From 865da6a06659a12fe762264265fc4264b94dd071 Mon Sep 17 00:00:00 2001 From: qai Date: Thu, 22 Jun 2023 12:08:01 -0400 Subject: [PATCH 1/5] - extended ReactionRoleType, added validation functions - comments about stoichiometry convention --- ord_schema/validations.py | 17 ++++++++++++++--- proto/reaction.proto | 10 ++++++++++ 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/ord_schema/validations.py b/ord_schema/validations.py index 1d95e789..415b1cae 100644 --- a/ord_schema/validations.py +++ b/ord_schema/validations.py @@ -783,9 +783,17 @@ def validate_reaction_workup(message: reaction_pb2.ReactionWorkup): def validate_reaction_outcome(message: reaction_pb2.ReactionOutcome): # pylint: disable=singleton-comparison - # Can only have one desired product - if sum(product.is_desired_product for product in message.products) > 1: - warnings.warn("Cannot have more than one desired product!", ValidationError) + # *Usually* there should be at most one PRODUCT & is_desired_product + ndp = sum( + product.is_desired_product for product in message.products + if product.reaction_role == reaction_pb2.ReactionRole.ReactionRoleType.PRODUCT + ) + if ndp > 1: + warnings.warn( + f"Usually at most one (reaction_role == PRODUCT & is_desired_product) product, but we have: {ndp}", + ValidationWarning + ) + # Check key values for product analyses # NOTE(ccoley): Could use any(), but using expanded loops for clarity analysis_keys = list(message.analyses.keys()) @@ -820,6 +828,9 @@ def validate_product_compound(message: reaction_pb2.ProductCompound): except ValueError as error: warnings.warn(str(error), ValidationWarning) + if message.is_desired_product: + if message.reaction_role == reaction_pb2.ReactionRole.ReactionRoleType.SIDE_PRODUCT: + warnings.warn("a product cannot be (SIDE_PRODUCT & is_desired_product)", ValidationError) def validate_texture(message: reaction_pb2.ProductCompound.Texture): check_type_and_details(message) diff --git a/proto/reaction.proto b/proto/reaction.proto index a5c85477..9917f120 100644 --- a/proto/reaction.proto +++ b/proto/reaction.proto @@ -261,6 +261,7 @@ message Compound { // properties of the compound (e.g., molecular weight), heuristic estimates // of physical properties (e.g., ClogP), optimized geometries (e.g., through // DFT), and calculated stereoelectronic descriptors. + // Convention: also put stoichiometry ratio/coefficient here, see https://github.com/open-reaction-database/ord-schema/issues/683 map features = 7; // Compounds may be assayed for quality control; analytical data should be // defined in the analyses map. @@ -287,6 +288,14 @@ message ReactionRole { // A product can be any species produced by the reaction, whether desired // or undesired. PRODUCT = 8; + // When there is only one intended chemical equation. + // - The products of the intended equation includes one and only one desired product and a set of byproducts. + // - If a product of this *reaction* is not in the right side of the intended equation, it is a side product. + // - The desired product has reaction_role == PRODUCT and is_desired_product == True + // - A byproduct has reaction_role == BYPRODUCT and is_desired_product == True + // - A side product has reaction_role == SIDE_PRODUCT and is_desired_product == False + BYPRODUCT = 9; + SIDE_PRODUCT = 10; } } @@ -887,6 +896,7 @@ message ProductCompound { } Texture texture = 5; // Any features (e.g., calculated descriptors) of the product compound. + // Convention: also put stoichiometry ratio/coefficient here, see https://github.com/open-reaction-database/ord-schema/issues/683 map features = 6; // Specify the role the ProductCompound played in the reaction. This // aids in constructing proper reaction SMILES and product lists. From 4a05814309d6f73e71129bdfc9d364f637b6b2f2 Mon Sep 17 00:00:00 2001 From: qai Date: Tue, 4 Jul 2023 20:01:54 -0400 Subject: [PATCH 2/5] - move stoichiometry convention to README.md --- README.md | 17 +++++++++++++++++ proto/reaction.proto | 2 -- 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 74098c04..cdb045fc 100644 --- a/README.md +++ b/README.md @@ -39,3 +39,20 @@ $ pip install -e . If you make changes to the protocol buffer definitions, [install](https://grpc.io/docs/protoc-installation/) `protoc` and run `./compile_proto_wrappers.sh` to rebuild the wrappers. + +## Conventions + +### 1. convention: compound stoichiometry + +##### Created: 2023.07.04 + +##### Last updated: 2023.07.04 + +##### Description: +1. The preferred field for compound stoichiometry is the map `Compound.features` or `ProductCompound.features`. +2. The key should be "stoichiometric_coefficient" or "stoichiometric_ratio". +3. The value should be a Data mesaage with its float_value representing the compound's stoichiometric coefficient or ratio.SInformation about also put stoichiometry ratio/coefficient here + +##### Related links: +[#683](https://github.com/open-reaction-database/ord-schema/issues/683) +[#684](https://github.com/open-reaction-database/ord-schema/pull/684) \ No newline at end of file diff --git a/proto/reaction.proto b/proto/reaction.proto index 9917f120..0e2ea1d4 100644 --- a/proto/reaction.proto +++ b/proto/reaction.proto @@ -261,7 +261,6 @@ message Compound { // properties of the compound (e.g., molecular weight), heuristic estimates // of physical properties (e.g., ClogP), optimized geometries (e.g., through // DFT), and calculated stereoelectronic descriptors. - // Convention: also put stoichiometry ratio/coefficient here, see https://github.com/open-reaction-database/ord-schema/issues/683 map features = 7; // Compounds may be assayed for quality control; analytical data should be // defined in the analyses map. @@ -896,7 +895,6 @@ message ProductCompound { } Texture texture = 5; // Any features (e.g., calculated descriptors) of the product compound. - // Convention: also put stoichiometry ratio/coefficient here, see https://github.com/open-reaction-database/ord-schema/issues/683 map features = 6; // Specify the role the ProductCompound played in the reaction. This // aids in constructing proper reaction SMILES and product lists. From 590a1f66d479f7dc8afea511cd4c5bb355c5787c Mon Sep 17 00:00:00 2001 From: qai Date: Wed, 5 Jul 2023 17:45:12 -0400 Subject: [PATCH 3/5] update comments on `reaction_role` --- proto/reaction.proto | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/proto/reaction.proto b/proto/reaction.proto index 0e2ea1d4..d9b08100 100644 --- a/proto/reaction.proto +++ b/proto/reaction.proto @@ -287,12 +287,11 @@ message ReactionRole { // A product can be any species produced by the reaction, whether desired // or undesired. PRODUCT = 8; - // When there is only one intended chemical equation. - // - The products of the intended equation includes one and only one desired product and a set of byproducts. - // - If a product of this *reaction* is not in the right side of the intended equation, it is a side product. - // - The desired product has reaction_role == PRODUCT and is_desired_product == True - // - A byproduct has reaction_role == BYPRODUCT and is_desired_product == True - // - A side product has reaction_role == SIDE_PRODUCT and is_desired_product == False + // When there is one intended chemical equation: + // - Set `is_desired_product=True` to indicate a desired product. + // - Use BYPRODUCT to indicate a chemical species that is an expected result of the reaction but is not the product of interest. + // - Use SIDE_PRODUCT to indicate the product of a side reaction. + // - See https://doi.org/10.1021/op300317g for a discussion of these terms. BYPRODUCT = 9; SIDE_PRODUCT = 10; } From 32b31cd273bf0e6a43ed446cda2403b1792a7b0a Mon Sep 17 00:00:00 2001 From: qai Date: Sun, 9 Jul 2023 21:20:41 -0400 Subject: [PATCH 4/5] `compile_proto_wrappers.sh && format.sh` - libprotoc 22.3 - Ubuntu clang-format version 14.0.0-1ubuntu1 - go version go1.20.5 linux/amd64 - Ubuntu clang-format version 14.0.0-1ubuntu1 --- js/ord-schema/proto/dataset_pb.js | 14 +- js/ord-schema/proto/reaction_pb.js | 42 +- js/ord-schema/proto/test_pb.js | 20 +- ord_schema/proto/dataset_pb2.py | 32 +- ord_schema/proto/reaction_pb2.py | 1108 ++++++---------------------- ord_schema/proto/test_pb2.py | 179 +---- ord_schema/validations.py | 8 +- proto/reaction.proto | 3 +- 8 files changed, 326 insertions(+), 1080 deletions(-) diff --git a/js/ord-schema/proto/dataset_pb.js b/js/ord-schema/proto/dataset_pb.js index 6e4bb2b3..056d50fb 100644 --- a/js/ord-schema/proto/dataset_pb.js +++ b/js/ord-schema/proto/dataset_pb.js @@ -29,13 +29,13 @@ var jspb = require('google-protobuf'); var goog = jspb; -var global = (function() { - if (this) { return this; } - if (typeof window !== 'undefined') { return window; } - if (typeof global !== 'undefined') { return global; } - if (typeof self !== 'undefined') { return self; } - return Function('return this')(); -}.call(null)); +var global = + (typeof globalThis !== 'undefined' && globalThis) || + (typeof window !== 'undefined' && window) || + (typeof global !== 'undefined' && global) || + (typeof self !== 'undefined' && self) || + (function () { return this; }).call(null) || + Function('return this')(); var ord$schema_proto_reaction_pb = require('../../ord-schema/proto/reaction_pb.js'); goog.object.extend(proto, ord$schema_proto_reaction_pb); diff --git a/js/ord-schema/proto/reaction_pb.js b/js/ord-schema/proto/reaction_pb.js index 6f6274da..ab8bb7c4 100644 --- a/js/ord-schema/proto/reaction_pb.js +++ b/js/ord-schema/proto/reaction_pb.js @@ -29,13 +29,13 @@ var jspb = require('google-protobuf'); var goog = jspb; -var global = (function() { - if (this) { return this; } - if (typeof window !== 'undefined') { return window; } - if (typeof global !== 'undefined') { return global; } - if (typeof self !== 'undefined') { return self; } - return Function('return this')(); -}.call(null)); +var global = + (typeof globalThis !== 'undefined' && globalThis) || + (typeof window !== 'undefined' && window) || + (typeof global !== 'undefined' && global) || + (typeof self !== 'undefined' && self) || + (function () { return this; }).call(null) || + Function('return this')(); goog.exportSymbol('proto.ord.Amount', null, global); goog.exportSymbol('proto.ord.Amount.KindCase', null, global); @@ -1793,7 +1793,8 @@ proto.ord.Reaction.prototype.getInputsMap = function(opt_noLazyCreate) { */ proto.ord.Reaction.prototype.clearInputsMap = function() { this.getInputsMap().clear(); - return this;}; + return this; +}; /** @@ -4673,7 +4674,8 @@ proto.ord.Compound.prototype.getFeaturesMap = function(opt_noLazyCreate) { */ proto.ord.Compound.prototype.clearFeaturesMap = function() { this.getFeaturesMap().clear(); - return this;}; + return this; +}; /** @@ -4695,7 +4697,8 @@ proto.ord.Compound.prototype.getAnalysesMap = function(opt_noLazyCreate) { */ proto.ord.Compound.prototype.clearAnalysesMap = function() { this.getAnalysesMap().clear(); - return this;}; + return this; +}; @@ -4811,7 +4814,9 @@ proto.ord.ReactionRole.ReactionRoleType = { WORKUP: 5, INTERNAL_STANDARD: 6, AUTHENTIC_STANDARD: 7, - PRODUCT: 8 + PRODUCT: 8, + BYPRODUCT: 9, + SIDE_PRODUCT: 10 }; @@ -6719,7 +6724,8 @@ proto.ord.ReactionSetup.prototype.getAutomationCodeMap = function(opt_noLazyCrea */ proto.ord.ReactionSetup.prototype.clearAutomationCodeMap = function() { this.getAutomationCodeMap().clear(); - return this;}; + return this; +}; /** @@ -12704,7 +12710,8 @@ proto.ord.ReactionOutcome.prototype.getAnalysesMap = function(opt_noLazyCreate) */ proto.ord.ReactionOutcome.prototype.clearAnalysesMap = function() { this.getAnalysesMap().clear(); - return this;}; + return this; +}; @@ -13268,7 +13275,8 @@ proto.ord.ProductCompound.prototype.getFeaturesMap = function(opt_noLazyCreate) */ proto.ord.ProductCompound.prototype.clearFeaturesMap = function() { this.getFeaturesMap().clear(); - return this;}; + return this; +}; /** @@ -15076,7 +15084,8 @@ proto.ord.Analysis.prototype.getDataMap = function(opt_noLazyCreate) { */ proto.ord.Analysis.prototype.clearDataMap = function() { this.getDataMap().clear(); - return this;}; + return this; +}; /** @@ -15597,7 +15606,8 @@ proto.ord.ReactionProvenance.prototype.getReactionMetadataMap = function(opt_noL */ proto.ord.ReactionProvenance.prototype.clearReactionMetadataMap = function() { this.getReactionMetadataMap().clear(); - return this;}; + return this; +}; diff --git a/js/ord-schema/proto/test_pb.js b/js/ord-schema/proto/test_pb.js index 19c9bc62..4109ceaf 100644 --- a/js/ord-schema/proto/test_pb.js +++ b/js/ord-schema/proto/test_pb.js @@ -29,13 +29,13 @@ var jspb = require('google-protobuf'); var goog = jspb; -var global = (function() { - if (this) { return this; } - if (typeof window !== 'undefined') { return window; } - if (typeof global !== 'undefined') { return global; } - if (typeof self !== 'undefined') { return self; } - return Function('return this')(); -}.call(null)); +var global = + (typeof globalThis !== 'undefined' && globalThis) || + (typeof window !== 'undefined' && window) || + (typeof global !== 'undefined' && global) || + (typeof self !== 'undefined' && self) || + (function () { return this; }).call(null) || + Function('return this')(); goog.exportSymbol('proto.ord_test.Enum', null, global); goog.exportSymbol('proto.ord_test.Enum.EnumValues', null, global); @@ -1822,7 +1822,8 @@ proto.ord_test.Map.prototype.getValuesMap = function(opt_noLazyCreate) { */ proto.ord_test.Map.prototype.clearValuesMap = function() { this.getValuesMap().clear(); - return this;}; + return this; +}; @@ -2103,7 +2104,8 @@ proto.ord_test.MapNested.prototype.getChildrenMap = function(opt_noLazyCreate) { */ proto.ord_test.MapNested.prototype.clearChildrenMap = function() { this.getChildrenMap().clear(); - return this;}; + return this; +}; goog.object.extend(exports, proto.ord_test); diff --git a/ord_schema/proto/dataset_pb2.py b/ord_schema/proto/dataset_pb2.py index aae692d7..7631dd23 100644 --- a/ord_schema/proto/dataset_pb2.py +++ b/ord_schema/proto/dataset_pb2.py @@ -16,10 +16,9 @@ # Generated by the protocol buffer compiler. DO NOT EDIT! # source: ord-schema/proto/dataset.proto """Generated protocol buffer code.""" +from google.protobuf.internal import builder as _builder from google.protobuf import descriptor as _descriptor from google.protobuf import descriptor_pool as _descriptor_pool -from google.protobuf import message as _message -from google.protobuf import reflection as _reflection from google.protobuf import symbol_database as _symbol_database # @@protoc_insertion_point(imports) @@ -31,29 +30,14 @@ DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x1eord-schema/proto/dataset.proto\x12\x03ord\x1a\x1ford-schema/proto/reaction.proto\"x\n\x07\x44\x61taset\x12\x0c\n\x04name\x18\x01 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\x02 \x01(\t\x12 \n\treactions\x18\x03 \x03(\x0b\x32\r.ord.Reaction\x12\x14\n\x0creaction_ids\x18\x04 \x03(\t\x12\x12\n\ndataset_id\x18\x05 \x01(\t\"i\n\x0e\x44\x61tasetExample\x12\x12\n\ndataset_id\x18\x01 \x01(\t\x12\x13\n\x0b\x64\x65scription\x18\x02 \x01(\t\x12\x0b\n\x03url\x18\x03 \x01(\t\x12!\n\x07\x63reated\x18\x04 \x01(\x0b\x32\x10.ord.RecordEventb\x06proto3') - - -_DATASET = DESCRIPTOR.message_types_by_name['Dataset'] -_DATASETEXAMPLE = DESCRIPTOR.message_types_by_name['DatasetExample'] -Dataset = _reflection.GeneratedProtocolMessageType('Dataset', (_message.Message,), { - 'DESCRIPTOR' : _DATASET, - '__module__' : 'ord_schema.proto.dataset_pb2' - # @@protoc_insertion_point(class_scope:ord.Dataset) - }) -_sym_db.RegisterMessage(Dataset) - -DatasetExample = _reflection.GeneratedProtocolMessageType('DatasetExample', (_message.Message,), { - 'DESCRIPTOR' : _DATASETEXAMPLE, - '__module__' : 'ord_schema.proto.dataset_pb2' - # @@protoc_insertion_point(class_scope:ord.DatasetExample) - }) -_sym_db.RegisterMessage(DatasetExample) - +_globals = globals() +_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) +_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'ord_schema.proto.dataset_pb2', _globals) if _descriptor._USE_C_DESCRIPTORS == False: DESCRIPTOR._options = None - _DATASET._serialized_start=72 - _DATASET._serialized_end=192 - _DATASETEXAMPLE._serialized_start=194 - _DATASETEXAMPLE._serialized_end=299 + _globals['_DATASET']._serialized_start=72 + _globals['_DATASET']._serialized_end=192 + _globals['_DATASETEXAMPLE']._serialized_start=194 + _globals['_DATASETEXAMPLE']._serialized_end=299 # @@protoc_insertion_point(module_scope) diff --git a/ord_schema/proto/reaction_pb2.py b/ord_schema/proto/reaction_pb2.py index aebc0df2..395264aa 100644 --- a/ord_schema/proto/reaction_pb2.py +++ b/ord_schema/proto/reaction_pb2.py @@ -16,10 +16,9 @@ # Generated by the protocol buffer compiler. DO NOT EDIT! # source: ord-schema/proto/reaction.proto """Generated protocol buffer code.""" +from google.protobuf.internal import builder as _builder from google.protobuf import descriptor as _descriptor from google.protobuf import descriptor_pool as _descriptor_pool -from google.protobuf import message as _message -from google.protobuf import reflection as _reflection from google.protobuf import symbol_database as _symbol_database # @@protoc_insertion_point(imports) @@ -28,652 +27,11 @@ -DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x1ford-schema/proto/reaction.proto\x12\x03ord\"\xd9\x03\n\x08Reaction\x12,\n\x0bidentifiers\x18\x01 \x03(\x0b\x32\x17.ord.ReactionIdentifier\x12)\n\x06inputs\x18\x02 \x03(\x0b\x32\x19.ord.Reaction.InputsEntry\x12!\n\x05setup\x18\x03 \x01(\x0b\x32\x12.ord.ReactionSetup\x12+\n\nconditions\x18\x04 \x01(\x0b\x32\x17.ord.ReactionConditions\x12!\n\x05notes\x18\x05 \x01(\x0b\x32\x12.ord.ReactionNotes\x12.\n\x0cobservations\x18\x06 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DESCRIPTOR.message_types_by_name['ProductMeasurement'] -_PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS = _PRODUCTMEASUREMENT.nested_types_by_name['MassSpecMeasurementDetails'] -_PRODUCTMEASUREMENT_SELECTIVITY = _PRODUCTMEASUREMENT.nested_types_by_name['Selectivity'] -_DATETIME = DESCRIPTOR.message_types_by_name['DateTime'] -_ANALYSIS = DESCRIPTOR.message_types_by_name['Analysis'] -_ANALYSIS_DATAENTRY = _ANALYSIS.nested_types_by_name['DataEntry'] -_REACTIONPROVENANCE = DESCRIPTOR.message_types_by_name['ReactionProvenance'] -_REACTIONPROVENANCE_REACTIONMETADATAENTRY = _REACTIONPROVENANCE.nested_types_by_name['ReactionMetadataEntry'] -_PERSON = DESCRIPTOR.message_types_by_name['Person'] -_RECORDEVENT = DESCRIPTOR.message_types_by_name['RecordEvent'] -_TIME = DESCRIPTOR.message_types_by_name['Time'] -_MASS = DESCRIPTOR.message_types_by_name['Mass'] -_MOLES = DESCRIPTOR.message_types_by_name['Moles'] -_VOLUME = DESCRIPTOR.message_types_by_name['Volume'] -_CONCENTRATION = 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_TEMPERATURECONDITIONS_TEMPERATURECONTROL.enum_types_by_name['TemperatureControlType'] -_TEMPERATURECONDITIONS_TEMPERATUREMEASUREMENT_TEMPERATUREMEASUREMENTTYPE = _TEMPERATURECONDITIONS_TEMPERATUREMEASUREMENT.enum_types_by_name['TemperatureMeasurementType'] -_PRESSURECONDITIONS_PRESSURECONTROL_PRESSURECONTROLTYPE = _PRESSURECONDITIONS_PRESSURECONTROL.enum_types_by_name['PressureControlType'] -_PRESSURECONDITIONS_ATMOSPHERE_ATMOSPHERETYPE = _PRESSURECONDITIONS_ATMOSPHERE.enum_types_by_name['AtmosphereType'] -_PRESSURECONDITIONS_PRESSUREMEASUREMENT_PRESSUREMEASUREMENTTYPE = _PRESSURECONDITIONS_PRESSUREMEASUREMENT.enum_types_by_name['PressureMeasurementType'] -_STIRRINGCONDITIONS_STIRRINGRATE_STIRRINGRATETYPE = _STIRRINGCONDITIONS_STIRRINGRATE.enum_types_by_name['StirringRateType'] -_STIRRINGCONDITIONS_STIRRINGMETHODTYPE = _STIRRINGCONDITIONS.enum_types_by_name['StirringMethodType'] -_ILLUMINATIONCONDITIONS_ILLUMINATIONTYPE = _ILLUMINATIONCONDITIONS.enum_types_by_name['IlluminationType'] -_ELECTROCHEMISTRYCONDITIONS_ELECTROCHEMISTRYCELL_ELECTROCHEMISTRYCELLTYPE = _ELECTROCHEMISTRYCONDITIONS_ELECTROCHEMISTRYCELL.enum_types_by_name['ElectrochemistryCellType'] -_ELECTROCHEMISTRYCONDITIONS_ELECTROCHEMISTRYTYPE = _ELECTROCHEMISTRYCONDITIONS.enum_types_by_name['ElectrochemistryType'] -_FLOWCONDITIONS_TUBING_TUBINGTYPE = _FLOWCONDITIONS_TUBING.enum_types_by_name['TubingType'] -_FLOWCONDITIONS_FLOWTYPE = _FLOWCONDITIONS.enum_types_by_name['FlowType'] -_REACTIONWORKUP_REACTIONWORKUPTYPE = _REACTIONWORKUP.enum_types_by_name['ReactionWorkupType'] -_PRODUCTCOMPOUND_TEXTURE_TEXTURETYPE = _PRODUCTCOMPOUND_TEXTURE.enum_types_by_name['TextureType'] -_PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS_MASSSPECMEASUREMENTTYPE = _PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS.enum_types_by_name['MassSpecMeasurementType'] -_PRODUCTMEASUREMENT_SELECTIVITY_SELECTIVITYTYPE = _PRODUCTMEASUREMENT_SELECTIVITY.enum_types_by_name['SelectivityType'] -_PRODUCTMEASUREMENT_PRODUCTMEASUREMENTTYPE = _PRODUCTMEASUREMENT.enum_types_by_name['ProductMeasurementType'] -_ANALYSIS_ANALYSISTYPE = _ANALYSIS.enum_types_by_name['AnalysisType'] -_TIME_TIMEUNIT = _TIME.enum_types_by_name['TimeUnit'] -_MASS_MASSUNIT = _MASS.enum_types_by_name['MassUnit'] -_MOLES_MOLESUNIT = _MOLES.enum_types_by_name['MolesUnit'] -_VOLUME_VOLUMEUNIT = _VOLUME.enum_types_by_name['VolumeUnit'] -_CONCENTRATION_CONCENTRATIONUNIT = _CONCENTRATION.enum_types_by_name['ConcentrationUnit'] -_PRESSURE_PRESSUREUNIT = _PRESSURE.enum_types_by_name['PressureUnit'] -_TEMPERATURE_TEMPERATUREUNIT = _TEMPERATURE.enum_types_by_name['TemperatureUnit'] -_CURRENT_CURRENTUNIT = _CURRENT.enum_types_by_name['CurrentUnit'] -_VOLTAGE_VOLTAGEUNIT = _VOLTAGE.enum_types_by_name['VoltageUnit'] -_LENGTH_LENGTHUNIT = _LENGTH.enum_types_by_name['LengthUnit'] -_WAVELENGTH_WAVELENGTHUNIT = _WAVELENGTH.enum_types_by_name['WavelengthUnit'] -_FLOWRATE_FLOWRATEUNIT = _FLOWRATE.enum_types_by_name['FlowRateUnit'] -Reaction = _reflection.GeneratedProtocolMessageType('Reaction', (_message.Message,), { - - 'InputsEntry' : _reflection.GeneratedProtocolMessageType('InputsEntry', (_message.Message,), { - 'DESCRIPTOR' : _REACTION_INPUTSENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Reaction.InputsEntry) - }) - , - 'DESCRIPTOR' : _REACTION, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Reaction) - }) -_sym_db.RegisterMessage(Reaction) -_sym_db.RegisterMessage(Reaction.InputsEntry) - -ReactionIdentifier = _reflection.GeneratedProtocolMessageType('ReactionIdentifier', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONIDENTIFIER, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionIdentifier) - }) -_sym_db.RegisterMessage(ReactionIdentifier) - -ReactionInput = _reflection.GeneratedProtocolMessageType('ReactionInput', (_message.Message,), { - - 'AdditionSpeed' : _reflection.GeneratedProtocolMessageType('AdditionSpeed', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONINPUT_ADDITIONSPEED, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionInput.AdditionSpeed) - }) - , - - 'AdditionDevice' : _reflection.GeneratedProtocolMessageType('AdditionDevice', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONINPUT_ADDITIONDEVICE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionInput.AdditionDevice) - }) - , - 'DESCRIPTOR' : _REACTIONINPUT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionInput) - }) -_sym_db.RegisterMessage(ReactionInput) -_sym_db.RegisterMessage(ReactionInput.AdditionSpeed) -_sym_db.RegisterMessage(ReactionInput.AdditionDevice) - -Amount = _reflection.GeneratedProtocolMessageType('Amount', (_message.Message,), { - 'DESCRIPTOR' : _AMOUNT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Amount) - }) -_sym_db.RegisterMessage(Amount) - -UnmeasuredAmount = _reflection.GeneratedProtocolMessageType('UnmeasuredAmount', (_message.Message,), { - 'DESCRIPTOR' : _UNMEASUREDAMOUNT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.UnmeasuredAmount) - }) -_sym_db.RegisterMessage(UnmeasuredAmount) - -CrudeComponent = _reflection.GeneratedProtocolMessageType('CrudeComponent', (_message.Message,), { - 'DESCRIPTOR' : _CRUDECOMPONENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.CrudeComponent) - }) -_sym_db.RegisterMessage(CrudeComponent) - -Compound = _reflection.GeneratedProtocolMessageType('Compound', (_message.Message,), { - - 'Source' : _reflection.GeneratedProtocolMessageType('Source', (_message.Message,), { - 'DESCRIPTOR' : _COMPOUND_SOURCE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Compound.Source) - }) - , - - 'FeaturesEntry' : _reflection.GeneratedProtocolMessageType('FeaturesEntry', (_message.Message,), { - 'DESCRIPTOR' : _COMPOUND_FEATURESENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Compound.FeaturesEntry) - }) - , - - 'AnalysesEntry' : _reflection.GeneratedProtocolMessageType('AnalysesEntry', (_message.Message,), { - 'DESCRIPTOR' : _COMPOUND_ANALYSESENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Compound.AnalysesEntry) - }) - , - 'DESCRIPTOR' : _COMPOUND, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Compound) - }) -_sym_db.RegisterMessage(Compound) -_sym_db.RegisterMessage(Compound.Source) -_sym_db.RegisterMessage(Compound.FeaturesEntry) -_sym_db.RegisterMessage(Compound.AnalysesEntry) - -ReactionRole = _reflection.GeneratedProtocolMessageType('ReactionRole', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONROLE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionRole) - }) -_sym_db.RegisterMessage(ReactionRole) - -CompoundPreparation = _reflection.GeneratedProtocolMessageType('CompoundPreparation', (_message.Message,), { - 'DESCRIPTOR' : _COMPOUNDPREPARATION, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.CompoundPreparation) - }) -_sym_db.RegisterMessage(CompoundPreparation) - -CompoundIdentifier = _reflection.GeneratedProtocolMessageType('CompoundIdentifier', (_message.Message,), { - 'DESCRIPTOR' : _COMPOUNDIDENTIFIER, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.CompoundIdentifier) - }) -_sym_db.RegisterMessage(CompoundIdentifier) - -Vessel = _reflection.GeneratedProtocolMessageType('Vessel', (_message.Message,), { - 'DESCRIPTOR' : _VESSEL, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Vessel) - }) -_sym_db.RegisterMessage(Vessel) - -VesselMaterial = _reflection.GeneratedProtocolMessageType('VesselMaterial', (_message.Message,), { - 'DESCRIPTOR' : _VESSELMATERIAL, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.VesselMaterial) - }) -_sym_db.RegisterMessage(VesselMaterial) - -VesselAttachment = _reflection.GeneratedProtocolMessageType('VesselAttachment', (_message.Message,), { - 'DESCRIPTOR' : _VESSELATTACHMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.VesselAttachment) - }) -_sym_db.RegisterMessage(VesselAttachment) - -VesselPreparation = _reflection.GeneratedProtocolMessageType('VesselPreparation', (_message.Message,), { - 'DESCRIPTOR' : _VESSELPREPARATION, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.VesselPreparation) - }) -_sym_db.RegisterMessage(VesselPreparation) - -ReactionSetup = _reflection.GeneratedProtocolMessageType('ReactionSetup', (_message.Message,), { - - 'AutomationCodeEntry' : _reflection.GeneratedProtocolMessageType('AutomationCodeEntry', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONSETUP_AUTOMATIONCODEENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionSetup.AutomationCodeEntry) - }) - , - - 'ReactionEnvironment' : _reflection.GeneratedProtocolMessageType('ReactionEnvironment', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONSETUP_REACTIONENVIRONMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionSetup.ReactionEnvironment) - }) - , - 'DESCRIPTOR' : _REACTIONSETUP, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionSetup) - }) -_sym_db.RegisterMessage(ReactionSetup) -_sym_db.RegisterMessage(ReactionSetup.AutomationCodeEntry) -_sym_db.RegisterMessage(ReactionSetup.ReactionEnvironment) - -ReactionConditions = _reflection.GeneratedProtocolMessageType('ReactionConditions', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONCONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionConditions) - }) -_sym_db.RegisterMessage(ReactionConditions) - -TemperatureConditions = _reflection.GeneratedProtocolMessageType('TemperatureConditions', (_message.Message,), { - - 'TemperatureControl' : _reflection.GeneratedProtocolMessageType('TemperatureControl', (_message.Message,), { - 'DESCRIPTOR' : _TEMPERATURECONDITIONS_TEMPERATURECONTROL, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.TemperatureConditions.TemperatureControl) - }) - , - - 'TemperatureMeasurement' : _reflection.GeneratedProtocolMessageType('TemperatureMeasurement', (_message.Message,), { - 'DESCRIPTOR' : _TEMPERATURECONDITIONS_TEMPERATUREMEASUREMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.TemperatureConditions.TemperatureMeasurement) - }) - , - 'DESCRIPTOR' : _TEMPERATURECONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.TemperatureConditions) - }) -_sym_db.RegisterMessage(TemperatureConditions) -_sym_db.RegisterMessage(TemperatureConditions.TemperatureControl) -_sym_db.RegisterMessage(TemperatureConditions.TemperatureMeasurement) - -PressureConditions = _reflection.GeneratedProtocolMessageType('PressureConditions', (_message.Message,), { - - 'PressureControl' : _reflection.GeneratedProtocolMessageType('PressureControl', (_message.Message,), { - 'DESCRIPTOR' : _PRESSURECONDITIONS_PRESSURECONTROL, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.PressureConditions.PressureControl) - }) - , - - 'Atmosphere' : _reflection.GeneratedProtocolMessageType('Atmosphere', (_message.Message,), { - 'DESCRIPTOR' : _PRESSURECONDITIONS_ATMOSPHERE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.PressureConditions.Atmosphere) - }) - , - - 'PressureMeasurement' : _reflection.GeneratedProtocolMessageType('PressureMeasurement', (_message.Message,), { - 'DESCRIPTOR' : _PRESSURECONDITIONS_PRESSUREMEASUREMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.PressureConditions.PressureMeasurement) - }) - , - 'DESCRIPTOR' : _PRESSURECONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.PressureConditions) - }) -_sym_db.RegisterMessage(PressureConditions) -_sym_db.RegisterMessage(PressureConditions.PressureControl) -_sym_db.RegisterMessage(PressureConditions.Atmosphere) -_sym_db.RegisterMessage(PressureConditions.PressureMeasurement) - -StirringConditions = _reflection.GeneratedProtocolMessageType('StirringConditions', (_message.Message,), { - - 'StirringRate' : _reflection.GeneratedProtocolMessageType('StirringRate', (_message.Message,), { - 'DESCRIPTOR' : _STIRRINGCONDITIONS_STIRRINGRATE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.StirringConditions.StirringRate) - }) - , - 'DESCRIPTOR' : _STIRRINGCONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.StirringConditions) - }) -_sym_db.RegisterMessage(StirringConditions) -_sym_db.RegisterMessage(StirringConditions.StirringRate) - -IlluminationConditions = _reflection.GeneratedProtocolMessageType('IlluminationConditions', (_message.Message,), { - 'DESCRIPTOR' : _ILLUMINATIONCONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.IlluminationConditions) - }) -_sym_db.RegisterMessage(IlluminationConditions) - -ElectrochemistryConditions = _reflection.GeneratedProtocolMessageType('ElectrochemistryConditions', (_message.Message,), { - - 'ElectrochemistryMeasurement' : _reflection.GeneratedProtocolMessageType('ElectrochemistryMeasurement', (_message.Message,), { - 'DESCRIPTOR' : _ELECTROCHEMISTRYCONDITIONS_ELECTROCHEMISTRYMEASUREMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ElectrochemistryConditions.ElectrochemistryMeasurement) - }) - , - - 'ElectrochemistryCell' : _reflection.GeneratedProtocolMessageType('ElectrochemistryCell', (_message.Message,), { - 'DESCRIPTOR' : _ELECTROCHEMISTRYCONDITIONS_ELECTROCHEMISTRYCELL, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ElectrochemistryConditions.ElectrochemistryCell) - }) - , - 'DESCRIPTOR' : _ELECTROCHEMISTRYCONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ElectrochemistryConditions) - }) -_sym_db.RegisterMessage(ElectrochemistryConditions) -_sym_db.RegisterMessage(ElectrochemistryConditions.ElectrochemistryMeasurement) -_sym_db.RegisterMessage(ElectrochemistryConditions.ElectrochemistryCell) - -FlowConditions = _reflection.GeneratedProtocolMessageType('FlowConditions', (_message.Message,), { - - 'Tubing' : _reflection.GeneratedProtocolMessageType('Tubing', (_message.Message,), { - 'DESCRIPTOR' : _FLOWCONDITIONS_TUBING, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.FlowConditions.Tubing) - }) - , - 'DESCRIPTOR' : _FLOWCONDITIONS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.FlowConditions) - }) -_sym_db.RegisterMessage(FlowConditions) -_sym_db.RegisterMessage(FlowConditions.Tubing) - -ReactionNotes = _reflection.GeneratedProtocolMessageType('ReactionNotes', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONNOTES, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionNotes) - }) -_sym_db.RegisterMessage(ReactionNotes) - -ReactionObservation = _reflection.GeneratedProtocolMessageType('ReactionObservation', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONOBSERVATION, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionObservation) - }) -_sym_db.RegisterMessage(ReactionObservation) - -ReactionWorkup = _reflection.GeneratedProtocolMessageType('ReactionWorkup', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONWORKUP, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionWorkup) - }) -_sym_db.RegisterMessage(ReactionWorkup) - -ReactionOutcome = _reflection.GeneratedProtocolMessageType('ReactionOutcome', (_message.Message,), { - - 'AnalysesEntry' : _reflection.GeneratedProtocolMessageType('AnalysesEntry', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONOUTCOME_ANALYSESENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionOutcome.AnalysesEntry) - }) - , - 'DESCRIPTOR' : _REACTIONOUTCOME, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionOutcome) - }) -_sym_db.RegisterMessage(ReactionOutcome) -_sym_db.RegisterMessage(ReactionOutcome.AnalysesEntry) - -ProductCompound = _reflection.GeneratedProtocolMessageType('ProductCompound', (_message.Message,), { - - 'Texture' : _reflection.GeneratedProtocolMessageType('Texture', (_message.Message,), { - 'DESCRIPTOR' : _PRODUCTCOMPOUND_TEXTURE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductCompound.Texture) - }) - , - - 'FeaturesEntry' : _reflection.GeneratedProtocolMessageType('FeaturesEntry', (_message.Message,), { - 'DESCRIPTOR' : _PRODUCTCOMPOUND_FEATURESENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductCompound.FeaturesEntry) - }) - , - 'DESCRIPTOR' : _PRODUCTCOMPOUND, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductCompound) - }) -_sym_db.RegisterMessage(ProductCompound) -_sym_db.RegisterMessage(ProductCompound.Texture) -_sym_db.RegisterMessage(ProductCompound.FeaturesEntry) - -ProductMeasurement = _reflection.GeneratedProtocolMessageType('ProductMeasurement', (_message.Message,), { - - 'MassSpecMeasurementDetails' : _reflection.GeneratedProtocolMessageType('MassSpecMeasurementDetails', (_message.Message,), { - 'DESCRIPTOR' : _PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductMeasurement.MassSpecMeasurementDetails) - }) - , - - 'Selectivity' : _reflection.GeneratedProtocolMessageType('Selectivity', (_message.Message,), { - 'DESCRIPTOR' : _PRODUCTMEASUREMENT_SELECTIVITY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductMeasurement.Selectivity) - }) - , - 'DESCRIPTOR' : _PRODUCTMEASUREMENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ProductMeasurement) - }) -_sym_db.RegisterMessage(ProductMeasurement) -_sym_db.RegisterMessage(ProductMeasurement.MassSpecMeasurementDetails) -_sym_db.RegisterMessage(ProductMeasurement.Selectivity) - -DateTime = _reflection.GeneratedProtocolMessageType('DateTime', (_message.Message,), { - 'DESCRIPTOR' : _DATETIME, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.DateTime) - }) -_sym_db.RegisterMessage(DateTime) - -Analysis = _reflection.GeneratedProtocolMessageType('Analysis', (_message.Message,), { - - 'DataEntry' : _reflection.GeneratedProtocolMessageType('DataEntry', (_message.Message,), { - 'DESCRIPTOR' : _ANALYSIS_DATAENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Analysis.DataEntry) - }) - , - 'DESCRIPTOR' : _ANALYSIS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Analysis) - }) -_sym_db.RegisterMessage(Analysis) -_sym_db.RegisterMessage(Analysis.DataEntry) - -ReactionProvenance = _reflection.GeneratedProtocolMessageType('ReactionProvenance', (_message.Message,), { - - 'ReactionMetadataEntry' : _reflection.GeneratedProtocolMessageType('ReactionMetadataEntry', (_message.Message,), { - 'DESCRIPTOR' : _REACTIONPROVENANCE_REACTIONMETADATAENTRY, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionProvenance.ReactionMetadataEntry) - }) - , - 'DESCRIPTOR' : _REACTIONPROVENANCE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.ReactionProvenance) - }) -_sym_db.RegisterMessage(ReactionProvenance) -_sym_db.RegisterMessage(ReactionProvenance.ReactionMetadataEntry) - -Person = _reflection.GeneratedProtocolMessageType('Person', (_message.Message,), { - 'DESCRIPTOR' : _PERSON, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Person) - }) -_sym_db.RegisterMessage(Person) - -RecordEvent = _reflection.GeneratedProtocolMessageType('RecordEvent', (_message.Message,), { - 'DESCRIPTOR' : _RECORDEVENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.RecordEvent) - }) -_sym_db.RegisterMessage(RecordEvent) - -Time = _reflection.GeneratedProtocolMessageType('Time', (_message.Message,), { - 'DESCRIPTOR' : _TIME, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Time) - }) -_sym_db.RegisterMessage(Time) - -Mass = _reflection.GeneratedProtocolMessageType('Mass', (_message.Message,), { - 'DESCRIPTOR' : _MASS, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Mass) - }) -_sym_db.RegisterMessage(Mass) - -Moles = _reflection.GeneratedProtocolMessageType('Moles', (_message.Message,), { - 'DESCRIPTOR' : _MOLES, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Moles) - }) -_sym_db.RegisterMessage(Moles) - -Volume = _reflection.GeneratedProtocolMessageType('Volume', (_message.Message,), { - 'DESCRIPTOR' : _VOLUME, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Volume) - }) -_sym_db.RegisterMessage(Volume) - -Concentration = _reflection.GeneratedProtocolMessageType('Concentration', (_message.Message,), { - 'DESCRIPTOR' : _CONCENTRATION, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Concentration) - }) -_sym_db.RegisterMessage(Concentration) - -Pressure = _reflection.GeneratedProtocolMessageType('Pressure', (_message.Message,), { - 'DESCRIPTOR' : _PRESSURE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Pressure) - }) -_sym_db.RegisterMessage(Pressure) - -Temperature = _reflection.GeneratedProtocolMessageType('Temperature', (_message.Message,), { - 'DESCRIPTOR' : _TEMPERATURE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Temperature) - }) -_sym_db.RegisterMessage(Temperature) - -Current = _reflection.GeneratedProtocolMessageType('Current', (_message.Message,), { - 'DESCRIPTOR' : _CURRENT, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Current) - }) -_sym_db.RegisterMessage(Current) - -Voltage = _reflection.GeneratedProtocolMessageType('Voltage', (_message.Message,), { - 'DESCRIPTOR' : _VOLTAGE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Voltage) - }) -_sym_db.RegisterMessage(Voltage) - -Length = _reflection.GeneratedProtocolMessageType('Length', (_message.Message,), { - 'DESCRIPTOR' : _LENGTH, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Length) - }) -_sym_db.RegisterMessage(Length) - -Wavelength = _reflection.GeneratedProtocolMessageType('Wavelength', (_message.Message,), { - 'DESCRIPTOR' : _WAVELENGTH, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Wavelength) - }) -_sym_db.RegisterMessage(Wavelength) - -FlowRate = _reflection.GeneratedProtocolMessageType('FlowRate', (_message.Message,), { - 'DESCRIPTOR' : _FLOWRATE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.FlowRate) - }) -_sym_db.RegisterMessage(FlowRate) - -Percentage = _reflection.GeneratedProtocolMessageType('Percentage', (_message.Message,), { - 'DESCRIPTOR' : _PERCENTAGE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Percentage) - }) -_sym_db.RegisterMessage(Percentage) - -FloatValue = _reflection.GeneratedProtocolMessageType('FloatValue', (_message.Message,), { - 'DESCRIPTOR' : _FLOATVALUE, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.FloatValue) - }) -_sym_db.RegisterMessage(FloatValue) - -Data = _reflection.GeneratedProtocolMessageType('Data', (_message.Message,), { - 'DESCRIPTOR' : _DATA, - '__module__' : 'ord_schema.proto.reaction_pb2' - # @@protoc_insertion_point(class_scope:ord.Data) - }) -_sym_db.RegisterMessage(Data) +DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x1ford-schema/proto/reaction.proto\x12\x03ord\"\xd9\x03\n\x08Reaction\x12,\n\x0bidentifiers\x18\x01 \x03(\x0b\x32\x17.ord.ReactionIdentifier\x12)\n\x06inputs\x18\x02 \x03(\x0b\x32\x19.ord.Reaction.InputsEntry\x12!\n\x05setup\x18\x03 \x01(\x0b\x32\x12.ord.ReactionSetup\x12+\n\nconditions\x18\x04 \x01(\x0b\x32\x17.ord.ReactionConditions\x12!\n\x05notes\x18\x05 \x01(\x0b\x32\x12.ord.ReactionNotes\x12.\n\x0cobservations\x18\x06 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\x01(\t\x12\x0e\n\x06\x66ormat\x18\x07 \x01(\tB\x06\n\x04kindb\x06proto3') +_globals = globals() +_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) +_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'ord_schema.proto.reaction_pb2', _globals) if _descriptor._USE_C_DESCRIPTORS == False: DESCRIPTOR._options = None @@ -693,232 +51,232 @@ _ANALYSIS_DATAENTRY._serialized_options = b'8\001' _REACTIONPROVENANCE_REACTIONMETADATAENTRY._options = None _REACTIONPROVENANCE_REACTIONMETADATAENTRY._serialized_options = b'8\001' - _REACTION._serialized_start=41 - _REACTION._serialized_end=514 - _REACTION_INPUTSENTRY._serialized_start=449 - _REACTION_INPUTSENTRY._serialized_end=514 - _REACTIONIDENTIFIER._serialized_start=517 - _REACTIONIDENTIFIER._serialized_end=812 - _REACTIONIDENTIFIER_REACTIONIDENTIFIERTYPE._serialized_start=658 - _REACTIONIDENTIFIER_REACTIONIDENTIFIERTYPE._serialized_end=798 - _REACTIONINPUT._serialized_start=815 - _REACTIONINPUT._serialized_end=1643 - 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_globals['_PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS_MASSSPECMEASUREMENTTYPE']._serialized_start=13173 + _globals['_PRODUCTMEASUREMENT_MASSSPECMEASUREMENTDETAILS_MASSSPECMEASUREMENTTYPE']._serialized_end=13281 + _globals['_PRODUCTMEASUREMENT_SELECTIVITY']._serialized_start=13322 + _globals['_PRODUCTMEASUREMENT_SELECTIVITY']._serialized_end=13507 + _globals['_PRODUCTMEASUREMENT_SELECTIVITY_SELECTIVITYTYPE']._serialized_start=13421 + _globals['_PRODUCTMEASUREMENT_SELECTIVITY_SELECTIVITYTYPE']._serialized_end=13507 + _globals['_PRODUCTMEASUREMENT_PRODUCTMEASUREMENTTYPE']._serialized_start=13510 + _globals['_PRODUCTMEASUREMENT_PRODUCTMEASUREMENTTYPE']._serialized_end=13666 + _globals['_DATETIME']._serialized_start=13750 + _globals['_DATETIME']._serialized_end=13775 + _globals['_ANALYSIS']._serialized_start=13778 + _globals['_ANALYSIS']._serialized_end=14366 + _globals['_ANALYSIS_DATAENTRY']._serialized_start=14026 + _globals['_ANALYSIS_DATAENTRY']._serialized_end=14080 + _globals['_ANALYSIS_ANALYSISTYPE']._serialized_start=14083 + _globals['_ANALYSIS_ANALYSISTYPE']._serialized_end=14339 + _globals['_REACTIONPROVENANCE']._serialized_start=14369 + _globals['_REACTIONPROVENANCE']._serialized_end=14760 + _globals['_REACTIONPROVENANCE_REACTIONMETADATAENTRY']._serialized_start=14694 + _globals['_REACTIONPROVENANCE_REACTIONMETADATAENTRY']._serialized_end=14760 + _globals['_PERSON']._serialized_start=14762 + _globals['_PERSON']._serialized_end=14854 + _globals['_RECORDEVENT']._serialized_start=14856 + _globals['_RECORDEVENT']._serialized_end=14944 + _globals['_TIME']._serialized_start=14947 + _globals['_TIME']._serialized_end=15128 + _globals['_TIME_TIMEUNIT']._serialized_start=15034 + _globals['_TIME_TIMEUNIT']._serialized_end=15104 + _globals['_MASS']._serialized_start=15131 + _globals['_MASS']._serialized_end=15323 + _globals['_MASS_MASSUNIT']._serialized_start=15218 + _globals['_MASS_MASSUNIT']._serialized_end=15299 + _globals['_MOLES']._serialized_start=15326 + _globals['_MOLES']._serialized_end=15522 + _globals['_MOLES_MOLESUNIT']._serialized_start=15416 + _globals['_MOLES_MOLESUNIT']._serialized_end=15498 + _globals['_VOLUME']._serialized_start=15525 + _globals['_VOLUME']._serialized_end=15729 + _globals['_VOLUME_VOLUMEUNIT']._serialized_start=15618 + _globals['_VOLUME_VOLUMEUNIT']._serialized_end=15705 + _globals['_CONCENTRATION']._serialized_start=15732 + _globals['_CONCENTRATION']._serialized_end=15949 + _globals['_CONCENTRATION_CONCENTRATIONUNIT']._serialized_start=15846 + _globals['_CONCENTRATION_CONCENTRATIONUNIT']._serialized_end=15925 + _globals['_PRESSURE']._serialized_start=15952 + _globals['_PRESSURE']._serialized_end=16199 + _globals['_PRESSURE_PRESSUREUNIT']._serialized_start=16051 + _globals['_PRESSURE_PRESSUREUNIT']._serialized_end=16175 + _globals['_TEMPERATURE']._serialized_start=16202 + _globals['_TEMPERATURE']._serialized_end=16409 + _globals['_TEMPERATURE_TEMPERATUREUNIT']._serialized_start=16310 + _globals['_TEMPERATURE_TEMPERATUREUNIT']._serialized_end=16385 + _globals['_CURRENT']._serialized_start=16412 + _globals['_CURRENT']._serialized_end=16591 + _globals['_CURRENT_CURRENTUNIT']._serialized_start=16508 + _globals['_CURRENT_CURRENTUNIT']._serialized_end=16567 + _globals['_VOLTAGE']._serialized_start=16594 + _globals['_VOLTAGE']._serialized_end=16769 + _globals['_VOLTAGE_VOLTAGEUNIT']._serialized_start=16690 + _globals['_VOLTAGE_VOLTAGEUNIT']._serialized_end=16745 + _globals['_LENGTH']._serialized_start=16772 + _globals['_LENGTH']._serialized_end=16981 + _globals['_LENGTH_LENGTHUNIT']._serialized_start=16865 + _globals['_LENGTH_LENGTHUNIT']._serialized_end=16957 + _globals['_WAVELENGTH']._serialized_start=16984 + _globals['_WAVELENGTH']._serialized_end=17177 + _globals['_WAVELENGTH_WAVELENGTHUNIT']._serialized_start=17089 + _globals['_WAVELENGTH_WAVELENGTHUNIT']._serialized_end=17153 + _globals['_FLOWRATE']._serialized_start=17180 + _globals['_FLOWRATE']._serialized_end=17468 + _globals['_FLOWRATE_FLOWRATEUNIT']._serialized_start=17280 + _globals['_FLOWRATE_FLOWRATEUNIT']._serialized_end=17444 + _globals['_PERCENTAGE']._serialized_start=17470 + _globals['_PERCENTAGE']._serialized_end=17550 + _globals['_FLOATVALUE']._serialized_start=17552 + _globals['_FLOATVALUE']._serialized_end=17632 + _globals['_DATA']._serialized_start=17635 + _globals['_DATA']._serialized_end=17796 # @@protoc_insertion_point(module_scope) diff --git a/ord_schema/proto/test_pb2.py b/ord_schema/proto/test_pb2.py index b2b8cfc5..9a8e9cfe 100644 --- a/ord_schema/proto/test_pb2.py +++ b/ord_schema/proto/test_pb2.py @@ -16,10 +16,9 @@ # Generated by the protocol buffer compiler. DO NOT EDIT! # source: ord-schema/proto/test.proto """Generated protocol buffer code.""" +from google.protobuf.internal import builder as _builder from google.protobuf import descriptor as _descriptor from google.protobuf import descriptor_pool as _descriptor_pool -from google.protobuf import message as _message -from google.protobuf import reflection as _reflection from google.protobuf import symbol_database as _symbol_database # @@protoc_insertion_point(imports) @@ -30,119 +29,9 @@ DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x1bord-schema/proto/test.proto\x12\x08ord_test\"\xaf\x01\n\x06Scalar\x12\x13\n\x0bint32_value\x18\x01 \x01(\x05\x12\x13\n\x0bint64_value\x18\x02 \x01(\x03\x12\x18\n\x0b\x66loat_value\x18\x03 \x01(\x02H\x00\x88\x01\x01\x12\x14\n\x0cstring_value\x18\x04 \x01(\t\x12\x13\n\x0b\x62ytes_value\x18\x05 \x01(\x0c\x12\x17\n\nbool_value\x18\x06 \x01(\x08H\x01\x88\x01\x01\x42\x0e\n\x0c_float_valueB\r\n\x0b_bool_value\" \n\x0eRepeatedScalar\x12\x0e\n\x06values\x18\x01 \x03(\x02\"f\n\x04\x45num\x12(\n\x05value\x18\x01 \x01(\x0e\x32\x19.ord_test.Enum.EnumValues\"4\n\nEnumValues\x12\x0f\n\x0bUNSPECIFIED\x10\x00\x12\t\n\x05\x46IRST\x10\x01\x12\n\n\x06SECOND\x10\x02\"w\n\x0cRepeatedEnum\x12\x31\n\x06values\x18\x01 \x03(\x0e\x32!.ord_test.RepeatedEnum.EnumValues\"4\n\nEnumValues\x12\x0f\n\x0bUNSPECIFIED\x10\x00\x12\t\n\x05\x46IRST\x10\x01\x12\n\n\x06SECOND\x10\x02\"V\n\x06Nested\x12%\n\x05\x63hild\x18\x01 \x01(\x0b\x32\x16.ord_test.Nested.Child\x1a%\n\x05\x43hild\x12\x12\n\x05value\x18\x01 \x01(\x02H\x00\x88\x01\x01\x42\x08\n\x06_value\"i\n\x0eRepeatedNested\x12\x30\n\x08\x63hildren\x18\x01 \x03(\x0b\x32\x1e.ord_test.RepeatedNested.Child\x1a%\n\x05\x43hild\x12\x12\n\x05value\x18\x01 \x01(\x02H\x00\x88\x01\x01\x42\x08\n\x06_value\"_\n\x03Map\x12)\n\x06values\x18\x01 \x03(\x0b\x32\x19.ord_test.Map.ValuesEntry\x1a-\n\x0bValuesEntry\x12\x0b\n\x03key\x18\x01 \x01(\t\x12\r\n\x05value\x18\x02 \x01(\x02:\x02\x38\x01\"\xb3\x01\n\tMapNested\x12\x33\n\x08\x63hildren\x18\x01 \x03(\x0b\x32!.ord_test.MapNested.ChildrenEntry\x1a%\n\x05\x43hild\x12\x12\n\x05value\x18\x01 \x01(\x02H\x00\x88\x01\x01\x42\x08\n\x06_value\x1aJ\n\rChildrenEntry\x12\x0b\n\x03key\x18\x01 \x01(\t\x12(\n\x05value\x18\x02 \x01(\x0b\x32\x19.ord_test.MapNested.Child:\x02\x38\x01\x62\x06proto3') - - -_SCALAR = DESCRIPTOR.message_types_by_name['Scalar'] -_REPEATEDSCALAR = DESCRIPTOR.message_types_by_name['RepeatedScalar'] -_ENUM = DESCRIPTOR.message_types_by_name['Enum'] -_REPEATEDENUM = DESCRIPTOR.message_types_by_name['RepeatedEnum'] -_NESTED = DESCRIPTOR.message_types_by_name['Nested'] -_NESTED_CHILD = _NESTED.nested_types_by_name['Child'] -_REPEATEDNESTED = DESCRIPTOR.message_types_by_name['RepeatedNested'] -_REPEATEDNESTED_CHILD = _REPEATEDNESTED.nested_types_by_name['Child'] -_MAP = DESCRIPTOR.message_types_by_name['Map'] -_MAP_VALUESENTRY = _MAP.nested_types_by_name['ValuesEntry'] -_MAPNESTED = DESCRIPTOR.message_types_by_name['MapNested'] -_MAPNESTED_CHILD = _MAPNESTED.nested_types_by_name['Child'] -_MAPNESTED_CHILDRENENTRY = _MAPNESTED.nested_types_by_name['ChildrenEntry'] -_ENUM_ENUMVALUES = _ENUM.enum_types_by_name['EnumValues'] -_REPEATEDENUM_ENUMVALUES = _REPEATEDENUM.enum_types_by_name['EnumValues'] -Scalar = _reflection.GeneratedProtocolMessageType('Scalar', (_message.Message,), { - 'DESCRIPTOR' : _SCALAR, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Scalar) - }) -_sym_db.RegisterMessage(Scalar) - -RepeatedScalar = _reflection.GeneratedProtocolMessageType('RepeatedScalar', (_message.Message,), { - 'DESCRIPTOR' : _REPEATEDSCALAR, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.RepeatedScalar) - }) -_sym_db.RegisterMessage(RepeatedScalar) - -Enum = _reflection.GeneratedProtocolMessageType('Enum', (_message.Message,), { - 'DESCRIPTOR' : _ENUM, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Enum) - }) -_sym_db.RegisterMessage(Enum) - -RepeatedEnum = _reflection.GeneratedProtocolMessageType('RepeatedEnum', (_message.Message,), { - 'DESCRIPTOR' : _REPEATEDENUM, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.RepeatedEnum) - }) -_sym_db.RegisterMessage(RepeatedEnum) - -Nested = _reflection.GeneratedProtocolMessageType('Nested', (_message.Message,), { - - 'Child' : _reflection.GeneratedProtocolMessageType('Child', (_message.Message,), { - 'DESCRIPTOR' : _NESTED_CHILD, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Nested.Child) - }) - , - 'DESCRIPTOR' : _NESTED, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Nested) - }) -_sym_db.RegisterMessage(Nested) -_sym_db.RegisterMessage(Nested.Child) - -RepeatedNested = _reflection.GeneratedProtocolMessageType('RepeatedNested', (_message.Message,), { - - 'Child' : _reflection.GeneratedProtocolMessageType('Child', (_message.Message,), { - 'DESCRIPTOR' : _REPEATEDNESTED_CHILD, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.RepeatedNested.Child) - }) - , - 'DESCRIPTOR' : _REPEATEDNESTED, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.RepeatedNested) - }) -_sym_db.RegisterMessage(RepeatedNested) -_sym_db.RegisterMessage(RepeatedNested.Child) - -Map = _reflection.GeneratedProtocolMessageType('Map', (_message.Message,), { - - 'ValuesEntry' : _reflection.GeneratedProtocolMessageType('ValuesEntry', (_message.Message,), { - 'DESCRIPTOR' : _MAP_VALUESENTRY, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Map.ValuesEntry) - }) - , - 'DESCRIPTOR' : _MAP, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.Map) - }) -_sym_db.RegisterMessage(Map) -_sym_db.RegisterMessage(Map.ValuesEntry) - -MapNested = _reflection.GeneratedProtocolMessageType('MapNested', (_message.Message,), { - - 'Child' : _reflection.GeneratedProtocolMessageType('Child', (_message.Message,), { - 'DESCRIPTOR' : _MAPNESTED_CHILD, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.MapNested.Child) - }) - , - - 'ChildrenEntry' : _reflection.GeneratedProtocolMessageType('ChildrenEntry', (_message.Message,), { - 'DESCRIPTOR' : _MAPNESTED_CHILDRENENTRY, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.MapNested.ChildrenEntry) - }) - , - 'DESCRIPTOR' : _MAPNESTED, - '__module__' : 'ord_schema.proto.test_pb2' - # @@protoc_insertion_point(class_scope:ord_test.MapNested) - }) -_sym_db.RegisterMessage(MapNested) -_sym_db.RegisterMessage(MapNested.Child) -_sym_db.RegisterMessage(MapNested.ChildrenEntry) - +_globals = globals() +_builder.BuildMessageAndEnumDescriptors(DESCRIPTOR, _globals) +_builder.BuildTopDescriptorsAndMessages(DESCRIPTOR, 'ord_schema.proto.test_pb2', _globals) if _descriptor._USE_C_DESCRIPTORS == False: DESCRIPTOR._options = None @@ -150,34 +39,34 @@ _MAP_VALUESENTRY._serialized_options = b'8\001' _MAPNESTED_CHILDRENENTRY._options = None _MAPNESTED_CHILDRENENTRY._serialized_options = b'8\001' - _SCALAR._serialized_start=42 - _SCALAR._serialized_end=217 - _REPEATEDSCALAR._serialized_start=219 - _REPEATEDSCALAR._serialized_end=251 - _ENUM._serialized_start=253 - _ENUM._serialized_end=355 - _ENUM_ENUMVALUES._serialized_start=303 - _ENUM_ENUMVALUES._serialized_end=355 - _REPEATEDENUM._serialized_start=357 - _REPEATEDENUM._serialized_end=476 - _REPEATEDENUM_ENUMVALUES._serialized_start=303 - _REPEATEDENUM_ENUMVALUES._serialized_end=355 - _NESTED._serialized_start=478 - _NESTED._serialized_end=564 - _NESTED_CHILD._serialized_start=527 - _NESTED_CHILD._serialized_end=564 - _REPEATEDNESTED._serialized_start=566 - _REPEATEDNESTED._serialized_end=671 - _REPEATEDNESTED_CHILD._serialized_start=527 - _REPEATEDNESTED_CHILD._serialized_end=564 - _MAP._serialized_start=673 - _MAP._serialized_end=768 - _MAP_VALUESENTRY._serialized_start=723 - _MAP_VALUESENTRY._serialized_end=768 - _MAPNESTED._serialized_start=771 - _MAPNESTED._serialized_end=950 - _MAPNESTED_CHILD._serialized_start=527 - _MAPNESTED_CHILD._serialized_end=564 - _MAPNESTED_CHILDRENENTRY._serialized_start=876 - _MAPNESTED_CHILDRENENTRY._serialized_end=950 + _globals['_SCALAR']._serialized_start=42 + _globals['_SCALAR']._serialized_end=217 + _globals['_REPEATEDSCALAR']._serialized_start=219 + _globals['_REPEATEDSCALAR']._serialized_end=251 + _globals['_ENUM']._serialized_start=253 + _globals['_ENUM']._serialized_end=355 + _globals['_ENUM_ENUMVALUES']._serialized_start=303 + _globals['_ENUM_ENUMVALUES']._serialized_end=355 + _globals['_REPEATEDENUM']._serialized_start=357 + _globals['_REPEATEDENUM']._serialized_end=476 + _globals['_REPEATEDENUM_ENUMVALUES']._serialized_start=303 + _globals['_REPEATEDENUM_ENUMVALUES']._serialized_end=355 + _globals['_NESTED']._serialized_start=478 + _globals['_NESTED']._serialized_end=564 + _globals['_NESTED_CHILD']._serialized_start=527 + _globals['_NESTED_CHILD']._serialized_end=564 + _globals['_REPEATEDNESTED']._serialized_start=566 + _globals['_REPEATEDNESTED']._serialized_end=671 + _globals['_REPEATEDNESTED_CHILD']._serialized_start=527 + _globals['_REPEATEDNESTED_CHILD']._serialized_end=564 + _globals['_MAP']._serialized_start=673 + _globals['_MAP']._serialized_end=768 + _globals['_MAP_VALUESENTRY']._serialized_start=723 + _globals['_MAP_VALUESENTRY']._serialized_end=768 + _globals['_MAPNESTED']._serialized_start=771 + _globals['_MAPNESTED']._serialized_end=950 + _globals['_MAPNESTED_CHILD']._serialized_start=527 + _globals['_MAPNESTED_CHILD']._serialized_end=564 + _globals['_MAPNESTED_CHILDRENENTRY']._serialized_start=876 + _globals['_MAPNESTED_CHILDRENENTRY']._serialized_end=950 # @@protoc_insertion_point(module_scope) diff --git a/ord_schema/validations.py b/ord_schema/validations.py index 415b1cae..d57cdbea 100644 --- a/ord_schema/validations.py +++ b/ord_schema/validations.py @@ -785,13 +785,14 @@ def validate_reaction_outcome(message: reaction_pb2.ReactionOutcome): # pylint: disable=singleton-comparison # *Usually* there should be at most one PRODUCT & is_desired_product ndp = sum( - product.is_desired_product for product in message.products - if product.reaction_role == reaction_pb2.ReactionRole.ReactionRoleType.PRODUCT + product.is_desired_product + for product in message.products + if product.reaction_role == reaction_pb2.ReactionRole.ReactionRoleType.PRODUCT ) if ndp > 1: warnings.warn( f"Usually at most one (reaction_role == PRODUCT & is_desired_product) product, but we have: {ndp}", - ValidationWarning + ValidationWarning, ) # Check key values for product analyses @@ -832,6 +833,7 @@ def validate_product_compound(message: reaction_pb2.ProductCompound): if message.reaction_role == reaction_pb2.ReactionRole.ReactionRoleType.SIDE_PRODUCT: warnings.warn("a product cannot be (SIDE_PRODUCT & is_desired_product)", ValidationError) + def validate_texture(message: reaction_pb2.ProductCompound.Texture): check_type_and_details(message) diff --git a/proto/reaction.proto b/proto/reaction.proto index d9b08100..4430be36 100644 --- a/proto/reaction.proto +++ b/proto/reaction.proto @@ -289,7 +289,8 @@ message ReactionRole { PRODUCT = 8; // When there is one intended chemical equation: // - Set `is_desired_product=True` to indicate a desired product. - // - Use BYPRODUCT to indicate a chemical species that is an expected result of the reaction but is not the product of interest. + // - Use BYPRODUCT to indicate a chemical species that is an expected result + // of the reaction but is not the product of interest. // - Use SIDE_PRODUCT to indicate the product of a side reaction. // - See https://doi.org/10.1021/op300317g for a discussion of these terms. BYPRODUCT = 9; From d9f8b589b4509e8e4d832af412e9944426deabd4 Mon Sep 17 00:00:00 2001 From: qai Date: Sun, 9 Jul 2023 21:46:55 -0400 Subject: [PATCH 5/5] `compile_proto_wrappers.sh && format.sh` - libprotoc 22.3 - Ubuntu clang-format version 14.0.0-1ubuntu1 - go version go1.20.5 linux/amd64 - Ubuntu clang-format version 14.0.0-1ubuntu1 --- js/ord-schema/proto/reaction_pb.js | 50 +++++++++++- ord_schema/proto/reaction_pb2.py | 124 ++++++++++++++--------------- 2 files changed, 111 insertions(+), 63 deletions(-) diff --git a/js/ord-schema/proto/reaction_pb.js b/js/ord-schema/proto/reaction_pb.js index ab8bb7c4..44bb9046 100644 --- a/js/ord-schema/proto/reaction_pb.js +++ b/js/ord-schema/proto/reaction_pb.js @@ -15191,7 +15191,8 @@ proto.ord.ReactionProvenance.toObject = function(includeInstance, msg) { recordCreated: (f = msg.getRecordCreated()) && proto.ord.RecordEvent.toObject(includeInstance, f), recordModifiedList: jspb.Message.toObjectList(msg.getRecordModifiedList(), proto.ord.RecordEvent.toObject, includeInstance), - reactionMetadataMap: (f = msg.getReactionMetadataMap()) ? f.toObject(includeInstance, proto.ord.Data.toObject) : [] + reactionMetadataMap: (f = msg.getReactionMetadataMap()) ? f.toObject(includeInstance, proto.ord.Data.toObject) : [], + isMined: jspb.Message.getBooleanFieldWithDefault(msg, 10, false) }; if (includeInstance) { @@ -15270,6 +15271,10 @@ proto.ord.ReactionProvenance.deserializeBinaryFromReader = function(msg, reader) jspb.Map.deserializeBinary(message, reader, jspb.BinaryReader.prototype.readString, jspb.BinaryReader.prototype.readMessage, proto.ord.Data.deserializeBinaryFromReader, "", new proto.ord.Data()); }); break; + case 10: + var value = /** @type {boolean} */ (reader.readBool()); + msg.setIsMined(value); + break; default: reader.skipField(); break; @@ -15363,6 +15368,13 @@ proto.ord.ReactionProvenance.serializeBinaryToWriter = function(message, writer) if (f && f.getLength() > 0) { f.serializeBinary(9, writer, jspb.BinaryWriter.prototype.writeString, jspb.BinaryWriter.prototype.writeMessage, proto.ord.Data.serializeBinaryToWriter); } + f = /** @type {boolean} */ (jspb.Message.getField(message, 10)); + if (f != null) { + writer.writeBool( + 10, + f + ); + } }; @@ -15610,6 +15622,42 @@ proto.ord.ReactionProvenance.prototype.clearReactionMetadataMap = function() { }; +/** + * optional bool is_mined = 10; + * @return {boolean} + */ +proto.ord.ReactionProvenance.prototype.getIsMined = function() { + return /** @type {boolean} */ (jspb.Message.getBooleanFieldWithDefault(this, 10, false)); +}; + + +/** + * @param {boolean} value + * @return {!proto.ord.ReactionProvenance} returns this + */ +proto.ord.ReactionProvenance.prototype.setIsMined = function(value) { + return jspb.Message.setField(this, 10, value); +}; + + +/** + * Clears the field making it undefined. + * @return {!proto.ord.ReactionProvenance} returns this + */ +proto.ord.ReactionProvenance.prototype.clearIsMined = function() { + return jspb.Message.setField(this, 10, undefined); +}; + + +/** + * Returns whether this field is set. + * @return {boolean} + */ +proto.ord.ReactionProvenance.prototype.hasIsMined = function() { + return jspb.Message.getField(this, 10) != null; +}; + + diff --git a/ord_schema/proto/reaction_pb2.py b/ord_schema/proto/reaction_pb2.py index 395264aa..c3eb9c9d 100644 --- a/ord_schema/proto/reaction_pb2.py +++ b/ord_schema/proto/reaction_pb2.py @@ -27,7 +27,7 @@ -DESCRIPTOR = _descriptor_pool.Default().AddSerializedFile(b'\n\x1ford-schema/proto/reaction.proto\x12\x03ord\"\xd9\x03\n\x08Reaction\x12,\n\x0bidentifiers\x18\x01 \x03(\x0b\x32\x17.ord.ReactionIdentifier\x12)\n\x06inputs\x18\x02 \x03(\x0b\x32\x19.ord.Reaction.InputsEntry\x12!\n\x05setup\x18\x03 \x01(\x0b\x32\x12.ord.ReactionSetup\x12+\n\nconditions\x18\x04 \x01(\x0b\x32\x17.ord.ReactionConditions\x12!\n\x05notes\x18\x05 \x01(\x0b\x32\x12.ord.ReactionNotes\x12.\n\x0cobservations\x18\x06 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_globals['_LENGTH']._serialized_end=17017 + _globals['_LENGTH_LENGTHUNIT']._serialized_start=16901 + _globals['_LENGTH_LENGTHUNIT']._serialized_end=16993 + _globals['_WAVELENGTH']._serialized_start=17020 + _globals['_WAVELENGTH']._serialized_end=17213 + _globals['_WAVELENGTH_WAVELENGTHUNIT']._serialized_start=17125 + _globals['_WAVELENGTH_WAVELENGTHUNIT']._serialized_end=17189 + _globals['_FLOWRATE']._serialized_start=17216 + _globals['_FLOWRATE']._serialized_end=17504 + _globals['_FLOWRATE_FLOWRATEUNIT']._serialized_start=17316 + _globals['_FLOWRATE_FLOWRATEUNIT']._serialized_end=17480 + _globals['_PERCENTAGE']._serialized_start=17506 + _globals['_PERCENTAGE']._serialized_end=17586 + _globals['_FLOATVALUE']._serialized_start=17588 + _globals['_FLOATVALUE']._serialized_end=17668 + _globals['_DATA']._serialized_start=17671 + _globals['_DATA']._serialized_end=17832 # @@protoc_insertion_point(module_scope)