ARC Converters

Auto-deployed collection of ARC converters for converting ARCs to end-point repositories.

General workflow

Converters in this repository are simple fsx script files that share a common structure
When pushed to the main branch, they get automatically compiled and released
Now they are accessible using the ArcCommander, which makes use of the common structure to to run a streamlined conversion

Contribution Guide

Guidelines

Create issue with background information about the converter you want to add. This also serves as a place for discussion.
Fork this repository.
Create a feature branch.
Clone your fork-branch.
Add/Update ONE new converter.
Test your converter locally.
Commit, push and sync your branch.
- 👀 Add your issue id (for example #32) to your commit so it is automatically linked.
Open a pull request referencing your issue. 🎉

Create a converter

Start with adding a file to the converters folder. It MUST follow the naming scheme arc-convert-<FORMATNAME>.fsx.
Go into the file and add a reference to arcIO.NET
Add a create() function which has the converter body as return value

The converter body must be of type ARCconverter(located in arcIO.NET.Converter), selecting the return type you want. Your code could now look like this:

#r "nuget: arcIO.NET, 0.1.0-preview.5" 
#r "nuget: FSharp.Data, 5.0.2"

open ISADotNet
open ISADotNet.QueryModel
open ISADotNet.QueryModel.Linq.Spreadsheet
open arcIO.NET.Converter
open FsSpreadsheet.DSL
open FSharp.Data

let create() = ARCconverter.ARCtoXLSX (
    fun i s a ->
     
    )

Note, that all converters take a QInvestigation, a QStudy and a QAssay as input. Which study and assay are selected to be converted is decided by the ArcCommander when running the conversion.

Now fill out the converter body as you wish, the return type being determined by the format case you specified.
- Documentation about the ISADotNet Querymodel can be found here
- Documentation about the FsSpreadsheet DSL can be found here
- Documentation about the LitXML DSL can be found here

Test a converter

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Run a deployed converter

Released converters can be run by the ArcCommander using the syntax:

arc convert geo

Check out arc convert --help for additional info.

Allowed references

Only references to libraries referenced by the ArcCommander are allowed:

#r "nuget: arcIO.NET, 0.1.0-preview.5" 
#r "nuget: FSharp.Data, 5.0.2"
#r "nuget: LitXml"

Note, that arcIO.NET is always required and already comes packed with all dependencies for using the ISADotNet QueryModel and parsing to Spreadsheet based output formats.

nfdi4plants/converters