# Ask Oe With Ego

> Asks a medical question on OpenEvidence via ego-browser (or appends a follow-up to a thread), makes it public, then mints a scalable multi-turn HTML plus BibTeX/CSL-JSON/AMA bibliography with references verified through the Crossref API. Split into an ego-only capture step and a fully standalone transform step. Use when the user wants to ask OpenEvidence, add a follow-up, get a shareable link, an HTML export, and/or citations (.bib / CSL / AMA).

- Skill: `htlin222/ask-oe-with-ego` (Agent Skill, multi-file: 4 files)
- Install (CLI): `npx skillmds@latest add htlin222/ask-oe-with-ego`
- Raw SKILL.md: https://api.skillmd.com/api/skills/htlin222/ask-oe-with-ego/raw
- Safety review: WARNING
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Web & Frontend
- Author: htlin222 (https://skillmd.com/u/htlin222)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/htlin222/ask-oe-with-ego

---


# Ask OpenEvidence with ego-browser

Two layers, deliberately split:

1. **Capture — needs ego (`scripts/dump.mjs`).** Reuses the user's real, DataDome-trusted OpenEvidence session to ask/publish and snapshot the rendered SPA DOM into `oe-<id>.dump.json`. This is the *only* step that touches openevidence.com. A headless Playwright/Puppeteer would trip DataDome here (webdriver + fingerprint + datacenter IP + no clearance cookie) — ego works because it *is* the user's trusted browser.
2. **Transform — fully standalone (`scripts/oe-transform.mjs`).** Plain Node (≥18, global `fetch`), **no ego, no browser**. Reads a dump, resolves every reference through the **Crossref API** (PMIDs converted via NCBI first), and writes `oe-<id>.html` + `.bib` + `.csl.json` + `.ama.txt`. Only outbound calls are Crossref + NCBI (open APIs, no DataDome).

The HTML is thread-aware: one card per turn, nested TOC + scrollspy, citation popovers (AMA text), reference back-links with ×N counts, reading-progress bar, theme toggle, and toolbar **⬇ .bib / ⬇ CSL / ⬇ AMA** downloads. A single answer is a 1-turn thread — same pipeline.

## Preflight — is ego installed?

The capture step needs the `ego-browser` CLI. Check first:

```bash
command -v ego-browser >/dev/null 2>&1 && echo "EGO OK" || echo "EGO MISSING"
```

If **EGO MISSING**, **guide the user through installing ego-lite following [`references/install.md`](references/install.md)** — briefly: download the Mac build from **https://lite.ego.app/download?auto=1**, drag it into Applications, launch and complete onboarding (it auto-writes the `ego-browser` skill into `~/.claude/skills/` and migrates the user's login/cookies/profile — the source of the DataDome-trusted session), then `/ego-browser` + Full access. Re-run the check, then retry Round 2a. Do **not** substitute a headless browser — OpenEvidence sits behind DataDome-class protection and automated browsers get blocked; ego passes because it reuses the user's trusted session. Note: if a `oe-<id>.dump.json` already exists, **Round 2b (transform) still runs without ego** — offer that.

## Verified facts (don't re-discover)

- **Ask box**: `textarea[placeholder="Ask a medical question..."]`. **Follow-up box**: `textarea[placeholder="Ask a follow-up question..."]`. Submit with **Enter**.
- **Every turn mints a NEW `/ask/<uuid>` URL** rendering the whole thread up to that turn — export the **latest** id.
- **Flaky first paint** → `dump.mjs` reloads before parsing.
- **Public** = ask URL once set: `Share` → radio `input[value="ANYONE_WITH_LINK"]` → `Done`.
- **Per-turn refs**: parse via an ordered token stream (`compareDocumentPosition`); a turn's numbered refs are **only the external anchors AFTER its `References` heading** (the one before it is the figure source link — excluding it keeps citation numbers aligned; `refCount === max citation number`). Citations restart at [1] each turn.
- **Crossref**: `api.crossref.org/works/{doi}/transform/application/vnd.citationstyles.csl+json`. Set env `CROSSREF_MAILTO` to join the polite pool (optional). PMID→DOI via NCBI `esummary`. CSL-JSON `title` is a **string**; container names may contain `<scp>` etc. (strip tags).
- **ego Node runtime ignores shell env** → pass inputs via `scripts/params.json` (a file). `oe-transform.mjs` instead takes the dump path as **argv[2]** (it's plain Node).
- **ESM**: both scripts use `import`/`await import('node:fs')`, not `require`. Absolute paths (cwd is `/` under ego).

## Inputs

- New thread: `QUESTION`. Follow-up: `FOLLOWUP` + existing `ARTICLE_ID`.
- `QUESTIONS` — every turn's question, in order (card titles). New: `[QUESTION]`. Follow-up: `[...prior, FOLLOWUP]`. Unknown earlier turns fall back to `Turn N`.
- `OUT_DIR` — default `$HOME/oe-answers` (omit it in params.json to use the default).

## Round 1 — new thread (ego): submit the question

```bash
ego-browser nodejs <<'EOF'
const task = await useOrCreateTaskSpace('openevidence ask')
await openOrReuseTab('https://www.openevidence.com/', { wait: true, timeout: 40 })
await waitForLoad(); await wait(2)
const QUESTION = `<<<QUESTION>>>`
await click('textarea[placeholder="Ask a medical question..."]', { label: 'focus ask box' })
await fillInput('textarea[placeholder="Ask a medical question..."]', QUESTION)
await wait(0.5); await pressKey('Enter'); await wait(4)
const m = ((await pageInfo()).url||'').match(/\/ask\/([0-9a-f-]{16,})/)
cliLog('ARTICLE_ID: ' + (m ? m[1] : 'NONE'))
EOF
```

## Round F — follow-up (ego): append to a thread

```bash
ego-browser nodejs <<'EOF'
const task = await useOrCreateTaskSpace('openevidence ask')
const ARTICLE_ID = `<<<EXISTING THREAD ID>>>`
const FOLLOWUP   = `<<<FOLLOW-UP QUESTION>>>`
await gotoAndWait('https://www.openevidence.com/ask/' + ARTICLE_ID, { timeout: 45, settle: 3 }); await wait(2)
await click('textarea[placeholder="Ask a follow-up question..."]', { label: 'focus follow-up' })
await fillInput('textarea[placeholder="Ask a follow-up question..."]', FOLLOWUP)
await wait(0.5); await pressKey('Enter'); await wait(4)
const m = ((await pageInfo()).url||'').match(/\/ask\/([0-9a-f-]{16,})/)
cliLog('NEW_ARTICLE_ID: ' + (m ? m[1] : 'NONE'))
EOF
```

## Round 2 — capture (ego) → transform (standalone)

**2a. Write params, capture the DOM with ego:**

```bash
SKILL="$HOME/.claude/skills/ask-oe-with-ego"
# OUT_DIR is optional — omit it and dump.mjs defaults to $HOME/oe-answers.
cat > "$SKILL/scripts/params.json" <<'JSON'
{
  "ARTICLE_ID": "<<<LATEST TURN ID>>>",
  "QUESTIONS": ["<<<Q1 text>>>", "<<<Q2 text>>>"]
}
JSON
ego-browser nodejs < "$SKILL/scripts/dump.mjs"     # → oe-<id>.dump.json  (prints the exact NEXT command)
```

**2b. Transform standalone — no ego, no browser:**

```bash
node "$SKILL/scripts/oe-transform.mjs" "$HOME/oe-answers/oe-<LATEST TURN ID>.dump.json"
# → oe-<id>.html (+.bib .csl.json .ama.txt)  |  crossref:N/M
```

Step 2b runs anywhere Node ≥18 is present, on the `.dump.json` alone — that's the standalone half. If ego is missing but a dump exists, run only 2b.

## Storage (SQLite) — `scripts/store.mjs`

`oe-transform.mjs` **auto-persists every dump** into `scripts/oe-store.db` (built-in `node:sqlite`; best-effort, non-fatal if unavailable). This means you can re-render a thread later **without re-capturing from OpenEvidence** — no ego, no DataDome. The DB (and its `-wal`/`-shm` sidecars, plus transient `params.json`) is **`.gitignored`**.

```bash
SKILL="$HOME/.claude/skills/ask-oe-with-ego"
node "$SKILL/scripts/store.mjs" list                       # every stored thread (date, id, turns, refs, public, first Q)
node "$SKILL/scripts/store.mjs" get  <article_id> d.json   # export a stored dump back to JSON
node "$SKILL/scripts/oe-transform.mjs" d.json              # …then re-render offline from it
node "$SKILL/scripts/store.mjs" put  <dump.json>           # manual insert/upsert
node "$SKILL/scripts/store.mjs" rm   <article_id>          # delete
```

## Optional — cloud backup to Turso (`scripts/backup.mjs`)

**Entirely optional; nothing in the ask/transform/local-store flow depends on it.** It mirrors the local SQLite store to a [Turso](https://turso.tech) (libSQL) cloud DB using the `turso` CLI the user already authed — no app tokens, no npm client. Only reach for it when the user asks to back up / sync to the cloud.

Preflight (skip the whole feature if this fails — do **not** block anything else):

```bash
command -v turso >/dev/null 2>&1 && turso auth whoami >/dev/null 2>&1 && echo "TURSO OK" || echo "TURSO OFF"
```

If **TURSO OFF**, just tell the user cloud backup is available once they install + log in — `curl -sSfL https://get.tur.so/install.sh | bash` then `turso auth login` — and carry on; local `.db` is the source of truth regardless.

```bash
SKILL="$HOME/.claude/skills/ask-oe-with-ego"
node "$SKILL/scripts/backup.mjs" backup    # local oe-store.db → cloud (creates db first time, else upserts)
node "$SKILL/scripts/backup.mjs" status    # cloud row count + URL
node "$SKILL/scripts/backup.mjs" restore   # cloud → local (INSERT OR REPLACE)
```

Cloud db name defaults to `oe-store` (override with env `TURSO_DB`). `backup.mjs` self-checks the CLI/auth and exits with install guidance if absent — it never throws into the rest of the skill.

## After Round 2

- Report the public link and file paths; `SendUserFile([htmlPath], { display:'render', status:'normal' })` to show the page, attach `.bib`/`.csl.json`/`.ama.txt` on request.
- Close ego in a final heredoc: `await completeTaskSpace('openevidence ask', { keep: false })`.

## Adding more follow-ups

Repeat **Round F** on the latest id → **Round 2** with `QUESTIONS` extended. Renderer and bibliography scale to any turn count.

## Fallbacks

- **EGO MISSING** → capture can't run; hint install (see Preflight). Transform still works on an existing dump.
- **`oe-undefined.*` / empty dump** → `params.json` unread or `ARTICLE_ID` missing (env vars don't propagate — the file is the only channel).
- **Answer never completes** (dump poll exits low) → still streaming; rerun 2a.
- **`crossref:0`** → Crossref/NCBI unreachable; entries fall back to OpenEvidence-text synthesis (valid, less rich). Check network from the transform host.
- **Citations off by one** → a pre-`References` inline anchor slipped into a turn's ref list; the `inRefs` gate must exclude it.
- **Keep it private** → delete the Share block in `dump.mjs`; HTML then shows `Private`.