All File Changes

v475_preview to v475_preview2 (2024-11-25 to 2024-12-02) v475

• src/hg/hgLogin/hgLogin.c
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    8ac718f8496a6fbfbf00248a68e740a10c0bcf81 Tue Nov 26 00:42:19 2024 -0800
    This change accomodates upgrade to openssl3.3 and mariadb10 using custom-compiled libmariadb.a. These files are in /cluster/software/maridb and /cluster/software/openssl. refs #34014,#27440. It also handles the new mariadb 10 and 11 that have configuration with ssl turned on by default.
  • lines changed 1, context: html, text, full: html, text
    bbabbb31d85487865c08d16216e22f4112427513 Wed Nov 27 21:46:58 2024 -0800
    fix for older openssl that does not have macros.h
  • lines changed 5, context: html, text, full: html, text
    e9d64c75f7769ab7f411213c3689566b6fe74498 Fri Nov 29 00:33:03 2024 -0800
    fixes for MD5, evp functions mostly for OpenSSL3, not 1.1
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    eb529048797dc23f5dea4eeaa336578fabb67b98 Wed Nov 13 13:32:40 2024 -0800
    Adding a link to the Help menu to open a popup with all available javascript tutorials, refs #34208
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    9a2241a5a0066478af4577825340b57a2f42acd3 Mon Dec 2 09:42:01 2024 -0800
    Forgot to update the name of the basic tutorial in hgTracks.c, refs #34208
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    f24ed93b8e6b79c81b5733a26929f210ee4b7129 Mon Nov 25 22:53:22 2024 -0800
    Adding images to the new right-click features, refs #34855
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    eb529048797dc23f5dea4eeaa336578fabb67b98 Wed Nov 13 13:32:40 2024 -0800
    Adding a link to the Help menu to open a popup with all available javascript tutorials, refs #34208
  • lines changed 5, context: html, text, full: html, text
    4c6147a12865ea349d3d35610f9cb43aadd3a366 Wed Nov 13 15:27:28 2024 -0800
    Updating the name of the first tutorial now that we will be adding more. Making the first tutorial use the global object so I can call it from the new popup window with the rest of the tutorials. Moving a function to clean up the code. Updating the makefile with the new name change, refs #34290
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    4e620539ffe19c3fff4e3cd3d3f9070f42df342f Thu Nov 14 16:20:36 2024 -0800
    Changing the name of the function that generates the Tutorial popup to 'createTutorialPopup'. Removing the 'getDb()' function since it already exists it utils.js. Using the already existing function to open the Recommended Track Sets in the clinical tutorial. Making a change to only export the tutorials if they don't already exist. Making text changes to the popup, refs #34208
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    00a7706afb08c6e2523ea9645bd0f6bb25308593 Thu Nov 14 16:41:59 2024 -0800
    Adding more text changes that Lou suggested. Removing the basic tutorial link in the Help menu. Editing comments in the code, refs #34208
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    049a26b55b0a4001da527c7ddf6f37f7093285b8 Mon Dec 2 09:35:33 2024 -0800
    Moving the creation of the popup outside of the if statement. refs #34208
• src/hg/js/tutorials/basicTutorial.js
  • lines changed 267, context: html, text, full: html, text
    4c6147a12865ea349d3d35610f9cb43aadd3a366 Wed Nov 13 15:27:28 2024 -0800
    Updating the name of the first tutorial now that we will be adding more. Making the first tutorial use the global object so I can call it from the new popup window with the rest of the tutorials. Moving a function to clean up the code. Updating the makefile with the new name change, refs #34290
  • lines changed 3, context: html, text, full: html, text
    4e620539ffe19c3fff4e3cd3d3f9070f42df342f Thu Nov 14 16:20:36 2024 -0800
    Changing the name of the function that generates the Tutorial popup to 'createTutorialPopup'. Removing the 'getDb()' function since it already exists it utils.js. Using the already existing function to open the Recommended Track Sets in the clinical tutorial. Making a change to only export the tutorials if they don't already exist. Making text changes to the popup, refs #34208
  • lines changed 12, context: html, text, full: html, text
    45fe2c29fa638137639c0a9ede25442c8837ec82 Mon Dec 2 10:07:53 2024 -0800
    Updating the name of 'tour' to 'basicTour', refs #34208
• src/hg/js/tutorials/clinicalTutorial.js
  • lines changed 7, context: html, text, full: html, text
    eb529048797dc23f5dea4eeaa336578fabb67b98 Wed Nov 13 13:32:40 2024 -0800
    Adding a link to the Help menu to open a popup with all available javascript tutorials, refs #34208
  • lines changed 7, context: html, text, full: html, text
    4e620539ffe19c3fff4e3cd3d3f9070f42df342f Thu Nov 14 16:20:36 2024 -0800
    Changing the name of the function that generates the Tutorial popup to 'createTutorialPopup'. Removing the 'getDb()' function since it already exists it utils.js. Using the already existing function to open the Recommended Track Sets in the clinical tutorial. Making a change to only export the tutorials if they don't already exist. Making text changes to the popup, refs #34208
• src/hg/js/tutorials/hgTracksPopup.js
  • lines changed 62, context: html, text, full: html, text
    eb529048797dc23f5dea4eeaa336578fabb67b98 Wed Nov 13 13:32:40 2024 -0800
    Adding a link to the Help menu to open a popup with all available javascript tutorials, refs #34208
  • lines changed 18, context: html, text, full: html, text
    98487640ecf986c00fb0a13739323cc78d107601 Wed Nov 13 16:52:46 2024 -0800
    Updating the basic tutorial link to use the basic tutorial now that it is working. Updating the popup to have more descriptive text and other CSS options, refs #34208
  • lines changed 17, context: html, text, full: html, text
    93b4e6a3aeae8b052a7f2cbce148790b61274e86 Wed Nov 13 17:21:23 2024 -0800
    Check to see if you are on either hg38 or hg19 before starting the clinical tutorial. If not, go to hg38 and start the tutorial, refs #34208
  • lines changed 15, context: html, text, full: html, text
    4e620539ffe19c3fff4e3cd3d3f9070f42df342f Thu Nov 14 16:20:36 2024 -0800
    Changing the name of the function that generates the Tutorial popup to 'createTutorialPopup'. Removing the 'getDb()' function since it already exists it utils.js. Using the already existing function to open the Recommended Track Sets in the clinical tutorial. Making a change to only export the tutorials if they don't already exist. Making text changes to the popup, refs #34208
  • lines changed 5, context: html, text, full: html, text
    00a7706afb08c6e2523ea9645bd0f6bb25308593 Thu Nov 14 16:41:59 2024 -0800
    Adding more text changes that Lou suggested. Removing the basic tutorial link in the Help menu. Editing comments in the code, refs #34208
• src/hg/js/tutorials/makefile
  • lines changed 1, context: html, text, full: html, text
    eb529048797dc23f5dea4eeaa336578fabb67b98 Wed Nov 13 13:32:40 2024 -0800
    Adding a link to the Help menu to open a popup with all available javascript tutorials, refs #34208
  • lines changed 1, context: html, text, full: html, text
    4c6147a12865ea349d3d35610f9cb43aadd3a366 Wed Nov 13 15:27:28 2024 -0800
    Updating the name of the first tutorial now that we will be adding more. Making the first tutorial use the global object so I can call it from the new popup window with the rest of the tutorials. Moving a function to clean up the code. Updating the makefile with the new name change, refs #34290
• src/hg/js/tutorials/tutorial.js
  • lines changed 261, context: html, text, full: html, text
    4c6147a12865ea349d3d35610f9cb43aadd3a366 Wed Nov 13 15:27:28 2024 -0800
    Updating the name of the first tutorial now that we will be adding more. Making the first tutorial use the global object so I can call it from the new popup window with the rest of the tutorials. Moving a function to clean up the code. Updating the makefile with the new name change, refs #34290
• src/hg/lib/jksql.c
  • lines changed 12, context: html, text, full: html, text
    8ac718f8496a6fbfbf00248a68e740a10c0bcf81 Tue Nov 26 00:42:19 2024 -0800
    This change accomodates upgrade to openssl3.3 and mariadb10 using custom-compiled libmariadb.a. These files are in /cluster/software/maridb and /cluster/software/openssl. refs #34014,#27440. It also handles the new mariadb 10 and 11 that have configuration with ssl turned on by default.
  • lines changed 1, context: html, text, full: html, text
    8225f4a5bdc277983e65d138da3aa639c7502253 Wed Nov 27 21:21:44 2024 -0800
    oops one of the define tests was accidentally missing.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 1, context: html, text, full: html, text
    8985afa0bc2d3ae8f26c3aac86e5c796b814ce92 Sun Dec 1 20:51:39 2024 -0800
    show count while sendDownload refs #34370
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 17, context: html, text, full: html, text
    c81a4cfaf91dfa894a0f40aada6ad5ecfd8b4e5d Thu Nov 28 12:02:34 2024 -0800
    VGP update refs #34370
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    236eac75375604715a53bf6647694a563986e6ae Sun Dec 1 10:37:39 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    4737fd31279d3d74e590ba60ab2a29bf4b8f4764 Thu Nov 28 12:03:09 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    4737fd31279d3d74e590ba60ab2a29bf4b8f4764 Thu Nov 28 12:03:09 2024 -0800
    VGP update refs #34370
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    236eac75375604715a53bf6647694a563986e6ae Sun Dec 1 10:37:39 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 3, context: html, text, full: html, text
    7c0bb45884523d1077f0fab859f0ef2637776e8e Fri Nov 29 09:00:44 2024 -0800
    VGP update sent some to legacy refs #34370
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    e5c9ead38cc0cd9f33606fee751d2f0651cc83b4 Sun Dec 1 13:40:19 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    7c0bb45884523d1077f0fab859f0ef2637776e8e Fri Nov 29 09:00:44 2024 -0800
    VGP update sent some to legacy refs #34370
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    236eac75375604715a53bf6647694a563986e6ae Sun Dec 1 10:37:39 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    e0ea0d50158191088c5eb25c2ed669079ceedb33 Wed Nov 27 14:31:44 2024 -0800
    adding on per user request #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    236eac75375604715a53bf6647694a563986e6ae Sun Dec 1 10:37:39 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    4737fd31279d3d74e590ba60ab2a29bf4b8f4764 Thu Nov 28 12:03:09 2024 -0800
    VGP update refs #34370
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    236eac75375604715a53bf6647694a563986e6ae Sun Dec 1 10:37:39 2024 -0800
    VGP update refs #34370
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
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    9cd7cc7903e81265cfb09acd173ca9e385c05d06 Tue Nov 26 12:32:02 2024 -0800
    VGP update refs #34370
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    8ac718f8496a6fbfbf00248a68e740a10c0bcf81 Tue Nov 26 00:42:19 2024 -0800
    This change accomodates upgrade to openssl3.3 and mariadb10 using custom-compiled libmariadb.a. These files are in /cluster/software/maridb and /cluster/software/openssl. refs #34014,#27440. It also handles the new mariadb 10 and 11 that have configuration with ssl turned on by default.
• src/lib/https.c
  • lines changed 16, context: html, text, full: html, text
    8ac718f8496a6fbfbf00248a68e740a10c0bcf81 Tue Nov 26 00:42:19 2024 -0800
    This change accomodates upgrade to openssl3.3 and mariadb10 using custom-compiled libmariadb.a. These files are in /cluster/software/maridb and /cluster/software/openssl. refs #34014,#27440. It also handles the new mariadb 10 and 11 that have configuration with ssl turned on by default.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ed5575811e4af7344396c367fe5a934917e32882 Mon Dec 2 11:51:24 2024 -0800
    v475 preview2, refs #34871
• src/utils/twoBitDup/twoBitDup.c
  • lines changed 11, context: html, text, full: html, text
    8ac718f8496a6fbfbf00248a68e740a10c0bcf81 Tue Nov 26 00:42:19 2024 -0800
    This change accomodates upgrade to openssl3.3 and mariadb10 using custom-compiled libmariadb.a. These files are in /cluster/software/maridb and /cluster/software/openssl. refs #34014,#27440. It also handles the new mariadb 10 and 11 that have configuration with ssl turned on by default.
  • lines changed 1, context: html, text, full: html, text
    bbabbb31d85487865c08d16216e22f4112427513 Wed Nov 27 21:46:58 2024 -0800
    fix for older openssl that does not have macros.h
  • lines changed 5, context: html, text, full: html, text
    e9d64c75f7769ab7f411213c3689566b6fe74498 Fri Nov 29 00:33:03 2024 -0800
    fixes for MD5, evp functions mostly for OpenSSL3, not 1.1

• lines changed: 866
• files changed: 47