Fix: Honor EnvVarRequirement on workflow steps with --preserve-entire…

cwltool/job.py

@@ -511,11 +511,16 @@ def prepare_environment(
         elif runtimeContext.preserve_environment:
             self._preserve_environment_on_containers_warning(runtimeContext.preserve_environment)
 
-        env.update(self.extract_environment(runtimeContext, envVarReq))
-
         # Set required env vars
+        # Preserve host variables first.
+        env.update(self.extract_environment(runtimeContext, {}))
+
+        # Keep required CWL runtime vars deterministic.
         env.update(self._required_env())
 
+        # Allow explicit EnvVarRequirement to override defaults.
+        env.update(envVarReq)
+
         # Set on ourselves
         self.environment = env
 

tests/env-preserve-step-tool.cwl

@@ -0,0 +1,11 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+inputs: []
+baseCommand: env
+arguments: ["-0"]
+
+outputs:
+  env:
+    type: stdout

tests/env-preserve-step-wf.cwl

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: Workflow
+
+inputs: []
+
+outputs:
+  env:
+    type: File
+    outputSource: env_step/env
+
+steps:
+  env_step:
+    run: env-preserve-step-tool.cwl
+    in: []
+    out: [env]
+    requirements:
+      EnvVarRequirement:
+        envDef:
+          TMPDIR: /custom/tmpdir

tests/test_environment.py

@@ -1,5 +1,7 @@
 """Test passing of environment variables to tools."""
 
+import io
+import json
 import os
 from abc import ABC, abstractmethod
 from collections.abc import Callable, Mapping
@@ -9,13 +11,17 @@
 import pytest
 from packaging.version import Version
 
+from cwltool.env_to_stdout import deserialize_env
+from cwltool.main import main
 from cwltool.singularity import get_version
 
 from .util import (
     env_accepts_null,
+    get_data,
     get_tool_env,
     needs_docker,
     needs_singularity_not_apptainer,
+    working_directory,
 )
 
 # None => accept anything, just require the key is present
@@ -313,3 +319,70 @@ def test_preserve_all(
                 raise
             # Other variables can be overridden
             assert val == os.environ[vname]
+
+
+def test_preserve_entire_environment_honors_step_env_requirements(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+) -> None:
+    """Test that step EnvVarRequirement is honored with --preserve-entire-environment.
+
+    This test verifies the fix for the bug where EnvRequirements set on
+    workflow steps are not honored when using --preserve-entire-environment.
+    """
+    tmp_prefix = str(tmp_path / "canary")
+
+    # Create a simple test environment variable that should be preserved
+    extra_env = {
+        "TEST_PRESERVED_VAR": "should_be_preserved",
+    }
+
+    # Prepare arguments for cwltool
+    args = [
+        "--no-container",
+        f"--tmpdir-prefix={tmp_prefix}",
+        "--preserve-entire-environment",
+        get_data("tests/env-preserve-step-wf.cwl"),
+    ]
+
+    # Add extra env vars
+    for k, v in extra_env.items():
+        monkeypatch.setenv(k, v)
+
+    # Run cwltool
+    stdout = io.StringIO()
+    stderr = io.StringIO()
+
+    with working_directory(tmp_path):
+        rc = main(argsl=args, stdout=stdout, stderr=stderr)
+
+    assert (
+        rc == 0
+    ), f"cwltool failed with rc={rc}\nstdout:\n{stdout.getvalue()}\nstderr:\n{stderr.getvalue()}"
+
+    # Parse the output
+    output = json.loads(stdout.getvalue())
+    env_file = output["env"]["path"]
+
+    # Read and deserialize the environment from the file
+    with open(env_file) as f:
+        env = deserialize_env(f.read())
+
+    # Verify that the step's EnvVarRequirement is honored
+    # The step has: EnvVarRequirement with envDef: TMPDIR: /custom/tmpdir
+    # This should override the --tmpdir-prefix setting
+    assert "TMPDIR" in env, f"TMPDIR not found in environment. " f"Environment: {env}"
+    assert env["TMPDIR"] == "/custom/tmpdir", (
+        f"EnvVarRequirement value not set correctly. "
+        f"Expected '/custom/tmpdir', got {env.get('TMPDIR')!r} "
+        f"(This indicates the bug - step's EnvVarRequirement is being ignored)"
+    )
+
+    # Verify that preserved environment variables are also present
+    assert "TEST_PRESERVED_VAR" in env, (
+        f"Environment variable should be preserved with --preserve-entire-environment. "
+        f"Environment: {env}"
+    )
+    assert env["TEST_PRESERVED_VAR"] == "should_be_preserved", (
+        f"Preserved environment variable has wrong value. "
+        f"Expected 'should_be_preserved', got {env.get('TEST_PRESERVED_VAR')!r}"
+    )