The Knowledge Graph notebook

LinkedDataHub (LDH) is open source software you can use to manage data, create visualizations and build apps on RDF Knowledge Graphs.

What's new in LinkedDataHub v3? Watch this video for a feature overview:

We started the project with the intention to use it for Linked Data publishing, but gradually realized that we've built a multi-purpose data-driven platform.

We are building LinkedDataHub primarily for:

• researchers who need an RDF-native notebook that can consume and collect Linked Data and SPARQL documents and follows the FAIR principles
• developers who are looking for a declarative full stack framework for Knowledge Graph application development, with out-of-the-box UI and API

What makes LinkedDataHub unique is its completely data-driven architecture: applications and documents are defined as data, managed using a single generic HTTP API and presented using declarative technologies. The default application structure and user interface are provided, but they can be completely overridden and customized. Unless a custom server-side processing is required, no imperative code such as Java or JavaScript needs to be involved at all.

Follow the Get started guide to LinkedDataHub. The setup and basic configuration sections are provided below and should get you running.

Setup

Click to expand

Prerequisites

• bash shell 4.x. It should be included by default on Linux. On Windows you can install the Windows Subsystem for Linux.
• Java's keytool available on $PATH. It comes with the JDK.
• openssl available on $PATH
• uuidgen available on $PATH
• Docker installed. At least 8GB of memory dedicated to Docker is recommended.
• Docker Compose installed

Steps

1. Fork this repository and clone the fork into a folder
2. In the folder, create an .env file and fill out the missing values (you can use .env_sample as a template). For example:

   COMPOSE_CONVERT_WINDOWS_PATHS=1
   COMPOSE_PROJECT_NAME=linkeddatahub
   
   PROTOCOL=https
   PROXY_HTTP_PORT=81
   PROXY_HTTPS_PORT=4443
   HOST=localhost
   ABS_PATH=/
   
   OWNER_MBOX=john@doe.com
   OWNER_GIVEN_NAME=John
   OWNER_FAMILY_NAME=Doe
   OWNER_ORG_UNIT=My unit
   OWNER_ORGANIZATION=My org
   OWNER_LOCALITY=Copenhagen
   OWNER_STATE_OR_PROVINCE=Denmark
   OWNER_COUNTRY_NAME=DK
   

3. Setup SSL certificates/keys by running this from command line (replace $owner_cert_pwd and $secretary_cert_pwd with your own passwords):

   ./scripts/setup.sh .env ssl $owner_cert_pwd $secretary_cert_pwd 3650
   

   The script will create an ssl sub-folder where the SSL certificates and/or public keys will be placed.
4. Launch the application services by running this from command line:

   docker-compose up --build
   

   It will build LinkedDataHub's Docker image, start its container and mount the following sub-folders:
   • data where the triplestore(s) will persist RDF data
   • uploads where LDH stores content-hashed file uploads The first should take around half a minute as datasets are being loaded into triplestores. After a successful startup, the last line of the Docker log should read something like:

   linkeddatahub_1     | 09-Feb-2021 14:18:10.536 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [32609] milliseconds
   

5. Install ssl/owner/keystore.p12 into a web browser of your choice (password is the $owner_cert_pwd value supplied to setup.sh)
   • Google Chrome: Settings > Advanced > Manage Certificates > Import...
   • Mozilla Firefox: Options > Privacy > Security > View Certificates... > Import...
   • Apple Safari: The file is installed directly into the operating system. Open the file and import it using the Keychain Access tool (drag it to the local section).
   • Microsoft Edge: Does not support certificate management, you need to install the file into Windows. Read more here.
6. Open https://localhost:4443/ in that web browser

Notes

• You will likely get a browser warning such as Your connection is not private in Chrome or Warning: Potential Security Risk Ahead in Firefox due to the self-signed server certificate. Ignore it: click Advanced and Proceed or Accept the risk to proceed.
  • If this option does not appear in Chrome (as observed on some MacOS), you can open chrome://flags/#allow-insecure-localhost, switch Allow invalid certificates for resources loaded from localhost to Enabled and restart Chrome
• .env_sample and .env files might be invisible in MacOS Finder which hides filenames starting with a dot. You should be able to create it using Terminal however.
• On Linux your user may need to be a member of the docker group. Add it using

sudo usermod -aG docker ${USER}

and re-login with your user. An alternative, but not recommended, is to run

sudo docker-compose up

Configuration

Click to expand

Base URI

A common case is changing the base URI from the default https://localhost:4443/ to your own.

Lets use https://ec2-54-235-229-141.compute-1.amazonaws.com/linkeddatahub/ as an example. We need to split the URI into components and set them in the .env file using the following parameters:

PROTOCOL=https
HTTP_PORT=80
HTTPS_PORT=443
HOST=ec2-54-235-229-141.compute-1.amazonaws.com
ABS_PATH=/linkeddatahub/

ABS_PATH is required, even if it's just /.

Dataspaces

Dataspaces are configured in config/system-varnish.trig. Relative URIs will be resolved against the base URI configured in the .env file.

⚠️ Do not use blank nodes to identify applications or services. We recommend using the urn: URI scheme, since LinkedDataHub application resources are not accessible under their own dataspace.

Environment

LinkedDataHub supports a range of configuration options that can be passed as environment parameters in docker-compose.yml. The most common ones are:

CATALINA_OPTS

Tomcat's command line options

SELF_SIGNED_CERT

true if the server certificate is self-signed

SIGN_UP_CERT_VALIDITY

Validity of the WebID certificates of signed up users (not the owner's)

IMPORT_KEEPALIVE

The period for which the data import can keep an open HTTP connection before it times out, in ms. The larger files are being imported, the longer it has to be in order for the import to complete.

MAX_CONTENT_LENGTH

Maximum allowed size of the request body, in bytes

MAIL_SMTP_HOST

Hostname of the mail server

MAIL_SMTP_PORT

Port number of the mail server

GOOGLE_CLIENT_ID

OAuth 2.0 Client ID from Google. When provided, enables the Login with Google authentication method.

GOOGLE_CLIENT_SECRET

Client secret from Google

Reset

If you need to start fresh and wipe the existing setup (e.g. after configuring a new base URI), you can do that using

sudo rm -rf data uploads && docker-compose down -v

⚠️ This will remove the persisted data and files as well as Docker volumes.

Documentation

• Get started
• Reference
• User guide

Command line interface

LinkedDataHub CLI wraps the HTTP API into a set of shell scripts with convenient parameters. The scripts can be used for testing, automation, scheduled execution and such. It is usually much quicker to perform actions using CLI rather than the user interface, as well as easier to reproduce.

The scripts can be found in the scripts subfolder.

⚠️ The CLI scripts internally use Jena's CLI commands. Set up the Jena environment before running the scripts.

An environment variable JENA_HOME is used by all the command line tools to configure the class path automatically for you. You can set this up as follows:

On Linux / Mac

export JENA_HOME=the directory you downloaded Jena to
export PATH="$PATH:$JENA_HOME/bin"

Sample applications

Third party

• NOI OpenDataHub – tourism Knowledge Graph portal powered by LinkedDataHub and @ontop. Source code.

Demo apps

These demo applications can be installed into a LinkedDataHub instance using the provided CLI scripts.

⚠️ Before running app installation scripts that use LinkedDataHub's CLI scripts, set the SCRIPT_ROOT environmental variable to the scripts subfolder of your LinkedDataHub fork or clone. For example:

export SCRIPT_ROOT="/c/Users/namedgraph/WebRoot/AtomGraph/LinkedDataHub/scripts"

How to get involved

• contribute a new LDH application or modify one of ours
• work on good first issues
• work on the features in our Roadmap
• join our community

Test suite

LinkedDataHub includes an HTTP test suite. The server implementation is also covered by the Processor test suite.

Dependencies

Browser

• Saxon-JS
• OpenLayers
• Google Charts

Java

• Jersey
• XOM
• JavaMail
• Guava
• java-jwt
• ExpiringMap
• CSV2RDF
• Processor
• Web-Client

Docker

• atomgraph/nginx
• atomgraph/fuseki
• atomgraph/varnish
• namshi/smtp

Support

Please report issues if you've encountered a bug or have a feature request.

Commercial consulting, development, and support are available from AtomGraph.

Community

• linkeddatahub@groups.io (mailing list)
• @atomgraphhq on Twitter
• AtomGraph on LinkedIn
• W3C Declarative Linked Data Apps Community Group