14325: Merge branch 'master'

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

diff --git a/sdk/cwl/arvados_cwl/arvjob.py b/sdk/cwl/arvados_cwl/arvjob.py
index c6616c9873d62d1a6070b80cc2d3fd6ab7652cdf..69fe7e2a8f1b632675b16eeb3f6ad07ee76c00e8 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -2,6 +2,10 @@
 #
 # SPDX-License-Identifier: Apache-2.0
 
+from past.builtins import basestring
+from builtins import object
+from future.utils import viewitems
+
 import logging
 import re
 import copy
@@ -67,7 +71,7 @@ class ArvadosJob(JobBase):
                                                     keep_client=self.arvrunner.keep_client,
                                                     num_retries=self.arvrunner.num_retries)
                 script_parameters["task.vwd"] = {}
-                generatemapper = VwdPathMapper([self.generatefiles], "", "",
+                generatemapper = VwdPathMapper(self.generatefiles["listing"], "", "",
                                                separateDirs=False)
 
                 with Perf(metrics, "createfiles %s" % self.name):
@@ -243,7 +247,7 @@ class ArvadosJob(JobBase):
                                                                    api_client=self.arvrunner.api,
                                                                    keep_client=self.arvrunner.keep_client,
                                                                    num_retries=self.arvrunner.num_retries)
-                        log = logc.open(logc.keys()[0])
+                        log = logc.open(list(logc.keys())[0])
                         dirs = {
                             "tmpdir": "/tmpdir",
                             "outdir": "/outdir",
@@ -343,7 +347,7 @@ class RunnerJob(Runner):
             find_or_create=self.enable_reuse
         ).execute(num_retries=self.arvrunner.num_retries)
 
-        for k,v in job_spec["script_parameters"].items():
+        for k,v in viewitems(job_spec["script_parameters"]):
             if v is False or v is None or isinstance(v, dict):
                 job_spec["script_parameters"][k] = {"value": v}
 
@@ -386,19 +390,21 @@ class RunnerTemplate(object):
     }
 
     def __init__(self, runner, tool, job_order, enable_reuse, uuid,
-                 submit_runner_ram=0, name=None, merged_map=None):
+                 submit_runner_ram=0, name=None, merged_map=None,
+                 loadingContext=None):
         self.runner = runner
         self.embedded_tool = tool
         self.job = RunnerJob(
             runner=runner,
             tool=tool,
-            job_order=job_order,
             enable_reuse=enable_reuse,
             output_name=None,
             output_tags=None,
             submit_runner_ram=submit_runner_ram,
             name=name,
-            merged_map=merged_map)
+            merged_map=merged_map,
+            loadingContext=loadingContext)
+        self.job.job_order = job_order
         self.uuid = uuid
 
     def pipeline_component_spec(self):