[ARVADOS] created: 16eeca3890937e21e92893c077ffa8066cb5bd8f

[Git user]

        at  16eeca3890937e21e92893c077ffa8066cb5bd8f (commit)


commit 16eeca3890937e21e92893c077ffa8066cb5bd8f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Mon Aug 8 14:27:40 2016 -0400

    9552: import compute_checksums from cwltool.  Bump cwltool version.

diff --git a/build/run-build-packages.sh b/build/run-build-packages.sh
index e1c0ac3..fec4950 100755
--- a/build/run-build-packages.sh
+++ b/build/run-build-packages.sh
@@ -467,7 +467,7 @@ fpm_build schema_salad "" "" python 1.14.20160708181155
 fpm_build ruamel.yaml "" "" python 0.11.11 --python-setup-py-arguments "--single-version-externally-managed"
 
 # And for cwltool we have the same problem as for schema_salad. Ward, 2016-03-17
-fpm_build cwltool "" "" python 1.0.20160726135535
+fpm_build cwltool "" "" python 1.0.20160810161358
 
 # FPM eats the trailing .0 in the python-rdflib-jsonld package when built with 'rdflib-jsonld>=0.3.0'. Force the version. Ward, 2016-03-25
 fpm_build rdflib-jsonld "" "" python 0.3.0
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 99db9f1..8e964d3 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -9,6 +9,7 @@ import os
 import sys
 import threading
 import hashlib
+import functools
 import pkg_resources  # part of setuptools
 
 from cwltool.errors import WorkflowException
@@ -26,6 +27,7 @@ from .fsaccess import CollectionFsAccess
 
 from cwltool.process import shortname, UnsupportedRequirement
 from cwltool.pathmapper import adjustFileObjs
+from cwltool.draft2tool import compute_checksums
 from arvados.api import OrderedJsonModel
 
 logger = logging.getLogger('arvados.cwl-runner')
@@ -228,17 +230,7 @@ class ArvCwlRunner(object):
             raise WorkflowException("Workflow did not return a result.")
 
         if kwargs.get("compute_checksum"):
-            def compute_checksums(fileobj):
-                if "checksum" not in fileobj:
-                    checksum = hashlib.sha1()
-                    with self.fs_access.open(fileobj["location"], "rb") as f:
-                        contents = f.read(1024*1024)
-                        while contents != "":
-                            checksum.update(contents)
-                            contents = f.read(1024*1024)
-                    fileobj["checksum"] = "sha1$%s" % checksum.hexdigest()
-
-            adjustFileObjs(self.final_output, compute_checksums)
+            adjustFileObjs(self.final_output, functools.partial(compute_checksums, self.fs_access))
 
         return self.final_output
 
diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 9fcbdd7..60ea7ab 100644
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -32,7 +32,7 @@ setup(name='arvados-cwl-runner',
       # Make sure to update arvados/build/run-build-packages.sh as well
       # when updating the cwltool version pin.
       install_requires=[
-          'cwltool==1.0.20160726135535',
+          'cwltool==1.0.20160810161358',
           'arvados-python-client>=0.1.20160714204738',
       ],
       data_files=[

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