napistu 0.2.5.dev7__py3-none-any.whl → 0.3.1.dev1__py3-none-any.whl

napistu/mcp/config.py

@@ -0,0 +1,223 @@
+from pydantic import BaseModel, Field, computed_field, validator
+from typing import Optional
+import click
+from napistu.mcp.constants import MCP_DEFAULTS, MCP_PRODUCTION_URL
+
+
+class MCPServerConfig(BaseModel):
+    """Server-side MCP configuration with validation."""
+
+    host: str = Field(description="Host to bind server to")
+    port: int = Field(ge=1, le=65535, description="Port to bind server to")
+    server_name: str = Field(description="Server name")
+
+    @validator("host")
+    def validate_host(cls, v):
+        """Basic host validation."""
+        if not v or v.isspace():
+            raise ValueError("Host cannot be empty")
+        return v.strip()
+
+    @computed_field
+    @property
+    def bind_address(self) -> str:
+        """Full address for server binding."""
+        return f"{self.host}:{self.port}"
+
+
+class MCPClientConfig(BaseModel):
+    """Client-side MCP configuration with validation."""
+
+    host: str = Field(description="Target server host")
+    port: int = Field(ge=1, le=65535, description="Target server port")
+    use_https: bool = Field(description="Use HTTPS instead of HTTP")
+
+    @computed_field
+    @property
+    def base_url(self) -> str:
+        """Base URL for HTTP requests."""
+        protocol = "https" if self.use_https else "http"
+        return f"{protocol}://{self.host}:{self.port}"
+
+    @computed_field
+    @property
+    def mcp_url(self) -> str:
+        """Full MCP endpoint URL."""
+        return f"{self.base_url}{MCP_DEFAULTS.MCP_PATH}"
+
+
+# Preset configurations - no overrides needed
+def local_server_config() -> MCPServerConfig:
+    """Local development server configuration."""
+    return MCPServerConfig(
+        host=MCP_DEFAULTS.LOCAL_HOST,
+        port=MCP_DEFAULTS.LOCAL_PORT,
+        server_name=MCP_DEFAULTS.LOCAL_SERVER_NAME,
+    )
+
+
+def production_server_config() -> MCPServerConfig:
+    """Production server configuration."""
+    return MCPServerConfig(
+        host=MCP_DEFAULTS.PRODUCTION_HOST,
+        port=MCP_DEFAULTS.PRODUCTION_PORT,
+        server_name=MCP_DEFAULTS.PRODUCTION_SERVER_NAME,
+    )
+
+
+def local_client_config() -> MCPClientConfig:
+    """Local development client configuration."""
+    return MCPClientConfig(
+        host=MCP_DEFAULTS.LOCAL_HOST, port=MCP_DEFAULTS.LOCAL_PORT, use_https=False
+    )
+
+
+def production_client_config() -> MCPClientConfig:
+    """Production client configuration."""
+    # Parse production URL to extract host
+    production_host = MCP_PRODUCTION_URL.replace("https://", "").split("/")[0]
+    return MCPClientConfig(
+        host=production_host, port=MCP_DEFAULTS.HTTPS_PORT, use_https=True
+    )
+
+
+# Utility functions for CLI validation
+def validate_server_config_flags(
+    local: bool,
+    production: bool,
+    host: Optional[str],
+    port: Optional[int],
+    server_name: Optional[str],
+) -> MCPServerConfig:
+    """
+    Validate server configuration flags and return appropriate config.
+
+    Raises click.BadParameter if incompatible flags are used.
+    """
+    # Check for mutually exclusive presets
+    if local and production:
+        raise click.BadParameter("Cannot use both --local and --production flags")
+
+    # Check for preset + manual config conflicts
+    preset_used = local or production
+    manual_config_used = any(
+        [host is not None, port is not None, server_name is not None]
+    )
+
+    if preset_used and manual_config_used:
+        preset_name = "local" if local else "production"
+        raise click.BadParameter(
+            f"Cannot use --{preset_name} with manual host/port/server-name configuration. "
+            f"Use either preset flags OR manual configuration, not both."
+        )
+
+    # Return appropriate config
+    if local:
+        return local_server_config()
+    elif production:
+        return production_server_config()
+    else:
+        # Manual configuration - all required
+        if not all([host, port, server_name]):
+            raise click.BadParameter(
+                "Manual configuration requires --host, --port, and --server-name"
+            )
+        return MCPServerConfig(host=host, port=port, server_name=server_name)
+
+
+def validate_client_config_flags(
+    local: bool,
+    production: bool,
+    host: Optional[str],
+    port: Optional[int],
+    use_https: Optional[bool],
+) -> MCPClientConfig:
+    """
+    Validate client configuration flags and return appropriate config.
+
+    Raises click.BadParameter if incompatible flags are used.
+    """
+    # Check for mutually exclusive presets
+    if local and production:
+        raise click.BadParameter("Cannot use both --local and --production flags")
+
+    # Check for preset + manual config conflicts
+    preset_used = local or production
+    manual_config_used = any(
+        [host is not None, port is not None, use_https is not None]
+    )
+
+    if preset_used and manual_config_used:
+        preset_name = "local" if local else "production"
+        raise click.BadParameter(
+            f"Cannot use --{preset_name} with manual host/port/https configuration. "
+            f"Use either preset flags OR manual configuration, not both."
+        )
+
+    # Return appropriate config
+    if local:
+        return local_client_config()
+    elif production:
+        return production_client_config()
+    else:
+        # Manual configuration - all required
+        if not all([host is not None, port is not None, use_https is not None]):
+            raise click.BadParameter(
+                "Manual configuration requires --host, --port, and --https"
+            )
+        return MCPClientConfig(host=host, port=port, use_https=use_https)
+
+
+# Click option decorators for reuse
+def server_config_options(f):
+    """Decorator to add server configuration options to click commands."""
+    f = click.option(
+        "--production", is_flag=True, help="Use production server configuration"
+    )(f)
+    f = click.option(
+        "--local", is_flag=True, help="Use local development server configuration"
+    )(f)
+    f = click.option(
+        "--host",
+        type=str,
+        help="Host to bind server to (requires --port and --server-name)",
+    )(f)
+    f = click.option(
+        "--port",
+        type=int,
+        help="Port to bind server to (requires --host and --server-name)",
+    )(f)
+    f = click.option(
+        "--server-name", type=str, help="Server name (requires --host and --port)"
+    )(f)
+    return f
+
+
+def client_config_options(f):
+    """Decorator to add client configuration options to click commands."""
+    f = click.option("--production", is_flag=True, help="Connect to production server")(
+        f
+    )
+    f = click.option(
+        "--local", is_flag=True, help="Connect to local development server"
+    )(f)
+    f = click.option(
+        "--host",
+        type=str,
+        default=None,
+        help="Server host (requires --port and --https)",
+    )(f)
+    f = click.option(
+        "--port",
+        type=int,
+        default=None,
+        help="Server port (requires --host and --https)",
+    )(f)
+    f = click.option(
+        "--https",
+        is_flag=True,
+        default=None,
+        flag_value=True,
+        help="Use HTTPS (requires --host and --port)",
+    )(f)
+    return f

napistu/mcp/constants.py

@@ -31,6 +31,36 @@ TOOL_VARS = SimpleNamespace(
     SNIPPET="snippet",
 )
 
+# MCP Server Configuration Constants
+MCP_DEFAULTS = SimpleNamespace(
+    # Local development defaults
+    LOCAL_HOST="127.0.0.1",
+    LOCAL_PORT=8765,
+    # Production defaults
+    PRODUCTION_HOST="0.0.0.0",
+    PRODUCTION_PORT=8080,
+    # Server names
+    LOCAL_SERVER_NAME="napistu-local",
+    PRODUCTION_SERVER_NAME="napistu-production",
+    FULL_SERVER_NAME="napistu-full",
+    # Transport configuration
+    TRANSPORT="streamable-http",
+    MCP_PATH="/mcp",
+    # Standard protocol ports
+    HTTP_PORT=80,
+    HTTPS_PORT=443,
+)
+
+# Production server URL
+MCP_PRODUCTION_URL = "https://napistu-mcp-server-844820030839.us-west1.run.app"
+
+# Profile names (component configurations)
+MCP_PROFILES = SimpleNamespace(
+    EXECUTION="execution",  # execution only
+    DOCS="docs",  # docs + codebase + tutorials
+    FULL="full",  # all components
+)
+
 READMES = {
     "napistu": "https://raw.githubusercontent.com/napistu/napistu/main/README.md",
     "napistu-py": "https://raw.githubusercontent.com/napistu/napistu-py/main/README.md",
@@ -38,7 +68,20 @@ READMES = {
     "napistu/tutorials": "https://raw.githubusercontent.com/napistu/napistu/main/tutorials/README.md",
 }
 
-WIKI_ROOT = "https://raw.githubusercontent.com/napistu/napistu/main/docs/wiki"
+WIKI_PAGES = {
+    "Consensus",
+    "Data-Sources",
+    "Napistu-Graphs",
+    "Dev-Zone",
+    "Environment-Setup",
+    "Exploring-Molecular-Relationships-as-Networks",
+    "GitHub-Actions-napistu‐py",
+    "History",
+    "Model-Context-Protocol-(MCP)-server",
+    "Precomputed-distances",
+    "SBML",
+    "SBML-DFs",
+}
 
 NAPISTU_PY_READTHEDOCS = "https://napistu.readthedocs.io/en/latest"
 NAPISTU_PY_READTHEDOCS_API = NAPISTU_PY_READTHEDOCS + "/api.html"
@@ -61,7 +104,7 @@ REPOS_WITH_WIKI = [PACKAGE_DEFS.GITHUB_PROJECT_REPO]
 TUTORIAL_URLS = {
     "adding_data_to_graphs": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/adding_data_to_graphs.ipynb",
     "downloading_pathway_data": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/downloading_pathway_data.ipynb",
-    "formatting_sbml_dfs_as_cpr_graphs": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/formatting_sbml_dfs_as_cpr_graphs.ipynb",
+    "creating_a_napistu_graph": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/creating_a_napistu_graph.ipynb",
     "merging_models_into_a_consensus": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/merging_models_into_a_consensus.ipynb",
     "r_based_network_visualization": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/r_based_network_visualization.ipynb",
     "suggesting_mechanisms_with_networks": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/suggesting_mechanisms_with_networks.ipynb",