arc-export

Automatic building of a Docker container for exporting ARCs to various other ARC representations

Develop

Build

use VS or VSCode tooling or run dotnet build or dotnet test from the command line.

Test

This repo uses external arcs as fixtures to create and test the output. These are referenced as git submodules in /tests/fixtures.

To clone the repo with the submodules, use the following command:

git clone --recurse-submodules

If you have already cloned the repo, you can initialize the submodules with the following commands:

git submodule init
git submodule update

Note that the submodules are set on a specific commit, so do not update them.

To execute the tests run:

dotnet test

Run locally with dotnet

This assumes you have the git submodules cloned as described in the test section.

dotnet run --project ./src/arc-export/arc-export.fsproj -- -p ./tests/fixtures/ArcPrototype/ -f rocrate-metadata -f isa-json -f summary-markdown

Setup

local docker build

docker build . -t arc-export

docker run -v C:\Repos\ArcRepo:/arc arc-export:latest /arc-export -p arc

download container first

docker pull ghcr.io/nfdi4plants/arc-export:main

docker run -v C:\Repos\ArcRepo:/arc ghcr.io/nfdi4plants/arc-export:main /arc-export -p arc

Basic usage

Example

The following command executed from within the ARC (./) creates all three output files in a folder (arc-export) inside the ARC.

docker run --rm -v ./:/arc ghcr.io/nfdi4plants/arc-export:main /arc-export -p arc -f rocrate-metadata -f isa-json -f summary-markdown -o arc/arc-export

Output format Selection

Output format can be specified with the -f flag, followed by one of the following:

• isa-json will produce an arc-isa.json file following the ISA-JSON specification
• rocrate-metadata will produce an arc-ro-crate-metadata.json file following the ARC RO-Crate profile
• summary-markdown will produce an arc-summary.md file
• (experimental) rocrate-metadata-lfs will produce an arc-ro-crate-metadata.json file following the ARC RO-Crate profile, where all objects of type File which are tracked by git-lfs additionally contain the according SHA256 hash

E.g.

docker run -v C:\Repos\ArcRepo:/arc arc-export:latest /arc-export -p arc -f rocrate-metadata -f isa-json -f summary-markdown

will produce all three basic output files.

Help

USAGE: arc-export [--help] --arc-directory <path> [--out-directory <path>]
                  [--output-format <isa-json|rocrate-metadata|rocrate-metadata-lfs|summary-markdown>]

OPTIONS:

    --arc-directory, -p <path>
                          Specify a directory that contains the arc to convert.
    --out-directory, -o <path>
                          Optional. Specify a output directory for the invenio metadata record.
    --output-format, -f <isa-json|rocrate-metadata|summary-markdown>
                          Optional. Specify the output format. Default is ISA-JSON.
    --help                display this list of options.