pyobo 0.10.9__tar.gz → 0.10.11__tar.gz

{pyobo-0.10.9/src/pyobo.egg-info → pyobo-0.10.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.9
+Version: 0.10.11
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases

{pyobo-0.10.9 → pyobo-0.10.11}/docs/source/conf.py

@@ -58,7 +58,7 @@ author = "Charles Tapley Hoyt"
 #
 
 # The full version, including alpha/beta/rc tags.
-release = "0.10.9"
+release = "0.10.11"
 
 # The short X.Y version.
 parsed_version = re.match(

{pyobo-0.10.9 → pyobo-0.10.11}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyobo
-version = 0.10.9
+version = 0.10.11
 description = Handling and writing OBO
 long_description = file: README.rst
 url = https://github.com/pyobo/pyobo

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/alts.py

@@ -28,12 +28,15 @@ NO_ALTS = {
 
 @lru_cache()
 @wrap_norm_prefix
-def get_id_to_alts(prefix: str, force: bool = False) -> Mapping[str, List[str]]:
+def get_id_to_alts(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, List[str]]:
     """Get alternate identifiers."""
     if prefix in NO_ALTS:
         return {}
 
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="alt_ids.tsv", version=version)
     header = [f"{prefix}_id", "alt_id"]
 
@@ -51,26 +54,28 @@ def get_id_to_alts(prefix: str, force: bool = False) -> Mapping[str, List[str]]:
 
 @lru_cache()
 @wrap_norm_prefix
-def get_alts_to_id(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_alts_to_id(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get alternative id to primary id mapping."""
     return {
         alt: primary
-        for primary, alts in get_id_to_alts(prefix, force=force).items()
+        for primary, alts in get_id_to_alts(prefix, force=force, version=version).items()
         for alt in alts
     }
 
 
-def get_primary_curie(curie: str) -> Optional[str]:
+def get_primary_curie(curie: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the primary curie for an entity."""
     prefix, identifier = normalize_curie(curie)
-    primary_identifier = get_primary_identifier(prefix, identifier)
+    primary_identifier = get_primary_identifier(prefix, identifier, version=version)
     if primary_identifier is not None:
         return f"{prefix}:{primary_identifier}"
     return None
 
 
 @wrap_norm_prefix
-def get_primary_identifier(prefix: str, identifier: str) -> str:
+def get_primary_identifier(prefix: str, identifier: str, *, version: Optional[str] = None) -> str:
     """Get the primary identifier for an entity.
 
     :param prefix: The name of the resource
@@ -82,7 +87,7 @@ def get_primary_identifier(prefix: str, identifier: str) -> str:
     if prefix in NO_ALTS:  # TODO later expand list to other namespaces with no alts
         return identifier
 
-    alts_to_id = get_alts_to_id(prefix)
+    alts_to_id = get_alts_to_id(prefix, version=version)
     if alts_to_id and identifier in alts_to_id:
         return alts_to_id[identifier]
     return identifier

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/hierarchy.py

@@ -13,6 +13,7 @@ from .properties import get_filtered_properties_mapping
 from .relations import get_filtered_relations_df
 from ..identifier_utils import wrap_norm_prefix
 from ..struct import TypeDef, has_member, is_a, part_of
+from ..struct.reference import Reference
 
 __all__ = [
     "get_hierarchy",
@@ -24,7 +25,6 @@ __all__ = [
     "get_children",
 ]
 
-from ..struct.reference import Reference
 
 logger = logging.getLogger(__name__)
 
@@ -154,14 +154,16 @@ def _get_hierarchy_helper(
     return rv
 
 
-def is_descendent(prefix, identifier, ancestor_prefix, ancestor_identifier) -> bool:
+def is_descendent(
+    prefix, identifier, ancestor_prefix, ancestor_identifier, *, version: Optional[str] = None
+) -> bool:
     """Check that the first identifier has the second as a descendent.
 
     Check that go:0070246 ! natural killer cell apoptotic process is a
     descendant of go:0006915 ! apoptotic process::
     >>> assert is_descendent('go', '0070246', 'go', '0006915')
     """
-    descendants = get_descendants(ancestor_prefix, ancestor_identifier)
+    descendants = get_descendants(ancestor_prefix, ancestor_identifier, version=version)
     return descendants is not None and f"{prefix}:{identifier}" in descendants
 
 
@@ -224,13 +226,15 @@ def get_children(
     return set(hierarchy.predecessors(curie))
 
 
-def has_ancestor(prefix, identifier, ancestor_prefix, ancestor_identifier) -> bool:
+def has_ancestor(
+    prefix, identifier, ancestor_prefix, ancestor_identifier, *, version: Optional[str] = None
+) -> bool:
     """Check that the first identifier has the second as an ancestor.
 
     Check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process::
     >>> assert has_ancestor('go', '0006915', 'go', '0008219')
     """
-    ancestors = get_ancestors(prefix, identifier)
+    ancestors = get_ancestors(prefix, identifier, version=version)
     return ancestors is not None and f"{ancestor_prefix}:{ancestor_identifier}" in ancestors
 
 

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/metadata.py

@@ -4,7 +4,7 @@
 
 import logging
 from functools import lru_cache
-from typing import Mapping
+from typing import Mapping, Optional
 
 from .utils import get_version
 from ..getters import get_ontology
@@ -21,9 +21,12 @@ logger = logging.getLogger(__name__)
 
 @lru_cache()
 @wrap_norm_prefix
-def get_metadata(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_metadata(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get metadata for the ontology."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="metadata.json", version=version)
 
     @cached_json(path=path, force=force)

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/names.py

@@ -30,11 +30,11 @@ __all__ = [
 logger = logging.getLogger(__name__)
 
 
-def get_name_by_curie(curie: str) -> Optional[str]:
+def get_name_by_curie(curie: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the name for a CURIE, if possible."""
     prefix, identifier = normalize_curie(curie)
     if prefix and identifier:
-        return get_name(prefix, identifier)
+        return get_name(prefix, identifier, version=version)
     return None
 
 
@@ -69,20 +69,20 @@ def _help_get(
             NO_BUILD_PREFIXES.add(prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier)
+    primary_id = get_primary_identifier(prefix, identifier, version=version)
     return mapping.get(primary_id)
 
 
 @wrap_norm_prefix
-def get_name(prefix: str, identifier: str) -> Optional[str]:
+def get_name(prefix: str, identifier: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the name for an entity."""
-    return _help_get(get_id_name_mapping, prefix, identifier)
+    return _help_get(get_id_name_mapping, prefix, identifier, version=version)
 
 
 @lru_cache()
 @wrap_norm_prefix
 def get_ids(
-    prefix: str, force: bool = False, strict: bool = False, version: Optional[str] = None
+    prefix: str, *, force: bool = False, strict: bool = False, version: Optional[str] = None
 ) -> Set[str]:
     """Get the set of identifiers for this prefix."""
     if prefix == "ncbigene":
@@ -150,16 +150,18 @@ def get_id_name_mapping(
 
 @lru_cache()
 @wrap_norm_prefix
-def get_name_id_mapping(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_name_id_mapping(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get a name to identifier mapping for the OBO file."""
-    id_name = get_id_name_mapping(prefix=prefix, force=force)
+    id_name = get_id_name_mapping(prefix=prefix, force=force, version=version)
     return {v: k for k, v in id_name.items()}
 
 
 @wrap_norm_prefix
-def get_definition(prefix: str, identifier: str) -> Optional[str]:
+def get_definition(prefix: str, identifier: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the definition for an entity."""
-    return _help_get(get_id_definition_mapping, prefix, identifier)
+    return _help_get(get_id_definition_mapping, prefix, identifier, version=version)
 
 
 def get_id_definition_mapping(

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/relations.py

@@ -48,9 +48,11 @@ def get_relations_df(
     force: bool = False,
     wide: bool = False,
     strict: bool = True,
+    version: Optional[str] = None,
 ) -> pd.DataFrame:
     """Get all relations from the OBO."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="relations.tsv", version=version)
 
     @cached_df(path=path, dtype=str, force=force)
@@ -118,9 +120,11 @@ def get_id_multirelations_mapping(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    version: Optional[str] = None,
 ) -> Mapping[str, List[Reference]]:
     """Get the OBO file and output a synonym dictionary."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     ontology = get_ontology(prefix, force=force, version=version)
     return ontology.get_id_multirelations_mapping(typedef=typedef, use_tqdm=use_tqdm)
 
@@ -134,6 +138,7 @@ def get_relation_mapping(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    version: Optional[str] = None,
 ) -> Mapping[str, str]:
     """Get relations from identifiers in the source prefix to target prefix with the given relation.
 
@@ -147,7 +152,8 @@ def get_relation_mapping(
     >>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
     >>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
     """
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     ontology = get_ontology(prefix, force=force, version=version)
     return ontology.get_relation_mapping(
         relation=relation, target_prefix=target_prefix, use_tqdm=use_tqdm
@@ -163,6 +169,7 @@ def get_relation(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    **kwargs,
 ) -> Optional[str]:
     """Get the target identifier corresponding to the given relationship from the source prefix/identifier pair.
 
@@ -181,6 +188,7 @@ def get_relation(
         target_prefix=target_prefix,
         use_tqdm=use_tqdm,
         force=force,
+        **kwargs,
     )
     return relation_mapping.get(source_identifier)
 

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/species.py

@@ -22,13 +22,13 @@ logger = logging.getLogger(__name__)
 
 
 @wrap_norm_prefix
-def get_species(prefix: str, identifier: str) -> Optional[str]:
+def get_species(prefix: str, identifier: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the species."""
     if prefix == "uniprot":
         raise NotImplementedError
 
     try:
-        id_species = get_id_species_mapping(prefix)
+        id_species = get_id_species_mapping(prefix, version=version)
     except NoBuild:
         logger.warning("unable to look up species for prefix %s", prefix)
         return None
@@ -37,7 +37,7 @@ def get_species(prefix: str, identifier: str) -> Optional[str]:
         logger.warning("no results produced for prefix %s", prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier)
+    primary_id = get_primary_identifier(prefix, identifier, version=version)
     return id_species.get(primary_id)
 
 

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/typedefs.py

@@ -4,6 +4,7 @@
 
 import logging
 from functools import lru_cache
+from typing import Optional
 
 import pandas as pd
 
@@ -22,9 +23,12 @@ logger = logging.getLogger(__name__)
 
 @lru_cache()
 @wrap_norm_prefix
-def get_typedef_df(prefix: str, force: bool = False) -> pd.DataFrame:
+def get_typedef_df(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> pd.DataFrame:
     """Get an identifier to name mapping for the typedefs in an OBO file."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="typedefs.tsv", version=version)
 
     @cached_df(path=path, dtype=str, force=force)

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/api/xrefs.py

@@ -30,9 +30,16 @@ logger = logging.getLogger(__name__)
 
 
 @wrap_norm_prefix
-def get_xref(prefix: str, identifier: str, new_prefix: str, flip: bool = False) -> Optional[str]:
+def get_xref(
+    prefix: str,
+    identifier: str,
+    new_prefix: str,
+    *,
+    flip: bool = False,
+    version: Optional[str] = None,
+) -> Optional[str]:
     """Get the xref with the new prefix if a direct path exists."""
-    filtered_xrefs = get_filtered_xrefs(prefix, new_prefix, flip=flip)
+    filtered_xrefs = get_filtered_xrefs(prefix, new_prefix, flip=flip, version=version)
     return filtered_xrefs.get(identifier)
 
 
@@ -41,8 +48,8 @@ def get_xref(prefix: str, identifier: str, new_prefix: str, flip: bool = False)
 def get_filtered_xrefs(
     prefix: str,
     xref_prefix: str,
-    flip: bool = False,
     *,
+    flip: bool = False,
     use_tqdm: bool = False,
     force: bool = False,
     strict: bool = False,

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/aws.py

@@ -77,14 +77,19 @@ def upload_artifacts(
         upload_artifacts_for_prefix(prefix=prefix, bucket=bucket, s3_client=s3_client)
 
 
-def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
+def upload_artifacts_for_prefix(
+    *, prefix: str, bucket: str, s3_client=None, version: Optional[str] = None
+):
     """Upload compiled parts for the given prefix to AWS."""
     if s3_client is None:
         s3_client = boto3.client("s3")
 
+    if version is None:
+        version = get_version(prefix)
+
     logger.info("[%s] getting id->name mapping", prefix)
     get_id_name_mapping(prefix)
-    id_name_path = prefix_cache_join(prefix, name="names.tsv", version=get_version(prefix))
+    id_name_path = prefix_cache_join(prefix, name="names.tsv", version=version)
     if not id_name_path.exists():
         raise FileNotFoundError
     id_name_key = os.path.join(prefix, "cache", "names.tsv")
@@ -93,7 +98,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting id->synonyms mapping", prefix)
     get_id_synonyms_mapping(prefix)
-    id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=get_version(prefix))
+    id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=version)
     if not id_synonyms_path.exists():
         raise FileNotFoundError
     id_synonyms_key = os.path.join(prefix, "cache", "synonyms.tsv")
@@ -102,7 +107,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting xrefs", prefix)
     get_xrefs_df(prefix)
-    xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=get_version(prefix))
+    xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=version)
     if not xrefs_path.exists():
         raise FileNotFoundError
     xrefs_key = os.path.join(prefix, "cache", "xrefs.tsv")
@@ -111,7 +116,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting relations", prefix)
     get_relations_df(prefix)
-    relations_path = prefix_cache_join(prefix, name="relations.tsv", version=get_version(prefix))
+    relations_path = prefix_cache_join(prefix, name="relations.tsv", version=version)
     if not relations_path.exists():
         raise FileNotFoundError
     relations_key = os.path.join(prefix, "cache", "relations.tsv")
@@ -120,7 +125,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting properties", prefix)
     get_properties_df(prefix)
-    properties_path = prefix_cache_join(prefix, name="properties.tsv", version=get_version(prefix))
+    properties_path = prefix_cache_join(prefix, name="properties.tsv", version=version)
     if not properties_path.exists():
         raise FileNotFoundError
     properties_key = os.path.join(prefix, "cache", "properties.tsv")
@@ -129,7 +134,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting alternative identifiers", prefix)
     get_id_to_alts(prefix)
-    alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=get_version(prefix))
+    alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=version)
     if not alts_path.exists():
         raise FileNotFoundError
     alts_key = os.path.join(prefix, "cache", "alt_ids.tsv")

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/cli/lookup.py

@@ -76,9 +76,10 @@ def xrefs(prefix: str, target: str, force: bool, no_strict: bool, version: Optio
 @prefix_argument
 @verbose_option
 @force_option
-def metadata(prefix: str, force: bool):
+@version_option
+def metadata(prefix: str, force: bool, version: Optional[str]):
     """Print the metadata for the given namespace."""
-    metadata = get_metadata(prefix, force=force)
+    metadata = get_metadata(prefix, force=force, version=version)
     click.echo(json.dumps(metadata, indent=2))
 
 

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/constants.py

@@ -4,17 +4,13 @@
 
 import logging
 import re
-from functools import partial
-from typing import Callable
 
-import bioversions
 import pystow
 
 __all__ = [
     "RAW_DIRECTORY",
     "DATABASE_DIRECTORY",
     "SPECIES_REMAPPING",
-    "version_getter",
 ]
 
 logger = logging.getLogger(__name__)
@@ -85,11 +81,6 @@ SPECIES_RECORD = "5334738"
 SPECIES_FILE = "species.tsv.gz"
 
 
-def version_getter(name: str) -> Callable[[], str]:
-    """Make a function appropriate for getting versions."""
-    return partial(bioversions.get_version, name)
-
-
 NCBITAXON_PREFIX = "NCBITaxon"
 DATE_FORMAT = "%d:%m:%Y %H:%M"
 PROVENANCE_PREFIXES = {

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/sources/antibodyregistry.py

@@ -24,9 +24,10 @@ URL = "http://antibodyregistry.org/php/fileHandler.php"
 CHUNKSIZE = 20_000
 
 
-def get_chunks(force: bool = False) -> pd.DataFrame:
+def get_chunks(*, force: bool = False, version: Optional[str] = None) -> pd.DataFrame:
     """Get the BioGRID identifiers mapping dataframe."""
-    version = bioversions.get_version(PREFIX)
+    if version is None:
+        version = bioversions.get_version(PREFIX)
     df = ensure_df(
         PREFIX,
         url=URL,
@@ -47,7 +48,7 @@ class AntibodyRegistryGetter(Obo):
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return iter_terms(force=force)
+        return iter_terms(force=force, version=self._version_or_raise)
 
 
 def get_obo(*, force: bool = False) -> Obo:
@@ -74,9 +75,9 @@ SKIP = {
 }
 
 
-def iter_terms(force: bool = False) -> Iterable[Term]:
+def iter_terms(*, force: bool = False, version: Optional[str] = None) -> Iterable[Term]:
     """Iterate over antibodies."""
-    chunks = get_chunks(force=force)
+    chunks = get_chunks(force=force, version=version)
     needs_curating = set()
     # df['vendor'] = df['vendor'].map(bioregistry.normalize_prefix)
     it = tqdm(chunks, desc=f"{PREFIX}, chunkssize={CHUNKSIZE}")

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/sources/biogrid.py

@@ -2,12 +2,12 @@
 
 """Extract and convert BioGRID identifiers."""
 
+from functools import partial
 from typing import Mapping, Optional
 
 import bioversions
 import pandas as pd
 
-from pyobo.constants import version_getter
 from pyobo.resources.ncbitaxon import get_ncbitaxon_id
 from pyobo.utils.cache import cached_mapping
 from pyobo.utils.path import ensure_df, prefix_directory_join
@@ -61,7 +61,11 @@ def get_df() -> pd.DataFrame:
 
 @cached_mapping(
     path=prefix_directory_join(
-        PREFIX, "cache", "xrefs", name="ncbigene.tsv", version=version_getter(PREFIX)
+        PREFIX,
+        "cache",
+        "xrefs",
+        name="ncbigene.tsv",
+        version=partial(bioversions.get_version, PREFIX),
     ),
     header=["biogrid_id", "ncbigene_id"],
 )

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/sources/ccle.py

@@ -50,7 +50,7 @@ def iter_terms(version: Optional[str] = None, force: bool = False) -> Iterable[T
         yield term
 
 
-def get_version() -> str:
+def get_ccle_static_version() -> str:
     """Get the default version of CCLE's cell lines."""
     return "2019"
 
@@ -58,21 +58,21 @@ def get_version() -> str:
 def get_url(version: Optional[str] = None) -> str:
     """Get the cBioPortal URL for the given version of CCLE's cell lines."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     return f"https://cbioportal-datahub.s3.amazonaws.com/ccle_broad_{version}.tar.gz"
 
 
 def get_inner(version: Optional[str] = None) -> str:
     """Get the inner tarfile path."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     return f"ccle_broad_{version}/data_clinical_sample.txt"
 
 
 def ensure(version: Optional[str] = None, **kwargs) -> Path:
     """Ensure the given version is downloaded."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     url = get_url(version=version)
     return pystow.ensure("pyobo", "raw", PREFIX, version, url=url, **kwargs)
 
@@ -80,7 +80,7 @@ def ensure(version: Optional[str] = None, **kwargs) -> Path:
 def ensure_df(version: Optional[str] = None, force: bool = False) -> pd.DataFrame:
     """Get the CCLE clinical sample dataframe."""
     if version is None:
-        version = get_version()
+        version = get_ccle_static_version()
     path = ensure(version=version, force=force)
     inner_path = get_inner(version=version)
     with tarfile.open(path) as tf:

{pyobo-0.10.9 → pyobo-0.10.11}/src/pyobo/sources/expasy.py

@@ -4,11 +4,11 @@
 
 import logging
 from collections import defaultdict
-from typing import Dict, Iterable, Mapping, Optional, Set, Tuple
+from typing import Any, Dict, Iterable, Mapping, Optional, Set, Tuple
 
 from .utils import get_go_mapping
 from ..struct import Obo, Reference, Synonym, Term
-from ..struct.typedef import enables, has_member
+from ..struct.typedef import enables, has_member, term_replaced_by
 from ..utils.path import ensure_path
 
 __all__ = [
@@ -93,12 +93,29 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
 
     database_path = ensure_path(PREFIX, url=EXPASY_DATABASE_URL, version=version)
     with open(database_path) as file:
-        _data = get_database(file)
+        id_to_data = get_database(file)
 
     ec2go = get_ec2go(version=version)
 
     ec_code_to_alt_ids = {}
-    for ec_code, data in _data.items():
+    for ec_code, data in id_to_data.items():
+        if data.get("deleted"):
+            terms[ec_code] = Term(
+                reference=Reference(prefix=PREFIX, identifier=ec_code), is_obsolete=True
+            )
+            continue
+
+        transfer_ids = data.get("transfer_id")
+        if transfer_ids:
+            term = terms[ec_code] = Term(
+                reference=Reference(prefix=PREFIX, identifier=ec_code), is_obsolete=True
+            )
+            for transfer_id in transfer_ids:
+                term.append_relationship(
+                    term_replaced_by, Reference(prefix=PREFIX, identifier=transfer_id)
+                )
+            continue
+
         parent_ec_code = data["parent"]["identifier"]
         parent_term = terms[parent_ec_code]
 
@@ -210,7 +227,7 @@ def get_database(lines: Iterable[str]) -> Mapping:
     for groups in _group_by_id(lines):
         _, expasy_id = groups[0]
 
-        rv[expasy_id] = ec_data_entry = {
+        ec_data_entry: Dict[str, Any] = {
             "concept": {
                 "namespace": PREFIX,
                 "identifier": expasy_id,
@@ -230,10 +247,10 @@ def get_database(lines: Iterable[str]) -> Mapping:
             if descriptor == "//":
                 continue
             elif descriptor == DE and value == "Deleted entry.":
-                continue
+                ec_data_entry["deleted"] = True
             elif descriptor == DE and value.startswith("Transferred entry: "):
-                value = value[len("Transferred entry: ") :].rstrip()
-                ec_data_entry["transfer_id"] = value
+                value = value[len("Transferred entry: ") :].rstrip().rstrip(".")
+                ec_data_entry["transfer_id"] = value.split(" and ")
             elif descriptor == DE:
                 ec_data_entry["concept"]["name"] = value.rstrip(".")  # type:ignore
             elif descriptor == AN:
@@ -259,11 +276,7 @@ def get_database(lines: Iterable[str]) -> Mapping:
                         )
                     )
 
-    for expasy_id, data in rv.items():
-        transfer_id = data.pop("transfer_id", None)
-        if transfer_id is not None:
-            rv[expasy_id]["alt_ids"].append(transfer_id)  # type:ignore
-
+        rv[expasy_id] = ec_data_entry
     return rv