11332: Override relaxed path checks to be even more relaxed, and bump cwltool &

schema salad pin for hashes-in-filenames fix.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 36fe6efbb28ca7be90044e4e2ebd6368a73237ee..3b14701a9b9480cf6119e6d0e81e478e6da81214 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -11,6 +11,7 @@ import threading
 import hashlib
 import copy
 import json
+import re
 from functools import partial
 import pkg_resources  # part of setuptools
 
@@ -629,6 +630,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
 def add_arv_hints():
     cache = {}
+    cwltool.draft2tool.ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")
     res = pkg_resources.resource_stream(__name__, 'arv-cwl-schema.yml')
     cache["http://arvados.org/cwl"] = res.read()
     res.close()

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 49047fa14328271106608721c9fa22099dfcb5ae..1c10fe8196aba940495934169d559bb756cfda31 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -3,7 +3,6 @@ import urlparse
 from functools import partial
 import logging
 import json
-import re
 import subprocess
 
 from StringIO import StringIO
@@ -30,8 +29,6 @@ from . import done
 
 logger = logging.getLogger('arvados.cwl-runner')
 
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
-
 def trim_listing(obj):
     """Remove 'listing' field from Directory objects that are keep references.
 

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index d5a75a9441156b8a6a01a94a2b0d39dbae5e9b38..ed384d273e4542a89055327d79b3a04597dd7f86 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -48,8 +48,8 @@ setup(name='arvados-cwl-runner',
       # Note that arvados/build/run-build-packages.sh looks at this
       # file to determine what version of cwltool and schema-salad to build.
       install_requires=[
-          'cwltool==1.0.20170213175853',
-          'schema-salad==2.2.20170208112505',
+          'cwltool==1.0.20170224141733',
+          'schema-salad==2.2.20170222151604',
           'ruamel.yaml==0.13.7',
           'arvados-python-client>=0.1.20170112173420',
           'setuptools'