File Changes for angie

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

• src/hg/hgSession/sessionData.c
  • lines changed 7, context: html, text, full: html, text
    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/inc/soTerm.h
  • lines changed 10, 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
  • lines changed 7, 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/lib/soTerm.c
  • lines changed 100, 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
  • lines changed 23, 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/utils/binFromRange/binFromRange.c
  • lines changed 33, 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/makefile
  • lines changed 3, 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/jsonQuery/jsonQuery.c
  • lines changed 103, 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/makefile
  • lines changed 3, 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/makefile
  • lines changed 1, 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/inc/common.h
  • 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/hash.h
  • lines changed 3, 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]
  • lines changed 6, 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/jsonParse.h
  • lines changed 44, 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/jsonQuery.h
  • lines changed 57, 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/inc/localmem.h
  • lines changed 5, 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/lib/basicBed.c
  • lines changed 2, 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/common.c
  • lines changed 4, 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/lib/hash.c
  • lines changed 7, 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]
  • lines changed 42, 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/lib/jsonParse.c
  • lines changed 139, 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/lib/jsonQuery.c
  • lines changed 407, 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/lib/localmem.c
  • lines changed 5, 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.
  • lines changed 2, 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/makefile
  • lines changed 1, 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/lib/tests/expected/jsonQueryTest.out
  • lines changed 190, 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/lib/tests/input/jsonQueryTestJson.txt
  • lines changed 5, 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/lib/tests/input/jsonQueryTestPath.txt
  • lines changed 18, 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/lib/tests/jsonQueryTest.c
  • lines changed 169, 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/lib/tests/makefile
  • lines changed 11, 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.