Commits for hiram

v502_preview to v502_preview2 (2026-07-27 to 2026-08-04) v502

68af4c3f3932fa4eed67a3ec455ec7093ad488cd Mon Jul 27 14:42:39 2026 -0700

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text

e9382ceee474dffd408150b9dd9c014562e31d19 Tue Jul 28 12:14:57 2026 -0700

• better indexing for the "ncbiGene" track refs #34917
  • src/hg/utils/automation/gffAttrsToIx.py - lines changed 156, context: html, text, full: html, text

29d0226323cbd906d7f1788bdda8de0154d19b92 Tue Jul 28 12:36:56 2026 -0700

• improve the index for the NCBI GenBank gene track no redmine
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 5, context: html, text, full: html, text

6b009b167921316fed954336df03cd07d17e59f3 Tue Jul 28 12:37:35 2026 -0700

• script to find out of date trackData/ncbiGene/ data in GenArk hubs no redmine
  • src/hg/utils/automation/ncbiGeneCheckStale.py - lines changed 148, context: html, text, full: html, text

8e9524c62f000fc7a3ea638ae3d6f1e6cd077d54 Tue Jul 28 14:45:31 2026 -0700

• move one to legacy GCA_010909765.1_sAmbRad1 refs #29545
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text

2ee596b92ac7068713614f4322ce634cf6981036 Tue Jul 28 14:50:43 2026 -0700

• space in wrong location per claude code review no redmine
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

80484198a43b2152023cadd0b6abd26785ab69ea Wed Jul 29 14:53:53 2026 -0700

• now archiving versions of NCBI GenBank gene track when updated refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 118, context: html, text, full: html, text
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 384, context: html, text, full: html, text

629c77052d6b1f7def62cd6cd641b7f383eb8b2c Wed Jul 29 14:54:16 2026 -0700

• now archiving versions of NCBI GenBank gene track when updated refs #37958
  • src/hg/utils/automation/asmHubNcbiGene.pl - lines changed 83, context: html, text, full: html, text

5c6501db6f2650e1f23fb8d196b4c9c0b3fd8d10 Wed Jul 29 15:11:42 2026 -0700

• wire in the new procedure for doNcbiGene refs #37958
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 94, context: html, text, full: html, text
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 44, context: html, text, full: html, text

a213081a5106754b3f3ec4899c7b54ce3b6352f1 Wed Jul 29 16:01:33 2026 -0700

• claude fixing claude errors refs #37958
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/doNcbiGene.pl - lines changed 8, context: html, text, full: html, text

ff97a131bb3d4d6f2dae3d04c73afceab20233eb Wed Jul 29 16:12:23 2026 -0700

• better url link to the archive track hub refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 2, context: html, text, full: html, text

72db51d8eaa9689eab8ff9cd8b37261c1b1290da Wed Jul 29 16:20:00 2026 -0700

• stay on the server where the browser is do not go to genome.ucsc.edu refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 1, context: html, text, full: html, text

636dc23e0f0b10bb1f1be27b7936ec15b9be2f49 Wed Jul 29 21:53:06 2026 -0700

• hub link to the archive without duplicating the tracks refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 1, context: html, text, full: html, text

3c82ef9ff5d48182efda36c193dede849fd69c66 Wed Jul 29 21:57:48 2026 -0700

• rsync to hgdownload ignore archive/ refs #37958
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 6, context: html, text, full: html, text

19f3e5917459c97a2732f9c054cc4f12ef13b327 Wed Jul 29 22:22:54 2026 -0700

• add a date version to the ncbiGene track and can later get a more definate name out of the assembly_summary files refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 10, context: html, text, full: html, text

643fc5346b9416e784bdf9b169ae9405d651264d Thu Jul 30 15:37:45 2026 -0700

• definitions to load the assembly_summary files from NCBI refs #37958
  • src/hg/inc/assemblySummary.h - lines changed 115, context: html, text, full: html, text
  • src/hg/lib/assemblySummary.as - lines changed 42, context: html, text, full: html, text
  • src/hg/lib/assemblySummary.c - lines changed 596, context: html, text, full: html, text
  • src/hg/lib/assemblySummary.sql - lines changed 51, context: html, text, full: html, text

9946c4df9443f75376808598ada08daad38bec76 Thu Jul 30 15:40:51 2026 -0700

• obsolete asmSummary becomes assemblySummary refs #37958
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text

7024eeb90212e7787a66cca8dab92c8690834fb9 Thu Jul 30 17:12:27 2026 -0700

• adjustments for some odd rows refs #37958
  • src/hg/lib/assemblySummary.sql - lines changed 9, context: html, text, full: html, text

9b6210bc4e86c38aff5a505b3c40cb90e3a4b9b8 Fri Jul 31 13:37:13 2026 -0700

• pass relay secret string in http headers instead of in the URL and fixup a bare SQL injection refs #31811
  • src/hg/hubApi/apiUtils.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hubApi/dataApi.h - lines changed 4, context: html, text, full: html, text

5b2853df34ece1d773f2fd0625803005829f8649 Mon Aug 3 08:41:12 2026 -0700

• testing the assembly request system refs #31811
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 4, context: html, text, full: html, text

7b36bef91a2342823690eb89293c3ba19dec8d1e Mon Aug 3 08:51:36 2026 -0700

• testing assembly submit system refs #31811
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text

a71f33ea4a34a46a90957e9b59cd7235cbdff4e9 Mon Aug 3 15:56:12 2026 -0700

• adding annotation version notes correctly to ncbiGene.html description page refs #37958
  • src/hg/utils/automation/AsmHub.pm - lines changed 58, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 4, context: html, text, full: html, text

2593dae2a2f67c1a98c81a35a92a47cadaed33d7 Mon Aug 3 16:17:12 2026 -0700

• getting the ncbiGene/archive out refs #37958
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 10, context: html, text, full: html, text

2cf4774648ff468f2c26ddab4a2b1c24294f40ee Mon Aug 3 16:27:49 2026 -0700

• and symLink out the archive/ncbiGene to the hgdownload staging refs #37958
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 3, context: html, text, full: html, text

15c85bf89d6cbe8dcd3aea9e44e539b8b60825f2 Mon Aug 3 16:30:42 2026 -0700

• OK to send out archive directory now refs #37958
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 6, context: html, text, full: html, text

3163998d4c6f3bfbce543b1a04f11682db2f52d4 Mon Aug 3 16:40:18 2026 -0700

• include the archive/ncbiGene/*/hub.txt in the hgdownload push refs #37958
  • src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh - lines changed 6, context: html, text, full: html, text