[bugfix] Some dataset tooltips do not render to values

[abought]

Summary

Some portal dataset tooltips show code rather than values- see example.

This most often happens for phenotypes that contain special characters, like hyphens.

Details

When multiple datasets are in use, the plot uses namespaces to locate the correct data. LocusZoom has certain rules for syntax, and only allows limited sets of characters to be used for namespaces. (see regex, alphanumeric + underscores).

Speculative fix

I do not have a running instance, but the following may help:

Change the portal datasource creation code to remove special characters.

var source_name = phenotype.replace(/[^A-Za-z0-9_]/g, "")
dataSources.add(source_name, new broadAssociationSource(geneGetLZ, rawPhenotype,dataSetName,propertyName,makeDynamic));

You will then need to update layouts to reference the new namespace name correctly (lines of the form {namespace: { thing1: thing2 }}- here is one; there are probably others).

[benralexander]

Seems like a good idea, Andy. We will explore further.

On Wed, Oct 3, 2018 at 5:40 PM Andy Boughton notifications@github.com wrote:

Summary

Some portal dataset tooltips show code rather than values- see example. [image: screen shot 2018-10-03 at 5 19 48 pm] https://user-images.githubusercontent.com/2957073/46440157-8d6eb300-c730-11e8-8dc6-81300f33fa1e.png

This most often happens for phenotypes that contain special characters, like hyphens. Details

When multiple datasets are in use, the plot uses namespaces to locate the correct data. LocusZoom has certain rules for syntax, and only allows limited sets of characters to be used for namespaces. (see regex https://github.com/statgen/locuszoom/blob/c4b0be2d5f36416536739b8bcdc322d8f67cf78c/assets/js/app/Layouts.js#L64, alphanumeric + underscores). Speculative fix

I do not have a running instance, but the following may help:

Change the portal datasource creation https://github.com/broadinstitute/dig-diabetes-portal/blob/c2b8dcffa7977b42e072e8efdf4d0850e5e5b355/web-app/js/lib/dport/locusZoomPlot.js#L1690 code to remove special characters.

var sourcename = phenotype.replace(/[^A-Za-z0-9]/g, "") dataSources.add(source_name, new broadAssociationSource(geneGetLZ, rawPhenotype,dataSetName,propertyName,makeDynamic));

You will then need to update layouts to reference the new namespace name correctly (lines of the form {namespace: { thing1: thing2 }}- here is one https://github.com/broadinstitute/dig-diabetes-portal/blob/c2b8dcffa7977b42e072e8efdf4d0850e5e5b355/web-app/js/lib/dport/locusZoomPlot.js#L1199; there are probably others).

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[abought]

Thanks, Ben.

To make things easier, the next LZ.js release will add a warning message for situations like this: https://github.com/statgen/locuszoom/commit/82c4422c675e822f2416bd3051e30c39475f9abc

For now we will only warn, in order to avoid breaking sites like the portal. In later versions I would expect LZ.js to throw an error instead.