4d991e3416f4ac769408dfd2f65d8fdb0f7fae9b braney Wed Sep 16 12:36:41 2026 -0700 docent: a test for hgCollection, the one CGI nothing reached, refs #37892 hgCollection shares visibility logic with hgTracks by COPY rather than by call. hg/hgCollection/hgCollection.c carries its own isParentVisible() at line 269, a verbatim copy of the one in hg/lib/trackHub.c. Nine scripts in tests/regress caught the trackHub.c copy on the #37547 cart-visibility branch; nothing caught this one, and it was found by grep afterwards. This is the test that would have. The copy's reach is narrower than it first looks, and the script says so: its only caller is checkForVisible(), which builds the "Visible Tracks" folder at the top of the builder's source tree. It is NOT on the save path, so the bug drops a track you have on in the browser out of that shortcut folder and leaves a saved collection alone. The assertion sits on the FOLDER'S OWN jsTree CLASS, which turned out to be a cleaner statement of the bug than counting what is inside it. addVisibleTracks writes `,children:true` into the node only when checkForVisible() found something, so the folder renders jstree-open when the cart has visible tracks and jstree-leaf when it does not. The leaves inside it are then named as well. Three things the live page settled, each of which had been a guess: * The folder arrives OPEN. Clicking it CLOSES it. The first draft clicked. * A node's id is the track name, and the same id is used for that track under its group folder, so both selectors are scoped to li#visible. Unscoped, they would also match the copy under Regulation the moment anyone opened it. * wgEncodeBroadHistoneGm12878H3k4me1StdSig does not follow its siblings' naming. It is named in the assertion for that reason: a rename shows up here rather than quietly halving what this checks. The track cannot be chosen freely. It has to be a leaf whose container is hidden by default, or the test passes on a broken build (the rule in regress/README.txt: a top-level track is added as a stub whatever the cart says, and a default-visible child has its container in the list already). It also has to be one hgCollection will show at all -- trackCanBeAdded() at line 141 keeps only wig, bigWig and bedGraph leaves, which is why this names a cell-line leaf and not the multiWig container above it. wgEncodeRegMarkH3k4me1H1hesc is both. The noHas: names wgEncodeRegMarkH3k27acH1hesc, whose container IS visible by default: it says the hideKids reached hgCollection, so the has: is not passing because the whole superTrack came up on its own. The wait had to be restructured, and the reason generalises. Waiting for the folder's CHILDREN meant that a build with the bug -- where the folder is empty -- timed out after 15 seconds with a Playwright message instead of failing at the expect: with what it wanted. Waiting for either terminal state (jstree-open or jstree-leaf) fixes it: measured on genome-test the folder settles about 30ms after load whichever way it goes, and jstree-open lands about 11ms before the children, which is why the child check gets its own wait after the class has been asserted. Measured both ways. The same script with the track hidden fails in about a second: step 9 (expect) failed: nothing matches "li#visible.jstree-open"; 1 element(s) match "li#visible.jstree-leaf", wanted none README.txt describes it, drops hgCollection from "Still to write", and records what that section should now hold instead: a THIRD copy of isParentVisible(), in hg/lib/hgFind.c at line 2957, feeding isTrackVisible() at 2977. It decides whether a search result lands under "Visible Tracks" or "Hidden Tracks" on hgSearch, it is the same bug in the same shape, and it needs no login. 18 of 18 pass in tests/, and preflight resolves all four fixtures. diff --git src/hg/utils/docent/tests/README.txt src/hg/utils/docent/tests/README.txt index ce7cce1fa77..08df45d7358 100644 --- src/hg/utils/docent/tests/README.txt +++ src/hg/utils/docent/tests/README.txt @@ -1,210 +1,213 @@ Docent tests ------------ Run by hand, not by the kent tree's `make test`: make test # every *.docent.yaml here make test T=composite # just one make parity # one script FAST and slow, and twice over make derive # the derivation alone, against expected/ (no browser) make derive-accept # rewrite those baselines, then read `git diff expected/` make test TARGET=hgwdev-demo9 # the same scripts, against another server TARGET overrides the `target:` each script carries, for every target above, and takes the same values it does: a shorthand (rr, genome-test, hgwdev, hgwbeta), a bare hgwdev- sandbox or demo, or a full .../cgi-bin URL. It is how you try a suite against a branch build -- a sandbox, a ticket park from `ts`, a demo browser -- without editing the scripts. `make preflight TARGET=...` checks that server rather than the one the scripts name, so the fixture check and the run agree. Read a redirected run's failures with the server in mind. A script asserts what its OWN server draws, so a red one somewhere else can be the other machine's trackDb rather than a bug: a demo sandbox that carries only one assembly fails every script on the others, and a sandbox trackDb with a track the RR has not released changes what `exact: true` counts. Redirecting is for trying a suite elsewhere, not for moving it: the committed scripts stay pointed at the server they were written against, which is the one the nightly reads. `make preflight` prints how the target is configured, so the log says which server was driven AND how it differs from the one the scripts name: target https://hgwdev-braney.gi.ucsc.edu/cgi-bin /usr/local/apache/cgi-bin-braney/hg.conf central.db hgcentraltest db.trackDb trackDb_braney,trackDb curatedHubPrefix braney browser.quickLift on browser.quickLiftAlignments on browser.recTrackSets on Those are read off the hg.conf the server reads, following its includes the way hg/lib/hgConfig.c does, so the value printed is the EFFECTIVE one -- a sandbox conf that sets nothing still shows what it inherits from the shared conf it includes. Only a fixed list of settings is printed, because hg.conf includes hg.conf.private. It works for a server on this machine: genome-test, hgwdev, an hgwdev- sandbox or demo, or a ticket park from `ts` on 127.0.0.1 (looked up by port in its registry). For hgwbeta or the RR it says the conf cannot be read from here, which is true and is better than a guess. Even with that in the log, a config difference and a code difference can still look alike. The reliable way to tell them apart is to swap only the BINARY: drop a control build's CGIs into the same sandbox, leave its hg.conf alone, and re-run. If the failures follow the binary they are the code. Most tests drive a real browser against a real server, so they need the network and the shared Playwright install (/hive/groups/browser/uiTest/pw; see ../README.md). That is why none of this is part of the tree-wide test target: a broken network would fail the build. A test is an ordinary Docent script that asserts with `expect:`. It passes by exiting 0. `expect:` is the only verb that CHECKS anything, so a test with no `expect:` step in it tests nothing: `track:` accepts a name no assembly has and still exits 0. Other verbs do fail a run, so do not read the line above as "nothing else can stop it". A verb throws when it cannot do what it was told -- `mouseover:` cannot find the item, `loadSession:` cannot find the file, `drag:`, `convert:` and `go:` likewise -- and docent.js turns any step's throw into `step N (verb) failed` and exit 1. None of them looks at whether the page came out right, which is the part only `expect:` does. A script named *.xfail.docent.yaml is expected to FAIL, and the run fails if it passes. That is how a trap gets pinned rather than merely written down. `make derive` is the cheap half: DOCENT_DERIVE=1 resolves the `track:` steps against trackDb and prints the cart variables without opening a browser, in about a second. It is where Docent's own decisions live, and the baselines in expected/ are what catch a change to visVars() or tdbHideTargets() that a rendered page would hide. The trackDb listing is cached in $TMPDIR for a day (docent.js, TDB_TTL), and a cold fetch prints one provenance line that a warm run does not. That line would make the first `make derive` of the day differ from a baseline captured warm, for a reason that has nothing to do with trackDb changing, so the makefile strips it from both the run and the baseline. Everything else trackDb says about itself is kept, including the two lines that report a hub genome or an unreachable hubApi. What is covered --------------- selftest session: -> expect: -> loadSession:, on hg38 at SHH. Saves the cart, changes the view, restores it from the local file, checks rows both times. heavysession the same three steps as selftest, on a Recommended Track Set: 34 rows in, saved, moved away, loaded back, `exact: true` on both halves. selftest round-trips two rows, which barely reaches outIfNotPresent() in hgSession -- the function that writes a trackDb default for every track that is deliberately NOT in the cart, and the one a broken save-and-reload path shows up in. A path that dropped four rows left selftest green. firstrequest a track turned on has to be drawn by the request that turned it on, with no `go:`, `open:` or `convert:` in between. The bug it exists for lags by exactly one request, so any script that navigates before asserting reads a correct image and passes. It names wgEncodeRegMarkH3k4me1 for the reason in its header: a top-level track or a default-visible child would pass on the broken build too. + collection hgCollection, which no other script here or in regress/ reaches. It shares + visibility logic with hgTracks by COPY rather than by call: + hg/hgCollection/hgCollection.c carries its own isParentVisible(), a + verbatim copy of the one in hg/lib/trackHub.c, and it decides what goes in + the builder's "Visible Tracks" folder. Needs a login, so it is the one + script here that uses `login:`. Asserts on the folder's own jsTree class + first -- open when checkForVisible() found something, leaf when it did not + -- and then on the leaves inside it. composite clinvar with clinvarCnv hidden: the two-request split (#37953). One request would leave clinvarCnv_sel=1 and the CNV row drawn. views hideKids on the VIEW that holds the subtrack, with the sibling views hidden by name. Also covers the `_sel` checkbox, since the subtrack is `parent wgEncodeRegDnaseSignal off`, and pins the superTrack side effect below. views.xfail the same thing aimed at the COMPOSITE instead, which loses the row. Expected to fail. supertrack varsInPubs hideKids + one member: `exact: true`, because a test that only checked the member was present would pass with all six drawn. urllen {cCREs: hideKids} must not become the 1701-variable, 42,020-character GET that Apache answered with 414. Checks `noText: "Too Long"`, since a 414 renders as a perfectly good page; the derive baseline pins it at 3. customtrack addCustomTrack: with inline BED, tabs and newlines surviving the trip. scale a 3x run draws the same rows as a 1x one. ordered `ordered: true` on rows:, and the fact that a row which was not drawn is reported by rows: alone rather than failing the order check as well. ordered.xfail the same two rows named the wrong way round. Expected to fail -- a flag that cannot fail is not a check, it is a second copy of the set test. pagechecks the `expect:` checks that read the PAGE rather than the track image -- `url:`/`noUrl:` on the address, `has:`/`noHas:` on a CSS selector -- plus the positional form of `click:` (`{track:, frac:}`), which follows the item box nearest a point. All four exist for bugs that rows:, height: and text: cannot see: a search term's zero-width space stripped out of a URL (#36387), a center label attached to the wrong row (#37785), and an item that cannot be named at all because its track is `type bigBed 3` (#36335). pagechecks the same four aimed the wrong way at once. Expected to fail. The message .xfail names every check that failed, so one run says which of the four broke. colorchecks `color:`, the one check that reads the track IMAGE: is:/not: on the color a row is mostly drawn in, `part: label` for the center label instead of the items, `at:` for one item rather than the whole row, and the list form. It exists for #36212, where a track that sets both `itemRgb on` and `color` draws its items in the wrong one -- same rows, same height, same names, same tooltips, so nothing but the pixels can tell. colorchecks the same six aimed wrong, all in ONE expect: step so the message has to .xfail name all six. Expected to fail. The comment lists them in order; read the log rather than trusting the exit code. expectfail an assertion that is plainly false. Expected to fail -- if it ever passes, .xfail `expect:` has stopped throwing and every other test here means nothing. make parity FAST vs slow, and a rerun, on composite. FAST drops the dwells and the recording and must not change what the page ends up showing; the rerun catches state left behind in the cart. Two things these tests found ---------------------------- Worth knowing before writing more: * Turning on anything under a superTrack sends `=show`, and every OTHER member then comes up at its own trackDb visibility -- so `hide: all` is undone for them. views asserts wgEncodeRegMarkH3k27ac comes back, rather than working around it. Whether Docent should be cleverer here is an open question, not a settled one. * `hideKids` on a VIEW has to enumerate its leaves (a view holds no sub-containers to stop at), so views sends 188 variables in a 6,986-character request. That is under Apache's 8,190 limit with less room than is comfortable. Its `noText: "Too Long"` is what turns a future overflow into a clear failure instead of a strange one. Still to write -------------- mouseover: by item: on stacked items, and the timing case where a neighbour's tooltip is still up on arrival pinShot: several tooltips in one figure, cursors drawn convert: quickLift onto a GenArk haplotype, hideDefaults re-checked -- note a session taken after it cannot be checked in, see #38046 drag: each of then: zoom / highlight / cancel addHub:, addPublicHub: the two hub attach paths (a stable hub URL is the hard part) montage: panel order, lettering, a named shot that was never taken goShow: the suggestion menu, including a `pick:` that matches nothing loadSession: the three remote forms -- only the local-file form is covered the YAML lint `{item:name}` with no space warns and drops the argument. This needs a test that reads stderr, which the harness does not do yet. - hgCollection no script here or in regress/ reaches that CGI at all, and it shares - visibility logic with hgTracks by COPY rather than by call: - hg/hgCollection/hgCollection.c carries its own isParentVisible(), a - verbatim copy of the one in hg/lib/trackHub.c. The copy in trackHub.c - was caught by nine scripts in regress/ on the #37547 branch; the copy in - hgCollection.c was found by grep afterwards, and would have dropped a - container's children out of a saved collection in the same silent way. - A test needs a `collection:` verb: the page puts tracks into a - collection by dragging between two jsTrees, and `drag:` is the - genomic drag-select on the track image, not that. Its buttons are - #newCollection, #doNewCollection, #saveCollections and #discardChanges, - which is enough to open and save one but not to put a track in it. + hgFind's copy there is a THIRD copy of isParentVisible(), in hg/lib/hgFind.c at line + 2957, feeding isTrackVisible() at 2977. It decides category->visibility, + which is what puts a search result under "Visible Tracks" rather than + "Hidden Tracks" on hgSearch (hgSearch.c:174, js/hgSearch.js:44). Same + bug, same shape, and no login needed. wgEncodeGencodeBasicV49 is a + searchable subtrack three levels under a hidden container, which is the + right shape for it. A test that needs a stable server-side fixture (a hub, a custom track) should carry it in the script rather than assume something on disk. The one fixture that cannot be carried anywhere is a login. hgCollection refuses a visitor who is not signed in, and the login cookie is checked against a salted hash, so a script that needs that page uses the `login:` step, and the step reads an account from ~/.docentLogin. That file is one [section] per HGCENTRAL DATABASE, because an account is a row in gbMembers in one of them: genome-test, hgwdev, every sandbox and every ticket park read hgcentraltest and share one account, while hgwbeta and the RR are separate sets of accounts. Which central a server reads is read from its hg.conf rather than guessed from the host -- a sandbox can point itself somewhere else, and two on hgwdev do today. `make preflight` says which account and which central it resolved for the server being driven, and refuses a file that is readable by group or other. No password is ever printed and none can be written in a script. ../README.md under `login` has the format. colorchecks is the one exception, and the reason is worth knowing before someone else hits it. `color:` has to address a ROW by name, and a custom track cannot be addressed by name at all: hgTracks assigns its row id (`ct__`), which is why customtrack asserts on label text instead of on `rows:`. So an inline custom track -- the self-contained way to get a known color onto the page -- is the one fixture this check cannot use. It reads ~/public_html/docentFixtures/itemRgbHub/ instead, which tests/regress/rm36212.xfail needs anyway, and which `make preflight` checks is still there.