@cyanheads/pubmed-mcp-server 1.3.4 → 1.4.1

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/logic.js

@@ -2,7 +2,7 @@ import { ChartJSNodeCanvas } from "chartjs-node-canvas";
 import { z } from "zod";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-export const GeneratePubMedChartInputSchema = z.object({
+export const PubMedGenerateChartInputSchema = z.object({
     chartType: z
         .enum([
         "bar",
@@ -14,47 +14,47 @@ export const GeneratePubMedChartInputSchema = z.object({
         "radar",
         "polarArea",
     ])
-        .describe("Required. Specifies the type of chart to generate. Options: 'bar', 'line', 'scatter', 'pie', 'doughnut', 'bubble', 'radar', 'polarArea'."),
+        .describe("Specifies the type of chart to generate."),
     title: z
         .string()
         .optional()
-        .describe("Optional. The main title displayed above the chart. If omitted, no title is shown."),
+        .describe("The main title displayed above the chart."),
     width: z
         .number()
         .int()
         .positive()
         .optional()
         .default(800)
-        .describe("Optional. The width of the chart canvas in pixels. Must be a positive integer. Default: 800."),
+        .describe("The width of the chart canvas in pixels."),
     height: z
         .number()
         .int()
         .positive()
         .optional()
         .default(600)
-        .describe("Optional. The height of the chart canvas in pixels. Must be a positive integer. Default: 600."),
+        .describe("The height of the chart canvas in pixels."),
     dataValues: z
         .array(z.record(z.string(), z.any()))
         .min(1)
-        .describe("Required. An array of data objects used to plot the chart. Each object represents a data point or bar, structured as key-value pairs (e.g., [{ 'year': '2020', 'articles': 150 }, { 'year': '2021', 'articles': 180 }]). Must contain at least one data object."),
+        .describe("An array of data objects to plot the chart (e.g., [{ 'year': '2020', 'articles': 150 }])."),
     outputFormat: z
         .enum(["png"])
         .default("png")
-        .describe("Specifies the output format for the chart. Currently, only 'png' (Portable Network Graphics) is supported and is the default."),
+        .describe("Specifies the output format for the chart."),
     xField: z
         .string()
-        .describe("Required. The name of the field in `dataValues` to be used for the X-axis (horizontal). This field determines the categories or values along the bottom of the chart (e.g., 'year', 'geneName', 'publicationCount')."),
+        .describe("The field name from `dataValues` for the X-axis."),
     yField: z
         .string()
-        .describe("Required. The name of the field in `dataValues` to be used for the Y-axis (vertical). This field determines the values plotted upwards on the chart (e.g., 'articles', 'expressionLevel', 'citationCount')."),
+        .describe("The field name from `dataValues` for the Y-axis."),
     seriesField: z
         .string()
         .optional()
-        .describe("Optional. The name of the field in `dataValues` used to create multiple distinct lines or bar groups (series) on the same chart. Each unique value in this field will correspond to a separate dataset."),
+        .describe("The field name for creating multiple data series on the same chart."),
     sizeField: z
         .string()
         .optional()
-        .describe("Optional. For bubble charts. The name of the field in `dataValues` to use for encoding the size of the bubbles. Larger values in this field will result in larger bubbles (e.g., 'sampleSize', 'effectMagnitude')."),
+        .describe("For bubble charts, the field name for encoding bubble size."),
 });
 // Helper to group data by a series field
 function groupDataBySeries(data, xField, yField, seriesField) {
@@ -68,13 +68,13 @@ function groupDataBySeries(data, xField, yField, seriesField) {
     }
     return series;
 }
-export async function generatePubMedChartLogic(input, parentRequestContext) {
+export async function pubmedGenerateChartLogic(input, parentRequestContext) {
     const operationContext = requestContextService.createRequestContext({
         parentRequestId: parentRequestContext.requestId,
-        operation: "generatePubMedChartLogicExecution",
+        operation: "pubmedGenerateChartLogicExecution",
         input: sanitizeInputForLogging(input),
     });
-    logger.info(`Executing 'generate_pubmed_chart' with Chart.js. Chart type: ${input.chartType}`, operationContext);
+    logger.info(`Executing 'pubmed_generate_chart' with Chart.js. Chart type: ${input.chartType}`, operationContext);
     const { width, height, chartType, dataValues, xField, yField, title, seriesField, sizeField, } = input;
     const chartJSNodeCanvas = new ChartJSNodeCanvas({
         width,
@@ -191,3 +191,4 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         });
     }
 }
+//# sourceMappingURL=logic.js.map

package/dist/mcp-server/tools/pubmedGenerateChart/logic.js.map

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package/dist/mcp-server/tools/pubmedGenerateChart/registration.d.ts

@@ -0,0 +1,8 @@
+/**
+ * @fileoverview Registers the 'pubmed_generate_chart' tool with the MCP server.
+ * This tool now accepts parameterized input for generating charts.
+ * @module src/mcp-server/tools/pubmedGenerateChart/registration
+ */
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerPubMedGenerateChartTool(server: McpServer): Promise<void>;
+//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/pubmedGenerateChart/registration.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/registration.js

@@ -1,25 +1,21 @@
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
-import { GeneratePubMedChartInputSchema, generatePubMedChartLogic, } from "./logic.js";
-export async function registerGeneratePubMedChartTool(server) {
-    const operation = "registerGeneratePubMedChartTool";
-    const toolName = "generate_pubmed_chart";
-    const toolDescription = "Generates a customizable chart (PNG) from structured data. " +
-        "Supports 'bar', 'line', 'scatter', 'pie', 'doughnut', 'bubble', 'radar', and 'polarArea' plots. " +
-        "Requires data values and field mappings for axes. " +
-        "Optional parameters allow for titles and dimensions. " +
-        "Internally uses Chart.js and chartjs-node-canvas to produce a Base64-encoded PNG image.";
+import { PubMedGenerateChartInputSchema, pubmedGenerateChartLogic, } from "./logic.js";
+export async function registerPubMedGenerateChartTool(server) {
+    const operation = "registerPubMedGenerateChartTool";
+    const toolName = "pubmed_generate_chart";
+    const toolDescription = "Generates a customizable chart (PNG) from structured data. Supports various plot types and requires data values and field mappings for axes. Returns a Base64-encoded PNG image.";
     const context = requestContextService.createRequestContext({ operation });
     await ErrorHandler.tryCatch(async () => {
-        server.tool(toolName, toolDescription, GeneratePubMedChartInputSchema.shape, async (input, mcpProvidedContext) => {
+        server.tool(toolName, toolDescription, PubMedGenerateChartInputSchema.shape, async (input, mcpProvidedContext) => {
             const richContext = requestContextService.createRequestContext({
                 parentRequestId: context.requestId,
-                operation: "generatePubMedChartToolHandler",
+                operation: "pubmedGenerateChartToolHandler",
                 mcpToolContext: mcpProvidedContext,
                 input,
             });
             try {
-                const result = await generatePubMedChartLogic(input, richContext);
+                const result = await pubmedGenerateChartLogic(input, richContext);
                 return {
                     content: [
                         {
@@ -33,7 +29,7 @@ export async function registerGeneratePubMedChartTool(server) {
             }
             catch (error) {
                 const handledError = ErrorHandler.handleError(error, {
-                    operation: "generatePubMedChartToolHandler",
+                    operation: "pubmedGenerateChartToolHandler",
                     context: richContext,
                     input,
                     rethrow: false,
@@ -69,3 +65,4 @@ export async function registerGeneratePubMedChartTool(server) {
         critical: true,
     });
 }
+//# sourceMappingURL=registration.js.map

package/dist/mcp-server/tools/pubmedGenerateChart/registration.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"registration.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedGenerateChart/registration.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,iCAAiC,CAAC;AAC1E,OAAO,EACL,YAAY,EACZ,MAAM,EAEN,qBAAqB,GACtB,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAEL,8BAA8B,EAC9B,wBAAwB,GACzB,MAAM,YAAY,CAAC;AAEpB,MAAM,CAAC,KAAK,UAAU,+BAA+B,CACnD,MAAiB;IAEjB,MAAM,SAAS,GAAG,iCAAiC,CAAC;IACpD,MAAM,QAAQ,GAAG,uBAAuB,CAAC;IACzC,MAAM,eAAe,GACnB,kLAAkL,CAAC;IACrL,MAAM,OAAO,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC;IAE1E,MAAM,YAAY,CAAC,QAAQ,CACzB,KAAK,IAAI,EAAE;QACT,MAAM,CAAC,IAAI,CACT,QAAQ,EACR,eAAe,EACf,8BAA8B,CAAC,KAAK,EACpC,KAAK,EACH,KAA+B,EAC/B,kBAAuB,EACE,EAAE;YAC3B,MAAM,WAAW,GACf,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,eAAe,EAAE,OAAO,CAAC,SAAS;gBAClC,SAAS,EAAE,gCAAgC;gBAC3C,cAAc,EAAE,kBAAkB;gBAClC,KAAK;aACN,CAAC,CAAC;YAEL,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,wBAAwB,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;gBAClE,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,OAAO;4BACb,IAAI,EAAE,MAAM,CAAC,UAAU;4BACvB,QAAQ,EAAE,WAAW;yBACtB;qBACF;oBACD,OAAO,EAAE,KAAK;iBACf,CAAC;YACJ,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,YAAY,GAAG,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE;oBACnD,SAAS,EAAE,gCAAgC;oBAC3C,OAAO,EAAE,WAAW;oBACpB,KAAK;oBACL,OAAO,EAAE,KAAK;iBACf,CAAC,CAAC;gBAEH,MAAM,QAAQ,GACZ,YAAY,YAAY,QAAQ;oBAC9B,CAAC,CAAC,YAAY;oBACd,CAAC,CAAC,IAAI,QAAQ,CACV,aAAa,CAAC,cAAc,EAC5B,0DAA0D,EAC1D;wBACE,iBAAiB,EAAE,YAAY,CAAC,IAAI;wBACpC,oBAAoB,EAAE,YAAY,CAAC,OAAO;qBAC3C,CACF,CAAC;gBAER,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,MAAM;4BACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gCACnB,KAAK,EAAE;oCACL,IAAI,EAAE,QAAQ,CAAC,IAAI;oCACnB,OAAO,EAAE,QAAQ,CAAC,OAAO;oCACzB,OAAO,EAAE,QAAQ,CAAC,OAAO;iCAC1B;6BACF,CAAC;yBACH;qBACF;oBACD,OAAO,EAAE,IAAI;iBACd,CAAC;YACJ,CAAC;QACH,CAAC,CACF,CAAC;QACF,MAAM,CAAC,MAAM,CAAC,SAAS,QAAQ,eAAe,EAAE,OAAO,CAAC,CAAC;IAC3D,CAAC,EACD;QACE,SAAS;QACT,OAAO;QACP,SAAS,EAAE,aAAa,CAAC,qBAAqB;QAC9C,QAAQ,EAAE,IAAI;KACf,CACF,CAAC;AACJ,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/index.d.ts

@@ -4,3 +4,4 @@
  * @module src/mcp-server/tools/pubmedResearchAgent/index
  */
 export { registerPubMedResearchAgentTool } from "./registration.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedResearchAgent/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,+BAA+B,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/index.js

@@ -4,3 +4,4 @@
  * @module src/mcp-server/tools/pubmedResearchAgent/index
  */
 export { registerPubMedResearchAgentTool } from "./registration.js";
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedResearchAgent/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,+BAA+B,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/index.d.ts

@@ -5,3 +5,4 @@
 export * from "./inputSchema.js";
 export * from "./outputTypes.js";
 export * from "./planOrchestrator.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,kBAAkB,CAAC;AACjC,cAAc,kBAAkB,CAAC;AACjC,cAAc,uBAAuB,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/index.js

@@ -7,3 +7,4 @@ export * from "./outputTypes.js";
 export * from "./planOrchestrator.js";
 // Individual section prompt generators are not typically exported directly from here,
 // as they are used internally by the planOrchestrator.
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,cAAc,kBAAkB,CAAC;AACjC,cAAc,kBAAkB,CAAC;AACjC,cAAc,uBAAuB,CAAC;AACtC,sFAAsF;AACtF,uDAAuD"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.d.ts

@@ -109,3 +109,4 @@ export declare const PubMedResearchAgentInputSchema: z.ZodObject<{
     include_detailed_prompts_for_agent?: boolean | undefined;
 }>;
 export type PubMedResearchAgentInput = z.infer<typeof PubMedResearchAgentInputSchema>;
+//# sourceMappingURL=inputSchema.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"inputSchema.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,8BAA8B;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAiNzC,CAAC;AAEH,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAC5C,OAAO,8BAA8B,CACtC,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.js

@@ -147,3 +147,4 @@ export const PubMedResearchAgentInputSchema = z.object({
         .default(false) // Default to false, meaning the tool primarily structures the detailed input.
         .describe("If true, the tool will add more detailed instructive prompts/guidance within the output fields for a research agent. If false (default), it will primarily structure the provided inputs with minimal additional prompting."),
 });
+//# sourceMappingURL=inputSchema.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"inputSchema.js","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/inputSchema.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,MAAM,CAAC,MAAM,8BAA8B,GAAG,CAAC,CAAC,MAAM,CAAC;IACrD,8BAA8B;IAC9B,wBAAwB,EAAE,CAAC;SACxB,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,CAAC,2DAA2D,CAAC;IACxE,qBAAqB,EAAE,CAAC;SACrB,MAAM,EAAE;SACR,GAAG,CAAC,EAAE,CAAC;SACP,QAAQ,CACP,2KAA2K,CAC5K;IACH,iBAAiB,EAAE,CAAC;SACjB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;SACxB,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,CACP,qIAAqI,CACtI;IACH,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,qHAAqH,CACtH;IAEH,0CAA0C;IAC1C,8BAA8B,EAAE,CAAC;SAC9B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,mHAAmH,CACpH;IACH,6BAA6B,EAAE,CAAC;SAC7B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,uEAAuE,CACxE;IACH,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,8FAA8F,CAC/F;IACH,qBAAqB,EAAE,CAAC;SACrB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4EAA4E,CAC7E;IACH,oCAAoC,EAAE,CAAC;SACpC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;SACjB,QAAQ,EAAE;SACV,QAAQ,CAAC,uDAAuD,CAAC;IACpE,qCAAqC,EAAE,CAAC;SACrC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4HAA4H,CAC7H;IAEH,0BAA0B,EAAE,CAAC;SAC1B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,0FAA0F,CAC3F;IACH,oCAAoC,EAAE,CAAC;SACpC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IAEH,wBAAwB,EAAE,CAAC;SACxB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4HAA4H,CAC7H;IACH,sCAAsC,EAAE,CAAC;SACtC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,oGAAoG,CACrG;IACH,iCAAiC,EAAE,CAAC;SACjC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,oGAAoG,CACrG;IACH,yBAAyB,EAAE,CAAC;SACzB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,gHAAgH,CACjH;IACH,qBAAqB,EAAE,CAAC;SACrB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,uGAAuG,CACxG;IACH,2CAA2C,EAAE,CAAC;SAC3C,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,2EAA2E,CAC5E;IAEH,iDAAiD;IACjD,kCAAkC,EAAE,CAAC;SAClC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,6FAA6F,CAC9F;IACH,kCAAkC,EAAE,CAAC;SAClC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,qFAAqF,CACtF;IACH,iCAAiC,EAAE,CAAC;SACjC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+HAA+H,CAChI;IAEH,8CAA8C;IAC9C,yBAAyB,EAAE,CAAC;SACzB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,qHAAqH,CACtH;IACH,kCAAkC,EAAE,CAAC;SAClC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wGAAwG,CACzG;IACH,mCAAmC,EAAE,CAAC;SACnC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wGAAwG,CACzG;IACH,kCAAkC,EAAE,CAAC;SAClC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,6FAA6F,CAC9F;IAEH,8CAA8C;IAC9C,gCAAgC,EAAE,CAAC;SAChC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sFAAsF,CACvF;IACH,qCAAqC,EAAE,CAAC;SACrC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,6FAA6F,CAC9F;IACH,uCAAuC,EAAE,CAAC;SACvC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,6BAA6B,EAAE,CAAC;SAC7B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;IAEH,sCAAsC;IACtC,qCAAqC,EAAE,CAAC;SACrC,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,kEAAkE,CACnE;IACH,yBAAyB,EAAE,CAAC;SACzB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,kFAAkF,CACnF;IACH,yBAAyB,EAAE,CAAC;SACzB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+EAA+E,CAChF;IAEH,wDAAwD;IACxD,kCAAkC,EAAE,CAAC;SAClC,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC,CAAC,8EAA8E;SAC7F,QAAQ,CACP,6NAA6N,CAC9N;CACJ,CAAC,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.d.ts

@@ -104,3 +104,4 @@ export interface PubMedResearchPlanGeneratedOutput {
     phase_4_dissemination_and_iteration: Phase4Output;
     cross_cutting_considerations: CrossCuttingOutput;
 }
+//# sourceMappingURL=outputTypes.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"outputTypes.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,MAAM,WAAW,qBAAqB;IACpC,yBAAyB,CAAC,EAAE,MAAM,CAAC;IACnC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,iCAAiC,CAAC,EAAE,MAAM,CAAC;IAC3C,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,mCAAmC,CAAC,EAAE,MAAM,CAAC;IAC7C,8BAA8B,CAAC,EAAE,MAAM,CAAC;IACxC,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,2BAA2B,CAAC,EAAE,MAAM,CAAC;IACrC,wCAAwC,CAAC,EAAE,MAAM,CAAC;IAClD,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,kCAAkC,CAAC;IAC1C,yCAAyC,EAAE,qBAAqB,CAAC;IACjE,mCAAmC,EAAE,qBAAqB,CAAC;IAC3D,iDAAiD,EAAE,qBAAqB,CAAC;CAC1E;AAED,MAAM,WAAW,qBAAqB;IACpC,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,8BAA8B,CAAC,EAAE,MAAM,CAAC;IACxC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,yCAAyC,CAAC;IACjD,kCAAkC,EAAE,qBAAqB,CAAC;IAC1D,kCAAkC,EAAE,qBAAqB,CAAC;CAC3D;AAED,MAAM,WAAW,qBAAqB;IACpC,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,gCAAgC,CAAC,EAAE,MAAM,CAAC;IAC1C,+BAA+B,CAAC,EAAE,MAAM,CAAC;IACzC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,sCAAsC,CAAC;IAC9C,2BAA2B,EAAE,qBAAqB,CAAC;IACnD,+BAA+B,EAAE,qBAAqB,CAAC;CACxD;AAED,MAAM,WAAW,qBAAqB;IACpC,6BAA6B,CAAC,EAAE,MAAM,CAAC;IACvC,kCAAkC,CAAC,EAAE,MAAM,CAAC;IAC5C,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,oCAAoC,CAAC,EAAE,MAAM,CAAC;IAC9C,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,qBAAqB;IACpC,0BAA0B,CAAC,EAAE,MAAM,CAAC;IACpC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,sCAAsC,CAAC;IAC9C,+BAA+B,EAAE,qBAAqB,CAAC;IACvD,oCAAoC,EAAE,qBAAqB,CAAC;IAC5D,uCAAuC,EAAE,qBAAqB,CAAC;CAChE;AAED,MAAM,WAAW,mBAAmB;IAClC,kCAAkC,CAAC,EAAE,MAAM,CAAC;IAC5C,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CACpC;AACD,MAAM,WAAW,kBAAkB;IACjC,KAAK,EAAE,8BAA8B,CAAC;IACtC,OAAO,EAAE,mBAAmB,CAAC;CAC9B;AAED,MAAM,WAAW,iCAAiC;IAChD,UAAU,EAAE,MAAM,CAAC;IACnB,uCAAuC,CAAC,EAAE,MAAM,CAAC;IACjD,aAAa,EAAE;QACb,iBAAiB,EAAE,MAAM,EAAE,CAAC;QAC5B,+BAA+B,EAAE,MAAM,CAAC;QACxC,cAAc,CAAC,EAAE,MAAM,CAAC;QACxB,mCAAmC,EAAE,OAAO,CAAC;KAC9C,CAAC;IACF,+BAA+B,EAAE,YAAY,CAAC;IAC9C,sCAAsC,EAAE,YAAY,CAAC;IACrD,mCAAmC,EAAE,YAAY,CAAC;IAClD,mCAAmC,EAAE,YAAY,CAAC;IAClD,4BAA4B,EAAE,kBAAkB,CAAC;CAClD"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.js

@@ -5,3 +5,4 @@
  * @module pubmedResearchAgent/logic/outputTypes
  */
 export {};
+//# sourceMappingURL=outputTypes.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"outputTypes.js","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/outputTypes.ts"],"names":[],"mappings":"AAAA;;;;;GAKG"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.d.ts

@@ -8,3 +8,4 @@ import { RequestContext } from "../../../../utils/index.js";
 import type { PubMedResearchAgentInput } from "./inputSchema.js";
 import type { PubMedResearchPlanGeneratedOutput } from "./outputTypes.js";
 export declare function generateFullResearchPlanOutline(input: PubMedResearchAgentInput, parentRequestContext: RequestContext): PubMedResearchPlanGeneratedOutput;
+//# sourceMappingURL=planOrchestrator.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"planOrchestrator.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAEL,cAAc,EAGf,MAAM,4BAA4B,CAAC;AACpC,OAAO,KAAK,EAAE,wBAAwB,EAAE,MAAM,kBAAkB,CAAC;AACjE,OAAO,KAAK,EAYV,iCAAiC,EAClC,MAAM,kBAAkB,CAAC;AAuF1B,wBAAgB,+BAA+B,CAC7C,KAAK,EAAE,wBAAwB,EAC/B,oBAAoB,EAAE,cAAc,GACnC,iCAAiC,CAyVnC"}

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.js

@@ -258,3 +258,4 @@ Key responsibilities:
     };
     return removeEmptyObjectsRecursively(plan);
 }
+//# sourceMappingURL=planOrchestrator.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/pubmedResearchAgent/logic.d.ts

@@ -7,3 +7,4 @@
 import { RequestContext } from "../../../utils/index.js";
 import { PubMedResearchAgentInput, PubMedResearchPlanGeneratedOutput } from "./logic/index.js";
 export declare function pubmedResearchAgentLogic(input: PubMedResearchAgentInput, parentRequestContext: RequestContext): Promise<PubMedResearchPlanGeneratedOutput>;
+//# sourceMappingURL=logic.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"logic.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedResearchAgent/logic.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAEL,cAAc,EAGf,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAEL,wBAAwB,EACxB,iCAAiC,EAClC,MAAM,kBAAkB,CAAC;AAE1B,wBAAsB,wBAAwB,CAC5C,KAAK,EAAE,wBAAwB,EAC/B,oBAAoB,EAAE,cAAc,GACnC,OAAO,CAAC,iCAAiC,CAAC,CAyB5C"}

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

@@ -20,3 +20,4 @@ export async function pubmedResearchAgentLogic(input, parentRequestContext) {
     });
     return researchPlanOutline;
 }
+//# sourceMappingURL=logic.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/logic.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"logic.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedResearchAgent/logic.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EACL,MAAM,EAEN,qBAAqB,EACrB,uBAAuB,GACxB,MAAM,yBAAyB,CAAC;AACjC,OAAO,EACL,+BAA+B,GAGhC,MAAM,kBAAkB,CAAC;AAE1B,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,KAA+B,EAC/B,oBAAoC;IAEpC,MAAM,gBAAgB,GAAG,qBAAqB,CAAC,oBAAoB,CAAC;QAClE,eAAe,EAAE,oBAAoB,CAAC,SAAS;QAC/C,SAAS,EAAE,mCAAmC;QAC9C,KAAK,EAAE,uBAAuB,CAAC,KAAK,CAAC;KACtC,CAAC,CAAC;IAEH,MAAM,CAAC,IAAI,CACT,kFAAkF,KAAK,CAAC,iBAAiB,CAAC,IAAI,CAC5G,IAAI,CACL,EAAE,EACH,gBAAgB,CACjB,CAAC;IAEF,MAAM,mBAAmB,GAAG,+BAA+B,CACzD,KAAK,EACL,gBAAgB,CACjB,CAAC;IAEF,MAAM,CAAC,MAAM,CAAC,+CAA+C,EAAE;QAC7D,GAAG,gBAAgB;QACnB,YAAY,EAAE,KAAK,CAAC,wBAAwB;KAC7C,CAAC,CAAC;IAEH,OAAO,mBAAmB,CAAC;AAC7B,CAAC"}

package/dist/mcp-server/tools/pubmedResearchAgent/registration.d.ts

@@ -8,3 +8,4 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
  * @param server - The McpServer instance.
  */
 export declare function registerPubMedResearchAgentTool(server: McpServer): Promise<void>;
+//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/pubmedResearchAgent/registration.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"registration.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedResearchAgent/registration.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAepE;;;GAGG;AACH,wBAAsB,+BAA+B,CACnD,MAAM,EAAE,SAAS,GAChB,OAAO,CAAC,IAAI,CAAC,CAgFf"}

package/dist/mcp-server/tools/pubmedResearchAgent/registration.js

@@ -70,3 +70,4 @@ export async function registerPubMedResearchAgentTool(server) {
         critical: true,
     });
 }
+//# sourceMappingURL=registration.js.map

package/dist/mcp-server/tools/pubmedResearchAgent/registration.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/pubmedSearchArticles/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Barrel file for the pubmedSearchArticles tool.
+ * Exports the tool's registration function.
+ * @module src/mcp-server/tools/pubmedSearchArticles/index
+ */
+export { registerPubMedSearchArticlesTool } from "./registration.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/pubmedSearchArticles/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedSearchArticles/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,gCAAgC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/pubmedSearchArticles/index.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Barrel file for the pubmedSearchArticles tool.
+ * Exports the tool's registration function.
+ * @module src/mcp-server/tools/pubmedSearchArticles/index
+ */
+export { registerPubMedSearchArticlesTool } from "./registration.js";
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/pubmedSearchArticles/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedSearchArticles/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,gCAAgC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/{searchPubMedArticles → pubmedSearchArticles}/logic.d.ts

@@ -1,13 +1,13 @@
 /**
- * @fileoverview Logic for the searchPubMedArticles MCP tool.
+ * @fileoverview Logic for the pubmed_search_articles MCP tool.
  * Handles constructing ESearch and ESummary queries, interacting with
  * the NcbiService, and formatting the results.
- * @module src/mcp-server/tools/searchPubMedArticles/logic
+ * @module src/mcp-server/tools/pubmedSearchArticles/logic
  */
 import { z } from "zod";
 import { ParsedBriefSummary } from "../../../types-global/pubmedXml.js";
 import { RequestContext } from "../../../utils/index.js";
-export declare const SearchPubMedArticlesInputSchema: z.ZodObject<{
+export declare const PubMedSearchArticlesInputSchema: z.ZodObject<{
     queryTerm: z.ZodString;
     maxResults: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
     sortBy: z.ZodDefault<z.ZodOptional<z.ZodEnum<["relevance", "pub_date", "author", "journal_name"]>>>;
@@ -49,9 +49,9 @@ export declare const SearchPubMedArticlesInputSchema: z.ZodObject<{
     filterByPublicationTypes?: string[] | undefined;
     fetchBriefSummaries?: number | undefined;
 }>;
-export type SearchPubMedArticlesInput = z.infer<typeof SearchPubMedArticlesInputSchema>;
-export type SearchPubMedArticlesOutput = {
-    searchParameters: SearchPubMedArticlesInput;
+export type PubMedSearchArticlesInput = z.infer<typeof PubMedSearchArticlesInputSchema>;
+export type PubMedSearchArticlesOutput = {
+    searchParameters: PubMedSearchArticlesInput;
     effectiveESearchTerm: string;
     totalFound: number;
     retrievedPmidCount: number;
@@ -60,4 +60,5 @@ export type SearchPubMedArticlesOutput = {
     eSearchUrl: string;
     eSummaryUrl?: string;
 };
-export declare function searchPubMedArticlesLogic(input: SearchPubMedArticlesInput, parentRequestContext: RequestContext): Promise<SearchPubMedArticlesOutput>;
+export declare function pubmedSearchArticlesLogic(input: PubMedSearchArticlesInput, parentRequestContext: RequestContext): Promise<PubMedSearchArticlesOutput>;
+//# sourceMappingURL=logic.d.ts.map

package/dist/mcp-server/tools/pubmedSearchArticles/logic.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/{searchPubMedArticles → pubmedSearchArticles}/logic.js

@@ -1,8 +1,8 @@
 /**
- * @fileoverview Logic for the searchPubMedArticles MCP tool.
+ * @fileoverview Logic for the pubmed_search_articles MCP tool.
  * Handles constructing ESearch and ESummary queries, interacting with
  * the NcbiService, and formatting the results.
- * @module src/mcp-server/tools/searchPubMedArticles/logic
+ * @module src/mcp-server/tools/pubmedSearchArticles/logic
  */
 import { z } from "zod";
 import { getNcbiService } from "../../../services/NCBI/core/ncbiService.js";
@@ -10,7 +10,7 @@ import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
 import { extractBriefSummaries } from "../../../services/NCBI/parsing/index.js";
 import { sanitization } from "../../../utils/security/sanitization.js";
-export const SearchPubMedArticlesInputSchema = z.object({
+export const PubMedSearchArticlesInputSchema = z.object({
     queryTerm: z
         .string()
         .min(3, "Query term must be at least 3 characters")
@@ -27,7 +27,7 @@ export const SearchPubMedArticlesInputSchema = z.object({
         .enum(["relevance", "pub_date", "author", "journal_name"])
         .optional()
         .default("relevance")
-        .describe("Sorting criteria for results. Options: 'relevance' (default), 'pub_date', 'author', 'journal_name'. Note: Other sorting (e.g., last_author, title) may require client-side implementation or be future server enhancements."),
+        .describe("Sorting criteria for results. Options: 'relevance' (default), 'pub_date', 'author', 'journal_name'."),
     dateRange: z
         .object({
         minDate: z
@@ -47,11 +47,11 @@ export const SearchPubMedArticlesInputSchema = z.object({
             .describe("The type of date to filter by: 'pdat' (Publication Date), 'mdat' (Modification Date), 'edat' (Entrez Date). Default is 'pdat'."),
     })
         .optional()
-        .describe("Defines an optional date range for the search, including min/max dates and the type of date field to use."),
+        .describe("Defines an optional date range for the search."),
     filterByPublicationTypes: z
         .array(z.string())
         .optional()
-        .describe('An array of publication types to filter by (e.g., ["Review", "Clinical Trial"]). The server maps these to the appropriate Entrez query syntax (e.g., "Review"[Publication Type]).'),
+        .describe('An array of publication types to filter by (e.g., ["Review", "Clinical Trial"]).'),
     fetchBriefSummaries: z
         .number()
         .int()
@@ -59,16 +59,16 @@ export const SearchPubMedArticlesInputSchema = z.object({
         .max(50)
         .optional()
         .default(0)
-        .describe("Number of top PMIDs for which to fetch brief summaries using ESummary v2.0. Set to 0 to disable. Maximum is 50 for this tool. Default is 0."),
+        .describe("Number of top PMIDs for which to fetch brief summaries using ESummary. Set to 0 to disable. Max 50. Default 0."),
 });
-export async function searchPubMedArticlesLogic(input, parentRequestContext) {
+export async function pubmedSearchArticlesLogic(input, parentRequestContext) {
     const ncbiService = getNcbiService();
     const toolLogicContext = requestContextService.createRequestContext({
         parentRequestId: parentRequestContext.requestId,
-        operation: "searchPubMedArticlesLogic",
+        operation: "pubmedSearchArticlesLogic",
         input: sanitizeInputForLogging(input),
     });
-    logger.info("Executing searchPubMedArticles tool", toolLogicContext);
+    logger.info("Executing pubmed_search_articles tool", toolLogicContext);
     let effectiveQuery = sanitization.sanitizeString(input.queryTerm, {
         context: "text",
     });
@@ -157,7 +157,7 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
             });
         }
     }
-    logger.notice("Successfully executed searchPubMedArticles tool.", {
+    logger.notice("Successfully executed pubmed_search_articles tool.", {
         ...toolLogicContext,
         totalFound,
         retrievedPmidCount,
@@ -174,3 +174,4 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
         eSummaryUrl,
     };
 }
+//# sourceMappingURL=logic.js.map

package/dist/mcp-server/tools/pubmedSearchArticles/logic.js.map

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package/dist/mcp-server/tools/pubmedSearchArticles/registration.d.ts

@@ -0,0 +1,11 @@
+/**
+ * @fileoverview Registration for the pubmed_search_articles MCP tool.
+ * @module src/mcp-server/tools/pubmedSearchArticles/registration
+ */
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+/**
+ * Registers the pubmed_search_articles tool with the MCP server.
+ * @param server - The McpServer instance.
+ */
+export declare function registerPubMedSearchArticlesTool(server: McpServer): Promise<void>;
+//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/pubmedSearchArticles/registration.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/{searchPubMedArticles → pubmedSearchArticles}/registration.js

@@ -1,29 +1,29 @@
 /**
- * @fileoverview Registration for the searchPubMedArticles MCP tool.
- * @module src/mcp-server/tools/searchPubMedArticles/registration
+ * @fileoverview Registration for the pubmed_search_articles MCP tool.
+ * @module src/mcp-server/tools/pubmedSearchArticles/registration
  */
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
-import { SearchPubMedArticlesInputSchema, searchPubMedArticlesLogic, } from "./logic.js";
+import { PubMedSearchArticlesInputSchema, pubmedSearchArticlesLogic, } from "./logic.js";
 /**
- * Registers the searchPubMedArticles tool with the MCP server.
+ * Registers the pubmed_search_articles tool with the MCP server.
  * @param server - The McpServer instance.
  */
-export async function registerSearchPubMedArticlesTool(server) {
-    const operation = "registerSearchPubMedArticlesTool";
-    const toolName = "search_pubmed_articles";
-    const toolDescription = "Searches PubMed for articles using a query term and optional filters (max results, sort, date range, publication types). Uses NCBI ESearch to find PMIDs and ESummary (optional) for brief summaries. Returns a JSON object with search parameters, ESearch term, result counts, PMIDs, optional summaries (PMID, title, authors, source, dates), and E-utility URLs.";
+export async function registerPubMedSearchArticlesTool(server) {
+    const operation = "registerPubMedSearchArticlesTool";
+    const toolName = "pubmed_search_articles";
+    const toolDescription = "Searches PubMed for articles using a query term and optional filters (max results, sort, date range, publication types). Uses NCBI ESearch to find PMIDs and ESummary (optional) for brief summaries. Returns a JSON object with search parameters, ESearch term, result counts, PMIDs, optional summaries, and E-utility URLs.";
     const context = requestContextService.createRequestContext({ operation });
     await ErrorHandler.tryCatch(async () => {
-        server.tool(toolName, toolDescription, SearchPubMedArticlesInputSchema.shape, async (input, mcpProvidedContext) => {
+        server.tool(toolName, toolDescription, PubMedSearchArticlesInputSchema.shape, async (input, mcpProvidedContext) => {
             const richContext = requestContextService.createRequestContext({
                 parentRequestId: context.requestId,
-                operation: "searchPubMedArticlesToolHandler",
+                operation: "pubmedSearchArticlesToolHandler",
                 mcpToolContext: mcpProvidedContext,
                 input,
             });
             try {
-                const result = await searchPubMedArticlesLogic(input, richContext);
+                const result = await pubmedSearchArticlesLogic(input, richContext);
                 return {
                     content: [
                         { type: "text", text: JSON.stringify(result, null, 2) },
@@ -33,7 +33,7 @@ export async function registerSearchPubMedArticlesTool(server) {
             }
             catch (error) {
                 const handledError = ErrorHandler.handleError(error, {
-                    operation: "searchPubMedArticlesToolHandler",
+                    operation: "pubmedSearchArticlesToolHandler",
                     context: richContext,
                     input,
                     rethrow: false,
@@ -69,3 +69,4 @@ export async function registerSearchPubMedArticlesTool(server) {
         critical: true,
     });
 }
+//# sourceMappingURL=registration.js.map

package/dist/mcp-server/tools/pubmedSearchArticles/registration.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"registration.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedSearchArticles/registration.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,iCAAiC,CAAC;AAC1E,OAAO,EACL,YAAY,EACZ,MAAM,EAEN,qBAAqB,GACtB,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAEL,+BAA+B,EAC/B,yBAAyB,GAC1B,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,gCAAgC,CACpD,MAAiB;IAEjB,MAAM,SAAS,GAAG,kCAAkC,CAAC;IACrD,MAAM,QAAQ,GAAG,wBAAwB,CAAC;IAC1C,MAAM,eAAe,GACnB,iUAAiU,CAAC;IACpU,MAAM,OAAO,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC;IAE1E,MAAM,YAAY,CAAC,QAAQ,CACzB,KAAK,IAAI,EAAE;QACT,MAAM,CAAC,IAAI,CACT,QAAQ,EACR,eAAe,EACf,+BAA+B,CAAC,KAAK,EACrC,KAAK,EACH,KAAgC,EAChC,kBAAuB,EACE,EAAE;YAC3B,MAAM,WAAW,GACf,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,eAAe,EAAE,OAAO,CAAC,SAAS;gBAClC,SAAS,EAAE,iCAAiC;gBAC5C,cAAc,EAAE,kBAAkB;gBAClC,KAAK;aACN,CAAC,CAAC;YAEL,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,yBAAyB,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;gBACnE,OAAO;oBACL,OAAO,EAAE;wBACP,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;qBACxD;oBACD,OAAO,EAAE,KAAK;iBACf,CAAC;YACJ,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,YAAY,GAAG,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE;oBACnD,SAAS,EAAE,iCAAiC;oBAC5C,OAAO,EAAE,WAAW;oBACpB,KAAK;oBACL,OAAO,EAAE,KAAK;iBACf,CAAC,CAAC;gBAEH,MAAM,QAAQ,GACZ,YAAY,YAAY,QAAQ;oBAC9B,CAAC,CAAC,YAAY;oBACd,CAAC,CAAC,IAAI,QAAQ,CACV,aAAa,CAAC,cAAc,EAC5B,+DAA+D,EAC/D;wBACE,iBAAiB,EAAE,YAAY,CAAC,IAAI;wBACpC,oBAAoB,EAAE,YAAY,CAAC,OAAO;qBAC3C,CACF,CAAC;gBAER,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,MAAM;4BACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gCACnB,KAAK,EAAE;oCACL,IAAI,EAAE,QAAQ,CAAC,IAAI;oCACnB,OAAO,EAAE,QAAQ,CAAC,OAAO;oCACzB,OAAO,EAAE,QAAQ,CAAC,OAAO;iCAC1B;6BACF,CAAC;yBACH;qBACF;oBACD,OAAO,EAAE,IAAI;iBACd,CAAC;YACJ,CAAC;QACH,CAAC,CACF,CAAC;QACF,MAAM,CAAC,MAAM,CAAC,SAAS,QAAQ,eAAe,EAAE,OAAO,CAAC,CAAC;IAC3D,CAAC,EACD;QACE,SAAS;QACT,OAAO;QACP,SAAS,EAAE,aAAa,CAAC,qBAAqB;QAC9C,QAAQ,EAAE,IAAI;KACf,CACF,CAAC;AACJ,CAAC"}

package/dist/mcp-server/transports/auth/authFactory.d.ts

@@ -8,3 +8,4 @@ import { AuthStrategy } from "./strategies/authStrategy.js";
  * @throws {Error} If the auth mode is unknown or misconfigured.
  */
 export declare function createAuthStrategy(): AuthStrategy | null;
+//# sourceMappingURL=authFactory.d.ts.map