Commits for kent

v386_preview2 to v386_base (2019-08-05 to 2019-08-12) v386

8a1718c666e29d0d2e3bcd0712cfb5e1ef8202de Tue Aug 6 08:48:11 2019 -0700

• Making it so that the _s in the required fields is optional since it isn't there in the tables that efetch gets.
  • src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c - lines changed 85, context: html, text, full: html, text

a53c1529894f2a09cd68e914bee1cc264b9b8d6e Tue Aug 6 08:49:32 2019 -0700

• Adding some of the relation url to accession mapping from the hca code to here, since it is of more general use than just hca.
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 70, context: html, text, full: html, text

9a5c53c204f4d4c780f6e57dc88a58f7a84ea28c Tue Aug 6 08:50:23 2019 -0700

• Adding new function - fieldedTableAddHead.
  • src/inc/fieldedTable.h - lines changed 3, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 27, context: html, text, full: html, text

7c4cb76a5e34c074fd703685ff55c8dfa1ef3a92 Tue Aug 6 11:48:32 2019 -0700

• Fixed a big in a debugging/dump routine that caused core dumps on nulls.
  • src/lib/rqlParse.c - lines changed 1, context: html, text, full: html, text

36dcc59871b9d3c32a43919d2d6d26fef10e3d78 Tue Aug 6 11:50:28 2019 -0700

• Making rql interpreter handle string additions, which the parser was just merrily putting in leading to internalErrs during the eval phase. To support this adding a new rqlEvalCoerceToString function.
  • src/lib/rqlEval.c - lines changed 43, context: html, text, full: html, text

79166a599f16eb59cff176099fb8611ded59d466 Tue Aug 6 11:51:11 2019 -0700

• Adding new rqlEvalCoerceToString for things that want to evaluate a string rather than a boolean expression.
  • src/inc/rql.h - lines changed 4, context: html, text, full: html, text

0c1740e6f5e1784aff4a2dddf2bb6c96184059c3 Wed Aug 7 12:01:51 2019 -0700

• Got parser working mostly. Evaluator starting to work.
  • src/hg/oneShot/freen/freen.c - lines changed 777, context: html, text, full: html, text

752306bc53b89dd0a9b02e57bd330b64f3a3fcc8 Wed Aug 7 15:50:57 2019 -0700

• Adding in some actual built in functions. Starting to extract bits into a strex.h interface file.
  • src/hg/oneShot/freen/freen.c - lines changed 235, context: html, text, full: html, text
  • src/inc/strex.h - lines changed 24, context: html, text, full: html, text

a4f5eb337ffaa1e4e9eaf9b45aa3543932236906 Wed Aug 7 17:13:35 2019 -0700

• Added in parameter type and count checks to built in functions. Added three new functions: now(), md5(), and split()
  • src/hg/oneShot/freen/freen.c - lines changed 92, context: html, text, full: html, text

5b5114fd377cd50d1af59af46d6842ba3420b3cb Wed Aug 7 17:35:17 2019 -0700

• Making an error message less file-focused in parser.
  • src/lib/tokenizer.c - lines changed 2, context: html, text, full: html, text

6e7b8bdf6aeb604219a24f35cf1d303a0cb6edef Wed Aug 7 18:08:33 2019 -0700

• Librarifying strex string expression module that is going in for tabToTabDir to help sort through some of HCA madness.
  • src/hg/oneShot/freen/freen.c - lines changed 1014, context: html, text, full: html, text
  • src/inc/strex.h - lines changed 5, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/strex.c - lines changed 1042, context: html, text, full: html, text
  • src/lib/strex.doc - lines changed 19, context: html, text, full: html, text

dda48ab9b28de6442a016aadbd93198d6c69a46e Wed Aug 7 23:54:00 2019 -0700

• Fixed an inconsistency in memory handling in nextStringBetween. It is now safe in all cases to free the returned value.
  • src/lib/common.c - lines changed 2, context: html, text, full: html, text

3e84d05093eba8a6769aab1aa6a9dec09285c310 Wed Aug 7 23:56:07 2019 -0700

• Adding in strex language processing of the field source in the spec file.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 120, context: html, text, full: html, text

16d50b66c01e686c4d0d457e44536446f55b8bfe Thu Aug 8 11:29:11 2019 -0700

• Renaming two built in functions.
  • src/lib/strex.c - lines changed 11, context: html, text, full: html, text

1caf6ec14e3a0a6f010ec4b5fe5f90d366a64021 Thu Aug 8 11:30:36 2019 -0700

• Updating a doc to describe operators as well as functions, and also rename some of the builtins.
  • src/lib/strex.doc - lines changed 7, context: html, text, full: html, text

f61da046c20f8466eae52182f97abbdee6573ae4 Thu Aug 8 14:05:43 2019 -0700

• Minor edits and additions to doc.
  • src/lib/strex.doc - lines changed 2, context: html, text, full: html, text

1aa8e87e310d813960d2db2000ade0508ceb0539 Thu Aug 8 14:17:30 2019 -0700

• Improving commenting.
  • src/lib/strex.c - lines changed 21, context: html, text, full: html, text

86198e4f30bbabbb41efc97ccce663055308b5a2 Fri Aug 9 09:22:42 2019 -0700

• Starting rework on new test set. Deleted old spec that doesn't work any more.
  • src/tabFile/tabToTabDir/in.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/inSpec.ra - lines changed 23, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/in.tsv - lines changed 467, context: html, text, full: html, text

d7cb3ff035b797a86966dc555a651a2fd3ab76fe Fri Aug 9 09:23:24 2019 -0700

• Making a symbol with dots in it for input field name because we need to make sure it works.
  • src/tabFile/tabToTabDir/test/in.tsv - lines changed 1, context: html, text, full: html, text

9688a777a961ceeceddcfe70c6c290626408617c Fri Aug 9 09:58:26 2019 -0700

• Adding fileName and fileLineNumber to strexParseString to make error messages more informative.
  • src/inc/strex.h - lines changed 5, context: html, text, full: html, text
  • src/lib/strex.c - lines changed 5, context: html, text, full: html, text

8edba16387f9185fea5edb8a05ced28d32ce6a34 Fri Aug 9 09:59:33 2019 -0700

• Adding file name and line number to strexParseString. The line number isn't accurate yet, is at bottom of stanza.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 3, context: html, text, full: html, text

d7620abf791fd7d117a9c8b5a810a92274146c0a Fri Aug 9 12:34:44 2019 -0700

• Refactoring a bit to improve error reporting. Going from higher level to lower level .ra file parsing functions on the spec file so can keep track of line numbers when we are checking for errors better.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 54, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/a_strex_test.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/donor.tsv - lines changed 13, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/fluidics_chip.tsv - lines changed 17, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/project.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/sample.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/specimen.tsv - lines changed 15, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/spec.txt - lines changed 50, context: html, text, full: html, text

a7e81d5ffdafdbf237a7ecda1ce4ad77c8d37d70 Fri Aug 9 12:39:11 2019 -0700

• Oops, need to rename the test dir
  • src/tabFile/tabToTabDir/test/expected/a_strex_test.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/donor.tsv - lines changed 13, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/fluidics_chip.tsv - lines changed 17, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/project.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/sample.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/expected/specimen.tsv - lines changed 15, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/in.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/test/spec.txt - lines changed 50, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/a_strex_test.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/donor.tsv - lines changed 13, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/fluidics_chip.tsv - lines changed 17, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/project.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/sample.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/specimen.tsv - lines changed 15, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/in.tsv - lines changed 467, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/spec.txt - lines changed 50, context: html, text, full: html, text