[ARVADOS] created: ddbe4fd3a397a58ffe78487aee8525cca9627659

[Git user]

        at  ddbe4fd3a397a58ffe78487aee8525cca9627659 (commit)


commit ddbe4fd3a397a58ffe78487aee8525cca9627659
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 10 11:43:26 2017 -0400

    10827: Don't track file mutations.

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 46436b5..3182137 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -51,6 +51,17 @@ arvados.log_handler.setFormatter(logging.Formatter(
         '%(asctime)s %(name)s %(levelname)s: %(message)s',
         '%Y-%m-%d %H:%M:%S'))
 
+class NoopMutationManager(object):
+    def register_reader(self, stepname, obj):
+        pass
+    def release_reader(self, stepname, obj):
+        pass
+    def register_mutation(self, stepname, obj):
+        pass
+    def set_generation(self, obj):
+        pass
+
+
 class ArvCwlRunner(object):
     """Execute a CWL tool or workflow, submit work (using either jobs or
     containers API), wait for them to complete, and report output.
@@ -375,6 +386,7 @@ class ArvCwlRunner(object):
         kwargs["use_container"] = True
         kwargs["tmpdir_prefix"] = "tmp"
         kwargs["compute_checksum"] = kwargs.get("compute_checksum")
+        kwargs["mutation_manager"] = NoopMutationManager()
 
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"

commit 7162967c740adba9f6f04e49a1f423aac77c4f9d
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 10 11:31:56 2017 -0400

    10827: Fix imports

diff --git a/sdk/cwl/arvados_cwl/crunch_script.py b/sdk/cwl/arvados_cwl/crunch_script.py
index 65ef508..821abf9 100644
--- a/sdk/cwl/arvados_cwl/crunch_script.py
+++ b/sdk/cwl/arvados_cwl/crunch_script.py
@@ -19,7 +19,8 @@ import re
 import functools
 
 from arvados.api import OrderedJsonModel
-from cwltool.process import shortname, adjustFileObjs, adjustDirObjs, normalizeFilesDirs
+from cwltool.process import shortname
+from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
 from cwltool.load_tool import load_tool
 from cwltool.errors import WorkflowException
 

commit 32d28ed55e74e19d75112cdbd5ed7a78700b1a3f
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 10 11:16:18 2017 -0400

    10827: Bump cwltool & schema salad dependency.

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 2b11671..25b3cf9 100644
--- 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==1.0.20170413194156',
-          'schema-salad==2.5.20170328195758',
+          'cwltool==1.0.20170510151339',
+          'schema-salad==2.5.20170428142041',
           'typing==3.5.3.0',
           'ruamel.yaml==0.13.7',
           'arvados-python-client>=0.1.20170327195441',

commit 4644e14f4158e3fa288abf6d979d2526606e5615
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 10 11:08:36 2017 -0400

    10827: Add --validate, --print-dot and --enable-dev options (pass through to
    existing cwltool functionality).

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 3c7de77..46436b5 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -539,7 +539,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Time to wait for a Javascript expression to evaluate before giving an error, default 20s.",
                         type=float,
                         default=20)
-    parser.add_argument("--version", action="store_true", help="Print version and exit")
+
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--print-dot", action="store_true",
+                         help="Print workflow visualization in graphviz format and exit")
+    exgroup.add_argument("--version", action="store_true", help="Print version and exit")
+    exgroup.add_argument("--validate", action="store_true", help="Validate CWL document only.")
 
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--verbose", action="store_true", help="Default logging")
@@ -611,6 +616,10 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
                         "Default is 'continue'.", default="continue", choices=("stop", "continue"))
 
+    parser.add_argument("--enable-dev", action="store_true",
+                        help="Enable loading and running development versions "
+                             "of CWL spec.", default=False)
+
     parser.add_argument("workflow", type=str, nargs="?", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 

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