Add addition device types, and analysis types (#719)

* Add some addition device types, and analysis types

* Fix formatting errors

* Update the checkout action version

* Update js protobuf for updated schema

* Update the js and py files

* Update license

* Update license year to 2024

* Update license year to 2024

* Fix indention

* Update license year

---------

Co-authored-by: Ben Deadman <ben@bjdeadman.co.uk>

.github/workflows/run_tests.yml

@@ -25,7 +25,7 @@ jobs:
     env:
       PGDATA: $GITHUB_WORKSPACE/rdkit-postgres
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
         with:
           miniconda-version: 'latest'
@@ -58,7 +58,7 @@ jobs:
         os: [ ubuntu-latest, macos-14 ]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
@@ -74,7 +74,7 @@ jobs:
   test_proto_wrappers:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
@@ -101,7 +101,7 @@ jobs:
   test_js:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-node@v3
         with:
           node-version: '16.x'
@@ -113,7 +113,7 @@ jobs:
   test_publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'

js/ord-schema/index.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2022 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

js/ord-schema/proto/dataset_pb.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2023 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

js/ord-schema/proto/dataset_pb.test.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2022 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

js/ord-schema/proto/reaction_pb.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2023 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -2881,7 +2881,9 @@ proto.ord.ReactionInput.AdditionDevice.AdditionDeviceType = {
   NONE: 2,
   SYRINGE: 3,
   CANNULA: 4,
-  ADDITION_FUNNEL: 5
+  ADDITION_FUNNEL: 5,
+  PIPETTE: 6,
+  POSITIVE_DISPLACEMENT_PIPETTE: 7
 };
 
 /**
@@ -5509,7 +5511,8 @@ proto.ord.CompoundIdentifier.CompoundIdentifierType = {
   UNIPROT_ID: 13,
   PDB_ID: 14,
   AMINO_ACID_SEQUENCE: 15,
-  HELM: 16
+  HELM: 16,
+  MDL: 17
 };
 
 /**
@@ -15126,7 +15129,9 @@ proto.ord.Analysis.AnalysisType = {
   EPR: 20,
   XRD: 21,
   RAMAN: 22,
-  ED: 23
+  ED: 23,
+  OPTICAL_ROTATION: 24,
+  CAD: 25
 };
 
 /**

js/ord-schema/proto/reaction_pb.test.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2022 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

js/ord-schema/proto/test_pb.js

@@ -1,5 +1,5 @@
 /**
- * Copyright 2023 Open Reaction Database Project Authors
+ * Copyright 2024 Open Reaction Database Project Authors
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

ord_schema/proto/dataset_pb2.py

@@ -1,4 +1,4 @@
-# Copyright 2023 Open Reaction Database Project Authors
+# Copyright 2024 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

ord_schema/proto/dataset_pb2_test.py

@@ -1,4 +1,4 @@
-# Copyright 2020 Open Reaction Database Project Authors
+# Copyright 2024 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

ord_schema/proto/reaction_pb2.pyi

@@ -100,12 +100,16 @@ class ReactionInput(_message.Message):
             SYRINGE: _ClassVar[ReactionInput.AdditionDevice.AdditionDeviceType]
             CANNULA: _ClassVar[ReactionInput.AdditionDevice.AdditionDeviceType]
             ADDITION_FUNNEL: _ClassVar[ReactionInput.AdditionDevice.AdditionDeviceType]
+            PIPETTE: _ClassVar[ReactionInput.AdditionDevice.AdditionDeviceType]
+            POSITIVE_DISPLACEMENT_PIPETTE: _ClassVar[ReactionInput.AdditionDevice.AdditionDeviceType]
         UNSPECIFIED: ReactionInput.AdditionDevice.AdditionDeviceType
         CUSTOM: ReactionInput.AdditionDevice.AdditionDeviceType
         NONE: ReactionInput.AdditionDevice.AdditionDeviceType
         SYRINGE: ReactionInput.AdditionDevice.AdditionDeviceType
         CANNULA: ReactionInput.AdditionDevice.AdditionDeviceType
         ADDITION_FUNNEL: ReactionInput.AdditionDevice.AdditionDeviceType
+        PIPETTE: ReactionInput.AdditionDevice.AdditionDeviceType
+        POSITIVE_DISPLACEMENT_PIPETTE: ReactionInput.AdditionDevice.AdditionDeviceType
         TYPE_FIELD_NUMBER: _ClassVar[int]
         DETAILS_FIELD_NUMBER: _ClassVar[int]
         type: ReactionInput.AdditionDevice.AdditionDeviceType
@@ -335,6 +339,7 @@ class CompoundIdentifier(_message.Message):
         PDB_ID: _ClassVar[CompoundIdentifier.CompoundIdentifierType]
         AMINO_ACID_SEQUENCE: _ClassVar[CompoundIdentifier.CompoundIdentifierType]
         HELM: _ClassVar[CompoundIdentifier.CompoundIdentifierType]
+        MDL: _ClassVar[CompoundIdentifier.CompoundIdentifierType]
     UNSPECIFIED: CompoundIdentifier.CompoundIdentifierType
     CUSTOM: CompoundIdentifier.CompoundIdentifierType
     SMILES: CompoundIdentifier.CompoundIdentifierType
@@ -352,6 +357,7 @@ class CompoundIdentifier(_message.Message):
     PDB_ID: CompoundIdentifier.CompoundIdentifierType
     AMINO_ACID_SEQUENCE: CompoundIdentifier.CompoundIdentifierType
     HELM: CompoundIdentifier.CompoundIdentifierType
+    MDL: CompoundIdentifier.CompoundIdentifierType
     TYPE_FIELD_NUMBER: _ClassVar[int]
     DETAILS_FIELD_NUMBER: _ClassVar[int]
     VALUE_FIELD_NUMBER: _ClassVar[int]
@@ -1205,6 +1211,8 @@ class Analysis(_message.Message):
         XRD: _ClassVar[Analysis.AnalysisType]
         RAMAN: _ClassVar[Analysis.AnalysisType]
         ED: _ClassVar[Analysis.AnalysisType]
+        OPTICAL_ROTATION: _ClassVar[Analysis.AnalysisType]
+        CAD: _ClassVar[Analysis.AnalysisType]
     UNSPECIFIED: Analysis.AnalysisType
     CUSTOM: Analysis.AnalysisType
     LC: Analysis.AnalysisType
@@ -1229,6 +1237,8 @@ class Analysis(_message.Message):
     XRD: Analysis.AnalysisType
     RAMAN: Analysis.AnalysisType
     ED: Analysis.AnalysisType
+    OPTICAL_ROTATION: Analysis.AnalysisType
+    CAD: Analysis.AnalysisType
     class DataEntry(_message.Message):
         __slots__ = ["key", "value"]
         KEY_FIELD_NUMBER: _ClassVar[int]

ord_schema/proto/reaction_pb2_test.py

@@ -1,4 +1,4 @@
-# Copyright 2020 Open Reaction Database Project Authors
+# Copyright 2024 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

ord_schema/proto/test_pb2.py

@@ -1,4 +1,4 @@
-# Copyright 2023 Open Reaction Database Project Authors
+# Copyright 2024 Open Reaction Database Project Authors
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

proto/reaction.proto

@@ -152,6 +152,8 @@ message ReactionInput {
       SYRINGE = 3;
       CANNULA = 4;
       ADDITION_FUNNEL = 5;
+      PIPETTE = 6;
+      POSITIVE_DISPLACEMENT_PIPETTE = 7;
     }
     AdditionDeviceType type = 1;
     // Specify, e.g., "gas-tight" for SYRINGE or cannula material.
@@ -398,6 +400,9 @@ message CompoundIdentifier {
     AMINO_ACID_SEQUENCE = 15;
     // HELM; https://www.pistoiaalliance.org/helm-notation/.
     HELM = 16;
+    MDL = 17;
+    // MDL number e.g., MFCD00005972 for morpholine,
+    // often included on commercial supplier listings.
   }
   CompoundIdentifierType type = 1;
   string details = 2;
@@ -1087,6 +1092,8 @@ message Analysis {
     XRD = 21;  // X-ray diffraction, including single-crystal XRD.
     RAMAN = 22;  // Raman spectroscopy.
     ED = 23;  // Electron diffraction, including MicroED.
+    OPTICAL_ROTATION = 24;  // optical rotation.
+    CAD = 25;  // Charged Aerosol Detector.
   }
   AnalysisType type = 1;
   // Any details about analysis (e.g., NMR type, columns, gradients).