quadstore

v13.2.4

Published

8 days ago

Quadstore is a LevelDB-backed RDF graph database / triplestore for JavaScript runtimes (browsers, Node.js, Deno, Bun, ...) that implements the RDF/JS interfaces and supports SPARQL queries and querying across named graphs.

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teomurgi

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node deno bun browser triplestore quadstore graph rdf store level leveldb database sparql rdfjs RDF/JS triple quad

QUADSTORE

Quadstore is a LevelDB-backed RDF graph database / triplestore for JavaScript runtimes (browsers, Node.js, Deno, Bun, ...) written in TypeScript.

Implements the Sink, Source and Store RDF/JS interfaces for maximum interoperability with other RDF libraries
Supports SPARQL queries via quadstore-comunica, a tailored configuration and distribution of the Comunica querying framework
Natively capable of querying across named graphs

QUADSTORE

Example of basic usage

import { MemoryLevel } from 'memory-level';
import { DataFactory } from 'rdf-data-factory';
import { Quadstore } from 'quadstore';
import { Engine } from 'quadstore-comunica';

// Any implementation of AbstractLevel can be used.
const backend = new MemoryLevel();

// Implementation of the RDF/JS DataFactory interface
const df = new DataFactory();           

// Store and query engine are separate modules
const store = new Quadstore({backend, dataFactory: df});
const engine = new Engine(store);

// Open the store
await store.open();

// Put a single quad into the store using Quadstore's API
await store.put(df.quad(                      
  df.namedNode('http://example.com/subject'),
  df.namedNode('http://example.com/predicate'),
  df.namedNode('http://example.com/object'),
  df.defaultGraph(),
));

// Retrieves all quads using Quadstore's API  
const { items } = await store.get({});

// Retrieves all quads using RDF/JS Stream interfaces
const quadsStream = store.match(undefined, undefined, undefined, undefined);
quadsStream.on('data', quad => console.log(quad));

// Queries the store via RDF/JS Query interfaces
const bindingsStream = await engine.queryBindings('SELECT * {?s ?p ?o}');
bindingsStream.on('data', binding => console.log(binding));

Status

Active, under development.

Changelog

See CHANGELOG.md.

Roadmap

We're currently working on the following features:

optimizing SPARQL performance by pushing filters down from the engine to the persistence layer

We're also evaluating the following features for future developments:

RDF* (see also these slides)

Notes

uses Semantic Versioning, pre-releases are tagged accordingly;
requires Node.js >= 16.0.0.

Usage

Parsing and serializing RDF

quadstore is compatible with all parsers and serializers implementing the relevant RDF/JS interfaces, such as n3 and @rdfjs/formats. See https://rdf.js.org for an open list of such libraries.

For example, here is how to use n3 in order to parse a Turtle file into an instance of Quadstore in a streaming fashion, with full backpressure handling, using classic-level as the backend:

import { Quadstore } from 'quadstore';
import { ClassicLevel } from 'classic-level';
import { DataFactory, StreamParser } from 'n3';
const store = new Quadstore({
  backend: new ClassicLevel('/path/to/db'),
  dataFactory: DataFactory,
});
await store.open();
const reader = fs.createReadStream('/path/to/file.ttl');
const parser = new StreamParser({ format: 'text/turtle' });
await store.putStream(reader.pipe(parser), { batchSize: 100 });
await store.close();

quadstore does not include any RDF parsing and/or serialization capability by choice as no subset of formats would meet the requirements of every use case and shipping support for all mainstream RDF formats would result in exceedingly high bundle sizes.

Storage backends

quadstore can work with any storage backend that implements the AbstractLevel interface. An incomplete list of available backends is available at level/awesome#stores.

Note that quadstore is only compatible with abstract-level's API as of its 1.x versions. Packages whose semver major version number tracks that of abstract-level, such as classic-level and memory-level, must be used up to their most recent 1.x version. The switch to abstract-level version 2.x is tracked in #168.

Our test suite focuses on the following backends:

classic-level for persistent, on-disk storage using LevelDB
memory-level for volatile in-memory storage using red-black trees
~~rocksdb for persistent storage using RocksDB~~
- waiting for the rocks-level package to be published
@nxtedition/rocks-level for persistent, on-disk storage using RocksDB
- this is an alternative backend for RocksDB that tends to be 5% - 15% faster then classic-level but is maintained outside of the Level community and set of official packages
browser-level for browser-side persistent storage using IndexedDB. For more information about browser-side usage, see the Browser usage section

Data model and return values

Except for those related to the RDF/JS stream interfaces, quadstore's API is promise-based and all methods return objects that include both the actual query results and the relevant metadata.

Objects returned by quadstore's APIs have the type property set to one of the following values:

"VOID" - when there's no data returned by the database, such as with the put method;
"QUADS" - when a query returns a collection of quads;
"APPROXIMATE_SIZE" - when a query returns an approximate count of how many matching items are present.

For those methods that return objects with the type property set to "QUADS", quadstore provides query results either in streaming mode or in non-streaming mode.

Streaming methods such as getStream return objects with the iterator property set to an instance of AsyncIterator, an implementation of a subset of the stream.Readable interface.

Non-streaming methods such as get return objects with the items property set to an array of quads.

Quads are returned as and expected to be instances of the RDF/JS Quad interface as produced by the implementation of the RDF/JS DataFactory interface passed to the Quadstore constructor.

Matching patterns, such as those used in the get and getStream methods, are expected to be maps of term names to instances of the RDF/JS Term interface.

Quadstore class

const Quadstore = require('quadstore').Quadstore;
const store = new Quadstore(opts);

Instantiates a new store. Supported properties for the opts argument are:

opts.backend

The opts.backend option must be an instance of a leveldb backend. See storage backends.

opts.dataFactory

The dataFactory option must be an implementation of the RDF/JS DataFactory interface. Some of the available implementations:

opts.indexes

The opts.indexes option allows users to configure which indexes will be used by the store. If not set, the store will default to the following indexes:

[
  ['subject', 'predicate', 'object', 'graph'],
  ['object', 'graph', 'subject', 'predicate'],
  ['graph', 'subject', 'predicate', 'object'],
  ['object', 'subject', 'predicate', 'graph'],
  ['predicate', 'object', 'graph', 'subject'],
  ['graph', 'predicate', 'object', 'subject'],
];

This option, if present, must be set to an array of term arrays, each of which must represent one of the 24 possible permutations of the four terms subject, predicate, object and graph. Partial indexes are not supported.

The store will automatically select which index(es) to use for a given query based on the available indexes and the query itself. If no suitable index is found for a given query, the store will throw an error.

opts.prefixes

Also, Quadstore can be configured with a prefixes object that defines a reversible mapping of IRIs to abbreviated forms, with the intention of reducing the storage cost where common HTTP prefixes are known in advance.

The prefixes object defines a bijection using two functions expandTerm and compactIri, both of which take a string parameter and return a string, as in the following example:

opts.prefixes = {
  expandTerm: term => term.replace(/^ex:/, 'http://example.com/'),
  compactIri: iri => iri.replace(/^http:\/\/example\.com\//, 'ex:'),
}

This will replace the IRI http://example.com/a with ex:a in storage.

Access to the backend

The backend of a quadstore can be accessed with the db property, to perform additional storage operations independently of quads.

In order to perform write operations atomically with quad storage, the put, multiPut, del, multiDel, patch and multiPatch methods accept a preWrite option which defines a procedure to augment the batch, as in the following example:

await store.put(dataFactory.quad(/* ... */), {
  preWrite: batch => batch.put('my.key', Buffer.from('my.value'))
});

Quadstore.prototype.open()

This method opens the store and throws if the open operation fails for any reason.

Quadstore.prototype.close()

This method closes the store and throws if the open operation fails for any reason.

Quadstore.prototype.get()

const pattern = {graph: dataFactory.namedNode('ex://g')};
const { items } = await store.get(pattern);

Returns an array of all quads within the store matching the specified terms.

This method also accepts an optional opts parameter with the following optional properties:

opts.order: array of term names (e.g. ['object']) that represents the desired ordering criteria of returned quads. Equivalent to the ORDER BY clause in SQL.
opts.reverse: boolean value that indicates whether to return quads in ascending or descending order. Equivalent to ASC / DESC modifiers in SQL.
opts.limit: limit the number of returned quads to the specified value. Equivalent to LIMIT clause in SQL.

Range matching

quadstore supports range-based matching in addition to value-based matching. Ranges can be defined using the gt, gte, lt, lte properties:

const pattern = {
  object: {
    termType: 'Range',
    gt: dataFactory.literal('7', 'http://www.w3.org/2001/XMLSchema#integer')
  }
};
const { items } = await store.get(matchTerms);

Values for literal terms with the following numeric datatypes are matched against their numerical values rather than their literal representations:

http://www.w3.org/2001/XMLSchema#integer
http://www.w3.org/2001/XMLSchema#decimal
http://www.w3.org/2001/XMLSchema#double
http://www.w3.org/2001/XMLSchema#nonPositiveInteger
http://www.w3.org/2001/XMLSchema#negativeInteger
http://www.w3.org/2001/XMLSchema#long
http://www.w3.org/2001/XMLSchema#int
http://www.w3.org/2001/XMLSchema#short
http://www.w3.org/2001/XMLSchema#byte
http://www.w3.org/2001/XMLSchema#nonNegativeInteger
http://www.w3.org/2001/XMLSchema#unsignedLong
http://www.w3.org/2001/XMLSchema#unsignedInt
http://www.w3.org/2001/XMLSchema#unsignedShort
http://www.w3.org/2001/XMLSchema#unsignedByte
http://www.w3.org/2001/XMLSchema#positiveInteger

This is also the case for terms with the following date/time datatypes:

http://www.w3.org/2001/XMLSchema#dateTime

Quadstore.prototype.put()

await store.put(dataFactory.quad(/* ... */));

Stores a new quad. Does not throw or return an error if the quad already exists.

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.
opts.scope: this can be set to a Scope instance as returned by initScope() and loadScope(). If set, blank node labels will be changed to prevent blank node collisions. See Blank nodes and quad scoping.

Quadstore.prototype.multiPut()

await store.multiPut([
  dataFactory.quad(/* ... */),
  dataFactory.quad(/* ... */),
]);

Stores new quads. Does not throw or return an error if quads already exists.

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.
opts.scope: this can be set to a Scope instance as returned by initScope() and loadScope(). If set, blank node labels will be changed to prevent blank node collisions. See Blank nodes and quad scoping.

Quadstore.prototype.del()

This method deletes a single quad. It Does not throw or return an error if the specified quad is not present in the store.

await store.del(dataFactory.quad(/* ... */));

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.

Quadstore.prototype.multiDel()

This method deletes multiple quads. It Does not throw or return an error if the specified quads are not present in the store.

await store.multiDel([
  dataFactory.quad(/* ... */),
  dataFactory.quad(/* ... */),
]);

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.

Quadstore.prototype.patch()

This method deletes one quad and inserts another quad in a single operation. It Does not throw or return an error if the specified quads are not present in the store (delete) or already present in the store (update).

await store.patch(
  dataFactory.quad(/* ... */),  // will be deleted
  dataFactory.quad(/* ... */),  // will be inserted
);

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.

Quadstore.prototype.multiPatch()

This method deletes and inserts quads in a single operation. It Does not throw or return an error if the specified quads are not present in the store (delete) or already present in the store (update).

// will be deleted
const oldQuads = [ 
    dataFactory.quad(/* ... */),
    dataFactory.quad(/* ... */),
];

// will be inserted
const newQuads = [ // will be inserted
    dataFactory.quad(/* ... */),
    dataFactory.quad(/* ... */),
    dataFactory.quad(/* ... */),        
];

await store.multiPatch(oldQuads, newQuads);

This method also accepts an optional opts parameter with the following properties:

opts.preWrite: this can be set to a function which accepts a chainedBatch and performs additional backend operations atomically with the put operation. See Access to the backend for more information.

Quadstore.prototype.getStream()

const pattern = {graph: dataFactory.namedNode('ex://g')};
const { iterator } = await store.getStream(pattern);

Just as QuadStore.prototype.get(), this method supports range matching and the order, reverse and limit options.

Quadstore.prototype.putStream()

await store.putStream(readableStream);

Imports all quads coming through the specified stream.Readable into the store.

This method also accepts an optional opts parameter with the following properties:

opts.scope: this can be set to a Scope instance as returned by initScope() and loadScope(). If set, blank node labels will be changed to prevent blank node collisions. See Blank nodes and quad scoping.

Quadstore.prototype.delStream()

await store.delStream(readableStream);

Deletes all quads coming through the specified stream.Readable from the store.

Quadstore.prototype.match()

const subject = dataFactory.namedNode('http://example.com/subject');
const graph = dataFactory.namedNode('http://example.com/graph');
store.match(subject, null, null, graph)
  .on('error', (err) => {})
  .on('data', (quad) => {
    // Quad is produced using dataFactory.quad()
  })
  .on('end', () => {});

Implementation of the RDF/JS Source#match method. Supports range-based matching.

Quadstore.prototype.import()

const readableStream; // A stream.Readable of Quad() instances
store.import(readableStream)
  .on('error', (err) => {})
  .on('end', () => {});

Implementation of the RDF/JS Sink#import method.

Quadstore.prototype.remove()

const readableStream; // A stream.Readable of Quad() instances
store.remove(readableStream)
  .on('error', (err) => {})
  .on('end', () => {});

Implementation of the RDF/JS Store#remove method.

Quadstore.prototype.removeMatches()

const subject = dataFactory.namedNode('http://example.com/subject');
const graph = dataFactory.namedNode('http://example.com/graph');
store.removeMatches(subject, null, null, graph)
  .on('error', (err) => {})
  .on('end', () => {});

Implementation of the RDF/JS Sink#removeMatches method.

Blank nodes and quad scoping

Blank nodes are defined as existential variables in that they merely indicate the existence of an entity rather than act as references to the entity itself.

While the semantics of blank nodes can be rather confusing, one of the most practical consequences of their definition is that two blank nodes having the same label may not refer to the same entity unless both nodes come from the same logical set of quads.

As an example, here's two JSON-LD documents converted to N-Quads using the
JSON-LD playground:

{
  "@id": "http://example.com/bob",
  "foaf:knows": {
    "foaf:name": "Alice"
  }
}

<http://example.com/bob> <foaf:knows> _:b0 .
_:b0 <foaf:name> "Alice" .

{
  "@id": "http://example.com/alice",
  "foaf:knows": {
    "foaf:name": "Bob"
  }
}

<http://example.com/alice> <foaf:knows> _:b0 .
_:b0 <foaf:name> "Bob" .

The N-Quads equivalent for both of these documents contains a blank node with the b0 label. However, although the label is the same, these blank nodes indicate the existence of two different entities. Intuitively, we can say that a blank node is scoped to the logical grouping of quads that contains it, be it a single quad, a document or a stream.

As quadstore treats all write operations as if they were happening within the same scope, importing these two sets of quads would result in a collision of two unrelated blank nodes, leading to a corrupted dataset.

A good way to address these issues is to skolemize skolemize all blank nodes into IRIs / named nodes. However, this is not always possible and / or practical.

The initScope() method returns a Scope instance which can be passed to the put, multiPut and putStream methods. When doing so, quadstore will replace each occurrence of a given blank node with a different blank node having a randomly-generated label, preventing blank node collisions.

Each Scope instance keeps an internal cache of mappings between previously encountered blank nodes and their replacements, so that it is able to always return the same replacement blank node for a given label. Each new mapping is atomically persisted to the store together with its originating quad, leading each scope to be incrementally persisted to the store consistently with each successful put and multiPut operation. This allows scopes to be re-used even across process restarts via the loadScope() method.

Quadstore.prototype.initScope()

Initializes a new, empty scope.

const scope = await store.initScope();
await store.put(quad, { scope });
await store.multiPut(quads, { scope });
await store.putStream(stream, { scope });

Quadstore.prototype.loadScope()

Each Scope instance has an .id property that acts as its unique identifier. The loadScope() method can be used to re-hydrate a scope through its .id:

const scope = await store.initScope();
/* store scope.id somewhere */

/* read the previously-stored scope.id */
const scope = await store.loadScope(scopeId);

Quadstore.prototype.deleteScope()

Deletes all mappings of a given scope from the store.

const scope = await store.initScope();
/* ... */
await store.deleteScope(scope.id);

Quadstore.prototype.deleteAllScopes()

Deletes all mappings of all scopes from the store.

await store.deleteAllScopes();

SPARQL

SPARQL queries can be executed against a Quadstore instance using any query engine capable of querying across RDF/JS data sources.

An example of one such engine is quadstore-comunica, an engine built as a custom distribution and configuration of Comunica that implements the RDF/JS Query spec.:

Comunica is a knowledge graph querying framework. [...] Comunica is a meta query engine using which query engines can be created. It does this by providing a set of modules that can be wired together in a flexible manner. [...] Its primary goal is executing SPARQL queries over one or more interfaces.

In time, quadstore-comunica will be extended with custom query modules that will optimize query performance by pushing some matching and ordering operations down to quadstore itself.

import { MemoryLevel } from 'memory-level';
import { DataFactory } from 'rdf-data-factory';
import { Quadstore } from 'quadstore';
import { Engine } from 'quadstore-comunica';

const backend = new MemoryLevel();
const df = new DataFactory();
const store = new Quadstore({backend, dataFactory: df});
const engine = new Engine(store);

await store.open();

const bindingsStream = await engine.queryBindings('SELECT * {?s ?p ?o}');

More information on quadstore-comunica's repository.

Browser usage

The browser-level backend for levelDB offers support for browser-side persistent storage via IndexedDB.

quadstore can be bundled for browser-side usage via Webpack, preferably using version 5.x. The reference quadstore-browser is meant to help in getting to a working Webpack configuration and also hosts a pre-built bundle with everything that is required to use quadstore in browsers.

Deno usage

quadstore can be used with the Deno runtime via the skypack.dev CDN:

import { DataFactory } from 'https://cdn.skypack.dev/[email protected]';
import { Quadstore } from 'https://cdn.skypack.dev/[email protected]';
import { MemoryLevel } from 'https://cdn.skypack.dev/[email protected]';
import { Engine } from 'https://cdn.skypack.dev/[email protected]';

const backend = new MemoryLevel();
const dataFactory = new DataFactory();
const store = new Quadstore({ backend, dataFactory });
const engine = new Engine(store);

await store.open();
await store.put(dataFactory.quad(
        dataFactory.namedNode('ex://s'),
        dataFactory.namedNode('ex://p'),
        dataFactory.namedNode('ex://o'),
));
const stream = await engine.queryBindings('SELECT * WHERE { ?s ?p ?o }');
stream.on('data', (bindings) => console.log(bindings));

Example usage:

deno run quadstore-test.ts

Performance

Performance is evaluated at tracked at https://github.com/quadstorejs/quadstore-perf

LICENSE

MIT. See LICENSE.md.

Published

Vulnerabilities

Links

Maintainers

Keywords

Readme

QUADSTORE

Table of contents

Example of basic usage

Status

Changelog

Roadmap

Notes

Usage

Parsing and serializing RDF

Storage backends

Data model and return values

Quadstore class

opts.backend

opts.dataFactory

opts.indexes

opts.prefixes

Access to the backend

Quadstore.prototype.open()

Quadstore.prototype.close()

Quadstore.prototype.get()

Range matching

Quadstore.prototype.put()

Quadstore.prototype.multiPut()

Quadstore.prototype.del()

Quadstore.prototype.multiDel()

Quadstore.prototype.patch()

Quadstore.prototype.multiPatch()

Quadstore.prototype.getStream()

Quadstore.prototype.putStream()

Quadstore.prototype.delStream()

Quadstore.prototype.match()

Quadstore.prototype.import()

Quadstore.prototype.remove()

Quadstore.prototype.removeMatches()

Blank nodes and quad scoping

Quadstore.prototype.initScope()

Quadstore.prototype.loadScope()

Quadstore.prototype.deleteScope()

Quadstore.prototype.deleteAllScopes()

SPARQL

Browser usage

Deno usage

Performance

LICENSE