[Feature Request] process.json writer based on annotation table

[Brilator]

Is your feature request related to a problem? Please describe. Instead of writing process.json from scratch or using spawn - esp. for people who already have protocols laid out column-wise.

Describe the solution you'd like Would be helpful to have an exporter to write protocols to a 'process.json' based on a one-row SWATE table with values.

[Brilator]

Now that we're discussing the template <-> protocol connection again, this might be worth reviving. Just to rephrase: I want to be able to fill out an isa.assay.xlsx (e.g. based on SWATE template) and export this to process.json for reuse as routine protocol in other ARCs.

Maybe also ISAdotnet material? @HLWeil

[Brilator]

Actually, isn't the conversion of a single-row isa.assay.xlsx to isa.assay.json just that?

[Freymaurer]

Depends. If you mean "only the column-header" with single-row then it is a protocol, if you mean "header+exactly one more row with values" then it is a process 👍

[HLWeil]

Hey, this is a good idea. If you just want to export the headers, a file with a single process will be enough (An isa protocol does not store the units).

However, if you want to export a filled out table (with values), a single process will probably not suffice. This is because there might be different values set for the same param. This can not be represented by a single process. Therefore you would need a sequence of processes, or even an assay.json.

[HLWeil]

@Brilator I'm not quite sure what you mean by ISADotNet material?

[Freymaurer]

(An isa protocol does not store the units)

Thanks for chiming in @HLWeil, completly forgot that.

[Brilator]

@Brilator I'm not quite sure what you mean by ISADotNet material?

I meant wether this is something where ISADotNet could help to convert.

If you just want to export the headers, a file with a single process will be enough

Yes, I mean to export the headers including one process. Just like this https://github.com/nfdi4plants/ARCexample_protocols/blob/main/assays/Metabolomics/protocols/Protocol_MassSpec_001.json

[HLWeil]

I meant wether this is something where ISADotNet could help to convert.

If I got this correctly you meant to let the converter infer that the name in the sample column describes a material(extract)?

[Brilator]

Sorry, no. :D Scratch the word "material". It has nothing to do with biological material or ISA Model "material".

I thought this was an English expression - e.g. if a person is the perfect significant other to marry, one would call them wife/ husband material. https://www.urbandictionary.com/define.php?term=Wife%20Material https://www.urbandictionary.com/define.php?term=Husband%20Material

And along those lines, I was just wondering wether what you're building with ISADotNet would help in conversion / extraction of info from a user-filled isa.assay.xlsx.

[HLWeil]

Ohhh 😅 , my vocab parsing goes something like this 1. Check ISA Vocab -> 2. Check Street Slang Vocab -> 3. Check General Vocab 😄

Yeah that's definitely something for ISADotNet. @Freymaurer actually you already perform tasks in SWATE similar to this using ISADotNet, right?

And along those lines, I was just wondering wether what you're building with ISADotNet would help in conversion / extraction of info from a user-filled isa.assay.xlsx.

Yeah I'm currently working on a web api for the ISADotNet and other arc related functionalities. This will allow easy access to such conversion tasks from any programming language or tool

[Freymaurer]

The functionality already exists, and will be part of @HLWeil web api, as far as i understand it 👍

[Freymaurer]

In addition an export function to different isa.json types is part of release 0.5.0!