# -*- coding: utf-8 -*-
"""Utilities for interacting with data and the schema."""
import json
import logging
from collections import defaultdict
from functools import lru_cache
from operator import attrgetter
from pathlib import Path
from typing import List, Mapping, Optional, Set, Union
from .constants import (
BIOREGISTRY_PATH,
COLLECTIONS_PATH,
CONTEXTS_PATH,
METAREGISTRY_PATH,
MISMATCH_PATH,
)
from .schema import Collection, Context, Registry, Resource
logger = logging.getLogger(__name__)
def _read_metaregistry(path: Union[str, Path]) -> Mapping[str, Registry]:
with open(path, encoding="utf-8") as file:
data = json.load(file)
return {
registry.prefix: registry
for registry in (Registry(**record) for record in data["metaregistry"])
}
[docs]def registries() -> List[Registry]:
"""Get a list of registries in the Bioregistry."""
return sorted(read_metaregistry().values(), key=attrgetter("prefix"))
[docs]@lru_cache(maxsize=1)
def read_registry() -> Mapping[str, Resource]:
"""Read the Bioregistry as JSON."""
return _registry_from_path(BIOREGISTRY_PATH)
[docs]def resources() -> List[Resource]:
"""Get a list of resources in the Bioregistry."""
return sorted(read_registry().values(), key=attrgetter("prefix"))
def _registry_from_path(path: Union[str, Path]) -> Mapping[str, Resource]:
with open(path, encoding="utf-8") as file:
data = json.load(file)
for prefix, value in data.items():
value.setdefault("prefix", prefix)
return {prefix: Resource.parse_obj(value) for prefix, value in data.items()}
def add_resource(resource: Resource) -> None:
"""Add a resource to the registry.
:param resource: A resource object to write
:raises KeyError: if the prefix is already present in the registry
"""
registry = dict(read_registry())
if resource.prefix in registry:
raise KeyError(f"Tried to add duplicate prefix to the registry: {resource.prefix}")
registry[resource.prefix] = resource
# Clear the cache
read_registry.cache_clear()
write_registry(registry)
[docs]@lru_cache(maxsize=1)
def read_mismatches() -> Mapping[str, Mapping[str, str]]:
"""Read the mismatches as JSON."""
with MISMATCH_PATH.open() as file:
return json.load(file)
[docs]def is_mismatch(bioregistry_prefix: str, external_metaprefix: str, external_prefix: str) -> bool:
"""Return if the triple is a mismatch."""
return external_prefix in read_mismatches().get(bioregistry_prefix, {}).get(
external_metaprefix, {}
)
def write_mismatches(mismatches: Mapping[str, Mapping[str, str]]) -> None:
"""Read the mismatches as JSON."""
MISMATCH_PATH.write_text(
json.dumps(
mismatches,
indent=2,
sort_keys=True,
ensure_ascii=False,
)
)
[docs]@lru_cache(maxsize=1)
def read_collections() -> Mapping[str, Collection]:
"""Read the manually curated collections."""
return _collections_from_path(COLLECTIONS_PATH)
def _collections_from_path(path: Union[str, Path]) -> Mapping[str, Collection]:
with open(path, encoding="utf-8") as file:
data = json.load(file)
return {
collection.identifier: collection
for collection in (Collection(**record) for record in data["collections"])
}
def write_collections(collections: Mapping[str, Collection]) -> None:
"""Write the collections."""
values = [v for _, v in sorted(collections.items())]
for collection in values:
collection.resources = sorted(set(collection.resources))
with open(COLLECTIONS_PATH, encoding="utf-8", mode="w") as file:
json.dump(
{"collections": [c.dict(exclude_none=True) for c in values]},
file,
indent=2,
sort_keys=True,
ensure_ascii=False,
)
[docs]def write_registry(registry: Mapping[str, Resource], *, path: Optional[Path] = None) -> None:
"""Write to the Bioregistry."""
if path is None:
path = BIOREGISTRY_PATH
with path.open(mode="w", encoding="utf-8") as file:
json.dump(
{
key: resource.dict(exclude_none=True, exclude={"prefix"})
for key, resource in registry.items()
},
file,
indent=2,
sort_keys=True,
ensure_ascii=False,
)
def write_metaregistry(metaregistry: Mapping[str, Registry]) -> None:
"""Write to the metaregistry."""
values = [v for _, v in sorted(metaregistry.items())]
with open(METAREGISTRY_PATH, mode="w", encoding="utf-8") as file:
json.dump(
{"metaregistry": [m.dict(exclude_none=True) for m in values]},
fp=file,
indent=2,
sort_keys=True,
ensure_ascii=False,
)
[docs]def write_contexts(contexts: Mapping[str, Context]) -> None:
"""Write to contexts."""
with open(CONTEXTS_PATH, mode="w", encoding="utf-8") as file:
json.dump(
{key: context.dict(exclude_none=True) for key, context in contexts.items()},
fp=file,
indent=2,
sort_keys=True,
ensure_ascii=False,
)
def read_prefix_contributions(registry: Mapping[str, Resource]) -> Mapping[str, Set[str]]:
"""Get a mapping from contributor ORCID identifiers to prefixes."""
rv = defaultdict(set)
for prefix, resource in registry.items():
if resource.contributor and resource.contributor.orcid:
rv[resource.contributor.orcid].add(prefix)
for contributor in resource.contributor_extras or []:
if contributor.orcid:
rv[contributor.orcid].add(prefix)
return dict(rv)
def read_prefix_reviews(registry: Mapping[str, Resource]) -> Mapping[str, Set[str]]:
"""Get a mapping from reviewer ORCID identifiers to prefixes."""
rv = defaultdict(set)
for prefix, resource in registry.items():
if resource.reviewer and resource.reviewer.orcid:
rv[resource.reviewer.orcid].add(prefix)
return dict(rv)
def read_prefix_contacts(registry: Mapping[str, Resource]) -> Mapping[str, Set[str]]:
"""Get a mapping from contact ORCID identifiers to prefixes."""
rv = defaultdict(set)
for prefix, resource in registry.items():
contact_orcid = resource.get_contact_orcid()
if contact_orcid:
rv[contact_orcid].add(prefix)
return dict(rv)
def read_collections_contributions(collections: Mapping[str, Collection]) -> Mapping[str, Set[str]]:
"""Get a mapping from contributor ORCID identifiers to collections."""
rv = defaultdict(set)
for collection_id, resource in collections.items():
for author in resource.authors or []:
rv[author.orcid].add(collection_id)
return dict(rv)
def read_registry_contributions(metaregistry: Mapping[str, Registry]) -> Mapping[str, Set[str]]:
"""Get a mapping from contributor ORCID identifiers to collections."""
rv = defaultdict(set)
for metaprefix, resource in metaregistry.items():
if resource.contact and resource.contact.orcid:
rv[resource.contact.orcid].add(metaprefix)
return dict(rv)
def read_context_contributions(contexts: Mapping[str, Context]) -> Mapping[str, Set[str]]:
"""Get a mapping from contributor ORCID identifiers to contexts."""
rv = defaultdict(set)
for context_key, context in contexts.items():
for maintainer in context.maintainers:
rv[maintainer.orcid].add(context_key)
return dict(rv)
[docs]def read_contexts() -> Mapping[str, Context]:
"""Get a mapping from context keys to contexts."""
return _contexts_from_path(CONTEXTS_PATH)
def _contexts_from_path(path: Union[str, Path]) -> Mapping[str, Context]:
with open(path, encoding="utf-8") as file:
data = json.load(file)
return {key: Context(**data) for key, data in data.items()}