Commits for angie

v382_preview2 to v382_base (2019-05-13 to 2019-05-20) v382

9b45eef7290592e268733f18aaff0503cfa82d4a Mon May 13 12:08:31 2019 -0700

• jsonQuery: Use netLineFileOpen not lineFileOpen, to support URLs.
  • src/hg/utils/jsonQuery/jsonQuery.c - lines changed 2, context: html, text, full: html, text

279df51388cf7da5474142bc74457f671c74b0ac Tue May 14 09:26:57 2019 -0700

• dyStringQuoteString needs to escape the escape character in addition to the quote character.
  • src/lib/dystring.c - lines changed 1, context: html, text, full: html, text

5ab68cb3e725251bdcd2d9b835883af146f72dc7 Tue May 14 12:55:56 2019 -0700

• When loading custom tracks, if all have been removed then the ctfile_ var is also removed, so don't errAbort if it's gone.
  • src/hg/lib/customTrack.c - lines changed 2, context: html, text, full: html, text

2093b34d5abc0f995acd69d28f83a60afaa3f966 Wed May 15 17:11:04 2019 -0700

• Prevent bigWarn methods from crashing if given a NULL or empty error message. refs #22440 note 130
  • src/hg/hgTracks/bigWarn.c - lines changed 4, context: html, text, full: html, text

e9d2ca4c5a20a3ce7ffe2aca7b55b0d010ca7ce4 Wed May 15 17:11:34 2019 -0700

• Don't fail silently when unable to open VCF. refs #22440 note 130
  • src/hg/hgTracks/vcfTrack.c - lines changed 9, context: html, text, full: html, text

521dad5888fde0e10237c9c6b741e071cd0c5cee Tue May 14 09:47:56 2019 -0700

• hgSession: added CGI param hgS_sessionDataDbSuffix to randomize choice of customData db* when bulk-converting old saved sessions to use sessionDataDir/sessionDataDbPrefix. refs #22440
  • src/hg/hgSession/hgSession.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgSession/hgSession.h - lines changed 6, context: html, text, full: html, text
  • src/hg/hgSession/sessionData.c - lines changed 34, context: html, text, full: html, text

8b8805e978d9f3082c09351ee19bbad1ca09cac2 Tue May 14 10:38:44 2019 -0700

• When saving a session, if a table is not in customTrash then check whether it has already been saved to a customData* db. If not, just move on instead of aborting. refs #22440
  • src/hg/hgSession/sessionData.c - lines changed 26, context: html, text, full: html, text

e6254f8ad3cfeba60c7d09513ed6d560af47a5e0 Tue May 14 11:29:09 2019 -0700

• When saving a session, if hgPcrResult trash files are lost and removed from the cart var value, remove the cart var to prevent hgTracks from errAborting about bad cart var format. refs #22440
  • src/hg/hgSession/sessionData.c - lines changed 4, context: html, text, full: html, text

28d8f6e18b5c04a6f517bbb05e6a15d80f042dd9 Tue May 14 12:34:10 2019 -0700

• When saving a session, even if a ctfile or customComposite is already a symlink, scan it anyway in case it is an old session that points to customTrash db tables. refs #22440
  • src/hg/hgSession/sessionData.c - lines changed 1, context: html, text, full: html, text

94b3342ec1b9abe3993347c967b652f2e91ecf57 Thu May 16 12:18:49 2019 -0700

• When saving a trash path that is already a link, if it is a relative link (e.g. to ../../userdata/ct/xyz) then resolve it to a full path. refs #22440
  • src/hg/hgSession/sessionData.c - lines changed 13, context: html, text, full: html, text

8999273deebb9514bab0282c96011acb4355ecbd Fri May 17 13:25:31 2019 -0700

• Simplifying hgVai documentation disclaimer that it's not for medical use.
  • src/hg/htdocs/goldenPath/help/hgVaiHelpText.html - lines changed 2, context: html, text, full: html, text