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addDisciplines.js
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addDisciplines.js
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//Takes a csv will all higher taxa included and adds the Specify discipline to each
const csv = require('fast-csv')
const path = require('path')
var disciplines = [];
var disciplineFile = 'SpecifyDisciplines20191019.csv'
let taxonFile = "taxon_names_with_higher_classification_IE20191018.csv"
//read the disciplines
csv.fromPath(`./${disciplineFile}`, {headers: true})
.on("data", data => {
disciplines.push(data);
})
.on("error", err =>{
console.log('error reading disciplines file')
})
.on("end", () => {
//read the taxa
let taxa = []
csv.fromPath(`./${taxonFile}`, {headers: true})
.on("data", data => {
taxa.push(data);
})
.on("error", err =>{
console.log('error reading taxon file')
})
.on("end", () => {
let disciplineCounts = {}
taxa.forEach(taxon => {
taxon.specifyDiscipline = null
for(var discipline of disciplines){
let disciplineRank = discipline.Rank.toLowerCase().trim()
let disciplineTaxa = discipline.Taxa.split(',').map(t => t.trim())
if(taxon[disciplineRank] && disciplineTaxa.includes(taxon[disciplineRank])){
taxon.specifyDiscipline = discipline.Discipline
if(disciplineCounts[discipline.Discipline]){
disciplineCounts[discipline.Discipline]++
}
else{
disciplineCounts[discipline.Discipline] = 1
}
}
}
//note if we didnt find it
if(!taxon.specifyDiscipline){
if(disciplineCounts.none){
disciplineCounts.none++
}
else{
disciplineCounts.none = 1
}
}
})
//print some feedback
if(Object.keys(disciplineCounts).length > 0){
console.log('Counts per discipline:')
Object.keys(disciplineCounts).forEach(key =>{
console.log(key + ': ' + disciplineCounts[key])
})
}
//write out the results.
//NOTE this scrambles special characters if there is an intermediary .xlsx file
//in that copy and paste the last column back to the original csv
let outfile = taxonFile.replace(/\.csv$/, '_disciplines.csv')
csv.writeToPath(path.resolve(__dirname, outfile), taxa, {headers: true})
.on('error', err => console.error(err))
.on('finish', () => console.log('Done writing out results.'));
})
})