ISSUES FIXED: #4

@@ -0,0 +2,4 @@
+
+A powerful, reactive Agent Framework using RxPy streams for complex AI agent orchestration and message routing.
+
+[![PyPI Package](https://img.shields.io/pypi/v/cleveragents.svg)](https://pypi.org/project/cleveragents/)

@@ -0,0 +3,4 @@
+A powerful, reactive Agent Framework using RxPy streams for complex AI agent orchestration and message routing.
+
+[![PyPI Package](https://img.shields.io/pypi/v/cleveragents.svg)](https://pypi.org/project/cleveragents/)
+[![Travis-CI Build Status](https://img.shields.io/travis/cleverthis/cleveragents.svg)](https://travis-ci.org/cleverthis/cleveragents)

@@ -0,0 +29,4 @@
+### Install from PyPI
+
+```bash
+pip install cleveragents

@@ -0,0 +210,4 @@
+      provider: openai
+      model: gpt-4
+      api_key: "sk-your-key-here"
+```

@@ -0,0 +273,4 @@
+
+```bash
+# Run all tests
+python -m behave tests/features

@@ -0,0 +276,4 @@
+python -m behave tests/features
+
+# Run with coverage
+python -m pytest --cov=cleveragents

@@ -0,0 +279,4 @@
+python -m pytest --cov=cleveragents
+
+# Run with tox for multiple environments
+tox

@@ -0,0 +41,4 @@
+  - sources: [source_streams]
+    target: target_stream
+
+splits:

@@ -0,0 +61,4 @@
+  global:
+    variable_name: value
+```
+

@@ -0,0 +104,4 @@
+      safe_mode: true
+      timeout: 30
+```
+

@@ -0,0 +130,4 @@
+        input: sub_agent1
+        output: sub_stream1
+```
+

@@ -0,0 +145,4 @@
+    operators:
+      - type: map
+        params:
+          agent: agent_name

@@ -0,0 +177,4 @@
+- `replay`: Replay all previous values
+
+**Operators:**
+- `map`: Transform messages using agents or functions

@@ -0,0 +220,4 @@
+    parallel_execution: true
+    state_class: "my_module.MyState"
+```
+

@@ -0,0 +253,4 @@
+      preserve_subscriptions: true
+      preserve_checkpointing: true
+```
+

@@ -0,0 +1,190 @@
+agents:

@@ -0,0 +1,274 @@
+# Multi-Agent Paper Writer - Multiple Specialized Agents Working Together

@@ -294,7 +294,14 @@ class ReactiveCleverAgentsApp:
 
             # Set up observers for output and errors
             def on_output(msg: StreamMessage):

@@ -298,0 +300,4 @@
+                    print(f"\n[DEBUG] Empty output received\n")
+                else:
+                    # Check for tool execution commands
+                    processed_content = self._process_tool_commands(content_str)

@@ -338,3 +345,3 @@
 
                     # Give streams time to process
-                    await asyncio.sleep(0.1)
+                    await asyncio.sleep(2.0)

@@ -668,6 +664,151 @@ class ReactiveCleverAgentsApp:
             self.langgraph_bridge.create_hybrid_pipeline(config_dict)
             self.logger.debug(f"Created hybrid pipeline: {pipeline_name}")
 
+    def _sanitize_json_string(self, json_str: str) -> str:

@@ -671,0 +677,4 @@
+        Returns:
+            Sanitized JSON string with control characters properly escaped
+        """
+        import re

@@ -671,0 +678,4 @@
+            Sanitized JSON string with control characters properly escaped
+        """
+        import re
+        import json

@@ -671,0 +679,4 @@
+        """
+        import re
+        import json
+        

@@ -671,0 +686,4 @@
+            return json_str  # Already valid, no sanitization needed
+        except json.JSONDecodeError:
+            pass  # Need to sanitize
+        

@@ -671,0 +689,4 @@
+        
+        # Strategy: Find all quoted string values and escape control characters within them
+        # We need to be careful to only escape content inside string values, not the JSON structure
+        

@@ -671,0 +690,4 @@
+        # Strategy: Find all quoted string values and escape control characters within them
+        # We need to be careful to only escape content inside string values, not the JSON structure
+        
+        def escape_string_content(match):

@@ -671,0 +695,4 @@
+            # match.group(0) is the full match including quotes
+            # match.group(1) is the content inside the quotes
+            content = match.group(1)
+            

@@ -671,0 +705,4 @@
+            content = content.replace('\b', '\\b')
+            content = content.replace('\f', '\\f')
+            content = content.replace('"', '\\"')  # Escape quotes
+            

@@ -671,0 +712,4 @@
+        # Pattern to match quoted strings (both keys and values)
+        # This matches: "anything including newlines and special chars"
+        # We use a negative lookbehind to avoid matching escaped quotes
+        pattern = r'"((?:[^"\\]|\\.)*)"|"([^"]*(?:\n[^"]*)*)"'

@@ -671,0 +721,4 @@
+        
+        return sanitized
+    
+    def _process_tool_commands(self, content: str) -> str:

@@ -671,0 +727,4 @@
+        
+        Detects [TOOL_EXECUTE:tool_name] commands and executes actual tools.
+        """
+        import re

@@ -671,0 +728,4 @@
+        Detects [TOOL_EXECUTE:tool_name] commands and executes actual tools.
+        """
+        import re
+        import json

@@ -671,0 +729,4 @@
+        """
+        import re
+        import json
+        import asyncio

@@ -671,0 +734,4 @@
+        # Pattern to match tool execution commands
+        pattern = r'\[TOOL_EXECUTE:(\w+)\]\s*(\{[^}]+\})\s*\[/TOOL_EXECUTE\]'
+        
+        def execute_tool_sync(tool_name, tool_params):

@@ -671,0 +755,4 @@
+                
+                # Try to get the current running loop
+                try:
+                    loop = asyncio.get_running_loop()

@@ -671,0 +757,4 @@
+                try:
+                    loop = asyncio.get_running_loop()
+                    # We're already in an async context, create a task
+                    import concurrent.futures

@@ -671,0 +767,4 @@
+                    # No running loop, we can use asyncio.run
+                    result = asyncio.run(file_manager.process_message(tool_request, context))
+                
+                return f"\n✅ {result}"

@@ -671,0 +769,4 @@
+                
+                return f"\n✅ {result}"
+                
+            except Exception as e:

@@ -671,0 +770,4 @@
+                return f"\n✅ {result}"
+                
+            except Exception as e:
+                self.logger.error(f"Tool execution failed: {e}")

@@ -671,0 +790,4 @@
+                # Sanitize JSON string before parsing to handle LLM-generated malformed JSON
+                sanitized_params_str = self._sanitize_json_string(tool_params_str)
+                tool_params = json.loads(sanitized_params_str)
+                tool_result = execute_tool_sync(tool_name, tool_params)

@@ -671,0 +799,4 @@
+                    result_content[match.end():]
+                )
+            except json.JSONDecodeError as e:
+                self.logger.error(f"Failed to parse tool params: {e}")

@@ -671,0 +800,4 @@
+                )
+            except json.JSONDecodeError as e:
+                self.logger.error(f"Failed to parse tool params: {e}")
+                error_msg = f"\n❌ Error: Invalid tool parameters format"

@@ -0,0 +36,4 @@
+
+```bash
+git clone https://git.cleverthis.com/cleveragents/cleveragents-core
+cd cleveragents

@@ -194,0 +201,4 @@
+                # No event loop in current thread, create one
+                loop = asyncio.new_event_loop()
+                asyncio.set_event_loop(loop)
+            self._memory_lock_instance = asyncio.Lock()

@@ -338,3 +348,3 @@
 
                     # Give streams time to process
-                    await asyncio.sleep(0.1)
+                    await asyncio.sleep(2.0)

@@ -0,0 +1,167 @@
+#!/bin/bash

@@ -0,0 +30,4 @@
+# Run the legal contract analyzer
+python -m cleveragents run \
+  -c examples/legal_contract_metadata_extractor.yaml \
+  -p "sample_contract.txt" \

@@ -0,0 +53,4 @@
+if grep -q "FILE_LOADER AGENT" /tmp/contract_test_output.log; then
+    echo "✅ FILE_LOADER agent simulation found"
+else
+    echo "❌ FILE_LOADER agent simulation not found"

@@ -0,0 +59,4 @@
+if grep -q "TEXT_PREPROCESSOR AGENT\|CONTRACT_ANALYZER AGENT\|RISK_ASSESSOR AGENT\|JSON_FORMATTER AGENT" /tmp/contract_test_output.log; then
+    echo "✅ Analysis agent simulation found"
+else
+    echo "❌ Analysis agent simulation not found (may continue in next interaction)"

@@ -0,0 +70,4 @@
+if grep -q "TOOL_EXECUTE:file_read" /tmp/contract_test_output.log; then
+    echo "✅ File reading tool execution command found"
+else
+    echo "⚠️  File reading tool execution command not found"

@@ -0,0 +164,4 @@
+
+# Clean up
+rm -f /tmp/contract_test_output.log
+

@@ -0,0 +24,4 @@
+echo "Starting test..."
+echo ""
+
+cat << 'EOF' | timeout 120 python -m cleveragents interactive -c examples/multi_agent_paper_writer.yaml --unsafe 2>&1 | grep -v "^\[" | head -100

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+
+echo ""
+echo "=========================================="
+echo "Test Complete!"

@@ -0,0 +16,4 @@
+echo ""
+
+timeout 120 python -m cleveragents run \
+  -c examples/scientific_paper_writer_single_turn.yaml \

@@ -0,0 +20,4 @@
+    """Test suite for tool command processing with nested JSON."""
+
+    def test_simple_file_read_command(self):
+        """Test that simple file_read commands are detected correctly."""

@@ -0,0 +274,4 @@
+```bash
+# Run all tests
+python -m behave tests/features
+

@@ -0,0 +1,384 @@
+# Legal Contract Metadata Extractor - True Multi-Agent Analysis System

@@ -0,0 +1,495 @@
+# Legal Contract Metadata Extractor - LangGraph with Conditional Routing

@@ -155,1 +158,4 @@
+            elif self.config.get("memory_enabled", False):
+                # Fall back to agent's own memory if no context history
                 history = await self.get_memory("conversation_history", [])
+            

@@ -288,2 +295,3 @@
             with open(filepath, "r", encoding="utf-8") as f:
-                return f.read()
+                content = f.read()
+            

@@ -290,0 +300,4 @@
+            # but we add a prefix for clean terminal display
+            line_count = content.count('\n') + 1
+            char_count = len(content)
+            

@@ -290,0 +303,4 @@
+            
+            # Format: Special marker + metadata + full content
+            # The special marker helps identify this for clean display
+            return f"[FILE_READ_SUCCESS]📄 File: {filepath} | Lines: {line_count} | Size: {char_count} chars\n[FILE_CONTENT_START]\n{content}\n[FILE_CONTENT_END]"

@@ -294,3 +311,3 @@
         self, args: Dict[str, Any], context: Optional[Dict[str, Any]]
     ) -> str:
-        """File writing tool."""
+        """File writing tool with support for write, append, and insert modes."""

@@ -297,2 +313,4 @@
+        """File writing tool with support for write, append, and insert modes."""
         filepath = args.get("file", "")
         content = args.get("content", "")
+        mode = args.get("mode", "w")  # "w" (write/overwrite), "a" (append), "insert" (insert at position)

@@ -312,3 +336,1 @@
-            if filepath.startswith("/") and not (
-                context and context.get("_unsafe_mode", False)
-            ):
+            if filepath.startswith("/") and not unsafe_mode:

@@ -314,2 +336,3 @@
-            ):
+            if filepath.startswith("/") and not unsafe_mode:
+                logger.error("Absolute path blocked for %s", filepath)
                 raise ExecutionError("Unsafe file path blocked in safe mode")

@@ -321,0 +343,4 @@
+                with open(filepath, "w", encoding="utf-8") as f:
+                    f.write(content)
+                return f"Successfully wrote {len(content)} characters to {filepath}"
+            

@@ -321,0 +344,4 @@
+                    f.write(content)
+                return f"Successfully wrote {len(content)} characters to {filepath}"
+            
+            elif mode == "a":

@@ -321,0 +349,4 @@
+                with open(filepath, "a", encoding="utf-8") as f:
+                    f.write(content)
+                return f"Successfully appended {len(content)} characters to {filepath}"
+            

@@ -321,0 +352,4 @@
+            
+            elif mode == "insert":
+                # Insert mode - read existing content, insert at position, write back
+                try:

@@ -321,0 +354,4 @@
+                # Insert mode - read existing content, insert at position, write back
+                try:
+                    with open(filepath, "r", encoding="utf-8") as f:
+                        existing_lines = f.readlines()

@@ -321,0 +358,4 @@
+                except FileNotFoundError:
+                    # If file doesn't exist, create it with the content
+                    existing_lines = []
+                

@@ -321,0 +360,4 @@
+                    existing_lines = []
+                
+                # Determine insertion position
+                if position is None or position == "end":

@@ -321,0 +362,4 @@
+                # Determine insertion position
+                if position is None or position == "end":
+                    # Append at end
+                    existing_lines.append(content if content.endswith('\n') else content + '\n')

@@ -321,0 +371,4 @@
+                elif isinstance(position, int):
+                    # Insert at specific line number (1-indexed)
+                    line_idx = max(0, min(position - 1, len(existing_lines)))
+                    existing_lines.insert(line_idx, content if content.endswith('\n') else content + '\n')

@@ -321,0 +374,4 @@
+                    existing_lines.insert(line_idx, content if content.endswith('\n') else content + '\n')
+                    insert_location = line_idx + 1
+                else:
+                    raise ExecutionError(f"Invalid position '{position}'. Use 'start', 'end', or line number.")

@@ -321,0 +375,4 @@
+                    insert_location = line_idx + 1
+                else:
+                    raise ExecutionError(f"Invalid position '{position}'. Use 'start', 'end', or line number.")
+                

@@ -321,0 +379,4 @@
+                # Write back
+                with open(filepath, "w", encoding="utf-8") as f:
+                    f.writelines(existing_lines)
+                

@@ -321,0 +380,4 @@
+                with open(filepath, "w", encoding="utf-8") as f:
+                    f.writelines(existing_lines)
+                
+                return f"Successfully inserted {len(content)} characters at line {insert_location} in {filepath}"

@@ -321,0 +381,4 @@
+                    f.writelines(existing_lines)
+                
+                return f"Successfully inserted {len(content)} characters at line {insert_location} in {filepath}"
+            

@@ -321,0 +383,4 @@
+                return f"Successfully inserted {len(content)} characters at line {insert_location} in {filepath}"
+            
+            else:
+                raise ExecutionError(f"Invalid mode '{mode}'. Use 'w' (write), 'a' (append), or 'insert'.")

@@ -321,0 +384,4 @@
+            
+            else:
+                raise ExecutionError(f"Invalid mode '{mode}'. Use 'w' (write), 'a' (append), or 'insert'.")
+                

@@ -670,0 +714,4 @@
+        # Pattern to match any content between quotes, including newlines
+        pattern = r'"([^"\\]*(?:\\.[^"\\]*)*|[^"]*(?:\n[^"]*)*)"'
+
+        sanitized = re.sub(pattern, escape_string_content, json_str, flags=re.DOTALL)

@@ -670,0 +732,4 @@
+        try:
+            # Find the appropriate agent that can execute this tool
+            target_agent = None
+            for _, agent in self.agents.items():

@@ -730,8 +869,16 @@ class ReactiveCleverAgentsApp:
         # Execute graph
         try:
             print(f"Executing graph '{graph_name}'...")
+            

@@ -732,1 +871,4 @@
             print(f"Executing graph '{graph_name}'...")
+            
+            # Prepare metadata with unsafe mode and context
+            metadata: Dict[str, Any] = {"context": self.config.global_context}

@@ -733,0 +873,4 @@
+            # Prepare metadata with unsafe mode and context
+            metadata: Dict[str, Any] = {"context": self.config.global_context}
+            metadata["_unsafe_mode"] = self.unsafe
+            

@@ -393,12 +381,20 @@ class LangGraph:
                         {"messages": [{"role": "user", "content": input_data}]},
                         mode=StateUpdateMode.APPEND,
                     )
+                

@@ -151,1 +150,3 @@
-            agent_input = last_message.get("content", "")
+            # Check if this is a tool agent that should receive the last message
+            # (regardless of role) to process commands from other agents
+            from cleveragents.agents.tool import ToolAgent

@@ -152,0 +160,4 @@
+                    if msg.get("role") == "user":
+                        last_user_message = msg.get("content", "")
+                        break
+                

@@ -156,0 +171,4 @@
+            "conversation_history": state.messages,
+            "full_context": True
+        }
+        

@@ -0,0 +272,4 @@
+### Running Tests
+
+```bash
+# Run all tests

@@ -0,0 +294,4 @@
+tox -e py312-nocov
+
+# Individual test scripts:
+bash tests/scripts/test_single_turn_writer.sh

@@ -0,0 +295,4 @@
+
+# Individual test scripts:
+bash tests/scripts/test_single_turn_writer.sh
+bash tests/scripts/test_multi_agent_paper_writer_langgraph.sh

@@ -0,0 +296,4 @@
+# Individual test scripts:
+bash tests/scripts/test_single_turn_writer.sh
+bash tests/scripts/test_multi_agent_paper_writer_langgraph.sh
+bash tests/scripts/test_legal_contract_analyzer_langgraph.sh

@@ -0,0 +297,4 @@
+bash tests/scripts/test_single_turn_writer.sh
+bash tests/scripts/test_multi_agent_paper_writer_langgraph.sh
+bash tests/scripts/test_legal_contract_analyzer_langgraph.sh
+bash tests/scripts/test_paper_writer_section_by_section.sh

@@ -0,0 +299,4 @@
+bash tests/scripts/test_legal_contract_analyzer_langgraph.sh
+bash tests/scripts/test_paper_writer_section_by_section.sh
+bash tests/scripts/test_multi_agent_interactive.sh
+bash tests/scripts/test_legal_contract_analyzer.sh

@@ -297,2 +315,4 @@
+        """File writing tool with support for write, append, and insert modes."""
         filepath = args.get("file", "")
         content = args.get("content", "")
+        mode = args.get("mode", "w")  # "w" (write/overwrite), "a" (append), "insert" (insert at position)

@@ -71,3 +72,2 @@
         self.input_stream.pipe(
-            ops.map(self._process_wrapper),
-            ops.flat_map(lambda future: rx.from_future(future)),
+            ops.map(self._process_wrapper),  # type: ignore[arg-type]

@@ -72,2 +73,2 @@
-            ops.map(self._process_wrapper),
-            ops.flat_map(lambda future: rx.from_future(future)),
+            ops.map(self._process_wrapper),  # type: ignore[arg-type]
+            ops.flat_map(rx.from_future),  # type: ignore[arg-type]

@@ -285,3 +307,3 @@
                 )
 
-            return rx.create(subscribe)  # type: ignore
+            return rx.create(subscribe)  # type: ignore[no-untyped-call]

@@ -310,3 +332,3 @@
             return await result_future
 
-        return ops.map(process_value)
+        return ops.map(process_value)  # type: ignore[arg-type]

@@ -81,6 +83,58 @@ class ToolAgent(Agent):
             else:
                 raise AgentCreationError(f"Invalid tool configuration: {tool}")
 
+    def _extract_json_from_message(self, message: str) -> Optional[Dict[str, Any]]:

@@ -84,0 +118,4 @@
+                return None  # Not a dict
+            except json.JSONDecodeError:
+                # Code block had invalid JSON, raise error
+                raise

@@ -323,1 +346,4 @@
+                    f.write(content)
+                return f"Successfully wrote {len(content)} characters to {filepath}"
 
+            elif mode == "a":

@@ -324,0 +393,4 @@
+                    f"at line {insert_location} in {filepath}"
+                )
+            else:
+                raise ExecutionError(f"Invalid mode '{mode}'. Use 'w' (write), 'a' (append), or 'insert'.")

@@ -292,0 +464,4 @@
+        return prefix + cleaned_content
+
+    def _handle_insert_position(
+        self, filepath: str, cleaned_content: str, position: Union[None, int, Literal["start", "end"]]

@@ -321,0 +529,4 @@
+                    f.write(cleaned_content)
+                return f"Successfully wrote {len(cleaned_content)} characters to {filepath}"
+
+            elif mode == "a":

@@ -670,0 +705,4 @@
+
+        # ✅ NEW: Validate the sanitized result
+        if not is_valid_json(sanitized):
+            logger.warning(

@@ -20,3 +22,1 @@
-from rx import operators as ops
-from rx.core import Observer
-from rx.scheduler.eventloop import AsyncIOScheduler
+from rx.core import Observer  # type: ignore[attr-defined]

@@ -21,2 +22,2 @@
-from rx.core import Observer
-from rx.scheduler.eventloop import AsyncIOScheduler
+from rx.core import Observer  # type: ignore[attr-defined]
+from rx.scheduler.eventloop import AsyncIOScheduler  # type: ignore[attr-defined]

@@ -0,0 +40,4 @@
+cd cleveragents-core
+pip install -e .
+```
+

@@ -0,0 +191,4 @@
+# Google Gemini
+export GOOGLE_API_KEY="your-google-key"
+```
+```

@@ -196,0 +207,4 @@
+                if self._memory_lock_instance is None:
+                    try:
+                        loop = asyncio.get_event_loop()
+                    except RuntimeError:

@@ -84,0 +100,4 @@
+        message_stripped = message.strip()
+
+        # If message looks like JSON (starts with { and ends with }), it must be valid JSON
+        if message_stripped.startswith("{") and message_stripped.endswith("}"):

@@ -292,0 +377,4 @@
+        self, filepath: str, unsafe_mode: bool
+    ) -> None:
+        """Validate file path for safety in safe mode."""
+        if not self.safe_mode:

@@ -670,0 +724,4 @@
+            return f'"{content}"'
+
+        # Pattern to match any content between quotes, including newlines
+        pattern = r'"([^"\\]*(?:\\.[^"\\]*)*|[^"]*(?:\n[^"]*)*)"'

@@ -0,0 +154,4 @@
+        print("✅ TEST PASSED: Complex nested JSON from actual usage")
+
+    def test_old_pattern_would_fail(self):
+        """Verify that the old regex pattern would fail with nested JSON."""