diff --git a/config/basic.yaml b/config/basic.yaml index bbb8caef..4837f75c 100644 --- a/config/basic.yaml +++ b/config/basic.yaml @@ -59,7 +59,14 @@ paperoni: collection: $class: paperoni.collection.filecoll:FileCollection file: ${paperoni.data_path}/collection.json + embedding: + $class: paperoni.embed.cfg:Embedding + model: gemini-embedding-001 + api_key: ${paperoni.api_keys.gemini} server: + host: localhost + port: 8000 + protocol: http max_results: 10000 process_pool_executor: max_workers: 4 @@ -83,3 +90,7 @@ paperoni: search: [] validate: [search] dev: [] + mcp: + api_client: + $class: paperoni.mcp.client:PaperoniAPIClient + endpoint: ${paperoni.server.protocol}://${paperoni.server.host}:${paperoni.server.port} \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 39361cea..3b680a4a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,6 +40,7 @@ dependencies = [ "jinja2>=3.1.6", "easy-oauth", "markdown>=3.10", + "fastmcp>=2.14.2", ] [project.urls] diff --git a/src/paperoni/__main__.py b/src/paperoni/__main__.py index b73b50a7..b56e6377 100644 --- a/src/paperoni/__main__.py +++ b/src/paperoni/__main__.py @@ -43,6 +43,7 @@ from .config import config from .dash import History from .display import display, print_field, terminal_width +from .embed.embeddings import PaperEmbedding from .fulltext.locate import URL, locate_all from .fulltext.pdf import PDF, CachePolicies, get_pdf from .heuristics import simplify_paper @@ -617,6 +618,12 @@ class Search: # [alias: -f] flags: set[str] = None + # Semantic search query + query: str = None + + # Similarity threshold + similarity_threshold: float = 0.75 + # Whether to expand links expand_links: bool = False @@ -648,8 +655,19 @@ def run(self, coll: "Coll") -> list[Paper]: exclude_flags={f for f in flags if f.startswith("~")}, ) ] + + if self.query: + papers, similarities = zip( + *PaperEmbedding.semantic_search( + papers, self.query, self.similarity_threshold + ) + ) + else: + similarities = None + self.format(papers) - return papers + + return papers, similarities @dataclass class Import: @@ -851,7 +869,7 @@ class Login: """Retrieve an access token from the paperoni server.""" # Endpoint to login to - endpoint: str = "http://localhost:8000" + endpoint: str = None # Whether to use headless mode headless: bool = False @@ -860,8 +878,29 @@ def run(self): print_field("Access token", login(self.endpoint, self.headless)) +@dataclass +class MCP: + """MCP server for paperoni.""" + + # Paperoni API + endpoint: str = None + + transport: Literal["stdio", "http"] = "stdio" + host: str = "localhost" + port: int = 9000 + + def run(self): + from .mcp.server import create_mcp + + mcp = create_mcp(self.endpoint) + if self.transport == "stdio": + mcp.run(transport="stdio") + elif self.transport == "http": + mcp.run(transport="http", host=self.host, port=self.port) + + PaperoniCommand = TaggedUnion[ - Discover, Refine, Fulltext, Work, Coll, Batch, Focus, Serve, Login + Discover, Refine, Fulltext, Work, Coll, Batch, Focus, Serve, Login, MCP ] diff --git a/src/paperoni/config.py b/src/paperoni/config.py index de715fc4..7b474b55 100644 --- a/src/paperoni/config.py +++ b/src/paperoni/config.py @@ -11,7 +11,9 @@ from serieux.features.encrypt import Secret from .collection.abc import PaperCollection +from .embed.cfg import Embedding from .get import Fetcher, RequestsFetcher +from .mcp.client import PaperoniAPIClient from .model.focus import AutoFocus, Focuses from .prompt import GenAIPrompt, Prompt @@ -52,6 +54,13 @@ def __post_init__(self): self.process_pool = ProcessPoolExecutor(**self.process_pool_executor) +@dataclass(kw_only=True) +class MCP: + api_client: TaggedSubclass[PaperoniAPIClient] = field( + default_factory=PaperoniAPIClient + ) + + @dataclass class PaperoniConfig: cache_path: Path = None @@ -66,7 +75,9 @@ class PaperoniConfig: work_file: Path = None collection: TaggedSubclass[PaperCollection] = None reporters: list[TaggedSubclass[Reporter]] = field(default_factory=list) + embedding: TaggedSubclass[Embedding] = field(default_factory=Embedding) server: Server = field(default_factory=Server) + mcp: MCP = field(default_factory=MCP) def __post_init__(self): self.metadata: Meta[Path | list[Path] | Meta | Any] = Meta() diff --git a/src/paperoni/embed/cfg.py b/src/paperoni/embed/cfg.py new file mode 100644 index 00000000..00372625 --- /dev/null +++ b/src/paperoni/embed/cfg.py @@ -0,0 +1,75 @@ +"""Embedding service for semantic search using Google GenAI.""" + +import json +from dataclasses import dataclass +from pathlib import Path +from typing import BinaryIO + +from google import genai +from google.genai.types import EmbedContentResponse +from paperazzi.utils import _make_key as paperazzi_make_key, disk_cache, disk_store +from serieux.features.encrypt import Secret + + +@dataclass +class EmbedContentResponseSerializer: + @staticmethod + def dump(response: EmbedContentResponse, file_obj: BinaryIO): + model_dump = response.model_dump() + return file_obj.write( + json.dumps(model_dump, indent=2, ensure_ascii=False).encode("utf-8") + ) + + @staticmethod + def load(file_obj: BinaryIO) -> EmbedContentResponse: + data = json.load(file_obj) + return EmbedContentResponse.model_validate(data) + + +@dataclass +class Embedding: + """Service for generating and caching embeddings using Google GenAI.""" + + client: genai.Client = None + api_key: Secret[str] = None + model: str = None + + def __post_init__(self): + if self.client is None: + self.client = genai.Client(api_key=self.api_key or None) + + def embed( + self, contents: list[str], cache_dir: Path = None, **kwargs + ) -> list[EmbedContentResponse]: + """Embed content.""" + if cache_dir is not None: + embed = self._embed.update(cache_dir=cache_dir) + else: + embed = self._embed + + return list( + map( + lambda c: embed(self.client, model=self.model, content=c, **kwargs), + contents, + ) + ) + + @staticmethod + def _make_key(_: tuple, kwargs: dict) -> str: + kwargs = kwargs.copy() + kwargs.pop("client", None) + + return paperazzi_make_key(None, kwargs) + + @disk_store + @disk_cache( + cache_dir=Path("/tmp/embeddings"), + serializer=EmbedContentResponseSerializer, + make_key=_make_key, + ) + @staticmethod + def _embed( + client: genai.Client, *, model: str, content: str, **kwargs + ) -> EmbedContentResponse: + """Get embedding for text.""" + return client.models.embed_content(model=model, contents=[content], **kwargs) diff --git a/src/paperoni/embed/embeddings.py b/src/paperoni/embed/embeddings.py new file mode 100644 index 00000000..17a681d2 --- /dev/null +++ b/src/paperoni/embed/embeddings.py @@ -0,0 +1,62 @@ +from typing import Iterable + +import numpy as np +from google import genai +from google.genai.types import EmbedContentResponse + +from ..config import config +from ..model.classes import Paper + + +class PaperEmbedding: + @staticmethod + def semantic_search( + papers: Iterable[Paper], query: str, similarity_threshold: float = 0.75 + ) -> list[tuple[Paper, float]]: + """Semantic search for papers.""" + responses: Iterable[EmbedContentResponse] = map( + PaperEmbedding.get_paper_embedding, papers + ) + store = np.array([r.embeddings[0].values for r in responses]) + query_embedding = np.array( + config.embedding.embed( + [query], + cache_dir=None, + config=genai.types.EmbedContentConfig(task_type="SEMANTIC_SIMILARITY"), + )[0] + .embeddings[0] + .values + ) + + # Calculate Cosine Similarity + # Formula: (A dot B) / (||A|| * ||B||) + dot_products = np.dot(store, query_embedding) + norms = np.linalg.norm(store, axis=1) * np.linalg.norm(query_embedding) + similarities = dot_products / norms + + # Return sorted results + sorted_indices = np.argsort(similarities)[::-1] + return [ + (papers[i], similarities[i]) + for i in sorted_indices + if similarities[i] >= similarity_threshold + ] + + @staticmethod + def get_paper_embedding(paper: Paper) -> list[float] | None: + """Get embedding for a paper (title + abstract + topics).""" + parts = [paper.title] + + if paper.abstract: + parts.append(paper.abstract) + + if paper.topics: + topic_names = ", ".join(sorted(t.name.lower() for t in paper.topics)) + parts.append(f"Topics: {topic_names}") + content = "\n\n".join(parts) + + return config.embedding.embed( + [content], + cache_dir=config.data_path / "embeddings", + config=genai.types.EmbedContentConfig(task_type="SEMANTIC_SIMILARITY"), + )[0] diff --git a/src/paperoni/mcp/__init__.py b/src/paperoni/mcp/__init__.py new file mode 100644 index 00000000..ade835e6 --- /dev/null +++ b/src/paperoni/mcp/__init__.py @@ -0,0 +1 @@ +"""MCP server for paperoni.""" diff --git a/src/paperoni/mcp/client.py b/src/paperoni/mcp/client.py new file mode 100644 index 00000000..6c6cdd8b --- /dev/null +++ b/src/paperoni/mcp/client.py @@ -0,0 +1,122 @@ +"""HTTP client for paperoni REST API.""" + +import os +from dataclasses import dataclass, field +from datetime import date +from typing import Any + +from fastapi import HTTPException +from serieux.features.encrypt import Secret + +from ..get import Fetcher, RequestsFetcher + + +@dataclass +class PaperoniAPIClient: + """Client for interacting with paperoni REST API.""" + + endpoint: str + token: Secret[str] = os.getenv("PAPERONI_TOKEN") + fetch: Fetcher = field(default_factory=RequestsFetcher) + + def __post_init__(self): + self.headers = { + "Accept": "application/json", + } + if self.token is not None: + self.headers["Authorization"] = f"Bearer {self.token}" + + def search_papers( + self, + paper_id: int = None, + title: str = None, + institution: str = None, + author: str = None, + venue: str = None, + start_date: date = None, + end_date: date = None, + include_flags: list[str] = None, + exclude_flags: list[str] = None, + query: str = None, + similarity_threshold: float = 0.75, + offset: int = 0, + limit: int = 100, + ) -> dict[str, Any]: + params: dict[str, Any] = { + "offset": offset, + "limit": limit, + } + + if paper_id: + params["paper_id"] = paper_id + if title: + params["title"] = title + if institution: + params["institution"] = institution + if author: + params["author"] = author + if venue: + params["venue"] = venue + if start_date: + params["start_date"] = start_date.isoformat() + if end_date: + params["end_date"] = end_date.isoformat() + if include_flags: + params["include_flags"] = ",".join(include_flags) + if exclude_flags: + params["exclude_flags"] = ",".join(exclude_flags) + if query: + params["query"] = query + if similarity_threshold: + params["similarity_threshold"] = similarity_threshold + + url = f"{self.endpoint}/api/v1/search" + + try: + resp = self.fetch.read( + url, + format="json", + cache_into=None, + headers=self.headers, + params=params, + ) + resp.pop("total", None) + return resp + + except Exception as e: + if isinstance(e, HTTPException) and e.status_code == 404: + return { + "results": [], + "similarities": None, + "count": 0, + "next_offset": None, + } + raise + + def count_papers( + self, + paper_id: int = None, + title: str = None, + institution: str = None, + author: str = None, + venue: str = None, + start_date: date = None, + end_date: date = None, + include_flags: list[str] = None, + exclude_flags: list[str] = None, + ) -> int: + # Fetch first page to get total count + resp = self.search_papers( + paper_id=paper_id, + title=title, + institution=institution, + author=author, + venue=venue, + start_date=start_date, + end_date=end_date, + include_flags=include_flags, + exclude_flags=exclude_flags, + offset=0, + limit=1, # Only need the total count + ) + return resp.get("total", 0) diff --git a/src/paperoni/mcp/server.py b/src/paperoni/mcp/server.py new file mode 100644 index 00000000..baa7a4ec --- /dev/null +++ b/src/paperoni/mcp/server.py @@ -0,0 +1,127 @@ +"""MCP server implementation using fastmcp.""" + +from datetime import date + +from fastmcp import FastMCP + +from ..config import config +from .client import PaperoniAPIClient + + +def create_mcp(endpoint: str = None): + api_client = PaperoniAPIClient( + endpoint or config.mcp.api_client.endpoint, + token=config.mcp.api_client.token, + fetch=config.mcp.api_client.fetch, + ) + + mcp = FastMCP(name="Paperoni") + + @mcp.tool + def search_papers( + paper_id: int = None, + title: str = None, + institution: str = None, + author: str = None, + venue: str = None, + start_date: date = None, + end_date: date = None, + include_flags: list[str] = None, + exclude_flags: list[str] = None, + query: str = None, + similarity_threshold: float = 0.75, + offset: int = 0, + limit: int = 100, + ): + """Search for papers in the paperoni collection. + + This tool allows searching for papers using various filters including + semantic search, institution, venue, author, and date ranges. Results + include paper metadata (title, abstract, authors, venues, topics) but + exclude PDF content. + + If a query is provided, the results will be sorted by similarity score. + Note that unrelated papers may still be returned with a low similarity + score. + + Args: + paper_id: Paper ID + title: Title of the paper + institution: Institution of an author + author: Author of the paper + venue: Venue name (long or short) + start_date: Start date to consider + end_date: End date to consider + include_flags: Flags that must be present + exclude_flags: Flags that must not be present + query: Semantic search query + similarity_threshold: Similarity threshold (default: 0.75) + offset: Pagination offset (default: 0) + limit: Maximum number of results to return (default: 100) + + Returns: + Dictionary containing: + - results: List of paper objects with metadata + - similarities: List of similarity scores (None if no query was provided) + - count: Number of results in this page + - next_offset: Offset for next page (None if no more pages) + """ + + return api_client.search_papers( + paper_id=paper_id, + title=title, + institution=institution, + author=author, + venue=venue, + start_date=start_date, + end_date=end_date, + include_flags=include_flags, + exclude_flags=exclude_flags, + query=query, + similarity_threshold=similarity_threshold, + offset=offset, + limit=limit, + ) + + @mcp.tool + def count_papers( + paper_id: int = None, + title: str = None, + institution: str = None, + author: str = None, + venue: str = None, + start_date: date = None, + end_date: date = None, + include_flags: list[str] = None, + exclude_flags: list[str] = None, + ) -> int: + """Count papers matching criteria without fetching all results. + + Args: + paper_id: Paper ID + title: Title of the paper + institution: Institution of an author + author: Author of the paper + venue: Venue name (long or short) + start_date: Start date to consider + end_date: End date to consider + include_flags: Flags that must be present + exclude_flags: Flags that must not be present + + Returns: + Total count of matching papers + """ + + return api_client.count_papers( + paper_id=paper_id, + title=title, + institution=institution, + author=author, + venue=venue, + start_date=start_date, + end_date=end_date, + include_flags=include_flags, + exclude_flags=exclude_flags, + ) + + return mcp diff --git a/src/paperoni/web/restapi.py b/src/paperoni/web/restapi.py index e15a6fb9..4b77bc6f 100644 --- a/src/paperoni/web/restapi.py +++ b/src/paperoni/web/restapi.py @@ -33,10 +33,10 @@ def __call__(self, things): class PagingMixin: """Mixin for paging.""" - # Results offset + # Pagination offset offset: int = field(default=0) - # Max number of results to return - size: int = field(default=100) + # Maximum number of results to return + limit: int = field(default=100) _count: int | None = field(repr=False, compare=False, default=None) _next_offset: int | None = field(repr=False, compare=False, default=None) @@ -54,23 +54,23 @@ def slice( iterable: Iterable, *, offset: int = None, - size: int = None, + limit: int = None, ) -> Iterable: if offset is None: offset = self.offset or 0 - if size is None: - size = self.size or 100 + if limit is None: + limit = self.limit or 100 - size = min(size, config.server.max_results) + limit = min(limit, config.server.max_results) self._count = 0 self._next_offset = offset - for entry in itertools.islice(iterable, offset, offset + size): + for entry in itertools.islice(iterable, offset, offset + limit): self._count += 1 self._next_offset += 1 yield entry - if self._count < size: + if self._count < limit: # No more results self._next_offset = None @@ -108,6 +108,7 @@ class SearchResponse(PagingResponseMixin): """Response model for paper search.""" results: list[CollectionPaper] + similarities: list[float] | None @dataclass @@ -277,10 +278,14 @@ def _search(request: dict): coll = Coll(command=None) # Perform search using the collection's search method - all_matches = request.run(coll) + all_matches, similarities = request.run(coll) + + if similarities is not None: + similarities = list(request.slice(similarities)) + results = list(request.slice(all_matches)) - return results, request.count, request.next_offset, len(all_matches) + return results, similarities, request.count, request.next_offset, len(all_matches) def _work_view(request: dict): @@ -338,11 +343,15 @@ async def root(): ) async def search_papers(request: SearchRequest = Depends()): """Search for papers in the collection.""" - results, count, next_offset, total = await run_in_process_pool( + results, similarities, count, next_offset, total = await run_in_process_pool( _search, serialize(SearchRequest, request) ) return SearchResponse( - results=results, count=count, next_offset=next_offset, total=total + results=results, + similarities=similarities, + count=count, + next_offset=next_offset, + total=total, ) @app.get( diff --git a/tests/web/test_restapi.py b/tests/web/test_restapi.py index 32e962a9..6ad290f5 100644 --- a/tests/web/test_restapi.py +++ b/tests/web/test_restapi.py @@ -180,8 +180,8 @@ def test_search_endpoint( ["params", "count", "next_offset", "total"], [ ({}, 3, None, 3), - ({"offset": 0, "size": 2}, 2, 2, 3), - ({"offset": 2, "size": 2}, 1, None, 3), + ({"offset": 0, "limit": 2}, 2, 2, 3), + ({"offset": 2, "limit": 2}, 1, None, 3), ], ) def test_search_endpoint_pagination( @@ -197,7 +197,7 @@ def test_search_endpoint_pagination( user = app.client("seeker@website.web") with patch("paperoni.web.restapi.SearchRequest.run") as mock_run: - mock_run.return_value = mock_papers + mock_run.return_value = mock_papers, None response = user.get("/api/v1/search", **params) @@ -219,7 +219,7 @@ def test_search_endpoint_max_results_limit( with app_factory({"paperoni.server.max_results": 2}) as app: user = app.client("seeker@website.web") with patch("paperoni.web.restapi.SearchRequest.run") as mock_run: - mock_run.return_value = mock_papers + mock_run.return_value = mock_papers, None # Request more than max_results response = user.get("/api/v1/search", size=100) @@ -240,7 +240,7 @@ def test_search_endpoint_empty_results(app): user = app.client("seeker@website.web") with patch("paperoni.web.restapi.SearchRequest.run") as mock_run: - mock_run.return_value = [] + mock_run.return_value = [], None response = user.get("/api/v1/search") diff --git a/tests/web/test_restapi/test_search_endpoint_params0_.yml b/tests/web/test_restapi/test_search_endpoint_params0_.yml index ace3d0b0..af0b7c7b 100644 --- a/tests/web/test_restapi/test_search_endpoint_params0_.yml +++ b/tests/web/test_restapi/test_search_endpoint_params0_.yml @@ -5,9 +5,11 @@ expand_links: false flags: null institution: null + limit: 100 offset: 0 paper_id: null - size: 100 + query: null + similarity_threshold: 0.75 start_date: null title: null venue: null diff --git a/tests/web/test_restapi/test_search_endpoint_params1_.yml b/tests/web/test_restapi/test_search_endpoint_params1_.yml index 08695db0..5a26f74a 100644 --- a/tests/web/test_restapi/test_search_endpoint_params1_.yml +++ b/tests/web/test_restapi/test_search_endpoint_params1_.yml @@ -5,9 +5,11 @@ expand_links: false flags: null institution: null + limit: 100 offset: 0 paper_id: null - size: 100 + query: null + similarity_threshold: 0.75 start_date: null title: Machine Learning venue: null diff --git a/tests/web/test_restapi/test_search_endpoint_params2_.yml b/tests/web/test_restapi/test_search_endpoint_params2_.yml index 1c7fdb6c..bf85dc90 100644 --- a/tests/web/test_restapi/test_search_endpoint_params2_.yml +++ b/tests/web/test_restapi/test_search_endpoint_params2_.yml @@ -5,9 +5,11 @@ expand_links: false flags: null institution: null + limit: 100 offset: 0 paper_id: null - size: 100 + query: null + similarity_threshold: 0.75 start_date: null title: null venue: null diff --git a/tests/web/test_restapi/test_search_endpoint_params3_.yml b/tests/web/test_restapi/test_search_endpoint_params3_.yml index 87cc57c3..81afb763 100644 --- a/tests/web/test_restapi/test_search_endpoint_params3_.yml +++ b/tests/web/test_restapi/test_search_endpoint_params3_.yml @@ -5,9 +5,11 @@ expand_links: false flags: null institution: MIT + limit: 100 offset: 0 paper_id: null - size: 100 + query: null + similarity_threshold: 0.75 start_date: null title: null venue: null diff --git a/tests/web/test_restapi/test_search_endpoint_params4_.yml b/tests/web/test_restapi/test_search_endpoint_params4_.yml index f7bca506..dcff410e 100644 --- a/tests/web/test_restapi/test_search_endpoint_params4_.yml +++ b/tests/web/test_restapi/test_search_endpoint_params4_.yml @@ -5,9 +5,11 @@ expand_links: false flags: null institution: MIT + limit: 100 offset: 0 paper_id: null - size: 100 + query: null + similarity_threshold: 0.75 start_date: null title: Machine Learning venue: null diff --git a/uv.lock b/uv.lock index 44ecb4ce..afaabbab 100644 --- a/uv.lock +++ 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