@cyanheads/pubmed-mcp-server 1.0.13 → 1.0.14

package/README.md

@@ -3,7 +3,7 @@
 [![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg)](https://www.typescriptlang.org/)
 [![Model Context Protocol SDK](https://img.shields.io/badge/MCP%20SDK-1.12.0-green.svg)](https://github.com/modelcontextprotocol/typescript-sdk)
 [![MCP Spec Version](https://img.shields.io/badge/MCP%20Spec-2025--03--26-lightgrey.svg)](https://github.com/modelcontextprotocol/modelcontextprotocol/blob/main/docs/specification/2025-03-26/changelog.mdx)
-[![Version](https://img.shields.io/badge/Version-1.0.13-blue.svg)](./CHANGELOG.md)
+[![Version](https://img.shields.io/badge/Version-1.0.14-blue.svg)](./CHANGELOG.md)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 [![Status](https://img.shields.io/badge/Status-Beta-orange.svg)](https://github.com/cyanheads/pubmed-mcp-server/issues)
 [![GitHub](https://img.shields.io/github/stars/cyanheads/pubmed-mcp-server?style=social)](https://github.com/cyanheads/pubmed-mcp-server)

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

@@ -6,71 +6,73 @@ import { logger, requestContextService, sanitizeInputForLogging, } from "../../.
 export const GeneratePubMedChartInputSchema = z.object({
     chartType: z
         .enum(["bar", "line", "scatter"])
-        .describe("Type of chart to generate (e.g., 'bar', 'line', 'scatter')."),
-    title: z.string().optional().describe("Title for the chart."),
+        .describe("Required. Specifies the type of chart to generate. Options: 'bar', 'line', 'scatter'."),
+    title: z
+        .string()
+        .optional()
+        .describe("Optional. The main title displayed above the chart. If omitted, no title is shown."),
     width: z
         .number()
         .int()
         .positive()
         .optional()
         .default(400)
-        .describe("Width of the chart in pixels."),
+        .describe("Optional. The width of the chart canvas in pixels. Must be a positive integer. Default: 400."),
     height: z
         .number()
         .int()
         .positive()
         .optional()
         .default(300)
-        .describe("Height of the chart in pixels."),
+        .describe("Optional. The height of the chart canvas in pixels. Must be a positive integer. Default: 300."),
     dataValues: z
         .array(z.record(z.string(), z.any()))
         .min(1)
-        .describe("Array of data objects to plot. Each object is a record (e.g., { category: 'A', amount: 28 })."),
+        .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."),
     outputFormat: z
         .enum(["svg"])
         .default("svg")
-        .describe("Specifies the desired output format for the generated chart. " +
-        "Currently, only 'svg' (Scalable Vector Graphics) is supported."),
+        .describe("Specifies the output format for the chart. Currently, only 'svg' (Scalable Vector Graphics) is supported and is the default."),
     xField: z
         .string()
-        .describe("Field name for the X-axis (e.g., 'category', 'date', 'metric1')."),
+        .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')."),
     yField: z
         .string()
-        .describe("Field name for the Y-axis (e.g., 'amount', 'value', 'metric2')."),
+        .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')."),
     xFieldType: z
         .enum(["nominal", "ordinal", "quantitative", "temporal"])
         .optional()
-        .describe("Type of the X-axis field. Defaults appropriately for chart type if omitted (e.g., 'nominal' for bar, 'temporal' for line, 'quantitative' for scatter)."),
+        .describe("Optional. Specifies the data type of the X-axis field. Options: 'nominal' (categories), 'ordinal' (ordered categories), 'quantitative' (numerical), 'temporal' (dates/times). If omitted, a suitable default is chosen based on `chartType` (e.g., 'nominal' for bar charts, 'temporal' for line charts, 'quantitative' for scatter plots)."),
     yFieldType: z
         .enum(["nominal", "ordinal", "quantitative", "temporal"])
         .optional()
-        .describe("Type of the Y-axis field. Defaults to 'quantitative' if omitted."),
+        .describe("Optional. Specifies the data type of the Y-axis field. Options: 'nominal', 'ordinal', 'quantitative', 'temporal'. Defaults to 'quantitative' if omitted."),
     // Optional fields for various chart types
     colorField: z
         .string()
         .optional()
-        .describe("Optional field name for color encoding."),
+        .describe("Optional. The name of the field in `dataValues` to use for color encoding. This can differentiate bars, lines, or points by color based on the values in this field (e.g., 'studyType', 'country')."),
     colorFieldType: z
         .enum(["nominal", "ordinal", "quantitative", "temporal"])
         .optional()
-        .describe("Type of the color field if provided. Defaults to 'nominal'."),
+        .describe("Optional. Specifies the data type of the `colorField`. Options: 'nominal', 'ordinal', 'quantitative', 'temporal'. Defaults to 'nominal' if `colorField` is provided and this is omitted."),
     seriesField: z
         .string()
         .optional()
-        .describe("Optional field name for creating multiple lines/series (typically for line charts)."),
+        .describe("Optional. Primarily for line charts. The name of the field in `dataValues` used to create multiple distinct lines (series) on the same chart. Each unique value in this field will correspond to a separate line (e.g., 'drugName' to plot different drug efficacy trends). Often used with `colorField` implicitly or explicitly."),
     seriesFieldType: z
         .enum(["nominal", "ordinal", "quantitative", "temporal"])
         .optional()
-        .describe("Type of the series field if provided. Defaults to 'nominal'."),
+        .describe("Optional. Specifies the data type of the `seriesField`. Options: 'nominal', 'ordinal', 'quantitative', 'temporal'. Defaults to 'nominal' if `seriesField` is provided and this is omitted."),
     // Scatter plot specific optional fields (can be expanded)
     sizeField: z
         .string()
         .optional()
-        .describe("Optional field for encoding point size in scatter plots."),
+        .describe("Optional. For scatter plots. The name of the field in `dataValues` to use for encoding the size of the points. Larger values in this field will result in larger points on the scatter plot (e.g., 'sampleSize', 'effectMagnitude')."),
     sizeFieldType: z
         .enum(["quantitative", "ordinal"])
         .optional()
-        .describe("Type of the size field. Defaults to 'quantitative'."),
+        .describe("Optional. Specifies the data type of the `sizeField`. Options: 'quantitative', 'ordinal'. Defaults to 'quantitative' if `sizeField` is provided and this is omitted."),
     // shapeField: z.string().optional().describe("Optional field for encoding point shape in scatter plots."), // Future enhancement
     // shapeFieldType: z.enum(["nominal", "ordinal"]).optional().describe("Type of the shape field."), // Future enhancement
 });

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

@@ -5,10 +5,11 @@ export function registerGeneratePubMedChartTool(server) {
     const operation = "registerGeneratePubMedChartTool";
     const regContext = requestContextService.createRequestContext({ operation });
     try {
-        server.tool("generate_pubmed_chart", "Generates a chart image (SVG) from given input. " +
-            "Supports different chart types like 'bar', 'line', and 'scatter'. " +
-            "Provide data values and specify fields for axes and encoding. " +
-            "The tool constructs a Vega-Lite specification internally and renders it as an SVG.", GeneratePubMedChartInputSchema.shape, async (validatedInput, mcpProvidedContext) => {
+        server.tool("generate_pubmed_chart", "Generates a customizable chart (SVG) from structured data. " +
+            "Supports 'bar', 'line', and 'scatter' plots. " +
+            "Requires data values and field mappings for axes. " +
+            "Optional parameters allow for titles, dimensions, and color/size/series encoding. " +
+            "Internally uses Vega-Lite to produce an SVG image.", GeneratePubMedChartInputSchema.shape, async (validatedInput, mcpProvidedContext) => {
             const handlerRequestContext = requestContextService.createRequestContext({
                 parentRequestId: regContext.requestId,
                 operation: "generatePubMedChartToolHandler",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.0.13",
+  "version": "1.0.14",
   "description": "A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Built on the mcp-ts-template for robust, production-ready performance.",
   "main": "dist/index.js",
   "files": [