pyobo 0.10.9__py3-none-any.whl → 0.10.10__py3-none-any.whl

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/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/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.dist-info → pyobo-0.10.10.dist-info}/METADATA

@@ -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.dist-info → pyobo-0.10.10.dist-info}/RECORD

@@ -11,12 +11,12 @@ pyobo/obographs.py,sha256=JKE0a7e-gmxqdJoeX2zb_xQ6Tv5PAe60YhnIpAvrrYg,3758
 pyobo/plugins.py,sha256=dXWGoFuQktNeQUWSJlPz2a7FeLysggc9ry6auEZdw98,1227
 pyobo/reader.py,sha256=3VTWQMmA-AHi3RdA2jb48d2deXO-lYKqXbcMa9Qhi_4,21271
 pyobo/resource_utils.py,sha256=JBcJRihZhNwp78-qWZPrzSCGoYfyOjzBwMkfmOkO_no,4289
-pyobo/version.py,sha256=ONSzSms19NKy9Bl2q8M4P_Mlo0MkqMGJ7X1SKZuec4M,977
+pyobo/version.py,sha256=S2agZOhWCaqxb1jQk8O_DDd5X86GPoXvcBAAxtmCpsc,978
 pyobo/api/__init__.py,sha256=Hq8p5uPW8fFYG2KfLqUsHhtLkTPqE4TqItGkedZzvXM,1326
 pyobo/api/alts.py,sha256=xmAb-gGQCJ9MbaFvoNK6E-V0B3TV9hxulkfbkHIvOso,2617
 pyobo/api/hierarchy.py,sha256=2KtyTkqOKJzejNqVvlhPQD_w0fKzrOQp1BSx-Ina3t0,9413
 pyobo/api/metadata.py,sha256=62E7j0ZW3vYK2Rh-R7NCMKnChbYjZwPjVDoaE1AsCOc,1070
-pyobo/api/names.py,sha256=A5HprOfdt7twF2LfjdQQaIj3FNj4_GD7MZ7CrKllY5M,7559
+pyobo/api/names.py,sha256=m_5UjixlUS10FCrlmNoNJ8pI_z-YB2xqgROGvPGIQBY,7661
 pyobo/api/properties.py,sha256=BKqUgN8nTpYrc0fROdaGGkptELgjbGT6TC_N2X8FIQM,7813
 pyobo/api/relations.py,sha256=VEQCQjPamehyGaL-wFzUYH9OeVq9pVzj70sl9K3ttKw,5996
 pyobo/api/species.py,sha256=xRPRoD6n1wcDaqlC_tHLw3rKMWa4razWsSPNa228g_4,2181
@@ -70,7 +70,7 @@ pyobo/sources/dictybase_gene.py,sha256=EgWBwUZ83ev7x5Lp_nUkgSq2zumkDjJ7_13m3f6kJ
 pyobo/sources/drugbank.py,sha256=pb2IdVQF4FqDvefwRdqlDV5j6pR9R1b3rGxHC-GSWb4,11028
 pyobo/sources/drugbank_salt.py,sha256=hx16G41mP2KXT4fsAQRCRkJMGn-z5cafs-bwm4wMtwo,1783
 pyobo/sources/drugcentral.py,sha256=05mGolBIyKCxAYzpH9LY_ZQrTVnizup2JUiWi2wW9OI,3587
-pyobo/sources/expasy.py,sha256=h8RcFtRd4wHBDVHC7tK8C1dT2M0dCknhfoWao7DLOx4,9507
+pyobo/sources/expasy.py,sha256=Ul6DFtHKw3fU1ec93c9f29kXxod2Rn-jPWOYl1xrRa8,10051
 pyobo/sources/famplex.py,sha256=bn3WaJdrDf9BxsG9vnnnnGOwCrnrJ-vTMxOnxgrtUb4,5816
 pyobo/sources/flybase.py,sha256=0-BCNsp-L-CgGPN9VdJec6-8e4-fJuzaZAZiNra3ZUQ,5768
 pyobo/sources/geonames.py,sha256=XpSc-_6653MrjunVJhqbHHLtkT8kmbJZzfRuF6DoWU8,7929
@@ -161,9 +161,9 @@ pyobo/xrefdb/sources/intact.py,sha256=F0z6WrOwI79aZSuM5MsvQwzqoyzh9J0UuB4Mseoj9X
 pyobo/xrefdb/sources/ncit.py,sha256=unoIKJqdcfitTc6pU9P1SxJ1w8ax0iDjvEOlqe64nCY,3745
 pyobo/xrefdb/sources/pubchem.py,sha256=GaqgqtSV-T_P-900nL3alPx_ZB36MlmnEepOnZMONA4,780
 pyobo/xrefdb/sources/wikidata.py,sha256=bOI2zUkkLbmXvOMJZmVWq1xKlMCuL_3l1NVsaoJr1x4,3387
-pyobo-0.10.9.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
-pyobo-0.10.9.dist-info/METADATA,sha256=BDEySfczBniUX3mHWKWI4XC9uxrbB_XPCRhp3Q5I8uE,20045
-pyobo-0.10.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-pyobo-0.10.9.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
-pyobo-0.10.9.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
-pyobo-0.10.9.dist-info/RECORD,,
+pyobo-0.10.10.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
+pyobo-0.10.10.dist-info/METADATA,sha256=rzbhrEqNk6WZVG-Z6qDwkOaobEwleVjGz5m-tSB3Zqg,20046
+pyobo-0.10.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+pyobo-0.10.10.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
+pyobo-0.10.10.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.10.10.dist-info/RECORD,,