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