Mercurial > repos > bimib > cobraxy

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

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author bimib
date Wed, 06 Nov 2024 13:57:24 +0000
parents 7e703e546998
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146:88cf4543e210 147:3fca9b568faf
10 from typing import Union, Optional, List, Dict, Tuple, TypeVar 10 from typing import Union, Optional, List, Dict, Tuple, TypeVar
11 11
12 ERRORS = [] 12 ERRORS = []
13 ########################## argparse ########################################## 13 ########################## argparse ##########################################
14 ARGS :argparse.Namespace 14 ARGS :argparse.Namespace
15 def process_args() -> argparse.Namespace: 15 def process_args(args:List[str] = None) -> argparse.Namespace:
16 """ 16 """
17 Processes command-line arguments. 17 Processes command-line arguments.
18 18
19 Args: 19 Args:
20 args (list): List of command-line arguments. 20 args (list): List of command-line arguments.
59 59
60 parser.add_argument( 60 parser.add_argument(
61 '-ra', '--ras_output', 61 '-ra', '--ras_output',
62 type = str, 62 type = str,
63 required = True, help = 'ras output') 63 required = True, help = 'ras output')
64 64
65 return parser.parse_args() 65
66 return parser.parse_args(args)
66 67
67 ############################ dataset input #################################### 68 ############################ dataset input ####################################
68 def read_dataset(data :str, name :str) -> pd.DataFrame: 69 def read_dataset(data :str, name :str) -> pd.DataFrame:
69 """ 70 """
70 Read a dataset from a CSV file and return it as a pandas DataFrame. 71 Read a dataset from a CSV file and return it as a pandas DataFrame.
645 if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath) 646 if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)
646 647
647 # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed. 648 # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed.
648 return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) } 649 return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) }
649 650
650 def main() -> None: 651 def main(args:List[str] = None) -> None:
651 """ 652 """
652 Initializes everything and sets the program in motion based on the fronted input arguments. 653 Initializes everything and sets the program in motion based on the fronted input arguments.
653 654
654 Returns: 655 Returns:
655 None 656 None
656 """ 657 """
657 # get args from frontend (related xml) 658 # get args from frontend (related xml)
658 global ARGS 659 global ARGS
659 ARGS = process_args() 660 ARGS = process_args(args)
660 print(ARGS.rules_selector) 661 print(ARGS.rules_selector)
661 # read dataset 662 # read dataset
662 dataset = read_dataset(ARGS.input, "dataset") 663 dataset = read_dataset(ARGS.input, "dataset")
663 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) 664 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
664 665