crossref-local 0.3.1__py3-none-any.whl → 0.4.0__py3-none-any.whl

crossref_local/mcp_server.py

@@ -10,24 +10,27 @@ Usage:
 """
 
 import json
-from typing import Optional
 
 from fastmcp import FastMCP
 
-from . import search, get, count, info, __version__
-from .impact_factor import ImpactFactorCalculator
+
+from . import (
+    get as _get,
+    info as _info,
+    search as _search,
+)
 
 # Initialize MCP server
 mcp = FastMCP(
     name="crossref-local",
     instructions="Local CrossRef database with 167M+ works and full-text search. "
-    "Use search_works to find papers, get_work for DOI lookup, count_works for counts, "
-    "database_info for stats, and calculate_impact_factor for journal metrics.",
+    "Use search to find papers, search_by_doi for DOI lookup, enrich_dois to add "
+    "citation counts and references, and status for stats.",
 )
 
 
 @mcp.tool()
-def search_works(
+def search(
     query: str,
     limit: int = 10,
     offset: int = 0,
@@ -48,11 +51,11 @@ def search_works(
         JSON string with search results including total count and matching works.
 
     Examples:
-        search_works("machine learning")
-        search_works("CRISPR", limit=20)
-        search_works("neural network AND memory", with_abstracts=True)
+        search("machine learning")
+        search("CRISPR", limit=20)
+        search("neural network AND memory", with_abstracts=True)
     """
-    results = search(query, limit=min(limit, 100), offset=offset)
+    results = _search(query, limit=min(limit, 100), offset=offset)
 
     works_data = []
     for work in results.works:
@@ -80,7 +83,7 @@ def search_works(
 
 
 @mcp.tool()
-def get_work(doi: str, as_citation: bool = False) -> str:
+def search_by_doi(doi: str, as_citation: bool = False) -> str:
     """Get detailed information about a work by DOI.
 
     Args:
@@ -91,10 +94,10 @@ def get_work(doi: str, as_citation: bool = False) -> str:
         JSON string with work metadata, or formatted citation string.
 
     Examples:
-        get_work("10.1038/nature12373")
-        get_work("10.1126/science.aax0758", as_citation=True)
+        search_by_doi("10.1038/nature12373")
+        search_by_doi("10.1126/science.aax0758", as_citation=True)
     """
-    work = get(doi)
+    work = _get(doi)
 
     if work is None:
         return json.dumps({"error": f"DOI not found: {doi}"})
@@ -106,69 +109,277 @@ def get_work(doi: str, as_citation: bool = False) -> str:
 
 
 @mcp.tool()
-def count_works(query: str) -> str:
-    """Count matching works without fetching results.
+def status() -> str:
+    """Get database statistics and status.
 
-    Faster than search when you only need the count.
+    Returns:
+        JSON string with database path, work count, FTS index count, and citation count.
+    """
+    db_info = _info()
+    return json.dumps(db_info, indent=2)
+
+
+@mcp.tool()
+def enrich_dois(dois: list[str]) -> str:
+    """Enrich DOIs with full metadata including citation counts and references.
+
+    Use this after search() to get detailed metadata for papers.
+    The search() tool returns basic info (title, authors, year, journal).
+    This tool adds: citation_count, references, volume, issue, publisher, etc.
+
+    Typical workflow:
+    1. search("epilepsy seizure prediction") -> get DOIs
+    2. enrich_dois([doi1, doi2, ...]) -> get full metadata
 
     Args:
-        query: FTS5 search query
+        dois: List of DOIs to enrich (e.g., ["10.1038/nature12373", "10.1126/science.aax0758"])
 
     Returns:
-        JSON string with count.
+        JSON string with enriched works including citation_count and references.
 
     Examples:
-        count_works("CRISPR")
-        count_works("machine learning AND deep")
+        enrich_dois(["10.1038/nature12373"])
+        enrich_dois(["10.1038/s41467-017-02577-y", "10.1093/brain/aww019"])
     """
-    n = count(query)
-    return json.dumps({"query": query, "count": n})
+    from . import get_many as _get_many
+
+    works = _get_many(dois)
+
+    works_data = []
+    for work in works:
+        works_data.append(work.to_dict())
+
+    return json.dumps(
+        {
+            "requested": len(dois),
+            "found": len(works_data),
+            "works": works_data,
+        },
+        indent=2,
+    )
 
 
 @mcp.tool()
-def database_info() -> str:
-    """Get database statistics and status.
+def cache_create(
+    name: str,
+    query: str,
+    limit: int = 1000,
+) -> str:
+    """Create a paper cache from search query.
+
+    Fetches full metadata for papers matching query and saves to disk cache.
+    Use this to build a reusable paper collection for a research topic.
+
+    Args:
+        name: Cache name (e.g., "epilepsy", "alzheimers")
+        query: FTS search query
+        limit: Max papers to cache (default: 1000)
 
     Returns:
-        JSON string with database path, work count, FTS index count, and citation count.
+        JSON with cache info (path, paper count, size)
+
+    Example:
+        cache_create("epilepsy", "epilepsy seizure prediction", limit=500)
     """
-    db_info = info()
-    return json.dumps(db_info, indent=2)
+    from . import cache
+
+    info = cache.create(name, query=query, limit=limit)
+    return json.dumps(info.to_dict(), indent=2)
 
 
 @mcp.tool()
-def calculate_impact_factor(
-    journal: str,
-    year: int = 2023,
-    window: int = 2,
+def cache_query(
+    name: str,
+    fields: list[str] | None = None,
+    include_abstract: bool = False,
+    include_references: bool = False,
+    include_citations: bool = False,
+    year_min: int | None = None,
+    year_max: int | None = None,
+    journal: str | None = None,
+    limit: int | None = None,
 ) -> str:
-    """Calculate impact factor for a journal.
+    """Query cached papers with field filtering.
 
-    Impact factor = citations in target year / articles in window years.
+    Returns minimal data to reduce context usage. Specify only fields needed.
 
     Args:
-        journal: Journal name or ISSN (e.g., "Nature", "Science", "0028-0836")
-        year: Target year for citation count (default: 2023)
-        window: Number of years for article window (default: 2 for standard IF)
+        name: Cache name
+        fields: Explicit field list (e.g., ["doi", "title", "year"])
+        include_abstract: Include abstract (default: False)
+        include_references: Include references list (default: False)
+        include_citations: Include citation_count (default: False)
+        year_min: Filter by minimum year
+        year_max: Filter by maximum year
+        journal: Filter by journal name (substring match)
+        limit: Max results to return
 
     Returns:
-        JSON string with journal name, article count, citation count, and impact factor.
+        JSON array of filtered papers
 
     Examples:
-        calculate_impact_factor("Nature")
-        calculate_impact_factor("Science", year=2022)
-        calculate_impact_factor("Cell", window=5)  # 5-year impact factor
+        cache_query("epilepsy", fields=["doi", "title", "year"])
+        cache_query("epilepsy", year_min=2020, include_citations=True, limit=50)
+    """
+    from . import cache
+
+    papers = cache.query(
+        name,
+        fields=fields,
+        include_abstract=include_abstract,
+        include_references=include_references,
+        include_citations=include_citations,
+        year_min=year_min,
+        year_max=year_max,
+        journal=journal,
+        limit=limit,
+    )
+    return json.dumps({"count": len(papers), "papers": papers}, indent=2)
+
+
+@mcp.tool()
+def cache_stats(name: str) -> str:
+    """Get cache statistics.
+
+    Returns year distribution, top journals, citation stats without loading full data.
+
+    Args:
+        name: Cache name
+
+    Returns:
+        JSON with statistics (paper_count, year_range, top_journals, etc.)
+    """
+    from . import cache
+
+    stats = cache.stats(name)
+    return json.dumps(stats, indent=2)
+
+
+@mcp.tool()
+def cache_list() -> str:
+    """List all available caches.
+
+    Returns:
+        JSON array of cache info (name, path, paper_count, size)
+    """
+    from . import cache
+
+    caches = cache.list_caches()
+    return json.dumps([c.to_dict() for c in caches], indent=2)
+
+
+@mcp.tool()
+def cache_top_cited(
+    name: str,
+    n: int = 20,
+    year_min: int | None = None,
+    year_max: int | None = None,
+) -> str:
+    """Get top cited papers from cache.
+
+    Args:
+        name: Cache name
+        n: Number of papers to return
+        year_min: Filter by minimum year
+        year_max: Filter by maximum year
+
+    Returns:
+        JSON array of top cited papers
+    """
+    from .cache_viz import get_top_cited
+
+    papers = get_top_cited(name, n=n, year_min=year_min, year_max=year_max)
+    return json.dumps(papers, indent=2)
+
+
+@mcp.tool()
+def cache_citation_summary(name: str) -> str:
+    """Get citation statistics for cached papers.
+
+    Returns mean, median, max citations and counts of highly cited papers.
+
+    Args:
+        name: Cache name
+
+    Returns:
+        JSON with citation statistics
     """
-    try:
-        with ImpactFactorCalculator() as calc:
-            result = calc.calculate_impact_factor(
-                journal_identifier=journal,
-                target_year=year,
-                window_years=window,
-            )
-        return json.dumps(result, indent=2)
-    except Exception as e:
-        return json.dumps({"error": str(e)})
+    from .cache_viz import get_citation_summary
+
+    summary = get_citation_summary(name)
+    return json.dumps(summary, indent=2)
+
+
+@mcp.tool()
+def cache_plot_scatter(
+    name: str,
+    output: str,
+    top_n: int = 10,
+) -> str:
+    """Generate year vs citations scatter plot.
+
+    Saves plot to file and returns top cited papers.
+
+    Args:
+        name: Cache name
+        output: Output file path (png/pdf/svg)
+        top_n: Number of top papers to label on plot
+
+    Returns:
+        JSON with output path and top papers list
+    """
+    from .cache_viz import plot_year_citations
+
+    result = plot_year_citations(name, output=output, top_n=top_n)
+    return json.dumps(result, indent=2)
+
+
+@mcp.tool()
+def cache_plot_network(
+    name: str,
+    output: str,
+    max_nodes: int = 100,
+) -> str:
+    """Generate citation network visualization.
+
+    Creates interactive HTML graph showing citation relationships.
+
+    Args:
+        name: Cache name
+        output: Output HTML file path
+        max_nodes: Maximum papers to include
+
+    Returns:
+        JSON with network stats
+    """
+    from .cache_viz import plot_citation_network
+
+    result = plot_citation_network(name, output=output, max_nodes=max_nodes)
+    return json.dumps(result, indent=2)
+
+
+@mcp.tool()
+def cache_export(
+    name: str,
+    output_path: str,
+    format: str = "json",
+    fields: list[str] | None = None,
+) -> str:
+    """Export cache to file.
+
+    Args:
+        name: Cache name
+        output_path: Output file path
+        format: Export format (json, csv, bibtex, dois)
+        fields: Fields to include (for json/csv)
+
+    Returns:
+        JSON with output path
+    """
+    from . import cache
+
+    path = cache.export(name, output_path, format=format, fields=fields)
+    return json.dumps({"exported": path, "format": format})
 
 
 def run_server(

crossref_local/remote.py

@@ -199,6 +199,11 @@ class RemoteClient:
                     authors=item.get("authors", []),
                     year=item.get("year"),
                     journal=item.get("journal"),
+                    volume=item.get("volume"),
+                    issue=item.get("issue"),
+                    page=item.get("page"),
+                    abstract=item.get("abstract"),
+                    citation_count=item.get("citation_count"),
                 )
                 works.append(work)
             return works

crossref_local/server.py

@@ -4,11 +4,11 @@ This server provides proper full-text search using FTS5 index,
 unlike the Django API which only scans a limited subset.
 
 Usage:
-    crossref-local api                    # Run on default port 3333
+    crossref-local api                    # Run on default port 8333
     crossref-local api --port 8080        # Custom port
 
     # Or directly:
-    uvicorn crossref_local.server:app --host 0.0.0.0 --port 3333
+    uvicorn crossref_local.server:app --host 0.0.0.0 --port 8333
 """
 
 import time
@@ -18,14 +18,14 @@ from fastapi import FastAPI, Query, HTTPException
 from fastapi.middleware.cors import CORSMiddleware
 from pydantic import BaseModel
 
-from . import fts
+from . import fts, __version__
 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",
+    version=__version__,
 )
 
 # CORS middleware
@@ -61,7 +61,7 @@ class SearchResponse(BaseModel):
 
 class InfoResponse(BaseModel):
     name: str = "CrossRef Local API"
-    version: str = "1.1.0"
+    version: str = __version__
     status: str = "running"
     mode: str = "local"
     total_papers: int
@@ -75,7 +75,7 @@ def root():
     """API root with endpoint information."""
     return {
         "name": "CrossRef Local API",
-        "version": "1.1.0",
+        "version": __version__,
         "status": "running",
         "endpoints": {
             "health": "/health",
@@ -341,7 +341,7 @@ def api_stats_compat():
     }
 
 
-def run_server(host: str = "0.0.0.0", port: int = 3333):
+def run_server(host: str = "0.0.0.0", port: int = 8333):
     """Run the FastAPI server."""
     import uvicorn
 

{crossref_local-0.3.1.dist-info → crossref_local-0.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: crossref-local
-Version: 0.3.1
+Version: 0.4.0
 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
@@ -43,6 +43,12 @@ 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.
@@ -55,6 +61,22 @@ 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 +157,8 @@ 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 +181,56 @@ Found 4 matches in 128.4ms
 
 Start the FastAPI server:
 ```bash
-crossref-local api --host 0.0.0.0 --port 3333
+crossref-local run-server-http --host 0.0.0.0 --port 8333
 ```
 
 Endpoints:
 ```bash
 # Search works (FTS5)
-curl "http://localhost:3333/works?q=CRISPR&limit=10"
+curl "http://localhost:8333/works?q=CRISPR&limit=10"
 
 # Get by DOI
-curl "http://localhost:3333/works/10.1038/nature12373"
+curl "http://localhost:8333/works/10.1038/nature12373"
 
 # Batch DOI lookup
-curl -X POST "http://localhost:3333/works/batch" \
+curl -X POST "http://localhost:8333/works/batch" \
   -H "Content-Type: application/json" \
   -d '{"dois": ["10.1038/nature12373", "10.1126/science.aax0758"]}'
 
 # Database info
-curl "http://localhost:3333/info"
+curl "http://localhost:8333/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 8333:127.0.0.1:8333 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:8333")
+
+# 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 run-server-mcp
 ```
 
-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": ["run-server-mcp"],
       "env": {
         "CROSSREF_LOCAL_DB": "/path/to/crossref.db"
       }
@@ -215,12 +239,27 @@ 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 run-server-mcp -t http --host 0.0.0.0 --port 8082
+```
+```json
+{
+  "mcpServers": {
+    "crossref-remote": {
+      "url": "http://your-server:8082/mcp"
+    }
+  }
+}
+```
+
+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
+- `status` - Database statistics
 
 </details>
 

crossref_local-0.4.0.dist-info/RECORD

@@ -0,0 +1,27 @@
+crossref_local/__init__.py,sha256=eCvA9q-nZSWCIoMZxINV5xsboXovv4YeqZfjfLzi820,3696
+crossref_local/__main__.py,sha256=N1c1ESGgJkAwsSWXANUgmzxC1OJEIqw-cl9m4pmNP7s,110
+crossref_local/aio.py,sha256=En2btSn3euRbEYav1919gsmdC8iQaMbgGUso-IThCwo,5490
+crossref_local/api.py,sha256=4VGThHU3RZaH5dgjax69iUHfRlh7j91LaM00guDKtKs,7436
+crossref_local/cache.py,sha256=sMrmiUJr8-zRBDXnHg0M_3q3MpgzT7V1bqMKb5kpKVg,12291
+crossref_local/cache_export.py,sha256=DU44Rv894fZz6OnBETbgwYzwVOPg3zJ6sP85yE5EYbc,2519
+crossref_local/cache_viz.py,sha256=0VAHK-i1xR5StEYrJ_IAs0HSk0MQNVFi4EjPtlZEwTY,8498
+crossref_local/citations.py,sha256=QFahv84upNnXP_89A8bHxEbAdz7wHbh5LEniGcAiHas,12402
+crossref_local/cli.py,sha256=OMgrWviTT6Q9wLPWyhb9qDiRlVAJCuRDwDVpddyRPUk,16352
+crossref_local/cli_cache.py,sha256=8QykJ7-H313x7oKRw5fJ9Coay27Y8uBWGx5JR1VQ1_Y,6220
+crossref_local/cli_completion.py,sha256=yzqwMbGbbqXJQHdztuaqji-AdFTd8zDDhHeNGdw4NpU,7341
+crossref_local/cli_main.py,sha256=NgCGB5-ThofTRPoxxwZpsfCQTo5WIw8oP7zBSKhEiDQ,444
+crossref_local/cli_mcp.py,sha256=JBGveR_K7M_EzmHb3G9xr1IZPHAf-vvht-yAn5IzkQM,8524
+crossref_local/config.py,sha256=tBAqnnscLOIF5dobEjOA4b57OVfGeGhpnmRonYKt7ng,4839
+crossref_local/db.py,sha256=x7dXQXjsFN4LavtkNAKTNw1cUBMG-2h53-Z-Xlq6aoQ,3696
+crossref_local/fts.py,sha256=yZMh_vmtFentXKAFGTS4z7ZNNj7p_ItgfFP5i0yQltw,4448
+crossref_local/mcp_server.py,sha256=BN1BByTI54Rh-QoMZA2wUTV7lxdX-fLvoiEaH3YP-W0,10974
+crossref_local/models.py,sha256=b_yYb91O6RwEPpEqe2Wmdz12WIfE5itjEus4-fCLxLI,5476
+crossref_local/remote.py,sha256=Ju4NewXsw_cNX4vq6OeSu8fKtyf9CLwno-4uWkpwAOM,8638
+crossref_local/server.py,sha256=CpCZm5ZVLSPfcke1lGkvEOp1XsH6bUGm5M0i9pj343U,9059
+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-0.4.0.dist-info/METADATA,sha256=l-quaEeSKQwlveyZgKwZfW1SwyNsM9G8yZhGOHtGtMs,9508
+crossref_local-0.4.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+crossref_local-0.4.0.dist-info/entry_points.txt,sha256=1LhHFzJ7VWhNmGY6yIGDJ5EhKTYCyU7CbLEooXQWhLQ,116
+crossref_local-0.4.0.dist-info/RECORD,,

{crossref_local-0.3.1.dist-info → crossref_local-0.4.0.dist-info}/entry_points.txt

@@ -1,3 +1,3 @@
 [console_scripts]
-crossref-local = crossref_local.cli:main
+crossref-local = crossref_local.cli_main:main
 crossref-local-mcp = crossref_local.mcp_server:main

crossref_local-0.3.1.dist-info/RECORD

@@ -1,20 +0,0 @@
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