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Merged
merged 1 commit into from
Oct 26, 2024
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Move serialize to separate module #437

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42 changes: 2 additions & 40 deletions executorlib/shared/cache.py
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Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,14 @@
import hashlib
import importlib.util
import os
import queue
import re
import subprocess
import sys
from concurrent.futures import Future
from typing import Any, Tuple

import cloudpickle

from executorlib.shared.executor import get_command_path
from executorlib.shared.hdf import dump, get_output, load
from executorlib.shared.serialize import serialize_funct_h5


class FutureItem:
Expand Down Expand Up @@ -152,7 +149,7 @@ def execute_tasks_h5(
memory_dict=memory_dict,
file_name_dict=file_name_dict,
)
task_key, data_dict = _serialize_funct_h5(
task_key, data_dict = serialize_funct_h5(
task_dict["fn"], *task_args, **task_kwargs
)
if task_key not in memory_dict.keys():
Expand Down Expand Up @@ -228,41 +225,6 @@ def _get_execute_command(file_name: str, cores: int = 1) -> list:
return command_lst


def _get_hash(binary: bytes) -> str:
"""
Get the hash of a binary.

Args:
binary (bytes): The binary to be hashed.

Returns:
str: The hash of the binary.

"""
# Remove specification of jupyter kernel from hash to be deterministic
binary_no_ipykernel = re.sub(b"(?<=/ipykernel_)(.*)(?=/)", b"", binary)
return str(hashlib.md5(binary_no_ipykernel).hexdigest())


def _serialize_funct_h5(fn: callable, *args: Any, **kwargs: Any) -> Tuple[str, dict]:
"""
Serialize a function and its arguments and keyword arguments into an HDF5 file.

Args:
fn (callable): The function to be serialized.
*args (Any): The arguments of the function.
**kwargs (Any): The keyword arguments of the function.

Returns:
Tuple[str, dict]: A tuple containing the task key and the serialized data.

"""
binary_all = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
task_key = fn.__name__ + _get_hash(binary=binary_all)
data = {"fn": fn, "args": args, "kwargs": kwargs}
return task_key, data


def _check_task_output(
task_key: str, future_obj: Future, cache_directory: str
) -> Future:
Expand Down
40 changes: 40 additions & 0 deletions executorlib/shared/serialize.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,40 @@
import hashlib
import re
from typing import Any, Tuple

import cloudpickle


def serialize_funct_h5(fn: callable, *args: Any, **kwargs: Any) -> Tuple[str, dict]:
"""
Serialize a function and its arguments and keyword arguments into an HDF5 file.
Args:
fn (callable): The function to be serialized.
*args (Any): The arguments of the function.
**kwargs (Any): The keyword arguments of the function.
Returns:
Tuple[str, dict]: A tuple containing the task key and the serialized data.
"""
binary_all = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
task_key = fn.__name__ + _get_hash(binary=binary_all)
data = {"fn": fn, "args": args, "kwargs": kwargs}
return task_key, data
Comment on lines +8 to +24
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@coderabbitai coderabbitai bot Oct 26, 2024

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⚠️ Potential issue

Add input validation and error handling.

The function should validate inputs and handle serialization errors gracefully.

Consider applying these improvements:

 def serialize_funct_h5(fn: callable, *args: Any, **kwargs: Any) -> Tuple[str, dict]:
+    if not callable(fn):
+        raise TypeError("fn must be callable")
+    
+    try:
         binary_all = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
+    except Exception as e:
+        raise ValueError(f"Failed to serialize function and arguments: {str(e)}")
+
     task_key = fn.__name__ + _get_hash(binary=binary_all)
     data = {"fn": fn, "args": args, "kwargs": kwargs}
     return task_key, data
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
def serialize_funct_h5(fn: callable, *args: Any, **kwargs: Any) -> Tuple[str, dict]:
"""
Serialize a function and its arguments and keyword arguments into an HDF5 file.
Args:
fn (callable): The function to be serialized.
*args (Any): The arguments of the function.
**kwargs (Any): The keyword arguments of the function.
Returns:
Tuple[str, dict]: A tuple containing the task key and the serialized data.
"""
binary_all = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
task_key = fn.__name__ + _get_hash(binary=binary_all)
data = {"fn": fn, "args": args, "kwargs": kwargs}
return task_key, data
def serialize_funct_h5(fn: callable, *args: Any, **kwargs: Any) -> Tuple[str, dict]:
"""
Serialize a function and its arguments and keyword arguments into an HDF5 file.
Args:
fn (callable): The function to be serialized.
*args (Any): The arguments of the function.
**kwargs (Any): The keyword arguments of the function.
Returns:
Tuple[str, dict]: A tuple containing the task key and the serialized data.
"""
if not callable(fn):
raise TypeError("fn must be callable")
try:
binary_all = cloudpickle.dumps({"fn": fn, "args": args, "kwargs": kwargs})
except Exception as e:
raise ValueError(f"Failed to serialize function and arguments: {str(e)}")
task_key = fn.__name__ + _get_hash(binary=binary_all)
data = {"fn": fn, "args": args, "kwargs": kwargs}
return task_key, data



def _get_hash(binary: bytes) -> str:
"""
Get the hash of a binary.
Args:
binary (bytes): The binary to be hashed.
Returns:
str: The hash of the binary.
"""
# Remove specification of jupyter kernel from hash to be deterministic
binary_no_ipykernel = re.sub(b"(?<=/ipykernel_)(.*)(?=/)", b"", binary)
return str(hashlib.md5(binary_no_ipykernel).hexdigest())
Comment on lines +27 to +40
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@coderabbitai coderabbitai bot Oct 26, 2024

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🛠️ Refactor suggestion

Consider adding input validation and improving hash reliability.

The hash function could be more robust with input validation and a more reliable kernel path handling.

Consider these improvements:

 def _get_hash(binary: bytes) -> str:
+    if not isinstance(binary, bytes):
+        raise TypeError("Input must be bytes")
+
     # Remove specification of jupyter kernel from hash to be deterministic
-    binary_no_ipykernel = re.sub(b"(?<=/ipykernel_)(.*)(?=/)", b"", binary)
+    # Handle both Windows and Unix-style paths
+    binary_no_ipykernel = re.sub(
+        b"(?<=/ipykernel_|\\\\ipykernel_)(.*)(?=/|\\\\)",
+        b"",
+        binary
+    )
     return str(hashlib.md5(binary_no_ipykernel).hexdigest())

Also, consider adding a comment explaining why MD5 is sufficient for this use case:

# MD5 is used here for generating cache keys, not for security purposes

12 changes: 6 additions & 6 deletions tests/test_cache_shared.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,13 @@


try:
from executorlib.shared.hdf import dump
from executorlib.shared.cache import (
FutureItem,
execute_task_in_file,
_check_task_output,
_serialize_funct_h5,
)
from executorlib.shared.cache import execute_task_in_file
from executorlib.shared.hdf import dump
from executorlib.shared.serialize import serialize_funct_h5

skip_h5io_test = False
except ImportError:
Expand All @@ -29,7 +29,7 @@ class TestSharedFunctions(unittest.TestCase):
def test_execute_function_mixed(self):
cache_directory = os.path.abspath("cache")
os.makedirs(cache_directory, exist_ok=True)
task_key, data_dict = _serialize_funct_h5(
task_key, data_dict = serialize_funct_h5(
my_funct,
1,
b=2,
Expand All @@ -52,7 +52,7 @@ def test_execute_function_mixed(self):
def test_execute_function_args(self):
cache_directory = os.path.abspath("cache")
os.makedirs(cache_directory, exist_ok=True)
task_key, data_dict = _serialize_funct_h5(
task_key, data_dict = serialize_funct_h5(
my_funct,
1,
2,
Comment on lines +55 to 58
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@coderabbitai coderabbitai bot Oct 26, 2024

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🛠️ Refactor suggestion

Consider refactoring duplicate test code.

The test methods test_execute_function_args and test_execute_function_kwargs share significant code with test_execute_function_mixed. Consider extracting common test logic into a helper method to reduce duplication.

def _run_serialization_test(self, *args, **kwargs):
    cache_directory = os.path.abspath("cache")
    os.makedirs(cache_directory, exist_ok=True)
    
    task_key, data_dict = serialize_funct_h5(my_funct, *args, **kwargs)
    file_name = os.path.join(cache_directory, task_key + ".h5in")
    dump(file_name=file_name, data_dict=data_dict)
    execute_task_in_file(file_name=file_name)
    
    future_obj = Future()
    _check_task_output(
        task_key=task_key, 
        future_obj=future_obj, 
        cache_directory=cache_directory
    )
    
    self.assertTrue(future_obj.done())
    self.assertEqual(future_obj.result(), 3)
    future_file_obj = FutureItem(
        file_name=os.path.join(cache_directory, task_key + ".h5out")
    )
    self.assertTrue(future_file_obj.done())
    self.assertEqual(future_file_obj.result(), 3)

Then use it in your test methods:

def test_execute_function_mixed(self):
    self._run_serialization_test(1, b=2)

def test_execute_function_args(self):
    self._run_serialization_test(1, 2)

def test_execute_function_kwargs(self):
    self._run_serialization_test(a=1, b=2)

Also applies to: 78-81

Expand All @@ -75,7 +75,7 @@ def test_execute_function_args(self):
def test_execute_function_kwargs(self):
cache_directory = os.path.abspath("cache")
os.makedirs(cache_directory, exist_ok=True)
task_key, data_dict = _serialize_funct_h5(
task_key, data_dict = serialize_funct_h5(
my_funct,
a=1,
b=2,
Expand Down
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