Commits for hiram

v499_preview to v499_preview2 (2026-05-18 to 2026-05-25) v499

0201e8ea6a448b2124e117c5909ced7ff4a253c8 Tue May 19 13:43:53 2026 -0700

• adding login verification to the liftRequest functions refs #31811
  • src/hg/hubApi/dataApi.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 79, context: html, text, full: html, text
  • src/hg/js/liftRequest.js - lines changed 95, context: html, text, full: html, text

aa1713ed7bcb1b52032542f990363316cd7b1364 Wed May 20 11:21:58 2026 -0700

• Mac OSX does not have posix_fallocate() function
  • src/hg/lib/trackDbCache.c - lines changed 7, context: html, text, full: html, text

ab3163d7361d2f7bcf7beb522cd947f691196bf5 Wed May 20 21:17:25 2026 -0700

• move the bigBed and bigWig files to hgdownload refs #31811
  • src/hg/makeDb/trackDb/human/hg38/vgp577way.trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/vgp577way.trackDb.ra - lines changed 2, context: html, text, full: html, text

0f34cba6fd9a27695e4793b8352d4cfde21b12d3 Wed May 20 22:14:45 2026 -0700

• adding three rats per user request
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 5, context: html, text, full: html, text

70e3a28ad9458ae12f69bf99db04ad4d3e857792 Thu May 21 10:18:45 2026 -0700

• send failed doTrackDb logs to stderr email to cron refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 3, context: html, text, full: html, text

55d9b1b7504ff9c43ad1173ae981a27d9212d773 Thu May 21 11:48:01 2026 -0700

• cron job safe full path names to kent commands refs #31811
  • src/hg/utils/automation/asmHubTOGA.pl - lines changed 2, context: html, text, full: html, text

19f16e7908a8bca3aedae90340d499bce4ae8535 Thu May 21 11:48:50 2026 -0700

• reentrant save log files for the doTrackDb steps refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 8, context: html, text, full: html, text

9fac381fd49318efc76d205caddc9e3146b8541e Thu May 21 11:51:06 2026 -0700

• housekeeping script to verify liftOverChain and quickLiftChain tables are in synchronization - they should have the same pairs of fromDb and toDb refs #31811
  • src/hg/utils/otto/userRequests/verifyChainTables.py - lines changed 59, context: html, text, full: html, text

366bbd6166c2d220b559ae13307d7a60e9cee3a9 Thu May 21 14:43:49 2026 -0700

• ottoRequest table should be InnoDB and allow international characters for email addresses refs #31811
  • src/hg/lib/ottoRequest.sql - lines changed 4, context: html, text, full: html, text

ab84356e6829bc2a0d2939f232dadb6acdd92e2f Thu May 21 15:35:01 2026 -0700

• correctly get the "query" short and longLabel in the track statement refs #37380
  • src/hg/utils/automation/asmHubChainNetTrackDb.sh - lines changed 17, context: html, text, full: html, text

cff0574d507c40d5bd01f091ccf8edf75ef5e892 Thu May 21 19:33:26 2026 -0700

• need to receive error message in cron stderr when something does not push correctly refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 14, context: html, text, full: html, text

b82f144c8a3db1f34a7ffb2d453515b76bb84bd7 Thu May 21 19:41:57 2026 -0700

• must run as umask 002 while making files to avoid write permissions by other users in our group refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 3, context: html, text, full: html, text

b8c37065aeee89c5c9d074112afe9351dd72a3ad Thu May 21 19:56:22 2026 -0700

• show the cron times in the page refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 1, context: html, text, full: html, text

6ddaedca96e314bcd1607e69bcfa8fb228d22a3c Thu May 21 21:53:56 2026 -0700

• common functions moved to ottoLib.py and shared with ottoBuildGenArkHub.py and fixup the legacy clade situation refs #31811
  • src/hg/utils/otto/userRequests/ottoLib.py - lines changed 39, context: html, text, full: html, text
  • src/hg/utils/otto/userRequests/ottoRequestPush.py - lines changed 197, context: html, text, full: html, text

8f801f0b7d0b28d3adbc5f26fc7cb8976ac2830f Fri May 22 13:48:48 2026 -0700

• add the featureBits measurements to the user notification email refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestWatch.sh - lines changed 75, context: html, text, full: html, text

4f3c5867733dd64868cff1ce30538e86146009c8 Sat May 23 08:54:43 2026 -0700

• allow HPRCv2 and lowelab to become official beta tracks
  • src/hg/makeDb/trackDb/betaGenArk.txt - lines changed 2, context: html, text, full: html, text

a1ca00e26cc02777d80ab7b1e1c9c87d14a249eb Sat May 23 08:55:38 2026 -0700

• allow vgp577way HPRCv2 and lowelab to become official public tracks
  • src/hg/makeDb/trackDb/publicGenArk.txt - lines changed 3, context: html, text, full: html, text

785e9cccf3daee25d9e7c2fcfd0284b68323374d Sat May 23 18:20:53 2026 -0700

• add the otto user cron tab times refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 1, context: html, text, full: html, text

9e84b6fc13d60a1beb638f18050cb1fed5835410 Sun May 24 12:04:05 2026 -0700

• add a "hide/show completed" toggle and no longer need to protect via VPN IP with .htaccess now refs #31811
  • src/hg/utils/otto/userRequests/ottoRequestView.cgi - lines changed 34, context: html, text, full: html, text