Mercurial > repos > bgruening > run_jupyter_job
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/jupyter_job commit c21261bb8373090c26cf5195134b30538b5bc714
author | bgruening |
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date | Fri, 20 Jan 2023 10:49:03 +0000 |
parents | f4619200cb0a |
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import argparse import os import subprocess import warnings from zipfile import ZipFile import h5py import yaml from skl2onnx import convert_sklearn from skl2onnx.common.data_types import FloatTensorType warnings.filterwarnings("ignore") os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3' SKLEARN_MODELS = [ "sklearn.ensemble", "sklearn.tree", "sklearn.linear_model", "sklearn.svm", "sklearn.neighbors", "sklearn.preprocessing", "sklearn.cluster" ] TF_MODELS = [ "tensorflow.python.keras.engine.training.Model", "tensorflow.python.keras.engine.sequential.Sequential", "tensorflow.python.keras.engine.functional.Functional", "tensorflow.python.keras.layers", "keras.engine.functional.Functional", "keras.engine.sequential.Sequential", "keras.engine.training.Model", "keras.layers" ] ARRAYS = [ "numpy.ndarray", "list" ] DATAFRAME = [ "pandas.core.frame.DataFrame" ] SCALAR_TYPES = [ "int", "float", "str" ] def find_replace_paths(script_file, updated_data_dict): for item in updated_data_dict: g_path = updated_data_dict[item] script_file = script_file.replace(item, g_path) return script_file def update_ml_files_paths(old_file_paths, new_file_paths): if old_file_paths == "" or old_file_paths is None or new_file_paths == "" or new_file_paths is None: return dict() o_files = old_file_paths.split(",") n_files = new_file_paths.split(",") new_paths_dict = dict() for i, o_f in enumerate(o_files): new_paths_dict[o_f] = n_files[i] return new_paths_dict def read_loaded_file(new_paths_dict, p_loaded_file, a_file, w_dir, z_file): global_vars = dict() input_file = yaml.safe_load(p_loaded_file) code_string = open(input_file, "r").read() re_code_string = find_replace_paths(code_string, new_paths_dict) compiled_code = compile(re_code_string, input_file, 'exec') exec(compiled_code, global_vars) check_vars(w_dir, global_vars, a_file) zip_files(w_dir, z_file) def zip_files(w_dir, z_file): with ZipFile(z_file, 'w') as zip_file: for f_path in os.listdir(w_dir): zip_file.write(f_path) def create_model_path(curr_path, key): onnx_path = curr_path + "/model_outputs" if not os.path.exists(onnx_path): os.makedirs(onnx_path) onnx_model_path = curr_path + "/model_outputs/" + "onnx_model_{}.onnx".format(key) return onnx_model_path def save_sklearn_model(w_dir, key, obj): initial_type = [('float_input', FloatTensorType([None, 4]))] onx = convert_sklearn(obj, initial_types=initial_type) sk_model_path = create_model_path(w_dir, key) with open(sk_model_path, "wb") as f: f.write(onx.SerializeToString()) def save_tf_model(w_dir, key, obj): import tensorflow as tf tf_file_key = "tf_model_{}".format(key) tf_model_path = "{}/{}".format(w_dir, tf_file_key) if not os.path.exists(tf_model_path): os.makedirs(tf_model_path) # save model as tf model tf.saved_model.save(obj, tf_model_path) # save model as ONNX tf_onnx_model_p = create_model_path(w_dir, key) # OPSET level defines a level of tensorflow operations supported by ONNX python_shell_script = "python -m tf2onnx.convert --saved-model " + tf_model_path + " --output " + tf_onnx_model_p + " --opset 15 " # convert tf/keras model to ONNX and save it to output file subprocess.run(python_shell_script, shell=True, check=True) def save_primitives(payload, a_file): hf_file = h5py.File(a_file, "w") for key in payload: try: hf_file.create_dataset(key, data=payload[key]) except Exception as e: print(e) continue hf_file.close() def save_dataframe(payload, a_file): for key in payload: payload[key].to_hdf(a_file, key=key) def check_vars(w_dir, var_dict, a_file): if var_dict is not None: primitive_payload = dict() dataframe_payload = dict() for key in var_dict: obj = var_dict[key] obj_class = str(obj.__class__) # save tf model if len([item for item in TF_MODELS if item in obj_class]) > 0: save_tf_model(w_dir, key, obj) # save scikit-learn model elif len([item for item in SKLEARN_MODELS if item in obj_class]) > 0: save_sklearn_model(w_dir, key, obj) # save arrays and lists elif len([item for item in ARRAYS if item in obj_class]) > 0: if key not in primitive_payload: primitive_payload[key] = obj elif len([item for item in DATAFRAME if item in obj_class]) > 0: if key not in dataframe_payload: dataframe_payload[key] = obj elif len([item for item in SCALAR_TYPES if item in obj_class]) > 0: if key not in primitive_payload: primitive_payload[key] = obj save_primitives(primitive_payload, a_file) save_dataframe(dataframe_payload, a_file) if __name__ == "__main__": arg_parser = argparse.ArgumentParser() arg_parser.add_argument("-mlp", "--ml_paths", required=True, help="") arg_parser.add_argument("-ldf", "--loaded_file", required=True, help="") arg_parser.add_argument("-wd", "--working_dir", required=True, help="") arg_parser.add_argument("-oz", "--output_zip", required=True, help="") arg_parser.add_argument("-oa", "--output_array", required=True, help="") arg_parser.add_argument("-mlf", "--ml_h5_files", required=True, help="") # get argument values args = vars(arg_parser.parse_args()) ml_paths = args["ml_paths"] loaded_file = args["loaded_file"] array_output_file = args["output_array"] zip_output_file = args["output_zip"] working_dir = args["working_dir"] ml_h5_files = args["ml_h5_files"] new_paths_dict = update_ml_files_paths(ml_paths, ml_h5_files) read_loaded_file(new_paths_dict, loaded_file, array_output_file, working_dir, zip_output_file)