All File Changes

v470_base to v471_preview (2024-08-26 to 2024-09-02) v471

• confs/hgwbeta.hg.conf
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    4ca8f87911f50779530cd9ad9c30a4a6b1f40824 Sun Sep 1 01:12:01 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 3, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c
  • lines changed 1, context: html, text, full: html, text
    e435de108aa1574d959ee3fbc40d674f1bf49224 Mon Aug 26 15:32:43 2024 -0700
    Replacing references to hgwdev.soe.ucsc.edu, as that server name is deprecated. no ticket
• src/hg/checkHgFindSpec/checkHgFindSpec.c
  • lines changed 13, context: html, text, full: html, text
    5197ebd63b54192a79e5f001a5cb18d89822b542 Wed May 29 13:42:32 2024 -0700
    Improve genbank search performance, mostly by optimizing mysql queries down from one query per findSpec result into a single query that checks all the findSpec results
• src/hg/hgGetAnn/tests/makefile
  • lines changed 16, context: html, text, full: html, text
    e10c349f9e394f6dfa688a2c83111115428b9535 Wed Aug 28 23:49:05 2024 -0700
    sort unpredictable output results
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    c16dcfe8fda775ad079cddaef13a999da905c2ac Tue Aug 27 11:45:51 2024 -0700
    In table browser, when checking if a track has an hTableInfo so we can put up the identifiers configuration, check if the requested track is in the list of tracks for that assembly, rather than just assume native tracks will not have a period in the name, refs #34252
• src/hg/htdocs/assemblySearch.html
  • lines changed 2, context: html, text, full: html, text
    f7f79df1b3d0ebea41b0fa0436f0fe65160131ca Mon Aug 26 13:12:08 2024 -0700
    now honoring the back button and restoring the state from the saved state object refs #32596
  • lines changed 6, context: html, text, full: html, text
    929d72bd9fa34529245e7969d992a8977da365af Mon Aug 26 14:42:56 2024 -0700
    now with RefSeq representative and RefSeq latest selection options refs #32596
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    a213555a50875b9a04c3bb4a267a54bea2dd427f Thu Aug 29 14:02:39 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
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    00f1aed7796ee719e3468d4b4acfebfd4d542d1b Thu Aug 29 18:36:10 2024 -0700
    correctly follow URL arguments and better state save and restore refs #32589
  • lines changed 11, context: html, text, full: html, text
    4f491c033139d8b4f4a2b8b1c8fd76d0f775c090 Mon Sep 2 17:00:03 2024 -0700
    manage all the options in the html page URL and start providing a share this page link refs #32596
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    cab1b236636738fdd2743f6b59798b136e4ead86 Thu Aug 29 18:15:34 2024 -0700
    Adding ChrisL's wording clarifying the use of curly brackets when field names overlap, refs #34363
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    7312dbe29eb58ff58fb753cbbd66f48a399a823c Thu Aug 29 17:01:56 2024 -0700
    Announcement for downloading all track data in current region, refs #31817
• src/hg/htdocs/images/downloadCurrentRegion.gif
  • lines changed 0, context: html, text, full: html, text
    7312dbe29eb58ff58fb753cbbd66f48a399a823c Thu Aug 29 17:01:56 2024 -0700
    Announcement for downloading all track data in current region, refs #31817
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    d60488a87c95d6585dfdaa3c24016731e3ea0e74 Tue Aug 27 13:46:05 2024 -0700
    correcting small typo form CR, refs #34351
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    7312dbe29eb58ff58fb753cbbd66f48a399a823c Thu Aug 29 17:01:56 2024 -0700
    Announcement for downloading all track data in current region, refs #31817
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    7527d06e8b8ba674b81a99e0ee5115b662a4603f Thu Aug 29 18:53:57 2024 -0700
    restore word wrap to track control labels (#34299)
• src/hg/htdocs/style/assemblySearch.css
  • lines changed 6, context: html, text, full: html, text
    929d72bd9fa34529245e7969d992a8977da365af Mon Aug 26 14:42:56 2024 -0700
    now with RefSeq representative and RefSeq latest selection options refs #32596
  • lines changed 5, context: html, text, full: html, text
    a213555a50875b9a04c3bb4a267a54bea2dd427f Thu Aug 29 14:02:39 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
  • lines changed 5, context: html, text, full: html, text
    2f18a9c643ecf990e9525610fdda0a31620ca530 Fri Aug 30 22:40:54 2024 -0700
    first pass at highlighting the match strings refs #32596
• src/hg/hubApi/assemblyList.py
  • lines changed 76, context: html, text, full: html, text
    48466d5a0bfaa3fa457f5a9a07118c323de32b11 Wed Aug 28 18:08:34 2024 -0700
    fixed up to add the new columns refs #33720
• src/hg/hubApi/dataApi.h
  • lines changed 4, context: html, text, full: html, text
    08a042ae53f8a7ea0b6e15bee0b12fcf48a90a76 Thu Aug 29 14:07:38 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
• src/hg/hubApi/dbDb.clade.year.acc.tsv
  • lines changed 248, context: html, text, full: html, text
    f3268ea3b0d6776b704239565d21d110416c6859 Wed Aug 28 18:08:24 2024 -0700
    fixed up to add the new columns refs #33720
• src/hg/hubApi/findGenome.c
  • lines changed 28, context: html, text, full: html, text
    e39d2c40cdc3e17273b158602400481ae7d2d03d Wed Aug 28 18:44:07 2024 -0700
    correspond with the new table structure and properly output the number values refs #32596
  • lines changed 138, context: html, text, full: html, text
    08a042ae53f8a7ea0b6e15bee0b12fcf48a90a76 Thu Aug 29 14:07:38 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
  • lines changed 1, context: html, text, full: html, text
    2230b5a2bad0d3f408763a58dc5c2b6426aef810 Thu Aug 29 14:18:48 2024 -0700
    correctly allow in level=contig refs #32596
  • lines changed 2, context: html, text, full: html, text
    0c7c5e88d0ae39e0f8832fe919ea2b69c713ba50 Thu Aug 29 14:26:14 2024 -0700
    correctly add year specification when requested refs #32596
• src/hg/hubApi/hubApi.c
  • lines changed 1, context: html, text, full: html, text
    08a042ae53f8a7ea0b6e15bee0b12fcf48a90a76 Thu Aug 29 14:07:38 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
• src/hg/inc/assemblyList.h
  • lines changed 6, context: html, text, full: html, text
    8ecd4ec7a45dc9f84f487d829b648f69c05fa862 Wed Aug 28 15:11:22 2024 -0700
    adding four columns to the database table for more accurate search refs #32596
• src/hg/js/assemblySearch.js
  • lines changed 70, context: html, text, full: html, text
    f7f79df1b3d0ebea41b0fa0436f0fe65160131ca Mon Aug 26 13:12:08 2024 -0700
    now honoring the back button and restoring the state from the saved state object refs #32596
  • lines changed 28, context: html, text, full: html, text
    929d72bd9fa34529245e7969d992a8977da365af Mon Aug 26 14:42:56 2024 -0700
    now with RefSeq representative and RefSeq latest selection options refs #32596
  • lines changed 3, context: html, text, full: html, text
    0590a9eb0c4805669982971bc86d3a06f836a6a6 Mon Aug 26 14:50:02 2024 -0700
    clean lint refs #32596
  • lines changed 87, context: html, text, full: html, text
    a213555a50875b9a04c3bb4a267a54bea2dd427f Thu Aug 29 14:02:39 2024 -0700
    now with proper interface to assembly status, refSeq category, assembly level refs #32596
  • lines changed 20, context: html, text, full: html, text
    00f1aed7796ee719e3468d4b4acfebfd4d542d1b Thu Aug 29 18:36:10 2024 -0700
    correctly follow URL arguments and better state save and restore refs #32589
  • lines changed 72, context: html, text, full: html, text
    2f18a9c643ecf990e9525610fdda0a31620ca530 Fri Aug 30 22:40:54 2024 -0700
    first pass at highlighting the match strings refs #32596
  • lines changed 4, context: html, text, full: html, text
    e9b3ea0e4ed31141bd55cec9db0b086b40ed6253 Fri Aug 30 22:52:22 2024 -0700
    jshint to get rid of lint warnings refs #32596
  • lines changed 4, context: html, text, full: html, text
    c59c7c3aeda4d5ffae880f2225a27d6df1afc2ab Sat Aug 31 09:06:23 2024 -0700
    this may fix the highlight when the word has non-word characters around it refs #32596
  • lines changed 62, context: html, text, full: html, text
    4f491c033139d8b4f4a2b8b1c8fd76d0f775c090 Mon Sep 2 17:00:03 2024 -0700
    manage all the options in the html page URL and start providing a share this page link refs #32596
  • lines changed 2, context: html, text, full: html, text
    e7e09cd46e7371080ac8aaed6d63d6f3e16f61a5 Mon Sep 2 17:06:03 2024 -0700
    missing ; refs #32596
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    a76e089c36bb0ffb0877804fa4ae1c6eca75cbba Tue Aug 27 16:28:48 2024 -0700
    Adding an extra line that informs users they can remove specific highlights via right click. Refs #34353
• src/hg/js/subCfg.js
  • lines changed 33, context: html, text, full: html, text
    03880f57ab6b355ea905067c7e4662eb657e44a0 Mon Aug 26 15:45:07 2024 -0700
    Make sub-config hgTrackUi controls not force the schema link outside the web browser window, refs #28083
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    c1b6ecf40163e277df5e8a03490a039bf47f4e6b Tue Aug 27 10:58:54 2024 -0700
    Switch some jquery selectors to document.querySelector so periods can be used in the query, refs #34252
  • lines changed 5, context: html, text, full: html, text
    1361600878135dfd42eae968c25e0370eae423c6 Wed Aug 28 13:55:49 2024 -0700
    Remove tooltips from divs that will become dialog boxes, refs #33977
• src/hg/lib/assemblyList.as
  • lines changed 4, context: html, text, full: html, text
    8ecd4ec7a45dc9f84f487d829b648f69c05fa862 Wed Aug 28 15:11:22 2024 -0700
    adding four columns to the database table for more accurate search refs #32596
• src/hg/lib/assemblyList.c
  • lines changed 82, context: html, text, full: html, text
    8ecd4ec7a45dc9f84f487d829b648f69c05fa862 Wed Aug 28 15:11:22 2024 -0700
    adding four columns to the database table for more accurate search refs #32596
• src/hg/lib/assemblyList.sql
  • lines changed 5, context: html, text, full: html, text
    8ecd4ec7a45dc9f84f487d829b648f69c05fa862 Wed Aug 28 15:11:22 2024 -0700
    adding four columns to the database table for more accurate search refs #32596
• src/hg/lib/chromAlias.c
  • lines changed 4, context: html, text, full: html, text
    a58d6091194d0113ef52cd694579ec703924a79a Mon Aug 26 16:52:00 2024 -0700
    enable non-hub assemblies to use chromAlias.bb from /gbdb
• src/hg/lib/featureBits.c
  • lines changed 5, context: html, text, full: html, text
    e0cf10a674d7aac55aff8d39d169440716eb3f74 Fri Aug 30 04:50:27 2024 -0700
    show table browser only exons when track contains genes, refs #27633
• src/hg/lib/genePredReader.c
  • lines changed 4, context: html, text, full: html, text
    5197ebd63b54192a79e5f001a5cb18d89822b542 Wed May 29 13:42:32 2024 -0700
    Improve genbank search performance, mostly by optimizing mysql queries down from one query per findSpec result into a single query that checks all the findSpec results
• src/hg/lib/hgFind.c
  • lines changed 83, context: html, text, full: html, text
    5197ebd63b54192a79e5f001a5cb18d89822b542 Wed May 29 13:42:32 2024 -0700
    Improve genbank search performance, mostly by optimizing mysql queries down from one query per findSpec result into a single query that checks all the findSpec results
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    945864df07edb8a0b7d3670ee2382eff3520703e Mon Aug 26 12:09:24 2024 -0700
    Make gtex cis-eqtls track filter by tissue dropdown work, we were missing javascript includes, refs #28142
  • lines changed 6, context: html, text, full: html, text
    1b5b7141665917514316dc90311835d16cfc61e3 Mon Aug 26 14:33:37 2024 -0700
    allow configuration of bigBed filters on bigGenePred tracks
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 3, context: html, text, full: html, text
    77c1fd0753c5b43a3c10baa351ed40962be704cb Tue Aug 27 16:53:48 2024 -0700
    Small change to generateUsageStats.py was to improve how it splits character lines. Before if counts were high, e.g. track:1034, it would slice out last 2 numbers but keep the :10. For the assemblyStatsCron various changes were made as documented in the RM ticket. This script is a fairly big mess, and has a lot of room for improvement via functions, better commentings, not using bash to write out, and general optimizations like parsing files mutltiple times. However, it is only used internally for general exploratory overviews and thus it has not warranted a proper restructuring and cleaning. The primary motivation here was to add up counts from track usage across all hubs instead of only reporting the highest one. Refs #34266
• src/hg/logCrawl/dbTrackAndSearchUsage/makefile
  • lines changed 1, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/dbTrackAndSearchUsage/trimTrackLogs
  • lines changed 115, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/trimLogs/README
  • lines changed 9, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/trimLogs/makefile
  • lines changed 2, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/trimLogs/runTrimLogs.sh
  • lines changed 222, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/trimLogs/trimLogs.sh
  • lines changed 9, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/logCrawl/trimLogs/trimTrackLogs
  • lines changed 115, context: html, text, full: html, text
    01660f51199249d8a05b8e863bea2f551920d8c9 Tue Aug 27 14:56:15 2024 -0700
    Add log trimming scripts to source tree so QA can run them, refs Lou email
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 5, context: html, text, full: html, text
    b0a9fd1a6ba35808bf4bc132bedef37af1b83a2c Wed Aug 28 14:30:29 2024 -0700
    convert the tsv listing to json for external consumption refs $34337
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 66, context: html, text, full: html, text
    e57553ce0dfbc42dc541d63da811f273c27c5351 Mon Aug 26 18:38:24 2024 -0700
    an update to catch to BRC genome set list refs #34337
  • lines changed 2, context: html, text, full: html, text
    5777a21286dc4cf80343b9505ce0833fdc7dfb5c Tue Aug 27 12:10:32 2024 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/asmHubs/tsvToJson.py
  • lines changed 315, context: html, text, full: html, text
    b0a9fd1a6ba35808bf4bc132bedef37af1b83a2c Wed Aug 28 14:30:29 2024 -0700
    convert the tsv listing to json for external consumption refs $34337
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    5777a21286dc4cf80343b9505ce0833fdc7dfb5c Tue Aug 27 12:10:32 2024 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 93, context: html, text, full: html, text
    c5942eaefb011d7bc460d6ea713712e9cfe8382d Wed Aug 28 09:20:51 2024 -0700
    rework the list to better match the beginning list from Anton refs #34337
• src/hg/makeDb/doc/brcAsmHub/hub.txt
  • lines changed 1, context: html, text, full: html, text
    c5942eaefb011d7bc460d6ea713712e9cfe8382d Wed Aug 28 09:20:51 2024 -0700
    rework the list to better match the beginning list from Anton refs #34337
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 73, context: html, text, full: html, text
    e57553ce0dfbc42dc541d63da811f273c27c5351 Mon Aug 26 18:38:24 2024 -0700
    an update to catch to BRC genome set list refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 2, context: html, text, full: html, text
    b63c2009dee960a47fbf2e7d5e92259b92c3211a Tue Aug 27 12:26:11 2024 -0700
    clean up listings refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b63c2009dee960a47fbf2e7d5e92259b92c3211a Tue Aug 27 12:26:11 2024 -0700
    clean up listings refs #29545
• src/hg/makeDb/hgLoadWiggle/chkWiggleTable.sh
  • lines changed 4, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    8fd8e815893d5f97f33b065862e727273f13a7b6 Wed Aug 28 18:29:54 2024 -0700
    Add ncbiRefSeqLink.omimId to omimId rule. refs #34013
• src/hg/makeDb/trackDb/human/enigma.html
  • lines changed 145, context: html, text, full: html, text
    bbd23e87bdbc50a9ee58c32982ff7987cb943af6 Tue Sep 3 08:58:25 2024 -0700
    Removing these tracks from internal trackDb since they are to be released only as public hubs refs #34352
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • lines changed 11, context: html, text, full: html, text
    2880d7bfc0b590450e4acb4c30c77726706f7a94 Thu Aug 29 19:37:31 2024 -0700
    Remove links that result go to warning page, refs #28064
• src/hg/makeDb/trackDb/human/hg19/wgRna.html
  • lines changed 7, context: html, text, full: html, text
    2880d7bfc0b590450e4acb4c30c77726706f7a94 Thu Aug 29 19:37:31 2024 -0700
    Remove links that result go to warning page, refs #28064
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
  • lines changed 6, context: html, text, full: html, text
    bee16be80287b44ddd0d1efdb74de194101da898 Thu Aug 29 00:05:36 2024 -0700
    Updating track names for the gnomAD v4.1 constraint track, refs #34252
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    e435de108aa1574d959ee3fbc40d674f1bf49224 Mon Aug 26 15:32:43 2024 -0700
    Replacing references to hgwdev.soe.ucsc.edu, as that server name is deprecated. no ticket
• src/hg/makeDb/trackDb/human/trackDb.enigmaTracks.ra
  • lines changed 70, context: html, text, full: html, text
    bbd23e87bdbc50a9ee58c32982ff7987cb943af6 Tue Sep 3 08:58:25 2024 -0700
    Removing these tracks from internal trackDb since they are to be released only as public hubs refs #34352
• src/hg/makeDb/trackDb/mouseStrains.html
  • lines changed 1, context: html, text, full: html, text
    e435de108aa1574d959ee3fbc40d674f1bf49224 Mon Aug 26 15:32:43 2024 -0700
    Replacing references to hgwdev.soe.ucsc.edu, as that server name is deprecated. no ticket
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 5, context: html, text, full: html, text
    6548404563a511e928e6813b7569614d56526a29 Mon Sep 2 05:17:51 2024 -0700
    adding VSV accessions to clinvar track, refs #34377
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    886ae501407aadc5b12c409cfaddc901b658fb76 Mon Aug 26 17:38:01 2024 -0700
    Tweaking runtime of GeCC otto to be at the start of the day, no RM.
  • lines changed 13, context: html, text, full: html, text
    aa7a4f9cc860e6f8ab0e9d24de61a12089bf2da4 Tue Aug 27 05:27:58 2024 -0700
    updating otto crontab, after email from Hiram
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
  • lines changed 30, context: html, text, full: html, text
    e587dcbf8a830c0c391309cb48bad26b186331b8 Mon Aug 26 17:40:31 2024 -0700
    Adding a new function that checks the current running otto crontab vs. the one committed to git.
• src/hg/utils/otto/sarscov2phylo/annotatedNotDesignated
  • lines changed 2, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 2, context: html, text, full: html, text
    29784b8ab0b8c9ae4f639d4411320ca0bbb3238b Wed Aug 14 13:07:57 2024 -0700
    Added a couple JN.1 GBW artifact sites reported by @FedeGueli.
• src/hg/utils/otto/sarscov2phylo/designatedNotAnnotated
  • lines changed 32, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 6, context: html, text, full: html, text
    d6e143eb6277e6a8d5ffadccbb9538325f5d86af Wed Aug 14 13:12:26 2024 -0700
    Add check for format of data returned by server (sometimes error messages are returned as text without HTTP error codes)
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    9ea690d413932da6911d75a073d3a5d95673d7d4 Wed Aug 14 13:08:23 2024 -0700
    Added 24C (KP.3)
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 19, context: html, text, full: html, text
    8e712a67beb687070337c4739f6a3664c5cc8225 Wed Aug 14 13:10:23 2024 -0700
    Fix lineage check to compare vs. lineages actually annotated on the tree, not just lineages present in pango.clade-mutations.tsv.
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    e10c349f9e394f6dfa688a2c83111115428b9535 Wed Aug 28 23:49:05 2024 -0700
    sort unpredictable output results
• src/product/installer/browserSetup.sh
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    e435de108aa1574d959ee3fbc40d674f1bf49224 Mon Aug 26 15:32:43 2024 -0700
    Replacing references to hgwdev.soe.ucsc.edu, as that server name is deprecated. no ticket
• src/utils/qa/GS1.csh
  • lines changed 1, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/utils/qa/assemblyStatsCron.py
  • lines changed 183, context: html, text, full: html, text
    77c1fd0753c5b43a3c10baa351ed40962be704cb Tue Aug 27 16:53:48 2024 -0700
    Small change to generateUsageStats.py was to improve how it splits character lines. Before if counts were high, e.g. track:1034, it would slice out last 2 numbers but keep the :10. For the assemblyStatsCron various changes were made as documented in the RM ticket. This script is a fairly big mess, and has a lot of room for improvement via functions, better commentings, not using bash to write out, and general optimizations like parsing files mutltiple times. However, it is only used internally for general exploratory overviews and thus it has not warranted a proper restructuring and cleaning. The primary motivation here was to add up counts from track usage across all hubs instead of only reporting the highest one. Refs #34266
• src/utils/qa/checkErrorLogsAreUpToDate.py
  • lines changed 26, context: html, text, full: html, text
    2aea926850613e4fcef435265d32564573fdb613 Wed Aug 28 11:23:21 2024 -0700
    Adding the runTrimLogs.sh script made by ChrisL to the tree, this has been running for a few years now. It processes the raw error logs into a better format that can be ingested by the various stats scripts such as the monthly usage reports. Primarily it makes sure that any error log lines belonging to a single cart does not span multiple lines. The second script is a small addition to check if the error logs are no longer updating. This has come up various times over the years, most recently botht he asia and euro logs had not updated since May, roughly 4.5 months old. No RM.
• src/utils/qa/compareHgFindSpecs.csh
  • lines changed 1, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/utils/qa/igtc.csh
  • lines changed 1, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/utils/qa/imageComp.py
  • lines changed 45, context: html, text, full: html, text
    ab18d0d8e378370ecc459e1b3ec8f5d72996296f Wed Aug 28 13:54:21 2024 -0700
    Fixing up the run function which began to fail when wget'ing the hgRender image. The arguments going into subprocess were getting mangled. No RM, image comparison cron issue.
• src/utils/qa/knownGene.csh
  • lines changed 2, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
• src/utils/qa/makefile
  • lines changed 2, context: html, text, full: html, text
    2aea926850613e4fcef435265d32564573fdb613 Wed Aug 28 11:23:21 2024 -0700
    Adding the runTrimLogs.sh script made by ChrisL to the tree, this has been running for a few years now. It processes the raw error logs into a better format that can be ingested by the various stats scripts such as the monthly usage reports. Primarily it makes sure that any error log lines belonging to a single cart does not span multiple lines. The second script is a small addition to check if the error logs are no longer updating. This has come up various times over the years, most recently botht he asia and euro logs had not updated since May, roughly 4.5 months old. No RM.
  • lines changed 1, context: html, text, full: html, text
    87435ae48fec925550b10151ef921ef36d75bb67 Wed Aug 28 12:46:28 2024 -0700
    Removing this from this dir as it already exists in ~/kent/src/hg/logCrawl/trimLogs/.
• src/utils/qa/qaTestScript.py
  • lines changed 5, context: html, text, full: html, text
    a544a4d69366f2959772f89ecd0fb1acc6172171 Tue Sep 3 08:19:19 2024 -0700
    Adding HAL example to selenium qaTestScript, No RM
• src/utils/qa/runTrimLogs.sh
  • lines changed 222, context: html, text, full: html, text
    2aea926850613e4fcef435265d32564573fdb613 Wed Aug 28 11:23:21 2024 -0700
    Adding the runTrimLogs.sh script made by ChrisL to the tree, this has been running for a few years now. It processes the raw error logs into a better format that can be ingested by the various stats scripts such as the monthly usage reports. Primarily it makes sure that any error log lines belonging to a single cart does not span multiple lines. The second script is a small addition to check if the error logs are no longer updating. This has come up various times over the years, most recently botht he asia and euro logs had not updated since May, roughly 4.5 months old. No RM.
  • lines changed 222, context: html, text, full: html, text
    87435ae48fec925550b10151ef921ef36d75bb67 Wed Aug 28 12:46:28 2024 -0700
    Removing this from this dir as it already exists in ~/kent/src/hg/logCrawl/trimLogs/.
• src/utils/qa/weeklybld/boxRelease.csh
  • lines changed 2, context: html, text, full: html, text
    45337f0f68ec7ec4e44183884dde67e81163ec67 Mon Aug 26 16:07:20 2024 -0700
    More updates for soe hostname deprecation, no ticket
  • lines changed 2, context: html, text, full: html, text
    db1319f8cd957c4d24344eead9f5b0dca8b9e0c4 Tue Sep 3 10:02:59 2024 -0700
    changed some URLs in printfs to use .gi.
• src/utils/qa/weeklybld/buildEnv.csh
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    1bc4a2a3c7559ec72a8c25a915fab379f944f6e5 Tue Sep 3 10:06:00 2024 -0700
    v471 preview1
• src/utils/trackDbIndexBb/makefile
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    884237c8d813f6f328f75b139f8f26715452712f Mon Aug 26 14:09:56 2024 -0700
    properly remove destination file before running a blind cp -p to maintain correct permissions no redmine

• lines changed: 3369
• files changed: 107