Fix compatability with pyteomics Unimod

CHANGELOG.md

@@ -3,6 +3,22 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog][Keep a Changelog] and this project adheres to [Semantic Versioning][Semantic Versioning].
 
+## [Unreleased]
+
+| Name | Version | Checksum |
+|  :---: |  :---: |  :---: |
+| XLMOD.obo.gz | release/2019-10-28 | 4e577044551d277e4bbd62753fa15e08 |
+| gno.obo.gz | 2023-11-09 | 078de92750ee4956b705684253a66f97 |
+| go.obo.gz | releases/2023-11-15 | 1130d315870d82c1624f87b37305777b |
+| pato.obo.gz | releases/2023-05-18/pato.obo | 8a14f0e3b3318c13d029d84d693a01e3 |
+| psi-mod.obo.gz | - | 713e6dd17632d0388802f1b0e06800f0 |
+| psi-ms.obo.gz | 4.1.136 | 1d5aa08ea57762000d00a9300734a78c |
+| unimod_tables.xml.gz | - | efc94f333458012a77203d09a64d7d38 |
+| unit.obo.gz | releases/2023-05-25 | 5a04e9d871730a1ee04764055e841785 |
+
+### Added
+1. Add `by_id` method to `Unimod` for parity with `pyteomics`
+
 ## [v1.3.1]
 
 ### Changed

psims/controlled_vocabulary/unimod.py

@@ -1,3 +1,4 @@
+from typing import Union
 import warnings
 import re
 
@@ -760,7 +761,13 @@ def version(self):
         except Exception:
             return self.default_version
 
-    def get(self, identifier, strict=True):
+    def by_id(self, identifier: int):
+        mod = self.session.query(Modification).get(identifier)
+        if mod is None:
+            raise KeyError(identifier)
+        return mod
+
+    def get(self, identifier: Union[str, int], strict=True):
         is_explicit_accession = isinstance(identifier, basestring) and identifier.startswith("UNIMOD")
         try:
             # At least one Modification has an empty string code_name or ex_code_name, causing
@@ -772,10 +779,7 @@ def get(self, identifier, strict=True):
         if isinstance(identifier, int) or is_explicit_accession:
             if is_explicit_accession:
                 identifier = int(identifier.replace("UNIMOD:", ''))
-            mod = self.session.query(Modification).get(identifier)
-            if mod is None:
-                raise KeyError(identifier)
-            return mod
+            return self.by_id(identifier)
         elif isinstance(identifier, basestring):
             if strict:
                 mod = self.session.query(Modification).filter(

psims/controlled_vocabulary/vendor/record.json

@@ -4,12 +4,12 @@
     "version": "release/2019-10-28"
   },
   "gno.obo.gz": {
-    "checksum": "6178d787e38a8a1b5d7506e3c1a880d0",
-    "version": "2023-08-09"
+    "checksum": "078de92750ee4956b705684253a66f97",
+    "version": "2023-11-09"
   },
   "go.obo.gz": {
-    "checksum": "a827a54e43185170c973afe1add92941",
-    "version": "releases/2023-10-09"
+    "checksum": "1130d315870d82c1624f87b37305777b",
+    "version": "releases/2023-11-15"
   },
   "pato.obo.gz": {
     "checksum": "8a14f0e3b3318c13d029d84d693a01e3",
@@ -20,8 +20,8 @@
     "version": null
   },
   "psi-ms.obo.gz": {
-    "checksum": "3f58f845ef728dc3225a5a2df32fff3a",
-    "version": "4.1.135"
+    "checksum": "1d5aa08ea57762000d00a9300734a78c",
+    "version": "4.1.136"
   },
   "unimod_tables.xml.gz": {
     "checksum": "efc94f333458012a77203d09a64d7d38",