@yeyuan98/opencode-bioresearcher-plugin 1.6.0 → 1.6.4

package/dist/tools/db/tools.js

@@ -29,7 +29,8 @@ export const dbQuery = tool({
         sql: z.string().describe('SELECT SQL query to execute. Use named placeholders like :name for parameters.'),
         params: z.record(z.string(), z.any()).optional().describe('Named parameters as key-value pairs (e.g., { "status": "active", "limit": 10 })'),
     },
-    execute: async (args, _context) => {
+    execute: async (args, context) => {
+        await context.ask({ permission: "dbQuery", patterns: ["*"], always: ["*"], metadata: {} });
         try {
             const backend = await getOrCreateBackend();
             const validation = validateReadOnlyQuery(args.sql, backend.type);
@@ -59,7 +60,8 @@ export const dbListTables = tool({
 
 **Usage:** Call this first to discover what tables are available before using dbDescribeTable or dbQuery.`,
     args: {},
-    execute: async (_args, _context) => {
+    execute: async (args, context) => {
+        await context.ask({ permission: "dbListTables", patterns: ["*"], always: ["*"], metadata: {} });
         try {
             const backend = await getOrCreateBackend();
             const collections = await backend.listCollections();
@@ -90,7 +92,8 @@ export const dbDescribeTable = tool({
     args: {
         table_name: z.string().describe('Name of the table/collection to describe. Use dbListTables to see available tables.'),
     },
-    execute: async (args, _context) => {
+    execute: async (args, context) => {
+        await context.ask({ permission: "dbDescribeTable", patterns: ["*"], always: ["*"], metadata: {} });
         try {
             const backend = await getOrCreateBackend();
             const validation = validateCollectionName(args.table_name, backend.type);

package/dist/tools/misc/calculator.js

@@ -105,6 +105,7 @@ export const calculator = tool({
             .describe("Decimal places for result (0-15, default 3)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "calculator", patterns: ["*"], always: ["*"], metadata: {} });
         const validation = validateFormula(args.formula);
         if (!validation.valid) {
             return validation.error;

package/dist/tools/misc/json-extract.js

@@ -253,6 +253,7 @@ export const jsonExtract = tool({
         return_all: z.boolean().default(false).describe("If true, returns all JSON objects found as array; if false (default), returns first only")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "jsonExtract", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = path.isAbsolute(args.file_path)
                 ? args.file_path

package/dist/tools/misc/json-infer.js

@@ -145,6 +145,7 @@ export const jsonInfer = tool({
         strict: z.boolean().default(false).describe("If true, all fields are required; if false (default), fields are optional")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "jsonInfer", patterns: ["*"], always: ["*"], metadata: {} });
         let parsedData;
         try {
             parsedData = JSON.parse(args.data);

package/dist/tools/misc/json-validate.js

@@ -200,6 +200,7 @@ export const jsonValidate = tool({
         schema: z.string().describe("JSON Schema string or file path (auto-reads from file if path detected)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "jsonValidate", patterns: ["*"], always: ["*"], metadata: {} });
         let parsedData;
         let parsedSchema;
         let schemaString = args.schema;

package/dist/tools/misc/timer.js

@@ -8,6 +8,7 @@ export const blockingTimer = tool({
             .describe("Delay time in seconds (max 300 seconds)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "blockingTimer", patterns: ["*"], always: ["*"], metadata: {} });
         const MAX_DELAY = 300;
         if (args.delay > MAX_DELAY) {
             return 'Blocking timer must NOT exceed 300 seconds. DO YOU REALLY NEED THIS LONG WAIT?';

package/dist/tools/parser/obo/obo.js

@@ -165,6 +165,7 @@ export const parse_obo_file = tool({
             .describe('Enable verbose logging for debugging')
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "parse_obo_file", patterns: [args.filePath], always: ["*"], metadata: {} });
         const verbose = args.verbose ?? false;
         try {
             const { filePath, outputFileName = 'obo_output.csv', outputDir } = args;

package/dist/tools/parser/pubmed/pubmed.js

@@ -174,6 +174,7 @@ export const parse_pubmed_articleSet = tool({
             .describe('Enable verbose logging for debugging')
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "parse_pubmed_articleSet", patterns: [args.filePath], always: ["*"], metadata: {} });
         try {
             const { filePath, outputMode = 'single', outputFileName, outputDir, verbose = false } = args;
             if (verbose)

package/dist/tools/table/tools.js

@@ -9,6 +9,7 @@ export const tableGetSheetPreview = tool({
         sheet_name: z.string().optional().describe("Worksheet name (optional, uses first sheet by default)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableGetSheetPreview", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -32,6 +33,7 @@ export const tableListSheets = tool({
         file_path: z.string().describe("Path to table file (supports .xlsx, .ods, .csv formats)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableListSheets", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -49,6 +51,7 @@ export const tableGetHeaders = tool({
         sheet_name: z.string().optional().describe("Worksheet name (optional, uses first sheet by default)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableGetHeaders", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -74,6 +77,7 @@ export const tableGetCell = tool({
         cell_address: z.string().describe("Cell address (e.g., 'A1', 'B5')")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableGetCell", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -103,6 +107,7 @@ export const tableFilterRows = tool({
         max_results: z.number().default(100).describe("Maximum number of results to return")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableFilterRows", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -150,6 +155,7 @@ export const tableSearch = tool({
         max_results: z.number().default(50).describe("Maximum number of results to return")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableSearch", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -192,6 +198,7 @@ export const tableGetRange = tool({
         range: z.string().describe("Cell range (e.g., 'A1:C10', 'A1:B20')")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableGetRange", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -228,6 +235,7 @@ export const tableSummarize = tool({
         columns: z.array(z.string()).optional().describe("Specific columns to summarize (empty = all numeric columns)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableSummarize", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -268,6 +276,7 @@ export const tableGroupBy = tool({
         agg_type: z.enum(['sum', 'count', 'avg', 'min', 'max']).default('sum').describe("Aggregation type")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableGroupBy", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -331,6 +340,7 @@ export const tablePivotSummary = tool({
         agg: z.enum(['sum', 'count', 'avg', 'min', 'max']).default('sum').describe("Aggregation type")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tablePivotSummary", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -411,6 +421,7 @@ export const tableAppendRows = tool({
         rows: z.array(z.union([z.array(z.any()), z.record(z.string(), z.any())])).describe("Rows to append (array of arrays or array of objects)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableAppendRows", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -452,6 +463,7 @@ export const tableUpdateCell = tool({
         value: z.any().describe("Value to set")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableUpdateCell", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.readFile(resolvedPath);
@@ -516,6 +528,7 @@ export const tableCreateFile = tool({
         data: z.any().describe("Data to write (array of arrays or array of objects)")
     },
     execute: async (args, context) => {
+        await context.ask({ permission: "tableCreateFile", patterns: [args.file_path], always: ["*"], metadata: {} });
         try {
             const resolvedPath = resolvePath(args.file_path, context.directory);
             const workbook = XLSX.utils.book_new();

package/dist/version.d.ts

@@ -0,0 +1 @@
+export declare const PLUGIN_VERSION = "1.6.4";

package/dist/version.js

@@ -0,0 +1 @@
+export const PLUGIN_VERSION = "1.6.4";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@yeyuan98/opencode-bioresearcher-plugin",
-  "version": "1.6.0",
+  "version": "1.6.4",
   "description": "OpenCode plugin that adds a bioresearcher agent",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -12,6 +12,7 @@
     }
   },
   "scripts": {
+    "prebuild": "node -e \"const p=require('./package.json');require('fs').writeFileSync('src/version.ts','export const PLUGIN_VERSION = \\\"'+p.version+'\\\"\\n')\"",
     "build": "tsc && node -e \"const fs=require('fs');fs.rmSync('dist/skills',{recursive:true,force:true});fs.cpSync('skills','dist/skills',{recursive:true})\"",
     "typecheck": "tsc --noEmit"
   },
@@ -31,7 +32,6 @@
   ],
   "dependencies": {
     "@opencode-ai/plugin": "^1.14.0",
-    "effect": "4.0.0-beta.48",
     "fast-xml-parser": "^5.3.5",
     "mongodb": "^7.1.0",
     "mysql2": "^3.18.2",