Resolves bibliographic metadata by extracting a DOI from the first page of a PDF and fetching citation data (title, authors, journal, year, volume/issue/pages) from the CrossRef API, falling back to the PDF's own metadata when no DOI is found.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@rag-pipeline find papers on transformer architectures from 2023"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
🇵🇱 Polska wersja
A local, GPU-accelerated retrieval pipeline for research papers — parses PDFs with layout-aware chunking, pulls real bibliographic metadata (DOI → CrossRef), embeds with hybrid dense + sparse vectors, and stores everything in Qdrant for hybrid search with reranking. Built to be queried directly from Claude through an MCP server.
Dropping papers into a folder makes them invisible to search. This turns a pile of PDFs into something queryable: proper section/paragraph-aware chunks (not a naive character splitter), citation-ready metadata pulled automatically from CrossRef, and hybrid dense+sparse retrieval so both semantic and exact-term queries work — all exposed as MCP tools so Claude can search and ingest papers directly.
Related MCP server: Personal Research Assistant MCP
Layout-aware PDF parsing via Docling — chunks by paragraph/section instead of a naive character splitter, keeps page numbers and section headings per chunk.
Real bibliographic metadata — regex-extracts a DOI from page 1, resolves full citation data (title, authors, journal, year, volume/issue/pages) via the CrossRef API, falls back to the PDF's own metadata when no DOI is found.
Hybrid embeddings — dense (BAAI/bge-m3) + sparse (SPLADE, prithvida/Splade_PP_EN_v1) vectors per chunk, stored together in Qdrant for hybrid retrieval.
Background ingestion — a Redis + RQ worker so large PDFs don't block a request; GPU-enabled Docker container for embedding.
MCP server exposing two tools to Claude — search_papers (hybrid search with reranking) and ingest_paper (drop a PDF straight into the index) — meant to work as a research-paper memory Claude can query directly.
Dockerized — Qdrant + Redis + GPU-enabled API/worker containers via docker-compose.
Python · Docling (PDF parsing) · sentence-transformers (BGE-M3 dense embeddings) · fastembed (SPLADE sparse embeddings) · Qdrant (hybrid vector search) · Redis + RQ (background job queue) · FastAPI (planned API layer) · MCP (Model Context Protocol server for Claude) · Docker Compose, CUDA 12.9 GPU container.
Work in progress — not fully wired up end to end yet.
Works today: ingest.py runs standalone from the CLI — parse a PDF, pull its metadata, embed it (dense + sparse), and upsert into Qdrant. Point it at a running Qdrant instance and it works.
Missing: main.py, the FastAPI service that's supposed to expose /search, /ingest, and /health — the Dockerfile copies it, the Docker Compose healthcheck pings it, the RQ worker expects something to be enqueuing jobs for it, and mcp_server.py's two Claude tools both call it over HTTP at localhost:8000. Without it, the worker has nothing to consume, the MCP tools have no backend to talk to, and docker-compose up won't build (the API/worker image's build step copies a file that isn't there).
The docker-compose.yml bind mounts also still point at a Windows path (S:\RAG-data\...) from an earlier setup — adjust those to wherever you want Qdrant/Redis/model cache data to live before running it.
uv sync
# Qdrant needs to be running somewhere ingest.py can reach:
docker run -p 6333:6333 qdrant/qdrant
python ingest.py path/to/paper.pdfThe full pipeline (Docker Compose stack, /search and /ingest API, MCP tools) will work once main.py exists.
Ingest a PDF file from the local filesystem into the search index. The file is chunked, embedded (dense + sparse), and stored in Qdrant.
| Name | Required | Description | Default |
|---|---|---|---|
| file_path | Yes | Absolute or relative path to the PDF file. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries the full burden of disclosing effects. It clearly explains the processing pipeline: the file is chunked, embedded with dense + sparse vectors, and stored in Qdrant. This lets an agent anticipate side effects. It does not mention idempotence, duplicate handling, or failure behavior, but the core mutation is transparently described.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two tight sentences with no filler. The first sentence states the primary action and target, the second adds the important processing steps. Every word earns its place.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a single-parameter ingest operation, the description covers the core workflow and storage destination. It does not describe the return value or failure behavior, but given the simple input and lack of output schema, the definition is reasonably complete for an agent to invoke it correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema already provides 100% coverage for the single parameter file_path, including its type and that it is an absolute or relative path. The description adds little beyond the schema, reinforcing that the file is a local PDF. That meets the baseline of 3 but does not exceed it.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb ('Ingest'), a clear resource ('PDF file'), and a destination ('search index'). It also names the sibling (search_papers) implicitly by its focus on adding to an index, so an agent can distinguish ingest from search without extra context.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies when to use this tool (when a PDF needs to be added to the search index) versus the sibling search_papers (when querying is needed), but it never explicitly states 'use this when... use search_papers when...' or mentions any exclusions or prerequisites.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Search the ingested paper collection using a natural-language query. Returns the most relevant passages with page numbers and sources, ranked by a cross-encoder reranker.
| Name | Required | Description | Default |
|---|---|---|---|
| limit | No | Number of results to return (default 5). | |
| query | Yes | The search query in natural language. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries the full burden of behavioral disclosure. It reveals that results are passages rather than full papers, include page numbers and sources, and are ranked by a cross-encoder reranker, which meaningfully describes behavior beyond the tool name.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences with the main action front-loaded. The second sentence efficiently packs return format and ranking behavior. No unnecessary words or redundancy.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a simple two-parameter search tool with no output schema, the description adequately conveys what results include (passages, page numbers, sources, ranked order) and the scope (ingested collection). It does not specify the exact result data structure, but that is minor given the straightforward contract and the clear sibling relationship.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so the baseline is 3. The description reinforces that the query is natural-language but adds no new detail about the limit parameter or query formatting. It does not need to compensate for schema gaps.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb ('search') and resource ('ingested paper collection'), and clarifies that queries are natural-language. It also distinguishes itself from the sibling 'ingest_paper' by focusing on retrieval of already-ingested content rather than adding papers.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The phrase 'ingested paper collection' clearly implies this is for searching papers previously added, giving the agent a strong contextual signal about when to use it. However, it does not explicitly name the alternative or state exclusions, so it falls short of full routing guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
v0.1.0ingest_papersearch_papersScored across 2 tools
The two tools have completely distinct roles: one adds documents to the index, the other queries it. There is no overlap or ambiguity between ingestion and search.
Both tools follow a verb_noun pattern and are recognizable at a glance. The only minor inconsistency is that one uses the plural 'papers' while the other uses singular 'paper'.
Two tools is a thin surface, falling below the typical 3-15 well-scoped range. Each tool is essential for the core RAG workflow, but the set still feels minimal for anything beyond basic ingest-and-query usage.
The core ingest and search operations are present, giving agents the main RAG loop. However, there is no way to list, delete, or update ingested papers, which leaves obvious workflow gaps around managing the collection.
Search arXiv/Semantic Scholar/OpenAlex + medical evidence (PubMed/Europe PMC) + LaTeX/PDF tools.
Search arXiv and ACL Anthology, retrieve citations and references, and browse web sources to accel…
Search 340M+ academic papers — citation graphs, semantic similarity, and AI literature reviews.
Parse, extract, split, and ask over digital PDFs (text layer, no OCR) from Cursor and Claude.
