All File Changes

v471_preview to v471_preview2 (2024-09-02 to 2024-09-09) v471

• src/hg/cgilib/hgSeq.c
  • lines changed 3, context: html, text, full: html, text
    9d1afd2a9f40d137353e53d7f1d0df4ca25fe4b7 Wed Sep 4 16:04:11 2024 -0700
    removing hubId from table browser fasta output, refs #34396
• src/hg/hgTables/hgTables.c
  • lines changed 29, context: html, text, full: html, text
    c1322ce22bfb59b5f98bf6b2aeb72c08fa4632ff Tue Sep 3 16:52:30 2024 -0700
    no feedback from QA for a long time, so committing curl button now but putting under hg.conf control, refs #33415
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    c1322ce22bfb59b5f98bf6b2aeb72c08fa4632ff Tue Sep 3 16:52:30 2024 -0700
    no feedback from QA for a long time, so committing curl button now but putting under hg.conf control, refs #33415
• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    c1322ce22bfb59b5f98bf6b2aeb72c08fa4632ff Tue Sep 3 16:52:30 2024 -0700
    no feedback from QA for a long time, so committing curl button now but putting under hg.conf control, refs #33415
• src/hg/hgTables/seqOut.c
  • lines changed 14, context: html, text, full: html, text
    c1322ce22bfb59b5f98bf6b2aeb72c08fa4632ff Tue Sep 3 16:52:30 2024 -0700
    no feedback from QA for a long time, so committing curl button now but putting under hg.conf control, refs #33415
• src/hg/hgTracks/hgTracks.c
  • lines changed 38, context: html, text, full: html, text
    318d4af062fce87394472706e0ba1094698a2c96 Thu Sep 5 22:09:30 2024 -0700
    wordwrap track control short lables unless a label has words longer than 20 charters, then character-wrap that label. Also a slight increates in max-width to accomidates adding small images in the label. #34398
• src/hg/htdocs/assemblySearch.html
  • lines changed 22, context: html, text, full: html, text
    879450f84abeea7f424bde8ab9ad95669eef3b53 Thu Sep 5 10:12:26 2024 -0700
    upper case corrections refs #32596
  • lines changed 1, context: html, text, full: html, text
    d64d6f53f31908c3570247a94023297d44ce3ee4 Thu Sep 5 14:47:32 2024 -0700
    add prompt text to input box and correctly do not place + in front of - refs #32596
  • lines changed 11, context: html, text, full: html, text
    41b27825db55ab0699dacce3c18c34cf791e6428 Sat Sep 7 23:49:38 2024 -0700
    correctly manipulate the copy to clipboard link refs #32596
• src/hg/htdocs/indexMeetings.html
  • lines changed 12, context: html, text, full: html, text
    7992bee1958606208401a4b599bb7b60b080c292 Fri Sep 6 07:47:49 2024 -0700
    Updated meetings.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 17, context: html, text, full: html, text
    318d4af062fce87394472706e0ba1094698a2c96 Thu Sep 5 22:09:30 2024 -0700
    wordwrap track control short lables unless a label has words longer than 20 charters, then character-wrap that label. Also a slight increates in max-width to accomidates adding small images in the label. #34398
• src/hg/hubApi/findGenome.c
  • lines changed 74, context: html, text, full: html, text
    1fb288d9c135df7d88a8accc0792f2986afe17bc Tue Sep 3 17:59:08 2024 -0700
    correctly manage the special characters in a single word, to be done same for multiple words refs #32596
• src/hg/js/assemblySearch.js
  • lines changed 12, context: html, text, full: html, text
    879450f84abeea7f424bde8ab9ad95669eef3b53 Thu Sep 5 10:12:26 2024 -0700
    upper case corrections refs #32596
  • lines changed 20, context: html, text, full: html, text
    9c2d11ccfb0c87e3561b584b1413bd0e21f9b285 Thu Sep 5 14:30:47 2024 -0700
    correctly highlight a compound word even when * wildcard included refs #32596
  • lines changed 3, context: html, text, full: html, text
    d64d6f53f31908c3570247a94023297d44ce3ee4 Thu Sep 5 14:47:32 2024 -0700
    add prompt text to input box and correctly do not place + in front of - refs #32596
  • lines changed 63, context: html, text, full: html, text
    41b27825db55ab0699dacce3c18c34cf791e6428 Sat Sep 7 23:49:38 2024 -0700
    correctly manipulate the copy to clipboard link refs #32596
  • lines changed 8, context: html, text, full: html, text
    c9e09744ad3e9050ff9ab8395de4a2fc1196b016 Sun Sep 8 10:51:52 2024 -0700
    correctly trim white space from before and after the query string and correctly test for words beginning with + or - refs #32596
  • lines changed 6, context: html, text, full: html, text
    ea483f476722f14fa41edf8832074600ca8df8ce Sun Sep 8 17:19:36 2024 -0700
    prevent duplication of words in the result during the highlight process refs #32596
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 4, context: html, text, full: html, text
    5d4991083d9c6db272b7bc4113e859a172fd584a Tue Sep 3 11:28:15 2024 -0700
    adding a couple per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    09ce1698f3a2ff54d67e414af4bdf1c55161e773 Wed Sep 4 22:57:29 2024 -0700
    adding RSV per dinner conversation and a fish request from a user refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    09ce1698f3a2ff54d67e414af4bdf1c55161e773 Wed Sep 4 22:57:29 2024 -0700
    adding RSV per dinner conversation and a fish request from a user refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    92e476fe0e5f25177ade29caff17394262987d94 Thu Sep 5 13:45:43 2024 -0700
    updating one refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    5d4991083d9c6db272b7bc4113e859a172fd584a Tue Sep 3 11:28:15 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 3, context: html, text, full: html, text
    bd0f0d984ed310e0ff894232ed3bf777002bdbbf Tue Sep 3 14:35:04 2024 -0700
    updates kicked a couple genbanks out refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    bd0f0d984ed310e0ff894232ed3bf777002bdbbf Tue Sep 3 14:35:04 2024 -0700
    updates kicked a couple genbanks out refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    5d4991083d9c6db272b7bc4113e859a172fd584a Tue Sep 3 11:28:15 2024 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    09ce1698f3a2ff54d67e414af4bdf1c55161e773 Wed Sep 4 22:57:29 2024 -0700
    adding RSV per dinner conversation and a fish request from a user refs #29545
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    a822b7483006b3a66bc6138f6ab1c1301e99eafb Thu Sep 5 18:27:54 2024 -0700
    Removing the period from the 'gnomad_r4.1' URL, refs #34252
• src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 2, context: html, text, full: html, text
    4cfa3273efa7e2395a23185fffc3bdbd12ef6878 Sat Sep 7 23:59:53 2024 -0700
    committing hubtools command, refs #34405
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    be04c57ff4cf31e8e5e2a281bebffb8f5363173e Wed Sep 4 09:22:46 2024 -0700
    Forgot to remove the include when I removed the trackDb and html for the ENIGMA tracks, no RM.
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 1, context: html, text, full: html, text
    4cbeaf5dc4cfdbf36a4bf93685a95e2189102e7b Wed Sep 4 09:56:08 2024 -0700
    correct typo error in script for archiving files refs #33088
• src/hg/utils/otto/panelApp/genes.py
  • lines changed 8, context: html, text, full: html, text
    d6b6234e8be94844c6bea9f7d2ca73226dcd0c70 Tue Sep 3 11:31:25 2024 -0700
    small otto fix for panelapp, no redmine, monthly otto email
• src/utils/hubtools/hubtools
  • lines changed 527, context: html, text, full: html, text
    4cfa3273efa7e2395a23185fffc3bdbd12ef6878 Sat Sep 7 23:59:53 2024 -0700
    committing hubtools command, refs #34405
  • lines changed 7, context: html, text, full: html, text
    25f65ead57c47cccd8cdf73c1e17fd0c39390670 Sun Sep 8 00:17:45 2024 -0700
    basic fixes for hubt make subcmd, refs #34405
• src/utils/hubtools/makefile
  • lines changed 14, context: html, text, full: html, text
    4cfa3273efa7e2395a23185fffc3bdbd12ef6878 Sat Sep 7 23:59:53 2024 -0700
    committing hubtools command, refs #34405
  • lines changed 1, context: html, text, full: html, text
    bc9d6c2f136be652342f2a5ae1459a30701081c7 Sun Sep 8 00:11:57 2024 -0700
    small mistake in last commit
• src/utils/qa/imageComp.py
  • lines changed 54, context: html, text, full: html, text
    a3c4fadb8944c8193891308d15d46e703df7a617 Wed Sep 4 12:03:30 2024 -0700
    Updated this cron to use python3 instead of 2.7 while chasing down a pug that ended up being due to an expired certificate on dev. Overall it's a good thing as this was the last QA cron I am aware of that was running python 2.x. No RM.
  • lines changed 2, context: html, text, full: html, text
    45c93a8fe5d76c863b252d8f4f9b37690f584aa2 Mon Sep 9 09:44:45 2024 -0700
    Forgot to update the way the shell function was being caleld when I updated from python 2.7 which took in a list of variables to python3 with the bash command which just takes in one long string. No RM.
• src/utils/qa/qaTestScript.py
  • lines changed 1, context: html, text, full: html, text
    3b230b817ddd6750f452206254bc07ee7754024a Thu Sep 5 17:06:00 2024 -0700
    Copied Gerardo's links to the genecats directory. Changed the link for the script. No redmine
  • lines changed 11, context: html, text, full: html, text
    17825a7edae00c426167a3269f135ef1601f4c3b Mon Sep 9 09:03:57 2024 -0700
    Adding code to kill chromdriver processes that don't get closed, No RM
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    340c35bfebd8c9c48ea36dd69436d2219b0f4049 Tue Sep 10 10:32:24 2024 -0700
    v471 preview2

• lines changed: 993
• files changed: 41