more tmp_outdir_prefix

Author: mr-c

cwltool/executors.py

@@ -43,19 +43,18 @@ def run_jobs(self,
                  ):
         pass
 
-    def execute(self, t,  # type: Process
+    def execute(self,
+                t,                 # type: Process
                 job_order_object,  # type: Dict[Text, Any]
                 logger=_logger,
-                **kwargs  # type: Any
-                ):
-        # type: (...) -> Tuple[Dict[Text, Any], Text]
+                **kwargs           # type: Any
+                ):  # type: (...) -> Tuple[Dict[Text, Any], Text]
 
         if "basedir" not in kwargs:
             raise WorkflowException("Must provide 'basedir' in kwargs")
 
         finaloutdir = os.path.abspath(kwargs.get("outdir")) if kwargs.get("outdir") else None
-        kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"]) if kwargs.get(
-            "tmp_outdir_prefix") else tempfile.mkdtemp()
+        kwargs["outdir"] = tempfile.mkdtemp(prefix=kwargs.get("tmp_outdir_prefix"))
         self.output_dirs.add(kwargs["outdir"])
         kwargs["mutation_manager"] = MutationManager()
         kwargs["toplevel"] = True

cwltool/job.py

@@ -175,8 +175,14 @@ def _setup(self, kwargs):  # type: (Dict) -> None
             _logger.debug(u"[job %s] initial work dir %s", self.name,
                           json.dumps({p: self.generatemapper.mapper(p) for p in self.generatemapper.files()}, indent=4))
 
-    def _execute(self, runtime, env, rm_tmpdir=True, move_outputs="move", secret_store=None):
-        # type: (List[Text], MutableMapping[Text, Text], bool, Text, SecretStore) -> None
+    def _execute(self,
+                 runtime,                # type:List[Text]
+                 env,                    # type: MutableMapping[Text, Text]
+                 rm_tmpdir=True,         # type: bool
+                 move_outputs="move",    # type: Text
+                 secret_store=None,      # type: SecretStore
+                 tmp_outdir_prefix=None  # type: Text
+                ):  # type: (...) -> None
 
         scr, _ = get_feature(self, "ShellCommandRequirement")
 
@@ -228,14 +234,9 @@ def _execute(self, runtime, env, rm_tmpdir=True, move_outputs="move", secret_sto
             if builder is not None:
                 job_script_contents = builder.build_job_script(commands)
             rcode = _job_popen(
-                commands,
-                stdin_path=stdin_path,
-                stdout_path=stdout_path,
-                stderr_path=stderr_path,
-                env=env,
-                cwd=self.outdir,
-                job_script_contents=job_script_contents,
-            )
+                commands, stdin_path, stdout_path, stderr_path, env,
+                self.outdir, tempfile.mkdtemp(prefix=tmp_outdir_prefix),
+                job_script_contents)
 
             if self.successCodes and rcode in self.successCodes:
                 processStatus = "success"
@@ -415,16 +416,15 @@ def run(self, pull_image=True, rm_container=True,
 
 
 def _job_popen(
-        commands,  # type: List[Text]
-        stdin_path,  # type: Text
-        stdout_path,  # type: Text
-        stderr_path,  # type: Text
+        commands,                  # type: List[Text]
+        stdin_path,                # type: Text
+        stdout_path,               # type: Text
+        stderr_path,               # type: Text
         env,  # type: Union[MutableMapping[Text, Text], MutableMapping[str, str]]
-        cwd,  # type: Text
-        job_dir=None,  # type: Text
+        cwd,                       # type: Text
+        job_dir,                   # type: Text
         job_script_contents=None,  # type: Text
-):
-    # type: (...) -> int
+       ):  # type: (...) -> int
     if not job_script_contents and not FORCE_SHELLED_POPEN:
 
         stdin = None  # type: Union[IO[Any], int]
@@ -471,9 +471,6 @@ def _job_popen(
 
         return rcode
     else:
-        if job_dir is None:
-            job_dir = tempfile.mkdtemp(prefix="cwltooljob")
-
         if not job_script_contents:
             job_script_contents = SHELL_COMMAND_TEMPLATE
 

cwltool/workflow.py

@@ -179,14 +179,8 @@ def __init__(self, workflow, **kwargs):
         self.state = None  # type: Dict[Text, WorkflowStateItem]
         self.processStatus = None  # type: Text
         self.did_callback = False
-
-        if "outdir" in kwargs:
-            self.outdir = kwargs["outdir"]
-        elif "tmp_outdir_prefix" in kwargs:
-            self.outdir = tempfile.mkdtemp(prefix=kwargs["tmp_outdir_prefix"])
-        else:
-            # tmp_outdir_prefix defaults to tmp, so this is unlikely to be used
-            self.outdir = tempfile.mkdtemp()
+        self.outdir = kwargs.get("outdir")
+        self.outdir = tempfile.mkdtemp(prefix=kwargs.get("tmp_outdir_prefix"))
 
         self.name = uniquename(u"workflow %s" % kwargs.get("name", shortname(self.workflow.tool.get("id", "embedded"))))