443d7aad57553f2606be41a934cb4dab46019e09 braney Fri Sep 4 12:10:00 2026 -0700 docent: first eleven regression tests, one per fixed bug, refs #38252 Ten assert the behavior their ticket says is correct; the eleventh is an xfail. All eleven pass against genome-test, 40s for the set. rm35333 bigBed schema vs trackDb type mismatch, no SEGFAULT rm35920 wrong bigBed type in a hub, no crash and no garbage item label rm36029 a MAF displays after several phyloP tracks are on rm36331 quickLift of the GENCODE Archive container, no "Unknown database" rm36514 a chromosome search after a quickLift hop rm36702 quickLift hg19 to hs1, no "Unknown database" rm36798 the two OMIM tracks survive a configure submit rm37388 hgc on a quickLifted hub item, no connect to the source assembly rm37520 lifted tracks survive a hop to another genome and back rm37906 Neandertal tracks draw data in a narrow window on hg18 rm36540 is the xfail, and it is worth reading. The ticket is Closed, but the symptom is present on genome.ucsc.edu (v502), hgwbeta (v503) and genome-test (v503), measured with the reporter's own hub URL as well as with our copy of it: genome= instead of db= for a hub-backed assembly still reaches a query against a chromInfo table that does not exist. There is no fixed behavior to assert, so it is pinned as an xfail and the run fails if it ever starts passing. Six of these build their own state rather than loading the session their ticket names, which is deliberate: a session on someone's account can be renamed or deleted, and hgTracks answers a missing session with a 200 and an early-error page that every noText: assertion passes on. Where a session is genuinely the cheapest way to a state (rm37388), the script also asserts noText: "Could not find session" so that a deleted session fails loudly instead of quietly. Four traps cost a run each and are written into the scripts that hit them, since the next twenty-nine will hit them too: a container never gets an img_data_ row (the rows carry its children's names); a leaf track with no features at the ticket's position has no row either, so a lifted view is better checked by its own quickLiftChain; `track:` sends a plain name and cannot turn on a track in an ATTACHED hub, whose cart variable carries the hub prefix; and asking for one view of a composite turns its sibling views on as well. diff --git src/hg/utils/docent/tests/regress/rm36702.docent.yaml src/hg/utils/docent/tests/regress/rm36702.docent.yaml new file mode 100644 index 00000000000..1e972ac8377 --- /dev/null +++ src/hg/utils/docent/tests/regress/rm36702.docent.yaml @@ -0,0 +1,32 @@ +# #36702 -- QuickLift from hg19 to hs1 and to the human GenArk assemblies failed with +# +# Couldn't set connection database to hub_3671779_hs1 +# mySQL error 1049: Unknown database 'hub_3671779_hs1' +# +# The hub id in the message is per-run, so the assertion names the stem of the message and +# not the whole string. +# +# Self-contained: the ticket's steps are a cart reset and a convert, with no session and +# no particular track needed. One track is turned on anyway, so the lifted view has +# something to draw and the row check below can mean something. +# Asserts on `ncbiRefSeqCurated`, a leaf track (hg19 has no mane track). Naming a container here does not work: refSeqComposite +# is a compositeTrack, and a container never gets an img_data_ row of its own -- the rows +# carry its children's names (ncbiRefSeqCurated and the rest). Check a name against +# trackDb before asserting on it. +target: genome-test +db: hg19 +position: chr7:155604967-155612966 +reset: true +fast: true +steps: + - go: chr7:155604967-155612966 + - hide: all + - track: {ncbiRefSeqCurated: pack} + - expect: {rows: [ncbiRefSeqCurated], noText: "Warning/Error"} + + - convert: {to: hs1, quicklift: true} + - open: lift + + # Both halves matter. The failure was an early-error page that draws no image, so + # noText: on its own would have passed on exactly the page the bug produced. + - expect: {rows: [ncbiRefSeqCurated], noText: "Unknown database"}