diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml index b74724f6..9f3d33a0 100644 --- a/.github/workflows/run_tests.yml +++ b/.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' diff --git a/js/ord-schema/index.js b/js/ord-schema/index.js index a4790b67..626fda94 100644 --- a/js/ord-schema/index.js +++ b/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. diff --git a/js/ord-schema/proto/dataset_pb.js b/js/ord-schema/proto/dataset_pb.js index 056d50fb..bfc448ac 100644 --- a/js/ord-schema/proto/dataset_pb.js +++ b/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. diff --git a/js/ord-schema/proto/dataset_pb.test.js b/js/ord-schema/proto/dataset_pb.test.js index a4fec208..8459ac01 100644 --- a/js/ord-schema/proto/dataset_pb.test.js +++ b/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. diff --git a/js/ord-schema/proto/reaction_pb.js b/js/ord-schema/proto/reaction_pb.js index 5ff40f02..7452744c 100644 --- a/js/ord-schema/proto/reaction_pb.js +++ b/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 }; /** diff --git a/js/ord-schema/proto/reaction_pb.test.js b/js/ord-schema/proto/reaction_pb.test.js index 6b854517..b58a99af 100644 --- a/js/ord-schema/proto/reaction_pb.test.js +++ b/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. diff --git a/js/ord-schema/proto/test_pb.js b/js/ord-schema/proto/test_pb.js index 4109ceaf..f49d494f 100644 --- a/js/ord-schema/proto/test_pb.js +++ b/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. diff --git a/ord_schema/proto/dataset_pb2.py b/ord_schema/proto/dataset_pb2.py index 7631dd23..47e7c31e 100644 --- a/ord_schema/proto/dataset_pb2.py +++ b/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. diff --git a/ord_schema/proto/dataset_pb2_test.py b/ord_schema/proto/dataset_pb2_test.py index 9036339b..e99d4176 100644 --- a/ord_schema/proto/dataset_pb2_test.py +++ b/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. diff --git a/ord_schema/proto/reaction_pb2.py b/ord_schema/proto/reaction_pb2.py index d0858e42..a06f795b 100644 --- a/ord_schema/proto/reaction_pb2.py +++ b/ord_schema/proto/reaction_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. @@ -27,7 +27,7 @@ -DESCRIPTOR = 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b/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] diff --git a/ord_schema/proto/reaction_pb2_test.py b/ord_schema/proto/reaction_pb2_test.py index 30be2558..0559ed44 100644 --- a/ord_schema/proto/reaction_pb2_test.py +++ b/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. diff --git a/ord_schema/proto/test_pb2.py b/ord_schema/proto/test_pb2.py index 9a8e9cfe..cc845e96 100644 --- a/ord_schema/proto/test_pb2.py +++ b/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. diff --git a/proto/reaction.proto b/proto/reaction.proto index 469c74f5..74905b47 100644 --- a/proto/reaction.proto +++ b/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).