ord-schema 0.3.40

package/README.md

@@ -0,0 +1,3 @@
+# JavaScript wrappers for the Open Reaction Database schema
+
+See https://open-reaction-database.org for more information.

package/index.js

@@ -0,0 +1,19 @@
+/**
+ * Copyright 2022 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.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+"use strict";
+exports.dataset_pb = require('./proto/dataset_pb');
+exports.reaction_pb = require('./proto/reaction_pb');

package/package.json

@@ -0,0 +1,23 @@
+{
+  "name": "ord-schema",
+  "version": "0.3.40",
+  "description": "Schema for the Open Reaction Database",
+  "main": "index.js",
+  "scripts": {
+    "test": "jest"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/open-reaction-database/ord-schema.git"
+  },
+  "author": "Open Reaction Database Project Authors",
+  "license": "Apache-2.0",
+  "bugs": {
+    "url": "https://github.com/open-reaction-database/ord-schema/issues"
+  },
+  "homepage": "https://open-reaction-database.org",
+  "dependencies": {
+    "google-protobuf": "<3.20",
+    "jest": "^29.3.1"
+  }
+}

package/proto/dataset_pb.js

@@ -0,0 +1,626 @@
+/**
+ * Copyright 2022 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.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+// source: ord-schema/proto/dataset.proto
+/**
+ * @fileoverview
+ * @enhanceable
+ * @suppress {missingRequire} reports error on implicit type usages.
+ * @suppress {messageConventions} JS Compiler reports an error if a variable or
+ *     field starts with 'MSG_' and isn't a translatable message.
+ * @public
+ */
+// GENERATED CODE -- DO NOT EDIT!
+/* eslint-disable */
+// @ts-nocheck
+
+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 ord$schema_proto_reaction_pb = require('../../ord-schema/proto/reaction_pb.js');
+goog.object.extend(proto, ord$schema_proto_reaction_pb);
+goog.exportSymbol('proto.ord.Dataset', null, global);
+goog.exportSymbol('proto.ord.DatasetExample', null, global);
+/**
+ * Generated by JsPbCodeGenerator.
+ * @param {Array=} opt_data Optional initial data array, typically from a
+ * server response, or constructed directly in Javascript. The array is used
+ * in place and becomes part of the constructed object. It is not cloned.
+ * If no data is provided, the constructed object will be empty, but still
+ * valid.
+ * @extends {jspb.Message}
+ * @constructor
+ */
+proto.ord.Dataset = function(opt_data) {
+  jspb.Message.initialize(this, opt_data, 0, -1, proto.ord.Dataset.repeatedFields_, null);
+};
+goog.inherits(proto.ord.Dataset, jspb.Message);
+if (goog.DEBUG && !COMPILED) {
+  /**
+   * @public
+   * @override
+   */
+  proto.ord.Dataset.displayName = 'proto.ord.Dataset';
+}
+/**
+ * Generated by JsPbCodeGenerator.
+ * @param {Array=} opt_data Optional initial data array, typically from a
+ * server response, or constructed directly in Javascript. The array is used
+ * in place and becomes part of the constructed object. It is not cloned.
+ * If no data is provided, the constructed object will be empty, but still
+ * valid.
+ * @extends {jspb.Message}
+ * @constructor
+ */
+proto.ord.DatasetExample = function(opt_data) {
+  jspb.Message.initialize(this, opt_data, 0, -1, null, null);
+};
+goog.inherits(proto.ord.DatasetExample, jspb.Message);
+if (goog.DEBUG && !COMPILED) {
+  /**
+   * @public
+   * @override
+   */
+  proto.ord.DatasetExample.displayName = 'proto.ord.DatasetExample';
+}
+
+/**
+ * List of repeated fields within this message type.
+ * @private {!Array<number>}
+ * @const
+ */
+proto.ord.Dataset.repeatedFields_ = [3,4];
+
+
+
+if (jspb.Message.GENERATE_TO_OBJECT) {
+/**
+ * Creates an object representation of this proto.
+ * Field names that are reserved in JavaScript and will be renamed to pb_name.
+ * Optional fields that are not set will be set to undefined.
+ * To access a reserved field use, foo.pb_<name>, eg, foo.pb_default.
+ * For the list of reserved names please see:
+ *     net/proto2/compiler/js/internal/generator.cc#kKeyword.
+ * @param {boolean=} opt_includeInstance Deprecated. whether to include the
+ *     JSPB instance for transitional soy proto support:
+ *     http://goto/soy-param-migration
+ * @return {!Object}
+ */
+proto.ord.Dataset.prototype.toObject = function(opt_includeInstance) {
+  return proto.ord.Dataset.toObject(opt_includeInstance, this);
+};
+
+
+/**
+ * Static version of the {@see toObject} method.
+ * @param {boolean|undefined} includeInstance Deprecated. Whether to include
+ *     the JSPB instance for transitional soy proto support:
+ *     http://goto/soy-param-migration
+ * @param {!proto.ord.Dataset} msg The msg instance to transform.
+ * @return {!Object}
+ * @suppress {unusedLocalVariables} f is only used for nested messages
+ */
+proto.ord.Dataset.toObject = function(includeInstance, msg) {
+  var f, obj = {
+    name: jspb.Message.getFieldWithDefault(msg, 1, ""),
+    description: jspb.Message.getFieldWithDefault(msg, 2, ""),
+    reactionsList: jspb.Message.toObjectList(msg.getReactionsList(),
+    ord$schema_proto_reaction_pb.Reaction.toObject, includeInstance),
+    reactionIdsList: (f = jspb.Message.getRepeatedField(msg, 4)) == null ? undefined : f,
+    datasetId: jspb.Message.getFieldWithDefault(msg, 5, "")
+  };
+
+  if (includeInstance) {
+    obj.$jspbMessageInstance = msg;
+  }
+  return obj;
+};
+}
+
+
+/**
+ * Deserializes binary data (in protobuf wire format).
+ * @param {jspb.ByteSource} bytes The bytes to deserialize.
+ * @return {!proto.ord.Dataset}
+ */
+proto.ord.Dataset.deserializeBinary = function(bytes) {
+  var reader = new jspb.BinaryReader(bytes);
+  var msg = new proto.ord.Dataset;
+  return proto.ord.Dataset.deserializeBinaryFromReader(msg, reader);
+};
+
+
+/**
+ * Deserializes binary data (in protobuf wire format) from the
+ * given reader into the given message object.
+ * @param {!proto.ord.Dataset} msg The message object to deserialize into.
+ * @param {!jspb.BinaryReader} reader The BinaryReader to use.
+ * @return {!proto.ord.Dataset}
+ */
+proto.ord.Dataset.deserializeBinaryFromReader = function(msg, reader) {
+  while (reader.nextField()) {
+    if (reader.isEndGroup()) {
+      break;
+    }
+    var field = reader.getFieldNumber();
+    switch (field) {
+    case 1:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setName(value);
+      break;
+    case 2:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setDescription(value);
+      break;
+    case 3:
+      var value = new ord$schema_proto_reaction_pb.Reaction;
+      reader.readMessage(value,ord$schema_proto_reaction_pb.Reaction.deserializeBinaryFromReader);
+      msg.addReactions(value);
+      break;
+    case 4:
+      var value = /** @type {string} */ (reader.readString());
+      msg.addReactionIds(value);
+      break;
+    case 5:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setDatasetId(value);
+      break;
+    default:
+      reader.skipField();
+      break;
+    }
+  }
+  return msg;
+};
+
+
+/**
+ * Serializes the message to binary data (in protobuf wire format).
+ * @return {!Uint8Array}
+ */
+proto.ord.Dataset.prototype.serializeBinary = function() {
+  var writer = new jspb.BinaryWriter();
+  proto.ord.Dataset.serializeBinaryToWriter(this, writer);
+  return writer.getResultBuffer();
+};
+
+
+/**
+ * Serializes the given message to binary data (in protobuf wire
+ * format), writing to the given BinaryWriter.
+ * @param {!proto.ord.Dataset} message
+ * @param {!jspb.BinaryWriter} writer
+ * @suppress {unusedLocalVariables} f is only used for nested messages
+ */
+proto.ord.Dataset.serializeBinaryToWriter = function(message, writer) {
+  var f = undefined;
+  f = message.getName();
+  if (f.length > 0) {
+    writer.writeString(
+      1,
+      f
+    );
+  }
+  f = message.getDescription();
+  if (f.length > 0) {
+    writer.writeString(
+      2,
+      f
+    );
+  }
+  f = message.getReactionsList();
+  if (f.length > 0) {
+    writer.writeRepeatedMessage(
+      3,
+      f,
+      ord$schema_proto_reaction_pb.Reaction.serializeBinaryToWriter
+    );
+  }
+  f = message.getReactionIdsList();
+  if (f.length > 0) {
+    writer.writeRepeatedString(
+      4,
+      f
+    );
+  }
+  f = message.getDatasetId();
+  if (f.length > 0) {
+    writer.writeString(
+      5,
+      f
+    );
+  }
+};
+
+
+/**
+ * optional string name = 1;
+ * @return {string}
+ */
+proto.ord.Dataset.prototype.getName = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 1, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.setName = function(value) {
+  return jspb.Message.setProto3StringField(this, 1, value);
+};
+
+
+/**
+ * optional string description = 2;
+ * @return {string}
+ */
+proto.ord.Dataset.prototype.getDescription = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 2, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.setDescription = function(value) {
+  return jspb.Message.setProto3StringField(this, 2, value);
+};
+
+
+/**
+ * repeated Reaction reactions = 3;
+ * @return {!Array<!proto.ord.Reaction>}
+ */
+proto.ord.Dataset.prototype.getReactionsList = function() {
+  return /** @type{!Array<!proto.ord.Reaction>} */ (
+    jspb.Message.getRepeatedWrapperField(this, ord$schema_proto_reaction_pb.Reaction, 3));
+};
+
+
+/**
+ * @param {!Array<!proto.ord.Reaction>} value
+ * @return {!proto.ord.Dataset} returns this
+*/
+proto.ord.Dataset.prototype.setReactionsList = function(value) {
+  return jspb.Message.setRepeatedWrapperField(this, 3, value);
+};
+
+
+/**
+ * @param {!proto.ord.Reaction=} opt_value
+ * @param {number=} opt_index
+ * @return {!proto.ord.Reaction}
+ */
+proto.ord.Dataset.prototype.addReactions = function(opt_value, opt_index) {
+  return jspb.Message.addToRepeatedWrapperField(this, 3, opt_value, proto.ord.Reaction, opt_index);
+};
+
+
+/**
+ * Clears the list making it empty but non-null.
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.clearReactionsList = function() {
+  return this.setReactionsList([]);
+};
+
+
+/**
+ * repeated string reaction_ids = 4;
+ * @return {!Array<string>}
+ */
+proto.ord.Dataset.prototype.getReactionIdsList = function() {
+  return /** @type {!Array<string>} */ (jspb.Message.getRepeatedField(this, 4));
+};
+
+
+/**
+ * @param {!Array<string>} value
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.setReactionIdsList = function(value) {
+  return jspb.Message.setField(this, 4, value || []);
+};
+
+
+/**
+ * @param {string} value
+ * @param {number=} opt_index
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.addReactionIds = function(value, opt_index) {
+  return jspb.Message.addToRepeatedField(this, 4, value, opt_index);
+};
+
+
+/**
+ * Clears the list making it empty but non-null.
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.clearReactionIdsList = function() {
+  return this.setReactionIdsList([]);
+};
+
+
+/**
+ * optional string dataset_id = 5;
+ * @return {string}
+ */
+proto.ord.Dataset.prototype.getDatasetId = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 5, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.Dataset} returns this
+ */
+proto.ord.Dataset.prototype.setDatasetId = function(value) {
+  return jspb.Message.setProto3StringField(this, 5, value);
+};
+
+
+
+
+
+if (jspb.Message.GENERATE_TO_OBJECT) {
+/**
+ * Creates an object representation of this proto.
+ * Field names that are reserved in JavaScript and will be renamed to pb_name.
+ * Optional fields that are not set will be set to undefined.
+ * To access a reserved field use, foo.pb_<name>, eg, foo.pb_default.
+ * For the list of reserved names please see:
+ *     net/proto2/compiler/js/internal/generator.cc#kKeyword.
+ * @param {boolean=} opt_includeInstance Deprecated. whether to include the
+ *     JSPB instance for transitional soy proto support:
+ *     http://goto/soy-param-migration
+ * @return {!Object}
+ */
+proto.ord.DatasetExample.prototype.toObject = function(opt_includeInstance) {
+  return proto.ord.DatasetExample.toObject(opt_includeInstance, this);
+};
+
+
+/**
+ * Static version of the {@see toObject} method.
+ * @param {boolean|undefined} includeInstance Deprecated. Whether to include
+ *     the JSPB instance for transitional soy proto support:
+ *     http://goto/soy-param-migration
+ * @param {!proto.ord.DatasetExample} msg The msg instance to transform.
+ * @return {!Object}
+ * @suppress {unusedLocalVariables} f is only used for nested messages
+ */
+proto.ord.DatasetExample.toObject = function(includeInstance, msg) {
+  var f, obj = {
+    datasetId: jspb.Message.getFieldWithDefault(msg, 1, ""),
+    description: jspb.Message.getFieldWithDefault(msg, 2, ""),
+    url: jspb.Message.getFieldWithDefault(msg, 3, ""),
+    created: (f = msg.getCreated()) && ord$schema_proto_reaction_pb.RecordEvent.toObject(includeInstance, f)
+  };
+
+  if (includeInstance) {
+    obj.$jspbMessageInstance = msg;
+  }
+  return obj;
+};
+}
+
+
+/**
+ * Deserializes binary data (in protobuf wire format).
+ * @param {jspb.ByteSource} bytes The bytes to deserialize.
+ * @return {!proto.ord.DatasetExample}
+ */
+proto.ord.DatasetExample.deserializeBinary = function(bytes) {
+  var reader = new jspb.BinaryReader(bytes);
+  var msg = new proto.ord.DatasetExample;
+  return proto.ord.DatasetExample.deserializeBinaryFromReader(msg, reader);
+};
+
+
+/**
+ * Deserializes binary data (in protobuf wire format) from the
+ * given reader into the given message object.
+ * @param {!proto.ord.DatasetExample} msg The message object to deserialize into.
+ * @param {!jspb.BinaryReader} reader The BinaryReader to use.
+ * @return {!proto.ord.DatasetExample}
+ */
+proto.ord.DatasetExample.deserializeBinaryFromReader = function(msg, reader) {
+  while (reader.nextField()) {
+    if (reader.isEndGroup()) {
+      break;
+    }
+    var field = reader.getFieldNumber();
+    switch (field) {
+    case 1:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setDatasetId(value);
+      break;
+    case 2:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setDescription(value);
+      break;
+    case 3:
+      var value = /** @type {string} */ (reader.readString());
+      msg.setUrl(value);
+      break;
+    case 4:
+      var value = new ord$schema_proto_reaction_pb.RecordEvent;
+      reader.readMessage(value,ord$schema_proto_reaction_pb.RecordEvent.deserializeBinaryFromReader);
+      msg.setCreated(value);
+      break;
+    default:
+      reader.skipField();
+      break;
+    }
+  }
+  return msg;
+};
+
+
+/**
+ * Serializes the message to binary data (in protobuf wire format).
+ * @return {!Uint8Array}
+ */
+proto.ord.DatasetExample.prototype.serializeBinary = function() {
+  var writer = new jspb.BinaryWriter();
+  proto.ord.DatasetExample.serializeBinaryToWriter(this, writer);
+  return writer.getResultBuffer();
+};
+
+
+/**
+ * Serializes the given message to binary data (in protobuf wire
+ * format), writing to the given BinaryWriter.
+ * @param {!proto.ord.DatasetExample} message
+ * @param {!jspb.BinaryWriter} writer
+ * @suppress {unusedLocalVariables} f is only used for nested messages
+ */
+proto.ord.DatasetExample.serializeBinaryToWriter = function(message, writer) {
+  var f = undefined;
+  f = message.getDatasetId();
+  if (f.length > 0) {
+    writer.writeString(
+      1,
+      f
+    );
+  }
+  f = message.getDescription();
+  if (f.length > 0) {
+    writer.writeString(
+      2,
+      f
+    );
+  }
+  f = message.getUrl();
+  if (f.length > 0) {
+    writer.writeString(
+      3,
+      f
+    );
+  }
+  f = message.getCreated();
+  if (f != null) {
+    writer.writeMessage(
+      4,
+      f,
+      ord$schema_proto_reaction_pb.RecordEvent.serializeBinaryToWriter
+    );
+  }
+};
+
+
+/**
+ * optional string dataset_id = 1;
+ * @return {string}
+ */
+proto.ord.DatasetExample.prototype.getDatasetId = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 1, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.DatasetExample} returns this
+ */
+proto.ord.DatasetExample.prototype.setDatasetId = function(value) {
+  return jspb.Message.setProto3StringField(this, 1, value);
+};
+
+
+/**
+ * optional string description = 2;
+ * @return {string}
+ */
+proto.ord.DatasetExample.prototype.getDescription = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 2, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.DatasetExample} returns this
+ */
+proto.ord.DatasetExample.prototype.setDescription = function(value) {
+  return jspb.Message.setProto3StringField(this, 2, value);
+};
+
+
+/**
+ * optional string url = 3;
+ * @return {string}
+ */
+proto.ord.DatasetExample.prototype.getUrl = function() {
+  return /** @type {string} */ (jspb.Message.getFieldWithDefault(this, 3, ""));
+};
+
+
+/**
+ * @param {string} value
+ * @return {!proto.ord.DatasetExample} returns this
+ */
+proto.ord.DatasetExample.prototype.setUrl = function(value) {
+  return jspb.Message.setProto3StringField(this, 3, value);
+};
+
+
+/**
+ * optional RecordEvent created = 4;
+ * @return {?proto.ord.RecordEvent}
+ */
+proto.ord.DatasetExample.prototype.getCreated = function() {
+  return /** @type{?proto.ord.RecordEvent} */ (
+    jspb.Message.getWrapperField(this, ord$schema_proto_reaction_pb.RecordEvent, 4));
+};
+
+
+/**
+ * @param {?proto.ord.RecordEvent|undefined} value
+ * @return {!proto.ord.DatasetExample} returns this
+*/
+proto.ord.DatasetExample.prototype.setCreated = function(value) {
+  return jspb.Message.setWrapperField(this, 4, value);
+};
+
+
+/**
+ * Clears the message field making it undefined.
+ * @return {!proto.ord.DatasetExample} returns this
+ */
+proto.ord.DatasetExample.prototype.clearCreated = function() {
+  return this.setCreated(undefined);
+};
+
+
+/**
+ * Returns whether this field is set.
+ * @return {boolean}
+ */
+proto.ord.DatasetExample.prototype.hasCreated = function() {
+  return jspb.Message.getField(this, 4) != null;
+};
+
+
+goog.object.extend(exports, proto.ord);

package/proto/dataset_pb.test.js

@@ -0,0 +1,41 @@
+/**
+ * Copyright 2022 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.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+const ord_schema = require('..');
+
+test('round-trip', () => {
+    const dataset = new ord_schema.dataset_pb.Dataset();
+    dataset.setName('test');
+    dataset.setDescription('test dataset');
+    // Add a reaction directly to the dataset.
+    const reaction1 = dataset.addReactions();
+    const identifier1 = reaction1.addIdentifiers();
+    identifier1.setValue('C(C)Cl.Br>>C(C)Br.Cl');
+    identifier1.setType(ord_schema.reaction_pb.ReactionIdentifier.ReactionIdentifierType.REACTION_SMILES);
+    // Copy a reaction created elsewhere.
+    const reaction2 = new ord_schema.reaction_pb.Reaction();
+    const identifier2 = reaction2.addIdentifiers();
+    identifier2.setValue('amide coupling');
+    identifier2.setType(ord_schema.reaction_pb.ReactionIdentifier.ReactionIdentifierType.NAME);
+    dataset.addReactions(reaction2);
+    const serialized = dataset.serializeBinary();
+    const other = ord_schema.dataset_pb.Dataset.deserializeBinary(serialized);
+    expect(other.getName()).toBe('test');
+    expect(other.getDescription()).toBe('test dataset');
+    expect(other.getReactionsList()).toHaveLength(2);
+    expect(other.getReactionsList()[0].getIdentifiersList()[0].getType()).toBe(ord_schema.reaction_pb.ReactionIdentifier.ReactionIdentifierType.REACTION_SMILES);
+    expect(other.getReactionsList()[1].getIdentifiersList()[0].getType()).toBe(ord_schema.reaction_pb.ReactionIdentifier.ReactionIdentifierType.NAME);
+});