[ARVADOS] updated: e0fac5213f40fc00946f8ec5e4df42bebdf756d2

[Git user]

Summary of changes:
 crunch_scripts/cwl-runner       | 6 ++++--
 sdk/cwl/arvados_cwl/__init__.py | 6 +++---
 2 files changed, 7 insertions(+), 5 deletions(-)

       via  e0fac5213f40fc00946f8ec5e4df42bebdf756d2 (commit)
       via  5011827dbbe6b17606bf83338b99dd53789ae9cc (commit)
       via  0bce01f575822851da09f252b38d7009ed7a5ab0 (commit)
       via  1cde74c26fd6a7793a7bb1a9bd748ce06e37c455 (commit)
      from  53deed9cb00b94a69a3be1f959cbfda342646718 (commit)

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commit e0fac5213f40fc00946f8ec5e4df42bebdf756d2
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 18 22:08:48 2016 -0400

    8653: Fix pathmapper API

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 50c51b0..0533b5e 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -575,8 +575,8 @@ class ArvadosCommandTool(CommandLineTool):
     def makeJobRunner(self):
         return ArvadosJob(self.arvrunner)
 
-    def makePathMapper(self, reffiles, input_basedir, **kwargs):
-        return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+    def makePathMapper(self, reffiles, **kwargs):
+        return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
                              "$(task.keep)/%s",
                              "$(task.keep)/%s/%s",
                              **kwargs)

commit 5011827dbbe6b17606bf83338b99dd53789ae9cc
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 18 22:06:19 2016 -0400

    8653: Set basedir for CollectionFsAccess

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index fabb6db..c786fc1 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -58,6 +58,7 @@ try:
     args.debug = True
     args.quiet = False
     args.ignore_docker_for_reuse = False
+    args.basedir = os.getcwd()
     args.cwl_runner_job={"uuid": arvados.current_job()["uuid"], "state": arvados.current_job()["state"]}
     outputObj = runner.arvExecutor(t, job_order_object, **vars(args))
 
diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 61fa07e..50c51b0 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -67,8 +67,8 @@ class CollectionFsAccess(cwltool.process.StdFsAccess):
     """Implement the cwltool FsAccess interface for Arvados Collections."""
 
     def __init__(self, basedir):
+        super(CollectionFsAccess, self).__init__(basedir)
         self.collections = {}
-        self.basedir = basedir
 
     def get_collection(self, path):
         p = path.split("/")

commit 0bce01f575822851da09f252b38d7009ed7a5ab0
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 18 22:01:15 2016 -0400

    8653: Update load_tool in cwl-runner crunch script

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index 5e7982c..fabb6db 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -20,6 +20,7 @@ import json
 import argparse
 from arvados.api import OrderedJsonModel
 from cwltool.process import adjustFiles
+from cwltool.load_tool import load_tool
 
 # Print package versions
 logging.info(cwltool.main.versionstring())
@@ -48,7 +49,7 @@ try:
 
     runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
 
-    t = cwltool.main.load_tool(job_order_object, False, True, runner.arvMakeTool, True)
+    t = load_tool(job_order_object, runner.arvMakeTool)
 
     args = argparse.Namespace()
     args.project_uuid = arvados.current_job()["owner_uuid"]

commit 1cde74c26fd6a7793a7bb1a9bd748ce06e37c455
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed May 18 17:42:44 2016 -0400

    8653: Check that parameters are basestring before matching regex.

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index e011177..5e7982c 100755
--- a/crunch_scripts/cwl-runner
+++ b/crunch_scripts/cwl-runner
@@ -38,7 +38,7 @@ try:
     job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
 
     for k,v in job_order_object.items():
-        if arvados.util.keep_locator_pattern.match(v):
+        if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
             job_order_object[k] = {
                 "class": "File",
                 "path": keeppath(v)

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