# -*- coding: utf-8 -*-
"""Utilities for handling prefixes."""
import logging
from functools import wraps
from typing import Optional, Tuple, Union
import bioregistry
from .registries import (
curie_has_blacklisted_prefix,
curie_has_blacklisted_suffix,
curie_is_blacklisted,
remap_full,
remap_prefix,
)
__all__ = [
"normalize_curie",
"wrap_norm_prefix",
"standardize_ec",
]
logger = logging.getLogger(__name__)
class MissingPrefix(ValueError):
"""Raised on a missing prefix."""
def __init__(self, prefix, curie, xref=None, ontology=None):
self.prefix = prefix
self.curie = curie
self.xref = xref
self.ontology = ontology
self.reference = None
def __str__(self) -> str:
s = ""
if self.ontology:
s += f"[{self.ontology}] "
s += f"unhandled prefix {self.prefix} found in curie {self.curie}"
if self.xref:
s += f"/xref {self.xref}"
if self.reference is not None:
s += f" from {self.reference.curie}"
return s
def _normalize_prefix(prefix: str, *, curie=None, xref=None, strict: bool = True) -> Optional[str]:
"""Normalize a namespace and return, if possible."""
norm_prefix = bioregistry.normalize_prefix(prefix)
if norm_prefix is not None:
return norm_prefix
elif strict:
raise MissingPrefix(prefix=prefix, curie=curie, xref=xref)
else:
return None
BAD_CURIES = set()
[docs]def normalize_curie(
curie: str, *, strict: bool = True
) -> Union[Tuple[str, str], Tuple[None, None]]:
"""Parse a string that looks like a CURIE.
:param curie: A compact uniform resource identifier (CURIE)
:param strict: Should an exception be thrown if the CURIE can not be parsed w.r.t. the Bioregistry?
:return: A parse tuple or a tuple of None, None if not able to parse and not strict
- Normalizes the namespace
- Checks against a blacklist for the entire curie, for the namespace, and for suffixes.
"""
if curie_is_blacklisted(curie):
return None, None
if curie_has_blacklisted_prefix(curie):
return None, None
if curie_has_blacklisted_suffix(curie):
return None, None
# Remap the curie with the full list
curie = remap_full(curie)
# Remap node's prefix (if necessary)
curie = remap_prefix(curie)
try:
head_ns, identifier = curie.split(":", 1)
except ValueError: # skip nodes that don't look like normal CURIEs
if curie not in BAD_CURIES:
BAD_CURIES.add(curie)
logger.debug(f"could not split CURIE on colon: {curie}")
return None, None
# remove redundant prefix
if identifier.casefold().startswith(f"{head_ns.casefold()}:"):
identifier = identifier[len(head_ns) + 1 :]
norm_node_prefix = _normalize_prefix(head_ns, curie=curie, strict=strict)
if not norm_node_prefix:
return None, None
return norm_node_prefix, identifier
def wrap_norm_prefix(f):
"""Decorate a function that take in a prefix to auto-normalize, or return None if it can't be normalized."""
@wraps(f)
def _wrapped(prefix, *args, **kwargs):
norm_prefix = bioregistry.normalize_prefix(prefix)
if norm_prefix is None:
raise ValueError(f"Invalid prefix: {prefix}")
return f(norm_prefix, *args, **kwargs)
return _wrapped
def standardize_ec(ec: str) -> str:
"""Standardize an EC code identifier by removing all trailing dashes and dots."""
ec = ec.strip()
for _ in range(4):
ec = ec.rstrip("-").rstrip(".")
return ec