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335
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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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10 from typing import Any, Callable, Dict, Generic, List, Literal, Optional, TypeVar, Union
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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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14
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15 import zipfile
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16 import gzip
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17 import bz2
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18 from io import StringIO
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19
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339
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20 class ValueErr(Exception):
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21 def __init__(self, param_name, expected, actual):
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22 super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")
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23
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24 class PathErr(Exception):
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25 def __init__(self, path, message):
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26 super().__init__(f"Path error for '{path}': {message}")
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27
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335
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28 class FileFormat(Enum):
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29 """
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30 Encodes possible file extensions to conditionally save data in a different format.
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31 """
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32 DAT = ("dat",) # this is how galaxy treats all your files!
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33 CSV = ("csv",) # this is how most editable input data is written
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339
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34 TSV = ("tsv",) # this is how most editable input data is ACTUALLY written TODO:more support pls!!
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335
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35 SVG = ("svg",) # this is how most metabolic maps are written
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36 PNG = ("png",) # this is a common output format for images (such as metabolic maps)
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37 PDF = ("pdf",) # this is also a common output format for images, as it's required in publications.
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339
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38
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39 # Updated to include compressed variants
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40 XML = ("xml", "xml.gz", "xml.zip", "xml.bz2") # SBML files are XML files, sometimes compressed
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41 JSON = ("json", "json.gz", "json.zip", "json.bz2") # COBRA models can be stored as JSON files, sometimes compressed
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42
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335
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43 TXT = ("txt",) # this is how most output data is written
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44 PICKLE = ("pickle", "pk", "p") # this is how all runtime data structures are saved
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45
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339
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46 def __init__(self, *extensions):
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47 self.extensions = extensions
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48 # Store original extension when set via fromExt
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49 self._original_extension = None
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50
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335
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51 @classmethod
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339
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52 def fromExt(cls, ext: str) -> "FileFormat":
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335
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53 """
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54 Converts a file extension string to a FileFormat instance.
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55 Args:
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56 ext : The file extension as a string.
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57 Returns:
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58 FileFormat: The FileFormat instance corresponding to the file extension.
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59 """
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60 variantName = ext.upper()
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61 if variantName in FileFormat.__members__:
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62 instance = FileFormat[variantName]
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339
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63 instance._original_extension = ext
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335
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64 return instance
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65
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339
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66 variantName = ext.lower()
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335
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67 for member in cls:
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68 if variantName in member.value:
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339
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69 # Create a copy-like behavior by storing the original extension
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70 member._original_extension = ext
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335
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71 return member
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72
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73 raise ValueErr("ext", "a valid FileFormat file extension", ext)
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74
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75 def __str__(self) -> str:
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76 """
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77 (Private) converts to str representation. Good practice for usage with argparse.
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78 Returns:
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79 str : the string representation of the file extension.
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80 """
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339
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81 # If we have an original extension stored (for compressed files), use it
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82 if hasattr(self, '_original_extension') and self._original_extension:
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83 return self._original_extension
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84
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340
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85 # For XML and JSON without original extension, use the base extension
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86 if self == FileFormat.XML:
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87 return "xml"
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88 elif self == FileFormat.JSON:
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89 return "json"
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90
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339
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91 return self.value[-1]
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335
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92
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93 class FilePath():
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94 """
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95 Represents a file path. View this as an attempt to standardize file-related operations by expecting
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96 values of this type in any process requesting a file path.
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97 """
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339
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98 def __init__(self, filePath: str, ext: FileFormat, *, prefix="") -> None:
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335
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99 """
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100 (Private) Initializes an instance of FilePath.
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101 Args:
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102 path : the end of the path, containing the file name.
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103 ext : the file's extension.
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104 prefix : anything before path, if the last '/' isn't there it's added by the code.
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105 Returns:
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106 None : practically, a FilePath instance.
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107 """
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339
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108 self.ext = ext
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335
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109 self.filePath = filePath
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110
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339
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111 if prefix and prefix[-1] != '/':
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112 prefix += '/'
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335
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113 self.prefix = prefix
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114
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115 @classmethod
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339
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116 def fromStrPath(cls, path: str) -> "FilePath":
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335
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117 """
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118 Factory method to parse a string from which to obtain, if possible, a valid FilePath instance.
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119 It detects double extensions such as .json.gz and .xml.bz2, which are common in COBRA models.
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120 These double extensions are not supported for other file types such as .csv.
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121 Args:
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122 path : the string containing the path
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123 Raises:
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124 PathErr : if the provided string doesn't represent a valid path.
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125 Returns:
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126 FilePath : the constructed instance.
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127 """
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128 result = re.search(r"^(?P<prefix>.*\/)?(?P<name>.*)\.(?P<ext>[^.]*)$", path)
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129 if not result or not result["name"] or not result["ext"]:
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130 raise PathErr(path, "cannot recognize folder structure or extension in path")
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131
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132 prefix = result["prefix"] if result["prefix"] else ""
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133 name, ext = result["name"], result["ext"]
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134
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339
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135 # Check for double extensions (json.gz, xml.zip, etc.)
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335
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136 parts = path.split(".")
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137 if len(parts) >= 3:
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138 penultimate = parts[-2]
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139 last = parts[-1]
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339
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140 double_ext = f"{penultimate}.{last}"
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141
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142 # Try the double extension first
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143 try:
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144 ext_format = FileFormat.fromExt(double_ext)
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335
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145 name = ".".join(parts[:-2])
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339
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146 # Extract prefix if it exists
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147 if '/' in name:
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148 prefix = name[:name.rfind('/') + 1]
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149 name = name[name.rfind('/') + 1:]
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150 return cls(name, ext_format, prefix=prefix)
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151 except ValueErr:
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152 # If double extension doesn't work, fall back to single extension
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153 pass
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335
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154
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339
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155 # Single extension fallback (original logic)
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156 try:
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157 ext_format = FileFormat.fromExt(ext)
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158 return cls(name, ext_format, prefix=prefix)
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159 except ValueErr:
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160 raise PathErr(path, f"unsupported file extension: {ext}")
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335
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161
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162 def show(self) -> str:
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163 """
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164 Shows the path as a string.
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165 Returns:
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166 str : the path shown as a string.
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167 """
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168 return f"{self.prefix}{self.filePath}.{self.ext}"
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169
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339
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170 def __str__(self) -> str:
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171 return self.show()
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335
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172
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173 # ERRORS
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174 def terminate(msg :str) -> None:
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175 """
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176 Terminate the execution of the script with an error message.
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177
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178 Args:
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179 msg (str): The error message to be displayed.
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180
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181 Returns:
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182 None
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183 """
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184 sys.exit(f"Execution aborted: {msg}\n")
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185
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186 def logWarning(msg :str, loggerPath :str) -> None:
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187 """
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188 Log a warning message to an output log file and print it to the console. The final period and a
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189 newline is added by the function.
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190
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191 Args:
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192 s (str): The warning message to be logged and printed.
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193 loggerPath : The file path of the output log file. Given as a string, parsed to a FilePath and
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194 immediately read back (beware relative expensive operation, log with caution).
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195
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196 Returns:
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197 None
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198 """
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199 # building the path and then reading it immediately seems useless, but it's actually a way of
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200 # validating that reduces repetition on the caller's side. Besides, logging a message by writing
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201 # to a file is supposed to be computationally expensive anyway, so this is also a good deterrent from
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202 # mindlessly logging whenever something comes up, log at the very end and tell the user everything
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203 # that went wrong. If you don't like it: implement a persistent runtime buffer that gets dumped to
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204 # the file only at the end of the program's execution.
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205 with open(FilePath.fromStrPath(loggerPath).show(), 'a') as log: log.write(f"{msg}.\n")
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206
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207 class CustomErr(Exception):
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208 """
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209 Custom error class to handle exceptions in a structured way, with a unique identifier and a message.
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210 """
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211 __idGenerator = count()
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212 errName = "Custom Error"
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213 def __init__(self, msg :str, details = "", explicitErrCode = -1) -> None:
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214 """
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215 (Private) Initializes an instance of CustomErr.
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216
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217 Args:
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218 msg (str): Error message to be displayed.
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219 details (str): Informs the user more about the error encountered. Defaults to "".
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220 explicitErrCode (int): Explicit error code to be used. Defaults to -1.
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221
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222 Returns:
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223 None : practically, a CustomErr instance.
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224 """
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225 self.msg = msg
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226 self.details = details
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227
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228 self.id = max(explicitErrCode, next(CustomErr.__idGenerator))
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229
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230 def throw(self, loggerPath = "") -> None:
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231 """
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232 Raises the current CustomErr instance, logging a warning message before doing so.
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233
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234 Raises:
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235 self: The current CustomErr instance.
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236
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237 Returns:
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238 None
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239 """
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240 if loggerPath: logWarning(str(self), loggerPath)
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241 raise self
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242
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243 def abort(self) -> None:
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244 """
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245 Aborts the execution of the script.
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246
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247 Returns:
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248 None
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249 """
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250 terminate(str(self))
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251
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252 def __str__(self) -> str:
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253 """
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254 (Private) Returns a string representing the current CustomErr instance.
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255
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256 Returns:
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257 str: A string representing the current CustomErr instance.
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258 """
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259 return f"{CustomErr.errName} #{self.id}: {self.msg}, {self.details}."
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260
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261 class ArgsErr(CustomErr):
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262 """
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263 CustomErr subclass for UI arguments errors.
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264 """
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265 errName = "Args Error"
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266 def __init__(self, argName :str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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267 super().__init__(f"argument \"{argName}\" expected {expected} but got {actual}", msg)
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268
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269 class DataErr(CustomErr):
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270 """
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271 CustomErr subclass for data formatting errors.
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272 """
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273 errName = "Data Format Error"
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274 def __init__(self, fileName :str, msg = "no further details provided") -> None:
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275 super().__init__(f"file \"{fileName}\" contains malformed data", msg)
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276
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277 class PathErr(CustomErr):
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278 """
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279 CustomErr subclass for filepath formatting errors.
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280 """
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281 errName = "Path Error"
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282 def __init__(self, path :FilePath, msg = "no further details provided") -> None:
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283 super().__init__(f"path \"{path}\" is invalid", msg)
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284
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285 class ValueErr(CustomErr):
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286 """
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287 CustomErr subclass for any value error.
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288 """
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289 errName = "Value Error"
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290 def __init__(self, valueName: str, expected :Any, actual :Any, msg = "no further details provided") -> None:
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291 super().__init__("value " + f"\"{valueName}\" " * bool(valueName) + f"was supposed to be {expected}, but got {actual} instead", msg)
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292
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293 # RESULT
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294 T = TypeVar('T')
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295 E = TypeVar('E', bound = CustomErr) # should bind to Result.ResultErr but python happened!
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296 class Result(Generic[T, E]):
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297 class ResultErr(CustomErr):
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298 """
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299 CustomErr subclass for all Result errors.
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300 """
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301 errName = "Result Error"
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302 def __init__(self, msg = "no further details provided") -> None:
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303 super().__init__(msg)
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304 """
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305 Class to handle the result of an operation, with a value and a boolean flag to indicate
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306 whether the operation was successful or not.
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307 """
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308 def __init__(self, value :Union[T, E], isOk :bool) -> None:
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309 """
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310 (Private) Initializes an instance of Result.
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311
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312 Args:
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313 value (Union[T, E]): The value to be stored in the Result instance.
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314 isOk (bool): A boolean flag to indicate whether the operation was successful or not.
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315
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316 Returns:
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317 None : practically, a Result instance.
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318 """
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319 self.isOk = isOk
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320 self.isErr = not isOk
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321 self.value = value
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322
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323 @classmethod
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324 def Ok(cls, value :T) -> "Result":
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325 """
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326 Constructs a new Result instance with a successful operation.
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327
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328 Args:
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329 value (T): The value to be stored in the Result instance, set as successful.
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330
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331 Returns:
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332 Result: A new Result instance with a successful operation.
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333 """
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334 return Result(value, isOk = True)
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335
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336 @classmethod
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337 def Err(cls, value :E) -> "Result":
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338 """
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339 Constructs a new Result instance with a failed operation.
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340
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341 Args:
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342 value (E): The value to be stored in the Result instance, set as failed.
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343
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344 Returns:
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345 Result: A new Result instance with a failed operation.
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346 """
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347 return Result(value, isOk = False)
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348
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349 def unwrap(self) -> T:
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350 """
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351 Unwraps the value of the Result instance, if the operation was successful.
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352
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353 Raises:
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354 ResultErr: If the operation was not successful.
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355
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356 Returns:
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357 T: The value of the Result instance, if the operation was successful.
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358 """
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359 if self.isOk: return self.value
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360 raise Result.ResultErr(f"Unwrapped Result.Err : {self.value}")
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361
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362 def unwrapOr(self, default :T) -> T:
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363 """
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364 Unwraps the value of the Result instance, if the operation was successful, otherwise
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365 it returns a default value.
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366
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367 Args:
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368 default (T): The default value to be returned if the operation was not successful.
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369
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370 Returns:
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371 T: The value of the Result instance, if the operation was successful,
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372 otherwise the default value.
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373 """
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374 return self.value if self.isOk else default
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375
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376 def expect(self, err :"Result.ResultErr") -> T:
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377 """
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378 Expects that the value of the Result instance is successful, otherwise it raises an error.
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379
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380 Args:
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381 err (Exception): The error to be raised if the operation was not successful.
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382
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383 Raises:
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384 err: The error raised if the operation was not successful.
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385
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386 Returns:
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387 T: The value of the Result instance, if the operation was successful.
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388 """
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389 if self.isOk: return self.value
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390 raise err
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391
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392 U = TypeVar("U")
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393 def map(self, mapper: Callable[[T], U]) -> "Result[U, E]":
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394 """
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395 Maps the value of the current Result to whatever is returned by the mapper function.
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396 If the Result contained an unsuccessful operation to begin with it remains unchanged
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397 (a reference to the current instance is returned).
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398 If the mapper function panics the returned result instance will be of the error kind.
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399
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400 Args:
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401 mapper (Callable[[T], U]): The mapper operation to be applied to the Result value.
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402
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403 Returns:
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404 Result[U, E]: The result of the mapper operation applied to the Result value.
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405 """
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406 if self.isErr: return self
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407 try: return Result.Ok(mapper(self.value))
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408 except Exception as e: return Result.Err(e)
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409
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410 D = TypeVar("D", bound = "Result.ResultErr")
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411 def mapErr(self, mapper :Callable[[E], D]) -> "Result[T, D]":
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412 """
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413 Maps the error of the current Result to whatever is returned by the mapper function.
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414 If the Result contained a successful operation it remains unchanged
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415 (a reference to the current instance is returned).
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416 If the mapper function panics this method does as well.
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417
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418 Args:
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419 mapper (Callable[[E], D]): The mapper operation to be applied to the Result error.
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420
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421 Returns:
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422 Result[U, E]: The result of the mapper operation applied to the Result error.
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423 """
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424 if self.isOk: return self
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425 return Result.Err(mapper(self.value))
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426
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427 def __str__(self):
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428 return f"Result::{'Ok' if self.isOk else 'Err'}({self.value})"
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429
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430 # FILES
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431 def read_dataset(path :FilePath, datasetName = "Dataset (not actual file name!)") -> pd.DataFrame:
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432 """
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433 Reads a .csv or .tsv file and returns it as a Pandas DataFrame.
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434
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435 Args:
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436 path : the path to the dataset file.
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437 datasetName : the name of the dataset.
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438
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439 Raises:
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440 DataErr: If anything goes wrong when trying to open the file, if pandas thinks the dataset is empty or if
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441 it has less than 2 columns.
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442
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443 Returns:
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444 pandas.DataFrame: The dataset loaded as a Pandas DataFrame.
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445 """
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446 # I advise against the use of this function. This is an attempt at standardizing bad legacy code rather than
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447 # removing / replacing it to avoid introducing as many bugs as possible in the tools still relying on this code.
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448 # First off, this is not the best way to distinguish between .csv and .tsv files and Galaxy itself makes it really
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449 # hard to implement anything better. Also, this function's name advertizes it as a dataset-specific operation and
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450 # contains dubious responsibility (how many columns..) while being a file-opening function instead. My suggestion is
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451 # TODO: stop using dataframes ever at all in anything and find a way to have tight control over file extensions.
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452 try: dataset = pd.read_csv(path.show(), sep = '\t', header = None, engine = "python")
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453 except:
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454 try: dataset = pd.read_csv(path.show(), sep = ',', header = 0, engine = "python")
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455 except Exception as err: raise DataErr(datasetName, f"encountered empty or wrongly formatted data: {err}")
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456
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457 if len(dataset.columns) < 2: raise DataErr(datasetName, "a dataset is always meant to have at least 2 columns")
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458 return dataset
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459
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460 def readPickle(path :FilePath) -> Any:
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461 """
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462 Reads the contents of a .pickle file, which needs to exist at the given path.
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463
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464 Args:
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465 path : the path to the .pickle file.
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466
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467 Returns:
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468 Any : the data inside a pickle file, could be anything.
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469 """
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470 with open(path.show(), "rb") as fd: return pickle.load(fd)
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471
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472 def writePickle(path :FilePath, data :Any) -> None:
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473 """
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474 Saves any data in a .pickle file, created at the given path.
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475
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476 Args:
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477 path : the path to the .pickle file.
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478 data : the data to be written to the file.
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479
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480 Returns:
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481 None
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482 """
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483 with open(path.show(), "wb") as fd: pickle.dump(data, fd)
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484
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485 def readCsv(path :FilePath, delimiter = ',', *, skipHeader = True) -> List[List[str]]:
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486 """
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487 Reads the contents of a .csv file, which needs to exist at the given path.
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488
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489 Args:
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490 path : the path to the .csv file.
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491 delimiter : allows other subformats such as .tsv to be opened by the same method (\\t delimiter).
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492 skipHeader : whether the first row of the file is a header and should be skipped.
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493
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494 Returns:
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495 List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas.
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496 """
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497 with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:]
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498
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499 def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree:
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500 """
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501 Reads the contents of a .svg file, which needs to exist at the given path.
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502
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503 Args:
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504 path : the path to the .svg file.
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505
|
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506 Raises:
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507 DataErr : if the map is malformed.
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508
|
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509 Returns:
|
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|
510 Any : the data inside a svg file, could be anything.
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511 """
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|
512 try: return ET.parse(path.show())
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513 except (ET.XMLSyntaxError, ET.XMLSchemaParseError) as err:
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514 raise customErr if customErr else err
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515
|
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516 def writeSvg(path :FilePath, data:ET.ElementTree) -> None:
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517 """
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|
518 Saves svg data opened with lxml.etree in a .svg file, created at the given path.
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519
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520 Args:
|
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|
521 path : the path to the .svg file.
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|
|
522 data : the data to be written to the file.
|
|
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523
|
|
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524 Returns:
|
|
|
525 None
|
|
|
526 """
|
|
|
527 with open(path.show(), "wb") as fd: fd.write(ET.tostring(data))
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528
|
|
|
529 # UI ARGUMENTS
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|
530 class Bool:
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|
531 def __init__(self, argName :str) -> None:
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532 self.argName = argName
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533
|
|
|
534 def __call__(self, s :str) -> bool: return self.check(s)
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535
|
|
|
536 def check(self, s :str) -> bool:
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|
537 s = s.lower()
|
|
|
538 if s == "true" : return True
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|
|
539 if s == "false": return False
|
|
|
540 raise ArgsErr(self.argName, "boolean string (true or false, not case sensitive)", f"\"{s}\"")
|
|
|
541
|
|
|
542 class Float:
|
|
|
543 def __init__(self, argName = "Dataset values, not an argument") -> None:
|
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|
544 self.argName = argName
|
|
|
545
|
|
|
546 def __call__(self, s :str) -> float: return self.check(s)
|
|
|
547
|
|
|
548 def check(self, s :str) -> float:
|
|
|
549 try: return float(s)
|
|
|
550 except ValueError:
|
|
|
551 s = s.lower()
|
|
|
552 if s == "nan" or s == "none": return math.nan
|
|
|
553 raise ArgsErr(self.argName, "numeric string or \"None\" or \"NaN\" (not case sensitive)", f"\"{s}\"")
|
|
|
554
|
|
|
555 # MODELS
|
|
|
556 OldRule = List[Union[str, "OldRule"]]
|
|
|
557 class Model(Enum):
|
|
|
558 """
|
|
|
559 Represents a metabolic model, either custom or locally supported. Custom models don't point
|
|
|
560 to valid file paths.
|
|
|
561 """
|
|
|
562
|
|
|
563 Recon = "Recon"
|
|
|
564 ENGRO2 = "ENGRO2"
|
|
|
565 ENGRO2_no_legend = "ENGRO2_no_legend"
|
|
|
566 HMRcore = "HMRcore"
|
|
|
567 HMRcore_no_legend = "HMRcore_no_legend"
|
|
|
568 Custom = "Custom" # Exists as a valid variant in the UI, but doesn't point to valid file paths.
|
|
|
569
|
|
|
570 def __raiseMissingPathErr(self, path :Optional[FilePath]) -> None:
|
|
|
571 if not path: raise PathErr("<<MISSING>>", "it's necessary to provide a custom path when retrieving files from a custom model")
|
|
|
572
|
|
|
573 def getRules(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, OldRule]]:
|
|
|
574 """
|
|
|
575 Open "rules" file for this model.
|
|
|
576
|
|
|
577 Returns:
|
|
|
578 Dict[str, Dict[str, OldRule]] : the rules for this model.
|
|
|
579 """
|
|
|
580 path = customPath if self is Model.Custom else FilePath(f"{self.name}_rules", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
581 self.__raiseMissingPathErr(path)
|
|
|
582 return readPickle(path)
|
|
|
583
|
|
|
584 def getTranslator(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, str]]:
|
|
|
585 """
|
|
|
586 Open "gene translator (old: gene_in_rule)" file for this model.
|
|
|
587
|
|
|
588 Returns:
|
|
|
589 Dict[str, Dict[str, str]] : the translator dict for this model.
|
|
|
590 """
|
|
|
591 path = customPath if self is Model.Custom else FilePath(f"{self.name}_genes", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
|
|
|
592 self.__raiseMissingPathErr(path)
|
|
|
593 return readPickle(path)
|
|
|
594
|
|
|
595 def getMap(self, toolDir = ".", customPath :Optional[FilePath] = None) -> ET.ElementTree:
|
|
|
596 path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/")
|
|
|
597 self.__raiseMissingPathErr(path)
|
|
|
598 return readSvg(path, customErr = DataErr(path, f"custom map in wrong format"))
|
|
|
599
|
|
|
600 def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model:
|
|
|
601 if(self is Model.Custom):
|
|
|
602 return self.load_custom_model(customPath, customExtension)
|
|
|
603 else:
|
|
|
604 return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/models/").show())
|
|
|
605
|
|
|
606 def load_custom_model(self, file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model:
|
|
|
607 ext = ext if ext else file_path.ext
|
|
|
608 try:
|
|
|
609 if ext in FileFormat.XML:
|
|
|
610 return cobra.io.read_sbml_model(file_path.show())
|
|
|
611
|
|
|
612 if ext in FileFormat.JSON:
|
|
|
613 # Compressed files are not automatically handled by cobra
|
|
|
614 if(ext == "json"):
|
|
|
615 return cobra.io.load_json_model(file_path.show())
|
|
|
616 else:
|
|
|
617 return self.extract_json_model(file_path, ext)
|
|
|
618
|
|
|
619 except Exception as e: raise DataErr(file_path, e.__str__())
|
|
|
620 raise DataErr(file_path,
|
|
|
621 f"Fomat \"{file_path.ext}\" is not recognized, only JSON and XML files are supported.")
|
|
|
622
|
|
|
623
|
|
|
624 def extract_json_model(file_path:FilePath, ext :FileFormat) -> cobra.Model:
|
|
|
625 """
|
|
|
626 Extract json COBRA model from a compressed file (zip, gz, bz2).
|
|
|
627
|
|
|
628 Args:
|
|
|
629 file_path: File path of the model
|
|
|
630 ext: File extensions of class FileFormat (should be .zip, .gz or .bz2)
|
|
|
631
|
|
|
632 Returns:
|
|
|
633 cobra.Model: COBRApy model
|
|
|
634
|
|
|
635 Raises:
|
|
|
636 Exception: Extraction errors
|
|
|
637 """
|
|
|
638 ext_str = str(ext)
|
|
|
639
|
|
|
640 try:
|
|
|
641 if '.zip' in ext_str:
|
|
|
642 with zipfile.ZipFile(file_path.show(), 'r') as zip_ref:
|
|
|
643 with zip_ref.open(zip_ref.namelist()[0]) as json_file:
|
|
|
644 content = json_file.read().decode('utf-8')
|
|
|
645 return cobra.io.load_json_model(StringIO(content))
|
|
|
646 elif '.gz' in ext_str:
|
|
|
647 with gzip.open(file_path.show(), 'rt', encoding='utf-8') as gz_ref:
|
|
|
648 return cobra.io.load_json_model(gz_ref)
|
|
|
649 elif '.bz2' in ext_str:
|
|
|
650 with bz2.open(file_path.show(), 'rt', encoding='utf-8') as bz2_ref:
|
|
|
651 return cobra.io.load_json_model(bz2_ref)
|
|
|
652 else:
|
|
|
653 raise ValueError(f"Compression format not supported: {ext_str}. Supported: .zip, .gz and .bz2")
|
|
|
654
|
|
|
655 except Exception as e:
|
|
|
656 raise Exception(f"Error during model extraction: {str(e)}")
|
|
|
657
|
|
|
658
|
|
|
659
|
|
240
|
660 def __str__(self) -> str: return self.value |
