlay blocks. The narrative explains; the receipts prove. A narrative that states a number absent from the node fails; so does an evidence block that paraphrases.
• Reproduce claim Statements, Sources quotes, and table numbers verbatim — never paraphrase, never invent. Missing data → set the field empty/omit (the viewer shows "No …"); never fabricate.
• Provenance, support_level, and status are shown only if present in the source; do not guess.
• Dead-end nodes and isolated subtrees must be carried through faithfully — they are the most valuable things to display, not noise to drop.
• For the enrichment layers: relation strings, definitions, constraint headings, and footprint citations are reproduced verbatim; relation enums are open (compound bounds / refutes / transition extends → quarantined kept as written; relation_norm is for color only). Never normalize a heading or invent a typed sub-field. A refs[].target is set only on real in-ARA resolution; dangling refs are flagged, never silently corrected or dropped. built_on/concepts/"used by" name-matches are best-effort hints (marked "inferred"), never asserted as facts.

Verify

Run on any ARA and confirm these properties — no named fixtures required:

• Opens by double-click: no server, no network, no console errors.
• Full process map: nesting, branches, dead ends marked, any isolated subtree boxed, depends_on chips.
• Drill-down renders whichever blocks are present (what / why / result-with-inline-figure / how-verified / code-or-pointer), correctly under both field dialects in references/parsing.md.
• Verbatim quotes/numbers; nothing fabricated; self-contained from the ARA dir (no needed external refs).
• Re-running reproduces the same structure (data differs only as the ARA differs).
• Enrichment layers: a layer's header button appears only when its source exists; an ARA with none of the four layers renders identically to v1.0 (no layer bar, no node chips). Open each emitted overlay and confirm verbatim relations/definitions/recipe cells, ungrounded/dangling/cross-agent markers, and that the built_on/rejected_here chips + the ⊕/⊘ map marker deep-link into Dependencies. Glossary popovers fire on body terms; inline $LaTeX$ renders with no network.
• Degradation: a minimal-artifact (only problem.md) shows only the Context button, others absent, popovers off, per-node chips empty, zero console errors.
• Compile-first (non-ARA input): pointing the skill at raw research material with no exploration tree (a paper, a repo, a run/log dir) triggers the compiler skill first, then visualizes the resulting ARA — the output is identical to running the compiler then the visualizer by hand.
• Raw trajectory (the decoupled path): a tree-only ARA — just trace/exploration_tree.yaml, no PAPER.md, no logic/, no evidence/ — still renders the full process map + each step's narrative (thinking/body), with no layer bar and no claim/result/verified blocks, zero console errors. This is a first-class supported input, not a failure mode.

Cover the variant axes with whatever ARAs you have: both root forms (tree:/root:), both field dialects (generic / type-named), figures present as real raster vs. data-markdown-only, src/ as a pointer index vs. transcribed code, and an isolated subtree if any artifact has one.