19280: explicitly include/exclude primary

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d2486c164bec6e85176a416c45e50964deea8e6d..d2dfcf26bc0e9c8b2b1c98e12f339597ecd5f256 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -417,8 +417,14 @@ def upload_dependencies(arvrunner, name, document_loader,
 
     normalizeFilesDirs(sc)
 
-    if include_primary and "id" in workflowobj:
-        sc.append({"class": "File", "location": workflowobj["id"]})
+    if "id" in workflowobj:
+        defrg, _ = urllib.parse.urldefrag(workflowobj["id"])
+        if include_primary:
+            # make sure it's included
+            sc.append({"class": "File", "location": defrg})
+        else:
+            # make sure it's excluded
+            sc = [d for d in sc if d.get("location") != defrg]
 
     def visit_default(obj):
         def defaults_are_optional(f):