feat: add callback for log copying

Author: kannon92

cwltool/context.py

@@ -1,6 +1,7 @@
 """Shared context objects that replace use of kwargs."""
 import copy
 import os
+import shutil
 import tempfile
 import threading
 from typing import (
@@ -55,6 +56,21 @@ def make_tool_notimpl(
 
 default_make_tool = make_tool_notimpl
 
+# Move logs from log location to final output
+def log_handler(
+    outdir: str,
+    base_path_logs: str,
+    stdout_path: Optional[str],
+    stderr_path: Optional[str],
+) -> None:
+    if outdir != base_path_logs:
+        if stdout_path:
+            new_stdout_path = stdout_path.replace(base_path_logs, outdir)
+            shutil.copy2(stdout_path, new_stdout_path)
+        if stderr_path:
+            new_stderr_path = stderr_path.replace(base_path_logs, outdir)
+            shutil.copy2(stderr_path, new_stderr_path)
+
 
 class LoadingContext(ContextBase):
     def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
@@ -119,6 +135,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.rm_container = True  # type: bool
         self.move_outputs = "move"  # type: str
         self.log_dir = ""  # type: str
+        self.log_dir_handler = log_handler
         self.streaming_allowed: bool = False
 
         self.singularity = False  # type: bool

cwltool/job.py

@@ -31,7 +31,6 @@
     Union,
     cast,
 )
-
 import psutil
 import shellescape
 from prov.model import PROV
@@ -393,19 +392,9 @@ def stderr_stdout_log_path(
                         "'listing' in self.generatefiles but no "
                         "generatemapper was setup."
                     )
-            # Move logs from log location to final output
-            if self.outdir != self.base_path_logs:
-                if stdout_path:
-                    new_stdout_path = stdout_path.replace(
-                        self.base_path_logs, self.outdir
-                    )
-                    shutil.copy2(stdout_path, new_stdout_path)
-                if stderr_path:
-                    new_stderr_path = stderr_path.replace(
-                        self.base_path_logs, self.outdir
-                    )
-                    shutil.copy2(stderr_path, new_stderr_path)
-
+            runtimeContext.log_dir_handler(
+                self.outdir, self.base_path_logs, stdout_path, stderr_path
+            )
             outputs = self.collect_outputs(self.outdir, rcode)
             outputs = bytes2str_in_dicts(outputs)  # type: ignore
         except OSError as e: