From 6e45aef0eaea08b9fb3ba85783af8552757f8e6a Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Thu, 26 Jan 2023 12:56:12 -0500 Subject: [PATCH] 19385: Fix typo, passing with --fast-parser now Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- sdk/cwl/arvados_cwl/arvworkflow.py | 17 ++++++++++++----- sdk/cwl/setup.py | 4 ++-- 2 files changed, 14 insertions(+), 7 deletions(-) diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py index c38458833a..7b10c15af7 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 68a3446010..258f2c5ecb 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', -- 2.30.2