Improve binary file handling (#187)

* Additional changes and experiments for docker

* Fix comment

* Detect binnary file read and redirect to processing

* Add test

* Remove docker files

Author: wonderwhy-er

docker-mcp.yaml

@@ -71,6 +71,7 @@
     "cross-fetch": "^4.1.0",
     "fastest-levenshtein": "^1.0.16",
     "glob": "^10.3.10",
+    "isbinaryfile": "^5.0.4",
     "zod": "^3.24.1",
     "zod-to-json-schema": "^3.23.5"
   },

package-lock.json

@@ -414,6 +414,9 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
                         • start_process("wc -l /path/file.csv") → Line counting
                         • start_process("head -10 /path/file.csv") → File preview
                         
+                        BINARY FILE SUPPORT:
+                        For PDF, Excel, Word, archives, databases, and other binary formats, use process tools with appropriate libraries or command-line utilities.
+                        
                         INTERACTIVE PROCESSES FOR DATA ANALYSIS:
                         1. start_process("python3 -i") - Start Python REPL for data work
                         2. start_process("node -i") - Start Node.js REPL for JSON/JS
@@ -487,6 +490,9 @@ server.setRequestHandler(ListToolsRequestSchema, async () => {
                         4. Analyze: interact_with_process(pid, "print(df.describe())")
                         5. Continue: interact_with_process(pid, "df.groupby('column').size()")
                         
+                        BINARY FILE PROCESSING WORKFLOWS:
+                        Use appropriate Python libraries (PyPDF2, pandas, docx2txt, etc.) or command-line tools for binary file analysis.
+                        
                         SMART DETECTION:
                         - Automatically waits for REPL prompt (>>>, >, etc.)
                         - Detects errors and completion states

package.json

@@ -4,6 +4,7 @@ import os from 'os';
 import fetch from 'cross-fetch';
 import { createReadStream } from 'fs';
 import { createInterface } from 'readline';
+import { isBinaryFile } from 'isbinaryfile';
 import {capture} from '../utils/capture.js';
 import {withTimeout} from '../utils/withTimeout.js';
 import {configManager} from '../config-manager.js';
@@ -87,6 +88,22 @@ async function getDefaultReadLength(): Promise<number> {
     return config.fileReadLineLimit ?? 1000; // Default to 1000 lines if not set
 }
 
+/**
+ * Generate instructions for handling binary files
+ * @param filePath Path to the binary file
+ * @param mimeType MIME type of the file
+ * @returns Instruction message for the LLM
+ */
+function getBinaryFileInstructions(filePath: string, mimeType: string): string {
+    const fileName = path.basename(filePath);
+    
+    return `Cannot read binary file as text: ${fileName} (${mimeType})
+
+Use start_process + interact_with_process to analyze binary files with appropriate tools (Node.js or Python libraries, command-line utilities, etc.).
+
+The read_file tool only handles text files and images.`;
+}
+
 // Initialize allowed directories from configuration
 async function getAllowedDirs(): Promise<string[]> {
     try {
@@ -383,6 +400,17 @@ async function readFileWithSmartPositioning(filePath: string, offset: number, le
     const stats = await fs.stat(filePath);
     const fileSize = stats.size;
 
+    // Check if the file is binary (but allow images to pass through)
+    const { isImage } = await getMimeTypeInfo(filePath);
+    if (!isImage) {
+        const isBinary = await isBinaryFile(filePath);
+        if (isBinary) {
+            // Return instructions instead of trying to read binary content
+            const instructions = getBinaryFileInstructions(filePath, mimeType);
+            throw new Error(instructions);
+        }
+    }
+
     // Get total line count for enhanced status messages (only for smaller files)
     const totalLines = await getFileLineCount(filePath);
 
@@ -664,11 +692,20 @@ export async function readFileFromDisk(filePath: string, offset: number = 0, len
             try {
                 return await readFileWithSmartPositioning(validPath, offset, length, mimeType, true);
             } catch (error) {
-                // If UTF-8 reading fails, treat as binary and return base64 but still as text
-                const buffer = await fs.readFile(validPath);
-                const content = `Binary file content (base64 encoded):\n${buffer.toString('base64')}`;
-
-                return { content, mimeType: 'text/plain', isImage: false };
+                // If it's our binary file instruction error, return it as content
+                if (error instanceof Error && error.message.includes('Cannot read binary file as text:')) {
+                    return { content: error.message, mimeType: 'text/plain', isImage: false };
+                }
+                
+                // If UTF-8 reading fails for other reasons, also check if it's binary
+                const isBinary = await isBinaryFile(validPath);
+                if (isBinary) {
+                    const instructions = getBinaryFileInstructions(validPath, mimeType);
+                    return { content: instructions, mimeType: 'text/plain', isImage: false };
+                }
+                
+                // Only if it's truly not binary, then we have a real UTF-8 reading error
+                throw error;
             }
         }
     };