Oops, we were defaulting to preserving the entire environment!

Author: mr-c

cwltool/job.py

@@ -442,9 +442,9 @@ def run(self,
 
         env = self.environment
         vars_to_preserve = runtimeContext.preserve_environment
-        if runtimeContext.preserve_entire_environment is not None:
+        if runtimeContext.preserve_entire_environment is not False:
             vars_to_preserve = os.environ
-        if vars_to_preserve is not None:
+        if vars_to_preserve:
             for key, value in os.environ.items():
                 if key in vars_to_preserve and key not in env:
                     # On Windows, subprocess env can't handle unicode.

tests/env.cwl

@@ -0,0 +1,13 @@
+cwlVersion: v1.0
+class: CommandLineTool
+inputs: []
+requirements:
+  ShellCommandRequirement: {}
+baseCommand: echo
+arguments:
+  - valueFrom: >
+      {\\"env_count\\": \$(env | wc -l)}
+    shellQuote: False
+stdout: cwl.output.json
+outputs:
+  env_count: int

tests/test_examples.py

@@ -931,3 +931,12 @@ def test_optional_numeric_output_0():
     assert "completed success" in stderr
     assert error_code == 0
     assert json.loads(stdout)['out'] == 0
+
+def test_env_filtering():
+    test_file = "tests/env.cwl"
+    error_code, stdout, stderr = get_main_output(
+        [get_data(test_file)])
+
+    assert "completed success" in stderr
+    assert error_code == 0
+    assert json.loads(stdout)['env_count'] == 4