d033cea2063e9362949baf5b4d8b837597173a0d
max
Thu Sep 10 05:16:05 2026 -0700
Address the code review of the Sep 9 commits
Faceted composite: text that comes from a hub - a metadata column's
description, the name and title of a data type, and the values quoted back in
the "could not load the metadata" row - is put on the page as text rather than
as markup. The three places built their markup from template strings, so a
value carrying angle brackets or a quote was read as HTML: the column
description now goes through the shared htmlEncode() once where the header is
parsed, and the other two build their elements as nodes. The error row reads
better for it as well, since a value with brackets in it used to disappear from
the message that was meant to show it.
The saved UI state keys on the assembly as well as the metadata id. localStorage
is per-origin, so two assemblies whose tracks share a name were sharing one
entry, and a row order dragged on one came back on the other over a different
set of samples. hgTrackUi passes the database down for it. State saved under the
old key is dropped, which costs a facet selection or a page length.
Imprinting: the five subtrack description pages link back to the container as
hgTrackUi?db=$db&g=$parentTrack, without the hgsid. Native trackDb html is
substituted by hgTrackDb as it loads the table, where there is no cart, so
${hgsid} came out empty and the link read 'hgsid=&g=...'. Matches what the
Fiber-seq pages already do. The makeDoc note that described the old form is
updated with the reason.
UniProt otto: README.txt lists all eight things that reach runLog.txt. It had
four, and was missing LOCKED, along with PREFLIGHT-FAIL, END and INTERRUPTED.
refs #36210
refs #37599
refs #38300
diff --git src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html
index 880c29b42ef..62a41f22063 100644
--- src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html
+++ src/hg/makeDb/trackDb/human/hg38/methBaseAsm.html
@@ -1,19 +1,19 @@
<h2>Description</h2>
<p>
-Part of the <a href="hgTrackUi?db=$db&hgsid=${hgsid}&g=$parentTrack">Imprinting</a> track collection, this track summarizes allele-specific methylation (ASM) across
+Part of the <a href="hgTrackUi?db=$db&g=$parentTrack">Imprinting</a> track collection, this track summarizes allele-specific methylation (ASM) across
thousands of human methylomes. A region where one allele is methylated and the other is not in many
independent samples is a candidate imprinting control region.
</p>
<p>
Whole-genome bisulfite sequencing reads are long enough to cover several CpG
sites at once, so the methylation states of neighboring sites on the same DNA
molecule can be read together. When the reads at a locus fall into two clearly
separated groups, one mostly methylated and one mostly unmethylated, that locus
shows allele-specific methylation. This track shows, for every CpG site in the
genome, the fraction of MethBase2 human methylomes in which the site was called
part of an allelically methylated region (AMR). Values range from 0 to 1. High
values mean that many independent samples show two differently methylated
alleles at that site, which is the expected signature of a constitutive
imprinted region. Lower but non-zero values point at loci where allele-specific