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392
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1 import math
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2 import re
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3 import sys
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4 import csv
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5 import pickle
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6 import lxml.etree as ET
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7
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8 from enum import Enum
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9 from itertools import count
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408
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10 from typing import Any, Callable, Dict, Generic, List, Literal, Optional, TypeVar, Union, Set, Tuple
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392
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11
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12 import pandas as pd
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13 import cobra
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409
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14 from cobra import Model as cobraModel, Reaction, Metabolite
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392
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15
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16 import zipfile
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17 import gzip
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18 import bz2
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19 from io import StringIO
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20
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394
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21
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22
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392
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23 class ValueErr(Exception):
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24 def __init__(self, param_name, expected, actual):
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25 super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")
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26
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27 class PathErr(Exception):
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28 def __init__(self, path, message):
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29 super().__init__(f"Path error for '{path}': {message}")
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30
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31 class FileFormat(Enum):
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32 """
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33 Encodes possible file extensions to conditionally save data in a different format.
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34 """
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35 DAT = ("dat",) # this is how galaxy treats all your files!
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36 CSV = ("csv",) # this is how most editable input data is written
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37 TSV = ("tsv",) # this is how most editable input data is ACTUALLY written TODO:more support pls!!
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38 SVG = ("svg",) # this is how most metabolic maps are written
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39 PNG = ("png",) # this is a common output format for images (such as metabolic maps)
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40 PDF = ("pdf",) # this is also a common output format for images, as it's required in publications.
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41
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42 # Updated to include compressed variants
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43 XML = ("xml", "xml.gz", "xml.zip", "xml.bz2") # SBML files are XML files, sometimes compressed
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44 JSON = ("json", "json.gz", "json.zip", "json.bz2") # COBRA models can be stored as JSON files, sometimes compressed
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45 MAT = ("mat", "mat.gz", "mat.zip", "mat.bz2") # COBRA models can be stored as MAT files, sometimes compressed
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46 YML = ("yml", "yml.gz", "yml.zip", "yml.bz2") # COBRA models can be stored as YML files, sometimes compressed
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47
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48 TXT = ("txt",) # this is how most output data is written
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49 PICKLE = ("pickle", "pk", "p") # this is how all runtime data structures are saved
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50
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51 def __init__(self, *extensions):
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52 self.extensions = extensions
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53 # Store original extension when set via fromExt
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54 self._original_extension = None
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55
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56 @classmethod
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57 def fromExt(cls, ext: str) -> "FileFormat":
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58 """
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59 Converts a file extension string to a FileFormat instance.
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60 Args:
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61 ext : The file extension as a string.
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62 Returns:
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63 FileFormat: The FileFormat instance corresponding to the file extension.
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64 """
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65 variantName = ext.upper()
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66 if variantName in FileFormat.__members__:
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67 instance = FileFormat[variantName]
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68 instance._original_extension = ext
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69 return instance
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70
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71 variantName = ext.lower()
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72 for member in cls:
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73 if variantName in member.value:
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74 # Create a copy-like behavior by storing the original extension
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75 member._original_extension = ext
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76 return member
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77
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78 raise ValueErr("ext", "a valid FileFormat file extension", ext)
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79
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80 def __str__(self) -> str:
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81 """
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82 (Private) converts to str representation. Good practice for usage with argparse.
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83 Returns:
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84 str : the string representation of the file extension.
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85 """
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86 # If we have an original extension stored (for compressed files only), use it
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87 if hasattr(self, '_original_extension') and self._original_extension:
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88 return self._original_extension
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89
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90 # For XML, JSON, MAT and YML without original extension, use the base extension
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91 if self == FileFormat.XML:
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92 return "xml"
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93 elif self == FileFormat.JSON:
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94 return "json"
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95 elif self == FileFormat.MAT:
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96 return "mat"
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97 elif self == FileFormat.YML:
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98 return "yml"
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99
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100 return self.value[-1]
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101
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102 class FilePath():
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103 """
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104 Represents a file path. View this as an attempt to standardize file-related operations by expecting
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105 values of this type in any process requesting a file path.
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106 """
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107 def __init__(self, filePath: str, ext: FileFormat, *, prefix="") -> None:
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108 """
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109 (Private) Initializes an instance of FilePath.
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110 Args:
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111 path : the end of the path, containing the file name.
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112 ext : the file's extension.
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113 prefix : anything before path, if the last '/' isn't there it's added by the code.
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114 Returns:
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115 None : practically, a FilePath instance.
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116 """
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117 self.ext = ext
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118 self.filePath = filePath
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119
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120 if prefix and prefix[-1] != '/':
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121 prefix += '/'
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122 self.prefix = prefix
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123
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124 @classmethod
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125 def fromStrPath(cls, path: str) -> "FilePath":
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126 """
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127 Factory method to parse a string from which to obtain, if possible, a valid FilePath instance.
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128 It detects double extensions such as .json.gz and .xml.bz2, which are common in COBRA models.
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129 These double extensions are not supported for other file types such as .csv.
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130 Args:
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131 path : the string containing the path
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132 Raises:
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133 PathErr : if the provided string doesn't represent a valid path.
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134 Returns:
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135 FilePath : the constructed instance.
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136 """
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137 result = re.search(r"^(?P<prefix>.*\/)?(?P<name>.*)\.(?P<ext>[^.]*)$", path)
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138 if not result or not result["name"] or not result["ext"]:
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139 raise PathErr(path, "cannot recognize folder structure or extension in path")
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140
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141 prefix = result["prefix"] if result["prefix"] else ""
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142 name, ext = result["name"], result["ext"]
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143
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144 # Check for double extensions (json.gz, xml.zip, etc.)
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145 parts = path.split(".")
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146 if len(parts) >= 3:
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147 penultimate = parts[-2]
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148 last = parts[-1]
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149 double_ext = f"{penultimate}.{last}"
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150
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151 # Try the double extension first
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152 try:
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153 ext_format = FileFormat.fromExt(double_ext)
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154 name = ".".join(parts[:-2])
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155 # Extract prefix if it exists
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156 if '/' in name:
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157 prefix = name[:name.rfind('/') + 1]
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158 name = name[name.rfind('/') + 1:]
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159 return cls(name, ext_format, prefix=prefix)
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160 except ValueErr:
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161 # If double extension doesn't work, fall back to single extension
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162 pass
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163
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164 # Single extension fallback (original logic)
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165 try:
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166 ext_format = FileFormat.fromExt(ext)
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167 return cls(name, ext_format, prefix=prefix)
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168 except ValueErr:
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169 raise PathErr(path, f"unsupported file extension: {ext}")
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170
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171 def show(self) -> str:
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172 """
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173 Shows the path as a string.
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174 Returns:
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175 str : the path shown as a string.
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176 """
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177 return f"{self.prefix}{self.filePath}.{self.ext}"
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178
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179 def __str__(self) -> str:
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180 return self.show()
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181
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182 # ERRORS
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183 def terminate(msg :str) -> None:
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184 """
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185 Terminate the execution of the script with an error message.
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186
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187 Args:
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188 msg (str): The error message to be displayed.
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189
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190 Returns:
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191 None
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192 """
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193 sys.exit(f"Execution aborted: {msg}\n")
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194
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195 def logWarning(msg :str, loggerPath :str) -> None:
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196 """
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197 Log a warning message to an output log file and print it to the console. The final period and a
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198 newline is added by the function.
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199
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200 Args:
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201 s (str): The warning message to be logged and printed.
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202 loggerPath : The file path of the output log file. Given as a string, parsed to a FilePath and
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203 immediately read back (beware relative expensive operation, log with caution).
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204
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205 Returns:
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206 None
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207 """
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208 # building the path and then reading it immediately seems useless, but it's actually a way of
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209 # validating that reduces repetition on the caller's side. Besides, logging a message by writing
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210 # to a file is supposed to be computationally expensive anyway, so this is also a good deterrent from
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211 # mindlessly logging whenever something comes up, log at the very end and tell the user everything
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212 # that went wrong. If you don't like it: implement a persistent runtime buffer that gets dumped to
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213 # the file only at the end of the program's execution.
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214 with open(FilePath.fromStrPath(loggerPath).show(), 'a') as log: log.write(f"{msg}.\n")
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215
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216 class CustomErr(Exception):
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217 """
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218 Custom error class to handle exceptions in a structured way, with a unique identifier and a message.
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219 """
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220 __idGenerator = count()
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221 errName = "Custom Error"
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222 def __init__(self, msg :str, details = "", explicitErrCode = -1) -> None:
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223 """
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224 (Private) Initializes an instance of CustomErr.
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225
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226 Args:
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227 msg (str): Error message to be displayed.
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228 details (str): Informs the user more about the error encountered. Defaults to "".
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229 explicitErrCode (int): Explicit error code to be used. Defaults to -1.
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230
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231 Returns:
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232 None : practically, a CustomErr instance.
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233 """
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234 self.msg = msg
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235 self.details = details
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236
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237 self.id = max(explicitErrCode, next(CustomErr.__idGenerator))
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238
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239 def throw(self, loggerPath = "") -> None:
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240 """
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241 Raises the current CustomErr instance, logging a warning message before doing so.
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242
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243 Raises:
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244 self: The current CustomErr instance.
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245
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246 Returns:
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247 None
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248 """
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249 if loggerPath: logWarning(str(self), loggerPath)
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250 raise self
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251
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252 def abort(self) -> None:
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253 """
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254 Aborts the execution of the script.
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255
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256 Returns:
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257 None
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258 """
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259 terminate(str(self))
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260
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261 def __str__(self) -> str:
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262 """
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263 (Private) Returns a string representing the current CustomErr instance.
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264
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265 Returns:
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266 str: A string representing the current CustomErr instance.
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267 """
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268 return f"{CustomErr.errName} #{self.id}: {self.msg}, {self.details}."
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269
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270 class ArgsErr(CustomErr):
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271 """
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272 CustomErr subclass for UI arguments errors.
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273 """
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274 errName = "Args Error"
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275 def __init__(self, argName :str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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276 super().__init__(f"argument \"{argName}\" expected {expected} but got {actual}", msg)
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277
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278 class DataErr(CustomErr):
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279 """
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280 CustomErr subclass for data formatting errors.
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281 """
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282 errName = "Data Format Error"
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283 def __init__(self, fileName :str, msg = "no further details provided") -> None:
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284 super().__init__(f"file \"{fileName}\" contains malformed data", msg)
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285
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286 class PathErr(CustomErr):
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287 """
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288 CustomErr subclass for filepath formatting errors.
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289 """
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290 errName = "Path Error"
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291 def __init__(self, path :FilePath, msg = "no further details provided") -> None:
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292 super().__init__(f"path \"{path}\" is invalid", msg)
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293
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294 class ValueErr(CustomErr):
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295 """
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296 CustomErr subclass for any value error.
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297 """
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298 errName = "Value Error"
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299 def __init__(self, valueName: str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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300 super().__init__("value " + f"\"{valueName}\" " * bool(valueName) + f"was supposed to be {expected}, but got {actual} instead", msg)
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301
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302 # RESULT
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303 T = TypeVar('T')
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304 E = TypeVar('E', bound = CustomErr) # should bind to Result.ResultErr but python happened!
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305 class Result(Generic[T, E]):
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306 class ResultErr(CustomErr):
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307 """
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308 CustomErr subclass for all Result errors.
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309 """
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310 errName = "Result Error"
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311 def __init__(self, msg = "no further details provided") -> None:
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312 super().__init__(msg)
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313 """
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314 Class to handle the result of an operation, with a value and a boolean flag to indicate
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315 whether the operation was successful or not.
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316 """
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317 def __init__(self, value :Union[T, E], isOk :bool) -> None:
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318 """
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319 (Private) Initializes an instance of Result.
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320
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321 Args:
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322 value (Union[T, E]): The value to be stored in the Result instance.
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323 isOk (bool): A boolean flag to indicate whether the operation was successful or not.
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324
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325 Returns:
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326 None : practically, a Result instance.
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327 """
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328 self.isOk = isOk
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329 self.isErr = not isOk
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330 self.value = value
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331
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332 @classmethod
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333 def Ok(cls, value :T) -> "Result":
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334 """
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335 Constructs a new Result instance with a successful operation.
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336
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337 Args:
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338 value (T): The value to be stored in the Result instance, set as successful.
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339
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340 Returns:
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341 Result: A new Result instance with a successful operation.
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342 """
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343 return Result(value, isOk = True)
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344
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345 @classmethod
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346 def Err(cls, value :E) -> "Result":
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347 """
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348 Constructs a new Result instance with a failed operation.
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349
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350 Args:
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351 value (E): The value to be stored in the Result instance, set as failed.
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352
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353 Returns:
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354 Result: A new Result instance with a failed operation.
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355 """
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356 return Result(value, isOk = False)
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357
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358 def unwrap(self) -> T:
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359 """
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360 Unwraps the value of the Result instance, if the operation was successful.
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361
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362 Raises:
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363 ResultErr: If the operation was not successful.
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364
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365 Returns:
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366 T: The value of the Result instance, if the operation was successful.
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367 """
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368 if self.isOk: return self.value
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369 raise Result.ResultErr(f"Unwrapped Result.Err : {self.value}")
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370
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371 def unwrapOr(self, default :T) -> T:
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372 """
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373 Unwraps the value of the Result instance, if the operation was successful, otherwise
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374 it returns a default value.
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375
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376 Args:
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377 default (T): The default value to be returned if the operation was not successful.
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378
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379 Returns:
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380 T: The value of the Result instance, if the operation was successful,
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381 otherwise the default value.
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382 """
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383 return self.value if self.isOk else default
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384
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385 def expect(self, err :"Result.ResultErr") -> T:
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386 """
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387 Expects that the value of the Result instance is successful, otherwise it raises an error.
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388
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389 Args:
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390 err (Exception): The error to be raised if the operation was not successful.
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391
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392 Raises:
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393 err: The error raised if the operation was not successful.
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394
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395 Returns:
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396 T: The value of the Result instance, if the operation was successful.
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397 """
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398 if self.isOk: return self.value
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399 raise err
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400
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401 U = TypeVar("U")
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402 def map(self, mapper: Callable[[T], U]) -> "Result[U, E]":
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403 """
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404 Maps the value of the current Result to whatever is returned by the mapper function.
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405 If the Result contained an unsuccessful operation to begin with it remains unchanged
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406 (a reference to the current instance is returned).
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407 If the mapper function panics the returned result instance will be of the error kind.
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408
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409 Args:
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410 mapper (Callable[[T], U]): The mapper operation to be applied to the Result value.
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411
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412 Returns:
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413 Result[U, E]: The result of the mapper operation applied to the Result value.
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414 """
|
|
|
415 if self.isErr: return self
|
|
|
416 try: return Result.Ok(mapper(self.value))
|
|
|
417 except Exception as e: return Result.Err(e)
|
|
|
418
|
|
|
419 D = TypeVar("D", bound = "Result.ResultErr")
|
|
|
420 def mapErr(self, mapper :Callable[[E], D]) -> "Result[T, D]":
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|
|
421 """
|
|
|
422 Maps the error of the current Result to whatever is returned by the mapper function.
|
|
|
423 If the Result contained a successful operation it remains unchanged
|
|
|
424 (a reference to the current instance is returned).
|
|
|
425 If the mapper function panics this method does as well.
|
|
|
426
|
|
|
427 Args:
|
|
|
428 mapper (Callable[[E], D]): The mapper operation to be applied to the Result error.
|
|
|
429
|
|
|
430 Returns:
|
|
|
431 Result[U, E]: The result of the mapper operation applied to the Result error.
|
|
|
432 """
|
|
|
433 if self.isOk: return self
|
|
|
434 return Result.Err(mapper(self.value))
|
|
|
435
|
|
|
436 def __str__(self):
|
|
|
437 return f"Result::{'Ok' if self.isOk else 'Err'}({self.value})"
|
|
|
438
|
|
|
439 # FILES
|
|
|
440 def read_dataset(path :FilePath, datasetName = "Dataset (not actual file name!)") -> pd.DataFrame:
|
|
|
441 """
|
|
|
442 Reads a .csv or .tsv file and returns it as a Pandas DataFrame.
|
|
|
443
|
|
|
444 Args:
|
|
|
445 path : the path to the dataset file.
|
|
|
446 datasetName : the name of the dataset.
|
|
|
447
|
|
|
448 Raises:
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|
|
449 DataErr: If anything goes wrong when trying to open the file, if pandas thinks the dataset is empty or if
|
|
|
450 it has less than 2 columns.
|
|
|
451
|
|
|
452 Returns:
|
|
|
453 pandas.DataFrame: The dataset loaded as a Pandas DataFrame.
|
|
|
454 """
|
|
|
455 # I advise against the use of this function. This is an attempt at standardizing bad legacy code rather than
|
|
|
456 # removing / replacing it to avoid introducing as many bugs as possible in the tools still relying on this code.
|
|
|
457 # First off, this is not the best way to distinguish between .csv and .tsv files and Galaxy itself makes it really
|
|
|
458 # hard to implement anything better. Also, this function's name advertizes it as a dataset-specific operation and
|
|
|
459 # contains dubious responsibility (how many columns..) while being a file-opening function instead. My suggestion is
|
|
|
460 # TODO: stop using dataframes ever at all in anything and find a way to have tight control over file extensions.
|
|
|
461 try: dataset = pd.read_csv(path.show(), sep = '\t', header = None, engine = "python")
|
|
|
462 except:
|
|
|
463 try: dataset = pd.read_csv(path.show(), sep = ',', header = 0, engine = "python")
|
|
|
464 except Exception as err: raise DataErr(datasetName, f"encountered empty or wrongly formatted data: {err}")
|
|
|
465
|
|
|
466 if len(dataset.columns) < 2: raise DataErr(datasetName, "a dataset is always meant to have at least 2 columns")
|
|
|
467 return dataset
|
|
|
468
|
|
|
469 def readPickle(path :FilePath) -> Any:
|
|
|
470 """
|
|
|
471 Reads the contents of a .pickle file, which needs to exist at the given path.
|
|
|
472
|
|
|
473 Args:
|
|
|
474 path : the path to the .pickle file.
|
|
|
475
|
|
|
476 Returns:
|
|
|
477 Any : the data inside a pickle file, could be anything.
|
|
|
478 """
|
|
|
479 with open(path.show(), "rb") as fd: return pickle.load(fd)
|
|
|
480
|
|
|
481 def writePickle(path :FilePath, data :Any) -> None:
|
|
|
482 """
|
|
|
483 Saves any data in a .pickle file, created at the given path.
|
|
|
484
|
|
|
485 Args:
|
|
|
486 path : the path to the .pickle file.
|
|
|
487 data : the data to be written to the file.
|
|
|
488
|
|
|
489 Returns:
|
|
|
490 None
|
|
|
491 """
|
|
|
492 with open(path.show(), "wb") as fd: pickle.dump(data, fd)
|
|
|
493
|
|
|
494 def readCsv(path :FilePath, delimiter = ',', *, skipHeader = True) -> List[List[str]]:
|
|
|
495 """
|
|
|
496 Reads the contents of a .csv file, which needs to exist at the given path.
|
|
|
497
|
|
|
498 Args:
|
|
|
499 path : the path to the .csv file.
|
|
|
500 delimiter : allows other subformats such as .tsv to be opened by the same method (\\t delimiter).
|
|
|
501 skipHeader : whether the first row of the file is a header and should be skipped.
|
|
|
502
|
|
|
503 Returns:
|
|
|
504 List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas.
|
|
|
505 """
|
|
|
506 with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:]
|
|
|
507
|
|
|
508 def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree:
|
|
|
509 """
|
|
|
510 Reads the contents of a .svg file, which needs to exist at the given path.
|
|
|
511
|
|
|
512 Args:
|
|
|
513 path : the path to the .svg file.
|
|
|
514
|
|
|
515 Raises:
|
|
|
516 DataErr : if the map is malformed.
|
|
|
517
|
|
|
518 Returns:
|
|
|
519 Any : the data inside a svg file, could be anything.
|
|
|
520 """
|
|
|
521 try: return ET.parse(path.show())
|
|
|
522 except (ET.XMLSyntaxError, ET.XMLSchemaParseError) as err:
|
|
|
523 raise customErr if customErr else err
|
|
|
524
|
|
|
525 def writeSvg(path :FilePath, data:ET.ElementTree) -> None:
|
|
|
526 """
|
|
|
527 Saves svg data opened with lxml.etree in a .svg file, created at the given path.
|
|
|
528
|
|
|
529 Args:
|
|
|
530 path : the path to the .svg file.
|
|
|
531 data : the data to be written to the file.
|
|
|
532
|
|
|
533 Returns:
|
|
|
534 None
|
|
|
535 """
|
|
|
536 with open(path.show(), "wb") as fd: fd.write(ET.tostring(data))
|
|
|
537
|
|
|
538 # UI ARGUMENTS
|
|
|
539 class Bool:
|
|
|
540 def __init__(self, argName :str) -> None:
|
|
|
541 self.argName = argName
|
|
|
542
|
|
|
543 def __call__(self, s :str) -> bool: return self.check(s)
|
|
|
544
|
|
|
545 def check(self, s :str) -> bool:
|
|
|
546 s = s.lower()
|
|
|
547 if s == "true" : return True
|
|
|
548 if s == "false": return False
|
|
|
549 raise ArgsErr(self.argName, "boolean string (true or false, not case sensitive)", f"\"{s}\"")
|
|
|
550
|
|
|
551 class Float:
|
|
|
552 def __init__(self, argName = "Dataset values, not an argument") -> None:
|
|
|
553 self.argName = argName
|
|
|
554
|
|
|
555 def __call__(self, s :str) -> float: return self.check(s)
|
|
|
556
|
|
|
557 def check(self, s :str) -> float:
|
|
|
558 try: return float(s)
|
|
|
559 except ValueError:
|
|
|
560 s = s.lower()
|
|
|
561 if s == "nan" or s == "none": return math.nan
|
|
|
562 raise ArgsErr(self.argName, "numeric string or \"None\" or \"NaN\" (not case sensitive)", f"\"{s}\"")
|
|
|
563
|
|
|
564 # MODELS
|
|
|
565 OldRule = List[Union[str, "OldRule"]]
|
|
|
566 class Model(Enum):
|
|
|
567 """
|
|
|
568 Represents a metabolic model, either custom or locally supported. Custom models don't point
|
|
|
569 to valid file paths.
|
|
|
570 """
|
|
|
571
|
|
|
572 Recon = "Recon"
|
|
|
573 ENGRO2 = "ENGRO2"
|
|
|
574 ENGRO2_no_legend = "ENGRO2_no_legend"
|
|
|
575 HMRcore = "HMRcore"
|
|
|
576 HMRcore_no_legend = "HMRcore_no_legend"
|
|
|
577 Custom = "Custom" # Exists as a valid variant in the UI, but doesn't point to valid file paths.
|
|
|
578
|
|
|
579 def __raiseMissingPathErr(self, path :Optional[FilePath]) -> None:
|
|
|
580 if not path: raise PathErr("<<MISSING>>", "it's necessary to provide a custom path when retrieving files from a custom model")
|
|
|
581
|
|
|
582 def getRules(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, OldRule]]:
|
|
|
583 """
|
|
|
584 Open "rules" file for this model.
|
|
|
585
|
|
|
586 Returns:
|
|
|
587 Dict[str, Dict[str, OldRule]] : the rules for this model.
|
|
|
588 """
|
|
|
589 path = customPath if self is Model.Custom else FilePath(f"{self.name}_rules", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
590 self.__raiseMissingPathErr(path)
|
|
|
591 return readPickle(path)
|
|
|
592
|
|
|
593 def getTranslator(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, str]]:
|
|
|
594 """
|
|
|
595 Open "gene translator (old: gene_in_rule)" file for this model.
|
|
|
596
|
|
|
597 Returns:
|
|
|
598 Dict[str, Dict[str, str]] : the translator dict for this model.
|
|
|
599 """
|
|
|
600 path = customPath if self is Model.Custom else FilePath(f"{self.name}_genes", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
601 self.__raiseMissingPathErr(path)
|
|
|
602 return readPickle(path)
|
|
|
603
|
|
|
604 def getMap(self, toolDir = ".", customPath :Optional[FilePath] = None) -> ET.ElementTree:
|
|
|
605 path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/")
|
|
|
606 self.__raiseMissingPathErr(path)
|
|
|
607 return readSvg(path, customErr = DataErr(path, f"custom map in wrong format"))
|
|
|
608
|
|
|
609 def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model:
|
|
|
610 if(self is Model.Custom):
|
|
|
611 return self.load_custom_model(customPath, customExtension)
|
|
|
612 else:
|
|
|
613 return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/models/").show())
|
|
|
614
|
|
|
615 def load_custom_model(self, file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model:
|
|
|
616 ext = ext if ext else file_path.ext
|
|
|
617 try:
|
|
|
618 if str(ext) in FileFormat.XML.value:
|
|
|
619 return cobra.io.read_sbml_model(file_path.show())
|
|
|
620
|
|
|
621 if str(ext) in FileFormat.JSON.value:
|
|
|
622 # Compressed files are not automatically handled by cobra
|
|
|
623 if(ext == "json"):
|
|
|
624 return cobra.io.load_json_model(file_path.show())
|
|
|
625 else:
|
|
|
626 return self.extract_model(file_path, ext, "json")
|
|
|
627
|
|
|
628 if str(ext) in FileFormat.MAT.value:
|
|
|
629 # Compressed files are not automatically handled by cobra
|
|
|
630 if(ext == "mat"):
|
|
|
631 return cobra.io.load_matlab_model(file_path.show())
|
|
|
632 else:
|
|
|
633 return self.extract_model(file_path, ext, "mat")
|
|
|
634
|
|
|
635 if str(ext) in FileFormat.YML.value:
|
|
|
636 # Compressed files are not automatically handled by cobra
|
|
|
637 if(ext == "yml"):
|
|
|
638 return cobra.io.load_yaml_model(file_path.show())
|
|
|
639 else:
|
|
|
640 return self.extract_model(file_path, ext, "yml")
|
|
|
641
|
|
|
642 except Exception as e: raise DataErr(file_path, e.__str__())
|
|
|
643 raise DataErr(file_path,
|
|
|
644 f"Fomat \"{file_path.ext}\" is not recognized, only JSON, XML, MAT and YAML (.yml) files are supported.")
|
|
|
645
|
|
|
646
|
|
|
647 def extract_model(self, file_path:FilePath, ext :FileFormat, model_encoding:Literal["json", "mat", "yml"]) -> cobra.Model:
|
|
|
648 """
|
|
|
649 Extract JSON, MAT and YAML COBRA model from a compressed file (zip, gz, bz2).
|
|
|
650
|
|
|
651 Args:
|
|
|
652 file_path: File path of the model
|
|
|
653 ext: File extensions of class FileFormat (should be .zip, .gz or .bz2)
|
|
|
654
|
|
|
655 Returns:
|
|
|
656 cobra.Model: COBRApy model
|
|
|
657
|
|
|
658 Raises:
|
|
|
659 Exception: Extraction errors
|
|
|
660 """
|
|
|
661 ext_str = str(ext)
|
|
|
662
|
|
|
663 try:
|
|
|
664 if '.zip' in ext_str:
|
|
|
665 with zipfile.ZipFile(file_path.show(), 'r') as zip_ref:
|
|
|
666 with zip_ref.open(zip_ref.namelist()[0]) as json_file:
|
|
|
667 content = json_file.read().decode('utf-8')
|
|
|
668 if model_encoding == "json":
|
|
|
669 return cobra.io.load_json_model(StringIO(content))
|
|
|
670 elif model_encoding == "mat":
|
|
|
671 return cobra.io.load_matlab_model(StringIO(content))
|
|
|
672 elif model_encoding == "yml":
|
|
|
673 return cobra.io.load_yaml_model(StringIO(content))
|
|
|
674 else:
|
|
|
675 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
|
|
|
676 elif '.gz' in ext_str:
|
|
|
677 with gzip.open(file_path.show(), 'rt', encoding='utf-8') as gz_ref:
|
|
|
678 if model_encoding == "json":
|
|
|
679 return cobra.io.load_json_model(gz_ref)
|
|
|
680 elif model_encoding == "mat":
|
|
|
681 return cobra.io.load_matlab_model(gz_ref)
|
|
|
682 elif model_encoding == "yml":
|
|
|
683 return cobra.io.load_yaml_model(gz_ref)
|
|
|
684 else:
|
|
|
685 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
|
|
|
686 elif '.bz2' in ext_str:
|
|
|
687 with bz2.open(file_path.show(), 'rt', encoding='utf-8') as bz2_ref:
|
|
|
688 if model_encoding == "json":
|
|
|
689 return cobra.io.load_json_model(bz2_ref)
|
|
|
690 elif model_encoding == "mat":
|
|
|
691 return cobra.io.load_matlab_model(bz2_ref)
|
|
|
692 elif model_encoding == "yml":
|
|
|
693 return cobra.io.load_yaml_model(bz2_ref)
|
|
|
694 else:
|
|
|
695 raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
|
|
|
696 else:
|
|
|
697 raise ValueError(f"Compression format not supported: {ext_str}. Supported: .zip, .gz and .bz2")
|
|
|
698
|
|
|
699 except Exception as e:
|
|
|
700 raise Exception(f"Error during model extraction: {str(e)}")
|
|
|
701
|
|
|
702
|
|
|
703
|
|
394
|
704 def __str__(self) -> str: return self.value
|
|
|
705
|
|
|
706
|
|
|
707 def convert_genes(model,annotation):
|
|
|
708 from cobra.manipulation import rename_genes
|
|
|
709 model2=model.copy()
|
|
|
710 try:
|
|
|
711 dict_genes={gene.id:gene.notes[annotation] for gene in model2.genes}
|
|
|
712 except:
|
|
|
713 print("No annotation in gene dict!")
|
|
|
714 return -1
|
|
|
715 rename_genes(model2,dict_genes)
|
|
|
716
|
|
408
|
717 return model2
|
|
|
718
|
|
|
719
|
|
409
|
720 def build_cobra_model_from_csv(csv_path: str, model_id: str = "new_model") -> cobra.Model:
|
|
408
|
721 """
|
|
|
722 Costruisce un modello COBRApy a partire da un file CSV con i dati delle reazioni.
|
|
|
723
|
|
|
724 Args:
|
|
|
725 csv_path: Path al file CSV (separato da tab)
|
|
|
726 model_id: ID del modello da creare
|
|
|
727
|
|
|
728 Returns:
|
|
|
729 cobra.Model: Il modello COBRApy costruito
|
|
|
730 """
|
|
|
731
|
|
|
732 # Leggi i dati dal CSV
|
|
|
733 df = pd.read_csv(csv_path, sep='\t')
|
|
|
734
|
|
|
735 # Crea il modello vuoto
|
|
409
|
736 model = cobraModel(model_id)
|
|
408
|
737
|
|
|
738 # Dict per tenere traccia di metaboliti e compartimenti
|
|
|
739 metabolites_dict = {}
|
|
|
740 compartments_dict = {}
|
|
|
741
|
|
|
742 print(f"Costruendo modello da {len(df)} reazioni...")
|
|
|
743
|
|
|
744 # Prima passata: estrai metaboliti e compartimenti dalle formule delle reazioni
|
|
|
745 for idx, row in df.iterrows():
|
|
|
746 reaction_formula = str(row['Reaction']).strip()
|
|
|
747 if not reaction_formula or reaction_formula == 'nan':
|
|
|
748 continue
|
|
|
749
|
|
|
750 # Estrai metaboliti dalla formula della reazione
|
|
|
751 metabolites = extract_metabolites_from_reaction(reaction_formula)
|
|
|
752
|
|
|
753 for met_id in metabolites:
|
|
|
754 compartment = extract_compartment_from_metabolite(met_id)
|
|
|
755
|
|
|
756 # Aggiungi compartimento se non esiste
|
|
|
757 if compartment not in compartments_dict:
|
|
|
758 compartments_dict[compartment] = compartment
|
|
|
759
|
|
|
760 # Aggiungi metabolita se non esiste
|
|
|
761 if met_id not in metabolites_dict:
|
|
|
762 metabolites_dict[met_id] = Metabolite(
|
|
|
763 id=met_id,
|
|
|
764 compartment=compartment,
|
|
|
765 name=met_id.replace(f"_{compartment}", "").replace("__", "_")
|
|
|
766 )
|
|
|
767
|
|
|
768 # Aggiungi compartimenti al modello
|
|
|
769 model.compartments = compartments_dict
|
|
|
770
|
|
|
771 # Aggiungi metaboliti al modello
|
|
|
772 model.add_metabolites(list(metabolites_dict.values()))
|
|
|
773
|
|
|
774 print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti")
|
|
|
775
|
|
|
776 # Seconda passata: aggiungi le reazioni
|
|
|
777 reactions_added = 0
|
|
414
|
778 reactions_skipped = 0
|
|
408
|
779
|
|
|
780 for idx, row in df.iterrows():
|
|
415
|
781
|
|
|
782 reaction_id = str(row['ReactionID']).strip()
|
|
|
783 reaction_formula = str(row['Reaction']).strip()
|
|
|
784
|
|
|
785 # Salta reazioni senza formula
|
|
|
786 if not reaction_formula or reaction_formula == 'nan':
|
|
|
787 raise ValueError(f"Formula della reazione mancante {reaction_id}")
|
|
|
788
|
|
|
789 # Crea la reazione
|
|
|
790 reaction = Reaction(reaction_id)
|
|
|
791 reaction.name = reaction_id
|
|
|
792
|
|
|
793 # Imposta bounds
|
|
|
794 reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
|
|
|
795 reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
|
|
|
796
|
|
|
797 # Aggiungi gene rule se presente
|
|
|
798 if pd.notna(row['Rule']) and str(row['Rule']).strip():
|
|
|
799 reaction.gene_reaction_rule = str(row['Rule']).strip()
|
|
|
800
|
|
|
801 # Parse della formula della reazione
|
|
408
|
802 try:
|
|
415
|
803 parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
|
|
|
804 except Exception as e:
|
|
|
805 print(f"Errore nel parsing della reazione {reaction_id}: {e}")
|
|
|
806 reactions_skipped += 1
|
|
|
807 continue
|
|
|
808
|
|
|
809 # Aggiungi la reazione al modello
|
|
|
810 model.add_reactions([reaction])
|
|
|
811 reactions_added += 1
|
|
412
|
812
|
|
408
|
813
|
|
|
814 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni")
|
|
|
815
|
|
|
816 # Imposta l'obiettivo di biomassa
|
|
|
817 set_biomass_objective(model)
|
|
|
818
|
|
|
819 # Imposta il medium
|
|
|
820 set_medium_from_data(model, df)
|
|
|
821
|
|
|
822 print(f"Modello completato: {len(model.reactions)} reazioni, {len(model.metabolites)} metaboliti")
|
|
|
823
|
|
|
824 return model
|
|
|
825
|
|
|
826
|
|
|
827 # Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore)
|
|
|
828 def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
|
|
|
829 """
|
|
|
830 Estrae gli ID dei metaboliti da una formula di reazione.
|
|
|
831 Pattern robusto: cattura token che terminano con _<compartimento> (es. _c, _m, _e)
|
|
|
832 e permette che comincino con cifre o underscore.
|
|
|
833 """
|
|
|
834 metabolites = set()
|
|
|
835 # coefficiente opzionale seguito da un token che termina con _<letters>
|
|
|
836 pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+_[a-z]+)'
|
|
|
837 matches = re.findall(pattern, reaction_formula)
|
|
|
838 metabolites.update(matches)
|
|
|
839 return metabolites
|
|
|
840
|
|
|
841
|
|
|
842 def extract_compartment_from_metabolite(metabolite_id: str) -> str:
|
|
|
843 """
|
|
|
844 Estrae il compartimento dall'ID del metabolita.
|
|
|
845 """
|
|
|
846 # Il compartimento è solitamente l'ultima lettera dopo l'underscore
|
|
|
847 if '_' in metabolite_id:
|
|
|
848 return metabolite_id.split('_')[-1]
|
|
|
849 return 'c' # default cytoplasm
|
|
|
850
|
|
|
851
|
|
|
852 def parse_reaction_formula(reaction: Reaction, formula: str, metabolites_dict: Dict[str, Metabolite]):
|
|
|
853 """
|
|
|
854 Parsa una formula di reazione e imposta i metaboliti con i loro coefficienti.
|
|
|
855 """
|
|
|
856
|
|
|
857 if reaction.id == 'EX_thbpt_e':
|
|
|
858 print(reaction.id)
|
|
|
859 print(formula)
|
|
|
860 # Dividi in parte sinistra e destra
|
|
|
861 if '<=>' in formula:
|
|
|
862 left, right = formula.split('<=>')
|
|
|
863 reversible = True
|
|
|
864 elif '<--' in formula:
|
|
|
865 left, right = formula.split('<--')
|
|
|
866 reversible = False
|
|
|
867 left, right = left, right
|
|
|
868 elif '-->' in formula:
|
|
|
869 left, right = formula.split('-->')
|
|
|
870 reversible = False
|
|
|
871 elif '<-' in formula:
|
|
|
872 left, right = formula.split('<-')
|
|
|
873 reversible = False
|
|
|
874 left, right = left, right
|
|
|
875 else:
|
|
|
876 raise ValueError(f"Formato reazione non riconosciuto: {formula}")
|
|
|
877
|
|
|
878 # Parse dei metaboliti e coefficienti
|
|
|
879 reactants = parse_metabolites_side(left.strip())
|
|
|
880 products = parse_metabolites_side(right.strip())
|
|
|
881
|
|
|
882 # Aggiungi metaboliti alla reazione
|
|
|
883 metabolites_to_add = {}
|
|
|
884
|
|
|
885 # Reagenti (coefficienti negativi)
|
|
|
886 for met_id, coeff in reactants.items():
|
|
|
887 if met_id in metabolites_dict:
|
|
|
888 metabolites_to_add[metabolites_dict[met_id]] = -coeff
|
|
|
889
|
|
|
890 # Prodotti (coefficienti positivi)
|
|
|
891 for met_id, coeff in products.items():
|
|
|
892 if met_id in metabolites_dict:
|
|
|
893 metabolites_to_add[metabolites_dict[met_id]] = coeff
|
|
|
894
|
|
|
895 reaction.add_metabolites(metabolites_to_add)
|
|
|
896
|
|
|
897
|
|
|
898 def parse_metabolites_side(side_str: str) -> Dict[str, float]:
|
|
|
899 """
|
|
|
900 Parsa un lato della reazione per estrarre metaboliti e coefficienti.
|
|
|
901 """
|
|
|
902 metabolites = {}
|
|
|
903 if not side_str or side_str.strip() == '':
|
|
|
904 return metabolites
|
|
|
905
|
|
|
906 terms = side_str.split('+')
|
|
|
907 for term in terms:
|
|
|
908 term = term.strip()
|
|
|
909 if not term:
|
|
|
910 continue
|
|
|
911
|
|
|
912 # pattern allineato: coefficiente opzionale + id che termina con _<compartimento>
|
|
|
913 match = re.match(r'(?:(\d+\.?\d*)\s+)?([A-Za-z0-9_]+_[a-z]+)', term)
|
|
|
914 if match:
|
|
|
915 coeff_str, met_id = match.groups()
|
|
|
916 coeff = float(coeff_str) if coeff_str else 1.0
|
|
|
917 metabolites[met_id] = coeff
|
|
|
918
|
|
|
919 return metabolites
|
|
|
920
|
|
|
921
|
|
|
922
|
|
|
923 def set_biomass_objective(model: Model):
|
|
|
924 """
|
|
|
925 Imposta la reazione di biomassa come obiettivo.
|
|
|
926 """
|
|
|
927 biomass_reactions = [r for r in model.reactions if 'biomass' in r.id.lower()]
|
|
|
928
|
|
|
929 if biomass_reactions:
|
|
|
930 model.objective = biomass_reactions[0].id
|
|
|
931 print(f"Obiettivo impostato su: {biomass_reactions[0].id}")
|
|
|
932 else:
|
|
|
933 print("Nessuna reazione di biomassa trovata")
|
|
|
934
|
|
|
935
|
|
|
936 def set_medium_from_data(model: Model, df: pd.DataFrame):
|
|
|
937 """
|
|
|
938 Imposta il medium basato sulla colonna InMedium.
|
|
|
939 """
|
|
|
940 medium_reactions = df[df['InMedium'] == True]['ReactionID'].tolist()
|
|
|
941
|
|
|
942 medium_dict = {}
|
|
|
943 for rxn_id in medium_reactions:
|
|
|
944 if rxn_id in [r.id for r in model.reactions]:
|
|
|
945 reaction = model.reactions.get_by_id(rxn_id)
|
|
|
946 if reaction.lower_bound < 0: # Solo reazioni di uptake
|
|
|
947 medium_dict[rxn_id] = abs(reaction.lower_bound)
|
|
|
948
|
|
|
949 if medium_dict:
|
|
|
950 model.medium = medium_dict
|
|
|
951 print(f"Medium impostato con {len(medium_dict)} componenti")
|
|
|
952
|
|
|
953
|
|
|
954 def validate_model(model: Model) -> Dict[str, any]:
|
|
|
955 """
|
|
|
956 Valida il modello e fornisce statistiche di base.
|
|
|
957 """
|
|
|
958 validation = {
|
|
|
959 'num_reactions': len(model.reactions),
|
|
|
960 'num_metabolites': len(model.metabolites),
|
|
|
961 'num_genes': len(model.genes),
|
|
|
962 'num_compartments': len(model.compartments),
|
|
|
963 'objective': str(model.objective),
|
|
|
964 'medium_size': len(model.medium),
|
|
|
965 'reversible_reactions': len([r for r in model.reactions if r.reversibility]),
|
|
|
966 'exchange_reactions': len([r for r in model.reactions if r.id.startswith('EX_')]),
|
|
|
967 }
|
|
|
968
|
|
|
969 try:
|
|
|
970 # Test di crescita
|
|
|
971 solution = model.optimize()
|
|
|
972 validation['growth_rate'] = solution.objective_value
|
|
|
973 validation['status'] = solution.status
|
|
|
974 except Exception as e:
|
|
|
975 validation['growth_rate'] = None
|
|
|
976 validation['status'] = f"Error: {e}"
|
|
|
977
|
|
|
978 return validation
|
