ARCSummary

Create or update markdown content of ARCs dynamically

ARCSummary aims to facilitate the dynamic generation of markdown content. It serves as a up-to-date overview of the ARCs current state since all the information is derived from the content of an already established or starting investigation.

Setup

Clone this repository locally to run with or without docker.

ARCsummary currently supports two main subcommands:

• summary Updates your README.md to the current version
• summarymr Pushes the updated summary to a side branch and opens a MergeRequest onto the main branch.

Download and run Docker image

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

docker run -v "</path_to_your_arc>:/arc" ghcr.io/nfdi4plants/arc-summary:main summary -d /arc
docker run -v "</path_to_your_arc>:/arc" ghcr.io/nfdi4plants/arc-summary:main summarymr -d /arc -t your_access_token -i user/repository

Build and run Docker image

For reference as this is based on the docker setup provided by arc-export see the docs

docker build -t dockerimage:latest /path/to/ARCSummary 

docker run -v "</path_to_your_arc>:/arc" dockerimage:latest summary -d /arc
docker run -v "</path_to_your_arc>:/arc" dockerimage:latest summarymr -d /arc -t your_access_token -i user/repository

Build and run .NET app

cd /path/to/your/CLI
dotnet restore
dotnet build
dotnet run summary -d /path/to/your/arc
dotnet run summarymr -d /path/to/your/arc -t your_access_token -i user/repository

Update via YAML

Alternatively you can include an empty YML file at the following root of your arc ("../.arc/arc_summary.yml"), which will return the default order. A suitable theme can be chosen here. For example for the publication style just include:

publicationstyle

Create a custom format using the currently supported format:

Custom:
   - Investigation # Top-level information based on metadata
      - Title
      - Description
      - Contacts
      - Publication
   - TOC # Table of Contents
   - ProvenanceGraph 
      - AsISA # Flowchart comparing study & assay relationships
      - AsArcTables # Flowchart comparing ArcTable relationships
   - OverviewTable # Additional table based on metadata
   - Studies
      - Title
      - Description
      - Additionaldetails
      - Annotationheaders
   - Assays
      - Title
      - Description
      - Additionaldetails
      - Annotationheaders

The order and sections to include are at the user's discretion. All input is later interpreted in complete lowercase.

Help

For Summary:

By default summary appends the generated content to the preexisting README.md file. If you would like to create the markdown as a separate SUMMARY.md file from the preexisting one you can set the optional flag to --indiv true.

USAGE: ARCSummary summary [--help] --arc-directory <arcPath>
                          [--individualmd <bool>]

OPTIONS:

    --arc-directory, -d, -ap <arcPath>
                          Location of the ARC in the Filesystem                     
    --individualmd, --indiv <bool>
                          Creates an individual markdown separate from
                          preexisting if true
    --help                display this list of options.

For SummaryMR:

USAGE: ARCSummary summarymr [--help] --arc-directory <string> --token <string> --pathorid <string> [--commitmessage <string>] [--mrtitle <string>] [--sourcebranch <string>] [--targetbranch <string>] [--username <string>] [--useremail <string>] [--apiadress <string>]

OPTIONS:

    --arc-directory, -d <string> 
        MANDATORY: Location of the ARC in the Filesystem

    --token, -t <string>  
        MANDATORY: Personal access token for gitlab

    --pathorid, -i <string> 
        MANDATORY: ID or URL-encdoded path of the project after .org/, e.g. username/myprojectname

    --commitmessage, --message <string>
        OPTIONAL: Message to be used for the commit.

    --mrtitle, --title <string>
        OPTIONAL: Title of the Merge Request

    --sourcebranch <string>
        OPTIONAL: Name of the branch to which the commit should be pushed, and which will be the
                          source branch of the MR. Default is `arc-summary`

    --targetbranch <string>
        OPTIONAL: Name of the reference branch which is the target for the MR. Default is `main`

    --username, --name <string>
        OPTIONAL: Username to be used for the commit

    --useremail, --email <string>
        OPTIONAL: Email to be used for the commit

    --apiadress, --api <string>
        OPTIONAL: Testing Server URL
        
    --help 
        display this list of options.

Prompt generation

Currently ARCSummary supports the generation of three prompts: basic, enhanced and hybrid (enhanced + ToC) for use with ChatGPT

    basicprompt, -p1 <options>
        Generates a basic prompt based on arc-path for
        ai-asssisted paragraph on the investigations objectives
        
    enhancedprompt, -p2 <options>
        Generates a enhanced prompt based on arc-path for
        ai-asssisted paragraph on the investigations objectives

    hybridprompt, -p3 <options>
        Generates a enhanced + CoT prompt based on arc-path
        for ai-asssisted paragraph on the investigations objectives