Commits for hiram

v502_base to v503_preview (2026-08-10 to 2026-08-17) v503

7e3b5a8fb40226e35e2312321ac38f035e858e90 Tue Aug 11 08:26:14 2026 -0700

• running the asmAlias table update in otto cron job refs #31811
  • src/hg/utils/otto/genArk/asmAlias/runUpdate.sh - lines changed 60, context: html, text, full: html, text

01ee213725a474e44118c21fb0c3bd55b9197357 Tue Aug 11 08:27:06 2026 -0700

• running the asmAlias table update in otto cron job refs #31811
  • src/hg/utils/otto/genArk/asmAlias/asmAliasUpdate.py - lines changed 581, context: html, text, full: html, text

6963a302c775bfdaa4aeca21205b006a93219e15 Tue Aug 11 08:29:49 2026 -0700

• running the asmAlias table update in otto cron job refs #31811
  • src/hg/utils/otto/genArk/updateHgcentral.sh - lines changed 3, context: html, text, full: html, text

a44da9109b149669559c746cdee09821e279edf7 Tue Aug 11 13:10:42 2026 -0700

• better organization of the asmAlias update procedure refs #31811
  • src/hg/utils/otto/genArk/updateHgcentral.sh - lines changed 42, context: html, text, full: html, text

3a6f7a2ceb39e56238f5a5d3ffa8c40a6d39f14e Tue Aug 11 13:14:09 2026 -0700

• better organization of the asmAlias update procedure refs #31811
  • src/hg/utils/otto/genArk/asmAlias/runUpdate.sh - lines changed 1, context: html, text, full: html, text

f880f8b822d19c049867d38998c93a03566ba13f Wed Aug 12 13:26:46 2026 -0700

• fixing up errors found in code review refs #37946
  • src/hg/hubApi/apiUtils.c - lines changed 41, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 23, context: html, text, full: html, text

b8d17d29c4215bc9e7776173cbaa75d88f3ee9bd Wed Aug 12 15:34:01 2026 -0700

• fixups in response to code review refs #38001
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 55, context: html, text, full: html, text

889acd1c73910e973c8325bbd44cfc64bb63a1e3 Wed Aug 12 15:49:54 2026 -0700

• following advice in code review remove obsolete files refs #38005
  • src/hg/inc/asmSummary.h - lines changed 124, context: html, text, full: html, text
  • src/hg/lib/asmSummary.as - lines changed 41, context: html, text, full: html, text
  • src/hg/lib/asmSummary.c - lines changed 785, context: html, text, full: html, text
  • src/hg/lib/asmSummary.sql - lines changed 47, context: html, text, full: html, text

889633f4b77694a53dcca81fb28cdd07f4db297b Wed Aug 12 15:54:36 2026 -0700

• make the cleanup step safe for rerun == idempotent refs #38005
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 11, context: html, text, full: html, text

619974f143583b4a32568613691e447986a75ac2 Wed Aug 12 16:04:56 2026 -0700

• fixups per code review refs #38005
  • src/hg/lib/assemblySummary.as - lines changed 3, context: html, text, full: html, text

7a55a823e6fe9bc65ac0ecf5b6576e90fda64bcb Wed Aug 12 16:10:27 2026 -0700

• fixups per code review refs #38005
  • src/hg/utils/automation/gffAttrsToIx.py - lines changed 4, context: html, text, full: html, text

d937f06fd5b42ae4621cd7d6bf0d048ab2863a41 Wed Aug 12 16:14:10 2026 -0700

• fixups per code review refs #38005
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 4, context: html, text, full: html, text

1b64478747b87c045f07b9a56b2ca3179260e4c4 Wed Aug 12 16:20:20 2026 -0700

• protect a string substitution against odd characters per code review refs #38005
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 1, context: html, text, full: html, text

ade26bcbd0927eaae0c456182a97877752c0eb4a Wed Aug 12 16:23:05 2026 -0700

• fixup the web page system to function properly with modern hub syntax and fixing bugs from code review refs #38005
  • src/hg/hubApi/hubApi.c - lines changed 84, context: html, text, full: html, text

c40c049765198e994676eb5b0d8f5f63fb970896 Wed Aug 12 16:38:41 2026 -0700

• fix per code review refs #38005
  • src/hg/hubApi/apiUtils.c - lines changed 3, context: html, text, full: html, text

c6a1b5637442d52ab61dca03453d11bfdf0db338 Wed Aug 12 19:26:21 2026 -0700

• code review revealed spelling error refs #38005
  • src/hg/lib/jksql.c - lines changed 3, context: html, text, full: html, text

0fbe2a386b7e4408875e3877fd7add7358f6b11a Fri Aug 14 09:02:40 2026 -0700

• turn off asmAlias update until issue 38082 is fixed refs #38082
  • src/hg/utils/otto/genArk/asmAlias/runUpdate.sh - lines changed 4, context: html, text, full: html, text

d05963670ee4c6b2b54366dc284d32e2b7896356 Fri Aug 14 09:22:16 2026 -0700

• candidate for patch fixing automatic redirect from GCA to GCF assemblies for track or assembly hubs refs #38082
  • src/hg/lib/hubConnect.c - lines changed 73, context: html, text, full: html, text