All File Changes

v449_preview2 to v449_base (2023-05-30 to 2023-06-05) v449

• confs/hgwdev.hg.conf
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    ba1fafe109fc707dadb1bca851fa27a37132d378 Sun Jun 4 01:11:18 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/domains.c
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    43faba38f90334c149441ba95933697192aaa415 Wed May 31 16:12:49 2023 -0700
    Fixing pfam outlinks from hgGene and pfam hg19 track, refs #31364
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 39, context: html, text, full: html, text
    0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55 Fri Jun 2 11:40:19 2023 -0700
    Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 5, context: html, text, full: html, text
    0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55 Fri Jun 2 11:40:19 2023 -0700
    Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 18, context: html, text, full: html, text
    0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55 Fri Jun 2 11:40:19 2023 -0700
    Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 10, context: html, text, full: html, text
    f2b126d2fe65e705b4f6554f1c0c3b8dfb6d0a83 Wed May 31 12:37:39 2023 -0700
    Check our reconstructed ancestral base value vs. the tree's par (parental/parsimonious?) base value.
  • lines changed 24, context: html, text, full: html, text
    0c551e8432f5c9bbf86ac83e49a5c640ae7dbc55 Fri Jun 2 11:40:19 2023 -0700
    Add support for a couple Influenza A RefSeq assemblies -- only for segment 4 (HA gene, the "H" in serotypes like "H3N2") for now since we'll need another menu (or smart matching) in order to support all segments.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 25, context: html, text, full: html, text
    aa32b124d6e43ec6717547bed2b18c489a1d04c8 Fri Jun 2 11:35:49 2023 -0700
    If user uploads fasta with names that include characters with special meaning in Newick then replace those with _. Influenza sequence names often include serotype in parens e.g. (H3N2), (H5N6).
• src/hg/hgTracks/simpleTracks.c
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    2dc6f1ab04207b985c79dbb696dce361bf515f3e Tue May 30 16:36:21 2023 -0700
    add chromName to SELECT query for omimGene2
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    003ab3805f814b34afad5ef601beb2caa984d0ca Wed May 31 15:29:33 2023 -0700
    increase maxItemsInFullTrack to 10,000 from 1,000
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    7bc669f46f2444b07b01749af60c9de0b5808f2a Fri Jun 2 11:57:37 2023 -0700
    openssl s_client will not work right unless both the -trusted_first and -servername are provided.
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 30, context: html, text, full: html, text
    a8b92f8b8b7c3948f155fa9ff6a3e5ed46777fcc Thu Jun 1 03:02:36 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix backfilling trackDb change log, refs #31340
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    c8aba189173469b2ef7d3ed0a0bf8691945fbae6 Mon Jun 5 10:05:40 2023 -0700
    New version number v449
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 7, context: html, text, full: html, text
    f75439bec894097ce1bb4045cef78d224fa123e0 Wed May 31 22:01:06 2023 -0700
    adding some Influenza viruses per Angie request refs #29545
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    0f107bd81f62a5a2daf5fc7eaaed4227e16b9757 Sun Jun 4 21:14:35 2023 -0700
    adding 4 Clostridium tyrobutyricum bacteria per user request refs #29545
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    a1e862f69956074d966f6e7d22afec16c2b576a9 Sun Jun 4 22:36:47 2023 -0700
    adding 1 more Clostridium tyrobutyricum per user request refs #39545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    0f107bd81f62a5a2daf5fc7eaaed4227e16b9757 Sun Jun 4 21:14:35 2023 -0700
    adding 4 Clostridium tyrobutyricum bacteria per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    a1e862f69956074d966f6e7d22afec16c2b576a9 Sun Jun 4 22:36:47 2023 -0700
    adding 1 more Clostridium tyrobutyricum per user request refs #39545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    24877dd7342ffaf7f9e78ed592f527659b95e806 Tue May 30 14:02:27 2023 -0700
    given our limited set of clades here, malaria parasice P. falciparum should be in invertebrate instead of viral no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    24877dd7342ffaf7f9e78ed592f527659b95e806 Tue May 30 14:02:27 2023 -0700
    given our limited set of clades here, malaria parasice P. falciparum should be in invertebrate instead of viral no redmine
  • lines changed 8, context: html, text, full: html, text
    f75439bec894097ce1bb4045cef78d224fa123e0 Wed May 31 22:01:06 2023 -0700
    adding some Influenza viruses per Angie request refs #29545
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    43faba38f90334c149441ba95933697192aaa415 Wed May 31 16:12:49 2023 -0700
    Fixing pfam outlinks from hgGene and pfam hg19 track, refs #31364
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    c8aba189173469b2ef7d3ed0a0bf8691945fbae6 Mon Jun 5 10:05:40 2023 -0700
    New version number v449
• src/lib/https.c
  • lines changed 134, context: html, text, full: html, text
    5050bac019113baa2063ead726f78d5ae38af5f2 Thu Jun 1 00:51:16 2023 -0700
    Updating the whitelist after doing a full re-scan of all the error_log data available under /hive/data/inside/wwwstats/. Thanks to Lou for helping check for missing data.
  • lines changed 137, context: html, text, full: html, text
    e5fb628e596f737787c714b5b7cc74128a48daa2 Thu Jun 1 13:42:16 2023 -0700
    Removing domains that do not need to be on the https whitelist because a scan shows they work just fine. 137 removed leaving just 153.
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    9cac0646b62ac2cc4cfa2e0b8bd363370a5cd2d2 Fri Jun 2 13:29:03 2023 -0700
    Removing domains from the whitelist where the site no longer exists.
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    233372100fe94b4265cc557eb80b17aef2f7720a Sat Jun 3 17:38:52 2023 -0700
    openssl does not verify host name by default, so we need to set a flag and pass the host name. This also means that urls with IP addresses instead of hostname will now give an error, but the whitelist can now just have IP addresses and it all works out. I double checked the history and there never more than 2 IP addresses in the whitelist, and these have been restored from those and also the recent full logs scan. We can watch the logs for any new IP addresses, but not expecting much to turn up. Also LetsEncrypt and other providers do not allow the IP address in the cert.
• src/utils/qa/weeklybld/buildEnv.csh
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    d7ec1384dbb5536485734208f15d14711e3182a4 Mon Jun 5 10:04:42 2023 -0700
    v449 final build, refs #31355

• lines changed: 493
• files changed: 28