Commits for chmalee
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v498_preview2 to v498_base (2026-05-04 to 2026-05-11) v498
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b2b58edce8b1d75567737b05e21ba9103073c69d Mon May 4 12:11:37 2026 -0700
- Fix myVariants tracks to load via a hardcoded query rather than hRangeQuery because the tableName is already qualified with the database. Remove dead code after refactor. Fix table browser output for myVariants tracks for various options, refs #33808
- src/hg/hgTables/bedList.c - lines changed 5, context: html, text, full: html, text
- src/hg/hgTables/custom.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/filterFields.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 10, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 4, context: html, text, full: html, text
- src/hg/hgTracks/myVariantsTrack.c - lines changed 33, context: html, text, full: html, text
bd0d63cb1a33174b6f43b32a48fddad7850d0acc Mon May 4 14:05:56 2026 -0700
- Remove em-dashes and fix myVariants custom tracks to use encoded usernames in their track names and trash files instead of raw usernames, refs #33808
- src/hg/hgTracks/myVariantsTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/lib/myVariants.c - lines changed 27, context: html, text, full: html, text
fa0ff693583dbd90241f3bd3b2dce6eafd974d6a Mon May 4 14:17:20 2026 -0700
- Add a basic description page for myVariants tracks, refs #38808
- src/hg/htdocs/inc/myVariantsDesc.html - lines changed 51, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 7, context: html, text, full: html, text
30a4424ce1b185ef0e6e95969e0b688d686dfb8d Wed May 6 11:52:40 2026 -0700
- HubSpace assembly hub fixes: fixes 1,5,6,8 and prettify error messages, refs #37411
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 21, context: html, text, full: html, text
- src/hg/hgHubConnect/hooks/pre-finish.c - lines changed 3, context: html, text, full: html, text
- src/hg/js/hgMyData.js - lines changed 101, context: html, text, full: html, text
60527238f7fe8afc89824e93b0d8780f1bcf65ad Wed May 6 14:38:50 2026 -0700
- Rename my variants to my annotations where appropriate, refs #33808
- src/hg/hgCustom/hgCustom.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/config.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgc/myVariantsClick.c - lines changed 3, context: html, text, full: html, text
- src/hg/lib/myVariants.c - lines changed 2, context: html, text, full: html, text
46a7db400ddc1280555e0bc32ed09311e19efc65 Thu May 7 10:53:58 2026 -0700
- Reword some hubSpace assembly hub error message. Make the duration of some error message notifications longer, change some text around input about why certain inputs are disabled in certain situations, refs #37411
- src/hg/hgHubConnect/hooks/pre-create.c - lines changed 5, context: html, text, full: html, text
- src/hg/hgHubConnect/trackHubWizard.c - lines changed 1, context: html, text, full: html, text
c6c395f3e8c38023107bab00507ee605f140ecf8 Thu May 7 11:00:09 2026 -0700
- More variant|item to annotation labeling changes. One 'item' is left in because it seems more appropriate as the placeholder text, refs #33808
6eaa03a52d1610050bcacf6e3a56c3086677574d Thu May 7 11:02:34 2026 -0700
- Change create to add in the highlight menu for creating a myVariants item, refs #33808
1da15f230f81e48dd030f04649f186688cefd933 Thu May 7 11:58:06 2026 -0700
- Fix incorrect strncpy call in jsonParse with a better snippage of the input string that avoids a strncpy altogether, refs #37500
d338d5080783d2ac5828658fe17160668bf64cdb Thu May 7 15:05:24 2026 -0700
- Fixes from code review, refs #37500
- Revalidate shared myVariants tracks against hgcentral on every read
path (hgTracks, hgc, hgTables); cart-supplied owner/db/project no
longer trusted. New myVariantsResolveSharedTrack helper.
- Scope shared-track UPDATE statements by share->project/db so a
recipient can't edit rows outside the granted scope.
- Add hgsid CSRF check to myVariantsJsCommand; pass hgsid in the
hgTracks.js highlight Add-Annotation POST.
- HTML-escape owner-controlled fields in the canEdit branch of
doMyVariantsDetails (Chromosome, Project, project select options,
hidden text input).
- Validate targetUser against gbMembers when creating a share; return
a clear 400 on typos.
- Replace the concat(id,' ',name)='%s' lookup with parsed-id +
name verification.
- Remove cgiMakeColorVar / cgiMakeColorVarWithLabel; the canEdit form
uses spectrum.js (already loaded for the create dialog).
- Strip _hidden_* columns from hgTables field lists for shared tracks,
both the display path and the selected-fields read path.
- Make the per-assembly invariant explicit: myVariantsLoadItems and
doMyVariantsDetails bail out if share->db != current database.
- Memoize myVariantsSharedScopeWhere to avoid per-region hgcentral
round-trips on genome-wide hgTables queries.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
- src/hg/hgTables/filterFields.c - lines changed 36, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTables/joining.c - lines changed 2, context: html, text, full: html, text
- src/hg/hgTracks/myVariantsTrack.c - lines changed 104, context: html, text, full: html, text
- src/hg/hgc/myVariantsClick.c - lines changed 87, context: html, text, full: html, text
- src/hg/inc/myVariants.h - lines changed 29, context: html, text, full: html, text
- src/hg/lib/myVariants.c - lines changed 167, context: html, text, full: html, text
8cdfd0efc540471112f850be74da7b87a8bd9b1e Fri May 8 13:48:54 2026 -0700
- Fix zoom to exon/codon option not appearing for genePreds/bigGenePreds/bigBeds. This broke because of tooltip code that now moves tooltip text into a data-tooltip attribute instead of leaving the text in the title attribute, refs #37521
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