# The MIT License (MIT)
#
# Copyright (c) 2019, Moritz E. Beber.
# Copyright (c) 2018 Institute for Molecular Systems Biology, ETH Zurich.
# Copyright (c) 2018 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
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# of this software and associated documentation files (the "Software"), to deal
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# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
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# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# THE SOFTWARE.
"""Provide a MIRIAM compliant Identifiers.org namespace ORM model."""
from __future__ import annotations
import re
from typing import ClassVar, Dict, List, Optional, Pattern
from sqlalchemy import Boolean, Column, String
from sqlalchemy.orm import reconstructor, validates
from .base import Base
[docs]class Namespace(Base):
r"""
Define a MIRIAM compliant Identifiers.org namespace ORM model.
Attributes
----------
miriam_id : str
The MIRIAM namespace identifier for itself, e.g., MIR:00000567.
prefix : str
The MIRIAM namespace prefix, e.g., 'metanetx.chemical'.
pattern : str
The regular expression pattern to validate against identifiers in the
namespace, e.g., ``^(MNXM\d+|BIOMASS)$``.
embedded_prefix : bool
Whether or not identifiers of this namespace have an embedded `prefix`, e.g.,
'CHEBI:52971'.
name : str, optional
The namespace's common name.
description : str, optional
A short description of the namespace.
"""
__tablename__ = "namespaces"
miriam_id: str = Column(String(12), nullable=False, index=True, unique=True)
# The currently longest prefix on Identifiers.org is 22.
prefix: str = Column(String(22), nullable=False, index=True, unique=True)
pattern: str = Column(String, nullable=False)
embedded_prefix: bool = Column(Boolean, default=False, nullable=False)
name: Optional[str] = Column(String, nullable=True)
description: Optional[str] = Column(String, nullable=True)
# Define normal Python class variables.
_identifier_pattern: ClassVar[Pattern] = re.compile(r"^MIR:\d{8}$")
def __init__(self, **kwargs):
"""
Initialize a namespace object.
Notes
-----
While defining an init method is usually not necessary for SQLAlchemy
declarative models, we do it here to insert the `compiled_pattern` attribute.
"""
super().__init__(**kwargs)
self.compiled_pattern = re.compile(self.pattern)
[docs] def __repr__(self):
"""Return a string representation of the object."""
return f"{type(self).__name__}(prefix={self.prefix})"
[docs] @reconstructor
def init_on_load(self):
"""Compile the identifier pattern on load from database."""
self.compiled_pattern = re.compile(self.pattern)
[docs] @validates("miriam_id")
def validate_identifier(self, _, miriam_id: str) -> str:
"""Validate the MIRIAM identifier against the pattern."""
if self._identifier_pattern.match(miriam_id) is None:
raise ValueError(
f"The namespace's identifier '{miriam_id}' does not match the "
f"official pattern '^MIR:\\d{8}$'."
)
return miriam_id
[docs] @classmethod
def get_map(
cls, session, prefixes: Optional[List[str]] = None
) -> Dict[str, Namespace]:
"""
Extract a mapping from namespace prefix to ORM instances.
Parameters
----------
session : sqlalchemy.Session
A SQLAlchemy session giving access to a database.
prefixes : list of str, optional
The elements in the mapping can be restricted to specific namespaces by
their prefix (default return all).
Returns
-------
dict
A dictionary mapping from namespace prefix to ORM model instance.
"""
query = session.query(cls)
if prefixes is not None:
query = query.filter(cls.prefix.in_(prefixes))
return {ns.prefix: ns for ns in query}