projects
/
arvados.git
/ blobdiff
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
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
from future.utils import viewvalues, viewitems
import os
+import sys
import urllib.parse
from functools import partial
import logging
import json
import urllib.parse
from functools import partial
import logging
import json
-import subprocess32 as subprocess
from collections import namedtuple
from collections import namedtuple
-
from io import StringIO
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
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 = {}
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)
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:
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.load
s(f.read().decode()
)
def keepify(fileobj):
path = fileobj["location"]
if not path.startswith("keep:"):
def keepify(fileobj):
path = fileobj["location"]
if not path.startswith("keep:"):