Unified top-level search across all configured academic platforms.

Returns only cite_key + title + abstract + year + source for each paper. Papers without abstract are discarded. Defaults to last 5 years.

Args: query: Search query string. max_results_per_source: Max results to fetch from each selected source. sources: Source names, preset group, or 'all'. Groups: medical (pubmed,pmc,medrxiv), cs (arxiv,dblp,semantic), metadata (crossref,openalex). Or comma-separated individual names. year_from: Earliest publication year (default: current year - 5). Pass 0 to disable year filtering. year_to: Latest publication year (default: none). Returns: Aggregated dict with per-source stats, errors, and simplified papers.

Get paper metadata by DOI with multi-source fallback.

Tries CrossRef first (richest metadata), then Semantic Scholar (best abstract coverage) to backfill missing abstract. Only saves to local library when an abstract is available.

Args: doi: Digital Object Identifier (e.g., '10.1038/nature12373'). Returns: Paper metadata dict. Empty dict if not found at all.

Try source-native download, OA repositories, Unpaywall, then optional Sci-Hub.

Args: source: Source name (arxiv, medrxiv, semantic, crossref, pubmed, pmc, dblp, openalex). paper_id: Source-native paper identifier. doi: Optional DOI used for repository/unpaywall/Sci-Hub fallback. title: Optional title used for repository/Sci-Hub fallback when DOI is unavailable. save_path: Directory to save downloaded files. use_scihub: Whether to fallback to Sci-Hub after OA attempts fail. scihub_base_url: Sci-Hub mirror URL for fallback. Returns: Download path on success or explanatory error message.

Download a paper's PDF using its cite_key.

Looks up the paper in the local library by cite_key, checks for an existing local PDF, then falls back to download_paper.

Args: cite_key: The paper's cite_key (e.g. 'Kxq') from search results. save_path: Directory to save the PDF (default: /downloads). Returns: Path to the downloaded PDF, or an error message.

Download and extract full text from a paper using its cite_key.

Checks for cached full text first, then downloads the PDF and extracts text via pypdf. The extracted text is cached in the local library.

Args: cite_key: The paper's cite_key (e.g. 'Kxq') from search results. save_path: Directory for PDF download (default: /downloads). Returns: The extracted text content, or an error message.

Clear all cached search results.

Returns: Dict with number of cleared entries.

Search the local paper library (SQLite) by keyword.

Searches across title, authors, and abstract of all previously fetched papers. This is an offline operation — no network calls are made.

Args: keyword: Search keyword (matched against title/authors/abstract). limit: Maximum number of results to return (default: 50). Returns: List of matching paper records from the local library.

Get statistics about the local paper library.

Returns: Dict with total paper count, counts by source, PDF/fulltext coverage, and the database file path.

Initialize harness infrastructure for academic paper writing.

Creates the following structure in the project directory:

• CLAUDE.md: Project map for AI Agent (in project root)

• .harness/: Harness directory containing:

  • rules.md: Writing rules (R0-R9)

  • verify.py: Automated verification script

  • checks/: Verification rule implementations

  • specs/manuscript-spec.yaml: Configurable standards

  • checklist.md: Manual review checklist

  • Harness.md: Usage guide

Args: project_dir: Target project directory path. Defaults to current working directory. force: If True, overwrite existing .harness/ directory. Defaults to False.

Returns: JSON string with initialization status and next steps.

Verify a manuscript against harness rules.

Runs the harness verification script on the specified manuscript file and returns a JSON report of violations, warnings, and info messages.

Args: manuscript_path: Path to the manuscript markdown file. verbose: If True, include detailed violation information. Defaults to False.

Returns: JSON string with verification results including error count, warning count, and detailed violation information.

List all harness rules with their descriptions.

Returns a summary of all verification rules (R0-R9) including rule ID, name, severity, and brief description.

Returns: JSON string with list of all rules.