X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b7b9ea44ada30b1251fb10c872cb1da1d7c29bd0..e3483661acc3d26d4532a536bd40ed761c21d7d1:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 7107ba0a30..fea6adfacc 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -1,4 +1,8 @@
-from cwltool.draft2tool import CommandLineTool
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from cwltool.command_line_tool import CommandLineTool
 from .arvjob import ArvadosJob
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
@@ -11,7 +15,7 @@ class ArvadosCommandTool(CommandLineTool):
         self.arvrunner = arvrunner
         self.work_api = kwargs["work_api"]
 
-    def makeJobRunner(self):
+    def makeJobRunner(self, **kwargs):
         if self.work_api == "containers":
             return ArvadosContainer(self.arvrunner)
         elif self.work_api == "jobs":
@@ -20,7 +24,7 @@ class ArvadosCommandTool(CommandLineTool):
     def makePathMapper(self, reffiles, stagedir, **kwargs):
         # type: (List[Any], unicode, **Any) -> PathMapper
         if self.work_api == "containers":
-            return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+            return ArvPathMapper(self.arvrunner, reffiles+kwargs.get("extra_reffiles", []), kwargs["basedir"],
                                  "/keep/%s",
                                  "/keep/%s/%s",
                                  **kwargs)
@@ -31,10 +35,25 @@ class ArvadosCommandTool(CommandLineTool):
                                  **kwargs)
 
     def job(self, joborder, output_callback, **kwargs):
+
+        # Workaround for #13365
+        builderargs = kwargs.copy()
+        builderargs["toplevel"] = True
+        builderargs["tmp_outdir_prefix"] = ""
+        builder = self._init_job(joborder, **builderargs)
+        joborder = builder.job
+
         if self.work_api == "containers":
-            kwargs["outdir"] = "/var/spool/cwl"
-            kwargs["docker_outdir"] = "/var/spool/cwl"
+            dockerReq, is_req = self.get_requirement("DockerRequirement")
+            if dockerReq and dockerReq.get("dockerOutputDirectory"):
+                kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
+                kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
+            else:
+                kwargs["outdir"] = "/var/spool/cwl"
+                kwargs["docker_outdir"] = "/var/spool/cwl"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
             kwargs["docker_outdir"] = "$(task.outdir)"
+            kwargs["tmpdir"] = "$(task.tmpdir)"
+            kwargs["docker_tmpdir"] = "$(task.tmpdir)"
         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)