ArangoDB

Torc relies heavily on the multi-model database ArangoDB. It uses graphs to store relationships/dependencies between workflow objects and documents for user-defined data.

Torc provides a moderately-comprehensive set of CLI commands and a custom HTTP API endpoint with auto-generated client API libraries. The goal is for users to not be forced to deal with ArangoDB directly, but there are still cases where that may be required. The web UI is particularly beneficial for useful for running queries, visualizing workflow graphs, and making minor edits to documents.. arangodump/arangorestore are great for backups.

Arango tools

Here are documentation links for some of their tools:

• Web UI: https://www.arangodb.com/docs/stable/programs-web-interface.html

• Queries: https://www.arangodb.com/docs/stable/programs-web-interface-aql-editor.html

• Shell: https://www.arangodb.com/docs/stable/programs-arangosh.html

• Export: https://www.arangodb.com/docs/stable/programs-arangoexport.html

• Backups: https://www.arangodb.com/docs/stable/programs-arangodump.html

• HTTP API: https://www.arangodb.com/docs/stable/http/

Installation

The recommended way of running these tools is through Arango’s Docker container. You can also install it locally; refer to https://www.arangodb.com/download-major/.

Here are example commands with arangodump to test your installation.

Docker

$ docker run -it arangodb/arangodb:latest arangodump --help

apptainer

$ module load apptainer
$ apptainer run /datasets/images/arangodb/arangodb.sif arangodump --help

Warning

Some commands require access to the local filesystem. If you are currently on the HPC’s shared filesystem, you might need to bind-mount the directory so that the software inside the container can access it.

Example with bind mount:

$ apptainer run -B /scratch:/scratch /datasets/images/arangodb/arangodb.sif arangodump --help

Local

$ arangoexport --help