// addLocusMetadata.go provides a function to manually add locus metadata to the .json files.

package main

import "seekia/resources/geneticReferences/locusMetadata"

import "seekia/internal/helpers"
import "seekia/internal/localFilesystem"

import "encoding/json"

import "slices"

import "log"

func main(){

	/*

	//TODO: Add these loci
	//		They are on the X chromosome, and we haven't defined the syntax to deal with X chromosome loci yet.

	newLocusMetadataObject_1 := locusMetadata.LocusMetadata{
		RSIDsList: []int64{5957354},
		Chromosome: X,
		Position: 120305480,
		GeneNamesList: []string{"TMEM255A"},
		CompanyAliases: make(map[locusMetadata.GeneticsCompany][]string),
		References: make(map[string]string),
	}

	newLocusMetadataObject_2 := locusMetadata.LocusMetadata{
		RSIDsList: []int64{78542430},
		Chromosome: X,
		Position: 48259397,
		GeneNamesList: []string{"SSX1"},
		CompanyAliases: make(map[locusMetadata.GeneticsCompany][]string),
		References: make(map[string]string),
	}

	*/

	// This is a list of metadata objects to add to the locus metadata
	lociToAddList := []locusMetadata.LocusMetadata{
		//newLocusMetadataObject_1,
		//newLocusMetadataObject_2,
	}

	numberOfLociToAdd := len(lociToAddList)

	err := locusMetadata.InitializeLocusMetadataVariables()
	if (err != nil){
		log.Println("ERROR: " + err.Error())
		return
	}

	// Map Structure: Chromosome -> List of locus metadata objects to add
	lociToAddMap := make(map[int][]locusMetadata.LocusMetadata)

	for _, locusObject := range lociToAddList{

		// First we check to see if locus metadata already exists

		locusRSIDsList := locusObject.RSIDsList

		for _, rsID := range locusRSIDsList{

			exists, _, err := locusMetadata.GetLocusMetadata(rsID)
			if (err != nil){
				log.Println("ERROR: " + err.Error())
				return
			}
			if (exists == true){
				rsIDString := helpers.ConvertInt64ToString(rsID)
				log.Println("lociToAddList contains locus whose metadata already exists: " + rsIDString)
				return
			}
		}

		locusChromosome := locusObject.Chromosome

		existingList, exists := lociToAddMap[locusChromosome]
		if (exists == false){
			lociToAddMap[locusChromosome] = []locusMetadata.LocusMetadata{locusObject}
		} else {
			existingList = append(existingList, locusObject)
			lociToAddMap[locusChromosome] = existingList
		}
	}

	for chromosomeInt, locusMetadataObjectsToAddList := range lociToAddMap{

		existingLocusMetadataObjectsList, err := locusMetadata.GetLocusMetadataObjectsListByChromosome(chromosomeInt)
		if (err != nil) {
			log.Println(err)
			return
		}

		newLocusMetadataObjectsList := slices.Concat(existingLocusMetadataObjectsList, locusMetadataObjectsToAddList)

		newChromosomeFileBytes, err := json.MarshalIndent(newLocusMetadataObjectsList, "", "\t")
		if (err != nil){
			log.Println("ERROR: " + err.Error())
			return
		}

		currentChromosomeString := helpers.ConvertIntToString(chromosomeInt)		

		locusMetadataFilepath := "../../resources/geneticReferences/locusMetadata/"

		err = localFilesystem.CreateOrOverwriteFile(newChromosomeFileBytes, locusMetadataFilepath, "LocusMetadata_Chromosome" + currentChromosomeString + ".json")
		if (err != nil){
			log.Println("ERROR: " + err.Error())
			return
		}
	}

	numberOfAddedLociString := helpers.ConvertIntToString(numberOfLociToAdd)

	log.Println("Successfully added " + numberOfAddedLociString + " locus metadatas!")
}