13306: Changes to arvados-cwl-runner code after running futurize --stage2

[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 9a03372d32de9375e9401fe4fc4099dce61f1181..bd8ab1137e9b4eda0e006162812bf8ea12d7bc7d 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvjob.py
+++ b/sdk/cwl/arvados_cwl/arvjob.py
@@ -1,3 +1,5 @@
+from past.builtins import basestring
+from builtins import object
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: Apache-2.0
@@ -67,11 +69,11 @@ 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):
-                    for f, p in generatemapper.items():
+                    for f, p in list(generatemapper.items()):
                         if p.type == "CreateFile":
                             with vwd.open(p.target, "w") as n:
                                 n.write(p.resolved.encode("utf-8"))
@@ -85,7 +87,7 @@ class ArvadosJob(JobBase):
                                      trash_at=info["trash_at"],
                                      properties=info["properties"])
 
-                for f, p in generatemapper.items():
+                for f, p in list(generatemapper.items()):
                     if p.type == "File":
                         script_parameters["task.vwd"][p.target] = p.resolved
                     if p.type == "CreateFile":
@@ -243,7 +245,7 @@ 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",
@@ -296,10 +298,10 @@ class RunnerJob(Runner):
         a pipeline template or pipeline instance.
         """
 
-        if self.tool.tool["id"].startswith("keep:"):
-            self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
+        if self.embedded_tool.tool["id"].startswith("keep:"):
+            self.job_order["cwl:tool"] = self.embedded_tool.tool["id"][5:]
         else:
-            packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
+            packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map)
             wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
             self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
 
@@ -343,7 +345,7 @@ 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 list(job_spec["script_parameters"].items()):
             if v is False or v is None or isinstance(v, dict):
                 job_spec["script_parameters"][k] = {"value": v}
 
@@ -386,19 +388,21 @@ 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.tool = tool
+        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):
@@ -420,7 +424,7 @@ class RunnerTemplate(object):
         job_params = spec['script_parameters']
         spec['script_parameters'] = {}
 
-        for param in self.tool.tool['inputs']:
+        for param in self.embedded_tool.tool['inputs']:
             param = copy.deepcopy(param)
 
             # Data type and "required" flag...