All File Changes

v438_preview2 to v438_base (2022-10-03 to 2022-10-10) v438

• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 12, context: html, text, full: html, text
    6c5cc98477af424865533ac39e22adf968a2f98d Tue Oct 4 12:55:30 2022 -0700
    cdw fixes for sqlSafef v2, and a minor bug fix of Jims refactoring of facet code.
  • lines changed 9, context: html, text, full: html, text
    1d5cb6a53674b76c2f8d4f8413a69b10124d9cbc Wed Oct 5 16:02:16 2022 -0700
    Fixing a few more minor bugs for sqlSafef V2 in CIRM cdwWebBrowse.
  • lines changed 1, context: html, text, full: html, text
    1dfa3b9f97577f088af82ed02340c07886d690fd Fri Oct 7 16:52:26 2022 -0700
    Various bugfixes for sqlSafef v2 and some of Jims refactoring like adding fuseCsvFields so it can support multiple tables in the from list. Also fixed an encoding issue for sample labels that had a double-quote in them. Updated jquery.min.js to point to newer version 1.12.
  • lines changed 33, context: html, text, full: html, text
    dc56c85d424c91e5c9fa4a8c3ae12881cccdd278 Fri Oct 7 18:49:19 2022 -0700
    sqlSafef v2 shift sqlSanity call to just where needed.
• src/hg/hgConvert/hgConvert.c
  • lines changed 1, context: html, text, full: html, text
    702cc90549aa4b82a4318d5bfdca9ea55ed732ba Mon Oct 3 14:12:53 2022 -0700
    build URLs into curated assemblies on hubs
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    67e90fa07dafa6a5afe8d7eac8435064252a1b9e Wed Oct 5 13:48:43 2022 -0700
    make sure that hgGateway JSON support doesn't assume that a db is a mySQL database when looking for a geneSuggest track
• src/hg/hgTables/filterFields.c
  • lines changed 6, context: html, text, full: html, text
    13a162ac62b49cf2908da7d0bdd872e3f0010591 Mon Oct 3 11:47:30 2022 -0700
    special case the knownGene track in the table browser until we get bigBed support in the all.joiner structure
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    13a162ac62b49cf2908da7d0bdd872e3f0010591 Mon Oct 3 11:47:30 2022 -0700
    special case the knownGene track in the table browser until we get bigBed support in the all.joiner structure
• src/hg/hgTables/schema.c
  • lines changed 18, context: html, text, full: html, text
    13a162ac62b49cf2908da7d0bdd872e3f0010591 Mon Oct 3 11:47:30 2022 -0700
    special case the knownGene track in the table browser until we get bigBed support in the all.joiner structure
• src/hg/hgTracks/hgTracks.c
  • lines changed 93, context: html, text, full: html, text
    6743beb41fc441dc2c5c37fcd330d280d197c7b0 Mon Oct 3 14:29:11 2022 -0700
    make a few small style changes on hgTracks: removing a few buttons that are hardly used, merging the two help texts, refs #29676
  • lines changed 2, context: html, text, full: html, text
    1b711556384dac50aa5cb05ccb596e773de42f72 Tue Oct 4 03:11:45 2022 -0700
    a few more small style tweaks to buttons on hgTracks, refs #29676
  • lines changed 2, context: html, text, full: html, text
    e318a262fe4f44d261b12eaab18c5dbb957094b1 Fri Oct 7 13:02:47 2022 -0700
    tiny css tweak suggested by clay, refs #29676
• src/hg/hgc/barChartClick.c
  • lines changed 1, context: html, text, full: html, text
    41d6ade369a45eec328b82f119e44bfddd6d350b Tue Oct 4 10:45:17 2022 -0700
    Fix urlLabel bug for barChart tracks I introduced when adding variable substitution to urlLabel setting, refs #29954
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 11, context: html, text, full: html, text
    674141354338dfe084c2120ba9cdd69fdae35621 Tue Oct 4 16:02:03 2022 -0700
    Adding two missing URL parameters, refs #30077
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    521cc31b669f7747ef7e64c7b5fc0051eb106d24 Mon Oct 10 08:42:25 2022 -0700
    adding link to genome-announce, OKed by Lou, no redmine
• src/hg/htdocs/images/Monkeypox_virus.jpg
  • lines changed 0, context: html, text, full: html, text
    010fc087ca305aee363153bb9d523aaad727d928 Fri Oct 7 16:58:27 2022 -0700
    monkeypox virus from NIAID Integrated Research Facility (IRF) https://www.flickr.com/photos/niaid/52103767506/ refs #29811
• src/hg/htdocs/inc/garModal.html
  • lines changed 1, context: html, text, full: html, text
    a530401a5ad42da837f0138689f123053e689191 Mon Oct 10 09:50:19 2022 -0700
    better indicate in the message that there will be a process to review the request no redmine
• src/hg/htdocs/style/HGStyle.css
  • lines changed 8, context: html, text, full: html, text
    6743beb41fc441dc2c5c37fcd330d280d197c7b0 Mon Oct 3 14:29:11 2022 -0700
    make a few small style changes on hgTracks: removing a few buttons that are hardly used, merging the two help texts, refs #29676
  • lines changed 1, context: html, text, full: html, text
    eb574da054723ad68bb4b1aa2a99d7cab2717a5e Mon Oct 3 14:33:32 2022 -0700
    forgot one button type in previous CSS change, refs #29676
  • lines changed 37, context: html, text, full: html, text
    1b711556384dac50aa5cb05ccb596e773de42f72 Tue Oct 4 03:11:45 2022 -0700
    a few more small style tweaks to buttons on hgTracks, refs #29676
  • lines changed 14, context: html, text, full: html, text
    8476bbc207cfff3eeba979bb22d5cb5f0025164a Fri Oct 7 08:30:13 2022 -0700
    after feedback from QA, a tiny change to buttons, refs #29676
  • lines changed 11, context: html, text, full: html, text
    e318a262fe4f44d261b12eaab18c5dbb957094b1 Fri Oct 7 13:02:47 2022 -0700
    tiny css tweak suggested by clay, refs #29676
• src/hg/htdocs/training/index.html
  • lines changed 4, context: html, text, full: html, text
    bebdfc0578f9c113c1dfc2efbbd4c70675edd071 Wed Oct 5 16:52:18 2022 -0700
    removed completed workshops
• src/hg/htdocs/training/upcoming.html
  • lines changed 23, context: html, text, full: html, text
    bebdfc0578f9c113c1dfc2efbbd4c70675edd071 Wed Oct 5 16:52:18 2022 -0700
    removed completed workshops
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    1dfa3b9f97577f088af82ed02340c07886d690fd Fri Oct 7 16:52:26 2022 -0700
    Various bugfixes for sqlSafef v2 and some of Jims refactoring like adding fuseCsvFields so it can support multiple tables in the from list. Also fixed an encoding issue for sample labels that had a double-quote in them. Updated jquery.min.js to point to newer version 1.12.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    34dfbf4b8910ce44315ac4ac0fe7e3e6f08f4540 Mon Oct 10 10:07:25 2022 -0700
    New version number v438
• src/hg/js/hgGateway.js
  • lines changed 9, context: html, text, full: html, text
    33c36db157884a27c6557ec816985dfa55675757 Wed Oct 5 22:12:02 2022 -0700
    add onclick function to buttons of class copyLink no redmine
• src/hg/js/hgHubConnect.js
  • lines changed 2, context: html, text, full: html, text
    6f0e8cf11dd3ead8170cf978f2587b768bc1d55a Mon Oct 10 06:58:07 2022 -0700
    finally was able to reproduce a bug I've observed a few times: the event listener on SVGs does not always return the SVG but can also return the PATH element as the target, depending on where the user clicks. This lead to non-working copy click handler on the SVG icon. Fixed now. refs #29583
• src/hg/lib/chromInfo.c
  • lines changed 3, context: html, text, full: html, text
    361c03dcbf16893e92db9a168c4c976cfd5736e7 Wed Oct 5 16:31:47 2022 -0700
    make chromSeqFileExists() do as it says it does and check for the existence of the chromInfo table before querying it.
• src/hg/lib/facetedTable.c
  • lines changed 1, context: html, text, full: html, text
    1dfa3b9f97577f088af82ed02340c07886d690fd Fri Oct 7 16:52:26 2022 -0700
    Various bugfixes for sqlSafef v2 and some of Jims refactoring like adding fuseCsvFields so it can support multiple tables in the from list. Also fixed an encoding issue for sample labels that had a double-quote in them. Updated jquery.min.js to point to newer version 1.12.
• src/hg/lib/hubConnect.c
  • lines changed 14, context: html, text, full: html, text
    5a6c13c718520069fb7f74c633ab7192aaf04231 Mon Oct 3 17:04:22 2022 -0700
    default to using "public" if no curatedHubPrefix is set
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    2530ca0451b74a28dcf4abc8edaf10d49c48d6ce Mon Oct 3 14:28:01 2022 -0700
    add option for bigSnp to go into wiggle mode
• src/hg/lib/jksql.c
  • lines changed 18, context: html, text, full: html, text
    1dfa3b9f97577f088af82ed02340c07886d690fd Fri Oct 7 16:52:26 2022 -0700
    Various bugfixes for sqlSafef v2 and some of Jims refactoring like adding fuseCsvFields so it can support multiple tables in the from list. Also fixed an encoding issue for sample labels that had a double-quote in them. Updated jquery.min.js to point to newer version 1.12.
• src/hg/lib/tablesTables.c
  • lines changed 8, context: html, text, full: html, text
    6c5cc98477af424865533ac39e22adf968a2f98d Tue Oct 4 12:55:30 2022 -0700
    cdw fixes for sqlSafef v2, and a minor bug fix of Jims refactoring of facet code.
  • lines changed 1, context: html, text, full: html, text
    1d5cb6a53674b76c2f8d4f8413a69b10124d9cbc Wed Oct 5 16:02:16 2022 -0700
    Fixing a few more minor bugs for sqlSafef V2 in CIRM cdwWebBrowse.
  • lines changed 9, context: html, text, full: html, text
    1dfa3b9f97577f088af82ed02340c07886d690fd Fri Oct 7 16:52:26 2022 -0700
    Various bugfixes for sqlSafef v2 and some of Jims refactoring like adding fuseCsvFields so it can support multiple tables in the from list. Also fixed an encoding issue for sample labels that had a double-quote in them. Updated jquery.min.js to point to newer version 1.12.
  • lines changed 2, context: html, text, full: html, text
    dc56c85d424c91e5c9fa4a8c3ae12881cccdd278 Fri Oct 7 18:49:19 2022 -0700
    sqlSafef v2 shift sqlSanity call to just where needed.
• src/hg/makeDb/doc/asmHubs/README.txt
  • lines changed 74, context: html, text, full: html, text
    6d9006164b9b861ba1d199c9c81b6ea40ababc1c Tue Oct 4 12:26:41 2022 -0700
    update instructions to include how to add locally developed tracks to the GenArk hub
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    61d34db4f91fbd325f16c3e9a5b87f66c6d4b462 Tue Oct 4 11:57:47 2022 -0700
    adding soybean legacy assembly GCF_000004515.4_Glycine_max_v2.0 per user request for a liftOver refs #30089
  • lines changed 169, context: html, text, full: html, text
    2417266c7f2ef6fbaef4f292e8d160941225911e Wed Oct 5 10:47:32 2022 -0700
    clear up confusion of invertebrates with invertebrate only need one no redmine
  • lines changed 1, context: html, text, full: html, text
    83b8b215a8fb3c86ee95b43fba845bcba93e5ed3 Wed Oct 5 15:06:35 2022 -0700
    adding assembly per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    83b8b215a8fb3c86ee95b43fba845bcba93e5ed3 Wed Oct 5 15:06:35 2022 -0700
    adding assembly per user request refs #29545
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 26, context: html, text, full: html, text
    adea08b7a8578f96a2e819466754b24ad79645f6 Mon Oct 3 13:27:41 2022 -0700
    removing old panelApp makedoc, refs #25568
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 2, context: html, text, full: html, text
    41d12b7ab39ffce5eba5fce2715a7afbe51667d2 Tue Oct 4 18:53:05 2022 -0700
    added an obsolete soybean assembly per user request no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    61d34db4f91fbd325f16c3e9a5b87f66c6d4b462 Tue Oct 4 11:57:47 2022 -0700
    adding soybean legacy assembly GCF_000004515.4_Glycine_max_v2.0 per user request for a liftOver refs #30089
• src/hg/makeDb/doc/mpxvRivers/genbankAli.txt
  • lines changed 8, context: html, text, full: html, text
    f594c31c334b0bfb0a23df10f2792772e3f39a21 Mon Oct 10 06:28:40 2022 -0700
    genbank alignment track for mpxvRivers, #30111
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 42, context: html, text, full: html, text
    0787a7613d9959a9cb0956ba8d6810660da4c29b Tue Oct 4 06:40:09 2022 -0700
    removing old panelApp trackDb parts, refs#25568
• src/hg/makeDb/trackDb/human/hg38/gtexSnAtlas.html
  • lines changed 7, context: html, text, full: html, text
    e91a026f3d1a402b6d42c814dc56c6a15e9d1770 Mon Oct 3 17:48:59 2022 -0700
    Made a few minor edits to the gtexSnAtlas.html, refs #29954
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    48ac5b576269cb2e4a7ded271b3482535a4e98d9 Mon Oct 3 11:51:51 2022 -0700
    short term change to support "old style" knownGene queries in the table browser
• src/hg/makeDb/trackDb/human/hg38/recombRate2.html
  • lines changed 4, context: html, text, full: html, text
    54680f4b9b2738aa5e549b45fef5f4f9419e1f5b Mon Oct 3 13:10:32 2022 -0700
    fixing funny typo noticed by poor Po-Ru Loh in the docs page, refs #30044
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 8, context: html, text, full: html, text
    51ddfe5fe097fbbc36b76270a4a1e97ea798fa57 Tue Oct 4 06:22:49 2022 -0700
    updating panelAdd trackDb, refs#25568
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    2eaedbb507227d834dd9fc191bc029a140809974 Fri Oct 7 16:50:12 2022 -0700
    Adding maxWindowCov to make dbSnp density graph and tweaking cfg for more clarity, refs #29715
• src/hg/makeDb/trackDb/virus/mpxvRivers/genbankAli.html
  • lines changed 61, context: html, text, full: html, text
    f594c31c334b0bfb0a23df10f2792772e3f39a21 Mon Oct 10 06:28:40 2022 -0700
    genbank alignment track for mpxvRivers, #30111
• src/hg/makeDb/trackDb/virus/mpxvRivers/genbankAli.ra
  • lines changed 10, context: html, text, full: html, text
    f594c31c334b0bfb0a23df10f2792772e3f39a21 Mon Oct 10 06:28:40 2022 -0700
    genbank alignment track for mpxvRivers, #30111
• src/hg/makeDb/trackDb/virus/mpxvRivers/html/assembly.html
  • lines changed 19, context: html, text, full: html, text
    32fcbb4a69306091132bad1cedb83084e3c146fc Fri Oct 7 17:33:09 2022 -0700
    updated text refs #29811
• src/hg/makeDb/trackDb/virus/mpxvRivers/html/cpgIslands.html
  • lines changed 2, context: html, text, full: html, text
    52f94f1f0d21752b3d8bcd3d879f2315bb2a6b96 Fri Oct 7 17:52:39 2022 -0700
    updated cpgIsland doc refs #29811
• src/hg/makeDb/trackDb/virus/mpxvRivers/html/description.html
  • lines changed 53, context: html, text, full: html, text
    fdbcbd6f5c97950df0bba8c319d026f3a61d338b Fri Oct 7 17:24:53 2022 -0700
    change hub text to zombie text refs #29811
• src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.html
  • lines changed 4, context: html, text, full: html, text
    44c6f980e485e5a93041214e0b78552bb1dad79c Wed Oct 5 14:57:28 2022 -0700
    Slight edits for primer track QA refs #30012
• src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.ra
  • lines changed 2, context: html, text, full: html, text
    44c6f980e485e5a93041214e0b78552bb1dad79c Wed Oct 5 14:57:28 2022 -0700
    Slight edits for primer track QA refs #30012
• src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    988fb9e9a5d07d53f4d70ff428f6e282a7587399 Fri Oct 7 17:50:28 2022 -0700
    cpgIslands recalculated refs #29811
  • lines changed 3, context: html, text, full: html, text
    f594c31c334b0bfb0a23df10f2792772e3f39a21 Mon Oct 10 06:28:40 2022 -0700
    genbank alignment track for mpxvRivers, #30111
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 4, context: html, text, full: html, text
    2121928a798a7119f00eb7e198bd06cf4ea36d2f Wed Oct 5 10:14:36 2022 -0700
    correctly recognize the presence of the chain net files no redmine
• src/hg/utils/automation/asmHubGatewayPage.pl
  • lines changed 2, context: html, text, full: html, text
    41e19d9efe6e606e34c4a832adc63c24ed27285b Tue Oct 4 14:26:32 2022 -0700
    beginning to add a share this link to be fixed up with the copy to clipboard functions no redmine
  • lines changed 2, context: html, text, full: html, text
    1e0a7a0350cbd56b4525ad015b783ed9e091e46d Wed Oct 5 10:01:37 2022 -0700
    adding copy link button to gateway page no redmine
  • lines changed 1, context: html, text, full: html, text
    e9df5883fdd6fc3429b95c3f0df69ffd846766b6 Thu Oct 6 09:32:29 2022 -0700
    extra space and bold the link no redmine
• src/hg/utils/automation/asmHubNcbiGene.pl
  • lines changed 27, context: html, text, full: html, text
    4951a3f2ca22c980a415c231e59958197baec741 Wed Oct 5 10:41:05 2022 -0700
    correct Gene model labels on the ncbiGene (not really NCBI gene) track no redmine
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 17, context: html, text, full: html, text
    4951a3f2ca22c980a415c231e59958197baec741 Wed Oct 5 10:41:05 2022 -0700
    correct Gene model labels on the ncbiGene (not really NCBI gene) track no redmine
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 11, context: html, text, full: html, text
    f981cdb28308ceeb88a91fa7ea81fe86a8d96ed6 Mon Oct 3 12:52:00 2022 -0700
    Add a hubCheck test for the autoScale setting for bigWigs, refs #30057
• src/hg/utils/hubCheck/tests/expected/autoScaleHub.txt
  • lines changed 10, context: html, text, full: html, text
    f981cdb28308ceeb88a91fa7ea81fe86a8d96ed6 Mon Oct 3 12:52:00 2022 -0700
    Add a hubCheck test for the autoScale setting for bigWigs, refs #30057
• src/hg/utils/hubCheck/tests/input/autoScaleHub.txt
  • lines changed 54, context: html, text, full: html, text
    f981cdb28308ceeb88a91fa7ea81fe86a8d96ed6 Mon Oct 3 12:52:00 2022 -0700
    Add a hubCheck test for the autoScale setting for bigWigs, refs #30057
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    f981cdb28308ceeb88a91fa7ea81fe86a8d96ed6 Mon Oct 3 12:52:00 2022 -0700
    Add a hubCheck test for the autoScale setting for bigWigs, refs #30057
• src/hg/utils/otto/panelApp/genes.py
  • lines changed 40, context: html, text, full: html, text
    da377fdc8a33c352274795c5817d8d117e03ae10 Tue Oct 4 03:30:08 2022 -0700
    more panelApp fixes, partially found by QA, refs #25568
• src/hg/utils/otto/panelApp/updatePanelApp
  • lines changed 2, context: html, text, full: html, text
    da377fdc8a33c352274795c5817d8d117e03ae10 Tue Oct 4 03:30:08 2022 -0700
    more panelApp fixes, partially found by QA, refs #25568
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    34dfbf4b8910ce44315ac4ac0fe7e3e6f08f4540 Mon Oct 10 10:07:25 2022 -0700
    New version number v438
• src/lib/cheapcgi.c
  • lines changed 1, context: html, text, full: html, text
    1b711556384dac50aa5cb05ccb596e773de42f72 Tue Oct 4 03:11:45 2022 -0700
    a few more small style tweaks to buttons on hgTracks, refs #29676
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    c57a8c64367799fa0b6463f1c151670c3d923d66 Mon Oct 10 10:06:03 2022 -0700
    v438 final build, refs #30058

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• files changed: 76