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_<n>_ 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/rm36059.docent.yaml src/hg/utils/docent/tests/regress/rm36059.docent.yaml
new file mode 100644
index 00000000000..022297d22f2
--- /dev/null
+++ src/hg/utils/docent/tests/regress/rm36059.docent.yaml
@@ -0,0 +1,53 @@
+# #36059 -- clicking an item in a quickLifted GENCODE Versions track gave an error instead
+# of a details page:
+#
+#     Can't start query:
+#     select class from wgEncodeGencodeAttrsV48 where name = "ENST00000297261.7"
+#
+# because hgc looked for the GENCODE attribute tables in the destination assembly, where
+# they do not exist.  Gerardo's test case is SHH/ENST00000297261.7, and it is the one used
+# here.
+#
+# 26334016d4d is the fix and it is worth reading: re-vet wgEncodeGencode* in
+# trackHub.c:isVetted() so the hub stanza stops emitting `avoidHandler on` (without that,
+# hgc never reaches doGencodeGene and falls through to the generic showGenePos output);
+# take the MySQL connection from quickLiftDb, since the attrs, tag, pubMed, refSeq and
+# uniProt tables live in the source assembly; use trackHubSkipHubName() for the table name
+# and the Basic/Comp/PseudoGene/PolyA dispatch, which otherwise errAborted with
+# "BUG: gencodeClick on wrong database"; and lift the Position values through the chain so
+# the page shows destination coordinates.
+#
+# So there are three separate ways this page can be wrong and the step below names all
+# three.  The UniProtKB section is the one that says doGencodeGene actually ran: the
+# generic fallback prints a position and little else, so a test that only asked for the
+# transcript name would pass on it.
+#
+# The position is the fourth: measured on genome-test on 2026-09-12, ENST00000297261.7 is
+# chr7:155,799,980-155,812,463 on hg38 and the lifted page reads hs1 chr7:156,983,127-156,995,607.
+# Naming the source coordinate in noText: is what makes that half about the lift rather
+# than about the page having a position at all.
+proof:
+  - "assertion-only 2026-09-12 -- written from the ticket and from 26334016d4d, 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: {knownGeneArchive: show, knownGeneV48: pack}
+  - expect: {rows: [knownGeneV48], noText: "Warning/Error"}
+
+  - convert: {to: hs1, quicklift: true, hideDefaults: true}
+  - open: lift
+  - expect: {rows: [knownGeneV48], noText: "Warning/Error"}
+
+  - click: {track: knownGeneV48, item: "ENST00000297261.7"}
+  - expect:
+      text: "Comments and Description Text from UniProtKB"
+      noText: "Can't start query"
+  - expect: {text: "hs1 chr7:156,983,127-156,995,607"}
+  - expect: {noText: "BUG: gencodeClick on wrong database"}
+  - expect: {noText: "chr7:155,799,980-155,812,463"}