All File Changes

v333_base to v334_preview (2016-05-23 to 2016-05-31) v334

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    234cbc971a40527191604738758d89959bf0d7de Sun May 29 01:11:41 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 137, context: html, text, full: html, text
    828dfd29e4e889d90b7f9a32727a049316c5ec9e Thu May 26 16:53:20 2016 -0700
    modifying cdwGetFile to support direct file retrieval based on submitted
    file name suffix. Also handle users that are not logged in.
    
  • lines changed 9, context: html, text, full: html, text
    90450b465975ea12bd70c437aff595c2eaf7152e Fri May 27 15:47:29 2016 -0700
    make summary pages show up on cdwWebBrowse
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    4852312929fa9c19a75b5dadac63089b19c7c795 Tue May 24 01:50:48 2016 -0700
    Bumping version number.
    
  • lines changed 17, context: html, text, full: html, text
    90450b465975ea12bd70c437aff595c2eaf7152e Fri May 27 15:47:29 2016 -0700
    make summary pages show up on cdwWebBrowse
    
  • lines changed 9, context: html, text, full: html, text
    20e9958384e3a96fcc7621dd061a6bd8758395dc Fri May 27 16:36:24 2016 -0700
    small code reformat for cdwWebBrowse
    
  • lines changed 7, context: html, text, full: html, text
    2d7900ce2c3cd0e9ee381bf5ae0f8a4377e31906 Tue May 31 12:10:58 2016 -0700
    cirm: showing datasets without summary pages, only supressing link now
    
• src/hg/cirm/cdw/flowCharts/sqlToTxt/sqlToTxt.c
  • lines changed 370, context: html, text, full: html, text
    3a8a6ce38cecfb696f42bc38b5bc6ee155dfff0e Tue May 31 08:55:54 2016 -0700
    Revisiting the code to scan through SQL databases and print out a flowchart in .txt format, refs #16113
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 2, context: html, text, full: html, text
    9cffcde631a6ce922fac8bfcd5dcfceb3261224c Mon May 30 16:07:08 2016 -0700
    cirm: adding an ID column to the cdwDataset table
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    90450b465975ea12bd70c437aff595c2eaf7152e Fri May 27 15:47:29 2016 -0700
    make summary pages show up on cdwWebBrowse
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 3, context: html, text, full: html, text
    91cf488695bb021b9930ebc784240ec9e6aae839 Mon May 30 16:11:15 2016 -0700
    forgot two files in previous commit
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 20, context: html, text, full: html, text
    9cffcde631a6ce922fac8bfcd5dcfceb3261224c Mon May 30 16:07:08 2016 -0700
    cirm: adding an ID column to the cdwDataset table
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 276, context: html, text, full: html, text
    91cf488695bb021b9930ebc784240ec9e6aae839 Mon May 30 16:11:15 2016 -0700
    forgot two files in previous commit
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 12, context: html, text, full: html, text
    90450b465975ea12bd70c437aff595c2eaf7152e Fri May 27 15:47:29 2016 -0700
    make summary pages show up on cdwWebBrowse
    
• src/hg/cirm/cdw/wrangle/maniMani/makefile
  • lines changed 2, context: html, text, full: html, text
    b163860a0f24a8e6d9cb989c1ccda5930b923175 Tue May 31 09:02:13 2016 -0700
    Updating maniMani and it's makefile, refs #16113
    
• src/hg/cirm/cdw/wrangle/maniMani/maniMani
  • lines changed 236, context: html, text, full: html, text
    b163860a0f24a8e6d9cb989c1ccda5930b923175 Tue May 31 09:02:13 2016 -0700
    Updating maniMani and it's makefile, refs #16113
    
• src/hg/cirm/quakeLab/quakeBrainGeo1/meta.txt
  • lines changed 1, context: html, text, full: html, text
    342c1d87b18c545d8eaad404e3ed77a6fdd19a80 Tue May 24 01:52:07 2016 -0700
    Adding top level meta tag.
    
• src/hg/hgGene/gtex.c
  • lines changed 22, context: html, text, full: html, text
    e491b3ca6211e825e7f5b4e57a72a3e44574af63 Mon May 23 15:08:55 2016 -0700
    Build patch for hgGene failure on hg38 (trying to access ensGene for GTEx section)
    
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    0ada44855b610aa826c3839e41d9b48929f86951 Wed May 25 09:52:13 2016 -0700
    Logins are case-insensitive, but cookie-checking is case-sensitive, so when making cookies, use the correctly cased userName from gbMembers. fixes #17396
    
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 261, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
  • lines changed 4, context: html, text, full: html, text
    727438a3a76e2d885d82d1dd095c644c7e574b05 Fri May 27 16:43:41 2016 -0700
    Mustn't forget the comments and copyright/license info! refs #15312
    
• src/hg/hgPublicSessions/makefile
  • lines changed 17, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/hgSession/hgSession.c
  • lines changed 240, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
  • lines changed 7, context: html, text, full: html, text
    f62a8fddb1db00bd52535a93c620f265c249f61e Tue May 31 13:24:45 2016 -0700
    Only delete gallery image if a session was in the gallery, refs #15312
    
• src/hg/hgSession/hgSession.h
  • lines changed 1, context: html, text, full: html, text
    d04177d5318b0a62eb5fe22bc5df8d375ae293a0 Mon May 30 13:18:10 2016 -0700
    Always forget a file, refs #15312
    
• src/hg/hgTables/bedList.c
  • lines changed 2, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/filterFields.c
  • lines changed 13, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/hgTables.c
  • lines changed 8, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/hgTables.h
  • lines changed 23, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/identifiers.c
  • lines changed 1, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/intersect.c
  • lines changed 2, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/joining.c
  • lines changed 12, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/longRange.c
  • lines changed 216, context: html, text, full: html, text
    64749fda55b80788aa56530efd346434a2f964e8 Tue May 24 18:49:30 2016 -0700
    oops, forgot an add
    
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/hgTracks/longRangeTrack.c
  • lines changed 32, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
  • lines changed 1, context: html, text, full: html, text
    daf37eceb2063c6769c9e22a8e4a95fd99d05cd6 Wed May 25 09:06:40 2016 -0700
    fix compiler warning
    
  • lines changed 39, context: html, text, full: html, text
    916b1db3c50ed46600f8c13acb742cb9dd205f6d Fri May 27 17:11:10 2016 -0700
    support connections to other chroms in longRange display. Also,
    longTabix in trackHubs
    
• src/hg/hgTracks/multiWig.c
  • lines changed 0, context: html, text, full: html, text
    3d43a4606cb8ee1d443c153261d4f4b743815257 Wed May 25 16:40:59 2016 -0700
    fix space issue per code review
    
• src/hg/hgc/hgc.c
  • lines changed 28, context: html, text, full: html, text
    ee6ff3f35374f858b28b3f38d127f1800345a364 Tue May 24 09:41:04 2016 -0700
    fixing missing line wrap in bigBedClick refs #17370
    
  • lines changed 25, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
  • lines changed 5, context: html, text, full: html, text
    916b1db3c50ed46600f8c13acb742cb9dd205f6d Fri May 27 17:11:10 2016 -0700
    support connections to other chroms in longRange display. Also,
    longTabix in trackHubs
    
• src/hg/hgc/hgc.h
  • lines changed 5, context: html, text, full: html, text
    ee6ff3f35374f858b28b3f38d127f1800345a364 Tue May 24 09:41:04 2016 -0700
    fixing missing line wrap in bigBedClick refs #17370
    
• src/hg/hgc/pubs.c
  • lines changed 25, context: html, text, full: html, text
    a991e57ae48c928570964e830f7e8a5dd482151b Tue May 24 17:10:58 2016 -0700
    forgot to add file in previous commit
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 22, context: html, text, full: html, text
    d58b691f090336ed5d7917aec0232987afd73d42 Tue May 31 09:35:52 2016 -0700
    Adding some changes to BED format section per Cricket/ENCODE feedback refs #17423 #16646
    
• src/hg/htdocs/contacts.html
  • lines changed 2, context: html, text, full: html, text
    3bfbe377e68500c383be0d39b6496a412d7ba3b0 Thu May 26 09:22:26 2016 -0700
    added bug reports to this so that people might stop sending them to the Suggestion Box
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 11, context: html, text, full: html, text
    03e9975b90a3944ee7e2ea7d8c2cd5e4778aebd6 Tue May 24 09:52:21 2016 -0700
    Updating session expiration policy, refs #14724
    
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 1, context: html, text, full: html, text
    41778516c7b2268e158eae039f47517ea83b035b Wed May 25 12:33:46 2016 -0700
    Fixing typo code review #17386
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 154, context: html, text, full: html, text
    7c55e66e231665430afa58c0d51fe1827819062c Tue May 31 11:31:03 2016 -0700
    Adding more sessions to sessions gallery and rearranging order refs #1263 #15312
    
  • lines changed 28, context: html, text, full: html, text
    dd0099a1e2e83083f4d63fca3deb03a106f7b52e Tue May 31 12:59:07 2016 -0700
    Adding rearrangements to table of contents to Session Gallery refs #15312
    
• src/hg/htdocs/images/sort_asc.png
  • lines changed 0, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/htdocs/images/sort_asc_disabled.png
  • lines changed 0, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/htdocs/images/sort_both.png
  • lines changed 0, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/htdocs/images/sort_desc.png
  • lines changed 0, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/htdocs/images/sort_desc_disabled.png
  • lines changed 0, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/htdocs/mirror.html
  • lines changed 2, context: html, text, full: html, text
    82d56b8b777ea5f1aa8fe8e8fd5c2dda94599036 Wed May 25 14:15:42 2016 -0700
    adding genome-asia to code.
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/inc/geoMirror.h
  • lines changed 1, context: html, text, full: html, text
    82d56b8b777ea5f1aa8fe8e8fd5c2dda94599036 Wed May 25 14:15:42 2016 -0700
    adding genome-asia to code.
    
• src/hg/inc/longRange.h
  • lines changed 4, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/inc/sessionThumbnail.h
  • lines changed 25, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
  • lines changed 5, context: html, text, full: html, text
    727438a3a76e2d885d82d1dd095c644c7e574b05 Fri May 27 16:43:41 2016 -0700
    Mustn't forget the comments and copyright/license info! refs #15312
    
• src/hg/inc/trackDb.h
  • lines changed 6, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/js/staticDoc.js
  • lines changed 1, context: html, text, full: html, text
    82d56b8b777ea5f1aa8fe8e8fd5c2dda94599036 Wed May 25 14:15:42 2016 -0700
    adding genome-asia to code.
    
• src/hg/lib/geoMirror.c
  • lines changed 2, context: html, text, full: html, text
    82d56b8b777ea5f1aa8fe8e8fd5c2dda94599036 Wed May 25 14:15:42 2016 -0700
    adding genome-asia to code.
    
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    8dd9c1352b4461676b163531bf9e81bc4fb86c67 Thu May 26 13:35:57 2016 -0700
    clone a string that might be a literal
    
  • lines changed 4, context: html, text, full: html, text
    a88a9080cf75df027cbb2def2b5a965d4deb0cd7 Thu May 26 17:00:21 2016 -0700
    fixing a memory leak
    
• src/hg/lib/longRange.c
  • lines changed 28, context: html, text, full: html, text
    ea5b4301814c1df9f2a0f3b2d9e0d2f06b22635e Tue May 24 18:37:10 2016 -0700
    hgTables support , some display changes, and a better hgc
    page for longTabix
    
  • lines changed 3, context: html, text, full: html, text
    916b1db3c50ed46600f8c13acb742cb9dd205f6d Fri May 27 17:11:10 2016 -0700
    support connections to other chroms in longRange display. Also,
    longTabix in trackHubs
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/lib/namedSessionDb.as
  • lines changed 1, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/lib/namedSessionDb.sql
  • lines changed 1, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
• src/hg/lib/sessionThumbnail.c
  • lines changed 59, context: html, text, full: html, text
    10d24a04f2cc45af8484f29d35899bec2e53db46 Fri May 27 16:29:24 2016 -0700
    Initial commit of public session listing CGI hgPublicSessions and supporting changes to hgSession. refs #15312
    
  • lines changed 7, context: html, text, full: html, text
    727438a3a76e2d885d82d1dd095c644c7e574b05 Fri May 27 16:43:41 2016 -0700
    Mustn't forget the comments and copyright/license info! refs #15312
    
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    916b1db3c50ed46600f8c13acb742cb9dd205f6d Fri May 27 17:11:10 2016 -0700
    support connections to other chroms in longRange display. Also,
    longTabix in trackHubs
    
• src/hg/lib/wikiLink.c
  • lines changed 75, context: html, text, full: html, text
    3c9694bc8ed2b3d835de4985b9ee7f0eebf1bfe2 Wed May 25 13:50:18 2016 -0700
    If remote hgLogin is configured by specifying some other server in hg.conf's wiki.host, then just accept the remote host cookies with no validation. fixes #17397
    
  • lines changed 17, context: html, text, full: html, text
    5c93dde5814fddc96330bbdea7aa3f9ff374aedf Wed May 25 15:41:05 2016 -0700
    In order to support userNames with leading/trailing spaces, CGI-encode the userName store in the cookie, and CGI-decode before comparing it to gbMembers.userName. refs #17396 note-15, note-17
    
  • lines changed 4, context: html, text, full: html, text
    70688a29ce74bb1fafd03ef2dda79ef38ea2891b Wed May 25 16:44:20 2016 -0700
    Fixing bug that allowed faked wiki cookie name to override hgLogin name. refs #17397 note-8, note-9.
    
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 58, context: html, text, full: html, text
    287b99f249aff556c267674069a219791eb346b9 Mon May 23 10:42:11 2016 -0700
    liftOver per user request refs #17293
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 81, context: html, text, full: html, text
    a2c2e92fb72d14c1fa46dbaab90250d786707711 Fri May 27 10:34:31 2016 -0700
    lastz runs panPan2 to hg38 refs #16036
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 63, context: html, text, full: html, text
    63bc069ed38f4f9e7fcc3e27c345954e33464c9a Fri May 27 10:37:40 2016 -0700
    lastz runs panPan2 to hg38 refs #16036
    
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 19, context: html, text, full: html, text
    6ef0466c6789ed5a7cc298708c5aa368a846be13 Tue May 24 11:24:36 2016 -0700
    liftOvers panPan1 to and from panPan2 refs #16036
    
• src/hg/makeDb/doc/panPan2/initialBuild.txt
  • lines changed 9, context: html, text, full: html, text
    6ef0466c6789ed5a7cc298708c5aa368a846be13 Tue May 24 11:24:36 2016 -0700
    liftOvers panPan1 to and from panPan2 refs #16036
    
• src/hg/makeDb/outside/gtexHub/hub/hub.test.txt
  • lines changed 6, context: html, text, full: html, text
    0b48f94b7b7a92c84effe471c131b7084a84d0ac Wed May 25 10:19:20 2016 -0700
    Save test hub file
    
• src/hg/makeDb/outside/gtexHub/hub/hub.txt
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    505183be94d3a1bd1e8e475269ffe1c4d1f0fd2e Tue May 24 16:59:52 2016 -0700
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    ea1cbf03de1d013f8464a5454f99dccffed926bc Wed May 25 11:57:39 2016 -0700
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