@cyanheads/pubmed-mcp-server 1.1.4 → 1.2.2

package/dist/mcp-server/resources/echoResource/echoResourceLogic.d.ts

@@ -1,79 +0,0 @@
-/**
- * @fileoverview Defines the core logic, schemas, and types for the `echo` resource.
- * This module includes a Zod schema for query parameter validation, type definitions,
- * and the main processing function that constructs the resource response.
- * The echo resource is designed to return a message, typically extracted from the
- * request URI's path or query parameters, along with a timestamp.
- * @module src/mcp-server/resources/echoResource/echoResourceLogic
- */
-import { z } from "zod";
-import { type RequestContext } from "../../../utils/index.js";
-/**
- * Zod schema defining expected query parameters for the echo resource.
- *
- * This schema is intended for validating parameters passed via the URI's query string
- * (e.g., `echo://some_message?message=override_from_query&anotherParam=value`).
- * Path parameters, such as `{message}` in a template like `echo://{message}`,
- * are typically defined in the `ResourceTemplate` (see `registration.ts`) and
- * extracted by the MCP SDK from the URI path. The SDK merges these path
- * parameters into the `params` object passed to the handler.
- *
- * If a path parameter and a query parameter share the same name (e.g., 'message'),
- * the query parameter will take precedence over the path parameter. This schema
- * defines `message` as an optional query parameter.
- */
-export declare const EchoResourceQuerySchema: z.ZodObject<{
-    /**
-     * Optional message to be echoed back in the response.
-     * If the resource template also defines a 'message' path parameter,
-     * this query parameter will override the path parameter's value if both are present.
-     */
-    message: z.ZodOptional<z.ZodString>;
-}, "strip", z.ZodTypeAny, {
-    message?: string | undefined;
-}, {
-    message?: string | undefined;
-}>;
-/**
- * TypeScript type inferred from the {@link EchoResourceQuerySchema}.
- * Represents the validated query parameters that might be passed to the echo resource.
- */
-export type EchoResourceParams = z.infer<typeof EchoResourceQuerySchema>;
-/**
- * Defines the structure of the JSON payload returned by the `processEchoResource` function.
- * This object is typically JSON-stringified by the resource handler before being sent
- * as the resource content.
- *
- * @property message - The message that is being echoed. This could be from a path parameter,
- *   a query parameter (which takes precedence), or a default value.
- * @property timestamp - An ISO 8601 timestamp indicating when the response was generated.
- * @property requestUri - The full URI of the original resource request.
- */
-export interface EchoResourceResponsePayload {
-    /** The message that is being echoed. */
-    message: string;
-    /** An ISO 8601 timestamp indicating when the response was generated. */
-    timestamp: string;
-    /** The full URI of the original resource request. */
-    requestUri: string;
-}
-/**
- * Processes the core logic for an echo resource request.
- * It constructs a response payload containing a message (derived from path or query parameters),
- * the current timestamp, and the original request URI.
- *
- * The `params` argument is expected to contain validated query parameters. If the resource
- * template (e.g., `echo://{message}`) includes path parameters, the MCP SDK extracts
- * them and merges them into the `params` object. If a query parameter shares the same
- * name as a path parameter, the query parameter's value takes precedence. This function
- * assumes `params.message` will hold the definitive message.
- *
- * @param uri - The full URL object of the incoming resource request.
- * @param params - The validated query parameters for the request.
- *   This object also includes path parameters merged by the SDK, with query parameters
- *   taking precedence in case of name conflicts.
- * @param context - The request context, used for logging and tracing the operation.
- * @returns The data payload for the response.
- *   This payload is typically JSON-stringified by the calling handler.
- */
-export declare const processEchoResource: (uri: URL, params: EchoResourceParams, context: RequestContext) => EchoResourceResponsePayload;

package/dist/mcp-server/resources/echoResource/echoResourceLogic.js

@@ -1,82 +0,0 @@
-/**
- * @fileoverview Defines the core logic, schemas, and types for the `echo` resource.
- * This module includes a Zod schema for query parameter validation, type definitions,
- * and the main processing function that constructs the resource response.
- * The echo resource is designed to return a message, typically extracted from the
- * request URI's path or query parameters, along with a timestamp.
- * @module src/mcp-server/resources/echoResource/echoResourceLogic
- */
-import { z } from "zod";
-import { logger } from "../../../utils/index.js";
-/**
- * Zod schema defining expected query parameters for the echo resource.
- *
- * This schema is intended for validating parameters passed via the URI's query string
- * (e.g., `echo://some_message?message=override_from_query&anotherParam=value`).
- * Path parameters, such as `{message}` in a template like `echo://{message}`,
- * are typically defined in the `ResourceTemplate` (see `registration.ts`) and
- * extracted by the MCP SDK from the URI path. The SDK merges these path
- * parameters into the `params` object passed to the handler.
- *
- * If a path parameter and a query parameter share the same name (e.g., 'message'),
- * the query parameter will take precedence over the path parameter. This schema
- * defines `message` as an optional query parameter.
- */
-export const EchoResourceQuerySchema = z.object({
-    /**
-     * Optional message to be echoed back in the response.
-     * If the resource template also defines a 'message' path parameter,
-     * this query parameter will override the path parameter's value if both are present.
-     */
-    message: z
-        .string()
-        .optional()
-        .describe("Optional message to echo back in the response. If not provided, a default may be used or derived from the path."),
-});
-/**
- * Processes the core logic for an echo resource request.
- * It constructs a response payload containing a message (derived from path or query parameters),
- * the current timestamp, and the original request URI.
- *
- * The `params` argument is expected to contain validated query parameters. If the resource
- * template (e.g., `echo://{message}`) includes path parameters, the MCP SDK extracts
- * them and merges them into the `params` object. If a query parameter shares the same
- * name as a path parameter, the query parameter's value takes precedence. This function
- * assumes `params.message` will hold the definitive message.
- *
- * @param uri - The full URL object of the incoming resource request.
- * @param params - The validated query parameters for the request.
- *   This object also includes path parameters merged by the SDK, with query parameters
- *   taking precedence in case of name conflicts.
- * @param context - The request context, used for logging and tracing the operation.
- * @returns The data payload for the response.
- *   This payload is typically JSON-stringified by the calling handler.
- */
-export const processEchoResource = (uri, params, context) => {
-    // The `params.message` can originate from a query parameter (validated by `EchoResourceQuerySchema`)
-    // or a path parameter (e.g., from a template like `echo://{message_from_path}`).
-    // The MCP SDK merges these, with query parameters taking precedence over path parameters if names conflict.
-    // The fallback "Default message..." is a safeguard if no message is provided via path or query.
-    const messageToEcho = params.message || `Default echo from ${uri.pathname}`;
-    logger.debug("Processing echo resource logic.", {
-        ...context,
-        resourceUri: uri.href,
-        extractedMessage: messageToEcho,
-        queryParamMessage: params.message,
-    });
-    const responsePayload = {
-        message: messageToEcho,
-        timestamp: new Date().toISOString(),
-        requestUri: uri.href,
-    };
-    logger.debug("Echo resource processed successfully.", {
-        ...context,
-        responsePayloadSummary: {
-            messageLength: responsePayload.message.length,
-            uriEchoed: responsePayload.requestUri.length > 50
-                ? `${responsePayload.requestUri.substring(0, 47)}...`
-                : responsePayload.requestUri,
-        },
-    });
-    return responsePayload;
-};

package/dist/mcp-server/resources/echoResource/index.d.ts

@@ -1,13 +0,0 @@
-/**
- * @fileoverview Barrel file for the `echo` resource.
- * This file serves as the public interface for the echo resource module,
- * primarily exporting the `registerEchoResource` function. This function is
- * responsible for registering the echo resource, including its templates and handler,
- * with an MCP server instance. This makes the resource accessible to clients
- * via defined URI patterns.
- *
- * Consuming modules should import from this barrel file to access
- * the echo resource's registration capabilities.
- * @module src/mcp-server/resources/echoResource/index
- */
-export { registerEchoResource } from "./registration.js";

package/dist/mcp-server/resources/echoResource/index.js

@@ -1,13 +0,0 @@
-/**
- * @fileoverview Barrel file for the `echo` resource.
- * This file serves as the public interface for the echo resource module,
- * primarily exporting the `registerEchoResource` function. This function is
- * responsible for registering the echo resource, including its templates and handler,
- * with an MCP server instance. This makes the resource accessible to clients
- * via defined URI patterns.
- *
- * Consuming modules should import from this barrel file to access
- * the echo resource's registration capabilities.
- * @module src/mcp-server/resources/echoResource/index
- */
-export { registerEchoResource } from "./registration.js";

package/dist/mcp-server/resources/echoResource/registration.d.ts

@@ -1,30 +0,0 @@
-/**
- * @fileoverview Handles the registration of the `echo` resource with an MCP server instance.
- * This module defines the resource's template (URI structure), metadata (name, description, examples),
- * and the asynchronous handler function that processes `resources/read` requests matching the template.
- * It utilizes the MCP SDK's `server.resource()` method for registration and integrates
- * robust error handling using the project's `ErrorHandler` utility.
- * @module src/mcp-server/resources/echoResource/registration
- */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers the 'echo' resource and its handlers with the provided MCP server instance.
- *
- * This function defines:
- * 1.  The resource template (e.g., `echo://{message}`), which determines the URI structure.
- *     The `{message}` part is a path variable.
- * 2.  A `list` operation for the template to provide example/discoverable URIs.
- * 3.  Metadata for the resource, including its user-friendly name, description, MIME type,
- *     and example URIs.
- * 4.  The core asynchronous handler logic for `resources/read` requests that match the template.
- *     This handler processes the request and returns the resource content.
- *
- * Error handling is integrated throughout using `ErrorHandler.tryCatch` for robustness.
- *
- * @param server - The MCP server instance to register the resource with.
- * @returns A promise that resolves when the resource registration is complete. It does not return a value upon successful completion.
- * @throws {McpError} If the registration process fails critically, which might halt server startup.
- * @see {@link EchoResourceParams} for the type of parameters passed to the handler.
- * @see {@link processEchoResource} for the core resource logic.
- */
-export declare const registerEchoResource: (server: McpServer) => Promise<void>;

package/dist/mcp-server/resources/echoResource/registration.js

@@ -1,168 +0,0 @@
-/**
- * @fileoverview Handles the registration of the `echo` resource with an MCP server instance.
- * This module defines the resource's template (URI structure), metadata (name, description, examples),
- * and the asynchronous handler function that processes `resources/read` requests matching the template.
- * It utilizes the MCP SDK's `server.resource()` method for registration and integrates
- * robust error handling using the project's `ErrorHandler` utility.
- * @module src/mcp-server/resources/echoResource/registration
- */
-import { ResourceTemplate, } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
-import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
-import { processEchoResource, } from "./echoResourceLogic.js";
-/**
- * Registers the 'echo' resource and its handlers with the provided MCP server instance.
- *
- * This function defines:
- * 1.  The resource template (e.g., `echo://{message}`), which determines the URI structure.
- *     The `{message}` part is a path variable.
- * 2.  A `list` operation for the template to provide example/discoverable URIs.
- * 3.  Metadata for the resource, including its user-friendly name, description, MIME type,
- *     and example URIs.
- * 4.  The core asynchronous handler logic for `resources/read` requests that match the template.
- *     This handler processes the request and returns the resource content.
- *
- * Error handling is integrated throughout using `ErrorHandler.tryCatch` for robustness.
- *
- * @param server - The MCP server instance to register the resource with.
- * @returns A promise that resolves when the resource registration is complete. It does not return a value upon successful completion.
- * @throws {McpError} If the registration process fails critically, which might halt server startup.
- * @see {@link EchoResourceParams} for the type of parameters passed to the handler.
- * @see {@link processEchoResource} for the core resource logic.
- */
-export const registerEchoResource = async (server) => {
-    const resourceName = "echo-resource"; // Internal identifier for this resource registration.
-    const registrationContext = requestContextService.createRequestContext({
-        operation: "RegisterResource",
-        resourceName: resourceName,
-        moduleName: "EchoResourceRegistration",
-    });
-    logger.info(`Attempting to register resource: '${resourceName}'`, registrationContext);
-    await ErrorHandler.tryCatch(async () => {
-        // Define the resource template. This specifies the URI structure and supported operations.
-        // The URI `echo://{message}` uses RFC 6570 syntax, where `{message}` is a path variable.
-        const template = new ResourceTemplate("echo://{message}", {
-            /**
-             * Asynchronous handler for the `resources/list` operation associated with this template.
-             * It provides a list of example or discoverable resource URIs that match this template.
-             * This allows clients to discover how to interact with the echo resource.
-             *
-             * @returns A promise resolving to an object containing an array of resource descriptors.
-             */
-            list: async () => {
-                const listContext = requestContextService.createRequestContext({
-                    parentContext: registrationContext,
-                    operation: "ListEchoResourceExamples",
-                });
-                logger.debug("Executing list operation for echo resource template.", listContext);
-                // Return a static list of example URIs.
-                return {
-                    resources: [
-                        {
-                            uri: "echo://hello",
-                            name: "Default Echo Message",
-                            description: "A simple echo resource example using a default message.",
-                        },
-                        // Add more examples as needed
-                    ],
-                    // nextCursor could be used here if the list were paginated.
-                };
-            },
-            // The `complete` operation (for URI completion suggestions) is optional and not implemented here.
-        });
-        logger.debug(`Resource template created for '${resourceName}': ${template.uriTemplate}`, registrationContext);
-        // Register the resource with the server.
-        // This involves providing the registration name, the template, metadata, and the handler for read operations.
-        server.resource(resourceName, template, {
-            name: "Echo Message Resource",
-            description: "A simple echo resource that returns a message, optionally specified in the URI path.",
-            mimeType: "application/json",
-            examples: [
-                {
-                    name: "Basic echo",
-                    uri: "echo://hello",
-                    description: "Accesses the echo resource to echo the message 'hello'.",
-                },
-                {
-                    name: "Custom echo",
-                    uri: "echo://custom-message-here",
-                    description: "Accesses the echo resource to echo 'custom-message-here'.",
-                },
-            ],
-        }, 
-        /**
-         * Asynchronous handler for `resources/read` requests matching the `echo://{message}` template.
-         * This function is invoked by the MCP SDK when a client requests to read a resource
-         * whose URI matches the registered template.
-         *
-         * The SDK extracts path variables (like `{message}` from `echo://{message}`) from the URI.
-         * These path variables, along with any validated query parameters, are passed in the `params` object.
-         *
-         * @param uri - The full URL object of the resource being requested.
-         * @param params - An object containing parameters derived from the request.
-         *   For this resource, it's expected to include `message` extracted from the URI
-         *   path by the SDK. It conforms to {@link EchoResourceParams}.
-         * @returns A promise that resolves with the resource content, formatted as a `ReadResourceResult`.
-         *   This includes the URI, Base64 encoded content blob, and MIME type.
-         *   If an error is thrown from this handler, the SDK is responsible for catching it and
-         *   formatting an error response.
-         */
-        async (uri, params) => {
-            const handlerContext = requestContextService.createRequestContext({
-                parentContext: registrationContext,
-                operation: "HandleResourceRead",
-                resourceName: resourceName,
-                resourceUri: uri.href,
-                inputParamsSummary: params.message
-                    ? { messageLength: params.message.length }
-                    : { noMessageParam: true },
-            });
-            logger.debug(`Handling read request for resource '${resourceName}', URI: ${uri.href}`, handlerContext);
-            return await ErrorHandler.tryCatch(async () => {
-                const responseData = processEchoResource(uri, params, handlerContext);
-                logger.debug(`'${resourceName}' (URI: ${uri.href}) processed successfully. Preparing content.`, handlerContext);
-                // Construct the `ReadResourceResult` as expected by the MCP SDK.
-                // The content (blob) must be Base64 encoded.
-                return {
-                    contents: [
-                        {
-                            uri: uri.href,
-                            blob: Buffer.from(JSON.stringify(responseData)).toString("base64"),
-                            mimeType: "application/json",
-                        },
-                    ],
-                };
-            }, {
-                operation: `ExecutingCoreLogicFor_${resourceName}_Read`,
-                context: handlerContext,
-                input: { uri: uri.href, params },
-                errorMapper: (error) => {
-                    const baseErrorCode = error instanceof McpError
-                        ? error.code
-                        : BaseErrorCode.INTERNAL_ERROR;
-                    const errorMessage = `Error processing read request for resource '${uri.href}': ${error instanceof Error ? error.message : "An unknown error occurred"}`;
-                    return new McpError(baseErrorCode, errorMessage, {
-                        ...handlerContext,
-                        originalErrorName: error instanceof Error ? error.name : typeof error,
-                    });
-                },
-            });
-        });
-        logger.info(`Resource '${resourceName}' (template: '${template.uriTemplate}') registered successfully.`, registrationContext);
-    }, {
-        operation: `RegisteringResource_${resourceName}`,
-        context: registrationContext,
-        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
-        errorMapper: (error) => {
-            const errorMessage = `Failed to register resource '${resourceName}': ${error instanceof Error ? error.message : "An unknown error occurred during registration."}`;
-            const code = error instanceof McpError
-                ? error.code
-                : BaseErrorCode.INITIALIZATION_FAILED;
-            return new McpError(code, errorMessage, {
-                ...registrationContext,
-                originalErrorName: error instanceof Error ? error.name : typeof error,
-            });
-        },
-        critical: true,
-    });
-};

package/dist/mcp-server/tools/getPubMedArticleConnections/logic.d.ts

@@ -1,6 +0,0 @@
-/**
- * @fileoverview Core logic for the 'get_pubmed_article_connections' MCP tool.
- * This file now re-exports the main handler from the './logic/index.js' module.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic
- */
-export { handleGetPubMedArticleConnections } from "./logic/index.js";

package/dist/mcp-server/tools/getPubMedArticleConnections/logic.js

@@ -1,6 +0,0 @@
-/**
- * @fileoverview Core logic for the 'get_pubmed_article_connections' MCP tool.
- * This file now re-exports the main handler from the './logic/index.js' module.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic
- */
-export { handleGetPubMedArticleConnections } from "./logic/index.js";