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load CWL and Snakemake specification #537

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VMois opened this issue Aug 9, 2022 · 0 comments
Open

load CWL and Snakemake specification #537

VMois opened this issue Aug 9, 2022 · 0 comments

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@VMois
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VMois commented Aug 9, 2022

Originated from this analysis - #535 (comment)

With reana-client-go, we cannot load workflow specifications for CWL, Snakemake, and Yadage. Because of that, we will need to move specification loading to reana-server. Currently, Yadage is loaded in the start_workflow endpoint. We should also add loading of CWL and Snakemake specifications there. This change should nicely play with validation there.

Example of Yadage loading and other engines:

# This is necessary for GitLab integration
if workflow.type_ == "yadage":
_load_and_save_yadage_spec(
workflow, workflow_dict["operational_options"]
)
elif workflow.type_ in ["cwl", "snakemake"]:
reana_yaml_path = os.path.join(workflow.workspace_path, "reana.yaml")
workflow.reana_specification = load_reana_spec(
reana_yaml_path, workflow.workspace_path
)
Session.commit()

@VMois VMois added this to Backlog in Go-Client-Basics Aug 9, 2022
@audrium audrium removed this from Backlog in Go-Client-Basics Sep 21, 2022
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