All File Changes

v454_base to v455_preview (2023-09-18 to 2023-09-25) v455

• src/hg/cgilib/pcrResult.c
  • lines changed 12, context: html, text, full: html, text
    04a5652eeca73cbc1c426587576cf8d3b29a1f4c Mon Sep 18 15:57:17 2023 -0700
    Fix hgTracks and hgc crash when a users session has pcr results from both before we allowed multiple queries to stack and after, refs #32236
• src/hg/hgGene/wikiTrack.c
  • lines changed 5, context: html, text, full: html, text
    10afed273e6c71a7f8d42531fe5256e9b12a9b02 Wed Sep 20 17:22:14 2023 -0700
    hgGene - Making links work better to support http or https. refs #32257
• src/hg/hgPcr/hgPcr.c
  • lines changed 23, context: html, text, full: html, text
    67774b8e85d05089eb6482e1ea865c4298f4ac36 Tue Sep 19 09:41:09 2023 -0700
    When appending pcr results, if we would be writing to a file that is in a saved session, first copy the session pcr results into a new trash file, and then write our new results into that. This keeps the session unchanged, refs #32236
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 16, context: html, text, full: html, text
    1d06b717ad1e8ebd6db725b4c086373661a9d54b Mon Sep 18 15:56:53 2023 -0700
    For genes with multiple exons (or ribosomal slippage), list the PSL blocks as 'segments' in the Nextstrain JSON instead of single start/end.
• src/hg/hgTables/galaxy.c
  • lines changed 1, context: html, text, full: html, text
    95dfda627819b071eaa0032584c50e31d4e9bcd1 Tue Sep 19 23:30:30 2023 -0700
    Adding support for galaxy and https redirection. Detect the https protocol and add s using our built-in function for it.
  • lines changed 13, context: html, text, full: html, text
    e5259878fcab4eeda7e83203e858c606b9dacf26 Thu Sep 21 14:11:22 2023 -0700
    Disable hyperlinks hgTables output for Galaxy, show warning with explanation instead. refs #32257
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    95dfda627819b071eaa0032584c50e31d4e9bcd1 Tue Sep 19 23:30:30 2023 -0700
    Adding support for galaxy and https redirection. Detect the https protocol and add s using our built-in function for it.
  • lines changed 12, context: html, text, full: html, text
    e5259878fcab4eeda7e83203e858c606b9dacf26 Thu Sep 21 14:11:22 2023 -0700
    Disable hyperlinks hgTables output for Galaxy, show warning with explanation instead. refs #32257
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    e5259878fcab4eeda7e83203e858c606b9dacf26 Thu Sep 21 14:11:22 2023 -0700
    Disable hyperlinks hgTables output for Galaxy, show warning with explanation instead. refs #32257
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    25eac8765c2e8a7300a791d0fe33e91c33e3c31f Wed Sep 20 17:11:37 2023 -0700
    hgTables - Making links work better to support http or https. refs #32257
• src/hg/hgTables/schema.c
  • lines changed 3, context: html, text, full: html, text
    25eac8765c2e8a7300a791d0fe33e91c33e3c31f Wed Sep 20 17:11:37 2023 -0700
    hgTables - Making links work better to support http or https. refs #32257
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    276a54d43de46e302347b921531a45ef266b55d4 Fri Sep 22 05:02:12 2023 -0700
    adding link to parent track for composite children trackUi page, refs #32263
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    13d3916285b56ee1227ad8e262ee15d9ec7a5e47 Wed Sep 20 17:18:51 2023 -0700
    hgTracks - Making links work better to support http or https. refs #32257
• src/hg/hgTracks/imageV2.c
  • lines changed 9, context: html, text, full: html, text
    ca8d3560aa51bc5d7a508359ebdb6fbedbc48b05 Fri Sep 22 13:19:15 2023 -0700
    Put special check for br tags in item titles behind hg.conf control now that we have new mouseover code. Eventually the else statement can be removed entirely, refs Jonathan email
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    90052d845ed4c1e24963ad7cdc0161b29f50e1d3 Mon Sep 18 15:53:02 2023 -0700
    Fix bug that was printing 'matches to ucsc genes' when the pcr match was not to ucsc genes, just overlapping that position
  • lines changed 2, context: html, text, full: html, text
    a2e949c53e2fecb9c8bf9524ab8b58ce0dd4666f Wed Sep 20 18:03:55 2023 -0700
    hgc - Making links work better to support http or https. refs #32257
• src/hg/hgc/wikiTrack.c
  • lines changed 3, context: html, text, full: html, text
    5f8bc82be821519c5e8e171749918d99c617b1c8 Wed Sep 20 17:15:25 2023 -0700
    hgc - Making links work better to support http or https. refs #32257
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    ae31cb7c9cb0b29fe6a23e7f96e3ad2b8d55f9d3 Thu Sep 21 16:46:47 2023 -0700
    Fill in missing bedList field for narrowPeak custom tracks, refs #32262
• src/hg/lib/hgHgvs.c
  • lines changed 47, context: html, text, full: html, text
    bbca1ee6f90a46e7a139434849dbf32bd206b522 Thu Sep 21 12:27:34 2023 -0700
    First cut of adding a historical refseq transcripts track, and getting hgvs searching to work with them, refs #26016
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 61, context: html, text, full: html, text
    bbca1ee6f90a46e7a139434849dbf32bd206b522 Thu Sep 21 12:27:34 2023 -0700
    First cut of adding a historical refseq transcripts track, and getting hgvs searching to work with them, refs #26016
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 1, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    107533d5af106590ee9e2d6dc55c8477a1ee2714 Mon Sep 18 16:03:23 2023 -0700
    Code review edit, refs #32252
  • lines changed 1, context: html, text, full: html, text
    6ba2cd0411ddc6d25daac2cd023dd19c980b35d8 Mon Sep 18 16:10:39 2023 -0700
    Another code review edit, refs #32252
  • lines changed 15, context: html, text, full: html, text
    db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb Fri Sep 22 07:40:45 2023 -0700
    Move refSeqHistorical into hg38 trackDb instead of just the top level refSeqComposite, refs build email
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 4, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra
  • lines changed 1, context: html, text, full: html, text
    53c9b1c9d8a80e8ff416c79d68ee77c91ab0c36c Fri Sep 22 13:27:42 2023 -0700
    turn off logoMaf cuz braney wrote bad code that slows down the browser big time
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 15, context: html, text, full: html, text
    bbca1ee6f90a46e7a139434849dbf32bd206b522 Thu Sep 21 12:27:34 2023 -0700
    First cut of adding a historical refseq transcripts track, and getting hgvs searching to work with them, refs #26016
  • lines changed 15, context: html, text, full: html, text
    db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb Fri Sep 22 07:40:45 2023 -0700
    Move refSeqHistorical into hg38 trackDb instead of just the top level refSeqComposite, refs build email
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.err
  • lines changed 2, context: html, text, full: html, text
    fbcacfcd4a8baadb31fca8b07c8f831580c31c82 Fri Sep 22 14:48:04 2023 -0700
    Fix hgvsToVcf tests now that we can have a track with old sequences, refs Galt email
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 1, context: html, text, full: html, text
    fbcacfcd4a8baadb31fca8b07c8f831580c31c82 Fri Sep 22 14:48:04 2023 -0700
    Fix hgvsToVcf tests now that we can have a track with old sequences, refs Galt email
• src/lib/https.c
  • lines changed 4, context: html, text, full: html, text
    f7caab779a069561391990f87b6524c045067d29 Tue Sep 19 13:57:36 2023 -0700
    Increase timeout in https.c from 10 seconds to 90 seconds, Needed for C-language htmlPage Robots on https like hgNearTest and others.
  • lines changed 4, context: html, text, full: html, text
    37cf8f5370f6cc20f6994dc409d17a5970daf231 Tue Sep 19 16:17:25 2023 -0700
    For a little more conservative change, put the connection timeout in https.c back to default 10 seconds.
• src/product/installer/browserSetup.sh
  • lines changed 5, context: html, text, full: html, text
    8bf17b1c0edbe0abc9bf503871b442566fc22831 Thu Sep 21 01:11:28 2023 -0700
    removing sdsc download option from gbic, refs #32241
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    4d345df0f820d74be05391972ecc931c0ab91077 Mon Sep 25 10:55:04 2023 -0700
    v455 preview1, refs #32270

• lines changed: 302
• files changed: 38