Moved kill_processes to sandbox destructor (#140)

The order of object destruction in Python is undefined, so it is not
safe to call an external function inside a __del__ method. By moving the
function body directly inside the destructor we can avoid None reference
errors.

Author: GlassOfWhiskey

cwl_utils/sandboxjs.py

@@ -28,7 +28,7 @@
 from cwl_utils.errors import JavascriptException, WorkflowException
 from cwl_utils.loghandler import _logger
 from cwl_utils.types import CWLOutputType
-from cwl_utils.utils import kill_processes, singularity_supports_userns
+from cwl_utils.utils import singularity_supports_userns
 
 default_timeout = 20
 
@@ -101,7 +101,35 @@ def __init__(
 
     def __del__(self) -> None:
         try:
-            kill_processes(self.processes_to_kill)
+            while self.processes_to_kill:
+                process = self.processes_to_kill.popleft()
+                if isinstance(process.args, MutableSequence):
+                    args = process.args
+                else:
+                    args = [process.args]
+                cidfile = [
+                    str(arg).split("=")[1] for arg in args if "--cidfile" in str(arg)
+                ]
+                if cidfile:  # Try to be nice
+                    try:
+                        with open(cidfile[0]) as inp_stream:
+                            p = subprocess.Popen(  # nosec
+                                ["docker", "kill", inp_stream.read()],
+                                shell=False,  # nosec
+                            )
+                            try:
+                                p.wait(timeout=10)
+                            except subprocess.TimeoutExpired:
+                                p.kill()
+                    except FileNotFoundError:
+                        pass
+                if process.stdin:
+                    process.stdin.close()
+                try:
+                    process.wait(10)
+                except subprocess.TimeoutExpired:
+                    pass
+                process.kill()
         except TypeError:
             pass
 

cwl_utils/utils.py

@@ -6,9 +6,12 @@
 import urllib.parse
 import urllib.request
 from copy import deepcopy
+
+from ruamel.yaml.main import YAML
+from ruamel.yaml.parser import ParserError
+from ruamel.yaml.scanner import ScannerError
 from typing import (
     Any,
-    Deque,
     Dict,
     List,
     MutableMapping,
@@ -18,10 +21,6 @@
     Union,
 )
 
-from ruamel.yaml.main import YAML
-from ruamel.yaml.parser import ParserError
-from ruamel.yaml.scanner import ScannerError
-
 from cwl_utils.errors import MissingKeyField
 from cwl_utils.loghandler import _logger
 
@@ -78,37 +77,6 @@ def bytes2str_in_dicts(
     return inp
 
 
-def kill_processes(
-    processes_to_kill,  # type: Deque[subprocess.Popen[str]]
-) -> None:
-    while processes_to_kill:
-        process = processes_to_kill.popleft()
-        if isinstance(process.args, MutableSequence):
-            args = process.args
-        else:
-            args = [process.args]
-        cidfile = [str(arg).split("=")[1] for arg in args if "--cidfile" in str(arg)]
-        if cidfile:  # Try to be nice
-            try:
-                with open(cidfile[0]) as inp_stream:
-                    p = subprocess.Popen(  # nosec
-                        ["docker", "kill", inp_stream.read()], shell=False  # nosec
-                    )
-                    try:
-                        p.wait(timeout=10)
-                    except subprocess.TimeoutExpired:
-                        p.kill()
-            except FileNotFoundError:
-                pass
-        if process.stdin:
-            process.stdin.close()
-        try:
-            process.wait(10)
-        except subprocess.TimeoutExpired:
-            pass
-        process.kill()
-
-
 def load_linked_file(
     base_url: urllib.parse.ParseResult, link: str, is_import: bool = False
 ) -> Tuple[Any, urllib.parse.ParseResult]: