7aba31f14aed7f2620e4746b54f9569a5c93e1ad braney Sat Sep 12 15:07:34 2026 -0700 docent: ten regression tests for quickLift, on hgTracks and on hgc, refs #38252 Fourteen scripts here already lift something -- they are the ones that call `convert: {quicklift: true}` -- so these take the parts of the lift that had no test. Five read the lifted image and five read a details page: rm38032 the target keeps the source's track order. First use of `ordered:`, which was added to expect: for this bug rm38042 a ClinVar CNV running past the chains quickLift loads is clipped rather than dropped, so the spanned-item merge still has it rm37646 a lolly composite subtrack lifts, and its map boxes still carry its own track name -- the string the stale pop pointer clobbered rm36048 the spanned-item merge still works on a lifted DECIPHER track rm37815 "Hide all default tracks on the target" hides all six of hs1's own tracks and keeps the lifted one rm36059 a lifted GENCODE Versions item gives the real details page, in destination coordinates, with no "Can't start query" rm36370 a lifted knownGene click renders GeneReviews and Methods, the two sections the ticket says were missing rm36125 a lifted RefSeq item's page, and its Predicted Protein link returning SHH's peptide instead of a blank page rm36942 the Alignment Differences description, reached from a difference item: the four colors and the figure rm38146 the same page with a GenArk assembly as the SOURCE, down to the base alignment that reads query bases out of a two bit file All ten are assertion-only: every fix shipped long ago. make test is 57 of 57 green in 10m18s, up from 7m34s -- each script costs a convert, about 17 seconds, because no URL builds a quickLift hub. README.txt gains what the batch cost. A lifted row and map box carry a per-run hub__ prefix, so rows: matches by suffix and a has: selector must use a substring. Never assert a count an otto reload can move: rm38042 and rm36048 both read the merged-item box and leave its count (45 for ClinVar today) to a comment. And a details page prints the track's own labels whether or not it worked, so each hgc assertion names something only the fixed page has. Three candidates were rejected: #38033's "(N items could not be lifted)" label is only in the drawn image and the page JSON, where no expect: check reaches it; #37970 needs a broadPeak track and hg38 has none; #37974's center-label drag is pixels. diff --git src/hg/utils/docent/tests/regress/rm36125.docent.yaml src/hg/utils/docent/tests/regress/rm36125.docent.yaml new file mode 100644 index 00000000000..c8dacb6b346 --- /dev/null +++ src/hg/utils/docent/tests/regress/rm36125.docent.yaml @@ -0,0 +1,72 @@ +# #36125 -- the list of things that went wrong on NCBI RefSeq tracks after a QuickLift. +# The half asserted here is the one the ticket opens with: clicking an item in the UCSC +# RefSeq subtrack came back with +# +# Couldn't set connection database to hub_25071_hs1 +# mySQL error 1049: Unknown database 'hub_25071_hs1' +# +# because hgc took the destination hub genome for a MySQL database. The ticket's note-4 +# adds the two links that were still broken after the first pass: Predicted Protein came +# back blank and CDS FASTA alignment raised the same Unknown database error. Three +# commits: 2654a3d8584 (subtrack selection, Predicted Protein and CDS FASTA links), +# fabf13fff3e (the CCDS link routes to the source assembly with coordinates lifted back, +# and Get Genomic Sequence Near Gene reads the destination assembly at the lifted exon +# coordinates), and 1f88a89d5bb (the note on a quickLifted CCDS page). +# +# So this clicks the item and then follows the link the ticket's note-4 said came back +# blank. Both pages are asserted the same way: a positive text that only the real page +# has, and the ticket's own error string. The error page carries the track's labels in its +# own header, so a positive check on those alone would pass on it. +# +# NM_000193 is named without its version on purpose. hgTracks writes the unversioned +# accession into the map box (i=NM_000193) even though the label shows NM_000193.4, so the +# script does not break when RefSeq bumps the version. +proof: + - "assertion-only 2026-09-12 -- written from the ticket after the fix shipped" + +target: genome-test +db: hg38 +position: chr7:155799529-155812871 +reset: true +fast: true +steps: + - go: chr7:155799529-155812871 + - hide: all + - track: {refSeqComposite: pack, refGene: pack} + - expect: {rows: [refGene], noText: "Warning/Error"} + + - convert: {to: hs1, quicklift: true, hideDefaults: true} + - open: lift + - expect: {rows: [refGene], noText: "Warning/Error"} + + # The click the ticket was filed about. The position printed here is the destination + # one: NM_000193.4 is chr7:155,799,980-155,812,463 on hg38 and chr7:156,983,127-156,995,607 + # on hs1, measured on genome-test on 2026-09-12. The CCDS link beside it is the other + # half of fabf13fff3e -- it has to point back at the SOURCE assembly, because the ccdsGene + # handler cannot open the destination hub genome as a database. + - click: {track: refGene, item: "NM_000193"} + - expect: + text: "RefSeq Gene SHH" + noText: "Unknown database" + - expect: + text: "chr7:156983127-156995607" + has: 'a[href*="ccdsGene"][href*="db=hg38"]' + + # Two things about the links under the item. The CDS FASTA alignment link is gone on + # purpose -- hgPal would open the destination's hub-virtual db, and its coordinates are + # in destination space while the multiZ alignment lives in source coords, so hgc.c skips + # the link when liftDb is set. And Predicted Protein is routed to htcTranslatedPredMRna + # rather than htcTranslatedProtein, which is how the peptide comes from the lifted exons + # instead of the source assembly's refPep file. + - expect: + noText: "CDS FASTA alignment" + has: 'a[href*="htcTranslatedPredMRna"]' + - click: 'a:has-text("Predicted Protein")' + + # The blank page the ticket's note-4 reported. Asserting the sequence itself and not + # merely that the page is not empty: SHH's N terminus is a fact about the gene, so this + # says the peptide was translated from the destination assembly at the lifted exon + # coordinates and is the right gene, which is what fabf13fff3e and 2654a3d8584 changed. + - expect: + text: "MLLLARCLLLVLVSSLLVCSGLACGPGRGFGKRRHPKK" + noText: "Unknown database"