X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/504e09d413026fcac8ac94530134da2fce4dc0f2..f423aff73c1927a74e39c738e08bd6f1100a94c5:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 2239e0f9df..7bb66a158e 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -42,6 +42,7 @@ import schema_salad.validate as validate
 import arvados.collection
 from .util import collectionUUID
 import ruamel.yaml as yaml
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 
 import arvados_cwl.arvdocker
 from .pathmapper import ArvPathMapper, trim_listing, collection_pdh_pattern, collection_uuid_pattern
@@ -392,7 +393,7 @@ def upload_dependencies(arvrunner, name, document_loader,
             discovered_secondaryfiles[mapper.mapper(d).resolved] = discovered[d]
 
     if "$schemas" in workflowobj:
-        sch = []
+        sch = CommentedSeq()
         for s in workflowobj["$schemas"]:
             sch.append(mapper.mapper(s).resolved)
         workflowobj["$schemas"] = sch
@@ -424,8 +425,9 @@ def packed_workflow(arvrunner, tool, merged_map):
     A "packed" workflow is one where all the components have been combined into a single document."""
 
     rewrites = {}
-    packed = pack(tool.doc_loader, tool.doc_loader.fetch(tool.tool["id"]),
-                  tool.tool["id"], tool.metadata, rewrite_out=rewrites)
+    packed = pack(arvrunner.loadingContext, tool.tool["id"],
+                  rewrite_out=rewrites,
+                  loader=tool.doc_loader)
 
     rewrite_to_orig = {v: k for k,v in viewitems(rewrites)}