Commits for angie

v334_preview2 to v334_base (2016-06-06 to 2016-06-13) v334

69b427307c0ec0dcda1782182aae4b46ac50fb8e Mon Jun 6 10:31:34 2016 -0700

• Check database existence instead of just relying on dbDb.active because GBiB/GBiC may copy our dbDb, but have a limited set of species locally. fixes #17316
  
  • src/hg/hgGateway/hgGateway.c - lines changed 7, context: html, text, full: html, text

07236560bae97afc34102ff2ae4a19ea74e7a049 Wed Jun 8 17:00:49 2016 -0700

• Replacing some str* functions with safe* functions so that if there is buffer overflow, we'll errAbort instead of carrying on with unterminated strings. An undetected overflow in sqlQuickQuery caused strange behavior downstream. refs #17327 note-101
  
  • src/hg/lib/jksql.c - lines changed 4, context: html, text, full: html, text

d968686107101a1824d34a007a19c8d18b368b78 Wed Jun 8 17:06:40 2016 -0700

• Limit the length of gbMembers.keyList to avoid buffer overflow (and wasted space). refs #17327 notes 98, 100, 101.
  
  • src/hg/lib/wikiLink.c - lines changed 16, context: html, text, full: html, text

c6e8c8af66b4ea7a9df7e8cc9fc7cacb99b234a4 Thu Jun 9 11:35:42 2016 -0700

• Revert "Limit the length of gbMembers.keyList to avoid buffer overflow (and wasted space). refs #17327 notes 98, 100, 101."
  
  This reverts commit d968686107101a1824d34a007a19c8d18b368b78.
  
  • src/hg/lib/wikiLink.c - lines changed 16, context: html, text, full: html, text

d1039b8f7028add5bb676f882c003152d50d073a Thu Jun 9 11:35:45 2016 -0700

• Revert "Fixing bug that allowed faked wiki cookie name to override hgLogin name. refs #17397 note-8, note-9."
  
  This reverts commit 70688a29ce74bb1fafd03ef2dda79ef38ea2891b.
  
  • src/hg/lib/wikiLink.c - lines changed 4, context: html, text, full: html, text

1423f7d5003af35b06436d9c70130853ab9e7df8 Thu Jun 9 11:35:48 2016 -0700

• Revert "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"
  
  This reverts commit 5c93dde5814fddc96330bbdea7aa3f9ff374aedf.
  
  • src/hg/lib/wikiLink.c - lines changed 17, context: html, text, full: html, text

e284653caf49c71f8eb4539b0913f6a90c817907 Thu Jun 9 11:35:53 2016 -0700

• Revert "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"
  
  This reverts commit 3c9694bc8ed2b3d835de4985b9ee7f0eebf1bfe2.
  
  • src/hg/lib/wikiLink.c - lines changed 75, context: html, text, full: html, text

8072ac144242761fb980c914908b1c2697430f21 Thu Jun 9 11:35:56 2016 -0700

• Revert "Logins are case-insensitive, but cookie-checking is case-sensitive, so when making cookies, use the correctly cased userName from gbMembers. fixes #17396"
  
  This reverts commit 0ada44855b610aa826c3839e41d9b48929f86951.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 1, context: html, text, full: html, text

ce019544af5459e5d1074720e5368a0b5dcd2d2a Thu Jun 9 11:36:00 2016 -0700

• Revert "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"
  
  This reverts commit ecd6e5bc9b85bcbafb08da0c1dae876b284ba69c.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/autoUpgrade.h - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/wikiLink.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.as - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.c - lines changed 139, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.h - lines changed 66, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.sql - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 246, context: html, text, full: html, text
  • src/lib/common.c - lines changed 3, context: html, text, full: html, text

d48e7626ab0b366e8ce43fee17366fe7d6ba6e67 Thu Jun 9 11:36:06 2016 -0700

• Revert "Several revisions to login cookie-checking after helpful code review by Max:"
  
  This reverts commit 185dbcc2ba84d6eb1301163b926ebed3177cd379.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 77, context: html, text, full: html, text
  • src/hg/hgLogin/hgLogin.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgSession/hgSession.c - lines changed 3, context: html, text, full: html, text
  • src/hg/inc/wikiLink.h - lines changed 20, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 225, context: html, text, full: html, text

ca7124f136400ff4b651eae36478d4b7190864c5 Thu Jun 9 11:36:10 2016 -0700

• Revert "adding another column to the gbMemberToken table, refs #17327"
  
  This reverts commit 6628f59edcffa5a7778f380072eeaeca09a2f742.
  
  • src/hg/lib/gbMemberToken.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.c - lines changed 139, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.h - lines changed 66, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.sql - lines changed 1, context: html, text, full: html, text

d8a0894d79f6d5b97797d07e0ced60ee37f528c6 Thu Jun 9 11:36:13 2016 -0700

• Revert "duh, if loginSystem is not enabled, we cannot use the gbMembers table. refs #17327"
  
  This reverts commit 46b4e2937954d44c12dcb496a140608316959d21.
  
  • src/hg/lib/wikiLink.c - lines changed 10, context: html, text, full: html, text

a113b1eaec149fb32d3abfe886497b33c728d4f0 Thu Jun 9 11:36:18 2016 -0700

• Revert "Oops, cartLoadUserSession is called before cartWriteCookie, so it needs to call loginSystemValidateCookies first."
  
  This reverts commit ce16fc5a8df55c02029781b267936bde5110264e.
  
  • src/hg/lib/cart.c - lines changed 5, context: html, text, full: html, text

5faaad7e4a0cde71c69f9c73db7fe94cf5db8bdc Thu Jun 9 11:42:40 2016 -0700

• Revert "Added checking of wiki.loggedInCookie (numeric user ID) using random numbers as suggested by Max"
  
  This reverts commit a240964d6dfdd6f8661487b64538d33518d88501.
  
  Conflicts:
  src/hg/hgSession/hgSession.c
  -- doSessionDetail was moved up by Jonathan's changes, so it needed to be changed to get userName the old way.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 5, context: html, text, full: html, text
  • src/hg/hgSession/hgSession.c - lines changed 52, context: html, text, full: html, text
  • src/hg/inc/wikiLink.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gbMemberToken.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 231, context: html, text, full: html, text

8b036c75c1833e62d94b3f8a3d48fcadafd8103f Thu Jun 9 11:43:37 2016 -0700

• Revert "Check idx vs database -- temporary stopgap."
  
  This reverts commit 5615ffccc75fa3e3a6b1477b696c1488a407b865.
  
  • src/hg/lib/wikiLink.c - lines changed 12, context: html, text, full: html, text

cfd6179f57db3bce50099459572f9ced7369f3cb Fri Jun 10 12:07:00 2016 -0700

• When TB region=genome option is grayed out, add an explanatory note. refs #4458 notes 62, 72, 73.
  
  • src/hg/hgTables/mainPage.c - lines changed 2, context: html, text, full: html, text

61878cb225c4fafa3ba2d38af16330fbb57377ed Mon Jun 13 09:52:59 2016 -0700

• Basic documentation of tableBrowser noGenome support in TB and DI. refs #4458
  
  • src/hg/hgTables/usage.c - lines changed 9, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html - lines changed 14, context: html, text, full: html, text
  • src/hg/js/react/hgIntegrator/hgIntegrator.jsx - lines changed 9, context: html, text, full: html, text