pyobo 0.11.1__py3-none-any.whl → 0.12.0__py3-none-any.whl

pyobo/api/names.py

@@ -4,43 +4,54 @@ from __future__ import annotations
 
 import logging
 import subprocess
-from collections.abc import Mapping
+from collections.abc import Callable, Mapping
 from functools import lru_cache
-from typing import Callable, TypeVar
+from typing import Any, TypeVar
 
-from curies import Reference, ReferenceTuple
+import curies
+import pandas as pd
+import ssslm
+from pystow.cache import Cached
+from ssslm import LiteralMapping
+from typing_extensions import Unpack
 
 from .alts import get_primary_identifier
-from .utils import get_version
+from .utils import _get_pi, get_version_from_kwargs
+from ..constants import (
+    GetOntologyKwargs,
+    check_should_cache,
+    check_should_force,
+)
 from ..getters import NoBuildError, get_ontology
-from ..identifier_utils import normalize_curie, wrap_norm_prefix
-from ..utils.cache import cached_collection, cached_mapping, cached_multidict
-from ..utils.path import prefix_cache_join
+from ..identifier_utils import wrap_norm_prefix
+from ..struct import Reference
+from ..utils.cache import cached_collection, cached_df, cached_mapping
+from ..utils.io import multidict
+from ..utils.path import CacheArtifact, get_cache_path
 
 __all__ = [
-    "get_name",
-    "get_name_by_curie",
-    "get_ids",
-    "get_id_name_mapping",
-    "get_name_id_mapping",
     "get_definition",
     "get_id_definition_mapping",
-    "get_synonyms",
+    "get_id_name_mapping",
     "get_id_synonyms_mapping",
+    "get_ids",
+    "get_literal_mappings",
+    "get_literal_mappings_df",
+    "get_name",
+    "get_name_by_curie",
+    "get_name_id_mapping",
     "get_obsolete",
+    "get_obsolete_references",
+    "get_references",
+    "get_synonyms",
 ]
 
 logger = logging.getLogger(__name__)
 
 
-def get_name_by_curie(curie: str, *, version: str | None = None) -> str | None:
+def get_name_by_curie(curie: str, **kwargs: Any) -> str | None:
     """Get the name for a CURIE, if possible."""
-    if version is None:
-        version = get_version(curie.split(":")[0])
-    prefix, identifier = normalize_curie(curie)
-    if prefix and identifier:
-        return get_name(prefix, identifier, version=version)
-    return None
+    return get_name(curie, **kwargs)
 
 
 X = TypeVar("X")
@@ -50,108 +61,140 @@ NO_BUILD_LOGGED: set = set()
 
 
 def _help_get(
-    f: Callable[[str], Mapping[str, X]],
-    prefix: str,
-    identifier: str,
-    force: bool = False,
-    strict: bool = False,
-    version: str | None = None,
+    f: Callable[[str, Unpack[GetOntologyKwargs]], Mapping[str, X]],
+    reference: Reference,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> X | None:
     """Get the result for an entity based on a mapping maker function ``f``."""
     try:
-        mapping = f(prefix, force=force, strict=strict, version=version)  # type:ignore
+        mapping = f(reference.prefix, **kwargs)  # type:ignore
     except NoBuildError:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] unable to look up results with %s", prefix, f)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning("[%s] unable to look up results with %s", reference.prefix, f)
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
     except ValueError as e:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] value error while looking up results with %s: %s", prefix, f, e)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning(
+                "[%s] value error while looking up results with %s: %s", reference.prefix, f, e
+            )
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
 
     if not mapping:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] no results produced with %s", prefix, f)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning("[%s] no results produced with %s", reference.prefix, f)
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier, version=version)
+    primary_id = get_primary_identifier(reference, **kwargs)
     return mapping.get(primary_id)
 
 
-@wrap_norm_prefix
 def get_name(
-    prefix: str | Reference | ReferenceTuple,
+    prefix: str | curies.Reference | curies.ReferenceTuple,
     identifier: str | None = None,
     /,
-    *,
-    version: str | None = None,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the name for an entity."""
-    if isinstance(prefix, (ReferenceTuple, Reference)):
-        prefix, identifier = prefix.prefix, prefix.identifier
-    return _help_get(get_id_name_mapping, prefix, identifier, version=version)  # type:ignore
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_name_mapping, reference, **kwargs)
 
 
 @lru_cache
 @wrap_norm_prefix
-def get_ids(
-    prefix: str, *, force: bool = False, strict: bool = False, version: str | None = None
-) -> set[str]:
+def get_ids(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> set[str]:
     """Get the set of identifiers for this prefix."""
     if prefix == "ncbigene":
-        from ..sources.ncbigene import get_ncbigene_ids
+        from ..sources.ncbi.ncbigene import get_ncbigene_ids
 
         logger.info("[%s] loading name mappings", prefix)
         rv = get_ncbigene_ids()
         logger.info("[%s] done loading name mappings", prefix)
         return rv
 
-    if version is None:
-        version = get_version(prefix)
-    path = prefix_cache_join(prefix, name="ids.tsv", version=version)
-
-    @cached_collection(path=path, force=force)
-    def _get_ids() -> set[str]:
-        if force:
-            logger.info("[%s v%s] forcing reload for names", prefix, version)
-        else:
-            logger.debug(
-                "[%s v%s] no cached identifiers found. getting from OBO loader", prefix, version
-            )
-        ontology = get_ontology(prefix, force=force, strict=strict, version=version)
-        return ontology.get_ids()
+    return {
+        reference.identifier
+        for reference in get_references(prefix, **kwargs)
+        if reference.prefix == prefix
+    }
+
+
+class CachedReferences(Cached[list[Reference]]):
+    """Make a function lazily cache its return value as file."""
+
+    def load(self) -> list[Reference]:
+        """Load data from the cache as a list of strings.
+
+        :returns: A list of strings loaded from the cache
+        """
+        with open(self.path) as file:
+            return [Reference.from_curie(line.strip()) for line in file]
 
-    return set(_get_ids())
+    def dump(self, references: list[Reference]) -> None:
+        """Dump data to the cache as a list of strings.
+
+        :param references: The list of strings to dump
+        """
+        with open(self.path, "w") as file:
+            for reference in references:
+                print(reference.curie, file=file)
+
+
+@wrap_norm_prefix
+def get_references(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> set[Reference]:
+    """Get the set of identifiers for this prefix."""
+    if prefix == "ncbigene":
+        from ..sources.ncbi.ncbigene import get_ncbigene_ids
+
+        logger.info("[%s] loading identifiers ", prefix)
+        rv = {Reference(prefix="ncbigene", identifier=i) for i in get_ncbigene_ids()}
+        logger.info("[%s] done loading identifiers", prefix)
+        return rv
+
+    version = get_version_from_kwargs(prefix, kwargs)
+    # TODO pre-cache these!
+    path = get_cache_path(prefix, CacheArtifact.references, version=version)
+
+    @CachedReferences(
+        path=path,
+        force=check_should_force(kwargs),
+        cache=check_should_cache(kwargs),
+    )
+    def _get_references() -> list[Reference]:
+        ontology = get_ontology(prefix, **kwargs)
+        return sorted(ontology.iterate_references())
+
+    return set(_get_references())
 
 
 @lru_cache
 @wrap_norm_prefix
 def get_id_name_mapping(
-    prefix: str, *, force: bool = False, strict: bool = False, version: str | None = None
+    prefix: str,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> Mapping[str, str]:
     """Get an identifier to name mapping for the OBO file."""
     if prefix == "ncbigene":
-        from ..sources.ncbigene import get_ncbigene_id_to_name_mapping
+        from ..sources.ncbi.ncbigene import get_ncbigene_id_to_name_mapping
 
-        logger.info("[%s] loading name mappings", prefix)
+        logger.info("[%s] loading identifiers", prefix)
         rv = get_ncbigene_id_to_name_mapping()
-        logger.info("[%s] done loading name mappings", prefix)
+        logger.info("[%s] done loading identifiers", prefix)
         return rv
 
-    if version is None:
-        version = get_version(prefix)
-    path = prefix_cache_join(prefix, name="names.tsv", version=version)
+    version = get_version_from_kwargs(prefix, kwargs)
+    path = get_cache_path(prefix, CacheArtifact.names, version=version)
 
-    @cached_mapping(path=path, header=[f"{prefix}_id", "name"], force=force)
+    @cached_mapping(
+        path=path,
+        header=[f"{prefix}_id", "name"],
+        force=check_should_force(kwargs),
+        cache=check_should_cache(kwargs),
+    )
     def _get_id_name_mapping() -> Mapping[str, str]:
-        if force:
-            logger.debug("[%s v%s] forcing reload for names", prefix, version)
-        else:
-            logger.debug("[%s v%s] no cached names found. getting from OBO loader", prefix, version)
-        ontology = get_ontology(prefix, force=force, strict=strict, version=version)
+        ontology = get_ontology(prefix, **kwargs)
         return ontology.get_id_name_mapping()
 
     try:
@@ -167,89 +210,126 @@ def get_id_name_mapping(
 @lru_cache
 @wrap_norm_prefix
 def get_name_id_mapping(
-    prefix: str, *, force: bool = False, version: str | None = None
+    prefix: str,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> Mapping[str, str]:
     """Get a name to identifier mapping for the OBO file."""
-    id_name = get_id_name_mapping(prefix=prefix, force=force, version=version)
+    id_name = get_id_name_mapping(prefix, **kwargs)
     return {v: k for k, v in id_name.items()}
 
 
-@wrap_norm_prefix
 def get_definition(
-    prefix: str, identifier: str | None = None, *, version: str | None = None
+    prefix: str | curies.Reference | curies.ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the definition for an entity."""
-    if identifier is None:
-        prefix, _, identifier = prefix.rpartition(":")
-    return _help_get(get_id_definition_mapping, prefix, identifier, version=version)
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_definition_mapping, reference, **kwargs)
 
 
 def get_id_definition_mapping(
-    prefix: str,
-    *,
-    force: bool = False,
-    strict: bool = False,
-    version: str | None = None,
+    prefix: str, **kwargs: Unpack[GetOntologyKwargs]
 ) -> Mapping[str, str]:
     """Get a mapping of descriptions."""
-    if version is None:
-        version = get_version(prefix)
-    path = prefix_cache_join(prefix, name="definitions.tsv", version=version)
-
-    @cached_mapping(path=path, header=[f"{prefix}_id", "definition"], force=force)
+    version = get_version_from_kwargs(prefix, kwargs)
+    path = get_cache_path(prefix, CacheArtifact.definitions, version=version)
+
+    @cached_mapping(
+        path=path,
+        header=[f"{prefix}_id", "definition"],
+        force=check_should_force(kwargs),
+        cache=check_should_cache(kwargs),
+    )
     def _get_mapping() -> Mapping[str, str]:
         logger.info(
             "[%s v%s] no cached descriptions found. getting from OBO loader", prefix, version
         )
-        ontology = get_ontology(prefix, force=force, strict=strict, version=version)
+        ontology = get_ontology(prefix, **kwargs)
         return ontology.get_id_definition_mapping()
 
     return _get_mapping()
 
 
-def get_obsolete(
-    prefix: str,
-    *,
-    force: bool = False,
-    strict: bool = False,
-    version: str | None = None,
-) -> set[str]:
+@wrap_norm_prefix
+def get_obsolete(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> set[str]:
     """Get the set of obsolete local unique identifiers."""
-    if version is None:
-        version = get_version(prefix)
-    path = prefix_cache_join(prefix, name="obsolete.tsv", version=version)
-
-    @cached_collection(path=path, force=force)
-    def _get_obsolete() -> set[str]:
-        ontology = get_ontology(prefix, force=force, strict=strict, version=version)
-        return ontology.get_obsolete()
+    version = get_version_from_kwargs(prefix, kwargs)
+    # TODO pre-cache these!
+    path = get_cache_path(prefix, CacheArtifact.obsoletes, version=version)
+
+    @cached_collection(
+        path=path,
+        force=check_should_force(kwargs),
+        cache=check_should_cache(kwargs),
+    )
+    def _get_obsolete() -> list[str]:
+        ontology = get_ontology(prefix, **kwargs)
+        return sorted(ontology.get_obsolete())
 
     return set(_get_obsolete())
 
 
 @wrap_norm_prefix
-def get_synonyms(prefix: str, identifier: str) -> list[str] | None:
+def get_obsolete_references(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> set[Reference]:
+    """Get the set of obsolete references."""
+    return {
+        Reference(prefix=prefix, identifier=identifier)
+        for identifier in get_obsolete(prefix, **kwargs)
+    }
+
+
+def get_synonyms(
+    prefix: str | curies.Reference | curies.ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
+) -> list[str] | None:
     """Get the synonyms for an entity."""
-    return _help_get(get_id_synonyms_mapping, prefix, identifier)
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_synonyms_mapping, reference, **kwargs)
 
 
 @wrap_norm_prefix
 def get_id_synonyms_mapping(
-    prefix: str,
-    *,
-    force: bool = False,
-    strict: bool = False,
-    version: str | None = None,
+    prefix: str, **kwargs: Unpack[GetOntologyKwargs]
 ) -> Mapping[str, list[str]]:
     """Get the OBO file and output a synonym dictionary."""
-    if version is None:
-        version = get_version(prefix)
-    path = prefix_cache_join(prefix, name="synonyms.tsv", version=version)
-
-    @cached_multidict(path=path, header=[f"{prefix}_id", "synonym"], force=force)
-    def _get_multidict() -> Mapping[str, list[str]]:
-        logger.info("[%s v%s] no cached synonyms found. getting from OBO loader", prefix, version)
-        ontology = get_ontology(prefix, force=force, strict=strict, version=version)
-        return ontology.get_id_synonyms_mapping()
-
-    return _get_multidict()
+    df = get_literal_mappings_df(prefix=prefix, **kwargs)
+    prefix_with_colon = f"{prefix}:"
+    prefix_with_colon_len = len(prefix_with_colon)
+    # keep only literal mappings with the right prefix
+    df = df[df["curie"].str.startswith(prefix_with_colon)]
+    return multidict(
+        (curie[prefix_with_colon_len:], text) for curie, text in df[["curie", "text"]].values
+    )
+
+
+def get_literal_mappings(
+    prefix: str, *, skip_obsolete: bool = False, **kwargs: Unpack[GetOntologyKwargs]
+) -> list[LiteralMapping]:
+    """Get literal mappings."""
+    df = get_literal_mappings_df(prefix=prefix, **kwargs)
+    rv = ssslm.df_to_literal_mappings(df, reference_cls=Reference)
+    if skip_obsolete:
+        obsoletes = get_obsolete_references(prefix, **kwargs)
+        rv = [lm for lm in rv if lm.reference not in obsoletes]
+    return rv
+
+
+def get_literal_mappings_df(
+    prefix: str,
+    **kwargs: Unpack[GetOntologyKwargs],
+) -> pd.DataFrame:
+    """Get a literal mappings dataframe."""
+    version = get_version_from_kwargs(prefix, kwargs)
+    path = get_cache_path(prefix, CacheArtifact.literal_mappings, version=version)
+
+    @cached_df(
+        path=path, dtype=str, force=check_should_force(kwargs), cache=check_should_cache(kwargs)
+    )
+    def _df_getter() -> pd.DataFrame:
+        return get_ontology(prefix, **kwargs).get_literal_mappings_df()
+
+    return _df_getter()