Merge branch 'thehyve/fix-crunch-documentation' Fix a typo in Crunch Dispatch install...

[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 b667dac1ca5cec6f272c390be8fcd17e1628764c..8268300e75b66d6f82b999f649003ec3a0615bbf 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -2,7 +2,7 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
-from cwltool.draft2tool import CommandLineTool
+from cwltool.command_line_tool import CommandLineTool
 from .arvjob import ArvadosJob
 from .arvcontainer import ArvadosContainer
 from .pathmapper import ArvPathMapper
@@ -24,7 +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)
@@ -35,9 +35,21 @@ class ArvadosCommandTool(CommandLineTool):
                                  **kwargs)
 
     def job(self, joborder, output_callback, **kwargs):
+
+        # Workaround for #13365
+        builderargs = kwargs.copy()
+        builderargs["toplevel"] = True
+        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)"