e497eccfb431be6af38d22c5bc2bb0e745c89b2d braney Sat Sep 5 09:22:17 2026 -0700 docent: eight more regression scripts, one per fixed bug rm35580 "Show <alt> placed on its chromosome" errored on the window rm36061 DECIPHER SNVs details missing after a quickLift rm36335 a quickLifted GIAB item click printed a garbled "can't port" rm36340 a search-result click carried the source coordinate rm37491 hgConvert named subtracks the user never showed as not liftable rm37562 a stale lastPosition banner on the lifted search-results page rm37615 a quickLifted bigBed tooltip reported pre-lift coordinates rm37785 a squishyPack track stole a neighbouring track's center label Each asserts the behavior its ticket says is correct, on genome-test, and names in noText:/noUrl: the exact string the buggy build produced rather than a generic "Error". Where the last page has no track image the noText: is paired with a positive text: or url: check, because a bare noText: passes just as happily on a blank page or an early error. Four things found writing these, all of them recorded in the scripts: A ticket's stated position and its stated item can disagree. #36061 says to go to chr7:156,982,676-156,996,015 and click item 517898; that item is at chr7:155,803,191, and decipherSnvs draws nothing at all in the ticket's window. hideKids cannot express "the user deselected this subtrack". It writes a <track>=hide cart variable, and isSubtrackVisible() (hg/lib/trackHub.c) begins with overrideComposite = (NULL != cartOptionalString(cart, tdb->track)) and then forces enabled = TRUE, so the sibling counts as visible to hgConvert and lands back in the "failed to lift" warning. A first rm37491 failed on exactly that and looked like the bug being back. A deselected subtrack is <track>_sel=0 with no visibility variable, which is what hgTrackUi's checkbox writes and what the goto: in that script sets. #37615's fix is not the one the plan for this suite described. The first commit appended a note saying the coordinates came from the source assembly; the second replaced it with the real fix, which puts the TARGET coordinates in the tooltip. A test for the note would fail. decipherSnvs (SNVs) and decipher (CNVs) are two different members of the superTrack decipherContainer, and the row that turns up when the SNVs track draws nothing is the CNVs one, which reads like the same track under a shorter id. refs #38252 diff --git src/hg/utils/docent/tests/regress/rm36335.docent.yaml src/hg/utils/docent/tests/regress/rm36335.docent.yaml new file mode 100644 index 00000000000..53278e8fe39 --- /dev/null +++ src/hg/utils/docent/tests/regress/rm36335.docent.yaml @@ -0,0 +1,55 @@ +# #36335 -- clicking an item in a quickLifted GIAB Problematic Regions track errored. +# +# hg/hgc/bigBedClick.c:502 said +# +# errAbort("can't port %s", fields[3]); +# +# and for a bigBed3 -- which every GIAB subtrack is -- fields[] is only three long, so +# fields[3] read one past the end and the dialog carried whatever was on the stack there. +# It also fired far too often: with bedSize 3 there is no name filter, so every interval +# quickLiftGetIntervals returned went through the remap and a single unmappable item +# aborted the whole page. Fixed in c13d7b1af23 by skipping a NULL remap, then 01badfbaa97 +# for the stacked <BR>s that fix exposed. +# +# Brian's own repro from the ticket, which is one subtrack in pack rather than the whole +# composite: hg38, hide all, alldifficultregions to pack, QuickLift to hs1, go to +# chr7:156,982,676-156,996,015, click an item. +# +# The two halves of the assertion are the error string the ticket quoted and the details +# the fixed page prints. noText: on its own would pass on the buggy page, because that page +# renders perfectly well -- it just carries a garbled warning. text: on the position is +# what says the item was really found and remapped, and 233 bases at +# chr7:156,983,823-156,984,055 is the value recorded in the ticket when the fix was +# verified. +target: genome-test +db: hg38 +position: chr7:156982676-156996015 +reset: true +fast: true +steps: + - go: chr7:156982676-156996015 + - hide: all + - track: {alldifficultregions: pack} + + # Assert the source view first: with nothing drawn here the convert would have nothing to + # lift and the real assertion below could pass for the wrong reason. + - expect: {rows: [alldifficultregions], noText: "Warning/Error"} + + - convert: {to: hs1, quicklift: true} + - open: lift + - expect: {rows: [alldifficultregions], noText: "can't port"} + + # Positional, not named. These items cannot be named at all: type bigBed 3 has no name + # field, so hgTracks writes an EMPTY i= into the hgc href and gives every box the same + # title, "Start of Exon (1/1)". frac: 0.5 takes the box nearest the middle of the row, + # which is enough -- the bug aborted the whole page whenever ANY item in range failed to + # remap, so which one is clicked does not matter. + - click: {track: alldifficultregions, frac: 0.5} + + # "Genomic Size" is the field the ticket names as proof the page renders: the fix was + # verified by seeing Position and Genomic Size come up directly under the title. The + # buggy build never got that far -- errAbort stopped the page and printed the garbled + # "can't port" instead -- so this and the noText: are two halves of one check. + - expect: + text: "Genomic Size" + noText: "can't port"