Commits for angie

v381_base to v382_preview (2019-04-29 to 2019-05-06) v382

a8c88d64b3a8adf8d6b522247b89c327b36e2a66 Mon Apr 29 10:41:21 2019 -0700

• Don't create new userdata directory unless we have at least one file to store there. Thx Hiram
  • src/hg/hgSession/sessionData.c - lines changed 7, context: html, text, full: html, text

9d47270703d4b9b603127f6c41dc9f1e49b56708 Wed Apr 17 11:08:58 2019 -0700

• loadAndValidateBed: Don't errAbort on empty array when checking autoSql fields; empty arrays are valid.
  • src/lib/basicBed.c - lines changed 2, context: html, text, full: html, text

4d1e38588ee18350611bbe576a7ceb91d5812e65 Tue Apr 16 14:01:29 2019 -0700

• Added const to declarations of some char * function params that are not modified, so I can use const in calling routines.
  • src/inc/common.h - lines changed 2, context: html, text, full: html, text
  • src/inc/localmem.h - lines changed 5, context: html, text, full: html, text
  • src/lib/common.c - lines changed 4, context: html, text, full: html, text
  • src/lib/localmem.c - lines changed 5, context: html, text, full: html, text

bc5a73ec376d9d06861b8d07e7abfe615fc38501 Wed Apr 10 09:39:10 2019 -0700

• Added hashIntReset, to quickly remove & reset to 0 all integer values of a hash. [It can also NULL out hashEl pointers, but mem alloc issues should be considered]
  • src/inc/hash.h - lines changed 3, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 7, context: html, text, full: html, text

506484c03bae4b9a7d61c5a56b928e773a0c83a7 Tue Apr 16 14:02:22 2019 -0700

• Added hashNewLm/newHashLm so an external lm can be passed in and used for all hash allocations.
  • src/inc/hash.h - lines changed 6, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 42, context: html, text, full: html, text

92ff3a19fc5cacf7b92a1a25086d9300f7df53e0 Tue Apr 16 14:02:52 2019 -0700

• Added *Lm functions that optionally use lm to allocate memory. Removed unused jsonFindName* functions -- if needed in the future, jsonQuery will probably be easier to use.
  • src/inc/jsonParse.h - lines changed 44, context: html, text, full: html, text
  • src/lib/jsonParse.c - lines changed 139, context: html, text, full: html, text

b3d2a3a1d7e096b0f97a2a5295d4fa610336de04 Fri Oct 12 11:02:37 2018 -0700

• Adding jsonQuery, which extracts values from a jsonElement tree using a simple path notation e.g. "journals[publisher=Nature].articles[*].author[0].lastName". aside: slFreeList doesn't check for NULL. I think it should, but it's used in a zillion places so for now I'll just check before calling.
  • src/hg/utils/jsonQuery/jsonQuery.c - lines changed 103, context: html, text, full: html, text
  • src/hg/utils/jsonQuery/makefile - lines changed 3, context: html, text, full: html, text
  • src/inc/jsonQuery.h - lines changed 57, context: html, text, full: html, text
  • src/lib/jsonQuery.c - lines changed 407, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/tests/expected/jsonQueryTest.out - lines changed 190, context: html, text, full: html, text
  • src/lib/tests/input/jsonQueryTestJson.txt - lines changed 5, context: html, text, full: html, text
  • src/lib/tests/input/jsonQueryTestPath.txt - lines changed 18, context: html, text, full: html, text
  • src/lib/tests/jsonQueryTest.c - lines changed 169, context: html, text, full: html, text
  • src/lib/tests/makefile - lines changed 11, context: html, text, full: html, text

9a5c1dc41298119f9569b12985a34146212dfe1a Wed Apr 10 09:36:38 2019 -0700

• Added soTermStringIdToId, soTermCmp, and soTermToMisoLink, for use with new dbSNP data. refs #23283
  • src/hg/inc/soTerm.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/soTerm.c - lines changed 100, context: html, text, full: html, text

0c882cb50cc196e069a5df0f19cb83997d6d3882 Tue Apr 16 14:00:17 2019 -0700

• Added SO terms used in dbSNP b152 JSON, plus an soUnknown enum value for when no SO terms are assigned. Move up nc_transcript_variant in funcImpactOrder to be above up/downstream. refs #23283
  • src/hg/inc/soTerm.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/soTerm.c - lines changed 23, context: html, text, full: html, text

7c84fe77d95b0733fcd4b27d8cbdfc038c1a8d5c Wed May 1 09:47:25 2019 -0700

• lmCleanup: null out *pLm before freeing lm, to make valgrind --leak-check=full -v happy.
  • src/lib/localmem.c - lines changed 2, context: html, text, full: html, text

9f568df48c409c062eab6e3b2aa60bc8509bf120 Fri May 3 16:42:33 2019 -0700

• binFromRange: util to convert start and end coords into a SQL '(bin = ### or bin = ### ...)' condition. refs #23429
  • src/hg/utils/binFromRange/binFromRange.c - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/binFromRange/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text