Merge branch '14383-java-sdk-double-slash'. Fixes #14383.

[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 2a86a0556881f47a9abac2cdf743c5d7ecb74833..c0d165aa9eed4e5cbaeaf9d365a302957a3921b1 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -7,15 +7,19 @@ standard_library.install_aliases()
 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
@@ -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)
 
@@ -467,7 +471,7 @@ 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:"):