pyobo 0.10.9__tar.gz → 0.10.10__tar.gz

{pyobo-0.10.9/src/pyobo.egg-info → pyobo-0.10.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.9
+Version: 0.10.10
 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-0.10.10}/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 = "0.10.10"
 
 # The short X.Y version.
 parsed_version = re.match(

{pyobo-0.10.9 → pyobo-0.10.10}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyobo
-version = 0.10.9
+version = 0.10.10
 description = Handling and writing OBO
 long_description = file: README.rst
 url = https://github.com/pyobo/pyobo

{pyobo-0.10.9 → pyobo-0.10.10}/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
 
 
@@ -74,9 +74,9 @@ def _help_get(
 
 
 @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()

{pyobo-0.10.9 → pyobo-0.10.10}/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
 
 

{pyobo-0.10.9 → pyobo-0.10.10}/src/pyobo/version.py

@@ -14,7 +14,7 @@ __all__ = [
     "get_git_hash",
 ]
 
-VERSION = "0.10.9"
+VERSION = "0.10.10"
 
 
 def get_git_hash() -> str:

{pyobo-0.10.9 → pyobo-0.10.10/src/pyobo.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.9
+Version: 0.10.10
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases