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Errors in ProtVista component in Pharos #64

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KeithKelleher opened this issue Nov 28, 2020 · 0 comments
Open

Errors in ProtVista component in Pharos #64

KeithKelleher opened this issue Nov 28, 2020 · 0 comments

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@KeithKelleher
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We're seeing some errors in Pharos coming from the ProtVista component. For example this one, but it seems to happen on most proteins: https://pharos.ncats.nih.gov/targets/mapk1#sequence

TypeError: Cannot read property 'charAt' of undefined
at SVGCircleElement. (11-es2015.50e2a2f87d650b388ab3.js:39)
...

It's happening on this line of the VariantViewer.js
.attr('cy', function(d) {
return variantViewer.yScale(d.alternativeSequence.charAt(0));
})

It seems most variants have an alternativeSequence set, but some do not. I don't know if something changed in the data model that now allows some Variant objects to not have an alternativeSequence, or something else changed?

Printing things out for myself locally, here's an example from MAPK1 of a variant that passes without error:

alternativeSequence: "S"
begin: 87
codon: "AAT/AGT"
consequenceType: "missense"
cytogeneticBand: "22q11.22"
end: 87
genomicLocation: "NC_000022.11:g.21807706T>C"
locations: (4) [{…}, {…}, {…}, {…}]
mutatedType: "S"
predictions: (2) [{…}, {…}]
somaticStatus: 0
sourceType: "large_scale_study"
type: "VARIANT"
wildType: "N"
...

and the next one that is missing an alternativeSequence and throws the error:

begin: 88
consequenceType: "inframe deletion"
cytogeneticBand: "22q11.22"
descriptions: [{…}]
end: 88
genomicLocation: "NC_000022.11:g.21807702_21807704del"
locations: (2) [{…}, {…}]
somaticStatus: 0
sourceType: "large_scale_study"
type: "VARIANT"
wildType: "D"
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