ord-schema

library0.6.8jsnpmunverified

The `ord-schema` package provides JavaScript and TypeScript wrappers for interacting with the Open Reaction Database (ORD) schema. The ORD project standardizes the representation of chemical reaction data, facilitating data exchange, analysis, and machine learning applications within the chemistry domain. This library offers client-side tools, primarily built on Protocol Buffers (protobuf), to create, manipulate, and validate reaction data according to the ORD specification. Currently at version 0.4.7, the package has a consistent release cadence, often addressing internal tooling, dependency updates (like Protobuf), and minor bug fixes. Its core differentiator lies in enabling structured, interoperable chemical reaction data handling.

serialization data

npm install ord-schema

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · ORD-SCHEMA

ord-schema

serializationjavascriptv0.6.8

Install

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Import

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Disk

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Pass rate

0/ 6

Env Coverage0 / 6

glibc

18–22

musl

18–22

Install & Compatibility

Where this runs

tested against v? · npm install

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

node 18–226 runs

build_error

glibc

node 18–226 runs

build_error

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

Reaction

✓ import { Reaction } from 'ord-schema';

✗ import Reaction from 'ord-schema';

Main Protobuf message type for a chemical reaction. It is a named export.

validateReaction

✓ import { validateReaction } from 'ord-schema';

✗ import { validate } from 'ord-schema';

Utility function for schema validation of Reaction messages. Specific named export.

Reaction.toObject

✓ import { Reaction } from 'ord-schema'; const reaction = new Reaction(); const obj = reaction.toObject();

✗ import { toObject } from 'ord-schema'; // ... `toObject` is a method on Reaction instances, not a direct export.

Protobuf messages have methods like `toObject()` and `serializeBinary()`. These are instance methods, not top-level exports.

Demonstrates creating a new Reaction object, populating basic fields, performing client-side validation, and handling Protobuf serialization/deserialization.

import { Reaction, validateReaction, ReactionMeasurement, Product } from 'ord-schema'; const reaction = new Reaction(); reaction.setReactionId('my-unique-reaction-id'); const measurement = new ReactionMeasurement(); measurement.setOutcome('SUCCESS'); reaction.addMeasurements(measurement); const product = new Product(); product.setReactionProduct('my-product-smiles'); // Example SMILES string reaction.addProducts(product); // Add a textual description reaction.setText('A simple example reaction with one product and a success outcome.'); // Validate the reaction object against the schema try { validateReaction(reaction); console.log('Reaction is valid:', reaction.toObject()); } catch (error) { console.error('Reaction validation failed:', error); } // Example of serializing to binary (for sending over network/saving) const binaryData = reaction.serializeBinary(); console.log(`Serialized reaction to ${binaryData.length} bytes.`); // Example of deserializing from binary const deserializedReaction = Reaction.deserializeBinary(binaryData); console.log('Deserialized reaction ID:', deserializedReaction.getReactionId());

Debug

Known issues

breakingThe underlying `protobuf` dependency was updated from `v4` to `v5` in `ord-schema@0.4.4`. While efforts are made to ensure backward compatibility for generated code, direct usage of `protobufjs` APIs or interaction with other libraries that strictly depend on `protobufjs@4` might lead to unexpected behavior or dependency conflicts.

fix

Review your `package.json` for other `protobufjs` dependencies. If conflicts arise, consider upgrading other dependencies or using package manager overrides if possible. Thoroughly test your application after upgrading `ord-schema` to version `0.4.4` or later.

affects: >=0.4.4

gotchaDirect modification of Protobuf message objects returned by `get*()` methods (e.g., `reaction.getMeasurements()`) can lead to unexpected behavior or state management issues, as these often return references. Use `add*()` or `set*()` methods for collections, or create new instances for nested objects.

fix

Always use the provided setters (`set*`, `add*`) to modify Protobuf message fields. For example, instead of `reaction.getMeasurements()[0].setOutcome('FAILURE')`, create a new `ReactionMeasurement` or ensure you're modifying a detached copy if complex manipulation is needed.

affects: >=0.1.0

Errors

Common errors & fixes

TypeError: reaction.setReactionId is not a function

Attempting to call Protobuf setter methods on a plain JavaScript object or an uninitialized message.

fix

Ensure `reaction` is an instance of `ord-schema.Reaction`. Instantiate it with `const reaction = new Reaction();` before calling any Protobuf-specific methods.

Error: Reaction validation failed: Error: Reaction.reaction_id is required.

A required field in the ORD schema was not set or was set with an invalid value before calling `validateReaction`.

fix

Consult the ORD schema documentation for the specific message type (e.g., `Reaction`) to identify all required fields and their expected data types. Ensure all mandatory fields are populated correctly before validation.

Error: Cannot find module 'ord-schema/proto/ord_pb' or its corresponding type declarations.

Trying to import directly from internal Protobuf-generated paths instead of the main `ord-schema` entry point.

fix

Most common symbols like `Reaction`, `validateReaction`, etc., are re-exported directly from the root `ord-schema` package. Use `import { Reaction } from 'ord-schema';` instead of `import { Reaction } from 'ord-schema/proto/ord_pb';`.

Upgrade

Version history

0.6.8latest on npm

Audit

Dependencies

protobufjsrequiredUsed for Protocol Buffers message definition and serialization/deserialization.

Agent activity

4 hits · last 30 days

node

Resources

githubhttps://github.com/open-reaction-database/ord-schema ↗

packagehttps://www.npmjs.com/package/ord-schema ↗

homepagehttps://open-reaction-database.org ↗