"""Yaml parser for config objects"""
from functools import partial
from pathlib import Path
from typing import Callable, Union
import yaml
from pydantic import BaseModel
from graphein.grn.config import GRNGraphConfig, RegNetworkConfig, TRRUSTConfig
from graphein.molecule.config import MoleculeGraphConfig
from graphein.ppi.config import BioGridConfig, PPIGraphConfig, STRINGConfig
from graphein.protein.config import (
DSSPConfig,
GetContactsConfig,
ProteinGraphConfig,
ProteinMeshConfig,
)
[docs]def config_constructor(
loader: yaml.FullLoader, node: yaml.nodes.MappingNode
) -> BaseModel:
"""Construct a BaseModel config.
:param loader: Given yaml loader
:param type: yaml.FullLoader
:param loader: A mapping node
:param type: yaml.nodes.MappingNode
"""
arg_map = loader.construct_mapping(node, deep=True) if node.value else {}
return eval(node.tag[1:])(**arg_map)
[docs]def function_constructor(
loader: yaml.FullLoader,
tag_suffix: str,
node: Union[yaml.nodes.MappingNode, yaml.nodes.ScalarNode],
) -> Callable:
"""Construct a Callable. If function parameters are given, this returns a partial function.
:param loader: Given yaml loader
:param type: yaml.FullLoader
:param tag_suffix: The name after the !func: tag
:param type: str
:param loader: A mapping node if function parameters are given, a scalar node if not
:param type: Union[yaml.nodes.MappingNode, yaml.nodes.ScalarNode]
"""
arg_map = None
if isinstance(node, yaml.nodes.MappingNode):
arg_map = (
loader.construct_mapping(node, deep=True) if node.value else {}
)
node = yaml.nodes.ScalarNode(
node.tag, "", node.start_mark, node.end_mark
)
func = loader.construct_python_name(tag_suffix, node)
if arg_map:
func = partial(func, **arg_map)
return func
[docs]def get_loader() -> yaml.Loader:
"""Add constructors to PyYAML loader."""
# For Python-specific tags, you can use full_load(), which resolves all tags except those known to be unsafe;
# this includes all the tags listed here: https://pyyaml.org/wiki/PyYAMLDocumentation#yaml-tags-and-python-types
loader = yaml.FullLoader
configs = [
ProteinGraphConfig.__name__,
DSSPConfig.__name__,
ProteinMeshConfig.__name__,
GetContactsConfig.__name__,
TRRUSTConfig.__name__,
RegNetworkConfig.__name__,
GRNGraphConfig.__name__,
STRINGConfig.__name__,
BioGridConfig.__name__,
PPIGraphConfig.__name__,
MoleculeGraphConfig.__name__,
]
for config in configs:
loader.add_constructor(f"!{config}", config_constructor)
loader.add_multi_constructor("!func:", function_constructor)
return loader
[docs]def parse_config(path: Path) -> BaseModel:
"""
Parses a yaml configuration file into a config object.
:param path: Path to configuration file
:type path: pathlib.Path
"""
with open(path, "rb") as f:
yml_config = yaml.load(f, Loader=get_loader())
return yml_config