npm - @cyanheads/pubmed-mcp-server - Versions diffs - 1.3.5 → 1.4.3 - Mend

@cyanheads/pubmed-mcp-server 1.3.5 → 1.4.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (221) hide show

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/index.d.ts RENAMED Viewed

@@ -1,8 +1,8 @@
 /**
- * @fileoverview Barrel export for the 'generatePubMedChart' tool.
+ * @fileoverview Barrel export for the 'pubmed_generate_chart' tool.
  * This file re-exports the registration function for the tool,
  * making it easier to import and register with the MCP server.
- * @module src/mcp-server/tools/generatePubMedChart/index
+ * @module src/mcp-server/tools/pubmedGenerateChart/index
  */
 export * from "./registration.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/pubmedGenerateChart/index.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedGenerateChart/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,cAAc,mBAAmB,CAAC"}

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/index.js RENAMED Viewed

@@ -1,8 +1,8 @@
 /**
- * @fileoverview Barrel export for the 'generatePubMedChart' tool.
+ * @fileoverview Barrel export for the 'pubmed_generate_chart' tool.
  * This file re-exports the registration function for the tool,
  * making it easier to import and register with the MCP server.
- * @module src/mcp-server/tools/generatePubMedChart/index
+ * @module src/mcp-server/tools/pubmedGenerateChart/index
  */
 export * from "./registration.js";
 //# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/pubmedGenerateChart/index.js.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedGenerateChart/index.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,cAAc,mBAAmB,CAAC"}

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/logic.d.ts RENAMED Viewed

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import { RequestContext } from "../../../utils/index.js";
-export declare const GeneratePubMedChartInputSchema: z.ZodObject<{
+export declare const PubMedGenerateChartInputSchema: z.ZodObject<{
     chartType: z.ZodEnum<["bar", "line", "scatter", "pie", "doughnut", "bubble", "radar", "polarArea"]>;
     title: z.ZodOptional<z.ZodString>;
     width: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
@@ -34,11 +34,11 @@ export declare const GeneratePubMedChartInputSchema: z.ZodObject<{
     seriesField?: string | undefined;
     sizeField?: string | undefined;
 }>;
-export type GeneratePubMedChartInput = z.infer<typeof GeneratePubMedChartInputSchema>;
-export type GeneratePubMedChartOutput = {
+export type PubMedGenerateChartInput = z.infer<typeof PubMedGenerateChartInputSchema>;
+export type PubMedGenerateChartOutput = {
     base64Data: string;
     chartType: string;
     dataPoints: number;
 };
-export declare function generatePubMedChartLogic(input: GeneratePubMedChartInput, parentRequestContext: RequestContext): Promise<GeneratePubMedChartOutput>;
+export declare function pubmedGenerateChartLogic(input: PubMedGenerateChartInput, parentRequestContext: RequestContext): Promise<PubMedGenerateChartOutput>;
 //# sourceMappingURL=logic.d.ts.map

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/logic.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/logic.js RENAMED Viewed

@@ -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,
@@ -84,7 +84,9 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
             ChartJS.defaults.maintainAspectRatio = false;
         },
     });
-    const labels = [...new Set(dataValues.map((item) => item[xField]))];
+    const labels = [
+        ...new Set(dataValues.map((item) => item[xField])),
+    ];
     let datasets;
     if (seriesField) {
         const groupedData = groupDataBySeries(dataValues, xField, yField, seriesField);
@@ -94,7 +96,6 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                 const point = data.find((p) => p.x === label);
                 return point ? point.y : null;
             }),
-            // You can add backgroundColor, borderColor etc. here for styling
         }));
     }
     else {
@@ -130,7 +131,9 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                     data: dataValues.map((item) => ({
                         x: item[xField],
                         y: item[yField],
-                        r: chartType === "bubble" && sizeField ? item[sizeField] : undefined,
+                        r: chartType === "bubble" && sizeField
+                            ? item[sizeField]
+                            : undefined,
                     })),
                 },
             ];
@@ -184,10 +187,11 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         };
     }
     catch (error) {
-        throw new McpError(BaseErrorCode.INTERNAL_ERROR, `Chart generation failed: ${error.message || "Internal server error during chart generation."}`, {
+        const err = error;
+        throw new McpError(BaseErrorCode.INTERNAL_ERROR, `Chart generation failed: ${err.message || "Internal server error during chart generation."}`, {
             ...operationContext,
-            originalErrorName: error.name,
-            originalErrorMessage: error.message,
+            originalErrorName: err.name,
+            originalErrorMessage: err.message,
         });
     }
 }

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

@@ -0,0 +1 @@

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

@@ -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/{generatePubMedChart → pubmedGenerateChart}/registration.d.ts.map RENAMED Viewed

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

package/dist/mcp-server/tools/{generatePubMedChart → pubmedGenerateChart}/registration.js RENAMED Viewed

@@ -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,

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

@@ -0,0 +1 @@

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

	@@ -1 +1 @@
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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;AA4F1B,wBAAgB,+BAA+B,CAC7C,KAAK,EAAE,wBAAwB,EAC/B,oBAAoB,EAAE,cAAc,GACnC,iCAAiC,CA2VnC"}

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

@@ -35,7 +35,9 @@ function removeEmptyObjectsRecursively(obj) {
     }
     if (Array.isArray(obj)) {
         // If it's an array, recurse on each element and filter out empty objects/arrays
-        const newArr = obj.map(removeEmptyObjectsRecursively).filter((item) => {
+        const newArr = obj
+            .map(removeEmptyObjectsRecursively)
+            .filter((item) => {
             if (item === null || item === undefined)
                 return false;
             if (Array.isArray(item) && item.length === 0)
@@ -51,9 +53,10 @@ function removeEmptyObjectsRecursively(obj) {
     }
     // If it's an object, create a new object with non-empty properties
     const newObj = {};
-    for (const key in obj) {
-        if (Object.prototype.hasOwnProperty.call(obj, key)) {
-            const value = removeEmptyObjectsRecursively(obj[key]);
+    const objAsRecord = obj;
+    for (const key in objAsRecord) {
+        if (Object.prototype.hasOwnProperty.call(objAsRecord, key)) {
+            const value = removeEmptyObjectsRecursively(objAsRecord[key]);
             // Skip null or undefined values
             if (value === null || value === undefined) {
                 continue;

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/pubmedResearchAgent/registration.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/pubmedSearchArticles/index.d.ts ADDED Viewed

@@ -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/{searchPubMedArticles → pubmedSearchArticles}/index.d.ts.map RENAMED Viewed

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

@@ -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/{searchPubMedArticles → pubmedSearchArticles}/index.js.map RENAMED Viewed

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

@@ -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"]>>>;
@@ -29,7 +29,7 @@ export declare const SearchPubMedArticlesInputSchema: z.ZodObject<{
 }, "strip", z.ZodTypeAny, {
     queryTerm: string;
     maxResults: number;
-    sortBy: "relevance" | "pub_date" | "author" | "journal_name";
+    sortBy: "author" | "relevance" | "pub_date" | "journal_name";
     fetchBriefSummaries: number;
     dateRange?: {
         dateType: "pdat" | "mdat" | "edat";
@@ -40,7 +40,7 @@ export declare const SearchPubMedArticlesInputSchema: z.ZodObject<{
 }, {
     queryTerm: string;
     maxResults?: number | undefined;
-    sortBy?: "relevance" | "pub_date" | "author" | "journal_name" | undefined;
+    sortBy?: "author" | "relevance" | "pub_date" | "journal_name" | undefined;
     dateRange?: {
         minDate?: string | undefined;
         maxDate?: string | undefined;
@@ -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;
@@ -60,5 +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/{searchPubMedArticles → pubmedSearchArticles}/logic.d.ts.map RENAMED Viewed

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

@@ -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",
     });
@@ -146,18 +146,20 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
         }
         const eSummaryQueryString = new URLSearchParams(eSummaryQueryStringParams).toString();
         eSummaryUrl = `${eSummaryBase}?${eSummaryQueryString}`;
-        const eSummaryResponseXml = await ncbiService.eSummary(eSummaryParams, toolLogicContext);
+        const eSummaryResponseXml = (await ncbiService.eSummary(eSummaryParams, toolLogicContext));
         if (eSummaryResponseXml && eSummaryResponseXml.eSummaryResult) {
             briefSummaries = await extractBriefSummaries(eSummaryResponseXml.eSummaryResult, toolLogicContext);
         }
-        else if (eSummaryResponseXml && eSummaryResponseXml.ERROR) {
+        else if (eSummaryResponseXml &&
+            eSummaryResponseXml.eSummaryResult?.ERROR) {
             logger.warning("ESummary returned a top-level error", {
                 ...toolLogicContext,
-                errorDetails: eSummaryResponseXml.ERROR,
+                errorDetails: eSummaryResponseXml
+                    .eSummaryResult?.ERROR,
             });
         }
     }
-    logger.notice("Successfully executed searchPubMedArticles tool.", {
+    logger.notice("Successfully executed pubmed_search_articles tool.", {
         ...toolLogicContext,
         totalFound,
         retrievedPmidCount,

package/dist/mcp-server/tools/{searchPubMedArticles → pubmedSearchArticles}/logic.js.map RENAMED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/mcp-server/tools/pubmedSearchArticles/registration.d.ts ADDED Viewed

@@ -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/{searchPubMedArticles → pubmedSearchArticles}/registration.d.ts.map RENAMED Viewed

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