15028: Fix discover secondaryFiles after internal v1.1 update

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/executor.py b/sdk/cwl/arvados_cwl/executor.py
index c5fd7e3cf40890f56f3e21fb3abb397dea533aa5..badf589387c90b66b4b69365d62de9fce2a4aabd 100644 (file)
--- a/sdk/cwl/arvados_cwl/executor.py
+++ b/sdk/cwl/arvados_cwl/executor.py
@@ -550,6 +550,10 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
         if not runtimeContext.name:
             runtimeContext.name = self.name = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
 
+        # Upload local file references in the job order.
+        job_order = upload_job_order(self, "%s input" % runtimeContext.name,
+                                     tool, job_order)
+
         submitting = (runtimeContext.update_workflow or
                       runtimeContext.create_workflow or
                       (runtimeContext.submit and not
@@ -579,10 +583,6 @@ http://doc.arvados.org/install/install-api-server.html#disable_api_methods
         loadingContext.metadata = tool.metadata
         tool = load_tool(tool.tool, loadingContext)
 
-        # Upload local file references in the job order.
-        job_order = upload_job_order(self, "%s input" % runtimeContext.name,
-                                     tool, job_order)
-
         existing_uuid = runtimeContext.update_workflow
         if existing_uuid or runtimeContext.create_workflow:
             # Create a pipeline template or workflow record and exit.

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 3235f4763c36506184d90a74a60136474d30b1e4..04fd1c443f47a9dad3a3ac6089e92ba8276930e4 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -79,7 +79,7 @@ def find_defaults(d, op):
 def setSecondary(t, fileobj, discovered):
     if isinstance(fileobj, dict) and fileobj.get("class") == "File":
         if "secondaryFiles" not in fileobj:
-            fileobj["secondaryFiles"] = cmap([{"location": substitute(fileobj["location"], sf), "class": "File"} for sf in t["secondaryFiles"]])
+            fileobj["secondaryFiles"] = cmap([{"location": substitute(fileobj["location"], sf["pattern"]), "class": "File"} for sf in t["secondaryFiles"]])
             if discovered is not None:
                 discovered[fileobj["location"]] = fileobj["secondaryFiles"]
     elif isinstance(fileobj, list):