Stabilise reorganisation changes; include spreadsheet and sign-up improvements

[Don-Isdale]

This branch contains reorganisation changes (#190), which are working ok, but with some issues to be stabilised, spreadsheet improvements, particularly in error reporting to the frontend GUI. The aim of the PR is to track issues and prepare this branch for release. Some improvements to sign-up may be added, noted in #216.

[Don-Isdale]

reported Fri 2023Jan20 by G in Teams 'Pretzel meeting'

• [x] [/3H] problems with the SNP data 09:57 019a6c16 add cacheClearKey().

• [x] [/2H] after doing a zoom and then reset zoom, the paths outside the zoom do not draw back automatically they are re-drawn if you do a zoom on the axis you did the original zoom on, but not on the other 10:09 b3e0387b re-filter paths after reset zoom

• [x] [/3H] searching for a feature produces a triangle but it is coloured black (used to be coloured by block i think): 10:13 13610137 feature search triangle colour was black

• [x] gets coloured correctly after adding another axis (but then that axis has a black triangle): 10:14 Fixed above : 13610137

• [x] [/2H] Reset Zooms in the View tab no longer works 10:25 fe230218 re-connect Reset Zooms button in the View tab

• [x] [/2H] Unchecking "Show Zoom/Reset buttons" does nothing same for "Axis Ticks on Outer side" 10:26 b9d9f2ff re-connect checkbox : Show Zoom/Reset buttons [/3H] f81bf0a5 re-connect update of axis Zoom/Reset button colour : brushed, zoomed. [/1H] af4d7230 change to initialisation of previous change b9d9f2ff,f81bf0a5 [/5H] fdde9243 reconnect : Axis Ticks on Outer side [/1H] 5c26f1f8 re-connect .extended in axisSide(), 452a3af8

• [x] # Ticks slider doesn't work Graph Text Size doesn't do anything (I think this hasn't worked for a while) 10:27 Tested OK in 13610137

• [x] [/4H] not getting histogram after loading vcf and strange behavior if i zoom in 16:54 e23c6d8f add /usr/local/bin/ to PATH for bcftools 019a6c16 add cacheClearKey().

• there's been a bug for a while where doing a feature search often requires you to press search twice first time it does nothing 16:55

• • not reproduced, Feb01

• [x] has the black coloured feature here Fixed above : 13610137

• [x] [/1.5H] and histogram off the end of axis 17:00 Feb01 : not reproduced exactly, but mousewheel-zoom into VCF features counts histogram reduced the range instead of the domain. 0821425d fix scaling of feature counts histogram

• [ ] it seems much slower - maybe related to the SNP loading like i think it's trying to draw a load of snps at the top all the time the genetic maps aren't noticeably slower but the SNP data is 17:00 [/2H] 97b6fdf3 store vcf featuresCounts result in cache

• [x] reset zooms does nothing 17:00 fe230218 re-connect Reset Zooms button in the View tab.

• [x] [/2H] BLAST searching this marker, it works on main, not on dev:

  BobWhite_c1002_263 CCTTACAGGCAAACAGGTGGTGCACTTGGACTTCATGGTTCACACAGCTC 17:10 f117e913 update paths in dnaSequenceSearch.bash for lb4app

• [x] I uploaded a test map with 2 markers which are present in the Savannah_x_Rialto 7A map here. When I load it and brush over the first marker, there is a path in the paths table but no path is drawn: 17:13 Tested OK using CSV (table) upload :

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Added features :

• [x] [/3H] d796003c add axisFontSize slider for ticks text