fix: fix quoting of string arguments that are passed to spawned jobs (#60)

Co-authored-by: Christian Meesters <meesters@uni-mainz.de>

Author: johanneskoester

snakemake_interface_executor_plugins/utils.py

@@ -6,6 +6,7 @@
 import asyncio
 from collections import UserDict
 from pathlib import Path
+import re
 import shlex
 import threading
 from typing import Any, List
@@ -39,16 +40,25 @@ def format_cli_pos_arg(value, quote=True):
     elif not_iterable(value):
         return format_cli_value(value)
     else:
-        return join_cli_args(format_cli_value(v) for v in value)
+        return join_cli_args(
+            format_cli_value(v, quote_if_contains_whitespace=True) for v in value
+        )
 
 
-def format_cli_value(value: Any) -> str:
+def format_cli_value(value: Any, quote_if_contains_whitespace: bool = False) -> str:
     if isinstance(value, SettingsEnumBase):
         return value.item_to_choice()
     elif isinstance(value, Path):
         return shlex.quote(str(value))
     elif isinstance(value, str):
-        return shlex.quote(value)
+        if is_quoted(value):
+            # the value is already quoted, do not quote again
+            return value
+        elif quote_if_contains_whitespace and " " in value:
+            # may be expression
+            return repr(value)
+        else:
+            return value
     else:
         return repr(value)
 
@@ -99,3 +109,10 @@ async def async_lock(_lock: threading.Lock):
         yield  # the lock is held
     finally:
         _lock.release()
+
+
+_is_quoted_re = re.compile(r"^['\"].+['\"]")
+
+
+def is_quoted(value: str) -> bool:
+    return _is_quoted_re.match(value) is not None

tests/tests.py

@@ -3,6 +3,7 @@
 from snakemake_interface_common.plugin_registry.tests import TestRegistryBase
 from snakemake_interface_common.plugin_registry.plugin import PluginBase, SettingsBase
 from snakemake_interface_common.plugin_registry import PluginRegistryBase
+from snakemake_interface_executor_plugins.utils import format_cli_arg
 
 
 class TestRegistry(TestRegistryBase):
@@ -26,3 +27,30 @@ def validate_settings(self, settings: SettingsBase, plugin: PluginBase):
 
     def get_example_args(self) -> List[str]:
         return ["--cluster-generic-submit-cmd", "qsub"]
+
+
+def test_format_cli_arg_single_quote():
+    fmt = format_cli_arg("--default-resources", {"slurm_extra": "'--gres=gpu:1'"})
+    assert fmt == "--default-resources \"slurm_extra='--gres=gpu:1'\""
+
+
+def test_format_cli_arg_double_quote():
+    fmt = format_cli_arg("--default-resources", {"slurm_extra": '"--gres=gpu:1"'})
+    assert fmt == "--default-resources 'slurm_extra=\"--gres=gpu:1\"'"
+
+
+def test_format_cli_arg_int():
+    fmt = format_cli_arg("--default-resources", {"mem_mb": 200})
+    assert fmt == "--default-resources 'mem_mb=200'"
+
+
+def test_format_cli_arg_expr():
+    fmt = format_cli_arg(
+        "--default-resources", {"mem_mb": "min(2 * input.size_mb, 2000)"}
+    )
+    assert fmt == "--default-resources 'mem_mb=min(2 * input.size_mb, 2000)'"
+
+
+def test_format_cli_arg_list():
+    fmt = format_cli_arg("--config", ["foo={'bar': 1}"])
+    assert fmt == "--config \"foo={'bar': 1}\""