Merge remote-tracking branch 'origin/master' into 15106-trgm-text-search

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 3a3784050105585d31f4fd13b4e335c902c5c307..912faf0e875b45655de56355374cca025bcc7377 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -174,7 +174,7 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             if pattern is None:
                 continue
             sfpath = substitute(primary["location"], pattern)
-            required = builder.do_eval(sf["required"], context=primary)
+            required = builder.do_eval(sf.get("required"), context=primary)
 
             if fsaccess.exists(sfpath):
                 primary["secondaryFiles"].append({"location": sfpath, "class": "File"})
@@ -470,7 +470,16 @@ def upload_job_order(arvrunner, name, tool, job_order):
 
     # Make a copy of the job order and set defaults.
     builder_job_order = copy.copy(job_order)
-    fill_in_defaults(tool.tool["inputs"],
+
+    # fill_in_defaults throws an error if there are any
+    # missing required parameters, we don't want it to do that
+    # so make them all optional.
+    inputs_copy = copy.deepcopy(tool.tool["inputs"])
+    for i in inputs_copy:
+        if "null" not in i["type"]:
+            i["type"] = ["null"] + aslist(i["type"])
+
+    fill_in_defaults(inputs_copy,
                      builder_job_order,
                      arvrunner.fs_access)
     # Need to create a builder object to evaluate expressions.