Pp Zotero Research Library

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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:

   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:

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.

  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.

  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.

  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.

  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.

  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:

zotero-research-library-pp-cli which "<capability in your own words>"

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

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

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

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

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

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:

  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:

{
  "meta": {"source": "live" | "local", "synced_at": "...", "reason": "..."},
  "results": <data>
}

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 <dir> for one invocation, or set ZOTERO_RESEARCH_LIBRARY_HOME=<dir> 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:

  {
    "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:

zotero-research-library-pp-cli recall "<user's question>" --agent

The response envelope:

{
  "query": "...",
  "normalized": "<normalized form>",
  "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": ["<trial command>", "zotero-research-library-pp-cli learnings confirm 12"] }
  ],
  "playbook": {
    "query_family": "...",
    "playbook": {
      "steps": [ { "cmd": "<command with {slot} substitution>", "purpose": "..." } ],
      "entity_slots": ["$ENTITY"],
      "expected_tool_calls": 3
    },
    "slots_resolved": { "$ENTITY": { "token": "<live token>", "canonical": "<canonical>" } },
    "notes": "<workarounds + gotchas for this query family>"
  },
  "notes": "<duplicate surface for non-playbook callers>"
}

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 <id>` only after the trial verified the behavior.
       Reject a wrong candidate with `learnings reject <id>`.
    -> 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 <id> prints the candidate's full payload before materializing it - check that the printed payload matches the behavior you verified. learnings reject <id> 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:<canonical> (top-level): a structurally matching row exists but its canonical entity differs from the live query's. Treated as cold start; the warning carries the conflicting canonical as a hint, but the row is NOT promoted into Results.
• ambiguous_alias (top-level): a single query entity resolved to multiple canonicals (e.g., "Cards" → Arizona Cardinals + St. Louis Cardinals). Surface the ambiguity from context before committing to a resource.
• candidates_present (top-level): the envelope carries a candidates section. Handle it via the candidates branch in Step 2 before anything else.
• lookup_refresh_available (top-level): an entity in the query has no lookup row yet, but synced data could provide one. Run zotero-research-library-pp-cli sync to refresh entity lookups.
• Top-level no_learnings_for_query_family: the table had no rows above the Jaccard floor. Pure cold start.