[Feature Request] Add "derivesFrom" key in studies.materials.samples.

[xiaoranzhou]

Describe the bug
There is not "derivesFrom" key in the studies.materials.samples
When using the same ARC to generate ARC JSON,
ARCcommander's output has derivesFrom

                            "name": "CAM_01",
                            "factorValues": [...],
                            "derivesFrom": [
                                {
                                   
                                    "name": "DB_097",
                                    "characteristics": [

                                        {
                                          "category":{
                                            
                                          },
                                          "value":{
                                             "annotationValue":"Arabidopsis thaliana",
                                             "termSource":"",
                                             "termAccession":""
                                          }
                                       }
                                    ]
                                }
                            ]
                        }

But the new ISA json export from ARCtrl does not have "derivesFrom"

Here is the isa specification.

To Reproduce
Steps to reproduce the behavior:

1. Use the following js script to create an ISAJSON

import {Xlsx} from "@fslab/fsspreadsheet";
import * as ARC from '@nfdi4plants/arctrl';
import fs from "fs";
import path from "path";

// Write

export function normalizePathSeparators (str) {
  const normalizedPath = path.normalize(str)
  return normalizedPath.replace(/\\/g, '/');
}


export async function fulfillWriteContract (basePath, contract) {
    function ensureDirectory (filePath) {
        let dirPath = path.dirname(filePath)
        if (!fs.existsSync(dirPath)){
            fs.mkdirSync(dirPath, { recursive: true });
        }
    }
    const p = path.join(basePath,contract.Path)
    if (contract.Operation = "CREATE") {
        if (contract.DTO == undefined) {
            ensureDirectory(p)
            fs.writeFileSync(p, "")
        } else if (contract.DTOType == "ISA_Assay" || contract.DTOType == "ISA_Assay" || contract.DTOType == "ISA_Investigation") {
            ensureDirectory(p)
            await Xlsx.toFile(p, contract.DTO)
        } else if (contract.DTOType == "PlainText") {
            ensureDirectory(p)
            fs.writeFileSync(p, contract.DTO)
        } else {
            console.log("Warning: The given contract is not a correct ARC write contract: ", contract)
        }
    }
}

// Read

export async function fulfillReadContract (basePath, contract) {
  async function fulfill() {
      const normalizedPath = normalizePathSeparators(path.join(basePath, contract.Path))
      switch (contract.DTOType) {
          case "ISA_Assay":
          case "ISA_Study":
          case "ISA_Investigation":
              let fswb = await Xlsx.fromXlsxFile(normalizedPath)
              return fswb
              break;
          case "PlainText":
              let content = fs.readFile(normalizedPath)
              return content
              break;
          default:
              console.log(`Handling of ${contract.DTOType} in a READ contract is not yet implemented`)
      }
  }
  if (contract.Operation == "READ") {
      return await fulfill()
  } else {
      console.error(`Error (fulfillReadContract): "${contract}" is not a READ contract`)
  }
}



export function getAllFilePaths(basePath) {
  const filesList = []
  function loop (dir) {
      const files = fs.readdirSync(dir);
      for (const file of files) {
          const filePath = path.join(dir, file);
  
          if (fs.statSync(filePath).isDirectory()) {
              // If it's a directory, recursively call the function on that directory
              loop(filePath);
          } else {
              // If it's a file, calculate the relative path and add it to the list
              const relativePath = path.relative(basePath, filePath);
              const normalizePath = normalizePathSeparators(relativePath)
              filesList.push(normalizePath);
          }
      }
  }
  loop(basePath)
  return filesList;
}




// put it all together
async function read(basePath) {
    let allFilePaths = getAllFilePaths(basePath)
    // Initiates an ARC from FileSystem but no ISA info.
    let arc = ARC.ARC.fromFilePaths(allFilePaths)
    // Read contracts will tell us what we need to read from disc.
    let readContracts = arc.GetReadContracts()
    console.log(readContracts)
    let fcontracts = await Promise.all(
        readContracts.map(async (contract) => {
            let content = await fulfillReadContract(basePath, contract)
            contract.DTO = content
            return (contract) 
        })
    )
    arc.SetISAFromContracts(fcontracts);
    console.log(fcontracts);
    return arc
}

// execution

await read("Facultative-CAM-in-Talinum").then(
    arc =>  {try {
        fs.writeFileSync('isa-export.json', ARC.JsonController.Investigation.toISAJsonString(arc.ISA, void 0, true))
        // file written successfully
      } catch (err) {
        console.error(err);
      }}



)

2. Open export Search "derivesFrom" in the text and cannot found it.

Expected behavior
Have "derivesFrom" which links the sample and source.

[HLWeil]

Hey Xiaoran, thanks for issue.

Technically, the isa json we create follows the specification set by the isa-json schemas. Therefore I changed the name from "Bug" to "Feature Request".

But I see the need to include more features used by other isa-related tools (as with the #392).

[xiaoranzhou]

Hey Xiaoran, thanks for issue.

Technically, the isa json we create follows the specification set by the isa-json schemas. Therefore I changed the name from "Bug" to "Feature Request".

But I see the need to include more features used by other isa-related tools (as with the #392).

Hi Lukas,
Thanks for the fast and information. Yes, it is more of a feature request.
I have also found that some of the ids are different from the ISA JSON generated by ARCcommander.
Previously the ARC commander generated ISA JSON only has the name such as “CAM_01” and “CAM_01_ext”
In the new ISA-JSON, some prefix like “sample_” and “source_” were added to the CAM_01.
There are "#Sample_CAM", "#Source_CAM_01" and "#Sample_CAM_01_ext" exist and "#Source_CAM_01" exist only as an id in one input. Could you please explain their usage?