File Changes for hiram

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

• src/hg/hubApi/apiUtils.c
  • lines changed 11, 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/dataApi.h
  • lines changed 4, 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/inc/assemblySummary.h
  • lines changed 115, 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/lib/assemblySummary.as
  • lines changed 42, 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/lib/assemblySummary.c
  • lines changed 596, 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/lib/assemblySummary.sql
  • lines changed 51, 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
  • lines changed 9, 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/makefile
  • lines changed 1, context: html, text, full: html, text
    9946c4df9443f75376808598ada08daad38bec76 Thu Jul 30 15:40:51 2026 -0700
    obsolete asmSummary becomes assemblySummary refs #37958
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 10, context: html, text, full: html, text
    2593dae2a2f67c1a98c81a35a92a47cadaed33d7 Mon Aug 3 16:17:12 2026 -0700
    getting the ncbiGene/archive out refs #37958
  • lines changed 3, 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/sendToHgdownload.sh
  • lines changed 6, context: html, text, full: html, text
    3c82ef9ff5d48182efda36c193dede849fd69c66 Wed Jul 29 21:57:48 2026 -0700
    rsync to hgdownload ignore archive/ refs #37958
  • lines changed 6, context: html, text, full: html, text
    15c85bf89d6cbe8dcd3aea9e44e539b8b60825f2 Mon Aug 3 16:30:42 2026 -0700
    OK to send out archive directory now refs #37958
  • 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/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    68af4c3f3932fa4eed67a3ec455ec7093ad488cd Mon Jul 27 14:42:39 2026 -0700
    adding a couple per user request refs #29545
  • 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/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, 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/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    68af4c3f3932fa4eed67a3ec455ec7093ad488cd Mon Jul 27 14:42:39 2026 -0700
    adding a couple per user request refs #29545
  • lines changed 1, 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
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    2ee596b92ac7068713614f4322ce634cf6981036 Tue Jul 28 14:50:43 2026 -0700
    space in wrong location per claude code review no redmine
• src/hg/utils/automation/AsmHub.pm
  • lines changed 118, context: html, text, full: html, text
    80484198a43b2152023cadd0b6abd26785ab69ea Wed Jul 29 14:53:53 2026 -0700
    now archiving versions of NCBI GenBank gene track when updated refs #37958
  • lines changed 2, 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
  • lines changed 1, 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
  • 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
  • lines changed 10, 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
  • lines changed 58, 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/asmHubNcbiGene.pl
  • lines changed 83, 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/doAssemblyHub.pl
  • lines changed 5, 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
  • lines changed 94, context: html, text, full: html, text
    5c6501db6f2650e1f23fb8d196b4c9c0b3fd8d10 Wed Jul 29 15:11:42 2026 -0700
    wire in the new procedure for doNcbiGene refs #37958
  • lines changed 6, context: html, text, full: html, text
    a213081a5106754b3f3ec4899c7b54ce3b6352f1 Wed Jul 29 16:01:33 2026 -0700
    claude fixing claude errors refs #37958
  • lines changed 4, 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/doNcbiGene.pl
  • lines changed 384, context: html, text, full: html, text
    80484198a43b2152023cadd0b6abd26785ab69ea Wed Jul 29 14:53:53 2026 -0700
    now archiving versions of NCBI GenBank gene track when updated refs #37958
  • lines changed 44, context: html, text, full: html, text
    5c6501db6f2650e1f23fb8d196b4c9c0b3fd8d10 Wed Jul 29 15:11:42 2026 -0700
    wire in the new procedure for doNcbiGene refs #37958
  • lines changed 8, 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/gffAttrsToIx.py
  • lines changed 156, 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/ncbiGeneCheckStale.py
  • lines changed 148, 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