Commits for kent

v357_base to v358_preview (2017-10-30 to 2017-11-06) v358

6b6763ede646c2be8b8929c2a8700a4a68565cf1 Mon Jul 10 09:58:08 2017 -0700

• Creating a json output option.
  • src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c - lines changed 103, context: html, text, full: html, text

018ef2c233c992fbbc573da09f9d7a01799828ad Tue Jul 18 16:45:54 2017 -0700

• Testing jsonWriteDouble();
  • src/hg/oneShot/freen/freen.c - lines changed 11, context: html, text, full: html, text

165743602ab381693f1f340dd7c3693e6f662343 Tue Jul 18 16:46:34 2017 -0700

• Changing jsonWriteDouble printf format from %lf to %g for jsonWriteDouble.
  • src/lib/jsonWrite.c - lines changed 1, context: html, text, full: html, text

b16f8d69be2fe49227f2a1d72214228763bc53b6 Tue Jul 18 16:48:16 2017 -0700

• Making ttjMakeSubObj() handle null and empty prefix parameters.
  • src/lib/tagToJson.c - lines changed 9, context: html, text, full: html, text

7fb8f954d43e80d0ac739601d017df814e3d0aff Thu Aug 3 12:27:05 2017 -0700

• Updating copyright holder per HCA request.
  • src/hca/LICENSE - lines changed 1, context: html, text, full: html, text

f3256f82f0a5eb915068c65290675b315ee20678 Fri Sep 1 14:02:27 2017 -0700

• Adding table that describes how v2 metadata fields move to v3.
  • src/hca/hcaV2ToV3/2to3 - lines changed 134, context: html, text, full: html, text

31139fbd0ac42c06d02e2d534831d719de4b5a0d Fri Sep 1 15:51:19 2017 -0700

• Renaming stuff for going between metadata versions.
  • src/hca/hcaV2ToV3/2to3 - lines changed 134, context: html, text, full: html, text
  • src/hca/v2_v3/2to3 - lines changed 134, context: html, text, full: html, text

1c61e4ebd646d8f13315dedb80affecdf9f5048e Fri Sep 1 15:51:40 2017 -0700

• Renaming stuff for going between metadata versions.
  • src/hca/v2_v3/2to3 - lines changed 134, context: html, text, full: html, text
  • src/hca/v2v3/2to3 - lines changed 134, context: html, text, full: html, text

a4861751824ae955f43dd60d321eb0c70620c19d Fri Sep 1 19:41:44 2017 -0700

• LIttle utility to fix up project.contributor in v2-v3 conversion seems to work.
  • src/hca/v2v3/hcav2v3ModifyContributors/hcav2v3ModifyContributors.c - lines changed 69, context: html, text, full: html, text
  • src/hca/v2v3/hcav2v3ModifyContributors/makefile - lines changed 3, context: html, text, full: html, text

7ce01a443f1fc128226f3d50455c55b5fb0b9bce Fri Sep 1 19:57:00 2017 -0700

• Unpacking more arrays.
  • src/hca/v2v3/hcav2v3ModifyContributors/hcav2v3ModifyContributors.c - lines changed 20, context: html, text, full: html, text

af3667fbd0899dffdc14d5df62c63817a00c7a77 Sun Sep 3 11:20:28 2017 -0700

• Renaming conversion program that expanded in scope to indicate it's new scope.
  • src/hca/v2v3/hcav2v3ArraysToMidObject/hcav2v3ArraysToMidObject.c - lines changed 83, context: html, text, full: html, text
  • src/hca/v2v3/hcav2v3ArraysToMidObject/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/v2v3/hcav2v3ModifyContributors/hcav2v3ModifyContributors.c - lines changed 79, context: html, text, full: html, text
  • src/hca/v2v3/hcav2v3ModifyContributors/makefile - lines changed 3, context: html, text, full: html, text

859c57e6d9c604e8c085f8a5c982f0f291a07ecf Sun Sep 3 11:35:58 2017 -0700

• Adding a bunch more things that are now arrays of objects.
  • src/hca/v2v3/hcav2v3ArraysToMidObject/hcav2v3ArraysToMidObject.c - lines changed 10, context: html, text, full: html, text

6f2a2d9ff2a77477878405e84f84777a04d57615 Mon Sep 4 11:56:48 2017 -0700

• Figuring out ways to modify a few less and fixing a few ontology terms.
  • src/hca/v2v3/2to3 - lines changed 4, context: html, text, full: html, text

be508ea1e3d9043b295ee9b8826f89dc300a3851 Mon Sep 4 11:58:02 2017 -0700

• Using kentSrc define one more place to avoid future edits.
  • src/hg/cirm/cdw/makefile - lines changed 1, context: html, text, full: html, text

252af85ccb21ce96ba1b8ad64c20a902c01fbd75 Mon Sep 4 12:04:15 2017 -0700

• Starting to add better array support to tagStorm. In particular tagStormInfo will now generate schemas with [#] or [%] or [$] (that is type char surrounded by square brackets) when a field type has multiple values. It also treats each value in an array separately rather than the whole thing as a comma separated list. Finally, and this is where the most code modifications are, it is starting to treat tag names such as people.2.name as arrays of objects, in this case referring to the name of the second person in the people array.
  • src/inc/tagSchema.h - lines changed 10, context: html, text, full: html, text
  • src/inc/tagToSql.h - lines changed 1, context: html, text, full: html, text
  • src/lib/tagSchema.c - lines changed 77, context: html, text, full: html, text
  • src/lib/tagToSql.c - lines changed 24, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tagStormInfo.c - lines changed 14, context: html, text, full: html, text

de453283f2c66364b952d5e1745652fb37027008 Mon Sep 4 12:04:57 2017 -0700

• Testing some stuff for tagStorm array support.
  • src/hg/oneShot/freen/freen.c - lines changed 6, context: html, text, full: html, text

2d509b869695762f7b2c06e82f9dff7f02c27d10 Mon Sep 4 12:07:16 2017 -0700

• Updating test sets for new functionality.
  • src/tagStorm/tagStormInfo/tests/expected.counts - lines changed 11, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tests/expected.out - lines changed 4, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tests/expected.schema - lines changed 11, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tests/expected.vals - lines changed 33, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tests/test.in - lines changed 19, context: html, text, full: html, text

857a84306ccc2fc4f6147edd822d1153dba507da Mon Sep 4 12:08:25 2017 -0700

• Adding another verbose(2) level for debugging.
  • src/tabFile/tabQuery/tabQuery.c - lines changed 1, context: html, text, full: html, text

4e1c6cfbdfa69c61a2a02be485297e786e0a0c9c Mon Sep 4 14:10:31 2017 -0700

• Adapting tagStormCheck for internal arrays.
  • src/tagStorm/tagStormCheck/tagStormCheck.c - lines changed 6, context: html, text, full: html, text

ec4cc6c85b75e159916f9051de61e602c3cfc575 Tue Sep 5 12:33:28 2017 -0700

• Freen tests a function that is a little tricky used in building up tagStorm schemas involving arrays.
  • src/hg/oneShot/freen/freen.c - lines changed 43, context: html, text, full: html, text

d931a2f62577733ea2db68a37d8e31bc2160edf6 Tue Sep 5 16:03:30 2017 -0700

• Updating test set for new functionality.
  • src/tagStorm/tagStormCheck/test.schema - lines changed 5, context: html, text, full: html, text
  • src/tagStorm/tagStormCheck/test.tags - lines changed 14, context: html, text, full: html, text

4929a9a5c8d7170a976fb2189f6dbee664be7790 Tue Sep 5 16:04:39 2017 -0700

• Testing some of the tag storm array processing stuff for tagStormCheck
  • src/hg/oneShot/freen/freen.c - lines changed 73, context: html, text, full: html, text

984d361cb53c9f60541eb6395475cf3f11fc9e9a Tue Sep 5 16:08:04 2017 -0700

• Adding array handling to tagStormCheck. The hard part ended up being checking required fields.
  • src/inc/tagSchema.h - lines changed 17, context: html, text, full: html, text
  • src/lib/tagSchema.c - lines changed 53, context: html, text, full: html, text
  • src/lib/tagToSql.c - lines changed 1, context: html, text, full: html, text
  • src/tagStorm/tagStormCheck/tagStormCheck.c - lines changed 116, context: html, text, full: html, text
  • src/tagStorm/tagStormInfo/tagStormInfo.c - lines changed 1, context: html, text, full: html, text

f959d4aeea0c00a3116be9a62648a0d70a775fb8 Wed Sep 6 11:45:21 2017 -0700

• Adding shortcuts option
  • src/tagStorm/tagSchemaToJson/tagSchemaToJson.c - lines changed 58, context: html, text, full: html, text

f42040eda7ad73e000510a0c3750f42b55a60c83 Wed Sep 6 12:24:54 2017 -0700

• Improving shortcut handling.
  • src/tagStorm/tagSchemaToJson/tagSchemaToJson.c - lines changed 59, context: html, text, full: html, text

442874e2a5188ef0ca1da03d42c367727f98c372 Wed Sep 6 17:21:09 2017 -0700

• Fixing a few typos and missing things.
  • src/hca/v2v3/2to3 - lines changed 3, context: html, text, full: html, text

aff5997f4c5ffa408b6be5de0a94a2bee8ccb2d6 Wed Sep 6 17:22:00 2017 -0700

• Updating test.schema to reflect HCA V3 more closely.
  • src/tagStorm/tagSchemaToJson/test.schema - lines changed 114, context: html, text, full: html, text

f3fb971b8bb28090c5d0f8a72f4063dde9e67280 Thu Sep 7 11:02:00 2017 -0700

• Making descriptions work better with subobjects, and arrays of subobjects work better.
  • src/tagStorm/tagSchemaToJson/tagSchemaToJson.c - lines changed 34, context: html, text, full: html, text

822de6b51fb45bd9cea5f8c0e6e463f018e55db0 Thu Sep 7 13:20:48 2017 -0700

• Updating files[] array to lanes[] array as part of V2 -> V3 transition.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 103, context: html, text, full: html, text

46ab8cdb3b6354c753c458ffba1a31a7f3bcae9b Thu Sep 7 15:18:58 2017 -0700

• Handling .1. .2. .3. output as arrays.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 29, context: html, text, full: html, text

54233e68e0cb7825f81de963011e83849e128f38 Thu Sep 7 15:30:13 2017 -0700

• Adapting to some changed tag names.
  • src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 4, context: html, text, full: html, text

7e67a21cf569cafee3228bf6452e2e760ca7365f Thu Sep 7 15:31:01 2017 -0700

• Ooops, 'lanes' not lane.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 1, context: html, text, full: html, text

050e1358247ac10835441952c2e192613f07f834 Thu Sep 7 16:51:12 2017 -0700

• Starting to add ids if missing for protocols and donors. Protocol bits might still need some work.
  • src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c - lines changed 106, context: html, text, full: html, text

233236f4f7c048d8be8cf861d047909b10e2af5a Thu Sep 7 21:43:00 2017 -0700

• Removing old V2 protocol handling. V3 doesn't need the special case.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 37, context: html, text, full: html, text

40c64e7dd6319e8bba943fdfea4608e53b13ac27 Fri Sep 8 18:28:58 2017 -0700

• Removing debugging message
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 148, context: html, text, full: html, text

2ccd1bd9cee67dc597157a6e47d2694b93c954e6 Fri Sep 8 19:12:17 2017 -0700

• Handling another fringe case of dots in a characteristics name.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 29, context: html, text, full: html, text

56d0c91fd610d6ba5a163d165d7ee0c34ace8e4f Mon Oct 30 11:12:25 2017 -0700

• Final round of HCA v3 metadata changes. This includes separating out a barcode subobject and renaming the assay.seq.lane file oriented fields.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 45, context: html, text, full: html, text
  • src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 52, context: html, text, full: html, text
  • src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c - lines changed 4, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 14, context: html, text, full: html, text
  • src/hca/v2v3/2to3 - lines changed 4, context: html, text, full: html, text

30aecb6730202593ae34967fe4ce07647d9acdaa Mon Oct 30 11:29:38 2017 -0700

• Making pie charts have an 'other' slice that collects together the pieces that are really too small to label.
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 86, context: html, text, full: html, text

195a8f91ef9142b437a126f7a25634408f65f12c Wed Nov 1 15:24:20 2017 -0700

• Bumping cdwWebBrowse version number since it's changed a bit.
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text