Keywords

Research in context graph, Ricgraph, Ricgraph Explorer, Ricgraph REST API, Data enrichment, Data harvesting, Data linking, Enrichment, Graph, Graph database, Harvest, Harvest data, Harvester, Knowledge graph, Linked data, Metadata, Utrecht University, Visualization

Ricgraph in a container

This page describes how to install and run Ricgraph in a Podman container. A container is like a small box that holds an application and everything it needs to run, such as files and settings. It makes sure the application works the same on any computer. Podman is a tool for creating and running containers, and it is safe because it doesn’t need special permissions to work. This makes it a good choice for running programs quickly and reliably. For other Ricgraph install options start reading at Install and configure Ricgraph for a single user.

To install and run Ricgraph in a Podman container, follow these steps:

Return to main README.md file.

1 Notes on the Ricgraph Podman container

Warning: Do not use the Ricgraph Podman container in a production environment, since it does not provide a web server (such as Apache). If you would like to harvest a lot of items, you are better off using Ricgraph for a single user or Ricgraph as a server. The Ricgraph Podman container is ideal for instructional or personal use.

The Ricgraph Podman container has been designed in such a way that it is easy to use. This also means that some “good container design practices” have not been followed, in particular:

  • the harvested items are stored in the Ricgraph Podman container (usually, one would use data storage in the filesystem on the host);
  • Neo4j Community Edition and Ricgraph are in the same Ricgraph Podman container (usually, one would use separate containers).

So, do not use the Ricgraph Podman container in a production environment.

2 Install Podman

Only for this step you will need Administrator or root access on your machine. Choose one of the following:

  • Linux:
  • MacOS:
  • Windows: The following information might help you to install Podman on Windows. Note that you will need Administrator privileges.
    • For both the command line version and the Desktop GUI version of Podman, you will need Windows Subsystem for Linux (WSL) 2. Install it as follows:

      • Open a PowerShell (Admin) or Terminal (Admin).

      • Type:

        dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart
wsl --install --no-distribution
    Next, for the command line version of Podman:
    • Get Podman from the GitHub releases page https://github.com/containers/podman/releases, choose the latest version with file name extension .msi.
    • Install it by clicking on the downloaded file, follow the instructions.
    • Exit your Administrator privileges.
    • Open Windows PowerShell or Terminal and use the commands in the sections below.
    Or, for the Desktop GUI version of Podman:
    • Follow the instructions from Install GUI version Podman Desktop.
    • You might get a Windows Firewall message, asking “Do you want to allow public, private, and domain networks to access this app?”. Choose Private networks from the list and click “Allow”.
    • After installation of the Desktop GUI version of Podman, you will need to make a Virtual Machine to run Podman. Podman Desktop will ask you to do this. Follow the instructions.
    • I got a weird error during installation, but rebooting my Windows machine resolved it. Try it, if you get a similar message.
    • Note that Podman Desktop GUI also installs Podman command line version.
    • Exit your Administrator privileges.
    • Open Windows PowerShell or Terminal and use the commands in the sections below.
    • Or use Podman Desktop GUI to pull the Ricgraph image (for location see below) and to start it.

3 Install and run the Ricgraph Podman container

For the following commands, you will need a Terminal or Command line or PowerShell window. If you use the Podman Windows command line version, first start Windows Subsystem for Linux (WSL) by typing wsl in the Windows Terminal or PowerShell window.

The Ricgraph container is hosted on the GitHub Container repository https://ghcr.io/utrechtuniversity/ricgraph.

There are two ways to run the Ricgraph Podman container:

  1. You have not done a podman commit (see below).

    Run the latest (newest) version of the Ricgraph Podman container, and download it if you don’t have it:

    podman run --pull=newer --name ricgraph -d -p 3030:3030 ghcr.io/utrechtuniversity/ricgraph:latest

    If you get an error like Error: creating container storage: the container name “ricgraph” is already in use, type:

    podman run --pull=newer --replace --name ricgraph -d -p 3030:3030 ghcr.io/utrechtuniversity/ricgraph:latest

  2. You have done a podman commit (see below).

    Run the local version of the Ricgraph Podman container (do not use the --pull=newer flag):

    podman run --name ricgraph -d -p 3030:3030 ghcr.io/utrechtuniversity/ricgraph:latest

    If you get an error like Error: creating container storage: the container name “ricgraph” is already in use, type:

    podman run --replace --name ricgraph -d -p 3030:3030 ghcr.io/utrechtuniversity/ricgraph:latest

Starting the container takes about ten seconds. Explore items with Ricgraph Explorer, in your browser, go to http://localhost:3030.

If you started podman run for the first time, the container does not have data in it. You can observe this by going to the Ricgraph Explorer home page (http://localhost:3030), by scrolling down to the “About Ricgraph” section, and looking for the number of nodes and edges. The easiest method for getting data in it, is to run the multiple_harvest_demo.sh script that harvests a selection of research information of Utrecht University (from the data repository Yoda and the Research Software Directory). These two repositories do not need authentication keys. Running this script will take several minutes to complete. Type

podman exec -it ricgraph make run_bash_script

It is a design decision to store all harvested items in the Ricgraph container (see Notes on the Ricgraph Podman container), so make them permanent (i.e. also available after restart of the container) by typing:

podman commit ricgraph ghcr.io/utrechtuniversity/ricgraph:latest

Now restart the Ricgraph container to see the results:

podman restart ricgraph

Explore the harvested items with Ricgraph Explorer, in your browser, go to http://localhost:3030.

You can stop all containers by typing:

podman stop -a

To (re)start, use the podman run command above.

4 Advanced use of the Ricgraph Podman container

For the following commands, you will need a Terminal or Command line or PowerShell window. If you use the Podman Windows command line version, first start Windows Subsystem for Linux (WSL) by typing wsl in the Windows Terminal or PowerShell window.

Get the status of all containers:

podman ps

Remove all podman containers:

podman rmi -a -f

Use a bash shell “in” the Ricgraph Podman container:

podman exec -it ricgraph /bin/bash

To harvest other sources then Yoda and the Research Software Directory, you will need to modify the Ricgraph Podman container. You might need to add API keys to the Ricgraph initialization file ricgraph.ini. Follow these steps:

  • Execute a bash shell in the Ricgraph Podman container (see above). Do the following commands in the container (in the bash shell you just started).

  • Add API keys to ricgraph.ini, if necessary for the sources you would like to harvest. It is in /usr/local in the container. You can use vim (or vi) to edit it.

  • Go to the directory with harvest scripts:

    cd /app/ricgraph/harvest

  • Run a harvest script (they start with ‘harvest_’):

    python [name of harvest script]

    or create your own harvest script. For more information, read Ricgraph harvest scripts. You can also use the scripts that harvest multiple sources.

  • Make the data permanent in the container, see podman commit above.
    Note that the size of your container may explode if you harvest a lot of items.

  • Restart the container, see podman restart above.

You can also use Ricgraph Makefile targets.

For other useful commands, read the comment section of the Containerfile.

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