scitex 2.15.3__py3-none-any.whl → 2.15.4__py3-none-any.whl

scitex/cli/scholar/_crossref_scitex.py

@@ -1,142 +1,41 @@
 #!/usr/bin/env python3
-# Timestamp: 2026-01-24
+# Timestamp: 2026-01-29
 # File: src/scitex/cli/scholar/_crossref_scitex.py
-"""CrossRef-SciTeX CLI commands for scitex scholar.
+"""CrossRef-SciTeX CLI - Thin wrapper delegating to crossref-local.
 
-Provides access to the local CrossRef database (167M+ papers) via crossref-local.
-Branded as crossref-scitex to distinguish from official CrossRef API.
+This module provides access to the local CrossRef database (167M+ papers)
+by delegating directly to crossref-local CLI without any modifications.
 """
 
 from __future__ import annotations
 
-import json
 import sys
 
 import click
 
 
-@click.group("crossref-scitex")
-def crossref_scitex():
-    """
-    CrossRef-SciTeX database search (167M+ papers)
-
-    \b
-    Search and query the local CrossRef database via crossref-local.
-    Supports both direct DB access and HTTP API mode.
-
-    \b
-    Examples:
-        scitex scholar crossref-scitex search "deep learning"
-        scitex scholar crossref-scitex get 10.1038/nature12373
-        scitex scholar crossref-scitex count "epilepsy seizure"
-        scitex scholar crossref-scitex info
-    """
-    pass
-
-
-@crossref_scitex.command("search")
-@click.argument("query")
-@click.option("-n", "--limit", default=20, help="Maximum results (default: 20)")
-@click.option("--offset", default=0, help="Skip N results for pagination")
-@click.option("--year-min", type=int, help="Minimum publication year")
-@click.option("--year-max", type=int, help="Maximum publication year")
-@click.option("--enrich", is_flag=True, help="Add citation counts and references")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def search_cmd(query, limit, offset, year_min, year_max, enrich, as_json):
-    """
-    Search for papers in CrossRef database.
+@click.command(
+    "crossref-scitex",
+    context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all commands")
+@click.pass_context
+def crossref_scitex(ctx, help_recursive):
+    r"""CrossRef-SciTeX database search (167M+ papers).
 
     \b
-    Examples:
-        scitex scholar crossref-scitex search "hippocampal sharp wave ripples"
-        scitex scholar crossref search "deep learning" --limit 50
-        scitex scholar crossref search "CRISPR" --year-min 2020 --enrich
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        results = crossref.search(query, limit=limit, offset=offset)
-
-        if enrich:
-            results = crossref.enrich(results)
-
-        papers = []
-        for work in results:
-            if year_min and work.year and work.year < year_min:
-                continue
-            if year_max and work.year and work.year > year_max:
-                continue
-            papers.append(work)
-            if len(papers) >= limit:
-                break
-
-        if as_json:
-            output = {
-                "query": query,
-                "total": results.total,
-                "count": len(papers),
-                "papers": [
-                    {
-                        "doi": p.doi,
-                        "title": p.title,
-                        "authors": p.authors,
-                        "year": p.year,
-                        "journal": p.journal,
-                        "citation_count": p.citation_count,
-                    }
-                    for p in papers
-                ],
-            }
-            click.echo(json.dumps(output, indent=2))
-        else:
-            click.secho(
-                f"Found {results.total} papers for: {query}", fg="green", bold=True
-            )
-            click.echo()
-
-            for i, paper in enumerate(papers, 1):
-                authors = ", ".join(paper.authors[:3]) if paper.authors else "Unknown"
-                if paper.authors and len(paper.authors) > 3:
-                    authors += " et al."
-
-                click.secho(f"{i}. {paper.title}", fg="cyan", bold=True)
-                click.echo(f"   Authors: {authors}")
-                click.echo(
-                    f"   Year: {paper.year or 'N/A'} | Journal: {paper.journal or 'N/A'}"
-                )
-                click.echo(f"   DOI: {paper.doi}")
-                if paper.citation_count:
-                    click.echo(f"   Citations: {paper.citation_count}")
-                click.echo()
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
-
-
-@crossref_scitex.command("get")
-@click.argument("doi")
-@click.option("--citations", is_flag=True, help="Include citing papers")
-@click.option("--references", is_flag=True, help="Include referenced papers")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def get_cmd(doi, citations, references, as_json):
-    """
-    Get paper details by DOI.
+    Thin wrapper for crossref-local. All arguments passed directly.
+    Run 'crossref-local --help' for full options.
 
     \b
     Examples:
-        scitex scholar crossref get 10.1038/nature12373
-        scitex scholar crossref get 10.1126/science.aax0758 --citations
+        scitex scholar crossref-scitex search "deep learning" --abstracts
+        scitex scholar crossref-scitex search-by-doi 10.1038/nature12373
+        scitex scholar crossref-scitex status
+        scitex scholar crossref-scitex cache query "neural networks"
     """
     try:
-        from scitex.scholar import crossref_scitex as crossref
+        from crossref_local.cli import cli as crossref_cli
     except ImportError:
         click.secho(
             "crossref-local not installed. Install with: pip install crossref-local",
@@ -144,153 +43,13 @@ def get_cmd(doi, citations, references, as_json):
         )
         sys.exit(1)
 
-    try:
-        work = crossref.get(doi)
-
-        if work is None:
-            click.secho(f"DOI not found: {doi}", fg="red")
-            sys.exit(1)
-
-        if as_json:
-            output = {
-                "doi": work.doi,
-                "title": work.title,
-                "authors": work.authors,
-                "year": work.year,
-                "journal": work.journal,
-                "abstract": work.abstract,
-                "citation_count": work.citation_count,
-                "reference_count": work.reference_count,
-                "type": work.type,
-                "publisher": work.publisher,
-            }
-            if citations:
-                output["citing_dois"] = crossref.get_citing(doi)
-            if references:
-                output["referenced_dois"] = crossref.get_cited(doi)
-            click.echo(json.dumps(output, indent=2))
-        else:
-            click.secho(work.title, fg="cyan", bold=True)
-            click.echo()
-
-            if work.authors:
-                click.echo(f"Authors: {', '.join(work.authors)}")
-            click.echo(f"Year: {work.year or 'N/A'}")
-            click.echo(f"Journal: {work.journal or 'N/A'}")
-            click.echo(f"DOI: {work.doi}")
-            click.echo(f"Type: {work.type or 'N/A'}")
-            click.echo(f"Publisher: {work.publisher or 'N/A'}")
-            click.echo(f"Citations: {work.citation_count or 0}")
-            click.echo(f"References: {work.reference_count or 0}")
-
-            if work.abstract:
-                click.echo()
-                click.secho("Abstract:", bold=True)
-                click.echo(
-                    work.abstract[:500] + "..."
-                    if len(work.abstract) > 500
-                    else work.abstract
-                )
-
-            if citations:
-                citing = crossref.get_citing(doi)
-                click.echo()
-                click.secho(f"Citing papers ({len(citing)}):", bold=True)
-                for c_doi in citing[:10]:
-                    click.echo(f"  - {c_doi}")
-                if len(citing) > 10:
-                    click.echo(f"  ... and {len(citing) - 10} more")
-
-            if references:
-                cited = crossref.get_cited(doi)
-                click.echo()
-                click.secho(f"References ({len(cited)}):", bold=True)
-                for r_doi in cited[:10]:
-                    click.echo(f"  - {r_doi}")
-                if len(cited) > 10:
-                    click.echo(f"  ... and {len(cited) - 10} more")
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
+    # Handle --help-recursive by delegating to crossref-local
+    args = ctx.args
+    if help_recursive:
+        args = ["--help-recursive"]
 
-
-@crossref_scitex.command("count")
-@click.argument("query")
-def count_cmd(query):
-    """
-    Count papers matching a query.
-
-    \b
-    Examples:
-        scitex scholar crossref count "machine learning"
-        scitex scholar crossref count "CRISPR gene editing"
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        count = crossref.count(query)
-        click.echo(f"{count:,} papers match: {query}")
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
-
-
-@crossref_scitex.command("info")
-@click.option("--json", "as_json", is_flag=True, help="Output as JSON")
-def info_cmd(as_json):
-    """
-    Show CrossRef database configuration and status.
-
-    \b
-    Examples:
-        scitex scholar crossref info
-        scitex scholar crossref info --json
-    """
-    try:
-        from scitex.scholar import crossref_scitex as crossref
-    except ImportError:
-        click.secho(
-            "crossref-local not installed. Install with: pip install crossref-local",
-            fg="red",
-        )
-        sys.exit(1)
-
-    try:
-        info = crossref.info()
-        mode = crossref.get_mode()
-
-        if as_json:
-            info["mode"] = mode
-            click.echo(json.dumps(info, indent=2))
-        else:
-            click.secho("CrossRef Database Status", fg="cyan", bold=True)
-            click.echo()
-            click.echo(f"Mode: {mode}")
-            click.echo(f"Status: {info.get('status', 'unknown')}")
-
-            if "version" in info:
-                click.echo(f"Version: {info['version']}")
-
-            if "work_count" in info:
-                click.echo(f"Papers: {info['work_count']:,}")
-
-            if "db_path" in info:
-                click.echo(f"Database: {info['db_path']}")
-
-            if "api_url" in info:
-                click.echo(f"API URL: {info['api_url']}")
-
-    except Exception as e:
-        click.secho(f"Error: {e}", fg="red")
-        sys.exit(1)
+    # Delegate all arguments to crossref-local CLI
+    sys.exit(crossref_cli.main(args, standalone_mode=False))
 
 
 # EOF

scitex/cli/scholar/_openalex_scitex.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-29
+# File: src/scitex/cli/scholar/_openalex_scitex.py
+"""OpenAlex-SciTeX CLI - Thin wrapper delegating to openalex-local.
+
+This module provides access to the local OpenAlex database (284M+ works)
+by delegating directly to openalex-local CLI without any modifications.
+"""
+
+from __future__ import annotations
+
+import sys
+
+import click
+
+
+@click.command(
+    "openalex-scitex",
+    context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+)
+@click.option("--help-recursive", is_flag=True, help="Show help for all commands")
+@click.pass_context
+def openalex_scitex(ctx, help_recursive):
+    """
+    OpenAlex-SciTeX database search (284M+ works)
+
+    \b
+    Thin wrapper for openalex-local. All arguments passed directly.
+    Run 'openalex-local --help' for full options.
+
+    \b
+    Examples:
+        scitex scholar openalex-scitex search "machine learning"
+        scitex scholar openalex-scitex search-by-doi 10.1038/nature12373
+        scitex scholar openalex-scitex status
+    """
+    try:
+        from openalex_local.cli import cli as openalex_cli
+    except ImportError:
+        click.secho(
+            "openalex-local not installed. Install with: pip install openalex-local",
+            fg="red",
+        )
+        sys.exit(1)
+
+    # Handle --help-recursive by delegating to openalex-local
+    args = ctx.args
+    if help_recursive:
+        args = ["--help-recursive"]
+
+    # Delegate all arguments to openalex-local CLI
+    sys.exit(openalex_cli.main(args, standalone_mode=False))
+
+
+# EOF

scitex/scholar/__init__.py

@@ -1,5 +1,4 @@
-"""
-SciTeX Scholar - Scientific Literature Management Made Simple
+"""SciTeX Scholar - Scientific Literature Management Made Simple.
 
 This module provides a unified interface for:
 - Searching scientific literature across multiple sources
@@ -27,17 +26,17 @@ _missing = warn_module_deps("scholar")
 try:
     from scitex.scholar.auth import ScholarAuthManager
 except ImportError:
-    ScholarAuthManager = None
+    ScholarAuthManager = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.browser import ScholarBrowserManager
 except ImportError:
-    ScholarBrowserManager = None
+    ScholarBrowserManager = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.config import ScholarConfig
 except ImportError:
-    ScholarConfig = None
+    ScholarConfig = None  # type: ignore[misc,assignment]
 
 try:
     from scitex.scholar.core import Paper, Papers, Scholar
@@ -71,12 +70,17 @@ try:
 except ImportError:
     utils = None
 
-# CrossRef integration via crossref-local delegation (branded as crossref-scitex)
+# Local database integrations (crossref-local, openalex-local)
 try:
-    from . import crossref_scitex
+    from .local_dbs import crossref_scitex
 except ImportError:
     crossref_scitex = None
 
+try:
+    from .local_dbs import openalex_scitex
+except ImportError:
+    openalex_scitex = None
+
 __all__ = [
     "ScholarConfig",
     "ScholarEngine",
@@ -87,8 +91,9 @@ __all__ = [
     "Papers",
     "Scholar",
     "utils",
-    # CrossRef integration (167M+ papers via crossref-local)
-    "crossref_scitex",
+    # Local database integrations
+    "crossref_scitex",  # CrossRef (167M+ papers via crossref-local)
+    "openalex_scitex",  # OpenAlex (284M+ works via openalex-local)
 ]
 
 # # Import core classes for advanced users

scitex/scholar/_mcp/crossref_tool_schemas.py

@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-29
+# File: src/scitex/scholar/_mcp/crossref_tool_schemas.py
+"""CrossRef-Local tool schemas for MCP server.
+
+Provides access to 167M+ papers via crossref-local database.
+"""
+
+from __future__ import annotations
+
+import mcp.types as types
+
+__all__ = ["get_crossref_tool_schemas"]
+
+
+def get_crossref_tool_schemas() -> list[types.Tool]:
+    """Return CrossRef-Local tool schemas."""
+    return [
+        types.Tool(
+            name="crossref_search",
+            description=(
+                "Search CrossRef database (167M+ papers) via crossref-local. "
+                "Fast full-text search with year filtering and citation enrichment."
+            ),
+            inputSchema={
+                "type": "object",
+                "properties": {
+                    "query": {
+                        "type": "string",
+                        "description": "Search query string (full-text search)",
+                    },
+                    "limit": {
+                        "type": "integer",
+                        "description": "Maximum number of results",
+                        "default": 20,
+                    },
+                    "offset": {
+                        "type": "integer",
+                        "description": "Number of results to skip for pagination",
+                        "default": 0,
+                    },
+                    "year_min": {
+                        "type": "integer",
+                        "description": "Minimum publication year filter",
+                    },
+                    "year_max": {
+                        "type": "integer",
+                        "description": "Maximum publication year filter",
+                    },
+                    "enrich": {
+                        "type": "boolean",
+                        "description": "Add citation counts and references",
+                        "default": False,
+                    },
+                },
+                "required": ["query"],
+            },
+        ),
+        types.Tool(
+            name="crossref_get",
+            description="Get a paper by DOI from CrossRef database with optional citation data.",
+            inputSchema={
+                "type": "object",
+                "properties": {
+                    "doi": {
+                        "type": "string",
+                        "description": "DOI of the paper (e.g., '10.1038/nature12373')",
+                    },
+                    "include_citations": {
+                        "type": "boolean",
+                        "description": "Include list of DOIs that cite this paper",
+                        "default": False,
+                    },
+                    "include_references": {
+                        "type": "boolean",
+                        "description": "Include list of DOIs this paper references",
+                        "default": False,
+                    },
+                },
+                "required": ["doi"],
+            },
+        ),
+        types.Tool(
+            name="crossref_count",
+            description="Count papers matching a search query in CrossRef database.",
+            inputSchema={
+                "type": "object",
+                "properties": {
+                    "query": {
+                        "type": "string",
+                        "description": "Search query string",
+                    },
+                },
+                "required": ["query"],
+            },
+        ),
+        types.Tool(
+            name="crossref_citations",
+            description="Get citation relationships for a paper (citing papers and/or references).",
+            inputSchema={
+                "type": "object",
+                "properties": {
+                    "doi": {
+                        "type": "string",
+                        "description": "DOI of the paper",
+                    },
+                    "direction": {
+                        "type": "string",
+                        "description": "Citation direction: 'citing', 'cited', or 'both'",
+                        "enum": ["citing", "cited", "both"],
+                        "default": "citing",
+                    },
+                    "limit": {
+                        "type": "integer",
+                        "description": "Maximum results per direction",
+                        "default": 100,
+                    },
+                },
+                "required": ["doi"],
+            },
+        ),
+        types.Tool(
+            name="crossref_info",
+            description="Get CrossRef database configuration and status.",
+            inputSchema={
+                "type": "object",
+                "properties": {},
+            },
+        ),
+    ]
+
+
+# EOF