14886: Fixes mock issue between tests

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

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 38975052384af13528f96cb9ff051682aa14badd..e515ac2ce5e99f4ec75011b8ac51bfe2fc1bbff8 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -4,18 +4,22 @@
 
 from future import standard_library
 standard_library.install_aliases()
-from future.utils import viewvalues
+from future.utils import  viewvalues, viewitems
 
 import os
+import sys
 import urllib.parse
 from functools import partial
 import logging
 import json
-import subprocess32 as subprocess
 from collections import namedtuple
-
 from io import StringIO
 
+if os.name == "posix" and sys.version_info[0] < 3:
+    import subprocess32 as subprocess
+else:
+    import subprocess
+
 from schema_salad.sourceline import SourceLine, cmap
 
 from cwltool.command_line_tool import CommandLineTool
@@ -175,7 +179,7 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
-    for d in list(discovered.keys()):
+    for d in list(discovered):
         # Only interested in discovered secondaryFiles which are local
         # files that need to be uploaded.
         if d.startswith("file:"):
@@ -236,7 +240,7 @@ def packed_workflow(arvrunner, tool, merged_map):
     packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
                   tool.tool["id"], tool.metadata, rewrite_out=rewrites)
 
-    rewrite_to_orig = {v: k for k,v in list(rewrites.items())}
+    rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}
 
     def visit(v, cur_id):
         if isinstance(v, dict):
@@ -318,7 +322,7 @@ def upload_workflow_deps(arvrunner, tool):
                                      discovered_secondaryfiles=discovered_secondaryfiles)
             document_loader.idx[deptool["id"]] = deptool
             toolmap = {}
-            for k,v in list(pm.items()):
+            for k,v in pm.items():
                 toolmap[k] = v.resolved
             merged_map[deptool["id"]] = FileUpdates(toolmap, discovered_secondaryfiles)
 
@@ -467,15 +471,15 @@ class Runner(Process):
             if "cwl.output.json" in outc:
                 with outc.open("cwl.output.json", "rb") as f:
                     if f.size() > 0:
-                        outputs = json.load(f)
+                        outputs = json.loads(f.read().decode())
             def keepify(fileobj):
                 path = fileobj["location"]
                 if not path.startswith("keep:"):
                     fileobj["location"] = "keep:%s/%s" % (record["output"], path)
             adjustFileObjs(outputs, keepify)
             adjustDirObjs(outputs, keepify)
-        except Exception as e:
-            logger.exception("[%s] While getting final output object: %s", self.name, e)
+        except Exception:
+            logger.exception("[%s] While getting final output object", self.name)
             self.arvrunner.output_callback({}, "permanentFail")
         else:
             self.arvrunner.output_callback(outputs, processStatus)