X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/6c43be47cb3756a0e6ffc924572259d1a1c8f2c3..ad4344e21db3c894869d09fdcb09e3202bf9cf78:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index a2c5c9e498..987ce8967a 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -6,25 +6,37 @@ from .pathmapper import ArvPathMapper
 class ArvadosCommandTool(CommandLineTool):
     """Wrap cwltool CommandLineTool to override selected methods."""
 
-    def __init__(self, arvrunner, toolpath_object, crunch2, **kwargs):
+    def __init__(self, arvrunner, toolpath_object, **kwargs):
         super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
         self.arvrunner = arvrunner
-        self.crunch2 = crunch2
+        self.work_api = kwargs["work_api"]
 
     def makeJobRunner(self):
-        if self.crunch2:
+        if self.work_api == "containers":
             return ArvadosContainer(self.arvrunner)
-        else:
+        elif self.work_api == "jobs":
             return ArvadosJob(self.arvrunner)
 
-    def makePathMapper(self, reffiles, **kwargs):
-        if self.crunch2:
+    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",
                                  "/keep/%s/%s",
                                  **kwargs)
-        else:
+        elif self.work_api == "jobs":
             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
                                  "$(task.keep)/%s",
                                  "$(task.keep)/%s/%s",
                                  **kwargs)
+
+    def job(self, joborder, output_callback, **kwargs):
+        if self.work_api == "containers":
+            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)