Samplegeno & Assorted Fixes (samplegeno-ui-2)

[Bianca-Morris]

Started as just samplegeno fixes, but it was so small that I lumped in the other updates, too.

Changes:

Samplegeno Table

• Shorten ref genotype in header.
• Move ref shortening code out into own function (maybe should memoize/move to util?).

Filtering Table

• Make all columns narrower so more is shown at first.
• Incorporate scientific notation to 3 digits for gnomad column. (E.g. 1.20, 0.120. 0.0120, 1.2e-3, 1.2e-4 etc).
• If genes has more than one item (show all, but comma separate the different entries).
  • Note: Wasn't able to really test this as well as would like on local... need to deploy to get a better idea if it works. Ran into failed validation/infinite validation bug & XML error when attempting to add another gene item to a variant for testing on local. This may inform why some of those SV infinite validation issues were happening previously... incomplete error handling?)
  • Note 2: This column might also be a good candidate for memoization due to looping, string joining?
• Fix 3-row column word-wrapping and text overlap issues.
• Enabled sort for each field visible in each column; most seem to work except for coding effect, which... doesn't behave entirely as expected. Disabled sorting for variant, bamsnap.
• Add comma between "Gene" and "Transcript"
• Change capitalization of "GnomAD" to "gnomAD"

Case Search Table

• Update variant ingestion status to come from case.vcf_file.

Case Bioinformatics Tab

• Add comma decoration to large numeric values in stats section.
• Switch pedigree button to be a provenance button that links to current case.vcf_file's provenance graph

To-Do:

• Bump version before merge

[alexkb0009]

Code looks good! (Haven't tested on local / assuming working as expected)

[Bianca-Morris]

Just commented this out for the time being... not sure if the pedFileName is necessary anymore? I assume if no one gets upset about this not being visible anymore, it's not necessary.

[Bianca-Morris]

May need to do some more work here to make sure these values are always Numbers, not strings. For now, decorateNumberWithCommas falls back to returning the string value anyway, so worst case scenario, it just doesn't add commas/renders the number as it currently is.