9bd1a5356bcf1a68ea715e5b0d9c3731203f6d88 braney Sat Sep 26 12:12:14 2026 -0700 docent: hubUpload: verb, which drops files into the Hub Upload dashboard, and a value: check in expect: for what a form field holds, refs #37892, #38398 Nothing is uploaded by hubUpload:, so a run leaves nothing on the server. value: exists because a selector cannot read a field that a framework draws: it sets the value property, and [value=...] reads only the attribute. diff --git src/hg/utils/docent/README.md src/hg/utils/docent/README.md index ed701fa6081..c1a9617fc82 100644 --- src/hg/utils/docent/README.md +++ src/hg/utils/docent/README.md @@ -152,38 +152,39 @@ | `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. 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=<name>` 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 wiggle's per-pixel `mouseOver` span, which is the only way a track drawn as a graph -- a wiggle, or a bigBed/VCF/BAM in density mode -- can be addressed at all, since it has no per-item map box. It reads the spans `hg/js/hgTracks.js` fetches from a trash .json and skips the map-box search entirely, because a track's own center label is titled "Click to alter the display density of <track>" and would match any name the digits appear in. | | `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 `<name>.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. | | `click: {track: mane, item: "NM_000546.6"}` | **Click a track item** and follow its own map-box link, which is how the hgc details page is reached — a raw mouse click on the data area is swallowed by hgTracks' drag-select handler. Addressed the same way `mouseover:` is: by identity (`item:`/`title:`/`value:`) or by **position** (`at:`/`frac:`/`x:`), which takes the item box nearest that point. Position is the only way in for a track whose items cannot be named at all — every GIAB Problematic Regions subtrack is `type bigBed 3`, so hgTracks writes an empty `i=` into the hgc href and gives every box the same title, and `click: {track: alldifficultregions, frac: 0.5}` is then the way to open one. A bare string is a plain CSS selector click instead (`click: 'a:has-text("placed on its chromosome")'`), for a link on a page that has no track image. | | `click: {track: mane, item: "NM_000546.6", raw: true}` | **Press the mouse where a user presses it** and let the page answer, instead of following the item's link. A different gesture, not a slower route to the same page: hgTracks answers a real item click with an ajax **dialog** (`popUpHgcOrHgGene.hgc`), and a whole class of bug lives in that dialog rather than on the hgc page -- hgTracks hanging on the SECOND click of the same item (#36805). Following the href never opens a dialog, so it can never see one. With no item name, `raw:` is a **bare point on the row** (`frac:`/`at:`/`x:`), which is the only way to click a row that carries no hgc map boxes at all: a click on the **ruler** (#27113). Docent waits for whichever of the three answers arrives -- a navigation, a dialog, or a new image in place -- so it needs no sleep. Note that jQuery UI **hides** a dialog on close rather than removing it, so assert `has: "#hgcDialog:visible"`, not `has: "#hgcDialog"`. | | `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). A bare string is `to:`, so `convert: hs1` is a plain coordinate convert to hs1 -- `quicklift: true` is never implied. | | `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: <text-or-url>` | **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. | +| `hubUpload: {name: hub.txt, text: "..."}` | **Add files to Hub Upload** (hgHubConnect -> Hub Upload -> Upload) the way a user dropping them on the dashboard would. `{files: [{name:, text:}, ...]}` drops several at once, as one batch. Nothing is uploaded: the files wait in the dashboard, so a run leaves nothing on the server. The page needs a user, so a `login` step comes first; the verb fails with that hint when the Upload button never becomes clickable. It returns once uppy holds the files, so the next step can wait for what the page does with them, such as the file card that opens by itself for a single file. Optional `shot:`. | | `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. | | `login` | **Sign in through hgLogin**, for the pages that refuse a visitor who is not logged in -- hgCollection above all (`hgCollection.c` doMiddle: *You must be logged in to edit collections*), and the saving half of hgSession. The login cookie is validated against a salted hash (`login.cookieSalt`, `hg/lib/wikiLink.c`), so there is no cookie to hand the browser: a script that needs one of those pages has to sign in the way a person does. **The step takes no credentials and cannot be given any.** They are read from `~/.docentLogin` (override with `DOCENT_LOGIN_FILE`), **one section per hgcentral database** -- an account is a row in `gbMembers` in one of them, so that is the key, not the server and not the sandbox:<br><br>`[hgcentraltest]`<br>`user=docentTest`<br>`password=...`<br><br>genome-test, hgwdev, every `hgwdev-<name>` sandbox and every ticket park read hgcentraltest, so one account covers all of them; hgwbeta reads hgcentralbeta and the RR reads hgcentral. Which central a server reads is **read from its hg.conf**, not assumed from the host, because a sandbox can say so for itself -- 45 of the personal confs on hgwdev set `central.db=hgcentraltest` and two do not. A server whose conf is on another machine falls back to a small table (the RR, the two mirrors, hgwbeta), and `[default]` catches the rest. A run redirected with `DOCENT_TARGET` looks up the server it is really driving. The file is refused unless it is mode 0600 -- the rule `hg/lib/hgConfig.c` applies to `hg.conf`. `DOCENT_LOGIN_USER` + `DOCENT_LOGIN_PASSWORD` override the file for one run. **Against a ticket park, target its HTTPS port** (the http port + 1000): hgLogin writes its form action as `https://` on the port it was reached on, so on the http port the password never arrives and the run carries on logged out. Docent accepts the parks' shared self-signed certificate on a loopback target, and on no other. Nothing prints a password. A wrong password fails the step rather than carrying on logged out, because hgLogin answers one by drawing the same form again, which is a perfectly good page. Map form `login: {shot: signed_in}`. `make preflight` reports the account and the central it resolved, so a missing password is caught before the browser starts. | | `loadSession: https://example.org/settings.txt` | Start from a **saved state** instead of a clean cart, so one tour can begin where another ended and a bug report that arrives as a session link becomes a starting position. Four forms: a **settings file by URL** (as above), a **share link** (`loadSession: https://genome.ucsc.edu/s/Braney/hg38`), a **named session** (`loadSession: {user: Braney, name: hg38}`), or a **local file** written by an earlier `session:` (`loadSession: {file: saved}` → `sessions/<base>/saved.txt`, sent up through hgSession's own upload form, so the project's sessions need not be published at all). Quick and silent, like `hub:` — this is setup, not something the tour demonstrates; add `shot:` to capture where it lands. Whatever the form, the load is issued against `target:` — see **Sessions** for why a share link is not simply followed. | -| `expect: {rows: [ruler, mane]}` | **The one verb that can fail a run.** Everything else renders happily whatever it is handed, so a wrong figure is written over a right one and only an eye catches it. State the expectation instead and the run stops, non-zero, at the step that broke it. Checks, any combination: `rows:` (these were drawn — plain names, matched by suffix so a lifted `hub_<n>_mane` counts), `exact: true` (…and nothing else), `ordered: true` (…and in that order, top to bottom), `noRows:` (these were not), `height: 2000` (the still is no taller than that in pixels; `"<1200"`, `">=300"` for another comparison), `tip: "mismatch A->C"` (the tooltip now up says this, as a SUBSTRING -- an item's tooltip is markup and its tail can render differently from the title it came from), `noTip:` (...and does not say this, one string or a list. It is the delimiter `tip:` has no other way to carry: a wiggle's tooltip is a bare number, so `tip: "1"` is also satisfied by "1.5" and by "13", and naming the other digits and the decimal point leaves one number), `text:` / `noText:` (the page does / does not contain this, one string or a **list** of them — `noText: "Too Long"` catches the Apache 414 that renders as a perfectly good page), `url:` / `noUrl:` (the current address does / does not contain this — which CGI a click reached, or what a form put in the query string; `noUrl: "%E2%80%8B"` is the only way to see that a search term's zero-width space was stripped, since it is invisible in the page), `color:` (the color a track's row is actually **drawn** in -- `{track: crm4, is: "0,0,255"}`, or `not:` for one it must not be; `part: label` asks about the center label instead of the items, `at:`/`frac:`/`x:` about one item instead of the whole row, and a **list** states several rows in one step. The only check that reads the IMAGE, for a bug that leaves the page identical -- same rows, same height, same names, same tooltips), `has:` / `noHas:` (a CSS selector matches / matches nothing — for a bug whose whole signature is where something sits in the page's TREE, like a center label attached to the wrong row: same rows, same height, same pixels. Reach for these last, since an assertion on hgTracks' own ids breaks easily for reasons that are not bugs), `box:` (where an element sits on the SCREEN — `{sel: "#topRightLinks", inside: "#main-menu-whole"}`, plus `clear:` for what it must not overlap and `height:`/`width:` for its own size. The only check that reads a bounding box, for a bug that leaves every selector matching and every word of the page in place). A failure names every check that failed **and the rows actually drawn**. `warn: true` downgrades it to a warning for a check worth logging but not worth stopping a build over. | +| `expect: {rows: [ruler, mane]}` | **The one verb that can fail a run.** Everything else renders happily whatever it is handed, so a wrong figure is written over a right one and only an eye catches it. State the expectation instead and the run stops, non-zero, at the step that broke it. Checks, any combination: `rows:` (these were drawn — plain names, matched by suffix so a lifted `hub_<n>_mane` counts), `exact: true` (…and nothing else), `ordered: true` (…and in that order, top to bottom), `noRows:` (these were not), `height: 2000` (the still is no taller than that in pixels; `"<1200"`, `">=300"` for another comparison), `tip: "mismatch A->C"` (the tooltip now up says this, as a SUBSTRING -- an item's tooltip is markup and its tail can render differently from the title it came from), `noTip:` (...and does not say this, one string or a list. It is the delimiter `tip:` has no other way to carry: a wiggle's tooltip is a bare number, so `tip: "1"` is also satisfied by "1.5" and by "13", and naming the other digits and the decimal point leaves one number), `text:` / `noText:` (the page does / does not contain this, one string or a **list** of them — `noText: "Too Long"` catches the Apache 414 that renders as a perfectly good page), `url:` / `noUrl:` (the current address does / does not contain this — which CGI a click reached, or what a form put in the query string; `noUrl: "%E2%80%8B"` is the only way to see that a search term's zero-width space was stripped, since it is invisible in the page), `color:` (the color a track's row is actually **drawn** in -- `{track: crm4, is: "0,0,255"}`, or `not:` for one it must not be; `part: label` asks about the center label instead of the items, `at:`/`frac:`/`x:` about one item instead of the whole row, and a **list** states several rows in one step. The only check that reads the IMAGE, for a bug that leaves the page identical -- same rows, same height, same names, same tooltips), `value:` (what a form field holds now -- `{sel: "#positionInput", is: "chr7:1-100"}`, or `not:`, one or a list; the selector must name exactly one field. A selector cannot ask this, since a page that draws a field sets its value property and `[value=...]` reads only the attribute), `has:` / `noHas:` (a CSS selector matches / matches nothing — for a bug whose whole signature is where something sits in the page's TREE, like a center label attached to the wrong row: same rows, same height, same pixels. Reach for these last, since an assertion on hgTracks' own ids breaks easily for reasons that are not bugs), `box:` (where an element sits on the SCREEN — `{sel: "#topRightLinks", inside: "#main-menu-whole"}`, plus `clear:` for what it must not overlap and `height:`/`width:` for its own size. The only check that reads a bounding box, for a bug that leaves every selector matching and every word of the page in place). A failure names every check that failed **and the rows actually drawn**. `warn: true` downgrades it to a warning for a check worth logging but not worth stopping a build over. | | `session: source` | Write `sessions/<base>/<name>.txt`: the **whole cart at this step**, in the format hgSession's "save settings to a local file" produces, so anyone can load it and get this exact view. Every track's visibility, the attached hubs, the custom tracks, the window. Off the video and off the page — it is fetched over the tour's own cookies, so the tour is not disturbed and nothing appears in the mp4. With `sessionUrlBase:` set at the top of the file, the run also prints the ready-made load URL. See **Sessions**. | | `shot: source` | Write `<name>.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: <url>`, `click: <sel>`, `hover: <sel>`, `wait: <sel>`, `wait: {gone: <sel>}`, `sleep: <ms>`, and `fill: {<sel>: <text>}`, which empties a form field and types into it. `wait:` goes both ways on purpose. A script that asserts what a click did has to wait on the half of the answer that settles **last**, and that is not always the half that appears -- a handler can do its visible work inside the click dispatch and defer the rest to a `setTimeout(..., 0)`. Waiting for the wrong half returns a tick early and the assert reads a page that is still mid-answer, which arrives as a script that passes about half the time. `{gone:}` waits for a selector to leave the DOM, so the vanishing half can be the one waited on. tests/regress/rm38257.docent.yaml is the worked example.