8653: Set basedir for CollectionFsAccess

diff --git a/crunch_scripts/cwl-runner b/crunch_scripts/cwl-runner
index fabb6db058703450e0174018403d0131e1015f2f..c786fc10b1715e1c5912e13ee98011aa94dceab3 100755 (executable)
--- 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 61fa07e53e76523d04312eed6ad2ec7efac8f397..50c51b0671a389a86e95c6cb3e64c1f14b0e5e99 100644 (file)
--- 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("/")