Merge branch '9567-keep-web-session-test'

[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 0601fa656b476ffcaef26e9b4aad80869b294c30..7107ba0a301ff9a80cf03386f78817ec021b2fd9 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -9,22 +9,32 @@ class ArvadosCommandTool(CommandLineTool):
     def __init__(self, arvrunner, toolpath_object, **kwargs):
         super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
         self.arvrunner = arvrunner
-        self.crunch2 = (kwargs["work_api"] == "containers")
+        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)"
+        return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)