X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e378cc27decd91bf72309946b84c7346a75be7c1..0821f5481edd016a3744bb50d97a9e5b99cd1a0f:/sdk/cwl/arvados_cwl/runner.py?ds=inline

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 839239258d..a4132ca3f7 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -21,11 +21,22 @@ from .pathmapper import ArvPathMapper
 
 logger = logging.getLogger('arvados.cwl-runner')
 
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
+cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r".*")
+
+def trim_listing(obj):
+    """Remove 'listing' field from Directory objects that are keep references.
+
+    When Directory objects represent Keep references, it redundant and
+    potentially very expensive to pass fully enumerated Directory objects
+    between instances of cwl-runner (e.g. a submitting a job, or using the
+    RunInSingleContainer feature), so delete the 'listing' field when it is
+    safe to do so.
+    """
 
-def del_listing(obj):
     if obj.get("location", "").startswith("keep:") and "listing" in obj:
         del obj["listing"]
+    if obj.get("location", "").startswith("_:"):
+        del obj["location"]
 
 def upload_dependencies(arvrunner, name, document_loader,
                         workflowobj, uri, loadref_run):
@@ -84,8 +95,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                            name=name)
 
     def setloc(p):
-        if not p["location"].startswith("_:") and not p["location"].startswith("keep:"):
-            p["location"] = mapper.mapper(p["location"]).target
+        if "location" in p and (not p["location"].startswith("_:")) and (not p["location"].startswith("keep:")):
+            p["location"] = mapper.mapper(p["location"]).resolved
     adjustFileObjs(workflowobj, setloc)
     adjustDirObjs(workflowobj, setloc)
 
@@ -133,7 +144,7 @@ class Runner(object):
                                         self.job_order.get("id", "#"),
                                         False)
 
-        adjustDirObjs(self.job_order, del_listing)
+        adjustDirObjs(self.job_order, trim_listing)
 
         if "id" in self.job_order:
             del self.job_order["id"]