comparison COBRAxy/custom_data_generator.py @ 147:3fca9b568faf draft

Uploaded

146:88cf4543e210

import pickle
import argparse
import pandas as pd
import utils.general_utils as utils
import utils.rule_parsing  as rulesUtils
from typing import Optional, Tuple, Union, Dict
import utils.reaction_parsing as reactionUtils

ARGS : argparse.Namespace
def process_args() -> argparse.Namespace:
    """
    Interfaces the script of a module with its frontend, making the user's choices for
    various parameters available as values in code.

    Args:

    parser.add_argument("-obnds", "--out_bounds", type = str, required = True, help = "Output bounds")

    parser.add_argument("-id", "--input",   type = str, required = True, help = "Input model")
    parser.add_argument("-mn", "--name",    type = str, required = True, help = "Input model name")
    # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
    
    argsNamespace = parser.parse_args()
    argsNamespace.out_dir = "result"
    # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection

    return argsNamespace

################################- INPUT DATA LOADING -################################

        for key, value in data.items():
            writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })

###############################- ENTRY POINT -################################
def main() -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.
    
    Returns:
        None
    """
    # get args from frontend (related xml)
    global ARGS
    ARGS = process_args()

    # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this!
    if os.path.isdir(ARGS.out_dir) == False: os.makedirs(ARGS.out_dir)

    # load custom model
    model = load_custom_model(
        utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)

147:3fca9b568faf

import pickle
import argparse
import pandas as pd
import utils.general_utils as utils
import utils.rule_parsing  as rulesUtils
from typing import Optional, Tuple, Union, List, Dict
import utils.reaction_parsing as reactionUtils

ARGS : argparse.Namespace
def process_args(args:List[str] = None) -> argparse.Namespace:
    """
    Interfaces the script of a module with its frontend, making the user's choices for
    various parameters available as values in code.

    Args:

    parser.add_argument("-obnds", "--out_bounds", type = str, required = True, help = "Output bounds")

    parser.add_argument("-id", "--input",   type = str, required = True, help = "Input model")
    parser.add_argument("-mn", "--name",    type = str, required = True, help = "Input model name")
    # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
    parser.add_argument('-idop', '--output_path', type = str, default='result', help = 'output path for maps')
    argsNamespace = parser.parse_args(args)
    # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection

    return argsNamespace

################################- INPUT DATA LOADING -################################

        for key, value in data.items():
            writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })

###############################- ENTRY POINT -################################
def main(args:List[str] = None) -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.
    
    Returns:
        None
    """
    # get args from frontend (related xml)
    global ARGS
    ARGS = process_args(args)

    # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this!
    if os.path.isdir(ARGS.output_path) == False: os.makedirs(ARGS.output_path)

    # load custom model
    model = load_custom_model(
        utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)