679b48855a32f8ea1e1ea8ca3c095a0c2c7f6c7a
max
  Tue Sep 8 10:08:41 2026 -0700
detailsScript: add a scatterPlot plot type, and use it for pcLAI

Clicking a pcLAI window now shows where that window sits in the ancestry space
it was placed in: a scatterplot of the 1000 Genomes reference haplotypes with
the window's own PCA coordinate and its segment's coordinate marked on it. The
numbers were already on the details page and told a reader almost nothing.

New plot type scatterPlot (hg/js/hgc.scatterPlot.js), driven the same way as
histogram. Background points come from a JSON or TSV file named by dataUrl and
may carry a category, which colors them and builds a legend, and a label, which
is shown on mouseover. The cloud is drawn on a canvas, since these files hold
thousands of points and that many <circle> elements make the page crawl; axes
and the highlighted points stay SVG on top. Point lookup for the mouseover goes
through a cell index so a large file stays smooth.

Two additions serve every plot type, not just this one:

- exportFields, a config key listing further bigBed fields whose values are
passed to the module as a fieldValues object. Without it a plot needing two
coordinates would need them packed into one field, and pcLAI keeps them in
pca and pcaSegment. Only fields that exist in the bigBed are exported, at
most 32, and the JSON types are checked rather than asserted because
jsonListVal and jsonStringVal errAbort and this JSON is written by a hub.

- a config key ending in Url is treated as a file, by the convention
trackSettingIsFile() already uses, and a relative one is resolved against the
track's own bigDataUrl. The module does not fetch it directly; it asks
hgTrackUi for it, the route facetedComposite uses for its metadata. That
checks the canonicalized path against the hubs on the cart and reads it with
udc, so a hub-relative path works even for a hub loaded from a local path
(the GenArk /gbdb hubs), no CORS header is needed, and a file outside a
connected hub cannot be read. Verified that /etc/passwd, file://, a dot-dot
escape, an unattached hub and an unrelated host are all refused with 400.
When the session has file caching off, hgc now exports udcTimeout the way
hgTrackUi does and the module POSTs, so the browser cannot answer from cache.

Fixes a crash reachable from any hub: "detailsScript.<plotType>.<field> null"
segfaulted hgc, because jsonObjectVal returns NULL for a JSON null and the hash
routines dereference it. This hit the shipped histogram type too.

trackDbSettingsGen.py stopped reading a setting's description at the first
"Example:" paragraph and never read <ul> at all, so it dropped everything after
the first example and every list item. That silently truncated 226 of the 264
descriptions, including spectrum's minGrayLevel/scoreMin/scoreMax bullets, and
would have dropped this whole scatterPlot section. It now skips the Example
label instead of stopping, and folds list items in. No setting loses a word and
none gains or loses an example.

pcLAI wiring: the background file is the authors' published reference panel
(github.com/AI-sandbox/hprc-pclai reference_pca_metadata.tsv), converted by
hprc2annotMakePclaiRefPanel.py -- 3122 haplotypes, 21 populations, 94 KB, one
file for the collection since it is the reference space rather than per-assembly
data. The four values pcaSegment takes across all 460 assemblies turn out to be
the four continental cluster centres, so the highlighted segment dot always
lands on one of them.

genark: addContrib now rewrites a "...Url" inside a detailsScript value the same
way it rewrites bigDataUrl, and symlinks the collection's shared root-level data
files next to the docs, so contrib/<name>/<file> resolves in the deeper GenArk
layout. It writes the alpha tier only, leaving the assembly's default hub alone,
and clears any unmarked copy of the collection's stanzas that the assembly build
baked in, which would otherwise leave the hub declaring each track twice.

refs #35415

diff --git src/hg/js/makefile src/hg/js/makefile
index 2811ec574ad..97bd5d3c8e2 100644
--- src/hg/js/makefile
+++ src/hg/js/makefile
@@ -4,31 +4,31 @@
 
 SUBDIRS= external model react tutorials
 include subdirs.mk
 
 # UCSC js files must pass jshint
 UCSC_JS_FILES=ajax.js alleles.js assemblySearch.js autocomplete.js \
     autocompleteCat.js edwPersona.js facetedComposite.js \
     hgBlat.js hgSession.js hgCustom.js hgCollection.js  hgGateway.js hgGtexTrackSettings.js \
     hgHubConnect.js hgTracks.js hgc.js hgMyData.js hgPhyloPlace.js \
     hgVai.js hui.js jsHelper.js utils.js ddcl.js subCfg.js \
     encodeProject.js encodeDataSummary.js encodeDataMatrix.js encodeChipMatrix.js encodeMatrix.js d3.dendrograms.js \
 	cdwSummaryJs.js spectrum.min.js hgSearch.js lorax.js liftRequest.js \
 	myVariantsBlocks.js topLinks.js
 
 # ES6 module files loaded via dynamic import() on hgc details pages
-MODULE_FILES=hgc.histogram.js
+MODULE_FILES=hgc.histogram.js hgc.scatterPlot.js
 
 # STATIC files must pass jshint
 STATIC_FILES=staticDoc.js dbDbTaxonomy.js analytics.js
 
 # JQUERY files and other third pary files which have NOT BEEN TOUCHED by UCSC
 JQUERY_FILES_UNTOUCHED= \
     d3pie.min.js \
     jquery.js jquery.imgareaselect.js jquery-ui.js jquery.contextmenu.js \
     jquery.cookie.js jquery.watermark.js jquery.watermarkinput.js jquery.ui.colorPicker.js \
     jquery.floatheader.js jquery.rotateTableCellContent.js jquery.plugins.js \
     jquery.validate.min.js jquery.history.js jquery.treetable.js mousetrap.min.js dagre-d3.js \
     igv.min.js igvFileHelper.js
 
 # JQUERY or other third pary files which HAVE BEEN MODIFIED by UCSC
 JQUERY_FILES_MODIFIED=jquery.tablednd.js ui.dropdownchecklist.js