13108: Fix tracking tasks in flight

[arvados.git] / sdk / cwl / arvados_cwl / arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 7347eacaacd3044367460b43b889f004600651fd..de329796e42384a18d4f4f669103c3fcb8a982a5 100644 (file)
--- 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
@@ -11,13 +15,14 @@ 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":
             return ArvadosJob(self.arvrunner)
 
-    def makePathMapper(self, reffiles, **kwargs):
+    def makePathMapper(self, reffiles, stagedir, **kwargs):
+        # type: (List[Any], unicode, **Any) -> PathMapper
         if self.work_api == "containers":
             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
                                  "/keep/%s",
@@ -30,5 +35,17 @@ class ArvadosCommandTool(CommandLineTool):
                                  **kwargs)
 
     def job(self, joborder, output_callback, **kwargs):
-        kwargs["outdir"] = "$(task.outdir)"
+        if self.work_api == "containers":
+            dockerReq, is_req = self.get_requirement("DockerRequirement")
+            if dockerReq and dockerReq.get("dockerOutputDirectory"):
+                kwargs["outdir"] = dockerReq.get("dockerOutputDirectory")
+                kwargs["docker_outdir"] = dockerReq.get("dockerOutputDirectory")
+            else:
+                kwargs["outdir"] = "/var/spool/cwl"
+                kwargs["docker_outdir"] = "/var/spool/cwl"
+        elif self.work_api == "jobs":
+            kwargs["outdir"] = "$(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)