All File Changes

v483_base to v484_preview (2025-06-09 to 2025-06-16) v484

• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 48, context: html, text, full: html, text
    a6a06378c3b112aa02cfe53f1a3805cb46ce128e Wed Jun 11 09:39:31 2025 -0700
    Adding WUSTL preliminary milestones from NIMH, ADGC7_F_28 = Column F, Row 28 from xls SSPsyGene Milestones RM1MH138313 Dougherty_FY25
  • lines changed 28, context: html, text, full: html, text
    6b3f2776a5c2974cdc88331ae27397a9fa2a986a Thu Jun 12 11:50:06 2025 -0700
    ADGC7 milestones sorted to Aims and Quarterly dates, ex column D - 9/30/2025 = 10/01/2025
  • lines changed 8, context: html, text, full: html, text
    fd09c7432e1cc6b213b9c5a02342d1748a026ee3 Fri Jun 13 09:26:04 2025 -0700
    Cleaning date data [mermaid code tolerated incorrect month lengths]
• src/hg/hgApi/hgApi.c
  • lines changed 3, context: html, text, full: html, text
    97a48c4a38b1032011acc92c711dd5ed3f258620 Thu Jun 12 11:10:25 2025 -0700
    If we didn't find the requested item in the genePred, do not continue as if we had found it, refs #35799
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    4e5154cb7b0faf1d16fadc3ec9f14018c8aa7bd2 Mon Jun 16 10:58:41 2025 -0700
    clade menu was not working refs #35863
• src/hg/hgHubConnect/hooks/hooklib.c
  • lines changed 54, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/hgHubConnect/hooks/hooklib.h
  • lines changed 6, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 25, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 29, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 7, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    88176999b6871c27f9c57d05bf21298671b561bb Fri Jun 13 15:44:33 2025 -0700
    extending warning on table browser to gnomad tracks, refs #35899
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 8, context: html, text, full: html, text
    86748c94956144a80b6c9daa78adb5bb280f58d4 Tue Jun 10 17:20:58 2025 -0700
    ignore psl base change display settings for protein psl since they are not supported
  • lines changed 1, context: html, text, full: html, text
    e3d2a33b73538f57586c2308113f6de1fbfa910d Mon Jun 16 07:13:41 2025 -0700
    improving merged items mouseover, no redmine
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    1668938f2aaa79ea9567d86fda63dfbda39f5d83 Wed Jun 11 07:14:57 2025 -0700
    remove EPS text and replace with note about vector graphics, refs #29394
• src/hg/hgTracks/simpleTracks.c
  • lines changed 40, context: html, text, full: html, text
    c143e15a268ea9f8338dbde7f9f832cbdbacb5fb Fri Jun 13 17:30:18 2025 -0700
    color bedMethyl appropriately and add mouseOver
  • lines changed 5, context: html, text, full: html, text
    5ec0112a1ac3e2714a3e44d83bd9fffb225b8eb4 Mon Jun 16 03:00:29 2025 -0700
    make the decorator glyphs a little smaller on high zoom levels, refs #35750
• src/hg/hgc/bamClick.c
  • lines changed 22, context: html, text, full: html, text
    c46e05f162d1eaefe16a84d7df9d2afcaa2dd4bb Mon Jun 16 14:54:58 2025 -0700
    output BAM alignment type in hgc page
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    abc14f34612ed59a0b27a0bc355e43733ddf1407 Tue Jun 10 10:19:40 2025 -0700
    fixing dupl link on hgc page on bigGenePred refs #35895
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    483e785a1cef9c2bfe1f08030cbc781f353deffc Tue Jun 10 09:01:13 2025 -0700
    Doc'ing logoMaf option, refs #34064
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 10, context: html, text, full: html, text
    483e785a1cef9c2bfe1f08030cbc781f353deffc Tue Jun 10 09:01:13 2025 -0700
    Doc'ing logoMaf option, refs #34064
  • lines changed 1, context: html, text, full: html, text
    8c5c91f825e66e6e351615d262d9136bb90edb30 Tue Jun 10 09:41:18 2025 -0700
    Adding logoMaf to bigMaf file type as well, refs #34064
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 150, context: html, text, full: html, text
    5239d7622b288c5d897ca855808844b16c183833 Tue Jun 10 16:00:17 2025 -0700
    Releasing and announcing the EVA Release 7, refs #35504
  • lines changed 1, context: html, text, full: html, text
    544eb50d2b311bbf70c92df72f98043a6fd0b57d Tue Jun 10 16:17:20 2025 -0700
    Fixing sacCer3 line for newsarch, refs #35504
  • lines changed 3, context: html, text, full: html, text
    e59602f7535ae9f199be704a7ee31e75f78eba69 Thu Jun 12 12:18:23 2025 -0700
    Fixing typos and making edits to the EVA Release 7 announcement, #35504
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    5239d7622b288c5d897ca855808844b16c183833 Tue Jun 10 16:00:17 2025 -0700
    Releasing and announcing the EVA Release 7, refs #35504
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    7cfe90e46b4537117f9b026d8e8508b55fe3462c Tue Jun 10 12:14:18 2025 -0700
    oops forgot to commit file in previous commit
• src/hg/inc/userdata.h
  • lines changed 3, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/js/ui.dropdownchecklist.js
  • lines changed 3, context: html, text, full: html, text
    e4d45c038f7a0e2e47610b4604b4d2908a8696cc Mon Jun 16 12:21:15 2025 -0700
    Add missing call to update the actual select when clear filters is clicked, refs #35906
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    d1727a7299087e0e936222db77097cfd936ddc2e Thu Jun 12 14:55:42 2025 -0700
    Don't double encode items on the url if they are already encoded, refs #35799
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    c143e15a268ea9f8338dbde7f9f832cbdbacb5fb Fri Jun 13 17:30:18 2025 -0700
    color bedMethyl appropriately and add mouseOver
• src/hg/lib/userdata.c
  • lines changed 34, context: html, text, full: html, text
    544b4db19ee0f7f92c9d338d6900c34a53d9f032 Wed Jun 11 15:45:15 2025 -0700
    Add back the good parts of b318572799b35, mostly have the pre-create hook set the upload path so we don't have to move files around in the pre-finish hook
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 596, context: html, text, full: html, text
    60926b22b0e71a92f99d8ed72f494a0689f06fa4 Sat Jun 14 12:20:50 2025 -0700
    cattle (GCF_002263795.3) to wildyak/pig/horse/dog/sugar_glider/rabbit/hedgehog lastz/chain/net run for user, refs #35794
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    09ef85ca632c16e69f78df3c0c0c3341cfe47fee Tue Jun 10 12:05:17 2025 -0700
    adding on per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    031ecd610e5aedea24a47b593927a304928c2172 Tue Jun 10 15:00:40 2025 -0700
    adding two for the BRC project 34337
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    acdf4cc28a8651e554426c493d06380e2bacf895 Wed Jun 11 17:04:29 2025 -0700
    adding updated HPRC assemblies and a user request refs #35415
  • lines changed 1, context: html, text, full: html, text
    d055acf1b67fcd434c4c7e2ddec719b35aba9390 Mon Jun 16 11:02:17 2025 -0700
    add one per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    acdf4cc28a8651e554426c493d06380e2bacf895 Wed Jun 11 17:04:29 2025 -0700
    adding updated HPRC assemblies and a user request refs #35415
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d08295645530efa8f0499aeb90c99bbd148d1f81 Mon Jun 9 14:14:09 2025 -0700
    catching up to BRC project list refs #34337
  • lines changed 3, context: html, text, full: html, text
    8eee5585408be4638d72c8edc91d10cde921c3ff Wed Jun 11 15:06:14 2025 -0700
    catching up to BRC project list refs #34337
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    acdf4cc28a8651e554426c493d06380e2bacf895 Wed Jun 11 17:04:29 2025 -0700
    adding updated HPRC assemblies and a user request refs #35415
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 69, context: html, text, full: html, text
    acdf4cc28a8651e554426c493d06380e2bacf895 Wed Jun 11 17:04:29 2025 -0700
    adding updated HPRC assemblies and a user request refs #35415
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    09ef85ca632c16e69f78df3c0c0c3341cfe47fee Tue Jun 10 12:05:17 2025 -0700
    adding on per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    031ecd610e5aedea24a47b593927a304928c2172 Tue Jun 10 15:00:40 2025 -0700
    adding two for the BRC project 34337
  • lines changed 13, context: html, text, full: html, text
    d055acf1b67fcd434c4c7e2ddec719b35aba9390 Mon Jun 16 11:02:17 2025 -0700
    add one per user request refs #29545
• src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
  • lines changed 66, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/hgLoadMaf/tests/expected/testDot.tab
  • lines changed 17, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/hgLoadMaf/tests/expected/testPipe.tab
  • lines changed 17, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/hgLoadMaf/tests/input/testDot.maf
  • lines changed 74, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/hgLoadMaf/tests/input/testPipe.maf
  • lines changed 74, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/hgLoadMaf/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    4ad0e02ecf9b2e9dd03c37e72dcec0915d3d9d3e Wed Jun 11 06:02:25 2025 -0700
    allowing dot in MAF files and also a pipe character, email with Hiram, ticket is coming
• src/hg/makeDb/trackDb/evaSnp.alpha.ra
  • lines changed 132, context: html, text, full: html, text
    5239d7622b288c5d897ca855808844b16c183833 Tue Jun 10 16:00:17 2025 -0700
    Releasing and announcing the EVA Release 7, refs #35504
• src/hg/makeDb/trackDb/evaSnp.ra
  • lines changed 29, context: html, text, full: html, text
    5239d7622b288c5d897ca855808844b16c183833 Tue Jun 10 16:00:17 2025 -0700
    Releasing and announcing the EVA Release 7, refs #35504
• src/hg/makeDb/trackDb/human/hg38/hicAndMicroC.html
  • lines changed 1, context: html, text, full: html, text
    5e412867b72db8c2e65c2c090dc0682d257fa737 Tue Jun 10 16:15:24 2025 -0700
    Adding an anchor for the Data Access section, refs #35861
• src/hg/makeDb/trackDb/human/hg38/unusualcons.html
  • lines changed 20, context: html, text, full: html, text
    53da311c2aa0cff3f0feee6d90e52ff7e0ec6ca5 Fri Jun 13 14:59:48 2025 -0700
    Making the track name bold and moving the definition to a new line to make the section less cluttered. Changing < and > to HTML entities, refs #35703
  • lines changed 33, context: html, text, full: html, text
    c2e552afa0d0574db2c2d93b51cd87b6484c4ddb Fri Jun 13 15:59:17 2025 -0700
    Adding links to the papers mentioned in the description for each track, refs #35703
  • lines changed 21, context: html, text, full: html, text
    9ed3e168a16f43599dd0e095304e54e049d99294 Mon Jun 16 13:58:13 2025 -0700
    Creating links to the download files in the Methods section for the Unusual Conservation track for hg38, refs #35703
  • lines changed 1, context: html, text, full: html, text
    105d8432645205ff11f4152e7ff9f30b25d11e9d Mon Jun 16 14:05:00 2025 -0700
    Removing strange encodings from one of the references, refs #35703
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    7947ad20b75e839bd0bb944db858bc73b56e568f Mon Jun 16 05:36:01 2025 -0700
    XSS prevention in error message output for errAbort(), refs #34157
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    5239d7622b288c5d897ca855808844b16c183833 Tue Jun 10 16:00:17 2025 -0700
    Releasing and announcing the EVA Release 7, refs #35504
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
  • lines changed 109, context: html, text, full: html, text
    7000bc69be5351f65c48d434bcc477b8d6d7cc05 Mon Jun 16 20:26:59 2025 -0700
    the database trackDb construction does not like the chain net views mixed up they must be the stanza right before their subTracks refs #35898
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    6fe0e58c664dd4f9849fb222de0a82bb5de61c61 Mon Jun 16 20:47:30 2025 -0700
    the database trackDb construction does not like the chain net views mixed up they must be the stanza right before their subTracks refs #35898
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 4, context: html, text, full: html, text
    bab676a6dc1396b8c361770f3dea490fb91243d1 Sun Jun 15 09:57:26 2025 -0700
    do not make symlinks in /gbdb/GCx_.../...
• src/hg/utils/automation/makefile
  • lines changed 1, context: html, text, full: html, text
    3f0c0274dd461da6dc0b76ab564723d0601952aa Mon Jun 16 20:28:59 2025 -0700
    should be delivering asmHubChainNetTrackDb.pl refs #35898
• src/lib/errAbort.c
  • lines changed 42, context: html, text, full: html, text
    7947ad20b75e839bd0bb944db858bc73b56e568f Mon Jun 16 05:36:01 2025 -0700
    XSS prevention in error message output for errAbort(), refs #34157
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    bab7d44dff52482307f68080744610101262b0d7 Mon Jun 16 07:29:18 2025 -0700
    reformatting previous commit in kent style
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    e5c2df7918c8e87602d4a525636dfcf6a2f77076 Mon Jun 16 08:02:09 2025 -0700
    making code a little nicer, refs #34157
• src/parasol/lib/paraMessage.c
  • lines changed 4, context: html, text, full: html, text
    25c163a7c73c6c9186ff840b2f214ab0de93bdb3 Thu Jun 12 18:07:36 2025 -0700
    Revert "fix for overflowing packet issue when paraHub restarts but most jobs are run on just one node." Hiram reports it did not fix the problem. This reverts commit f727e7c1325f863157c57d88ba0a1c3cf65b1478.
• src/parasol/paraNode/paraNode.c
  • lines changed 30, context: html, text, full: html, text
    25c163a7c73c6c9186ff840b2f214ab0de93bdb3 Thu Jun 12 18:07:36 2025 -0700
    Revert "fix for overflowing packet issue when paraHub restarts but most jobs are run on just one node." Hiram reports it did not fix the problem. This reverts commit f727e7c1325f863157c57d88ba0a1c3cf65b1478.
• src/product/installer/browserSetup.sh
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    a2b91b291a7c3823ff9e634612fcd85e9b8fd4b8 Mon Jun 16 07:15:47 2025 -0700
    clarifying docs after chris email, no redmine
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    a71e83c30508f8e59f523b495c263902c397aa3c Mon Jun 16 07:22:55 2025 -0700
    a warning for installs on osx, reported by chris, no redmine
• src/utils/qa/check_Tables_Metadata.py
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    04cadaf097f071cb3fd88866691fb1133b6d4bc5 Mon Jun 16 22:47:03 2025 -0700
    Commenting out the blatServers filtering to remove domain part due to Hiram updating the blatServers.hgcentral table on hgnfs1 for all host names, refs #35846
• src/utils/qa/qaTestScript.py
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    0b6c42c4114cc99b527d9fc8e4146ed8718658df Mon Jun 16 14:02:31 2025 -0700
    Updating the selenium qaTestScript to fix local mode issue, add a function that hovers the blue bar menu and clicks a menu item, comment out hgGeneGraph testing, update split table test, login as QAtester to test hgCollection, and update GenArk Rabbit Hub testing, No RM
• src/utils/qa/weeklybld/buildEnv.csh
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    cfec22009e749f14fed44493ec3c77d4e0c730e4 Mon Jun 16 23:11:40 2025 -0700
    v484 preview1, refs #35819

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• files changed: 73