[arvados] updated: 2.1.0-3013-g88d70b6d8

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Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

       via  88d70b6d852d2347a958b7e76de3f47df2699e70 (commit)
      from  9f39acdc1d65d8b2714ffccd51a0311e6df9ec4a (commit)

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commit 88d70b6d852d2347a958b7e76de3f47df2699e70
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri Nov 11 09:53:18 2022 -0500

    19688: Make sure CommandLineTool gets wrapped properly
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index c0b479c37..7f9c3c348 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -61,10 +61,26 @@ def make_wrapper_workflow(arvRunner, main, packed, project_uuid, name):
         "run": "keep:%s/workflow.json#main" % pdh
     }
 
+    newinputs = []
+    for i in main["inputs"]:
+        inp = {}
+        # Make sure to only copy known fields that are meaningful at
+        # the workflow level. In practice this ensures that if we're
+        # wrapping a CommandLineTool we don't grab inputBinding.
+        # Right now also excludes extension fields, which is fine,
+        # Arvados doesn't currently look for any extension fields on
+        # input parameters.
+        for f in ("type", "label", "secondaryFiles", "streamable",
+                  "doc", "id", "format", "loadContents",
+                  "loadListing", "default"):
+            if f in i:
+                inp[f] = i[f]
+        newinputs.append(inp)
+
     wrapper = {
         "class": "Workflow",
         "id": "#main",
-        "inputs": main["inputs"],
+        "inputs": newinputs,
         "outputs": [],
         "steps": [step]
     }

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