Deal with mypy

Author: stxue1

cwltool/command_line_tool.py

@@ -877,15 +877,10 @@ def remove_prefix(s: str, prefix: str) -> str:
                         keydict[cls] = r
 
             # If there are environmental variables to preserve, add it to the key
-            env_def = dict(cast(Mapping[str, str], keydict.get("EnvVarRequirement", {})))
-            env_requirement, _ = self.get_requirement("EnvVarRequirement")
-            if env_requirement:
-                for req in cast(list[CWLObjectType], env_requirement["envDef"]):
-                    env_name = cast(str, req["envName"])
-                    env_value = cast(str, req["envValue"])
-                    env_def[env_name] = env_value
+            env_var_requirement = cast(dict[str, str], keydict.get("EnvVarRequirement", {}))
+            env_def = cast(CWLObjectType, self.get_requirement("EnvVarRequirement")[0])
             if runtimeContext.preserve_environment is not None:
-                env_def = JobBase.extract_environment(runtimeContext, env_def)
+                env_def.update(JobBase.extract_environment(runtimeContext, env_var_requirement))
 
             if env_def:
                 keydict["EnvVarRequirement"] = env_def

cwltool/job.py

@@ -472,7 +472,7 @@ def _preserve_environment_on_containers_warning(
     @staticmethod
     def extract_environment(
         runtimeContext: RuntimeContext, envVarReq: Mapping[str, str]
-    ) -> dict[str, str]:
+    ) -> Mapping[str, str]:
         """
         Extract environment variables that should be preserved
         """
@@ -490,7 +490,7 @@ def extract_environment(
                         f"Attempting to preserve environment variable {key!r} which is not present"
                     )
         # Apply EnvVarRequirement
-        env.update()
+        env.update(envVarReq)
 
         return env