Source code for pyenzyme.enzymeml.core.exceptions

# File:
# Project: core
# Author: Jan Range
# License: BSD-2 clause
# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart

import yaml

from typing import Union, Optional

[docs]class SpeciesNotFoundError(Exception): """Raised when a species hasnt been found in a specific element""" def __init__( self, species_id: str, enzymeml_part: str, message: str = "Species ID has not been found", ): self.species_id = species_id self.enzymeml_part = enzymeml_part self.message = message super().__init__(self.message) def __str__(self) -> str: return f"{self.species_id} in {self.enzymeml_part} -> {self.message}"
[docs]class MeasurementDataSpeciesIdentifierError(Exception): """Raised when either no ID has been assigned to a measurementData""" def __init__(self, both: Optional[list] = None): if both: self.message = f"Both reactant ({both[0]}) and protein ({both[1]}) have been ID assigned to a measurement. Please specifiy either one of those." else: self.message = ( "Neither a reactant not protein has been ID assigned to measurement." ) super().__init__(self.message) def __str__(self) -> str: return self.message
[docs]class ParticipantIdentifierError(Exception): """Raised when an ID does not match the expected format""" def __init__(self, id: str, prefix: str) -> None: self.prefix = prefix = id def __str__(self) -> str: return f"Identifier '{}' does not match the expected format of '{self.prefix}[digits]'."
[docs]class ECNumberError(Exception): """Raised when an EC number does not match the pattern convenrtion""" def __init__(self, ecnumber: str): self.ecnumber = ecnumber def __str__(self) -> str: return f"EC number {self.ecnumber} does not match the pattern. Please specifify as X.X.X.X"
[docs]class DataError(Exception): """Raised when incomplete data has been assigned to a replicate""" pass
[docs]class ChEBIIdentifierError(Exception): """Raised when the CHEBI ID is incorrect.""" def __init__(self, chebi_id: Union[str, int]) -> None: self.chebi_id = chebi_id def __str__(self) -> str: return f"ChEBI ID {self.chebi_id} is invalid. Please provide a valid ChEBI ID."
[docs]class UniProtIdentifierError(Exception): """Raised when the UniProt ID is incorrect.""" def __init__(self, uniprotid: Union[str, int]) -> None: self.uniprotid = uniprotid def __str__(self) -> str: return f"UniProt ID {self.uniprotid} is invalid. Please provide a valid UniProt ID."