25ff975568a24a89dc2dcd4836875a448beaec9f braney Thu Aug 6 15:23:11 2026 -0700 Docent: hide a composite as a unit under hideKids, and warn on an over-long nav, refs #37892 `{cCREs: hideKids}` on hg38 sent 1701 cart variables in a 42,020-character GET. The walk behind hideKids went to true leaves, straight through the ENCODE4 Core Collection composite, and enumerated all 850 of its ENCFF subtracks. Apache's LimitRequestLine is 8190, so the server answered 414 and the next shot: photographed "Request-URI Too Long" -- and nothing failed: the page loaded, the still got written, the build exited 0. Only looking at the figure caught it. Hiding a composite already reaches its subtracks, so the expansion now stops at the first container that propagates its own visibility and keeps descending only through superTracks, which do not. hubApi never lists a superTrack container, so the flag tdbParse already sets when it synthesizes one answers the question without new data. That step is two variables now. This is a separate walk rather than a change to tdbLeaves, whose other caller resolves a container to a row on the page and does need true leaves -- a composite has no img_data_ of its own. nav() also warns when a URL passes 7800 characters. A 414 is not an exception, it is a page, so the run continues and the damage is a wrong figure; the one thing that helps is saying so at the time. diff --git src/hg/utils/docent/README.md src/hg/utils/docent/README.md index df4a2c4bfc9..2b1f3df22b2 100644 --- src/hg/utils/docent/README.md +++ src/hg/utils/docent/README.md @@ -1,281 +1,281 @@ # Docent — a language for authoring guided tours of the Genome Browser A **docent** leads a tour and explains what you are looking at. A Docent script is that tour, written down: an ordered list of high-level verbs (`go`, `hide`, `track`, `mouseover`, `convert`, `drag`, `shot`) that drive a real browser against a real server. `docent.js` renders one script into two things at once: - a **silent mp4** of the whole tour, and - a named **PNG still** at every `shot:` marker. So a published figure is literally a frame of the tour, and the two can never drift apart. The surface syntax is YAML — so ordinary editors highlight it and no one has to learn a new parser — but the language is the verb vocabulary layered on top, not the serialization. Scripts are named `.docent.yaml` (a bare `.docent` works too). The verbs deliberately encode *browser mechanics* rather than selectors: `convert:` knows that the Hide-defaults checkbox reverts when the Assembly menu reloads, `track: {clinvar: pack}` asks trackDb which containers and checkboxes that implies, and `mouseover:` knows that a lifted track's DOM id gains a per-run `hub__` prefix. The author writes intent; the renderer deals with the UI. ## Run ``` PLAYWRIGHT_BROWSERS_PATH=~/pwrec/browsers NODE_PATH=~/pwrec/node_modules \ node docent.js AP1.docent.yaml ``` Needs `playwright`, `js-yaml`, and `ffmpeg`. At UCSC these live in a shared install at `~braney/pwrec` (`pwrec/browsers` for Chromium, `pwrec/node_modules` for the modules) — point the two variables above anywhere you have them. Outputs, relative to the script's own directory: - mp4 → `../.mp4` (override with `mp4:` or a second argument) - stills → `stills//.png` (override with `stills:`) `docent.mk` in this directory has the make rules — include it from a project that keeps a set of scripts and it rebuilds only the ones whose source changed. See the usage comment at the top of that file. ## Top of file (all optional) ```yaml target: genome-test # or rr, hgwdev, hgwbeta, hgwdev-, or a full https://.../cgi-bin db: hg38 # source assembly position: chr7:155.8M # starting position (tracked from then on; `go:` sets it too) reset: true # cartReset first (clean cart + fresh quickLift hub) size: [1000, 760] # viewport pix: 850 # browser image width pace: 1.2 # seconds to dwell after each step shotHold: 2.2 # extra seconds the video pauses at a shot trackAnim: false # skip the visible dropdown gesture on `track:` (nav only) fast: false # true = figures only: no dwells, no cursor animation, no mp4 scale: 1 # >1 = print-resolution stills (see Print resolution) pinMouseovers: false # record every mouseover for `pinShot:` (see below) mp4: ../myname.mp4 # override output paths if you want stills: stills/AP1 ``` `target:` defaults to genome-test, so a script that forgets to say where it runs will not quietly hit someone's personal sandbox. ## Print resolution A screen still is about 120 dpi across a journal's 7-inch column — fine on a monitor, too coarse to print. `scale:` (or `DOCENT_SCALE=k`, or `make hires`) renders **the same tour with k times the pixels**, which is not the same thing as enlarging the stills afterwards: a still only ever has the pixels it was drawn with, so every layer is asked to draw more of them. ``` make hires # every scenario at 3x -> stills.hires// make hires SCALE=2 # 2x make hires BASES=BP1 # one scenario DOCENT_SCALE=3 DOCENT_STILLS=stills.hires DOCENT_FAST=1 node docent.js BP1.docent.yaml ``` What k does: - **deviceScaleFactor: k**, with the viewport left at its 1x CSS size. The page lays out exactly as at 1x — same line breaks, same jQuery-dialog width, same tooltip placement — and all of it rasterizes with k times the pixels. - **`pix` × k, `textSize` stepped up with it** (hgTracks' size ladder: 6, 8, 10, 12, 14, 18, 24, 34; 3x lands exactly on 24). The server draws a genuinely wider image, and the bigger font keeps its layout decisions proportional — tick spacing, room for labels, how features pack into rows. A wider image with an 8px font would be a different picture, not a bigger one. - **`zoom: 1/k` on the image table**, handing that wider image the 1x amount of layout space, so one image pixel lands on one device pixel. Native resolution, no resampling. - **The tooltip font is pinned back to its 1x size.** hgTracks takes the tooltip's font-size from the browser text size (`window.browserTextSize` → `hg/js/utils.js` `addMouseover`), which `textSize × k` has just tripled — and then the device pixel ratio scales the same text a second time. Left alone, a 3x still gets tooltips 3x too big: the popups swamp the figure and the last one pinned falls off the crop. - **Every drawn row asks for k times its height** (`.heightPer`, sent after each view change for the rows the page actually drew). A track with a FIXED PIXEL height does not follow `pix` or `textSize` — a bigLolly or wiggle row is a pixel count from trackDb/the cart — so a 128px row that was 15% of an 850px image would be 5% of a 2550px one. That is how ClinVar's lollipop row came out a sliver with unreadable y-axis labels. It is asked of the **drawn** row names, which is the only way to reach a **lifted/quickLift view**, whose tracks are hub tracks under names trackDb never saw. Each track's own `maxHeightPixels` still clamps the request, so **a fixed-height track needs a ceiling in trackDb to grow**: without one the default (128) is also the maximum and the request is silently clamped. Everything hgTracks reports about the image — map-box coords, mouseOver spans, `insideX` — is in the pixels the server drew, so it goes through the image's natural-to-displayed ratio before it becomes a page coordinate. That is why a `mouseover: {item: ...}` lands on the same feature at 3x as at 1x. Two things to expect: - **No mp4.** A scaled run is a figure run; build the video from an unscaled run of the same script. - **Densely packed tracks come out shorter.** hgTracks' font metrics are not perfectly linear across the size ladder, so a 24px font is a little narrower than three 8px ones and `pack` fits the same features into fewer rows. Same window, same tracks, same items, slightly roomier picture. Use `DOCENT_STILLS=` (what `make hires` does) so a print render lands beside the screen stills instead of overwriting them. ## Steps `steps:` is an ordered list. Each item is a bare verb or a one-key map. | Step | What it does | |------|--------------| | `gateway` | Open hgGateway for `db`. | | `go` | Click **GO** with the default position (no typing). | | `go: chr7:155799529-155812871` | Go straight to a position in hgTracks. | | `goShow: BRCA1` | **Demonstrates the position change through the UI** (vs. `go:` which navs there directly): the cursor glides to the **position box** and the term is **typed on screen**, then the page finishes the job — **Search** on hgTracks, the arrow on hgGateway — so one verb covers either page. Takes a **gene name** or a **position** (or anything else the box accepts: HGVS, an accession). Bare string, or map form `goShow: {gene: SHH, shot: source}` / `goShow: {position: "chr7:155,799,529-155,812,871", shot: source}` — quote coords in the map form (unquoted commas split a `{..}` flow map). | | `goShow: {gene: TP53, pick: "NR_176326"}` | A **gene name** goes through the browser's own **suggestion menu**, the way a user does it: Docent waits out the hgSuggest ajax, then clicks the matching row, so you land on the gene (not the search-results page) and the video shows the dropdown. Default match is the exact gene symbol; `pick:` selects a specific row by a substring of its text when the term is ambiguous (a `pick:` that matches nothing warns and falls back to the plain gene match). If nothing ever matches, the typed term is submitted as-is — that may land on the **search-results page**, which is legal, and a `click:` can take it from there. | | `hide: all` | Click **Hide all**. | | `track: {mane: pack}` | Set a track's visibility (`hide/dense/squish/pack/full`). The mouse visibly glides to that track's control dropdown, opens it, and picks the mode (then the state is applied). | | `track: {dbSnp155Common: pack}` | A subtrack by name: trackDb's view and composite above it come along, so this is the whole "common dbSNP" config. (`dbSnp155` is a *different*, off-by-default subtrack — all variants — not an alias for the composite.) | | `track: {clinvar: pack, clinvarCnv: hide}` | Composite: the container's mode reaches its subtracks, so name only the deviations. Docent adds the containers above and the `_sel` checkbox from trackDb — see **Track names come from trackDb**. | -| `track: {varsInPubs: hideKids, pubtator: pack}` | **superTrack: show one member only.** `hideKids` is not a visibility — it means *hide everything under this container*, so the child named alongside it is left the only one drawn. A superTrack needs this because, unlike a composite, its own mode does **not** reach its children: each comes up at its own trackDb visibility, so `{varsInPubs: show}` draws all eight of its members and an earlier `hide: all` does not stick. The expansion skips any child the step names itself and is sent in a round of its own **after** the rest — a subtrack hide travelling in the same request as its container can be dropped by the cart (#37953), so the container goes on first and the hides follow. Works on a composite or view too, where it deselects (`_sel=0`) rather than just hiding. `hideKids` alone (no child named) simply empties the container. | +| `track: {varsInPubs: hideKids, pubtator: pack}` | **superTrack: show one member only.** `hideKids` is not a visibility — it means *hide everything under this container*, so the child named alongside it is left the only one drawn. A superTrack needs this because, unlike a composite, its own mode does **not** reach its children: each comes up at its own trackDb visibility, so `{varsInPubs: show}` draws all eight of its members and an earlier `hide: all` does not stick. The expansion skips any child the step names itself and is sent in a round of its own **after** the rest — a subtrack hide travelling in the same request as its container can be dropped by the cart (#37953), so the container goes on first and the hides follow. Works on a composite or view too, where it deselects (`_sel=0`) rather than just hiding. `hideKids` alone (no child named) simply empties the container. The expansion stops at the first container that propagates its own visibility, so a composite under the superTrack is hidden as a unit rather than enumerated: `{cCREs: hideKids}` on hg38 sends two variables, not the 1701 that naming all 850 subtracks of the ENCODE4 Core Collection would take (which overran Apache's request-line limit and returned a 414 page in place of the view). | | `track: {anyTrackName: dense}` | Any track by its **trackDb** name. A name trackDb doesn't have (hub, custom track, quickLift target) is sent literally as `name=mode`. | | `mouseover: {track: dbSnp155Common, item: rs28406051}` | Hover a **named** item to raise its tooltip. `item:` matches the item's map box (its `&i=` HREF or its TITLE) and hovers that rectangle's center — so it lands on the **correct row** even when items are stacked, which a bare coordinate can't do. It then waits for **that item's own tooltip**, not merely for a tooltip: the browser shows one 500 ms after `mouseenter` and hides it 500 ms after `mouseleave` (`hg/js/utils.js`), so the cursor gliding in crosses other items and one of THEIR tooltips can still be on screen on arrival — which is how an Alignment Differences mismatch got pinned as its neighbour's "identical". The expected text comes from the item's own map box, rendered the way the tooltip renders it (the attribute holds markup and undecoded entities), and `DOCENT_ROWS=1` warns if it never appears. `title: "SHH"` matches the TITLE text only; `value: "..."` matches a JSON `mouseOver` span (wig/dense tracks). | | `mouseover: {track: mane, at: chr7:155805900}` | Hover by **position** when you don't need a specific item: genomic coord (`at:`), a fraction across the view (`frac: 0.5`), or a raw pixel (`x: 400`); the y is forced to the middle of that track's row (cannot disambiguate stacked items). Optional on any `mouseover`: `hold: 2.5` (seconds to dwell) and `shot: tip_mane` (capture the image **plus** the tooltip in one still). | | `mouseover: {track: dbSnp155Common, item: rs28406051, pin: true}` | `pin: true` **records** that tooltip (its text + position) so a later `pinShot:` can show several mouseovers open together in one figure. Nothing is added to the recorded page, so the **mp4 is unaffected** (it still shows only the transient native tooltip). Set `pinMouseovers: true` at the top of the file to record every mouseover by default (`pin: false` opts one out). Records accumulate within a view and are cleared on the next nav. | | `pinShot: all_tips` | Write `.png` with **all recorded (pinned) tooltips open at once**, each with a **cursor drawn at the point it was raised from** — so the figure says which feature every tooltip belongs to instead of leaving the reader to infer it from the anchor. Rendered on a throwaway page that shares the session (same cart/view) — never on the recorded page — so it never appears in the mp4. Consumes the recorded set (clears it). Place it after the `mouseover` steps whose tooltips you want shown together, before any nav/zoom. Map form `pinShot: {name: all_tips, cursors: false}` drops the pointers. | | `convert: {to: GCA_018466845.2, quicklift: true, hideDefaults: true}` | View→Convert, then **type the target into the page's own "Search for target genome" bar** and click the suggestion (`search:` overrides what is typed, `pick:` disambiguates the menu); the Assembly dropdown is checked afterwards and only opened by hand if the search didn't land there. QuickLift on, **re-checks Hide-defaults** (it reverts when the Assembly menu reloads), Submit. `to:` accepts an accession or a label fragment (`2257.pat`, matched against the dropdown text). | | `convert: {to: ..., shot: convert_filled}` | `shot:` inside `convert:` captures the Convert page, which no other verb can reach. A bare name is the **filled-in page just before Submit**. The map form names up to three moments: `shot: {opened: a, filled: b, result: c}` — `opened` as the page comes up, `filled` ready to Submit, `result` the conversion-result page (whose coordinate link `open: lift` clicks). These are viewport stills, so they show the page from the top. | | `hub: https://example.org/hub.txt` | **Quick, silent** attach of a track hub by URL (`hgTracks?hubUrl=...`): connects the hub so its tracks are available at their hub-declared visibility. Follow with `track:` to turn specific ones on. Map form `hub: {url: ..., db: hg38, position: chr7:...}` overrides the db/position (default: current `db` + last position). | | `addHub: https://example.org/hub.txt` | **Demonstrates the attach through the UI** (for the figure/video): opens My Data → Track Hubs, clicks the **Connected Hubs** tab, types the URL into the box, and clicks **Add Hub** — cursor glides and the URL is typed on screen. Then, on the "Hub Connect Successful" page, it **clicks the `Open:` link for `db`** so the demo ends on the browser with the hub loaded. Map form `addHub: {url: ..., db: hg38, shot: loaded}` sets which assembly to open and captures the still on that tracks view. Use `hub:` instead when you just need the hub attached without showing the steps. | | `addCustomTrack: ` | **Demonstrates loading a custom track via the UI**: opens My Data → Custom Tracks, types the track data (or a data URL) into the paste box, clicks **Submit**, then clicks through to the browser (**Go to first annotation**). Bare string is the data or URL; map form `addCustomTrack: {data: "track ...\nchr7 ...", db: hg38, goto: first, shot: loaded}` (use `url:` for a data URL, `goto: current` to land on **Return to current position** instead). Data is inserted literally (tabs/newlines preserved). In YAML, a multi-line track uses a block scalar: `addCustomTrack: |` then the indented lines. | | `addPublicHub: GTEx` | **Demonstrates connecting a PUBLIC hub via the UI**: opens My Data → Track Hubs, the **Public Hubs** tab, types the search terms, clicks **Search Public Hubs**, then clicks **Connect** on the matching hub row, and finally **clicks the `Open:` link for `db`** to land on the browser. Bare string is the search term (also used to match the row). A search usually returns several hubs, so use the map form `addPublicHub: {search: "GTEx", match: "GTEx Analysis Hub", db: hg38, shot: loaded}` to pick the exact hub by a substring of its row text (`match:` defaults to `search:`) and the assembly to open. If no row matches it **won't connect** (warns and stops) rather than pick the wrong hub. | | `drag: chr7:155,805,900-155,806,950` | Emulates the **Shift+drag-select** gesture: the cursor sweeps across the selection (a visible selection box is drawn) and the browser's own drag-select dialog is raised, then a button is clicked. The argument is one genomic region, `chrom:start-end`; a bare range **zooms**. For any other action, or to pass other keys, put the region under `range:` and quote it — unquoted commas split a `{..}` flow map: `drag: {range: "chr7:155,805,900-155,806,950", shot: dragselect, then: highlight}`. Endpoints that are not genomic coordinates are given as a fraction (`fromFrac:`/`toFrac:`) or raw px (`fromX:`/`toX:`) instead. Optional `track:` picks the row the box is drawn over; default is the top of the image. `shot: dragselect` captures the open dialog. `then:` = `zoom` (default → **Zoom In**) \| `highlight` (→ Single Highlight) \| `cancel` (Escape, view unchanged). (A real button-held drag would just pan, so the dialog is driven directly.) | | `open: lift` | Click the returned coordinate link → the lifted view. | | `zoom: out` / `zoom: in` | One zoom step (2×). | | `montage: {name: figure1, shots: [source, lifted]}` | Compose stills already written this run into **one multi-panel PNG**, which is what a journal wants for a figure with parts (A), (B), and so on. Panels are stacked in order and lettered automatically; `labels: [Before, After]` overrides the letters, `labels: false` drops them, `direction: horizontal` puts them side by side, and `gap:` / `labelSize:` tune the spacing and lettering. Composed at deviceScaleFactor 1 with every panel at its **natural pixel size**, so the composite is pixel-for-pixel its inputs: a `make hires` montage is print resolution because the panels were, not because anything was upscaled. Panels narrower than the widest are left-aligned and padded, never stretched. A named shot that was never taken is warned about and skipped. Put it last, after the `shot:`/`pinShot:` steps it names. | | `shot: source` | Write `.png` **and** pause the video here. On a tracks page the still is the track image (`#imgTbl`), plus any open tooltip/dialog. On any other page (an hgc detail page, an external page a link led to) it is the **viewport only — the top of the page**, never the whole scrolling document. | Escape hatches for anything the verbs don't cover: `goto: `, `click: `, `hover: `, `wait: `, `sleep: `. ## Speed A full run is a real browser against a real server, and most of its wall clock is the pacing that makes the *video* watchable, not work. Measured on BP1 (15 steps, 4 stills): **64 s**, of which ~40 s is dwells, cursor animation and dropdown theatrics, ~23 s is page loads, and ~1 s is the mp4 transcode. So when you are iterating on the **figures**, skip the video: make FAST=1 BP1 # or DOCENT_FAST=1, or `fast: true` in the script FAST drops the dwells (`pace`, `shotHold`, mouseover holds), moves the cursor in one jump, skips the dropdown open/highlight, and records no video, so there is no mp4 to transcode either — **24 s** instead of 64 s for BP1. The stills carry the same content; a couple of things about them are incidental rather than identical, so build normally for the figures you publish: - the drawn cursor rests wherever the last real action left it, which is not where the skipped animation would have left it; - a `pinShot:` crop is the bounding box of the image plus the pinned tooltips, so it can come out a few pixels taller or shorter. `DOCENT_TIME=1` prints where the time actually went, slowest step first — worth a look before assuming a script is slow for a reason you can fix. Two more things that help: - `make -j6` builds scenarios in parallel. Each run has its own browser, context and cart, so they don't interfere; the trackDb cache is written via a temp file and renamed, so concurrent runs can't read a half-written one. - The trackDb cache holds the *derived* index (a few MB), not hubApi's reply (~30 MB for hg38), so it is quick to re-read on every run. It refreshes daily; delete `$TMPDIR/docent-tdb-*` to force it. ## Gotchas The renderer lints for one YAML trap before it opens a browser: in a flow map a colon needs a trailing space, so `{item:name5568747}` parses as the single key `"item:name5568747"` and the intended `item:` argument is silently dropped — the verb then quietly falls back to a default. Any argument key containing a `:` gets a warning. Quote genomic coordinates inside a `{...}` flow map. An unquoted comma in `chr7:155,805,900` splits the map. `goShow:` with a gene name can't just wait for the suggestion menu to appear and click a row. The box shows **Recent** positions immediately, so an early click picks a previously-visited position instead of the gene, and when the hgSuggest results arrive the menu is re-rendered, which invalidates any row picked before that. Docent therefore polls until a row actually matches the term *and* the menu has stopped changing, ranks real hits above Recent rows, and addresses the row by index at click time. ## Track names come from trackDb Name tracks exactly as trackDb does — `mane`, `clinvar`, `clinvarCnv`, `dbSnp155Common`. Docent keeps **no table** of per-track cart variables; it fetches the trackDb of the server it is driving (hubApi `/list/tracks`, cached in `$TMPDIR` for a day) and derives what a `track:` step has to send: - **containers above the track** come along — a composite or view gets the mode you asked for, a superTrack gets `show`; - **the subtrack checkbox** (`_sel`) is stated explicitly, 1 for a visible mode and 0 for `hide`, because for a composite child the checkbox is what actually decides; - **nothing is pushed downward**: a container's visibility already reaches its selected children (`clinvar: pack` draws the SNVs, the CNVs and the submitted interpretations), so a script only names its *deviations* from trackDb — e.g. `track: {clinvar: pack, clinvarCnv: hide}`; - **`hide` never propagates upward** — hiding one subtrack must not turn its composite off. A step that names both a composite and something under it is applied in **two requests**, container first. hgTracks reshapes a composite when its container visibility changes, and that wipes per-subtrack overrides arriving in the same request (`clinvar=pack&clinvarCnv=hide` alone leaves `clinvarCnv_sel=1` and the CNV row still drawn). Names trackDb doesn't know — attached hubs, custom tracks, and everything on a quickLift target (a hub genome, which is not in the listing at all) — fall back to a literal `name=mode`, which is all Docent can honestly do for them. Set `DOCENT_ROWS=1` to log the rows hgTracks actually drew after each step (and the suggestion menus a `goShow:`/`convert:` search saw). That answers "why is that subtrack still there" and "why is my `mouseover:` track not shown" directly, instead of by guessing: DOCENT_ROWS=1 make BP1 track: clinvar=pack rows: ruler, mane, clinvarMain, clinvarCnv, clinvarSubLolly track: clinvarCnv=hide clinvarCnv_sel=0 rows: ruler, mane, clinvarMain, clinvarSubLolly It does the same for `mouseover:` — which map boxes matched the name, where the cursor went, the tooltip that was expected from the box, and the one that actually came up: item "4.3.157828209.157828210" in quickLiftChain: 1 map box(es) match (1 in row), centers x=[288] -> hovering (288,216), expecting tip "mismatch A->C" tip at (288,216): "mismatch A->C" **After a Convert/quickLift** the target's tracks are served from a hub, so their DOM ids gain a dynamic `hub__` prefix (e.g. `hub_191568_quickLiftChain`) that changes every run. `mouseover:` resolves the track by **suffix**, so you still just write the plain name — e.g. `track: quickLiftChain` (the Alignment Differences track) hits `hub_191568_quickLiftChain` automatically. ## Where this is headed Today a step reaches the browser as CGI variables — `hideTracks=1&clinvar=pack&...` — which is why the verbs have to know each composite's parameter set by heart. Once the cart can be handed a structured blob (#37838, "Store cart contents as JSON"), a Docent step can name the state it wants instead of assembling a pile of `_sel=1` variables, and the shortcut table above mostly goes away. Docent is meant to be an early consumer of that work. The same reason argues for the tour, not the video, being the durable artifact: a script that describes a state and a route through it can just as well drive a live in-browser tutorial as an mp4. ## Scripts in the wild The Current Protocols quickLift paper keeps six of these (`BP1`, `AP1`–`AP3`, `SP1`, `SP2`) in its own repo, under `currentProtocols/figures/scripts/`, and builds them with the `docent.mk` rules here. `BP1.docent.yaml` is a good one to read first: gateway → hide all → set two tracks → drag-select and zoom → Convert with quickLift → open the lifted view → pin two tooltips into one figure → click through to hgc and out to dbSNP.