cobraxy: COBRAxy/src/utils/general

comparison COBRAxy/src/utils/general_utils.py @ 539:2fb97466e404 draft

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author	francesco_lapi
date	Sat, 25 Oct 2025 14:55:13 +0000
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+:2fb97466e404
+"""
+General utilities for COBRAxy.
+This module provides:
+- File and path helpers (FileFormat, FilePath)
+- Error and result handling utilities (CustomErr, Result)
+- Basic I/O helpers (CSV/TSV, pickle, SVG)
+- Lightweight CLI argument parsers (Bool, Float)
+- Model loader utilities for COBRA models, including compressed formats
+"""
+import math
+import re
+import sys
+import csv
+import pickle
+import lxml.etree as ET
+from enum import Enum
+from itertools import count
+from typing import Any, Callable, Dict, Generic, List, Literal, Optional, TypeVar, Union, Tuple
+import pandas as pd
+import cobra
+import zipfile
+import gzip
+import bz2
+from io import StringIO
+from typing import Any, Callable, Dict, Generic, List, Literal, Optional, TypeVar, Union, Tuple
+class ValueErr(Exception):
+def __init__(self, param_name, expected, actual):
+super().__init__(f"Invalid value for {param_name}: expected {expected}, got {actual}")
+class PathErr(Exception):
+def __init__(self, path, message):
+super().__init__(f"Path error for '{path}': {message}")
+class FileFormat(Enum):
+"""
+Encodes possible file extensions to conditionally save data in a different format.
+"""
+DAT    = ("dat",)
+CSV    = ("csv",)
+TSV    = ("tsv",)
+SVG    = ("svg",)
+PNG    = ("png",)
+PDF    = ("pdf",)
+# Compressed variants for common model formats
+XML    = ("xml", "xml.gz", "xml.zip", "xml.bz2")
+JSON   = ("json", "json.gz", "json.zip", "json.bz2")
+MAT    = ("mat", "mat.gz", "mat.zip", "mat.bz2")
+YML    = ("yml", "yml.gz", "yml.zip", "yml.bz2")
+TXT    = ("txt",)
+PICKLE = ("pickle", "pk", "p")
+def __init__(self, *extensions):
+self.extensions = extensions
+# Store original extension when set via fromExt
+self._original_extension = None
+@classmethod
+def fromExt(cls, ext: str) -> "FileFormat":
+"""
+Converts a file extension string to a FileFormat instance.
+Args:
+ext : The file extension as a string.
+Returns:
+FileFormat: The FileFormat instance corresponding to the file extension.
+"""
+variantName = ext.upper()
+if variantName in FileFormat.__members__:
+instance = FileFormat[variantName]
+instance._original_extension = ext
+return instance
+variantName = ext.lower()
+for member in cls:
+if variantName in member.value:
+# Create a copy-like behavior by storing the original extension
+member._original_extension = ext
+return member
+raise ValueErr("ext", "a valid FileFormat file extension", ext)
+def __str__(self) -> str:
+"""
+(Private) converts to str representation. Good practice for usage with argparse.
+Returns:
+str : the string representation of the file extension.
+"""
+if hasattr(self, '_original_extension') and self._original_extension:
+return self._original_extension
+if self == FileFormat.XML:
+return "xml"
+elif self == FileFormat.JSON:
+return "json"
+elif self == FileFormat.MAT:
+return "mat"
+elif self == FileFormat.YML:
+return "yml"
+return self.value[-1]
+class FilePath():
+"""
+Represents a file path with format-aware helpers.
+"""
+def __init__(self, filePath: str, ext: FileFormat, *, prefix="") -> None:
+"""
+Initialize FilePath.
+Args:
+path: File name stem.
+ext: File extension (FileFormat).
+prefix: Optional directory path (trailing '/' auto-added).
+"""
+self.ext = ext
+self.filePath = filePath
+if prefix and prefix[-1] != '/':
+prefix += '/'
+self.prefix = prefix
+@classmethod
+def fromStrPath(cls, path: str) -> "FilePath":
+"""
+Parse a string path into a FilePath, supporting double extensions for models (e.g., .json.gz).
+Args:
+path : the string containing the path
+Raises:
+PathErr : if the provided string doesn't represent a valid path.
+Returns:
+FilePath : the constructed instance.
+"""
+result = re.search(r"^(?P<prefix>.*\/)?(?P<name>.*)\.(?P<ext>[^.]*)$", path)
+if not result or not result["name"] or not result["ext"]:
+raise PathErr(path, "cannot recognize folder structure or extension in path")
+prefix = result["prefix"] if result["prefix"] else ""
+name, ext = result["name"], result["ext"]
+parts = path.split(".")
+if len(parts) >= 3:
+penultimate = parts[-2]
+last = parts[-1]
+double_ext = f"{penultimate}.{last}"
+try:
+ext_format = FileFormat.fromExt(double_ext)
+name = ".".join(parts[:-2])
+if '/' in name:
+prefix = name[:name.rfind('/') + 1]
+name = name[name.rfind('/') + 1:]
+return cls(name, ext_format, prefix=prefix)
+except ValueErr:
+pass
+try:
+ext_format = FileFormat.fromExt(ext)
+return cls(name, ext_format, prefix=prefix)
+except ValueErr:
+raise PathErr(path, f"unsupported file extension: {ext}")
+def show(self) -> str:
+"""
+Shows the path as a string.
+Returns:
+str : the path shown as a string.
+"""
+return f"{self.prefix}{self.filePath}.{self.ext}"
+def __str__(self) -> str:
+return self.show()
+# ERRORS
+def terminate(msg :str) -> None:
+"""
+Terminate the execution of the script with an error message.
+Args:
+msg (str): The error message to be displayed.
+Returns:
+None
+"""
+sys.exit(f"Execution aborted: {msg}\n")
+def logWarning(msg :str, loggerPath :str) -> None:
+"""
+Log a warning message to an output log file and print it to the console. The final period and a
+newline is added by the function.
+Args:
+msg (str): The warning message to be logged and printed.
+loggerPath : The file path of the output log file. Given as a string, parsed to a FilePath and
+immediately read back (beware relative expensive operation, log with caution).
+Returns:
+None
+"""
+# Note: validates path via FilePath; keep logging minimal to avoid overhead.
+with open(FilePath.fromStrPath(loggerPath).show(), 'a') as log: log.write(f"{msg}.\n")
+class CustomErr(Exception):
+"""
+Custom error class to handle exceptions in a structured way, with a unique identifier and a message.
+"""
+__idGenerator = count()
+errName = "Custom Error"
+def __init__(self, msg :str, details = "", explicitErrCode = -1) -> None:
+"""
+(Private) Initializes an instance of CustomErr.
+Args:
+msg (str): Error message to be displayed.
+details (str): Informs the user more about the error encountered. Defaults to "".
+explicitErrCode (int): Explicit error code to be used. Defaults to -1.
+Returns:
+None : practically, a CustomErr instance.
+"""
+self.msg     = msg
+self.details = details
+self.id = max(explicitErrCode, next(CustomErr.__idGenerator))
+def throw(self, loggerPath = "") -> None:
+"""
+Raises the current CustomErr instance, optionally logging it first.
+Args:
+loggerPath (str): Optional path to a log file to append this error before raising.
+Raises:
+self: The current CustomErr instance.
+Returns:
+None
+"""
+if loggerPath:
+logWarning(str(self), loggerPath)
+raise self
+def abort(self) -> None:
+"""
+Aborts the execution of the script.
+Returns:
+None
+"""
+terminate(str(self))
+def __str__(self) -> str:
+"""
+(Private) Returns a string representing the current CustomErr instance.
+Returns:
+str: A string representing the current CustomErr instance.
+"""
+return f"{CustomErr.errName} #{self.id}: {self.msg}, {self.details}."
+class ArgsErr(CustomErr):
+"""
+CustomErr subclass for UI arguments errors.
+"""
+errName = "Args Error"
+def __init__(self, argName :str, expected :Any, actual :Any, msg = "no further details provided") -> None:
+super().__init__(f"argument \"{argName}\" expected {expected} but got {actual}", msg)
+class DataErr(CustomErr):
+"""
+CustomErr subclass for data formatting errors.
+"""
+errName = "Data Format Error"
+def __init__(self, fileName :str, msg = "no further details provided") -> None:
+super().__init__(f"file \"{fileName}\" contains malformed data", msg)
+class PathErr(CustomErr):
+"""
+CustomErr subclass for filepath formatting errors.
+"""
+errName = "Path Error"
+def __init__(self, path :FilePath, msg = "no further details provided") -> None:
+super().__init__(f"path \"{path}\" is invalid", msg)
+class ValueErr(CustomErr):
+"""
+CustomErr subclass for any value error.
+"""
+errName = "Value Error"
+def __init__(self, valueName: str, expected :Any, actual :Any, msg = "no further details provided") -> None:
+super().__init__("value " + f"\"{valueName}\" " * bool(valueName) + f"was supposed to be {expected}, but got {actual} instead", msg)
+# RESULT
+T = TypeVar('T')
+E = TypeVar('E', bound = CustomErr) # should bind to Result.ResultErr but python happened!
+class Result(Generic[T, E]):
+class ResultErr(CustomErr):
+"""
+CustomErr subclass for all Result errors.
+"""
+errName = "Result Error"
+def __init__(self, msg = "no further details provided") -> None:
+super().__init__(msg)
+"""
+Class to handle the result of an operation, with a value and a boolean flag to indicate
+whether the operation was successful or not.
+"""
+def __init__(self, value :Union[T, E], isOk :bool) -> None:
+"""
+Initialize an instance of Result.
+Args:
+value (Union[T, E]): The value to be stored in the Result instance.
+isOk (bool): A boolean flag to indicate whether the operation was successful or not.
+Returns:
+None : practically, a Result instance.
+"""
+self.isOk  = isOk
+self.isErr = not isOk
+self.value = value
+@classmethod
+def Ok(cls,  value :T) -> "Result":
+"""
+Construct a successful Result.
+Args:
+value (T): The value to be stored in the Result instance, set as successful.
+Returns:
+Result: A new Result instance with a successful operation.
+"""
+return Result(value, isOk = True)
+@classmethod
+def Err(cls, value :E) -> "Result":
+"""
+Construct a failed Result.
+Args:
+value (E): The value to be stored in the Result instance, set as failed.
+Returns:
+Result: A new Result instance with a failed operation.
+"""
+return Result(value, isOk = False)
+def unwrap(self) -> T:
+"""
+Unwraps the value of the Result instance, if the operation was successful.
+Raises:
+ResultErr: If the operation was not successful.
+Returns:
+T: The value of the Result instance, if the operation was successful.
+"""
+if self.isOk: return self.value
+raise Result.ResultErr(f"Unwrapped Result.Err : {self.value}")
+def unwrapOr(self, default :T) -> T:
+"""
+Unwraps the value of the Result instance, if the operation was successful, otherwise
+it returns a default value.
+Args:
+default (T): The default value to be returned if the operation was not successful.
+Returns:
+T: The value of the Result instance, if the operation was successful,
+otherwise the default value.
+"""
+return self.value if self.isOk else default
+def expect(self, err :"Result.ResultErr") -> T:
+"""
+Expects that the value of the Result instance is successful, otherwise it raises an error.
+Args:
+err (Exception): The error to be raised if the operation was not successful.
+Raises:
+err: The error raised if the operation was not successful.
+Returns:
+T: The value of the Result instance, if the operation was successful.
+"""
+if self.isOk: return self.value
+raise err
+U = TypeVar("U")
+def map(self, mapper: Callable[[T], U]) -> "Result[U, E]":
+"""
+Maps the value of the current Result to whatever is returned by the mapper function.
+If the Result contained an unsuccessful operation to begin with it remains unchanged
+(a reference to the current instance is returned).
+If the mapper function panics the returned result instance will be of the error kind.
+Args:
+mapper (Callable[[T], U]): The mapper operation to be applied to the Result value.
+Returns:
+Result[U, E]: The result of the mapper operation applied to the Result value.
+"""
+if self.isErr: return self
+try: return Result.Ok(mapper(self.value))
+except Exception as e: return Result.Err(e)
+D = TypeVar("D", bound = "Result.ResultErr")
+def mapErr(self, mapper :Callable[[E], D]) -> "Result[T, D]":
+"""
+Maps the error of the current Result to whatever is returned by the mapper function.
+If the Result contained a successful operation it remains unchanged
+(a reference to the current instance is returned).
+If the mapper function panics this method does as well.
+Args:
+mapper (Callable[[E], D]): The mapper operation to be applied to the Result error.
+Returns:
+Result[U, E]: The result of the mapper operation applied to the Result error.
+"""
+if self.isOk: return self
+return Result.Err(mapper(self.value))
+def __str__(self):
+return f"Result::{'Ok' if self.isOk else 'Err'}({self.value})"
+# FILES
+def readPickle(path :FilePath) -> Any:
+"""
+Reads the contents of a .pickle file, which needs to exist at the given path.
+Args:
+path : the path to the .pickle file.
+Returns:
+Any : the data inside a pickle file, could be anything.
+"""
+with open(path.show(), "rb") as fd: return pickle.load(fd)
+def writePickle(path :FilePath, data :Any) -> None:
+"""
+Saves any data in a .pickle file, created at the given path.
+Args:
+path : the path to the .pickle file.
+data : the data to be written to the file.
+Returns:
+None
+"""
+with open(path.show(), "wb") as fd: pickle.dump(data, fd)
+def readCsv(path :FilePath, delimiter = ',', *, skipHeader = True) -> List[List[str]]:
+"""
+Reads the contents of a .csv file, which needs to exist at the given path.
+Args:
+path : the path to the .csv file.
+delimiter : allows other subformats such as .tsv to be opened by the same method (\\t delimiter).
+skipHeader : whether the first row of the file is a header and should be skipped.
+Returns:
+List[List[str]] : list of rows from the file, each parsed as a list of strings originally separated by commas.
+"""
+with open(path.show(), "r", newline = "") as fd: return list(csv.reader(fd, delimiter = delimiter))[skipHeader:]
+def findIdxByName(header: List[str], name: str, colName="name") -> Optional[int]:
+"""
+Find the indices of the 'ReactionID' column and a user-specified column name
+within the header row of a tabular file.
+Args:
+header (List[str]): The header row, as a list of column names.
+name (str): The name of the column to look for (e.g. 'GPR').
+colName (str, optional): Label used in error messages for clarity. Defaults to "name".
+Returns:
+Tuple[int, int]: A tuple containing:
+- The index of the 'ReactionID' column.
+- The index of the requested column `name`.
+Raises:
+ValueError: If 'ReactionID' or the requested column `name` is not found in the header.
+Notes:
+Both 'ReactionID' and the requested column are mandatory for downstream processing.
+"""
+col_index = {col_name: idx for idx, col_name in enumerate(header)}
+if name not in col_index or "ReactionID" not in col_index:
+raise ValueError(f"Tabular file must contain 'ReactionID' and {name} columns.")
+id_idx = col_index["ReactionID"]
+idx_gpr = col_index[name]
+return id_idx, idx_gpr
+def readSvg(path :FilePath, customErr :Optional[Exception] = None) -> ET.ElementTree:
+"""
+Reads the contents of a .svg file, which needs to exist at the given path.
+Args:
+path : the path to the .svg file.
+Raises:
+DataErr : if the map is malformed.
+Returns:
+Any : the data inside a svg file, could be anything.
+"""
+try: return ET.parse(path.show())
+except (ET.XMLSyntaxError, ET.XMLSchemaParseError) as err:
+raise customErr if customErr else err
+def writeSvg(path :FilePath, data:ET.ElementTree) -> None:
+"""
+Saves svg data opened with lxml.etree in a .svg file, created at the given path.
+Args:
+path : the path to the .svg file.
+data : the data to be written to the file.
+Returns:
+None
+"""
+with open(path.show(), "wb") as fd: fd.write(ET.tostring(data))
+# UI ARGUMENTS
+class Bool:
+"""Simple boolean CLI argument parser accepting 'true' or 'false' (case-insensitive)."""
+def __init__(self, argName :str) -> None:
+self.argName = argName
+def __call__(self, s :str) -> bool: return self.check(s)
+def check(self, s :str) -> bool:
+s = s.lower()
+if s == "true" : return True
+if s == "false": return False
+raise ArgsErr(self.argName, "boolean string (true or false, not case sensitive)", f"\"{s}\"")
+class Float:
+"""Float CLI argument parser supporting NaN and None keywords (case-insensitive)."""
+def __init__(self, argName = "Dataset values, not an argument") -> None:
+self.argName = argName
+def __call__(self, s :str) -> float: return self.check(s)
+def check(self, s :str) -> float:
+try: return float(s)
+except ValueError:
+s = s.lower()
+if s == "nan" or s == "none": return math.nan
+raise ArgsErr(self.argName, "numeric string or \"None\" or \"NaN\" (not case sensitive)", f"\"{s}\"")
+# MODELS
+OldRule = List[Union[str, "OldRule"]]
+class Model(Enum):
+"""
+Represents a metabolic model, either custom or locally supported. Custom models don't point
+to valid file paths.
+"""
+Recon   = "Recon"
+ENGRO2  = "ENGRO2"
+ENGRO2_no_legend = "ENGRO2_no_legend"
+HMRcore = "HMRcore"
+HMRcore_no_legend = "HMRcore_no_legend"
+Custom  = "Custom"
+def __raiseMissingPathErr(self, path :Optional[FilePath]) -> None:
+if not path: raise PathErr("<<MISSING>>", "it's necessary to provide a custom path when retrieving files from a custom model")
+def getRules(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, OldRule]]:
+"""
+Open "rules" file for this model.
+Returns:
+Dict[str, Dict[str, OldRule]] : the rules for this model.
+"""
+path = customPath if self is Model.Custom else FilePath(f"{self.name}_rules", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
+self.__raiseMissingPathErr(path)
+return readPickle(path)
+def getTranslator(self, toolDir :str, customPath :Optional[FilePath] = None) -> Dict[str, Dict[str, str]]:
+"""
+Open "gene translator (old: gene_in_rule)" file for this model.
+Returns:
+Dict[str, Dict[str, str]] : the translator dict for this model.
+"""
+path = customPath if self is Model.Custom else FilePath(f"{self.name}_genes", FileFormat.PICKLE, prefix = f"{toolDir}/local/pickle files/")
+self.__raiseMissingPathErr(path)
+return readPickle(path)
+def getMap(self, toolDir = ".", customPath :Optional[FilePath] = None) -> ET.ElementTree:
+"""Open the SVG metabolic map for this model."""
+path = customPath if self is Model.Custom else FilePath(f"{self.name}_map", FileFormat.SVG, prefix = f"{toolDir}/local/svg metabolic maps/")
+self.__raiseMissingPathErr(path)
+return readSvg(path, customErr = DataErr(path, f"custom map in wrong format"))
+def getCOBRAmodel(self, toolDir = ".", customPath :Optional[FilePath] = None, customExtension :Optional[FilePath]=None)->cobra.Model:
+"""Load the COBRA model for this enum variant (supports Custom with explicit path/extension)."""
+if(self is Model.Custom):
+return self.load_custom_model(customPath, customExtension)
+else:
+return cobra.io.read_sbml_model(FilePath(f"{self.name}", FileFormat.XML, prefix = f"{toolDir}/local/models/").show())
+def load_custom_model(self, file_path :FilePath, ext :Optional[FileFormat] = None) -> cobra.Model:
+"""Load a COBRA model from a custom path, supporting XML, JSON, MAT, and YML (compressed or not)."""
+ext = ext if ext else file_path.ext
+try:
+if str(ext) in FileFormat.XML.value:
+return cobra.io.read_sbml_model(file_path.show())
+if str(ext) in FileFormat.JSON.value:
+# Compressed files are not automatically handled by cobra
+if(ext == "json"):
+return cobra.io.load_json_model(file_path.show())
+else:
+return self.extract_model(file_path, ext, "json")
+if str(ext) in FileFormat.MAT.value:
+# Compressed files are not automatically handled by cobra
+if(ext == "mat"):
+return cobra.io.load_matlab_model(file_path.show())
+else:
+return self.extract_model(file_path, ext, "mat")
+if str(ext) in FileFormat.YML.value:
+# Compressed files are not automatically handled by cobra
+if(ext == "yml"):
+return cobra.io.load_yaml_model(file_path.show())
+else:
+return self.extract_model(file_path, ext, "yml")
+except Exception as e: raise DataErr(file_path, e.__str__())
+raise DataErr(file_path,
+f"Fomat \"{file_path.ext}\" is not recognized, only JSON, XML, MAT and YAML (.yml) files are supported.")
+def extract_model(self, file_path:FilePath, ext :FileFormat, model_encoding:Literal["json", "mat", "yml"]) -> cobra.Model:
+"""
+Extract JSON, MAT and YAML COBRA model from a compressed file (zip, gz, bz2).
+Args:
+file_path: File path of the model
+ext: File extensions of class FileFormat (should be .zip, .gz or .bz2)
+Returns:
+cobra.Model: COBRApy model
+Raises:
+Exception: Extraction errors
+"""
+ext_str = str(ext)
+try:
+if '.zip' in ext_str:
+with zipfile.ZipFile(file_path.show(), 'r') as zip_ref:
+with zip_ref.open(zip_ref.namelist()[0]) as json_file:
+content = json_file.read().decode('utf-8')
+if model_encoding == "json":
+return cobra.io.load_json_model(StringIO(content))
+elif model_encoding == "mat":
+return cobra.io.load_matlab_model(StringIO(content))
+elif model_encoding == "yml":
+return cobra.io.load_yaml_model(StringIO(content))
+else:
+raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
+elif '.gz' in ext_str:
+with gzip.open(file_path.show(), 'rt', encoding='utf-8') as gz_ref:
+if model_encoding == "json":
+return cobra.io.load_json_model(gz_ref)
+elif model_encoding == "mat":
+return cobra.io.load_matlab_model(gz_ref)
+elif model_encoding == "yml":
+return cobra.io.load_yaml_model(gz_ref)
+else:
+raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
+elif '.bz2' in ext_str:
+with bz2.open(file_path.show(), 'rt', encoding='utf-8') as bz2_ref:
+if model_encoding == "json":
+return cobra.io.load_json_model(bz2_ref)
+elif model_encoding == "mat":
+return cobra.io.load_matlab_model(bz2_ref)
+elif model_encoding == "yml":
+return cobra.io.load_yaml_model(bz2_ref)
+else:
+raise ValueError(f"Unsupported model encoding: {model_encoding}. Supported: json, mat, yml")
+else:
+raise ValueError(f"Compression format not supported: {ext_str}. Supported: .zip, .gz and .bz2")
+except Exception as e:
+raise Exception(f"Error during model extraction: {str(e)}")
+def __str__(self) -> str: return self.value

Mercurial > repos > bimib > cobraxy

comparison COBRAxy/src/utils/general_utils.py @ 539:2fb97466e404 draft