Added timeout and limit to script entries

action_schema.xsd

@@ -33,6 +33,8 @@
     Single script that runs once and completes.
     Output is stored in context until explicitly deleted.
     Used for one-time operations like file manipulation.
+    Single scripts are limited to 1024 characters and 1 second timeout by default.
+    These limits can be changed with attributes.
     Example:
     <single>
       ls /
@@ -43,6 +45,8 @@
       <xs:sequence>
         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="skip"/>
       </xs:sequence>
+      <xs:attribute name="timeout" type="xs:float" use="optional"/>
+      <xs:attribute name="limit" type="xs:integer" use="optional"/>
     </xs:complexType>
   </xs:element>
 
@@ -51,6 +55,8 @@
     After a command is issued, all repeat scripts in context are run again.
     Useful for monitoring changing files or viewing results immediately after changing a file.
     Repeat scripts should execute quickly to avoid blocking the agent.
+    Repeat scripts are limited to 1024 characters and 1 second timeout by default.
+    These limits can be changed with attributes.
     Example:
     <repeat>
       ls /
@@ -61,6 +67,8 @@
       <xs:sequence>
         <xs:any minOccurs="0" maxOccurs="unbounded" processContents="skip"/>
       </xs:sequence>
+      <xs:attribute name="timeout" type="xs:float" use="optional"/>
+      <xs:attribute name="limit" type="xs:integer" use="optional"/>
     </xs:complexType>
   </xs:element>
 
@@ -83,6 +91,7 @@
 
   <!--
     Read all available text on stdin and store it in context.
+    Do this only if the context indicates there is data in the stdin buffer.
     Example:
     <read_stdin/>
   -->
@@ -93,6 +102,7 @@
   <!--
     Write to stdout.
     This is your main way of contacting the user.
+    Make sure you have properly reasoned about what to say and if it is necessary before issuing a write_stdout command.
     Example:
     <write_stdout>
       Hello world!

sia/background_entry.py

@@ -17,14 +17,19 @@ class BackgroundEntry(Entry):
         _exit_code: Exit code when process completes
     """
     
-    def __init__(self, script: str, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            script: str,
+        ):
         """
         Initialize a new background entry.
         
         Args:
-            script: The script/command to execute
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            script: The script/command to execute
         """
         super().__init__(id, timestamp)
         self._script = script

sia/parse_error_entry.py

@@ -8,15 +8,21 @@ class ParseErrorEntry(Entry):
     Entry type for parse and validation errors.
     """
     
-    def __init__(self, content: str, error: str, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            content: str,
+            error: str,
+        ):
         """
         Initialize a new parse error entry.
         
         Args:
-            content: Original content that failed to parse
-            error: Error message describing the failure
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            content: Original content that failed to parse
+            error: Error message describing the failure
         """
         super().__init__(id, timestamp)
         self._content = content

sia/read_entry.py

@@ -13,14 +13,19 @@ class ReadEntry(Entry):
         _read: Whether content has been read
     """
     
-    def __init__(self, io_buffer, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            io_buffer,
+        ):
         """
         Initialize a new read entry.
         
         Args:
-            io_buffer: Buffer to use for IO operations
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            io_buffer: Buffer to use for IO operations
         """
         super().__init__(id, timestamp)
         self._content = ""

sia/reasoning_entry.py

@@ -11,14 +11,19 @@ class ReasoningEntry(Entry):
         _content: The reasoning text
     """
     
-    def __init__(self, content: str, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            content: str,
+        ):
         """
         Initialize a new reasoning entry.
         
         Args:
-            content: The reasoning text
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            content: The reasoning text
         """
         super().__init__(id, timestamp)
         self._content = content

sia/repeat_entry.py

@@ -8,22 +8,46 @@ from .entry import Entry
 class RepeatEntry(Entry):
     """
     Entry type for scripts that are executed on every update.
+
+    Attributes:
+        script: The script/command to execute
+        timeout: Maximum time to wait for script execution
+        limit: Maximum number of characters to capture from stdout/stderr
+        stdout: Captured standard output from script execution
+        stderr: Captured standard error from script execution
+        exit_code: Process exit code after completion
+        _executed: Whether the script has been executed
     """
+
+    default_timeout = 1
+    default_limit = 1024
     
-    def __init__(self, script: str, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            script: str,
+            timeout: Optional[float],
+            limit: Optional[int],
+        ):
         """
         Initialize a new repeat entry.
         
         Args:
-            script: The script/command to execute
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            script: The script/command to execute
+            timeout: Maximum time to wait for script execution
+            limit: Maximum number of characters to capture from stdout/stderr
         """
         super().__init__(id, timestamp)
         self._script = script
+        self._timeout = timeout or self.default_timeout
+        self._limit = limit or self.default_limit
         self._stdout = ""
         self._stderr = ""
         self._exit_code: Optional[int] = None
+        self._timed_out = False
 
     @property
     def script(self) -> str:
@@ -50,15 +74,20 @@ class RepeatEntry(Entry):
         Execute the script and update the output.
         Captures stdout, stderr and exit code from each execution.
         """
-        process = subprocess.run(
-            self._script,
-            shell=True,
-            capture_output=True,
-            text=True
-        )
-        self._stdout = process.stdout
-        self._stderr = process.stderr
-        self._exit_code = process.returncode
+        try:
+            process = subprocess.run(
+                self._script,
+                timeout=self._timeout,
+                shell=True,
+                capture_output=True,
+                text=True
+            )
+            self._stdout = process.stdout
+            self._stderr = process.stderr
+            self._exit_code = process.returncode
+        except subprocess.TimeoutExpired as e:
+            self._timed_out = True
+
 
     def generate_context(self) -> ET.Element:
         """
@@ -69,12 +98,20 @@ class RepeatEntry(Entry):
         """
         element = ET.Element("repeat", {
             "id": self.id,
-            "exit_code": str(self._exit_code) if self._exit_code is not None else "-1"
         })
         element.text = self.script
-        stdout_elem = ET.SubElement(element, "stdout")
-        stdout_elem.text = self._stdout
-        stderr_elem = ET.SubElement(element, "stderr")
-        stderr_elem.text = self._stderr
+        if self._exit_code is not None:
+            element.set("exit_code", str(self._exit_code))
+        if self._timed_out:
+            element.set("timed_out", "true")
+        else:
+            if len(self._stdout) > self._limit:
+                element.set("stdout_truncated", "true")
+            stdout_elem = ET.SubElement(element, "stdout")
+            stdout_elem.text = self._stdout[:self._limit]
+            if len(self._stderr) > self._limit:
+                element.set("stderr_truncated", "true")
+            stderr_elem = ET.SubElement(element, "stderr")
+            stderr_elem.text = self._stderr[:self._limit]
         
         return element

sia/response_parser.py

@@ -54,15 +54,15 @@ class ResponseParser:
         try:
             root = ET.fromstring(xml.strip())
         except ET.ParseError as e:
-            return ParseErrorEntry(xml, f"Invalid XML: {str(e)}", entry_id, timestamp)
+            return ParseErrorEntry(entry_id, timestamp, xml, f"Invalid XML: {str(e)}")
         
         try:
             if root.tag == 'delete':
                 target_id = root.get('id')
                 if not target_id:
-                    return ParseErrorEntry(xml, "Delete command missing required 'id' attribute", entry_id, timestamp)
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Delete command missing required 'id' attribute")
                 if len(root.attrib) > 1:
-                    return ParseErrorEntry(xml, "Delete command should only have 'id' attribute", entry_id, timestamp)
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Delete command should only have 'id' attribute")
                 return DeleteCommand(target_id)
 
             elif root.tag == 'stop':
@@ -70,34 +70,46 @@ class ResponseParser:
                 
             elif root.tag == 'background':
                 if len(root) != 0 or root.attrib or root.text is None or root.text.strip() == '':
-                    return ParseErrorEntry(xml, "Background entry requires (only) script content", entry_id, timestamp)
-                return BackgroundEntry(root.text, entry_id, timestamp)
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Background entry requires (only) script content")
+                return BackgroundEntry(entry_id, timestamp, root.text)
                 
             elif root.tag == 'repeat':
-                if len(root) != 0 or root.attrib or root.text is None or root.text.strip() == '':
-                    return ParseErrorEntry(xml, "Repeat entry requires (only) script content", entry_id, timestamp)
-                return RepeatEntry(root.text, entry_id, timestamp)
+                if len(root) != 0 or root.text is None or root.text.strip() == '':
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Repeat entry requires (only) script content")
+                if len(root.attrib) > 2 or any(k not in ('timeout', 'limit') for k in root.attrib):
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Repeat entry only accepts 'timeout' and 'limit' attributes")
+                timeout = root.get('timeout')
+                limit = root.get('limit')
+                timeout = float(timeout) if timeout is not None else None
+                limit = int(limit) if limit is not None else None
+                return RepeatEntry(entry_id, timestamp, root.text, timeout, limit)
                 
             elif root.tag == 'single':
-                if len(root) != 0 or root.attrib or root.text is None or root.text.strip() == '':
-                    return ParseErrorEntry(xml, "Single entry requires (only) script content", entry_id, timestamp)
-                return SingleEntry(root.text, entry_id, timestamp)
-                
+                if len(root) != 0 or root.text is None or root.text.strip() == '':
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Single entry requires (only) script content")
+                if len(root.attrib) > 2 or any(k not in ('timeout', 'limit') for k in root.attrib):
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Single entry only accepts 'timeout' and 'limit' attributes")
+                timeout = root.get('timeout')
+                limit = root.get('limit')
+                timeout = float(timeout) if timeout is not None else None
+                limit = int(limit) if limit is not None else None
+                return SingleEntry(entry_id, timestamp, root.text, timeout, limit)
+
             elif root.tag == 'reasoning':
                 if len(root) != 0 or root.attrib or root.text is None or root.text.strip() == '':
-                    return ParseErrorEntry(xml, "Reasoning entry requires (only) text content", entry_id, timestamp)
-                return ReasoningEntry(root.text, entry_id, timestamp)
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Reasoning entry requires (only) text content")
+                return ReasoningEntry(entry_id, timestamp, root.text)
                 
             elif root.tag == 'read_stdin':
-                return ReadEntry(self.io_buffer, entry_id, timestamp)
+                return ReadEntry(entry_id, timestamp, self.io_buffer)
                 
             elif root.tag == 'write_stdout':
                 if len(root) != 0 or root.attrib or root.text is None or root.text.strip() == '':
-                    return ParseErrorEntry(xml, "Write stdout entry requires (only) text content", entry_id, timestamp)
-                return WriteEntry(root.text, self.io_buffer, entry_id, timestamp)
+                    return ParseErrorEntry(entry_id, timestamp, xml, "Write stdout entry requires (only) text content")
+                return WriteEntry(entry_id, timestamp, root.text, self.io_buffer)
                 
             else:
-                return ParseErrorEntry(xml, f"Unknown root element: {root.tag}", entry_id, timestamp)
+                return ParseErrorEntry(entry_id, timestamp, xml, f"Unknown root element: {root.tag}")
                 
         except Exception as e:
-            return ParseErrorEntry(xml, f"Error parsing response: {str(e)}", entry_id, timestamp)
+            return ParseErrorEntry(entry_id, timestamp, xml, f"Error parsing response: {str(e)}")

sia/single_entry.py

@@ -11,27 +11,44 @@ class SingleEntry(Entry):
     
     Attributes:
         script: The script/command to execute
+        timeout: Maximum time to wait for script execution
+        limit: Maximum number of characters to capture from stdout/stderr
         stdout: Captured standard output from script execution
         stderr: Captured standard error from script execution 
         exit_code: Process exit code after completion
         _executed: Whether the script has been executed
     """
+
+    default_timeout = 1
+    default_limit = 1024
     
-    def __init__(self, script: str, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            script: str,
+            timeout: Optional[float],
+            limit: Optional[int],
+        ):
         """
         Initialize a new single shot entry.
         
         Args:
-            script: The script/command to execute
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            script: The script/command to execute
+            timeout: Maximum time to wait for script execution
+            limit: Maximum number of characters to capture from stdout/stderr
         """
         super().__init__(id, timestamp)
         self._script = script
+        self._timeout = timeout or self.default_timeout
+        self._limit = limit or self.default_limit
         self._stdout = ""
         self._stderr = ""
         self._exit_code: Optional[int] = None
         self._executed = False
+        self._timed_out = False
 
     @property
     def script(self) -> str:
@@ -60,16 +77,20 @@ class SingleEntry(Entry):
         """
         if self._executed:
             return
-        process = subprocess.run(
-            self.script,
-            shell=True,
-            capture_output=True,
-            text=True
-        )
-        self._stdout = process.stdout
-        self._stderr = process.stderr
-        self._exit_code = process.returncode
         self._executed = True
+        try:
+            process = subprocess.run(
+                self._script,
+                timeout=self._timeout,
+                shell=True,
+                capture_output=True,
+                text=True
+            )
+            self._stdout = process.stdout
+            self._stderr = process.stderr
+            self._exit_code = process.returncode
+        except subprocess.TimeoutExpired as e:
+            self._timed_out = True
 
     def generate_context(self) -> ET.Element:
         """
@@ -82,10 +103,16 @@ class SingleEntry(Entry):
             "id": self.id,
         })
         element.text = self.script
-        if self._executed:
-            stdout_elem = ET.SubElement(element, "stdout")
-            stdout_elem.text = self._stdout
-            stderr_elem = ET.SubElement(element, "stderr")
-            stderr_elem.text = self._stderr
+        if self._timed_out:
+            element.set("timed_out", "true")
+        elif self._executed:
             element.set("exit_code", str(self._exit_code))
+            if len(self._stdout) > self._limit:
+                element.set("stdout_truncated", "true")
+            stdout_elem = ET.SubElement(element, "stdout")
+            stdout_elem.text = self._stdout[:self._limit]
+            if len(self._stderr) > self._limit:
+                element.set("stderr_truncated", "true")
+            stderr_elem = ET.SubElement(element, "stderr")
+            stderr_elem.text = self._stderr[:self._limit]
         return element

sia/write_entry.py

@@ -2,6 +2,7 @@ from datetime import datetime
 import xml.etree.ElementTree as ET
 
 from .entry import Entry
+from .io_buffer import IOBuffer
 
 class WriteEntry(Entry):
     """
@@ -13,15 +14,21 @@ class WriteEntry(Entry):
         _written: Whether the content has been written
     """
     
-    def __init__(self, content: str, io_buffer, id: str, timestamp: datetime):
+    def __init__(
+            self,
+            id: str,
+            timestamp: datetime,
+            content: str,
+            io_buffer: IOBuffer,
+        ):
         """
         Initialize a new write entry.
         
         Args:
-            content: Text to write to stdout
-            io_buffer: Buffer to use for IO operations
             id: Unique identifier for this entry
             timestamp: Creation timestamp for this entry
+            content: Text to write to stdout
+            io_buffer: Buffer to use for IO operations
         """
         super().__init__(id, timestamp)
         self.content = content

system_prompt.md

@@ -30,6 +30,7 @@ Scripts and their output appear in the context.
 You can use a script for starting a detached process that runs in the background.
 All processes can be managed by the usual Linux tools.
 The scripts defined in the script actions all run in a `bash` shell.
+You are logged in as root.
 
 # File system
 
@@ -71,6 +72,9 @@ Inspect your previous actions in detail.
 If something didn't work, try to understand why and don't repeat the same mistake.
 Don't delete mistakes until you understand them.
 
+If you notice parse_error entries in the context you have made a mistake.
+Reason about the error before trying again.
+
 # User interaction
 
 You are always working for a user.

test/background_entry_test.py

@@ -40,7 +40,7 @@ class BackgroundEntryTest(unittest.TestCase):
                 
     def test_initialization(self):
         """Test entry initialization"""
-        entry = BackgroundEntry("echo test", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "echo test")
         context = entry.generate_context()
         
         # Initial context should have script but no pid or exit_code
@@ -50,7 +50,7 @@ class BackgroundEntryTest(unittest.TestCase):
         
     def test_short_running_process(self):
         """Test execution of a quick process"""
-        entry = BackgroundEntry("echo 'test'", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "echo 'test'")
         
         # Wait for process to complete
         def is_complete(ctx):
@@ -74,7 +74,7 @@ class BackgroundEntryTest(unittest.TestCase):
             '"'
         )
         
-        entry = BackgroundEntry(script, self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, script)
         
         # Wait for process to complete
         def has_all_output(ctx):
@@ -85,7 +85,7 @@ class BackgroundEntryTest(unittest.TestCase):
         
     def test_process_failure(self):
         """Test handling of process failures"""
-        entry = BackgroundEntry("nonexistentcommand", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "nonexistentcommand")
         
         # Wait for process to fail
         def has_failed(ctx):
@@ -100,7 +100,7 @@ class BackgroundEntryTest(unittest.TestCase):
         
     def test_cleanup_running_process(self):
         """Test cleanup of running process"""
-        entry = BackgroundEntry("sleep 10", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "sleep 10")
         
         # Wait for process to start
         def has_started(ctx):
@@ -122,7 +122,7 @@ class BackgroundEntryTest(unittest.TestCase):
             
     def test_cleanup_completed_process(self):
         """Test cleanup of already completed process"""
-        entry = BackgroundEntry("echo test", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "echo test")
         
         # Wait for completion
         def is_complete(ctx):
@@ -135,7 +135,7 @@ class BackgroundEntryTest(unittest.TestCase):
         
     def test_multiple_cleanup_calls(self):
         """Test that multiple cleanup calls are safe"""
-        entry = BackgroundEntry("sleep 10", self.test_id, self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "sleep 10")
         
         # Wait for process to start
         def has_started(ctx):

test/base_agent_test.py

@@ -145,8 +145,9 @@ class BaseAgentTest(unittest.TestCase):
         self.assertEqual(len(list(root)), 0)
         
     def test_compile_context_with_entries(self):
-        # Add test entry to working memory
-        entry = ReasoningEntry("test reasoning", "test-id", self.test_timestamp)
+        """Test context compilation with a single entry."""
+        # Add test entry to working memory - note id and timestamp are now first
+        entry = ReasoningEntry("test-id", self.test_timestamp, "test reasoning")
         self.agent._working_memory.add_entry(entry)
         
         context = self.agent._compile_context()
@@ -166,9 +167,9 @@ class BaseAgentTest(unittest.TestCase):
         
     def test_multiple_entries(self):
         """Test handling multiple entries in working memory."""
-        # Add multiple entries
+        # Add multiple entries - note id and timestamp are now first
         entries = [
-            ReasoningEntry(f"test {i}", f"id-{i}", self.test_timestamp)
+            ReasoningEntry(f"id-{i}", self.test_timestamp, f"test {i}")
             for i in range(3)
         ]
         
@@ -186,4 +187,4 @@ class BaseAgentTest(unittest.TestCase):
         self.assertEqual(len(reasoning_elems), 3)
         for i, elem in enumerate(reasoning_elems):
             self.assertEqual(elem.get("id"), f"id-{i}")
-            self.assertEqual(elem.text.strip(), f"test {i}")
+            self.assertEqual(elem.text.strip(), f"test {i}")

test/delete_command_test.py

@@ -8,8 +8,6 @@ from sia.delete_command import DeleteCommand
 from sia.reasoning_entry import ReasoningEntry
 from sia.background_entry import BackgroundEntry
 
-
-
 class DeleteCommandTest(unittest.TestCase):
     def setUp(self):
         """Set up test cases with a fresh working memory"""
@@ -31,7 +29,7 @@ class DeleteCommandTest(unittest.TestCase):
     def test_delete_running_background_entry(self):
         """Test deleting a background entry that is still running"""
         # Create and start background process
-        entry = BackgroundEntry("sleep 10", "test-id", self.test_timestamp)
+        entry = BackgroundEntry(self.test_id, self.test_timestamp, "sleep 10")
         self.memory.add_entry(entry)
         
         # Wait for process to start
@@ -58,7 +56,7 @@ class DeleteCommandTest(unittest.TestCase):
     def test_delete_existing_entry(self):
         """Test deleting an existing entry"""
         # Add test entry
-        entry = ReasoningEntry("test content", self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, "test content")
         self.memory.add_entry(entry)
         
         # Execute delete command

test/parse_error_entry_test.py

@@ -13,31 +13,35 @@ class ParseErrorEntryTest(unittest.TestCase):
         """Test entry initialization"""
         content = "invalid content"
         error = "parsing failed"
-        entry = ParseErrorEntry(content, error, self.test_id, self.test_timestamp)
+        entry = ParseErrorEntry(self.test_id, self.test_timestamp, content, error)
         
         self.assertEqual(entry.id, self.test_id)
         self.assertEqual(entry.timestamp, self.test_timestamp)
+        self.assertEqual(entry.content, content)
+        self.assertEqual(entry.error, error)
         
     def test_update_does_nothing(self):
         """Test that update operation has no effect"""
         content = "invalid content"
         error = "parsing failed"
-        entry = ParseErrorEntry(content, error, self.test_id, self.test_timestamp)
+        entry = ParseErrorEntry(self.test_id, self.test_timestamp, content, error)
         
         # Store initial state
-        initial_context = entry.content
+        initial_content = entry.content
+        initial_error = entry.error
         
         # Perform update
         entry.update()
         
         # Verify state hasn't changed
-        self.assertEqual(entry.content, initial_context)
+        self.assertEqual(entry.content, initial_content)
+        self.assertEqual(entry.error, initial_error)
         
     def test_generate_context(self):
         """Test XML context generation"""
         content = "invalid content"
         error = "parsing failed"
-        entry = ParseErrorEntry(content, error, self.test_id, self.test_timestamp)
+        entry = ParseErrorEntry(self.test_id, self.test_timestamp, content, error)
         
         element = entry.generate_context()
         
@@ -48,26 +52,26 @@ class ParseErrorEntryTest(unittest.TestCase):
         # Verify error element
         error_elem = element.find("error")
         self.assertIsNotNone(error_elem)
-        self.assertEqual(error_elem.text, f"{error}")
+        self.assertEqual(error_elem.text, error)
         
         # Verify content element
         content_elem = element.find("content")
         self.assertIsNotNone(content_elem)
-        self.assertEqual(content_elem.text, f"{content}")
+        self.assertEqual(content_elem.text, content)
         
     def test_special_characters(self):
         """Test handling content and errors with special characters"""
         content = "Special content: \n\t\r\'\"\\"
         error = "Special error: \n\t\r\'\"\\"
-        entry = ParseErrorEntry(content, error, self.test_id, self.test_timestamp)
+        entry = ParseErrorEntry(self.test_id, self.test_timestamp, content, error)
         
         element = entry.generate_context()
-        self.assertEqual(element.find("content").text, f"{content}")
-        self.assertEqual(element.find("error").text, f"{error}")
+        self.assertEqual(element.find("content").text, content)
+        self.assertEqual(element.find("error").text, error)
         
     def test_empty_content_and_error(self):
         """Test handling empty content and error messages"""
-        entry = ParseErrorEntry("", "", self.test_id, self.test_timestamp)
+        entry = ParseErrorEntry(self.test_id, self.test_timestamp, "", "")
         
         element = entry.generate_context()
         self.assertEqual(element.find("content").text, "")

test/read_entry_test.py

@@ -13,7 +13,7 @@ class ReadEntryTest(unittest.TestCase):
         
     def test_initialization(self):
         """Test entry initialization"""
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         
         self.assertEqual(entry.content, "")
         self.assertEqual(entry.id, self.test_id)
@@ -24,7 +24,7 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "test message"
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, test_input)
@@ -35,7 +35,7 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "initial input"
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         initial_content = entry.content
         
@@ -47,7 +47,7 @@ class ReadEntryTest(unittest.TestCase):
         
     def test_empty_input(self):
         """Test reading when no input is available"""
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, "")
@@ -57,7 +57,7 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "Special chars: \n\t\r\'\"\\"
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, test_input)
@@ -67,14 +67,14 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "x" * 10000
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, test_input)
         
     def test_generate_context_before_read(self):
         """Test XML context generation before reading"""
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         element = entry.generate_context()
         
         # Verify XML structure
@@ -87,7 +87,7 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "test message"
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         element = entry.generate_context()
         
@@ -101,7 +101,7 @@ class ReadEntryTest(unittest.TestCase):
         test_input = "Hello 世界 😊"
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, test_input)
@@ -113,7 +113,7 @@ class ReadEntryTest(unittest.TestCase):
         Line 3"""
         self.io_buffer.append_stdin(test_input)
         
-        entry = ReadEntry(self.io_buffer, self.test_id, self.test_timestamp)
+        entry = ReadEntry(self.test_id, self.test_timestamp, self.io_buffer)
         entry.update()
         
         self.assertEqual(entry.content, test_input)

test/reasoning_entry_test.py

@@ -12,7 +12,7 @@ class ReasoningEntryTest(unittest.TestCase):
     def test_initialization(self):
         """Test entry initialization"""
         content = "test reasoning"
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         self.assertEqual(entry.content, content)
         self.assertEqual(entry.id, self.test_id)
@@ -21,7 +21,7 @@ class ReasoningEntryTest(unittest.TestCase):
     def test_update_does_nothing(self):
         """Test that update operation has no effect"""
         content = "test reasoning"
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         # Store initial state
         initial_content = entry.generate_context().text
@@ -35,7 +35,7 @@ class ReasoningEntryTest(unittest.TestCase):
     def test_generate_context(self):
         """Test XML context generation"""
         content = "test reasoning"
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         element = entry.generate_context()
         
@@ -47,14 +47,14 @@ class ReasoningEntryTest(unittest.TestCase):
     def test_special_characters(self):
         """Test handling reasoning text with special characters"""
         content = "Special reasoning: \n\t\r\'\"\\"
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         element = entry.generate_context()
         self.assertEqual(element.text, f"{content}")
         
     def test_empty_content(self):
         """Test handling empty reasoning text"""
-        entry = ReasoningEntry("", self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, "")
         
         element = entry.generate_context()
         self.assertEqual(element.text, "")
@@ -62,7 +62,7 @@ class ReasoningEntryTest(unittest.TestCase):
     def test_large_content(self):
         """Test handling large reasoning text"""
         content = "x" * 10000
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         element = entry.generate_context()
         self.assertEqual(element.text, f"{content}")
@@ -72,7 +72,7 @@ class ReasoningEntryTest(unittest.TestCase):
         content = """Line 1
         Line 2
         Line 3"""
-        entry = ReasoningEntry(content, self.test_id, self.test_timestamp)
+        entry = ReasoningEntry(self.test_id, self.test_timestamp, content)
         
         element = entry.generate_context()
         self.assertEqual(element.text, f"{content}")

test/repeat_entry_test.py

@@ -28,7 +28,7 @@ class RepeatEntryTest(unittest.TestCase):
     def test_initialization(self):
         """Test entry initialization"""
         script = "echo test"
-        entry = RepeatEntry(script, self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, script, None, None)
         
         self.assertEqual(entry.script, script)
         self.assertEqual(entry.stdout, "")
@@ -40,7 +40,7 @@ class RepeatEntryTest(unittest.TestCase):
     def test_successful_execution(self):
         """Test successful script execution"""
         script = "echo 'test'"
-        entry = RepeatEntry(script, self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         
         # Verify entry state
@@ -50,7 +50,7 @@ class RepeatEntryTest(unittest.TestCase):
         
     def test_failed_execution(self):
         """Test failed script execution with invalid command"""
-        entry = RepeatEntry("nonexistentcommand", self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, "nonexistentcommand", None, None)
         entry.update()
         
         # Verify entry state
@@ -78,7 +78,7 @@ class RepeatEntryTest(unittest.TestCase):
             f'"'
         )
         
-        entry = RepeatEntry(script, self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, script, None, None)
         
         # Run update multiple times
         outputs = []
@@ -92,13 +92,13 @@ class RepeatEntryTest(unittest.TestCase):
     def test_generate_context(self):
         """Test XML context generation"""
         script = "echo 'test'"
-        entry = RepeatEntry(script, self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         element = entry.generate_context()
         # Verify XML structure
         self.assertEqual(element.tag, "repeat")
         self.assertEqual(element.get("id"), self.test_id)
-        self.assertEqual(element.text, f"{script}")
+        self.assertEqual(element.text, script)
         self.assertEqual(element.get("exit_code"), "0")
         stdout_text = element.find("stdout").text
         self.assertEqual(stdout_text, "test\n")
@@ -124,7 +124,7 @@ class RepeatEntryTest(unittest.TestCase):
             f'"'
         )
         
-        entry = RepeatEntry(script, self.test_id, self.test_timestamp)
+        entry = RepeatEntry(self.test_id, self.test_timestamp, script, None, None)
         
         # Execute multiple times and verify output changes
         entry.update()

test/single_entry_test.py

@@ -26,7 +26,7 @@ class SingleEntryTest(unittest.TestCase):
     def test_initialization(self):
         """Test entry initialization"""
         script = "echo test"
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         
         self.assertEqual(entry.script, script)
         self.assertEqual(entry.stdout, "")
@@ -40,7 +40,7 @@ class SingleEntryTest(unittest.TestCase):
         """Test successful script execution"""
         script = "echo 'test'"
             
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         
         # Verify entry state
@@ -51,7 +51,7 @@ class SingleEntryTest(unittest.TestCase):
         
     def test_failed_execution(self):
         """Test failed script execution with invalid command"""
-        entry = SingleEntry("nonexistentcommand", self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, "nonexistentcommand", None, None)
         entry.update()
         
         # Verify entry state
@@ -64,7 +64,7 @@ class SingleEntryTest(unittest.TestCase):
         """Test script that creates a file"""
         script = f"echo 'test' > {self.test_filename}"
             
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         
         # Verify file was created and contains expected content
@@ -77,7 +77,7 @@ class SingleEntryTest(unittest.TestCase):
         """Test that script only executes once"""
         script = f"echo 'test' >> {self.test_filename}"
             
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         
         # Run update multiple times
         entry.update()
@@ -92,7 +92,7 @@ class SingleEntryTest(unittest.TestCase):
             
     def test_generate_context_before_execution(self):
         """Test XML context generation before execution"""
-        entry = SingleEntry("echo test", self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, "echo test", None, None)
         element = entry.generate_context()
         
         # Verify XML structure
@@ -109,7 +109,7 @@ class SingleEntryTest(unittest.TestCase):
         """Test XML context generation after execution"""
         script = "echo 'test'"
             
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         element = entry.generate_context()
         
@@ -128,7 +128,7 @@ class SingleEntryTest(unittest.TestCase):
         """Test executing multiple commands in one script"""
         script = f"echo 'first' > {self.test_filename} && echo 'second' >> {self.test_filename}"
             
-        entry = SingleEntry(script, self.test_id, self.test_timestamp)
+        entry = SingleEntry(self.test_id, self.test_timestamp, script, None, None)
         entry.update()
         
         # Verify file contains both lines

test/stop_command_test.py

@@ -27,7 +27,7 @@ class StopCommandTest(unittest.TestCase):
     def test_stop_command_cleanup(self):
         """Test stop command cleans up and removes all entries"""
         # Add background process
-        entry = BackgroundEntry("sleep 10", "test-id", self.test_timestamp)
+        entry = BackgroundEntry("test-id", self.test_timestamp, "sleep 10")
         self.memory.add_entry(entry)
         
         # Wait for process to start and get PID

test/working_memory_test.py

@@ -123,10 +123,10 @@ class WorkingMemoryTest(unittest.TestCase):
         
         # Add different types of entries
         entries = [
-            ReasoningEntry("test reasoning", "reasoning-1", self.test_timestamp),
-            ParseErrorEntry("bad content", "error msg", "error-1", self.test_timestamp),
-            ReadEntry(io_buffer, "read-1", self.test_timestamp),
-            WriteEntry("test output", io_buffer, "write-1", self.test_timestamp)
+            ReasoningEntry("reasoning-1", self.test_timestamp, "test reasoning"),
+            ParseErrorEntry("error-1", self.test_timestamp, "bad content", "error msg"),
+            ReadEntry("read-1", self.test_timestamp, io_buffer),
+            WriteEntry("write-1", self.test_timestamp, "test output", io_buffer)
         ]
         
         for entry in entries:
@@ -161,7 +161,7 @@ class WorkingMemoryTest(unittest.TestCase):
     def test_remove_entry_cleanup(self):
         """Test that removing an entry triggers cleanup"""
         # Create and start background process
-        entry = BackgroundEntry("sleep 10", "test-id", self.test_timestamp)
+        entry = BackgroundEntry("test-id", self.test_timestamp, "sleep 10")
         self.memory.add_entry(entry)
         
         # Wait for process to start and get PID
@@ -181,7 +181,7 @@ class WorkingMemoryTest(unittest.TestCase):
         # Add multiple background processes
         pids = []
         for i in range(3):
-            entry = BackgroundEntry("sleep 10", f"id-{i}", self.test_timestamp)
+            entry = BackgroundEntry(f"id-{i}", self.test_timestamp, "sleep 10")
             self.memory.add_entry(entry)
             self.assertTrue(self.wait_for_process_start(entry))
             context = entry.generate_context()
@@ -201,7 +201,7 @@ class WorkingMemoryTest(unittest.TestCase):
     def test_cleanup_on_memory_deletion(self):
         """Test that deleting memory properly cleans up all entries"""
         # Add a background process
-        entry = BackgroundEntry("sleep 10", "test-id", self.test_timestamp)
+        entry = BackgroundEntry("test-id", self.test_timestamp, "sleep 10")
         self.memory.add_entry(entry)
         
         # Wait for process to start and get PID
@@ -221,7 +221,7 @@ class WorkingMemoryTest(unittest.TestCase):
         """Test getting all entries"""
         # Add multiple entries
         entries = [
-            ReasoningEntry(f"content {i}", f"id-{i}", self.test_timestamp)
+            ReasoningEntry(f"id-{i}", self.test_timestamp, f"content {i}")
             for i in range(3)
         ]
         
@@ -239,7 +239,7 @@ class WorkingMemoryTest(unittest.TestCase):
     def test_get_entries_returns_copy(self):
         """Test that get_entries returns a copy of the list"""
         # Add an entry
-        entry = ReasoningEntry("test content", "test-id", self.test_timestamp)
+        entry = ReasoningEntry("test-id", self.test_timestamp, "test content")
         self.memory.add_entry(entry)
         
         # Get entries and modify the returned list

test/write_entry_test.py

@@ -14,7 +14,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_initialization(self):
         """Test entry initialization"""
         content = "test message"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         
         self.assertEqual(entry.content, content)
         self.assertEqual(entry.id, self.test_id)
@@ -25,7 +25,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_single_write(self):
         """Test writing content once"""
         content = "test message"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         
         # Perform update and verify content was written
         entry.update()
@@ -35,7 +35,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_multiple_updates(self):
         """Test that content is only written once even with multiple updates"""
         content = "test message"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         
         # Perform multiple updates
         entry.update()
@@ -52,7 +52,7 @@ class WriteEntryTest(unittest.TestCase):
         
     def test_empty_content(self):
         """Test writing empty content"""
-        entry = WriteEntry("", self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, "", self.io_buffer)
         entry.update()
         
         self.assertEqual(self.io_buffer.get_stdout(), "")
@@ -61,7 +61,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_special_characters(self):
         """Test writing content with special characters"""
         content = "Special chars: \n\t\r\'\"\\"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         entry.update()
         
         self.assertEqual(self.io_buffer.get_stdout(), content)
@@ -69,7 +69,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_large_content(self):
         """Test writing large content"""
         content = "x" * 10000
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         entry.update()
         
         self.assertEqual(self.io_buffer.get_stdout(), content)
@@ -77,7 +77,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_generate_context(self):
         """Test XML context generation"""
         content = "test message"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         
         # Generate context before writing
         element = entry.generate_context()
@@ -97,7 +97,7 @@ class WriteEntryTest(unittest.TestCase):
     def test_unicode_content(self):
         """Test writing Unicode content"""
         content = "Hello 世界 😊"
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         entry.update()
         
         self.assertEqual(self.io_buffer.get_stdout(), content)
@@ -107,7 +107,7 @@ class WriteEntryTest(unittest.TestCase):
         content = """Line 1
         Line 2
         Line 3"""
-        entry = WriteEntry(content, self.io_buffer, self.test_id, self.test_timestamp)
+        entry = WriteEntry(self.test_id, self.test_timestamp, content, self.io_buffer)
         entry.update()
         
         self.assertEqual(self.io_buffer.get_stdout(), content)