crossref-local 0.3.1__py3-none-any.whl → 0.5.0__py3-none-any.whl

crossref_local/server.py

@@ -1,352 +1,8 @@
-"""FastAPI server for CrossRef Local with FTS5 search.
+#!/usr/bin/env python3
+"""Backward compatibility: re-export from _server."""
 
-This server provides proper full-text search using FTS5 index,
-unlike the Django API which only scans a limited subset.
+from ._server import app, run_server, DEFAULT_PORT, DEFAULT_HOST
 
-Usage:
-    crossref-local api                    # Run on default port 3333
-    crossref-local api --port 8080        # Custom port
+__all__ = ["app", "run_server", "DEFAULT_PORT", "DEFAULT_HOST"]
 
-    # Or directly:
-    uvicorn crossref_local.server:app --host 0.0.0.0 --port 3333
-"""
-
-import time
-from typing import Optional, List
-
-from fastapi import FastAPI, Query, HTTPException
-from fastapi.middleware.cors import CORSMiddleware
-from pydantic import BaseModel
-
-from . import fts
-from .db import get_db
-from .models import Work
-
-app = FastAPI(
-    title="CrossRef Local API",
-    description="Fast full-text search across 167M+ scholarly works",
-    version="1.1.0",
-)
-
-# CORS middleware
-app.add_middleware(
-    CORSMiddleware,
-    allow_origins=["*"],
-    allow_methods=["*"],
-    allow_headers=["*"],
-)
-
-
-class WorkResponse(BaseModel):
-    doi: str
-    title: Optional[str] = None
-    authors: List[str] = []
-    year: Optional[int] = None
-    journal: Optional[str] = None
-    issn: Optional[str] = None
-    volume: Optional[str] = None
-    issue: Optional[str] = None
-    page: Optional[str] = None
-    abstract: Optional[str] = None
-    citation_count: Optional[int] = None
-
-
-class SearchResponse(BaseModel):
-    query: str
-    total: int
-    returned: int
-    elapsed_ms: float
-    results: List[WorkResponse]
-
-
-class InfoResponse(BaseModel):
-    name: str = "CrossRef Local API"
-    version: str = "1.1.0"
-    status: str = "running"
-    mode: str = "local"
-    total_papers: int
-    fts_indexed: int
-    citations: int
-    database_path: str
-
-
-@app.get("/")
-def root():
-    """API root with endpoint information."""
-    return {
-        "name": "CrossRef Local API",
-        "version": "1.1.0",
-        "status": "running",
-        "endpoints": {
-            "health": "/health",
-            "info": "/info",
-            "search": "/works?q=<query>",
-            "get_by_doi": "/works/{doi}",
-            "batch": "/works/batch",
-        },
-    }
-
-
-@app.get("/health")
-def health():
-    """Health check endpoint."""
-    db = get_db()
-    return {
-        "status": "healthy",
-        "database_connected": db is not None,
-        "database_path": str(db.db_path) if db else None,
-    }
-
-
-@app.get("/info", response_model=InfoResponse)
-def info():
-    """Get database statistics."""
-    db = get_db()
-
-    row = db.fetchone("SELECT COUNT(*) as count FROM works")
-    work_count = row["count"] if row else 0
-
-    try:
-        row = db.fetchone("SELECT COUNT(*) as count FROM works_fts")
-        fts_count = row["count"] if row else 0
-    except Exception:
-        fts_count = 0
-
-    try:
-        row = db.fetchone("SELECT COUNT(*) as count FROM citations")
-        citation_count = row["count"] if row else 0
-    except Exception:
-        citation_count = 0
-
-    return InfoResponse(
-        total_papers=work_count,
-        fts_indexed=fts_count,
-        citations=citation_count,
-        database_path=str(db.db_path),
-    )
-
-
-@app.get("/works", response_model=SearchResponse)
-def search_works(
-    q: str = Query(..., description="Search query (FTS5 syntax supported)"),
-    limit: int = Query(10, ge=1, le=100, description="Max results"),
-    offset: int = Query(0, ge=0, description="Skip first N results"),
-):
-    """
-    Full-text search across works.
-
-    Uses FTS5 index for fast searching across titles, abstracts, and authors.
-    Supports FTS5 query syntax like AND, OR, NOT, "exact phrases".
-
-    Examples:
-        /works?q=machine learning
-        /works?q="neural network" AND hippocampus
-        /works?q=CRISPR&limit=20
-    """
-    start = time.perf_counter()
-
-    try:
-        results = fts.search(q, limit=limit, offset=offset)
-    except Exception as e:
-        raise HTTPException(status_code=400, detail=f"Search error: {e}")
-
-    elapsed_ms = (time.perf_counter() - start) * 1000
-
-    return SearchResponse(
-        query=q,
-        total=results.total,
-        returned=len(results.works),
-        elapsed_ms=round(elapsed_ms, 2),
-        results=[
-            WorkResponse(
-                doi=w.doi,
-                title=w.title,
-                authors=w.authors,
-                year=w.year,
-                journal=w.journal,
-                issn=w.issn,
-                volume=w.volume,
-                issue=w.issue,
-                page=w.page,
-                abstract=w.abstract,
-                citation_count=w.citation_count,
-            )
-            for w in results.works
-        ],
-    )
-
-
-@app.get("/works/{doi:path}", response_model=Optional[WorkResponse])
-def get_work(doi: str):
-    """
-    Get work metadata by DOI.
-
-    Examples:
-        /works/10.1038/nature12373
-        /works/10.1016/j.cell.2020.01.001
-    """
-    db = get_db()
-    metadata = db.get_metadata(doi)
-
-    if metadata is None:
-        raise HTTPException(status_code=404, detail=f"DOI not found: {doi}")
-
-    work = Work.from_metadata(doi, metadata)
-
-    return WorkResponse(
-        doi=work.doi,
-        title=work.title,
-        authors=work.authors,
-        year=work.year,
-        journal=work.journal,
-        issn=work.issn,
-        volume=work.volume,
-        issue=work.issue,
-        page=work.page,
-        abstract=work.abstract,
-        citation_count=work.citation_count,
-    )
-
-
-class BatchRequest(BaseModel):
-    dois: List[str]
-
-
-class BatchResponse(BaseModel):
-    requested: int
-    found: int
-    results: List[WorkResponse]
-
-
-@app.post("/works/batch", response_model=BatchResponse)
-def get_works_batch(request: BatchRequest):
-    """
-    Get multiple works by DOI.
-
-    Request body: {"dois": ["10.1038/...", "10.1016/..."]}
-    """
-    db = get_db()
-    results = []
-
-    for doi in request.dois:
-        metadata = db.get_metadata(doi)
-        if metadata:
-            work = Work.from_metadata(doi, metadata)
-            results.append(
-                WorkResponse(
-                    doi=work.doi,
-                    title=work.title,
-                    authors=work.authors,
-                    year=work.year,
-                    journal=work.journal,
-                    abstract=work.abstract,
-                    citation_count=work.citation_count,
-                )
-            )
-
-    return BatchResponse(
-        requested=len(request.dois),
-        found=len(results),
-        results=results,
-    )
-
-
-# For backwards compatibility with existing API endpoints
-@app.get("/api/search/")
-def api_search_compat(
-    title: Optional[str] = None,
-    q: Optional[str] = None,
-    doi: Optional[str] = None,
-    limit: int = 10,
-):
-    """Backwards-compatible search endpoint."""
-    query = title or q
-
-    if doi:
-        # DOI lookup
-        try:
-            work = get_work(doi)
-            return {
-                "query": {"doi": doi},
-                "results": [work.model_dump()],
-                "total": 1,
-                "returned": 1,
-            }
-        except HTTPException:
-            return {"query": {"doi": doi}, "results": [], "total": 0, "returned": 0}
-
-    if not query:
-        raise HTTPException(
-            status_code=400, detail="Specify q, title, or doi parameter"
-        )
-
-    # Call fts.search directly (not the endpoint function)
-    results = fts.search(query, limit=limit, offset=0)
-    return {
-        "query": {
-            "title": query,
-            "doi": None,
-            "year": None,
-            "authors": None,
-            "limit": limit,
-        },
-        "results": [
-            WorkResponse(
-                doi=w.doi,
-                title=w.title,
-                authors=w.authors,
-                year=w.year,
-                journal=w.journal,
-                issn=w.issn,
-                volume=w.volume,
-                issue=w.issue,
-                page=w.page,
-                abstract=w.abstract,
-                citation_count=w.citation_count,
-            ).model_dump()
-            for w in results.works
-        ],
-        "total": results.total,
-        "returned": len(results.works),
-    }
-
-
-@app.get("/api/stats/")
-def api_stats_compat():
-    """Backwards-compatible stats endpoint."""
-    db = get_db()
-
-    row = db.fetchone("SELECT COUNT(*) as count FROM works")
-    work_count = row["count"] if row else 0
-
-    # Get table names
-    tables = []
-    for row in db.fetchall("SELECT name FROM sqlite_master WHERE type='table'"):
-        tables.append(row["name"])
-
-    # Get index names
-    indices = []
-    for row in db.fetchall("SELECT name FROM sqlite_master WHERE type='index'"):
-        if row["name"]:
-            indices.append(row["name"])
-
-    return {
-        "total_papers": work_count,
-        "database_size_mb": None,
-        "year_range": None,
-        "total_journals": 0,
-        "total_citations": None,
-        "tables": tables,
-        "indices": indices,
-    }
-
-
-def run_server(host: str = "0.0.0.0", port: int = 3333):
-    """Run the FastAPI server."""
-    import uvicorn
-
-    uvicorn.run(app, host=host, port=port)
-
-
-if __name__ == "__main__":
-    run_server()
+# EOF

{crossref_local-0.3.1.dist-info → crossref_local-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: crossref-local
-Version: 0.3.1
+Version: 0.5.0
 Summary: Local CrossRef database with 167M+ works and full-text search
 Project-URL: Homepage, https://github.com/ywatanabe1989/crossref_local
 Project-URL: Repository, https://github.com/ywatanabe1989/crossref_local
@@ -18,6 +18,7 @@ Classifier: Topic :: Database
 Classifier: Topic :: Scientific/Engineering
 Requires-Python: >=3.10
 Requires-Dist: click>=8.0
+Requires-Dist: rich>=13.0
 Provides-Extra: all
 Requires-Dist: fastapi>=0.100; extra == 'all'
 Requires-Dist: fastmcp>=0.4; extra == 'all'
@@ -43,11 +44,20 @@ Requires-Dist: networkx>=3.0; extra == 'viz'
 Requires-Dist: pyvis>=0.3; extra == 'viz'
 Description-Content-Type: text/markdown
 
+<!-- ---
+!-- Timestamp: 2026-01-16 19:15:51
+!-- Author: ywatanabe
+!-- File: /home/ywatanabe/proj/crossref-local/README.md
+!-- --- -->
+
 # CrossRef Local
 
 Local CrossRef database with 167M+ scholarly works, full-text search, and impact factor calculation.
 
+[![PyPI version](https://badge.fury.io/py/crossref-local.svg)](https://badge.fury.io/py/crossref-local)
+[![Documentation](https://readthedocs.org/projects/crossref-local/badge/?version=latest)](https://crossref-local.readthedocs.io/en/latest/)
 [![Tests](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml/badge.svg)](https://github.com/ywatanabe1989/crossref-local/actions/workflows/test.yml)
+[![Coverage](https://codecov.io/gh/ywatanabe1989/crossref-local/branch/main/graph/badge.svg)](https://codecov.io/gh/ywatanabe1989/crossref-local)
 [![Python](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 
@@ -55,6 +65,22 @@ Local CrossRef database with 167M+ scholarly works, full-text search, and impact
   <img src="examples/readme_figure.png" alt="CrossRef Local Demo" width="800"/>
 </p>
 
+<details>
+<summary><strong>MCP Demo Video</strong></summary>
+
+<p align="center">
+  <a href="https://scitex.ai/media/videos/crossref-local-v0.3.1-demo.mp4">
+    <img src="examples/demo_mcp_out/crossref-local-v0.3.1-demo-thumbnail_6m55s.png" alt="Demo Video Thumbnail" width="600"/>
+  </a>
+</p>
+
+Live demonstration of MCP server integration with Claude Code for `epilepsy seizure prediction` literature review:
+- Full-text search on title, abstracts, and keywords across 167M papers (22ms response)
+
+📄 [Full demo documentation](examples/demo_mcp.org) | 📊 [Generated diagrams](examples/demo_mcp_out/)
+
+</details>
+
 <details>
 <summary><strong>Why CrossRef Local?</strong></summary>
 
@@ -135,9 +161,8 @@ async def main():
 
 ```bash
 crossref-local search "CRISPR genome editing" -n 5
-crossref-local get 10.1038/nature12373
-crossref-local impact-factor Nature -y 2023  # IF: 54.067
-crossref-local info  # Database stats
+crossref-local search-by-doi 10.1038/nature12373
+crossref-local status  # Configuration and database stats
 ```
 
 With abstracts (`-a` flag):
@@ -160,53 +185,68 @@ Found 4 matches in 128.4ms
 
 Start the FastAPI server:
 ```bash
-crossref-local api --host 0.0.0.0 --port 3333
+crossref-local relay --host 0.0.0.0 --port 31291
 ```
 
 Endpoints:
 ```bash
 # Search works (FTS5)
-curl "http://localhost:3333/works?q=CRISPR&limit=10"
+curl "http://localhost:31291/works?q=CRISPR&limit=10"
 
 # Get by DOI
-curl "http://localhost:3333/works/10.1038/nature12373"
+curl "http://localhost:31291/works/10.1038/nature12373"
 
 # Batch DOI lookup
-curl -X POST "http://localhost:3333/works/batch" \
+curl -X POST "http://localhost:31291/works/batch" \
   -H "Content-Type: application/json" \
   -d '{"dois": ["10.1038/nature12373", "10.1126/science.aax0758"]}'
 
+# Citation endpoints
+curl "http://localhost:31291/citations/10.1038/nature12373/citing"
+curl "http://localhost:31291/citations/10.1038/nature12373/cited"
+curl "http://localhost:31291/citations/10.1038/nature12373/count"
+
+# Collection endpoints
+curl "http://localhost:31291/collections"
+curl -X POST "http://localhost:31291/collections" \
+  -H "Content-Type: application/json" \
+  -d '{"name": "my_papers", "query": "CRISPR", "limit": 100}'
+curl "http://localhost:31291/collections/my_papers/download?format=bibtex"
+
 # Database info
-curl "http://localhost:3333/info"
+curl "http://localhost:31291/info"
 ```
 
-Remote access via SSH tunnel:
+HTTP mode (connect to running server):
 ```bash
-# On local machine
-ssh -L 3333:127.0.0.1:3333 nas
+# On local machine (if server is remote)
+ssh -L 31291:127.0.0.1:31291 your-server
 
 # Python client
-from crossref_local import configure_remote
-configure_remote("http://localhost:3333")
+from crossref_local import configure_http
+configure_http("http://localhost:31291")
+
+# Or via CLI
+crossref-local --http search "CRISPR"
 ```
 
 </details>
 
 <details>
-<summary><strong>MCP Server (Claude Desktop)</strong></summary>
+<summary><strong>MCP Server</strong></summary>
 
-Run as MCP server for Claude Desktop integration:
+Run as MCP (Model Context Protocol) server:
 ```bash
-crossref-local serve
+crossref-local mcp start
 ```
 
-Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
+Local MCP client configuration:
 ```json
 {
   "mcpServers": {
     "crossref-local": {
       "command": "crossref-local",
-      "args": ["serve"],
+      "args": ["mcp", "start"],
       "env": {
         "CROSSREF_LOCAL_DB": "/path/to/crossref.db"
       }
@@ -215,12 +255,36 @@ Add to Claude Desktop config (`~/.config/claude/claude_desktop_config.json`):
 }
 ```
 
+Remote MCP via HTTP (recommended):
+```bash
+# On server: start persistent MCP server
+crossref-local mcp start -t http --host 0.0.0.0 --port 8082
+```
+```json
+{
+  "mcpServers": {
+    "crossref-remote": {
+      "url": "http://your-server:8082/mcp"
+    }
+  }
+}
+```
+
+Diagnose setup:
+```bash
+crossref-local mcp doctor        # Check dependencies and database
+crossref-local mcp list-tools    # Show available MCP tools
+crossref-local mcp installation  # Show client config examples
+```
+
+See [docs/remote-deployment.md](docs/remote-deployment.md) for systemd and Docker setup.
+
 Available tools:
-- `search_works` - Full-text search across 167M+ papers
-- `get_work` - Get paper by DOI
-- `count_works` - Count matching papers
-- `database_info` - Database statistics
-- `calculate_impact_factor` - Journal impact factor
+- `search` - Full-text search across 167M+ papers
+- `search_by_doi` - Get paper by DOI
+- `enrich_dois` - Add citation counts and references to DOIs
+- `status` - Database statistics
+- `cache_*` - Paper collection management
 
 </details>
 

crossref_local-0.5.0.dist-info/RECORD

@@ -0,0 +1,47 @@
+crossref_local/__init__.py,sha256=bOn6qJob4okwkLzzIoEGQj0I-amIBSr89iWrbkYEJns,3691
+crossref_local/__main__.py,sha256=N1c1ESGgJkAwsSWXANUgmzxC1OJEIqw-cl9m4pmNP7s,110
+crossref_local/aio.py,sha256=_vDHFoE2n6GqO3j6pGeCaJVVe5I5L3M0tuMlW8IgGx8,1255
+crossref_local/cache.py,sha256=yQpnRRBsHx2pluIPPfJlrakeuCC8TysKXrfA3ohdxSg,13321
+crossref_local/cli.py,sha256=2pWJK_vnO1IIwUrMB3K8KW94ZWfkEF7TLSxMsaR-LrI,137
+crossref_local/jobs.py,sha256=1tyaFRjyQGVi8xqk5nYga7maIFq2qYTroBGwAeN5DFc,4835
+crossref_local/mcp_server.py,sha256=YmUd3xKqSDnW6sYDC7KRpZ7sSTnbTnxxGw9s_5lqIt8,185
+crossref_local/remote.py,sha256=PmvUq87mC76sM9BL9RczOaXtvwHoqMc_dN5PJCYT18M,239
+crossref_local/server.py,sha256=SKoQ-cOoZjdXm24Sv1CFu3F8UclbD6QstfQb-7l2xtA,215
+crossref_local/_aio/__init__.py,sha256=z5_RNd9PTQUslI5LWOCn0711s8cIRX7N-Y-S-JyutAU,371
+crossref_local/_aio/_impl.py,sha256=uG5r0d92EcPDqB52w4Wjb7kf1GmjHrLEELHINmNXnJc,5626
+crossref_local/_cache/__init__.py,sha256=QSSTVWB_zNU3JQRdnBCzHuIl93WM3udgO2NkRlgm9M0,272
+crossref_local/_cache/export.py,sha256=ZyZS1vWZE9ui9weywejnBFI2FzNV1r1Q_3XXPiFIj3M,3028
+crossref_local/_cache/utils.py,sha256=D3sg7MoXZs4aC2OvagVgmOVMZjm1Xqy1ulGbs0_F914,2502
+crossref_local/_cache/viz.py,sha256=0VAHK-i1xR5StEYrJ_IAs0HSk0MQNVFi4EjPtlZEwTY,8498
+crossref_local/_cli/__init__.py,sha256=NS07Eo93dRAuO5vxGwGwS0ctvZxMMkF_py09bzIk3Hk,175
+crossref_local/_cli/cache.py,sha256=8QykJ7-H313x7oKRw5fJ9Coay27Y8uBWGx5JR1VQ1_Y,6220
+crossref_local/_cli/cli.py,sha256=w7rJ4ZtetSr6TRz2f2vyHqZylq5vXM8O9KB61gScbFM,16903
+crossref_local/_cli/completion.py,sha256=yzqwMbGbbqXJQHdztuaqji-AdFTd8zDDhHeNGdw4NpU,7341
+crossref_local/_cli/main.py,sha256=NgCGB5-ThofTRPoxxwZpsfCQTo5WIw8oP7zBSKhEiDQ,444
+crossref_local/_cli/mcp.py,sha256=yjUoq3hvu2OofYf_D29_NXoTvkhxz5QbWAuWv6U-H8U,11427
+crossref_local/_cli/mcp_server.py,sha256=jZJwhiTavgTHcJctXpafPgy3aIT49-rdIZ-4i88myeU,10989
+crossref_local/_core/__init__.py,sha256=6xKO9y3VOuTF1f83uyQ48HWhszYpPfWZj94t0q0rEgk,940
+crossref_local/_core/api.py,sha256=YogfhBHDIqT-hdEI-iDe_-py13Vp6F4GW8q0psLDRyQ,7781
+crossref_local/_core/citations.py,sha256=4ERCTVkZu6kesZRazaWcTpUUeYz0rs97NwFZAYcLdKA,12765
+crossref_local/_core/config.py,sha256=T-2EX4EDoCLaOAmViBKGQuNvoJP8x7cvZOvmAcNrQms,5475
+crossref_local/_core/db.py,sha256=KLlcdNWLnKSexc0cuRZGsBLmJUnXeEaD_CBcXhbPXLg,3832
+crossref_local/_core/fts.py,sha256=Ti1EdSsrIQMDFTynyoiqC2bi_nHtPZ6uOyj5ERcxiQk,4515
+crossref_local/_core/models.py,sha256=4b8153r7xDBcmTQFsIeSLD1jJm4KvuUkKTLixB7lccM,5562
+crossref_local/_impact_factor/__init__.py,sha256=pcgVCPogBisANYE5Vp2PHVGPgxoMsSXr-6utqVE97-4,559
+crossref_local/_impact_factor/calculator.py,sha256=eZ13URAZzPdRyAQpS8zXe_T33e2lm_gQhtoJCXbfIGM,15977
+crossref_local/_impact_factor/journal_lookup.py,sha256=Ztx6ZeWxfmPvA3KfcW5h_yz01XPstIdk91j3nu2Q-qw,8846
+crossref_local/_remote/__init__.py,sha256=bTA_bed9XsA0HDArm1o0WagsasxN0atzXdRI6I-r7Pk,1412
+crossref_local/_remote/base.py,sha256=gvvvq7uGrG1IOQEZ5ZhWWuakg9Fl_GdkAaU1AfCmtzY,11258
+crossref_local/_remote/collections.py,sha256=840HkakS_AtZbmRMYP-GpUX4S5oJ9jaJXzjivQgyozU,5022
+crossref_local/_server/__init__.py,sha256=4fTk1r__5uWhC6XABVDV7PTPdglFIV32hr9KZ5WbKc8,3869
+crossref_local/_server/middleware.py,sha256=6tdrfFCOA06i0HIDtrHZthY8DXbKy8rMEWHf-3Ve8-Y,926
+crossref_local/_server/models.py,sha256=gjnE-MK4XtfdN_obMyqT5xjNXPa3F-BPrgMrrg908KY,2580
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