--- name: pp-zotero-research-library description: "Your entire Zotero research library, searchable offline — version-based incremental sync into SQLite with full-text search no other Zotero tool has. Trigger phrases: `search my Zotero library`, `what does my library say about`, `find papers about`, `sync my Zotero library`, `what did I add to Zotero this week`, `get the citation for`, `use zotero-research-library`, `run zotero cli`." author: "Eric Rash" license: "Apache-2.0" argument-hint: " [args] | install cli|mcp" allowed-tools: "Read Bash" metadata: openclaw: requires: bins: - zotero-research-library-pp-cli install: - kind: go bins: [zotero-research-library-pp-cli] module: github.com/mvanhorn/printing-press-library/library/productivity/zotero-research-library/cmd/zotero-research-library-pp-cli --- # Zotero — Printing Press CLI ## Prerequisites: Install the CLI This skill drives the `zotero-research-library-pp-cli` binary. **You must verify the CLI is installed before invoking any command from this skill.** If it is missing, install it first: 1. Install via the Printing Press installer. It defaults binaries to `$HOME/.local/bin` on macOS/Linux and `%LOCALAPPDATA%\Programs\PrintingPress\bin` on Windows: ```bash npx -y @mvanhorn/printing-press-library install zotero-research-library --cli-only ``` 2. Verify: `zotero-research-library-pp-cli --version` 3. Ensure the reported install directory is on `$PATH` for the agent/runtime that will invoke this skill. If the `npx` install fails (no Node, offline, etc.), fall back to a direct Go install (requires Go 1.26.5 or newer). This installs into `$GOPATH/bin` (default `$HOME/go/bin`), so add that directory to `$PATH` instead: ```bash go install github.com/mvanhorn/printing-press-library/library/productivity/zotero-research-library/cmd/zotero-research-library-pp-cli@latest ``` If `--version` reports "command not found" after install, the runtime cannot see the binary directory on `$PATH`. Do not proceed with skill commands until verification succeeds. zotero-research-library-pp-cli mirrors your library into a local SQLite cache using the API's version cursors, then answers research-grounding questions offline: ranked full-text search with snippets, collection trees, recent-additions triage, and Better BibTeX citekey lookups. What the Web API meters at 100 items a page, your cache answers in milliseconds. ## When to Use This CLI Use this CLI whenever a task needs the user's own research library: grounding answers in their curated corpus, finding citations, browsing collections, or exporting BibTeX. It is the substrate for research-grounding workflows — search the local cache first, fall back to live API or open web only when the cache misses. ## Anti-triggers Do not use this CLI for: - Do not use this CLI to create, modify, or delete items in Zotero — it is read-only against the API - Do not use it for PDF download or attachment file retrieval; it indexes extracted text only - Do not use it for open-web literature search — it covers the user's own library ## Unique Capabilities These capabilities aren't available in any other tool for this API. ### Research grounding that compounds - **`ground`** — Ranked full-text search over your synced library — title, abstract, creators, tags, and attachment full text — answered offline in under a second, with snippets and citation-ready metadata. _Reach for this when asked what the user's own library says about a topic._ ```bash zotero-research-library-pp-cli ground "hamstring injury prevention" --limit 10 --agent ``` - **`items recent`** — What landed in the library recently, sorted by dateAdded from the local cache, with a --days cutoff and pipeable keys. _Use for weekly triage of new additions._ ```bash zotero-research-library-pp-cli items recent --days 7 --agent ``` - **`collections tree`** — Renders the full collection hierarchy with per-node item counts in one command — a shape the flat API cannot return in one call. _Use for a hierarchical overview of how the library is organized._ ```bash zotero-research-library-pp-cli collections tree --counts --agent ``` ### Manuscript plumbing - **`cite`** — Resolves a Better BibTeX citekey to its item from the local cache and exports citekey-faithful BibTeX; sync backfills citekeys via the desktop's local JSON-RPC when available. _Use when a manuscript needs a citation by its Better BibTeX citekey._ ```bash zotero-research-library-pp-cli cite smithHamstring2024 --format bibtex ``` ### Agent-native plumbing - **`cache status`** — Sync cursors, row and FTS counts, and last-sync age from the local cache; 'cache reindex' rebuilds the FTS index from base tables with zero network. _Use to check cache freshness offline before trusting search results._ ```bash zotero-research-library-pp-cli cache status --agent ``` ## Command Reference **collections** — Hierarchical collections organizing the library - `zotero-research-library-pp-cli collections get` — One collection by key - `zotero-research-library-pp-cli collections items` — Items in a collection (including children) - `zotero-research-library-pp-cli collections list` — All collections - `zotero-research-library-pp-cli collections subcollections` — Subcollections of a collection - `zotero-research-library-pp-cli collections top` — Top-level collections **deleted** — Deletion tombstones for sync - `zotero-research-library-pp-cli deleted` — Keys of items/collections/searches/tags deleted since a library version **fulltext** — Full-text content index - `zotero-research-library-pp-cli fulltext` — Attachment keys whose full-text content changed since a version **items** — Bibliographic items in the library - `zotero-research-library-pp-cli items children` — Child notes and attachments of an item - `zotero-research-library-pp-cli items fulltext` — Full-text content of an attachment item - `zotero-research-library-pp-cli items get` — Get one item by key - `zotero-research-library-pp-cli items list` — List items. - `zotero-research-library-pp-cli items top` — Top-level items only (no child notes/attachments) - `zotero-research-library-pp-cli items trash` — Items in the trash **keys** — API key introspection - `zotero-research-library-pp-cli keys` — Resolve the current API key to userID, username, and access scopes (doctor probe + userID discovery) **searches** — Saved searches - `zotero-research-library-pp-cli searches get` — One saved search - `zotero-research-library-pp-cli searches list` — All saved searches **tags** — Tags across the library - `zotero-research-library-pp-cli tags` — All tags in the library ## Freshness Contract This printed CLI owns bounded freshness only for registered store-backed read command paths. In `--data-source auto` mode, those paths check `sync_state` and may run a bounded refresh before reading local data. `--data-source local` never refreshes. `--data-source live` reads the API and does not mutate the local store. Set `ZOTERO_RESEARCH_LIBRARY_NO_AUTO_REFRESH=1` to skip the freshness hook without changing source selection. Covered paths: - `zotero-research-library-pp-cli collections` - `zotero-research-library-pp-cli collections get` - `zotero-research-library-pp-cli collections list` - `zotero-research-library-pp-cli collections search` - `zotero-research-library-pp-cli deleted` - `zotero-research-library-pp-cli deleted get` - `zotero-research-library-pp-cli deleted list` - `zotero-research-library-pp-cli deleted search` - `zotero-research-library-pp-cli items` - `zotero-research-library-pp-cli items get` - `zotero-research-library-pp-cli items list` - `zotero-research-library-pp-cli items search` - `zotero-research-library-pp-cli searches` - `zotero-research-library-pp-cli searches get` - `zotero-research-library-pp-cli searches list` - `zotero-research-library-pp-cli searches search` - `zotero-research-library-pp-cli tags` - `zotero-research-library-pp-cli tags get` - `zotero-research-library-pp-cli tags list` - `zotero-research-library-pp-cli tags search` When JSON output uses the generated provenance envelope, freshness metadata appears at `meta.freshness`. Treat it as current-cache freshness for the covered command path, not a guarantee of complete historical backfill or API-specific enrichment. ### Finding the right command When you know what you want to do but not which command does it, ask the CLI directly: ```bash zotero-research-library-pp-cli which "" ``` `which` resolves a natural-language capability query to the best matching command from this CLI's curated feature index. Exit code `0` means at least one match; exit code `2` means no confident match — fall back to `--help` or use a narrower query. ## Recipes ### Research-grounding query ```bash zotero-research-library-pp-cli ground "return to play criteria" --limit 10 --agent --select key,title,creators,date,DOI ``` Offline ranked search with citation-ready fields; the first step of the grounding workflow. ### Full-text deep search ```bash zotero-research-library-pp-cli ground "nordic hamstring" --fulltext --agent ``` Extends the search into attachment full text and resolves hits to their parent papers. ### Weekly additions to BibTeX ```bash zotero-research-library-pp-cli items recent --days 7 --agent --select key,title ``` Fresh additions ready to pipe into an export. ### Scope a search to a collection ```bash zotero-research-library-pp-cli ground "acl injury" --collection HAMSTRING --limit 5 ``` Collection-scoped grounding using the local join table. ### Live server-side search fallback ```bash zotero-research-library-pp-cli items list --q "tendon" --qmode everything --limit 10 --json ``` When you need unsynced server state, the generated endpoint carries the API's full search grammar. ## Auth Setup Create an API key at zotero.org/settings/keys and set ZOTERO_API_KEY (or run auth set-token). The CLI resolves your numeric userID automatically via /keys/current and stores the library-prefixed base URL in config — you never need to look up your user ID. Run `zotero-research-library-pp-cli doctor` to verify setup. ## Agent Mode Add `--agent` to any command. Expands to: `--json --compact --no-input --no-color --yes`. - **Pipeable** — JSON on stdout, errors on stderr - **Filterable** — `--select` keeps a subset of fields. Dotted paths descend into nested structures; arrays traverse element-wise. Critical for keeping context small on verbose APIs: ```bash zotero-research-library-pp-cli collections list --agent --select id,name,status ``` - **Previewable** — `--dry-run` shows the request without sending - **Offline-friendly** — sync/search commands can use the local SQLite store when available - **Non-interactive** — never prompts, every input is a flag - **Read-only** — do not use this CLI for create, update, delete, publish, comment, upvote, invite, order, send, or other mutating requests ### Response envelope Commands that read from the local store or the API wrap output in a provenance envelope: ```json { "meta": {"source": "live" | "local", "synced_at": "...", "reason": "..."}, "results": } ``` Parse `.results` for data and `.meta.source` to know whether it's live or local. A human-readable `N results (live)` summary is printed to stderr only when stdout is a terminal AND no machine-format flag (`--json`, `--csv`, `--compact`, `--quiet`, `--plain`, `--select`) is set — piped/agent consumers and explicit-format runs get pure JSON on stdout. ## Paths and state Agents should treat the CLI's path resolver as part of the runtime contract: - Use `--home ` for one invocation, or set `ZOTERO_RESEARCH_LIBRARY_HOME=` to relocate all four path kinds under one root. - Use per-kind env vars only when a specific kind must diverge: `ZOTERO_RESEARCH_LIBRARY_CONFIG_DIR`, `ZOTERO_RESEARCH_LIBRARY_DATA_DIR`, `ZOTERO_RESEARCH_LIBRARY_STATE_DIR`, `ZOTERO_RESEARCH_LIBRARY_CACHE_DIR`. - Resolution order is per-kind env var, `--home`, `ZOTERO_RESEARCH_LIBRARY_HOME`, XDG (`XDG_CONFIG_HOME`, `XDG_DATA_HOME`, `XDG_STATE_HOME`, `XDG_CACHE_HOME`), then platform defaults. - `config` contains settings like `config.toml` and profiles. `data` contains `credentials.toml`, `data.db`, cookies, and auth sidecars. `state` contains persisted queries, jobs, and `teach.log`. `cache` contains regenerable HTTP/cache files. - Stored secrets live in `credentials.toml` under the data dir. Existing legacy `config.toml` secrets are read for compatibility and leave `config.toml` on the first auth write. - Run `zotero-research-library-pp-cli doctor --fail-on warn` to surface path and credential-location warnings. `agent-context` exposes a schema v4 `paths` block for agents that need the resolved dirs. - For MCP, pass relocation through the MCP host config. The MCP binary does not inherit CLI flags: ```json { "mcpServers": { "zotero-research-library": { "command": "zotero-research-library-pp-mcp", "env": { "ZOTERO_RESEARCH_LIBRARY_HOME": "/srv/zotero-research-library" } } } } ``` Fleet precedence: an inherited per-kind env var overrides an explicit `--home` for that kind. Use `ZOTERO_RESEARCH_LIBRARY_HOME` or per-kind vars as durable fleet levers, and use `--home` only for a single invocation. Relocation is not reversible by unsetting env vars; move files manually before clearing `ZOTERO_RESEARCH_LIBRARY_HOME`, or `doctor` will not find credentials left under the former root. ## Automatic learning This CLI ships a self-capturing learning loop. The CLI does its own bookkeeping: every invocation is journaled locally, a failed flag followed by a corrected retry auto-derives a `flag_alias` candidate, and a `teach` on a query family without a playbook auto-synthesizes a `playbook_candidate` from the session's journal. Your job is judgment only: `recall` first, act on surfaced candidates, `teach` the final answer, `playbook amend` when you observe a correction. You never record failures by hand. ### Step 1: `recall` before any discovery Before list/search/drill commands on a new user question, run: ```bash zotero-research-library-pp-cli recall "" --agent ``` The response envelope: ```json { "query": "...", "normalized": "", "query_entities": ["..."], "found": true | false, "match_score": 0.0, "results": [ { "resource_id": "...", "resource_type": "...", "venue": "...", "confidence": 2, "entity_match": "exact|partial|unknown", "source": "taught|preseed|pattern", "warnings": ["..."] } ], "mismatches": [ /* only when --debug-mismatches */ ], "warnings": [ /* top-level */ ], "candidates": [ { "id": 12, "class": "flag_alias | playbook_candidate", "summary": "...", "sightings": 3, "last_seen": "...", "rationale": "...", "next_action": ["", "zotero-research-library-pp-cli learnings confirm 12"] } ], "playbook": { "query_family": "...", "playbook": { "steps": [ { "cmd": "", "purpose": "..." } ], "entity_slots": ["$ENTITY"], "expected_tool_calls": 3 }, "slots_resolved": { "$ENTITY": { "token": "", "canonical": "" } }, "notes": "" }, "notes": "" } ``` Empty-store short-circuit: if the store has no learnings, playbooks, or candidates yet (recall finds nothing and `learnings list` and `learnings candidates` are both empty), skip recall for the rest of this session instead of taxing every query; resume recall-first once something has been taught. ### Step 2: decision tree Read `candidates`, `playbook`, `notes`, `results[0]`, and warnings in that order: ``` if Candidates present (warnings include "candidates_present"): -> candidates are try-then-confirm, never facts. Follow each candidate's two-step next_action verbatim: run the trial command first, then run `learnings confirm ` only after the trial verified the behavior. Reject a wrong candidate with `learnings reject `. -> NEVER re-teach something recall surfaced as a candidate; confirm or reject that candidate instead of teaching a duplicate. -> candidates ride alongside playbooks and resource hits, not instead of them; continue with the branches below after acting on them. if Playbook present: -> READ Playbook.notes verbatim FIRST (workarounds + gotchas the CLI surface doesn't expose) -> replay Playbook.steps in order, substituting Playbook.slots_resolved entries for the entity slot tokens. If a step's slot is unresolved, fall back to discovery for that step only. -> the Playbook's expected_tool_calls is a budget; if you find yourself running materially more, record the divergence via `zotero-research-library-pp-cli playbook amend` at end-of-session. elif Notes present (no Playbook): -> read Notes verbatim before any discovery step; they carry known gotchas for this query family even when no structured choreography exists yet. elif Found AND Results[0].EntityMatch == "exact" AND Results[0].Confidence >= 2: -> skip discovery; fetch live data for Results[*].ResourceID in parallel elif Found AND Results[0].EntityMatch == "partial": -> candidate hint, NOT a hit; read the resource title to validate before trusting elif (any row in Mismatches[] when --debug-mismatches was passed): -> treat as cold start; the stored learning is for a different entity (different canonical resolved from query_entities) else: // Found == false, no playbook, no notes -> cold start; run discovery normally; teach the answer afterward (Step 4). If the family has no playbook yet, that teach auto-synthesizes a playbook candidate from this session's journal - you do not need to record one by hand. ``` Playbook and Notes are orthogonal to the per-resource path. A recall response can carry both a Playbook AND a `Results[]` hit - use both: the Playbook tells you which choreography to run; the resource hits short-circuit specific steps. Default to skipping `mismatches`; pass `--debug-mismatches` only when investigating cold-start surprises. Candidate judgment details: `learnings confirm ` prints the candidate's full payload before materializing it - check that the printed payload matches the behavior you verified. `learnings reject ` tombstones the derivation signature so the same candidate does not resurface. The envelope carries only the few candidates worth acting on now; `zotero-research-library-pp-cli learnings candidates` lists the full open set. Graceful degradation: if `learnings confirm` is an unknown command, you are driving an older binary - ignore the candidates guidance and follow the rest of the protocol. ### Step 3: always read `warnings` - `low_confidence`: row exists at `confidence<2`. Treat as a hint, not a skip-discovery hit. - `resource_not_in_store`: the local store doesn't have the resource the learning points at. The match validator couldn't classify entities — direct-fetch and re-evaluate. - `cross_alias_match` (per-result): the row was taught under a different alias and matched the live query's canonical via `entity_lookups` (e.g., a "USA" teach satisfying a "United States" recall). Trust the resource_id. - `similar_shape_different_entity