Commits for lrnassar
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v497_preview to v497_preview2 (2026-04-06 to 2026-04-13) v497
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2059ffca9a9b74cd5ba9632a5835ae47d213b594 Tue Apr 7 11:04:02 2026 -0700
- Address CR feedback from #37315: fix broken color link, paraythroid typo, long lines,
and incorrect #Supported anchor. Remove dead weng-lab.github.io color link in 12 ENCODE4
track HTML files. Fix "paraythroid" to "parathyroid" in 3 HTML files and wgEncodeReg4.ra
labels. Break long lines in credits sections and availability paragraphs across hg38 and
mm10 track HTML files. Replace nonexistent #Supported anchor with FAQ/FAQformat.html in
contribTracks.html. refs #37315
- src/hg/htdocs/contribTracks.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 10, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.html - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfPeaks.html - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 9, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 8, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 9, context: html, text, full: html, text
dd40846f55b0cb21d346f2edbe51936f04007bb2 Tue Apr 7 11:07:15 2026 -0700
- Adding peak+signal data and new organ subtracks to hg38 ENCODE4 Regulation. refs #34923
Epigenetics composite: added 3,154 bigBed peak subtracks (was signal-only),
composite type changed from bigWig to bed 3, Data Type facet added.
TF ChIP composite: added 2,462 bigWig signal subtracks (was peak-only),
composite type changed from bigBed 5 to bed 3, Data Type facet added.
MultiWig organ-averaged tracks: added 15 new organ subtracks across ATAC (+2),
H3K4me3 (+3), H3K27ac (+4), CTCF (+6). Updated bone marrow tissue-only
subtracks for H3K4me3 and H3K27ac to use new separate tp. data files.
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 137, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 28388, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 24622, context: html, text, full: html, text
a1e8bd10892f1d84b1a9a16ddadc3a6ee3f01038 Tue Apr 7 11:22:52 2026 -0700
- Fix production lab credits to be assay-specific for ENCODE4 multiWig tracks. refs #34923
Each multiWig HTML page was using the full 13-lab Epigenetics list instead of
the assay-specific production labs from the hub. Updated DNase, ATAC, H3K4me3,
H3K27ac, and CTCF credits for hg38, and ATAC, H3K4me3, H3K27ac, and CTCF for
mm10 to match the hub's per-assay credits.
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 4, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 4, context: html, text, full: html, text
f9fa02315060e80003f55f78c770dea0830d128c Tue Apr 7 15:33:47 2026 -0700
- Make Recent Genomes and Connected Hubs cards keyboard-accessible on hgGateway. refs #37342
- src/hg/htdocs/style/jWest.css - lines changed 7, context: html, text, full: html, text
- src/hg/js/hgGateway.js - lines changed 15, context: html, text, full: html, text
9a1687b6341af06ee8e0746a9a502ba09cee8284 Tue Apr 7 16:11:57 2026 -0700
- Add missing form labels and aria-labels across hgTables pages and main site search. refs #37343
Main page search bar (index.html): aria-label on search input.
hgTables main page (mainPage.c): aria-label on Galaxy/GREAT checkboxes,
fix Position label to target radio button instead of text input, aria-label
on position text input.
hgTables user regions (userRegions.c): aria-label on paste textarea and
file upload input.
hgTables filter page (filterFields.c): aria-label on all per-field filter
dropdowns and text inputs across string, numeric, integer, and enum field types.
hgTables intersect page (intersect.c): label elements on all 6 radio buttons
and 2 complement checkboxes, aria-label on threshold text inputs.
- src/hg/hgTables/filterFields.c - lines changed 46, context: html, text, full: html, text
- src/hg/hgTables/intersect.c - lines changed 23, context: html, text, full: html, text
- src/hg/hgTables/mainPage.c - lines changed 8, context: html, text, full: html, text
- src/hg/hgTables/userRegions.c - lines changed 5, context: html, text, full: html, text
- src/hg/htdocs/index.html - lines changed 1, context: html, text, full: html, text
acace5022c846865a6e449fe1973e94504394cde Tue Apr 7 16:33:34 2026 -0700
- Add aria-labels to Base Position and supertrack/container dropdowns on hgTracks. refs #37344
New hideShowDropDownWithClassExtraAndLabel() passes label through to the
existing labeled dropdown function. superTrackDropDownWithExtra() now passes
tdb->shortLabel. Ruler dropdown updated in both hgTracks.c and config.c.
Brings hgTracks track dropdown label coverage from 69% to 100%.
- src/hg/hgTracks/config.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
f704665435dca39ec3f9022bf2584553f3fddf00 Wed Apr 8 09:30:19 2026 -0700
- Updating the annotated screenshot without the phylo tree, no RM.
- docs/tutorials/gatewayTutorial.md - lines changed 1, context: html, text, full: html, text
- src/hg/htdocs/images/tutorialImages/gatewayPageAnnotated.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
0b65049e315263b6d6c7a46f3f5c2894a8413e8c Wed Apr 8 16:13:38 2026 -0700
- Weng lab feedback on ENCODE4 Regulation tracks (hg38 + mm10). refs #34923
hg38 multiWig organ-averaged tracks: fix tissue-only vs all-biosamples data.
The Weng lab fixed a bug where both variants pointed to the same file. Now
83 tissue-only subtracks point to proper tp.{organ}.{Assay}.bigWig files,
80 former fake tissue-only subtracks converted to all-biosamples, and the
DNase nose organ added / lymphoid tissue all-biosamples removed to match hub.
Default subtracks changed from cell lines to tissue samples per Weng lab
request: hg38 uses brain/heart/liver, mm10 uses forebrain/heart/liver
postnatal 0 days C57BL/6. Applied to all 6 bigComposite tracks.
Organ colors updated: urinary bladder (194,33,39), mm10 intestine (121,92,166),
mm10 blood marrow (184,120,120) per Weng lab canonical color mapping. Added
ENCODE color mapping wiki link to all 12 multiWig HTML description pages.
Credits fixed: mm10 DNase production labs corrected from 6 to 2 PIs (Stam, Hardison).
mm10 supertrack developer list corrected (removed Greg Andrews per hub).
ENCODE3 Regulation tracks renamed with alpha tags. relatedTracks messages
updated. Biosample column in Epigenetics metadata TSVs cleaned of redundant
assay+type suffixes (3,154 hg38 + 1,178 mm10 entries).
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.alpha.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 967, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Atac.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Dnase.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkCtcf.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k27ac.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4MarkH3k4me3.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra - lines changed 18, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Txn.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.html - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegAtac.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegDnase.html - lines changed 6, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra - lines changed 40, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkCtcf.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k27ac.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegMarkH3k4me3.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra - lines changed 7, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra - lines changed 20, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/encode4RegTxn.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.alpha.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 4, context: html, text, full: html, text
7a4b3c8ae0be8a7a0f1df90dab1b606b0d9af10b Fri Apr 10 10:59:18 2026 -0700
- Fix duplicate priority in hg38 DNase multiWig all-biosamples section. refs #34923
DnaseAllOvary and DnaseAllSmallIntestine both had priority 33, and there was
a gap at priority 55 (leftover from nose insertion/lymphoid tissue removal).
Renumbered all DNase all-biosamples subtracks to be contiguous (25-64).
Feedback from code review.
- src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra - lines changed 22, context: html, text, full: html, text
5b55849bed022137ad7f399d96f6458dc7509a7e Fri Apr 10 11:51:52 2026 -0700
- Update ENCODE4 Regulation makedocs for hg38 and mm10. refs #34923
Updated to reflect all work through Weng lab feedback round 2: tp/ave fix,
tissue default subtracks, color fixes, credits audit, biosample cleanup,
ENCODE3 rename, relatedTracks, and current file/disk counts.
- src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 145, context: html, text, full: html, text
- src/hg/makeDb/doc/mm10.encode4.regulation.txt - lines changed 76, context: html, text, full: html, text
833be021d3df3caba9a3ef6e2a6ceb9d41e2162b Sat Apr 11 12:45:32 2026 -0700
- Increase Anthropic API retry resilience in mlqAutomate. Retries now wait longer
(5s/15s/45s/135s instead of 2s/4s/8s) to ride out transient 529 overload errors.
If retries are still exhausted, the script logs a clear error message and skips
the affected emails instead of crashing, so the next cron run picks them up. refs #36801
- src/utils/qa/mlqAutomate.py - lines changed 17, context: html, text, full: html, text
2762a10400229116f476c3f526712c2d0126ed0c Mon Apr 13 09:40:34 2026 -0700
- Fix gray organ count in hg38 makedoc per CR feedback. refs #34923
- src/hg/makeDb/doc/hg38/encode4.regulation.txt - lines changed 1, context: html, text, full: html, text
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