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Source code for galaxy.tools.expressions.evaluation

import json
import os
import subprocess

from .util import find_engine

FILE_DIRECTORY = os.path.normpath(os.path.dirname(os.path.join(__file__)))
NODE_ENGINE = os.path.join(FILE_DIRECTORY, "cwlNodeEngine.js")

[docs]def evaluate(config, input): application = find_engine(config) default_context = { "engineConfig": [], "job": {}, "context": None, "outdir": None, "tmpdir": None, } new_input = default_context new_input.update(input) sp = subprocess.Popen( [application, NODE_ENGINE], shell=False, close_fds=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE ) input_str = f"{json.dumps(new_input)}\n\n" input_bytes = input_str.encode("utf-8") (stdoutdata, stderrdata) = sp.communicate(input_bytes) if sp.returncode != 0: message = f"Expression engine returned non-zero exit code on evaluation of\n{json.dumps(new_input, indent=4)}{stdoutdata}{stderrdata}" raise Exception(message) rval_raw = stdoutdata.decode("utf-8") return json.loads(rval_raw)