File Changes for hiram

v499_base to v500_preview (2026-06-01 to 2026-06-08) v500

• src/hg/htdocs/liftRequest.html
  • lines changed 1, context: html, text, full: html, text
    fc7664f673106948bb09c9f03ce8d10746f66d24 Thu Jun 4 14:32:25 2026 -0700
    should be simple include of gbPageStart.html not the gbPageStartHardcoded.html refs #31811
• src/hg/hubApi/apiUtils.c
  • lines changed 4, context: html, text, full: html, text
    6861403ca8a731be04bb0dc4be79f7272a35b73f Mon Jun 1 10:52:06 2026 -0700
    using otto profile to talk to hgcentral refs #31811liftOver.c
  • lines changed 1, context: html, text, full: html, text
    146388a6797bd5eae6a0be47eb976007fce54358 Thu Jun 4 16:03:49 2026 -0700
    correctly disconnect from hgcentraltest refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 51, context: html, text, full: html, text
    623b40a3d4c25c552af92d88aed99c5427446f36 Mon Jun 1 12:12:37 2026 -0700
    avoid race condition using INSERT WHERE NOT EXISTS refs #31811
  • lines changed 15, context: html, text, full: html, text
    fe99a2d141b3f2d33e8706c1061d59015e0c571d Thu Jun 4 14:39:19 2026 -0700
    correct detection of login status and correct use of local hgcentraltest when not on one of the RR servers refs #31811
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ebbf5e4ced6bccc61fd43049a2d33c77a0c7a6e2 Fri Jun 5 11:03:27 2026 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    330702087f98389c3d5b6a1ec0fd7ad56d3bd563 Thu Jun 4 16:15:48 2026 -0700
    add several per user request and otto testing refs #31811
  • lines changed 1, context: html, text, full: html, text
    07c7876ca4f755b24a430c16208a879de9ae614c Fri Jun 5 11:02:32 2026 -0700
    adding one per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    57469ac0b93684608b744610b3c42646f232144c Fri Jun 5 11:59:05 2026 -0700
    fixup a legacy assembly refs #29545
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 2, context: html, text, full: html, text
    c91de9787fcb7f202a9e294d4e9e8734938d5389 Wed Jun 3 10:52:32 2026 -0700
    do not add the toga V1 tracks when the TOGAv2 is available refs #35776
• src/hg/utils/otto/userRequests/devAndRR.sh
  • lines changed 2, context: html, text, full: html, text
    305a444f30710dc5de4595a349fca62c4ba34503 Wed Jun 3 12:21:14 2026 -0700
    do NOT need to check the one on hgwdev, this would duplicate things refs #31811
• src/hg/utils/otto/userRequests/kegAlignLastz.sh
  • lines changed 10, context: html, text, full: html, text
    957b916c9cb686a1e2f21c8702db24369623cb85 Tue Jun 2 12:33:46 2026 -0700
    correct primate score matrix for lastz input refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
  • lines changed 38, context: html, text, full: html, text
    30701e4c2c2ad71f0d597ad9629da75c6a35dfba Wed Jun 3 14:31:24 2026 -0700
    fix the legacy construction procedure refs #31811
• src/hg/utils/otto/userRequests/ottoRequestPush.py
  • lines changed 67, context: html, text, full: html, text
    481b82eaafcf77f9b82bce0159ff84e9284c3325 Tue Jun 2 10:36:03 2026 -0700
    correctly capturing any stderr or stdout and only send it to cron stderr in case of error refs #31811