[arvados] updated: 2.5.0-29-g4f3739a49

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Summary of changes:
 sdk/cwl/arvados_cwl/arvworkflow.py | 22 ++++++++++++++++++----
 sdk/cwl/setup.py                   |  4 ++--
 2 files changed, 20 insertions(+), 6 deletions(-)

       via  4f3739a4967959db6783408d8aad2137b9ebdab5 (commit)
       via  6e45aef0eaea08b9fb3ba85783af8552757f8e6a (commit)
       via  a5bb9338a46680c3976544618d0a3fd5f0b65a96 (commit)
      from  fb27923f7ce22eddde0852d24d6c94323de41330 (commit)

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commit 4f3739a4967959db6783408d8aad2137b9ebdab5
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Fri Jan 27 10:02:09 2023 -0500

    19385: Update cwl dependencies to stable releases
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz at curii.com>

diff --git a/sdk/cwl/setup.py b/sdk/cwl/setup.py
index 258f2c5ec..9af61a3d9 100644
--- 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==3.1.20230126160225',
-          'schema-salad==8.3.20230109181937.dev8+g5bb37c3',
+          'cwltool==3.1.20230127121939',
+          'schema-salad==8.4.20230127112827',
           'arvados-python-client{}'.format(pysdk_dep),
           'ciso8601 >= 2.0.0',
           'networkx < 2.6',

commit 6e45aef0eaea08b9fb3ba85783af8552757f8e6a
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Jan 26 12:56:12 2023 -0500

    19385: Fix typo, passing with --fast-parser now
    
    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 c38458833..7b10c15af 100644
--- 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 68a344601..258f2c5ec 100644
--- 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',

commit a5bb9338a46680c3976544618d0a3fd5f0b65a96
Author: Peter Amstutz <peter.amstutz at curii.com>
Date:   Thu Jan 26 11:06:23 2023 -0500

    19385: fast-parser fixups
    
    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 e850ebcb2..c38458833 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -188,7 +188,12 @@ def update_refs(d, baseuri, urlexpander, merged_map, jobmapper, set_block_style,
             else:
                 update_refs(s, baseuri, urlexpander, merged_map, jobmapper, set_block_style, runtimeContext, prefix, replacePrefix)
     elif isinstance(d, MutableMapping):
-        if "id" in d:
+        for field in ("id", "name"):
+            if isinstance(d.get(field), str) and d[field].startswith("_:"):
+                # blank node reference, was added in automatically, can get rid of it.
+                del d[field]
+
+        if "id" in d and not 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)
@@ -353,6 +358,8 @@ def new_upload_workflow(arvRunner, tool, job_order, project_uuid,
 
     col.save_new(name=toolname, owner_uuid=arvRunner.project_uuid, ensure_unique_name=True, properties=properties)
 
+    logger.info("Workflow uploaded to %s", col.manifest_locator())
+
     adjustDirObjs(job_order, trim_listing)
     adjustFileObjs(job_order, trim_anonymous_location)
     adjustDirObjs(job_order, trim_anonymous_location)

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