def run(environment_path=None):
if expression is None:
raise Exception("Python library cwltool must be available to evaluate expressions.")
if environment_path is None:
environment_path = os.environ.get("GALAXY_EXPRESSION_INPUTS")
with open(environment_path) as f:
raw_inputs = json.load(f)
outputs = raw_inputs["outputs"]
inputs = raw_inputs.copy()
del inputs["outputs"]
result = evaluate(None, inputs)
if '__error_message' in result:
raise Exception(result['__error_message'])
for output in outputs:
path = output["path"]
from_expression = output["from_expression"]
# if it is just a simple value, short-cut all the interpolation
# interpolate seems to fail with None values so this worksaround
# that for now.
if from_expression in result:
output_value = result[from_expression]
else:
from_expression = f"$({from_expression})"
output_value = expression.interpolate(from_expression, result)
with open(path, "w") as f:
json.dump(output_value, f)
def run(environment_path=None):
if expression is None:
raise Exception("Python library cwltool must be available to evaluate expressions.")
if environment_path is None:
environment_path = os.environ.get("GALAXY_EXPRESSION_INPUTS")
with open(environment_path, "r") as f:
raw_inputs = json.load(f)
outputs = raw_inputs["outputs"]
inputs = raw_inputs.copy()
del inputs["outputs"]
result = evaluate(None, inputs)
for output in outputs:
path = output["path"]
from_expression = "$(" + output["from_expression"] + ")"
output_value = expression.interpolate(from_expression, result)
with open(path, "w") as f:
json.dump(output_value, f)
def test_evaluate():
input = {"script": "{return 5;}"}
assert evaluate(None, input) == 5