File Changes for hiram

v500_preview to v500_preview2 (2026-06-08 to 2026-06-15) v500

• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 27, context: html, text, full: html, text
    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
• src/hg/htdocs/liftRequest.html
  • lines changed 3, context: html, text, full: html, text
    61272f4594c12ee485b70df7be66fa282e8b378f Wed Jun 10 07:27:54 2026 -0700
    fixup issues from claude code review refs #31811
• src/hg/hubApi/tests/findGenome.README.txt
  • lines changed 159, context: html, text, full: html, text
    eb8aca4b2f05a4fac87c19f0015c0fdc830a2b09 Mon Jun 15 09:49:28 2026 -0700
    corresponding information about the use of the findGenome.sh script
• src/hg/hubApi/tests/findGenome.sh
  • lines changed 336, context: html, text, full: html, text
    847b1a96e008aecae23d9f20e250c22efd10dbe1 Mon Jun 15 09:45:56 2026 -0700
    useful script to test performance and accuracy of the "findGenome" functions, can be used before and after changes to verify functionality remains correct.
• src/hg/lib/assemblyList.sql
  • lines changed 6, context: html, text, full: html, text
    6c8386587f9dc2eb3a34db1018d8fd52361c2b4d Fri Jun 12 13:48:55 2026 -0700
    better indexes on assemblyList table to improve search performance
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    596fc9e27b7266b9692723e059731fa8ff2bbd11 Fri Jun 12 11:24:40 2026 -0700
    do not need the central db connection until after the captcha verification - this appears to eliminate all SQL connection for failed robot contacts
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    b0e65cd4657431971b78d34a7451ec55eae082ed Tue Jun 9 16:22:13 2026 -0700
    adding a couple per user request refs #29545
• src/hg/utils/automation/kegAlign.json.ga
  • lines changed 64, context: html, text, full: html, text
    31734e42148b0358ee38a154aa343e2d1c0b258f Thu Jun 11 17:20:55 2026 -0700
    kegAlign updated to accept scoring matrix refs #31811
• src/hg/utils/otto/genArk/addAssemblyList.sh
  • lines changed 10, context: html, text, full: html, text
    01f8a6872a8d3679c29e63adac60c59f6a86c0c9 Fri Jun 12 15:14:45 2026 -0700
    correctly reloading assemblyList table with new indexes and no interference with the running system
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    6e13fa20c66e496bcd2200d52235e093bd26d240 Sat Jun 13 22:41:40 2026 -0700
    explicity use a read-only kent mirror script
• src/hg/utils/otto/readOnlyKentMirror
  • lines changed 32, context: html, text, full: html, text
    95364ad664672b64da007a4fc25b0c51e9f23a30 Sat Jun 13 22:40:07 2026 -0700
    script to keep otto source tree up to date
  • lines changed 19, context: html, text, full: html, text
    12b69accc1d28a01e01c1cf7444d3b97e752aa82 Sat Jun 13 22:55:19 2026 -0700
    correct typo error and check for all error condition exits
• src/hg/utils/otto/sandboxupdate
  • lines changed 41, context: html, text, full: html, text
    13d2aa231f56c354b17528b8d72c541b1f98b2e6 Fri Jun 12 15:30:36 2026 -0700
    existing script in the otto user account HOME/bin/
  • lines changed 26, context: html, text, full: html, text
    3b97fd6c57d705abd88608cc5b277d264dae31ef Fri Jun 12 15:50:57 2026 -0700
    correct fetch update of the otto user sandbox
  • lines changed 26, context: html, text, full: html, text
    0b81e64efebcdb9ce7dc37f00868010ddcf70d56 Sat Jun 13 22:46:52 2026 -0700
    restore the original meaning of this script
  • lines changed 7, context: html, text, full: html, text
    a5d8d437fd8a70311ca85fb0f9ce8b27fbe1c459 Sat Jun 13 22:58:10 2026 -0700
    correct email address for error message
• src/hg/utils/otto/userRequests/asmRequestWatch.sh
  • lines changed 133, context: html, text, full: html, text
    87aafb03635a2e1ea4821bb1a2e41b640c867799 Mon Jun 8 13:11:17 2026 -0700
    initial script for assembly watch refs #31811
  • lines changed 46, context: html, text, full: html, text
    7133bbf60ed53ab306628d72050c9379ee74a9f1 Mon Jun 8 14:23:43 2026 -0700
    watch for an assembly build to have begun refs #31811
  • lines changed 28, context: html, text, full: html, text
    9ffda9e5b601497b1ddcda75d5bbf377c1156713 Mon Jun 8 14:32:29 2026 -0700
    watch for a build to have completed refs #31811
  • lines changed 110, context: html, text, full: html, text
    c54bbc1b2596adbb4bf4fcd278a531224c1d4624 Mon Jun 8 15:23:59 2026 -0700
    add checking for the files to go through the system refs #31811
  • lines changed 10, context: html, text, full: html, text
    90297a90d259da8b7e7d48e7bf8600994e6a09a6 Wed Jun 10 07:23:05 2026 -0700
    minor fixups per claude code review refs #31811
  • lines changed 1, context: html, text, full: html, text
    862b3b53dd2a3e4011560f989ac1c18310d4ffc4 Thu Jun 11 15:55:44 2026 -0700
    better email subject construction refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
  • lines changed 18, context: html, text, full: html, text
    bbbd8958d58ef4d08410683f00b476095fda53cc Fri Jun 12 16:05:30 2026 -0700
    improved source tree update refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
  • lines changed 28, context: html, text, full: html, text
    b8e0ec67d7da42dbdd9837bb11833cdc6b761b31 Mon Jun 8 14:50:45 2026 -0700
    eliminate the checkIp and reset STATUS_NAMES to liftStatus refs #31811
  • lines changed 20, context: html, text, full: html, text
    77f91b38ab166f2adfefbdff3c2cbd50c2591cd0 Mon Jun 8 15:21:14 2026 -0700
    correct status labels to differeniate liftOver vs. assembly status refs #31811
  • lines changed 6, context: html, text, full: html, text
    90297a90d259da8b7e7d48e7bf8600994e6a09a6 Wed Jun 10 07:23:05 2026 -0700
    minor fixups per claude code review refs #31811
  • lines changed 1, context: html, text, full: html, text
    8d11236cb4e555b9cbd549b86a097e7817682e49 Sat Jun 13 23:05:30 2026 -0700
    grammer correction per claude code review refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
  • lines changed 3, context: html, text, full: html, text
    862b3b53dd2a3e4011560f989ac1c18310d4ffc4 Thu Jun 11 15:55:44 2026 -0700
    better email subject construction refs #31811
  • lines changed 2, context: html, text, full: html, text
    e14c4963bf3ad0f67e9ecf82a081acae159d821b Sat Jun 13 23:03:16 2026 -0700
    restore the galaxy cleanup step refs #31811
• src/inc/common.h
  • lines changed 10, context: html, text, full: html, text
    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
  • lines changed 1, context: html, text, full: html, text
    5437603957fb22ab9ffb254c2978c2a02439b2e9 Wed Jun 10 07:14:01 2026 -0700
    fixup comments per claud code review refs #33554
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
  • lines changed 2, context: html, text, full: html, text
    5437603957fb22ab9ffb254c2978c2a02439b2e9 Wed Jun 10 07:14:01 2026 -0700
    fixup comments per claud code review refs #33554
• src/userApps/fetchKentSource.sh
  • lines changed 10, context: html, text, full: html, text
    edb6fc7755da47df33f2dce4af4fd0017385b7fc Thu Jun 11 12:55:46 2026 -0700
    hacking in the submodules for the htslib no redmine