From: Peter Amstutz <peter.amstutz@curii.com>
Date: Tue, 2 Aug 2022 16:40:27 +0000 (-0400)
Subject: 19280: explicitly include/exclude primary
X-Git-Tag: 2.5.0~103^2~2
X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/4e5838bd9e1a7baa5b3e53e97e308140e4b6105f

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 d2486c164b..d2dfcf26bc 100644
--- 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):