Return current configuration summary and enabled integrations.

Search Semantic Scholar, OpenAlex, Europe PMC, arXiv, Crossref, and DOAJ for a topic.

Find similar papers starting from a seed paper title or DOI.

Search a topic and render an interactive citation/relatedness graph as a self-contained HTML file.

Nodes are papers (size scales with citation count, color by year); edges connect papers that share keywords or a venue, plus similarity links radiating from the top result. Returns the local HTML path. Open it in a browser to explore or screenshot the landscape.

Download an open-access PDF and return a local preview.

Extract full text from a local PDF, save a text sidecar, and return top matching chunks.

Render selected PDF pages to PNG and return them as images the model can see.

The result is [metadata_dict, image, image, ...]: the dict keeps pdf_path and images (local PNG paths) for path-based clients, and the trailing image blocks let a vision-capable model inspect figures, tables, and layout directly. Set include_images=False to return only the paths.

Return a downloaded PDF's local path so a client can open the file when it needs it.

By default nothing is base64-inlined: the result is [metadata, resource_link] where metadata carries pdf_path / doc_id / page_count / size_bytes. The PDF stays on disk; clients that read local files (e.g. Claude Code) or fetch the paperpilot://pdf/{doc_id} resource use it without payload bloat. Set embed_base64=True to inline the PDF as an application/pdf resource for clients that read PDFs that way (Claude API integrations), bounded by max_mb / max_pages.

Return the exact extracted text of specific PDF pages (1-based) as plain JSON.

For fine-grained lookups over the wire (a single reference entry, a table, a footnote) without base64 and without filesystem/shell access. Use deep_read_topic first to get the pdf_path and the page mapping (deep_reads[*].chunk_manifest_path), then fetch the exact pages you need here.

Search LibGen mirrors for supplemental research material.

Resolve LibGen mirror links, download a PDF when possible, and return a preview.

Search Sci-Hub for papers by DOI, title, or keyword. Use search_type='doi', 'title', or 'keyword'. Requires SCIHUB_ENABLED=true.

Download a paper PDF via Sci-Hub using its DOI. Returns local path and text preview. Requires SCIHUB_ENABLED=true.

List Zotero collections visible to the configured web or local Zotero integration.

Run the end-to-end research workflow and optionally sync the result into Zotero. Set include_scihub=True to use Sci-Hub as a fallback for papers without open-access PDFs. Set write_graph=True to also render an interactive citation graph HTML (path returned as graph_path).

Search, download, extract full text, and return evidence chunks plus local PDF paths for direct inspection.

By default the result is just [result_dict]: it carries every downloaded PDF's local path in pdf_paths (and in deep_reads[].pdf_path / downloads[].pdf_path), so a client can open the files when needed without any base64 in the payload. Opt in to inline content when your client benefits: render_top_pages=True appends the top paper's relevant pages as images (vision models); attach_top_pdf=True embeds its PDF as an application/pdf resource (Claude API style). include_scihub=True adds a Sci-Hub fallback; write_graph=True also renders a citation graph (path in graph_path).