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/rm38146.docent.yaml src/hg/utils/docent/tests/regress/rm38146.docent.yaml
new file mode 100644
index 00000000000..a0168c8b413
--- /dev/null
+++ src/hg/utils/docent/tests/regress/rm38146.docent.yaml
@@ -0,0 +1,50 @@
+# #38146 -- a quickLift whose SOURCE is a GenArk assembly worked, but clicking either of
+# the alignment links on the difference track errored with
+#
+#     Couldn't connect to database 'GCA_002844635.1' on 'localhost' as hguser.
+#     Unknown database 'GCA_002844635.1'
+#
+# Something took the GenArk accession for a MySQL database name instead of a hub genome.
+# Split out of #37974 so the center-label drag fix there could close separately.  Jairo's
+# case is the pig assembly GCA_002844635.1 (USMARCv1.0) lifted to susScr11, and it is the
+# one used here.
+#
+# 25c1787f5c2 is the fix: hgc reads the chain's query sequence from the two bit file
+# whenever the track names one, instead of opening the query assembly as a database.
+#
+# So the script goes all the way to the page that needed the sequence.  The details page
+# is the first half and the whole-window base alignment is the second, and only the second
+# actually reads query bases -- a test that stopped at the details page would pass on a
+# build that still could not produce the alignment.
+#
+# The GenArk assembly is reached by accession with no hubUrl, the way hgTracks resolves one
+# from the genark table, and nothing is turned on by hand: its default view carries the
+# tracks this lifts.
+proof:
+  - "assertion-only 2026-09-12 -- written from the ticket and from 25c1787f5c2, after the fix shipped"
+
+target: genome-test
+db: GCA_002844635.1
+reset: true
+fast: true
+steps:
+  - goto: "/cgi-bin/hgTracks?db=GCA_002844635.1&pix=1100"
+  - expect: {rows: [augustus], noText: "Warning/Error"}
+
+  - convert: {to: susScr11, quicklift: true, hideDefaults: true}
+  - open: lift
+  - expect: {rows: [quickLiftChain, augustus], noText: "Unknown database"}
+
+  # The details page.  The source assembly has to be named as a hub genome, with its own
+  # sequence name, rather than looked up as a database.
+  - click: {track: quickLiftChain, frac: 0.5}
+  - expect:
+      text: "GCA_002844635.1 position"
+      noText: "Unknown database"
+
+  # And the page that reads query bases out of the two bit.
+  - click: 'a:has-text("DNA sequence alignment of whole window")'
+  - expect:
+      text: "Only query sequence"
+      noText: "Couldn't connect to database"
+  - expect: {text: "Base Alignment: susScr11"}