78988553dd9b460c26f0b9f21f15a1aacfad9dab lrnassar Fri Aug 21 15:44:40 2026 -0700 Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001 Sentence-case the tissue names and the facet column titles, so the barChart facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the bigWig matrix reads "Spleen". Only the first character is upper-cased. Added sentenceCaseTissues.sh, which does the .facets and .categories files and is idempotent, since the hub still ships lower-case and this has to be replayed after any refetch. The count and color column names are deliberately left lower-case: barChartUi.c requires a field literally named "count" to load the file at all, and facetedTable.c keys its merge logic on "count", "color" and "val". Renaming the faceted columns means trackDb matches, so the stanzas now read barChartFacets Tissue,Timepoint. Set priority on the container children so the default-visible M21 TPM sorts first and the signal composite sorts last. The composite needs an explicit value; without one it inherits the superTrack's 0.6 and floats to the top. Fix the All reads view, which was inert. Every all-reads subtrack shipped parent off, so switching the view to full revealed nothing. The view's own visibility already gates drawing, so the subtrack state should not encode the view as well. The default image is unchanged at 78 unique-reads rep1 tracks, and switching the view to full now yields 156. This also makes the Rep 2 toggle symmetric across the two views. Rename the bigWig subGroup3 display label from Age to Timepoint, matching the barChart facet and the .facets column. The group name stays "age" because dimensions and sortOrder reference it by name. Add relatedTracks cross-links between the mm10 container and Tabula Muris. Not Tabula Muris Senis, which is not on the RR. Description pages: reorder the mm10 subtrack list to match the new display order, "sub tracks" to "subtracks", capitalise the colour legend tissue names, and correct the mm39 Il11ra2 note - the gene appears three times, two of them stacked at one position and sharing a details page, with the third 497 kb away. Makedocs record the casing step, its ordering constraint relative to the reorder and colour steps, and the count/color naming constraint. diff --git src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt index ef6fa45999b..735b227f512 100644 --- src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt +++ src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt @@ -190,16 +190,30 @@ # reapplied after any hub refetch. Originals are kept as *.bb.preStartFix. ~/kent/src/hg/makeDb/scripts/mouseDevTimecourse/fixBarChartStarts.sh mm39 \ /hive/data/outside/woldlab/mouseDevTimecourse/mm39/mouse_development_TPM_M21_mm39.bb \ /hive/data/outside/woldlab/mouseDevTimecourse/mm39/mouse_development_FPKM_M21_mm39.bb # liftOver accounting, for the description page: mm10 M21 has 55536 genes and # mm39 M21 has 55447, so 89 genes failed to lift from GRCm38 to GRCm39 and none # were gained. 42 of the 89 are on chr14, 40 of those within chr14:3.2-26.3 Mb; # the rest are scattered. 45 of the 89 carry Gm* or *Rik names. # One gene, Il11ra2, is duplicated in the # mm39 files: ENSMUSG00000078735.3 on mm10 chr4 and ENSMUSG00000095623.1 on the # unplaced scaffold chr4_JH584294_random both lift to mm39 chr4:42656355-42661893, # and their expression vectors are identical. Left in place as a known artifact. +# 2026-08-21 (Lou, QA #37001): sentence-case the tissue names and the facet column +# titles, matching mm10. Only the first character is upper-cased, and the count and +# color column names stay lower-case because hgTracks matches them by exact string. +# trackDb has to match the renamed columns: barChartFacets Tissue,Timepoint. +# Run this LAST, after curl -> reorder -> colour, since those snippets group on the +# lower-case tissue strings. + +~/kent/src/hg/makeDb/scripts/mouseDevTimecourse/sentenceCaseTissues.sh \ + /hive/data/outside/woldlab/mouseDevTimecourse/mm39/mouse_development_M21.facets \ + /hive/data/outside/woldlab/mouseDevTimecourse/mm39/mouse_development_M21.categories + +# Also set priority 1-2 on the two bigBarChart subtracks so the default-visible +# M21 TPM sorts first. + ##############################################################################