13681: Revert to yaml.round_trip_dump instead of json.dumps().

[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 35a068f91be7b28b7eebd0f32538e9222367d8a1..119acc30392ceb9f124a6d0101c0868beeb6c1ae 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -2,45 +2,59 @@
 #
 # 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
+from functools import partial
 
 class ArvadosCommandTool(CommandLineTool):
     """Wrap cwltool CommandLineTool to override selected methods."""
 
-    def __init__(self, arvrunner, toolpath_object, **kwargs):
-        super(ArvadosCommandTool, self).__init__(toolpath_object, **kwargs)
+    def __init__(self, arvrunner, toolpath_object, loadingContext):
+        super(ArvadosCommandTool, self).__init__(toolpath_object, loadingContext)
         self.arvrunner = arvrunner
-        self.work_api = kwargs["work_api"]
-
-    def makeJobRunner(self, use_container=True):
-        if self.work_api == "containers":
-            return ArvadosContainer(self.arvrunner)
-        elif self.work_api == "jobs":
-            return ArvadosJob(self.arvrunner)
-
-    def makePathMapper(self, reffiles, stagedir, **kwargs):
-        # type: (List[Any], unicode, **Any) -> PathMapper
-        if self.work_api == "containers":
-            return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+
+    def make_job_runner(self, runtimeContext):
+        if runtimeContext.work_api == "containers":
+            return partial(ArvadosContainer, self.arvrunner)
+        elif runtimeContext.work_api == "jobs":
+            return partial(ArvadosJob, self.arvrunner)
+        else:
+            raise Exception("Unsupported work_api %s", runtimeContext.work_api)
+
+    def make_path_mapper(self, reffiles, stagedir, runtimeContext, separateDirs):
+        if runtimeContext.work_api == "containers":
+            return ArvPathMapper(self.arvrunner, reffiles+runtimeContext.extra_reffiles, runtimeContext.basedir,
                                  "/keep/%s",
-                                 "/keep/%s/%s",
-                                 **kwargs)
-        elif self.work_api == "jobs":
-            return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+                                 "/keep/%s/%s")
+        elif runtimeContext.work_api == "jobs":
+            return ArvPathMapper(self.arvrunner, reffiles, runtimeContext.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)
+                                 "$(task.keep)/%s/%s")
+
+    def job(self, joborder, output_callback, runtimeContext):
+
+        # Workaround for #13365
+        builderargs = runtimeContext.copy()
+        builderargs.toplevel = True
+        builderargs.tmp_outdir_prefix = ""
+        builder = self._init_job(joborder, builderargs)
+        joborder = builder.job
+
+        runtimeContext = runtimeContext.copy()
+
+        if runtimeContext.work_api == "containers":
+            dockerReq, is_req = self.get_requirement("DockerRequirement")
+            if dockerReq and dockerReq.get("dockerOutputDirectory"):
+                runtimeContext.outdir = dockerReq.get("dockerOutputDirectory")
+                runtimeContext.docker_outdir = dockerReq.get("dockerOutputDirectory")
+            else:
+                runtimeContext.outdir = "/var/spool/cwl"
+                runtimeContext.docker_outdir = "/var/spool/cwl"
+        elif runtimeContext.work_api == "jobs":
+            runtimeContext.outdir = "$(task.outdir)"
+            runtimeContext.docker_outdir = "$(task.outdir)"
+            runtimeContext.tmpdir = "$(task.tmpdir)"
+            runtimeContext.docker_tmpdir = "$(task.tmpdir)"
+        return super(ArvadosCommandTool, self).job(joborder, output_callback, runtimeContext)