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Source code for galaxy_ext.expressions.handle_job

Execute an external process to evaluate expressions for Galaxy jobs.

Galaxy should be importable on sys.path .

import json
import logging
import os
import sys
import warnings

# insert *this* galaxy before all others on sys.path
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
warnings.filterwarnings("ignore", message=r"[\n.]DEPRECATION: Python 2", module="cwltool")

    from cwl_utils import expression
except ImportError:
    expression = None  # type: ignore[assignment]

from galaxy.tools.expressions import evaluate

log = logging.getLogger(__name__)

[docs]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)