19385: Fix typo, passing with --fast-parser now

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

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index c38458833acf0669c3de8ab1f3045339141e5f4c..7b10c15af752ba895454fe9cbb85283f32294ba7 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -193,7 +193,7 @@ def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, set_block_style,
                 # blank node reference, was added in automatically, can get rid of it.
                 del d[field]
 
-        if "id" in d and not d:
+        if "id" in d:
             baseuri = urlexpander(d["id"], baseuri, scoped_id=True)
         elif "name" in d and isinstance(d["name"], str):
             baseuri = urlexpander(d["name"], baseuri, scoped_id=True)
@@ -332,13 +332,20 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid,
             #print(yamlloader.dump(result, stream=sys.stdout))
             yamlloader.dump(result, stream=f)
 
+        with col.open(os.path.join("original", w[n+1:]), "wt") as f:
+            f.write(text)
+
+
     for w in include_files:
         with col.open(w[n+1:], "wb") as f1:
-            with open(uri_file_path(w), "rb") as f2:
-                dat = f2.read(65536)
-                while dat:
-                    f1.write(dat)
+            with col.open(os.path.join("original", w[n+1:]), "wb") as f3:
+                with open(uri_file_path(w), "rb") as f2:
                     dat = f2.read(65536)
+                    while dat:
+                        f1.write(dat)
+                        f3.write(dat)
+                        dat = f2.read(65536)
+
 
     toolname = tool.tool.get("label") or tool.metadata.get("label") or os.path.basename(tool.tool["id"])
     if git_info and git_info.get("http://arvados.org/cwl#gitDescribe"):

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 68a3446010bf79192a8f3b703c071f6d1c61ab23..258f2c5ecb50bfccc8b4593a7e099ad1bfb1a03b 100644 (file)
--- a/sdk/cwl/setup.py
+++ b/sdk/cwl/setup.py
@@ -36,8 +36,8 @@ setup(name='arvados-cwl-runner',
       # file to determine what version of cwltool and schema-salad to
       # build.
       install_requires=[
-          'cwltool==3.1.20230119183816',
-          'schema-salad==8.3.20230109181937.dev6+gca19f37',
+          'cwltool==3.1.20230126160225',
+          'schema-salad==8.3.20230109181937.dev8+g5bb37c3',
           'arvados-python-client{}'.format(pysdk_dep),
           'ciso8601 >= 2.0.0',
           'networkx < 2.6',