Update web VEP input detection in JavaScript (e111)

[nuno-agostinho]

1. Update JavaScript regex to validate VEP input formats.
2. Preview CAID¹ and Region input.

Related with:

• Detect input format using VEP code ensembl-variation#1026
• Fix web VEP input format detection ensembl-vep#1477

Footnotes

1. ENSVAR-5945: CAID is not currently supported in REST, so the preview will simply state that the variant ID was not found. ↩

[jyothishnt]

This regex looks complex.

1. Can you please break it down and also move it to a separate method?
2. If you are marking it case insensitive you don't need to capitalise ACGTN.
3. Please add in more examples of regions in the comments (line 269)

[nuno-agostinho]

Hey @jyothishnt, when you mention breaking it down, do you mean something like this?

var chrom  = "([^:]+)";
var pos    = "(\\d+)-(\\d+)";
var strand = "(:[-\+]?1)?";
var allele = "([a-z]{3,}|[ACGTN-]+)";

const re   = new RegExp(`^${chrom}:${pos}${strand}[\/:]${allele}$`, "i");
data[0].match(re);

[azangru]

Interesting. I had something rather like this in mind:

const parts = data[0].split(':');
const [chromosome, position, allele] = parts;
if (parts.length !== 3 || !chromosome || !position || !allele) {
  return;
}

const isValidPositionFormat = /^\d+-d+$/.test(position);
const isValidAlleleFormat = /^[a-z]{3,}$/i.test(allele) || /^[ACGTN-]+$/i.test(allele);

// chromosome has already been checked in the if-statemebt above
if (isValidPositionFormat && isValidAlleleFormat) {
  return 'region';
}

[azangru]

return;
...
return 'region';

Sorry, I meant return false or return true in my snippet above. I imagined it as a method that would be called inside of the if-condition that currently contains the long regex. Something like if (this.isRegionFormat(data)) { return 'region'; }.

[nakib103]

Hi @jyothishnt @azangru ,

Thanks for reviewing this PR.

• Breaking that function by splitting : has a problem because the elements are not always separated by :.

• This function implements the same logic as detect_format function used in ensembl-vep and ensembl-variation. Having same logic in different places was causing issue when we are doing updates in one places and the other place was not being updated. So, we recently made changes to have to only have one function in ensembl-variation -
  Fix web VEP input format detection ensembl-vep#1477
  Detect input format using VEP code ensembl-variation#1026
  Unfortunately we need to keep this function also (making changes in 2 places is better than 3 at least !). Saying all these things is prelude to saying it is better for us if we can keep the logic same as the other function so it is easy to update in future -
  https://github.com/Ensembl/ensembl-variation/blob/86bad9e537344c88df5fb04e8ee0fce0a7d59876/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm#L388

Let me know if that makes sense.

[azangru]

Breaking that function by splitting : has a problem because the elements are not always separated by :.

But your regular expression was also checking for the presence of :, wasn't it? If a string does not have a :, it would fail this particular check (parts.length will not equal 3), just as the regex would.

Anyway, if you have a strong preference for the long regex, I don't have any objections. It is not the new site, after all.

[nakib103]

This part of the regex allows the second : to be not present -
(:[-\+]?1)?[\/:]

Example here -
https://www.ensembl.org/info/docs/tools/vep/vep_formats.html#region

Yeah, it is better to not introduce a potential breaking changes for the current sites. Thanks!