A node parse-transform utility to remove authors from scientificNames in GBIF Backbone to use in ALA

gbif-backbone-parse-for-ala.js

//
// DEPRECATED
// Use: https://github.com/living-atlases/gbif-taxonomy-for-la
//
const parse = require("csv-parse/lib/es5");
const transform = require('stream-transform');
const fs = require('fs');

var readStream = fs.createReadStream("./gbif-backbone/Taxon.tsv.orig");

const parser = parse({
  quote: null,
  delimiter: '\t'
});

var atFirstLine = true;

const transformer = transform(function(record) {
  if (atFirstLine) {
    // we skip the first line
    atFirstLine = false;
  } else {
    const hasAuthor = record[6].length > 0;
    const hasCanonicalName = record[7].length > 0;
    const sciName = record[5];
    if (hasAuthor) {
      if (hasCanonicalName) record[5] = record[7];
      else {
        // no canonicalName so we try to remove author from sciName if it's there
        var pos = record[5].lastIndexOf(" " + record[6]);
        if (pos !== -1) {
           record[5] = record[5].substr(0, pos);
        }
      }
    }
  }
  return record.join('\t')+'\n';
});

readStream.on('open', function () {
  readStream.pipe(parser).pipe(transformer).pipe(process.stdout)
});

readStream.on('error', function(err) {
  readStream.end(err);
});

@rpfigueira lucky you! I So have to reindex my errors personal index ;-)

Back to this. I updated my gist following the @rpfigueira comment.
Before:

nameindexer --testSearch "Methanobrevibacter ruminantium"         
(...)
Search for name: Methanobrevibacter ruminantium
ID: 1000111
GUID: 1000111
Classification: "Balch & Wolfe, 1981 (Smith & Hungate, 1958)",Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobrevibacter
Scientific name: Methanobrevibacter ruminantium (Smith & Hungate, 1958) Balch & Wolfe, 1981
Authorship: Balch & Wolfe, 1981 (Smith & Hungate, 1958)
Rank: SPECIES
Synonym: null
Match type: exactMatch

and now:

nameindexer --testSearch "Methanobrevibacter ruminantium"                                                                                                                             
(...)
Search for name: Methanobrevibacter ruminantium
ID: 1000111
GUID: 1000111
Classification: "Balch & Wolfe, 1981 (Smith & Hungate, 1958)",Archaea,Euryarchaeota,Methanobacteria,Methanobacteriales,Methanobacteriaceae,Methanobrevibacter
Scientific name: Methanobrevibacter ruminantium
Authorship: Balch & Wolfe, 1981 (Smith & Hungate, 1958)
Rank: SPECIES
Synonym: null
Match type: exactMatch

Thanks!

The issue reported by Tim gbif/checklistbank#100