All File Changes

v333_preview2 to v333_base (2016-05-16 to 2016-05-23) v333

• src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c
  • lines changed 126, context: html, text, full: html, text
    337d09b1fb983b7363a53e80c0ca49227a6fd228 Tue May 17 13:14:10 2016 -0700
    adding cdwGetFile to the CDW to download a file. Also adding a
    "download" button to cdwWebBrowse that uses cdwGetFile. Fixing a stray
    include in cdwWebBrowse on the way.
    
  • lines changed 3, context: html, text, full: html, text
    01c0d4de2150d1d2f064806fb0887f4abbc32226 Tue May 17 13:17:56 2016 -0700
    fixing a cdw error message
    
• src/hg/cirm/cdw/cdwGetFile/makefile
  • lines changed 16, context: html, text, full: html, text
    337d09b1fb983b7363a53e80c0ca49227a6fd228 Tue May 17 13:14:10 2016 -0700
    adding cdwGetFile to the CDW to download a file. Also adding a
    "download" button to cdwWebBrowse that uses cdwGetFile. Fixing a stray
    include in cdwWebBrowse on the way.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 11, context: html, text, full: html, text
    8525cb4eb3c388aa18c992b9e9d48d91ebe5e358 Tue May 17 09:43:36 2016 -0700
    Fixing up the new data_set_id manifest override, refs #17344
    
  • lines changed 17, context: html, text, full: html, text
    423d70464b426c499ab5de32d7235ed7327adf53 Wed May 18 16:32:26 2016 -0700
    Adding checking for required fields with -test flag.
    
  • lines changed 36, context: html, text, full: html, text
    18fabd413b56d338ef8594db36efe7c067785e7c Wed May 18 17:19:29 2016 -0700
    Reworking Chris's data_set_id workaround by replacing tagStormUniqueIndex with tagStormIndexExtended call.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    337d09b1fb983b7363a53e80c0ca49227a6fd228 Tue May 17 13:14:10 2016 -0700
    adding cdwGetFile to the CDW to download a file. Also adding a
    "download" button to cdwWebBrowse that uses cdwGetFile. Fixing a stray
    include in cdwWebBrowse on the way.
    
  • lines changed 11, context: html, text, full: html, text
    7200ca703033fd3306817d972f8f1db22b4588b0 Tue May 17 14:05:01 2016 -0700
    fixing bug in cdwWebBrowse when user is not logged in
    
• src/hg/cirm/cdw/inc/cdwDataset.h
  • lines changed 67, context: html, text, full: html, text
    ea90c9f1e576521aa7d6f2e33b15092253f65e43 Tue May 17 13:13:56 2016 -0700
    Getting rid of a .h file that got merged into cdw.h.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 3, context: html, text, full: html, text
    337d09b1fb983b7363a53e80c0ca49227a6fd228 Tue May 17 13:14:10 2016 -0700
    adding cdwGetFile to the CDW to download a file. Also adding a
    "download" button to cdwWebBrowse that uses cdwGetFile. Fixing a stray
    include in cdwWebBrowse on the way.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 13, context: html, text, full: html, text
    337d09b1fb983b7363a53e80c0ca49227a6fd228 Tue May 17 13:14:10 2016 -0700
    adding cdwGetFile to the CDW to download a file. Also adding a
    "download" button to cdwWebBrowse that uses cdwGetFile. Fixing a stray
    include in cdwWebBrowse on the way.
    
• src/hg/cirm/cdw/lib/cdwTagStorm.c
  • lines changed 4, context: html, text, full: html, text
    bd907fd5cba4b3a331f41319dfbd502c77b29412 Wed May 18 16:30:46 2016 -0700
    Added a TODO in the right place to put a universal age field.
    
• src/hg/hgLogin/hgLogin.c
  • lines changed 77, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
  • lines changed 3, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/hgLogin/hgLogin.h
  • lines changed 1, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
• src/hg/hgTracks/bedTrack.c
  • lines changed 5, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/connectTrack.c
  • lines changed 143, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/longRangeTrack.c
  • lines changed 85, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/makefile
  • lines changed 2, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/hgc/hgc.c
  • lines changed 57, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
  • lines changed 32, context: html, text, full: html, text
    de438b6041d00b72be32bcdec70436a9d201baf2 Sat May 21 12:17:40 2016 -0700
    libify the guts of ave so I can use it in hgc
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 1, context: html, text, full: html, text
    798753c4a1ccbc6488631de49876db49f43406e3 Mon May 16 16:27:44 2016 -0700
    Adding missing pre tag to bigChain.html
    
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 6, context: html, text, full: html, text
    f7b90df2c3e209e1665933e59c48dcb8398d5b8a Wed May 18 09:55:17 2016 -0700
    Adding note about density graphs to help docs refs #952
    
• src/hg/htdocs/images/session.hg19.Dnase.png
  • lines changed 0, context: html, text, full: html, text
    87d26ae44251311eeb48a057cf164ff1639d76c7 Fri May 20 16:03:46 2016 -0700
    Adding a new session image for #1263
    
• src/hg/htdocs/images/session.hg19.TFBScluster.png
  • lines changed 0, context: html, text, full: html, text
    f4f1de432ff19de9c343b0c4182926b7ff51e79e Fri May 20 16:13:59 2016 -0700
    Adding a new session image for #1263
    
• src/hg/htdocs/images/session.hg19.enhancer.png
  • lines changed 0, context: html, text, full: html, text
    93826d60f303bb75706ac0e21ffbebbecc80d05b Fri May 20 15:49:39 2016 -0700
    Adding a new session image for #1263
    
• src/hg/htdocs/images/session.hg38.refGeneFrame.png
  • lines changed 0, context: html, text, full: html, text
    96b5d0cc148cd094d2ad94af3eedc94d56ed0724 Wed May 18 10:56:25 2016 -0700
    Adding a session image refs #1263
    
• src/hg/inc/autoUpgrade.h
  • lines changed 19, context: html, text, full: html, text
    0cedad8cd900ffc7748341d00d99a589f9d19880 Thu May 19 12:19:44 2016 -0700
    Separated out Galt's autoUpgrade code that robustly attempts to add a column to a table into a new lib module. refs #17336 note-11
    
  • lines changed 2, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/inc/longRange.h
  • lines changed 41, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    0be5973c33c20adcdf29ff2b52ba6b2d83eed89c Mon May 23 10:08:57 2016 -0700
    New version number v333
    
• src/hg/inc/wikiLink.h
  • lines changed 20, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
  • lines changed 4, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/lib/autoUpgrade.c
  • lines changed 107, context: html, text, full: html, text
    0cedad8cd900ffc7748341d00d99a589f9d19880 Thu May 19 12:19:44 2016 -0700
    Separated out Galt's autoUpgrade code that robustly attempts to add a column to a table into a new lib module. refs #17336 note-11
    
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    ce16fc5a8df55c02029781b267936bde5110264e Mon May 16 12:04:05 2016 -0700
    Oops, cartLoadUserSession is called before cartWriteCookie, so it needs to call loginSystemValidateCookies first.
    refs #17327
    
  • lines changed 4, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
• src/hg/lib/cartDb.c
  • lines changed 135, context: html, text, full: html, text
    0cedad8cd900ffc7748341d00d99a589f9d19880 Thu May 19 12:19:44 2016 -0700
    Separated out Galt's autoUpgrade code that robustly attempts to add a column to a table into a new lib module. refs #17336 note-11
    
• src/hg/lib/cgapAlias.as
  • lines changed 1, context: html, text, full: html, text
    72a1266960d040b2f07ae91e734a73482401e95f Tue May 17 16:53:44 2016 -0700
    Minor fixes and additions to wrap up mm10 UCSC Genes release, refs #15315
    
• src/hg/lib/gbMemberToken.as
  • lines changed 1, context: html, text, full: html, text
    6628f59edcffa5a7778f380072eeaeca09a2f742 Mon May 16 14:49:52 2016 -0700
    adding another column to the gbMemberToken table, refs #17327
    
  • lines changed 8, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/lib/gbMemberToken.c
  • lines changed 139, context: html, text, full: html, text
    6628f59edcffa5a7778f380072eeaeca09a2f742 Mon May 16 14:49:52 2016 -0700
    adding another column to the gbMemberToken table, refs #17327
    
  • lines changed 139, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/lib/gbMemberToken.h
  • lines changed 66, context: html, text, full: html, text
    6628f59edcffa5a7778f380072eeaeca09a2f742 Mon May 16 14:49:52 2016 -0700
    adding another column to the gbMemberToken table, refs #17327
    
  • lines changed 66, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/lib/gbMemberToken.sql
  • lines changed 1, context: html, text, full: html, text
    6628f59edcffa5a7778f380072eeaeca09a2f742 Mon May 16 14:49:52 2016 -0700
    adding another column to the gbMemberToken table, refs #17327
    
  • lines changed 14, context: html, text, full: html, text
    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/lib/hui.c
  • lines changed 15, context: html, text, full: html, text
    8757802b83b0fcf0cf1b071b2bebf4cf8b000c1b Mon May 16 14:39:03 2016 -0700
    Move metadata ahead of downloads and schema links for better presentation (as it is no longer a link). This was needed to keep ENCODE track UI pages pretty. refs #17314
    
  • lines changed 11, context: html, text, full: html, text
    84ca51e2468430ef920de07f05d33625af212411 Tue May 17 11:36:14 2016 -0700
    hiding track density options by default and showing upon click on checkbox, refs #952
    
  • lines changed 16, context: html, text, full: html, text
    23bb7c6df21dec94a2a711c14149da901647104a Tue May 17 15:02:54 2016 -0700
    use autoscale and maximum scaling mode for density graphs. Also, don't
    show the wiggle options unless folks have selected density graph
    
  • lines changed 3, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/lib/longRange.c
  • lines changed 90, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
  • lines changed 1, context: html, text, full: html, text
    0cedad8cd900ffc7748341d00d99a589f9d19880 Thu May 19 12:19:44 2016 -0700
    Separated out Galt's autoUpgrade code that robustly attempts to add a column to a table into a new lib module. refs #17336 note-11
    
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/hg/lib/wikiLink.c
  • lines changed 10, context: html, text, full: html, text
    46b4e2937954d44c12dcb496a140608316959d21 Mon May 16 13:58:14 2016 -0700
    duh, if loginSystem is not enabled, we cannot use the gbMembers table. refs #17327
    
  • lines changed 223, context: html, text, full: html, text
    185dbcc2ba84d6eb1301163b926ebed3177cd379 Thu May 19 04:42:20 2016 -0700
    Several revisions to login cookie-checking after helpful code review by Max:
    
    Use /dev/urandom instead of srand(clock1000()), duh.
    
    Instead of forming cookie strings in both wikiLink.c and hgLogin.c,
    form them all in wikiLink.c so they're consistent. The wikiLink
    routines now return (possibly empty) slName lists of cookie strings
    to be set.
    
    The login system uses new cookie names that default to a concatentation
    of central.cookie (which needs to have one name per central database,
    like hguid for RR hgcentral and hguid.genome-test for hgcentraltest)
    and either optional new config params login.tokenCookie and
    login.userNameCookie or central.cookie concatenated with hgLoginToken and
    hgLoginUserName (because login uses the central db, so it's different for
    hgwdev vs RR). If those cookies are not set but the wiki cookies are set,
    then we accept the wiki cookie values and send out the new cookies,
    removing the wiki cookies the first time that happens.
    
    The login system no longer depends on any wiki.* hg.conf settings.
    
    refs #17336, #17327
    
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    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/hg/makeDb/doc/hg38/hg38Patch7.txt
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    39547fc9e92ded4e129ddad7bcc88fbbea3a9fa3 Wed May 18 16:34:49 2016 -0700
    running up hg38 patch7 build refs #17134
    
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    f32c38d8a38e48bce9d141e6114193c3ac3be48e Thu May 19 16:19:55 2016 -0700
    almost done refs #17134
    
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    c986cbce8aa5d57093ad7c56ca6b169c51634209 Fri May 20 11:23:57 2016 -0700
    patch7 in the pushQ refs #17134
    
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    e604a23dfa4f5517340509e27959510a2109c1af Fri May 20 13:40:53 2016 -0700
    running up ncbiRefSeq gene track for GRCh38.p7 refs #13673
    
• src/hg/makeDb/doc/hg38/patchDescr.pl
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    c986cbce8aa5d57093ad7c56ca6b169c51634209 Fri May 20 11:23:57 2016 -0700
    patch7 in the pushQ refs #17134
    
• src/hg/makeDb/doc/mm10Patch4/mm10Patch4.txt
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    1c25478654cdc5230c1ac510539c133c0da3e0dc Tue May 17 13:04:53 2016 -0700
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    7f964899304489ba1dcc035d8aa430f45965c003 Tue May 17 14:18:18 2016 -0700
    adding some convenient and easy tracks refs #16414
    
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    8ce64912f5012a9363c0157a35aba45c78b8ef11 Tue May 17 15:16:54 2016 -0700
    adding downloads and documentation refs #16414
    
• src/hg/makeDb/doc/mm10Patch4/patchDescr.pl
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    8ce64912f5012a9363c0157a35aba45c78b8ef11 Tue May 17 15:16:54 2016 -0700
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• src/hg/makeDb/doc/mm10Patch4/readmeLines.pl
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    8ce64912f5012a9363c0157a35aba45c78b8ef11 Tue May 17 15:16:54 2016 -0700
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• src/hg/makeDb/doc/mm10Patch4/regionScan.pl
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    1c25478654cdc5230c1ac510539c133c0da3e0dc Tue May 17 13:04:53 2016 -0700
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• src/hg/makeDb/doc/mm10Patch4/scanAssemblyReport.pl
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    1c25478654cdc5230c1ac510539c133c0da3e0dc Tue May 17 13:04:53 2016 -0700
    working up mm10Patch4 refs #16414
    
• src/hg/makeDb/doc/panPan2/initialBuild.txt
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    3866b72feb88fee5d5da39b0c8a3f941221959fd Tue May 17 16:13:43 2016 -0700
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• src/hg/makeDb/doc/panPan2/ucscCompositeAgp.pl
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    3866b72feb88fee5d5da39b0c8a3f941221959fd Tue May 17 16:13:43 2016 -0700
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• src/hg/makeDb/doc/panPan2/unplaced.pl
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    3866b72feb88fee5d5da39b0c8a3f941221959fd Tue May 17 16:13:43 2016 -0700
    running up liftOvers refs #16036
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes16.csh
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    72a1266960d040b2f07ae91e734a73482401e95f Tue May 17 16:53:44 2016 -0700
    Minor fixes and additions to wrap up mm10 UCSC Genes release, refs #15315
    
• src/hg/makeDb/genbank/etc/align.dbs
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    62f87fe5998f2d4cd5bd7d6d1f9675235fe01e9b Tue May 17 16:02:06 2016 -0700
    Added panPan2 - Bonobo refs #16036
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    62f87fe5998f2d4cd5bd7d6d1f9675235fe01e9b Tue May 17 16:02:06 2016 -0700
    Added panPan2 - Bonobo refs #16036
    
• src/hg/makeDb/outside/gtexHub/hub/gtexHub.html
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    8148cb1c3778b1e26d31041e9f3366d4f1a2141a Wed May 18 10:03:36 2016 -0700
    Corrections to hub description after QA review. refs #15647
    
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    203c86b9ad42e2a826013690afd0770a1a063c75 Thu May 19 16:29:30 2016 -0700
    Add Contacts section, as per QA request. refs #15647
    
• src/hg/makeDb/outside/gtexHub/hub/hub.txt
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    09941914372abcd0dfa2ce98b78878d8d29963f9 Thu May 19 16:29:05 2016 -0700
    Correct sample count in title. refs #15647
    
• src/hg/makeDb/schema/all.joiner
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    72a1266960d040b2f07ae91e734a73482401e95f Tue May 17 16:53:44 2016 -0700
    Minor fixes and additions to wrap up mm10 UCSC Genes release, refs #15315
    
• src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html
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    ad15338c0ae37103c6aa449a14050b8ab390ee99 Wed May 18 15:07:13 2016 -0700
    add documentation for 5-way track refs #17180
    
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.5way.ra
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    ad15338c0ae37103c6aa449a14050b8ab390ee99 Wed May 18 15:07:13 2016 -0700
    add documentation for 5-way track refs #17180
    
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.chainNet.ra
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    ad15338c0ae37103c6aa449a14050b8ab390ee99 Wed May 18 15:07:13 2016 -0700
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• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra
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    ad15338c0ae37103c6aa449a14050b8ab390ee99 Wed May 18 15:07:13 2016 -0700
    add documentation for 5-way track refs #17180
    
• src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html
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    9dc9d719cd1c538a8c94ba5374b57ca4c117d0e3 Wed May 18 15:34:43 2016 -0700
    adding description page for 5-way refs #17180
    
• src/hg/makeDb/trackDb/human/hg38Patch7/description.html
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    a8194a279064ef6177ec3243f4b79442b9e2db8f Thu May 19 14:35:53 2016 -0700
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• src/hg/makeDb/trackDb/human/hg38Patch7/gap.html
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• src/hg/makeDb/trackDb/human/hg38Patch7/gold.html
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• src/hg/makeDb/trackDb/human/hg38Patch7/trackDb.ra
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    a8194a279064ef6177ec3243f4b79442b9e2db8f Thu May 19 14:35:53 2016 -0700
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• src/hg/makeDb/trackDb/human/trackDb.ra
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    b156247a138894909d6cbf525265930ea27f648b Mon May 16 12:40:06 2016 -0700
    Updating ClinVar release tags to display new desc page, refs #16122
    
• src/hg/makeDb/trackDb/makefile
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    1bf39d2a8b816fe2352f94eda5d7f226cf5dcec3 Tue May 17 09:49:07 2016 -0700
    adding mm10Patch4 to the haplotypes group refs #16414
    
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    a8194a279064ef6177ec3243f4b79442b9e2db8f Thu May 19 14:35:53 2016 -0700
    trackDb doc files for hg38Patch7 refs #17134
    
• src/hg/makeDb/trackDb/mouse/mm10/knownGeneOld8.html
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    72a1266960d040b2f07ae91e734a73482401e95f Tue May 17 16:53:44 2016 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.html
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    71d3933155b8205e482f26d4642b4a58cc75beb7 Tue May 17 14:39:32 2016 -0700
    adding mm10 patch4 html page with links to everything refs #16414
    
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• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
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    054a0f24fabbe20929806cf7e9cb3c5646b83e46 Tue May 17 13:02:47 2016 -0700
    adding mm10Patch4 tracks refs #16414
    
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    Updating search rules for old mm10 UCSC Genes, refs #15315
    
• src/hg/makeDb/trackDb/mouse/mm10Patch4/description.html
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    1bf39d2a8b816fe2352f94eda5d7f226cf5dcec3 Tue May 17 09:49:07 2016 -0700
    adding mm10Patch4 to the haplotypes group refs #16414
    
• src/hg/makeDb/trackDb/mouse/mm10Patch4/gap.html
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    1bf39d2a8b816fe2352f94eda5d7f226cf5dcec3 Tue May 17 09:49:07 2016 -0700
    adding mm10Patch4 to the haplotypes group refs #16414
    
• src/hg/makeDb/trackDb/mouse/mm10Patch4/gold.html
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    1bf39d2a8b816fe2352f94eda5d7f226cf5dcec3 Tue May 17 09:49:07 2016 -0700
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• src/hg/makeDb/trackDb/mouse/mm10Patch4/trackDb.ra
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    1bf39d2a8b816fe2352f94eda5d7f226cf5dcec3 Tue May 17 09:49:07 2016 -0700
    adding mm10Patch4 to the haplotypes group refs #16414
    
• src/inc/aveStats.h
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    de438b6041d00b72be32bcdec70436a9d201baf2 Sat May 21 12:17:40 2016 -0700
    libify the guts of ave so I can use it in hgc
    
• src/inc/bedTabix.h
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    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/lib/aveStats.c
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    de438b6041d00b72be32bcdec70436a9d201baf2 Sat May 21 12:17:40 2016 -0700
    libify the guts of ave so I can use it in hgc
    
• src/lib/bedTabix.c
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    7a89988d6fd56140fd0b43c0f60430a210c24570 Thu May 19 16:41:30 2016 -0700
    connecting things up for the long-range interaction display.
    
• src/lib/common.c
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    ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c Fri May 20 16:17:00 2016 -0700
    New random-token method for login (HT Max & Galt): instead of requiring a new table gbMemberToken, use autoUpgrade to add a new column (keyList) to gbMembers that contains a list of long random keys, analogous to userDb and sessionDb's sessionKey (see cartDb.c). The token cookie now includes both gbMembers.idx (for fast lookup) and the long random key, similar to the hguid cookie and hgsid CGI param. keyList is a list in order to support user login on multiple web clients. refs #17327 #17336 note-11
    
• src/lib/https.c
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    873ffe864441ef8d03629f751137f3f8114e8cbe Fri May 20 23:54:36 2016 -0700
    Fixes #17362. sigtimedwait not available on OSX. now uses sigwait.
    
• src/lib/makefile
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    de438b6041d00b72be32bcdec70436a9d201baf2 Sat May 21 12:17:40 2016 -0700
    libify the guts of ave so I can use it in hgc
    
• src/product/installer/README.md
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    d634731e4d646db3eaa0936c3f8651e0e6527b71 Wed May 18 16:23:00 2016 -0700
    various fixed to the browser installer script after feedback from Angie
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    4011a2fb6caca4a22ae491bcd79fe6756939c5d4 Thu May 19 09:42:34 2016 -0700
    generating a help page from the installer readme file, #14399
    
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• src/product/installer/browserSetup.sh
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    d634731e4d646db3eaa0936c3f8651e0e6527b71 Wed May 18 16:23:00 2016 -0700
    various fixed to the browser installer script after feedback from Angie
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    b522d99abfd3969e5c4757da1f53446acde6b29d Wed May 18 16:42:53 2016 -0700
    fixing the udr option and downloading udr now from hgdownload, thanks to
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    c409b1ef198cd2e87e742eab9a27fadefe3a92e4 Wed May 18 16:49:01 2016 -0700
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    929c1e1c0af12a04ef298d2b463cacf5647d6a63 Fri May 20 10:32:05 2016 -0700
    fixing 2bit and genbank errors, refs #14399
    
• src/product/installer/makefile
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    4011a2fb6caca4a22ae491bcd79fe6756939c5d4 Thu May 19 09:42:34 2016 -0700
    generating a help page from the installer readme file, #14399
    
• src/product/installer/staticPage.html
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    generating a help page from the installer readme file, #14399
    
• src/utils/ave/ave.c
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    de438b6041d00b72be32bcdec70436a9d201baf2 Sat May 21 12:17:40 2016 -0700
    libify the guts of ave so I can use it in hgc
    
• src/utils/qa/weeklybld/buildEnv.csh
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    a162d1da94ad9cf234a17d69b4459c4d8bdf19c2 Mon May 23 10:07:40 2016 -0700
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• src/utils/qa/weeklybld/userApps.sh
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