feat: Enable logging to host system as container runs

Author: kannon92

cwltool/argparser.py

@@ -40,6 +40,14 @@ def arg_parser() -> argparse.ArgumentParser:
         help="Output directory. The default is the current directory.",
     )
 
+    parser.add_argument(
+        "--log-host",
+        type=str,
+        default="",
+        help="Output directory. The default is the current directory.",
+    )
+
+
     parser.add_argument(
         "--parallel",
         action="store_true",

cwltool/context.py

@@ -118,6 +118,7 @@ def __init__(self, kwargs: Optional[Dict[str, Any]] = None) -> None:
         self.pull_image = True  # type: bool
         self.rm_container = True  # type: bool
         self.move_outputs = "move"  # type: str
+        self.log_host = ""
         self.streaming_allowed: bool = False
 
         self.singularity = False  # type: bool

cwltool/job.py

@@ -267,6 +267,9 @@ def _execute(
             menv.pass_through_env_vars(env)
             menv.set_env_vars(env)
 
+        outdir_stdout_stderr =  self.outdir if runtimeContext.log_host == "" else runtimeContext.log_host
+
+
         _logger.info(
             "[job %s] %s$ %s%s%s%s",
             self.name,
@@ -278,8 +281,8 @@ def _execute(
                 ]
             ),
             " < %s" % self.stdin if self.stdin else "",
-            " > %s" % os.path.join(self.outdir, self.stdout) if self.stdout else "",
-            " 2> %s" % os.path.join(self.outdir, self.stderr) if self.stderr else "",
+            " > %s" % os.path.join(outdir_stdout_stderr, self.stdout) if self.stdout else "",
+            " 2> %s" % os.path.join(outdir_stdout_stderr, self.stderr) if self.stderr else "",
         )
         if self.joborder is not None and runtimeContext.research_obj is not None:
             job_order = self.joborder
@@ -308,21 +311,22 @@ def _execute(
                     stdin_path = rmap[1]
 
             stderr_path = None
+            outdir_stdout_stderr =  self.outdir if runtimeContext.log_host == "" else runtimeContext.log_host
             if self.stderr is not None:
-                abserr = os.path.join(self.outdir, self.stderr)
+                abserr = os.path.join(outdir_stdout_stderr, self.stderr)
                 dnerr = os.path.dirname(abserr)
                 if dnerr and not os.path.exists(dnerr):
                     os.makedirs(dnerr)
                 stderr_path = abserr
 
             stdout_path = None
             if self.stdout is not None:
-                absout = os.path.join(self.outdir, self.stdout)
+                absout = os.path.join(outdir_stdout_stderr, self.stdout)
                 dnout = os.path.dirname(absout)
                 if dnout and not os.path.exists(dnout):
                     os.makedirs(dnout)
                 stdout_path = absout
-
+            _logger.debug("stderr: %s stdout: %s hostdir: %s", stderr_path, stdout_path, outdir_stdout_stderr)
             commands = [str(x) for x in runtime + self.command_line]
             if runtimeContext.secret_store is not None:
                 commands = cast(

cwltool/main.py

@@ -1262,6 +1262,9 @@ def main(
                 runtimeContext.move_outputs = "copy"
             runtimeContext.tmp_outdir_prefix = args.cachedir
 
+        if args.log_host:
+            runtimeContext.log_host = args.log_host
+
         runtimeContext.secret_store = getdefault(
             runtimeContext.secret_store, SecretStore()
         )