Merge branch 'main' into name-conflict-error

common-workflow-language · Dec 3, 2020 · 0074471 · 0074471
2 parents ab858ed + 70dafe0
commit 0074471
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/cwltool/command_line_tool.py b/cwltool/command_line_tool.py
@@ -1214,7 +1214,7 @@ def collect_output(
                     rfile = files.copy()
                     revmap(rfile)
                     if files["class"] == "Directory":
-                        ll = schema.get("loadListing") or builder.loadListing
+                        ll = binding.get("loadListing") or builder.loadListing
                         if ll and ll != "no_listing":
                             get_listing(fs_access, files, (ll == "deep_listing"))
                     else:

diff --git a/cwltool/job.py b/cwltool/job.py
@@ -379,7 +379,7 @@ def _execute(
                 stderr_path=stderr_path,
                 env=env,
                 cwd=self.outdir,
-                job_dir=runtimeContext.create_outdir(),
+                make_job_dir=lambda: runtimeContext.create_outdir(),
                 job_script_contents=job_script_contents,
                 timelimit=self.timelimit,
                 name=self.name,
@@ -909,7 +909,7 @@ def _job_popen(
     stderr_path: Optional[str],
     env: MutableMapping[str, str],
     cwd: str,
-    job_dir: str,
+    make_job_dir: Callable[[], str],
     job_script_contents: Optional[str] = None,
     timelimit: Optional[int] = None,
     name: Optional[str] = None,
@@ -1004,11 +1004,12 @@ def terminate():  # type: () -> None
             "stdin_path": stdin_path,
         }
 
-        with open(
-            os.path.join(job_dir, "job.json"), mode="w", encoding="utf-8"
-        ) as job_file:
-            json_dump(job_description, job_file, ensure_ascii=False)
+        job_dir = make_job_dir()
         try:
+            with open(
+                os.path.join(job_dir, "job.json"), mode="w", encoding="utf-8"
+            ) as job_file:
+                json_dump(job_description, job_file, ensure_ascii=False)
             job_script = os.path.join(job_dir, "run_job.bash")
             with open(job_script, "wb") as _:
                 _.write(job_script_contents.encode("utf-8"))

diff --git a/cwltool/process.py b/cwltool/process.py
@@ -824,6 +824,7 @@ def inc(d):  # type: (List[int]) -> None
 
         files = []  # type: List[CWLObjectType]
         bindings = CommentedSeq()
+        outdir = ""
         tmpdir = ""
         stagedir = ""
 
@@ -852,8 +853,8 @@ def inc(d):  # type: (List[int]) -> None
             tmpdir = runtime_context.docker_tmpdir or "/tmp"  # nosec
             stagedir = runtime_context.docker_stagedir or "/var/lib/cwl"
         else:
-            outdir = fs_access.realpath(runtime_context.get_outdir())
-            if self.tool["class"] != "Workflow":
+            if self.tool["class"] == "CommandLineTool":
+                outdir = fs_access.realpath(runtime_context.get_outdir())
                 tmpdir = fs_access.realpath(runtime_context.get_tmpdir())
                 stagedir = fs_access.realpath(runtime_context.get_stagedir())