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default network access for ICT to CLT conversion and handle single node wfb payload #291

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Oct 31, 2024
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default network access for ICT to CLT conversion and handle single node wfb payload #291

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10 changes: 8 additions & 2 deletions src/sophios/api/utils/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,9 @@ def extract_state(inp: Json) -> Json:
plugin = next((ict for ict in plugins if ict['pid'] == node_pid), None)
clt: Json = {}
if plugin:
clt = ict_to_clt(plugin)
# by default have network access true
# so we don't get runtime error for docker/container pull
clt = ict_to_clt(plugin, True)
# just have the clt payload in run
node['run'] = clt
inp_restrict = inp_inter['state']
Expand Down Expand Up @@ -165,7 +167,11 @@ def wfb_to_wic(inp: Json) -> Cwl:
workflow_temp["steps"].append(node) # node["cwlScript"] # Assume dict form
else: # A single node workflow
node = inp_restrict["nodes"][0]
workflow_temp = node["cwlScript"] if node.get("cwlScript") else node['run']
if node.get("cwlScript"):
workflow_temp = node["cwlScript"]
else:
workflow_temp["steps"] = []
workflow_temp["steps"].append(node)
return workflow_temp


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