Commits for kent

v350_base to v351_preview (2017-06-05 to 2017-06-12) v351

b168eec18c0cb3f2d06b1ccc59eb34776403f50e Wed May 31 18:05:09 2017 -0700

• Writing and testing new csvParseNext function.
  • src/hg/oneShot/freen/freen.c - lines changed 78, context: html, text, full: html, text
  • src/inc/csv.h - lines changed 9, context: html, text, full: html, text
  • src/lib/csv.c - lines changed 78, context: html, text, full: html, text

15f70a1451e9791fc080647cb8d913a5a6e0aa3b Wed May 31 18:17:40 2017 -0700

• Adding csvNeedsParsing
  • src/hg/oneShot/freen/freen.c - lines changed 6, context: html, text, full: html, text
  • src/inc/csv.h - lines changed 4, context: html, text, full: html, text
  • src/lib/csv.c - lines changed 9, context: html, text, full: html, text

d8b257c90191279ac9fcdea02f15f69b14f4315d Thu Jun 1 11:26:15 2017 -0700

• Downgrading debugging statements to verbose(2)
  • src/tagStorm/tagStormArrayToCsv/tagStormArrayToCsv.c - lines changed 2, context: html, text, full: html, text

ec6b7d8016ad341a64aacc6e7680214da34b6299 Thu Jun 1 12:17:14 2017 -0700

• Removing renaming and deleting bits. This will happen in another program specific to HCA. Skipping DATABASE level as it is always the same. Turning _1 _2 _3 etc into array.
  • src/hca/reformat/geoToTagStorm/geoToTagStorm.c - lines changed 87, context: html, text, full: html, text

20918bcae46467138245dd98cf4f2567e4fa18b8 Thu Jun 1 16:57:11 2017 -0700

• Making it by default collapse multiple tags with the same name in a stanza into a single comma-separated-list valued tag. The old behavior, which is occassionally useful, is avilable with the new expandArrays option.
  • src/hca/reformat/geoToTagStorm/geoToTagStorm.c - lines changed 91, context: html, text, full: html, text

4c2ca21cf82719c27ab53d4b1a00d8e90702747a Thu Jun 1 16:59:20 2017 -0700

• Oops forgot to add expandArrays to options[] table. Also downgrading some verbosities.
  • src/hca/reformat/geoToTagStorm/geoToTagStorm.c - lines changed 3, context: html, text, full: html, text

4b9efdf7b6d90698e486d8f1ccdd3132456ddc1b Thu Jun 1 17:11:31 2017 -0700

• Adding a test set.
  • src/hca/reformat/geoToTagStorm/expected.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/test.soft - lines changed 334, context: html, text, full: html, text

373475aaf70e6b0eb02c5464fe9110f25fe9f24c Thu Jun 1 17:55:34 2017 -0700

• Utility to HCAify a GEO tagStorm. Will still need SRA files attached.
  • src/hca/reformat/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 199, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/in.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/makefile - lines changed 3, context: html, text, full: html, text

32a7f051b082da240f3bc95d5419687a2d1fff93 Thu Jun 1 21:51:52 2017 -0700

• Adding hashReverseAllBucketLists, refactored out of hashExpand().
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 19, context: html, text, full: html, text

7fb5e1977f5ea547629e349327664dc83db47b4a Thu Jun 1 21:52:59 2017 -0700

• Adding a test set.
  • src/hca/reformat/geoStormToHcaStorm/out.tags - lines changed 1625, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/srxToSrr.tab - lines changed 48, context: html, text, full: html, text

2c7a7278b17c56cf7bb58e939a6f149530471c04 Thu Jun 1 21:54:02 2017 -0700

• Oops, meant to add expected.tags, not out.tags
  • src/hca/reformat/geoStormToHcaStorm/expected.tags - lines changed 204, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/out.tags - lines changed 1625, context: html, text, full: html, text

53af5fcd9de6582a30f2ab0405fb0c703fa38b91 Thu Jun 1 21:56:46 2017 -0700

• Adding srxToSrr.tab parameter and associated assay.sra_run tag. Renaming a few other tags in the output.
  • src/hca/reformat/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 44, context: html, text, full: html, text

76afc28e12ab0a404ba8f6668c8f02e4d53ee5a9 Thu Jun 1 23:07:57 2017 -0700

• Program to add several tags including the assay.files tag based on the sra_run and the paired_ends and single_cell.method tags.
  • src/hca/reformat/hcaAddSrrFiles/expected.tags - lines changed 216, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 133, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/test.tags - lines changed 207, context: html, text, full: html, text

3b03dacd234f1eb006be4ac3aade74f2c1b4cd24 Thu Jun 1 23:11:53 2017 -0700

• Oops, _1 _2, not _0 _1 in paired ends.
  • src/hca/reformat/hcaAddSrrFiles/expected.tags - lines changed 5, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 1, context: html, text, full: html, text

f65b9a7ca8bc46448f1893fe97f1598f9f5acdce Fri Jun 2 08:29:44 2017 -0700

• Renaming directory to something more specific.
  • src/hca/fromGeo/README - lines changed 1, context: html, text, full: html, text
  • src/hca/fromGeo/geoSoftToRaDir/geoSoftToRaDir.c - lines changed 154, context: html, text, full: html, text
  • src/hca/fromGeo/geoSoftToRaDir/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/expected.tags - lines changed 204, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 224, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/in.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/srxToSrr.tab - lines changed 48, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/expected.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/geoToHca.delete - lines changed 23, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/geoToHca.rename - lines changed 40, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 346, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/test.soft - lines changed 334, context: html, text, full: html, text
  • src/hca/fromGeo/hcaAddSrrFiles/expected.tags - lines changed 216, context: html, text, full: html, text
  • src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 133, context: html, text, full: html, text
  • src/hca/fromGeo/hcaAddSrrFiles/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/fromGeo/hcaAddSrrFiles/test.tags - lines changed 207, context: html, text, full: html, text
  • src/hca/reformat/geoSoftToRaDir/geoSoftToRaDir.c - lines changed 154, context: html, text, full: html, text
  • src/hca/reformat/geoSoftToRaDir/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/expected.tags - lines changed 204, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 224, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/in.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/reformat/geoStormToHcaStorm/srxToSrr.tab - lines changed 48, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/expected.tags - lines changed 249, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/geoToHca.delete - lines changed 23, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/geoToHca.rename - lines changed 40, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/geoToTagStorm.c - lines changed 346, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/reformat/geoToTagStorm/test.soft - lines changed 334, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/expected.tags - lines changed 216, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 133, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/reformat/hcaAddSrrFiles/test.tags - lines changed 207, context: html, text, full: html, text

4e3095bc06307daed680b0300031c9b8ec26c6ba Fri Jun 2 08:33:29 2017 -0700

• Making directory for programs that assist in conversion to HCA submission formats.
  • src/hca/toHca/README - lines changed 1, context: html, text, full: html, text

a66f882df960f69a6cdcb773299708756985d95c Fri Jun 2 08:55:46 2017 -0700

• Making a test set for hcaStormToBundles
  • src/hca/toHca/hcaStormToBundles/test.tags - lines changed 93, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587500_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587501_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587502_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587503_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587504_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir1/SRR3587505_1.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587500_2.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587501_2.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587502_2.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587503_2.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587504_2.fastq.gz - lines changed 1, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testFastqs/subdir2/SRR3587505_2.fastq.gz - lines changed 1, context: html, text, full: html, text

0b9219668c0793d20092ecd6128df8cf41025900 Fri Jun 2 14:16:34 2017 -0700

• First cut works. Need to add some special casing for the files[] still.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 361, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testIt - lines changed 3, context: html, text, full: html, text

fd67631b1660daf25b69d5a2df7643c4c75568b6 Fri Jun 2 14:23:31 2017 -0700

• Replacing local escaper with one from json library.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 10, context: html, text, full: html, text

2e2fe42ea116b0a37fe3bd4b1744a0998a4ccaa6 Fri Jun 2 14:24:09 2017 -0700

• Adding csvParse.
  • src/inc/csv.h - lines changed 3, context: html, text, full: html, text
  • src/lib/csv.c - lines changed 14, context: html, text, full: html, text

29fba277b1b4bc7e4d9ee3897b9e97fb73e30db7 Fri Jun 2 14:24:29 2017 -0700

• Fixing comment.
  • src/inc/tagStorm.h - lines changed 1, context: html, text, full: html, text

d0d7db3bc684ca5e714ddcab080de393f24d2687 Fri Jun 2 14:26:19 2017 -0700

• Some external files have been integrate into C code of geoStormToHcaStorm.
  • src/hca/fromGeo/geoToTagStorm/geoToHca.delete - lines changed 23, context: html, text, full: html, text
  • src/hca/fromGeo/geoToTagStorm/geoToHca.rename - lines changed 40, context: html, text, full: html, text

cbb6973cb9210c1b1395a638210a734794d0c920 Fri Jun 2 14:27:01 2017 -0700

• Leaving supplementary files in
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 1, context: html, text, full: html, text

7a07f877246c11849c7a6702688ca9513d4252be Fri Jun 2 14:27:40 2017 -0700

• Adding reference to LICENSE in README.
  • src/hca/README - lines changed 1, context: html, text, full: html, text

7380cf43b63d424791325dba3711392044723fea Fri Jun 2 14:28:23 2017 -0700

• Removing some debugging statements and fixing Offset/Size mixup.
  • src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c - lines changed 4, context: html, text, full: html, text

937dc7a7db8bb221cb28cf32ce99e05a19a92205 Fri Jun 2 14:30:08 2017 -0700

• Moving not so useful utility that has been superceded by geoToTagStorm to place where it doesn't need code review.
  • src/hca/fromGeo/geoSoftToRaDir/geoSoftToRaDir.c - lines changed 154, context: html, text, full: html, text
  • src/hca/fromGeo/geoSoftToRaDir/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/oneShot/geoSoftToRaDir/geoSoftToRaDir.c - lines changed 154, context: html, text, full: html, text
  • src/hca/oneShot/geoSoftToRaDir/makefile - lines changed 3, context: html, text, full: html, text

f29661c17a6bdc41aaa7cd7d4e8599be0910246b Fri Jun 2 14:35:05 2017 -0700

• Moving tagStormListLeaves to library.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 35, context: html, text, full: html, text
  • src/inc/tagStorm.h - lines changed 11, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 29, context: html, text, full: html, text

80391fd4f66e266ae5ac2b0bddcffbce9c5390e8 Fri Jun 2 14:39:06 2017 -0700

• Moving pathsInDirAndSubdirs to library.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 24, context: html, text, full: html, text
  • src/inc/portable.h - lines changed 3, context: html, text, full: html, text
  • src/lib/portimpl.c - lines changed 24, context: html, text, full: html, text

f7d7de0807a969111b230bce983369e2bca2eba7 Sat Jun 3 13:25:02 2017 -0700

• Starting directory for importing projects from HCA.
  • src/hca/fromArrayExpress/README - lines changed 1, context: html, text, full: html, text

fe441da309997cb46221c512dc7d7c32a99b998a Sat Jun 3 13:31:06 2017 -0700

• Adding test set for arrayExpressToTagStorm program.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/test.idf.txt - lines changed 32, context: html, text, full: html, text
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/test.sdrf.txt - lines changed 7, context: html, text, full: html, text

831bc70506c43ba97b550c4f8d001f130eef97a0 Sat Jun 3 16:02:05 2017 -0700

• Utility to convert ArrayExpress tab-sep-files to a tagStorm is fully half baked now. Handling first of two tab-sep-files.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 150, context: html, text, full: html, text

11f4fabd36716bcce6cc27b91464b27e48cd7682 Sat Jun 3 16:02:11 2017 -0700

• Utility to convert ArrayExpress tab-sep-files to a tagStorm is fully half baked now. Handling first of two tab-sep-files.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/makefile - lines changed 3, context: html, text, full: html, text

735cf928eb52e73b26027b1c9800a8922b3eb078 Sat Jun 3 17:07:49 2017 -0700

• Adding csvEscapeAndAppend
  • src/inc/csv.h - lines changed 6, context: html, text, full: html, text
  • src/lib/csv.c - lines changed 21, context: html, text, full: html, text

44f45592a7dacc9006180ccc5df5267467c15bb9 Sat Jun 3 17:35:43 2017 -0700

• First cut of parsing sdrf.txt file. Still got to deal better with term-source-refs and term-accessions.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 93, context: html, text, full: html, text

5f85700e04280b91f910b5b76ac2a06dff1d1f14 Sat Jun 3 18:20:47 2017 -0700

• Dealing with Term Source REF and Term Accession Number's dependency on previous fields.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 15, context: html, text, full: html, text

4fb316961e495d2667b021a8f8eb1e6b57f7522f Sat Jun 3 18:31:29 2017 -0700

• Dealing with repeated SecondaryAccession in idf files.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 11, context: html, text, full: html, text

f19c68a052a2712449f2bf6ce72f3d9c37f7785d Sat Jun 3 18:41:13 2017 -0700

• Relaxing some error checking that was causing problems, skip instead of errAbort.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 2, context: html, text, full: html, text

79eecd27f9665f13b7fb3658f19b2e25727974b8 Sat Jun 3 19:09:58 2017 -0700

• Changing date format to YYYY-MM-YY.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 57, context: html, text, full: html, text

a55f333a7f05e2bcc03278b79eb13de371c275e5 Sun Jun 4 13:54:40 2017 -0700

• Start of reformatter from arrayExpress to HCA tagStorm. Wow, a lot of renaming and still not done with that, nevermind the more structural changes.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 153, context: html, text, full: html, text
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/test.tags - lines changed 192, context: html, text, full: html, text

bbdcdd68f83d4f6ef38c7f1ba1e9a2a780cf1d29 Sun Jun 4 14:17:54 2017 -0700

• Have finished renaming and weeding pass for fields in our two examples at least. Still todo the reformatting.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 6, context: html, text, full: html, text

0a292e50dbc126ea297f1305b909920ced7765b0 Sun Jun 4 14:18:58 2017 -0700

• Handling Unit, which like the ontology term stuff, occurs anywhere and modifies previous fields.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 9, context: html, text, full: html, text

e59125514ee9cfa47168f772f1f6dbea3fa5ac04 Sun Jun 4 20:28:55 2017 -0700

• Dealing with finding assay.seq.machine.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 32, context: html, text, full: html, text

89ba7232309a06a09398d9207f71da284258ba66 Sun Jun 4 23:00:02 2017 -0700

• Dealing with idf.Person* tags. Also turning some weeding of redundant terms to more conservative 'replaceWithFirstChoice.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 127, context: html, text, full: html, text

94f2c56cfbb4432f3152f3fc00b7c060e501e878 Sun Jun 4 23:20:15 2017 -0700

• Dealng with secondary accessions.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 39, context: html, text, full: html, text

4d5d2ba756aab35dd74626d7514a8c77fdc319b6 Mon Jun 5 00:03:51 2017 -0700

• Coping with DDJB trace accessions and combining text and data supplementary files into a single array.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 41, context: html, text, full: html, text

ed1a3ec8c86add73020e7592b4cd8675b962868e Mon Jun 5 07:50:03 2017 -0700

• Dealing with seq.paired_ends, rna.strand, and improving seq.molecule.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 68, context: html, text, full: html, text

58fcdf39c0eb2d0d7418116727e30cc904398a0b Tue Jun 6 17:16:04 2017 -0700

• Handling sample.donor.age, sample.donor.body_mass_index, sample.donor.age. Also swapping . for _ in contact.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 25, context: html, text, full: html, text

a905cf6faa256af0adad4809d68b6ef2c5639314 Thu Jun 8 21:59:00 2017 -0700

• Handling protocols.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 115, context: html, text, full: html, text

3ffa8a1e5efde2b3e3600249290f0d8293a6d035 Thu Jun 8 23:15:20 2017 -0700

• Adding a line accidentally deleted back into test set.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/test.tags - lines changed 1, context: html, text, full: html, text

8b00e74bab400cad7e2a56d57f268281ea9c56ca Thu Jun 8 23:17:01 2017 -0700

• Removing trailing underbar from array express field names. Removing required fields in sdrf since they vary so much between submissions.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 11, context: html, text, full: html, text

f8b86d1a5a8ad658ce2179cfd9011d841af2adfd Thu Jun 8 23:17:40 2017 -0700

• Adding a line accidentally deleted back into test set.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/test.idf.txt - lines changed 1, context: html, text, full: html, text

98d5d71a7d203bcdb4779b73645f9465d1e20ce9 Thu Jun 8 23:21:03 2017 -0700

• Quite a few small changes. Adding project uuid. Making a combined address tag to be more euro-friendly. Refactoring tag storm tree traversal code so don't need 6 lines to wrap every routine that traverses the tree.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 72, context: html, text, full: html, text
  • src/hca/fromGeo/geoStormToHcaStorm/makefile - lines changed 1, context: html, text, full: html, text

fef6b0e6ceee0f85c4a88300de55419d379901a5 Thu Jun 8 23:22:46 2017 -0700

• Adding plural to some tag names made from arrays. Keeping program from reversing order of things.
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 9, context: html, text, full: html, text

53b998b52efc314f64d9d03bc6e3cb49269a38c3 Thu Jun 8 23:26:06 2017 -0700

• Much more complete implementation. Will create json arrays[] automatically if it's a tagStorm array better. Makes type field semi credibly inside of files object array.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 122, context: html, text, full: html, text

9f9ad5fdcccb6e5f697a016d2957bbe4757f7e87 Thu Jun 8 23:27:02 2017 -0700

• Changing to index1_reads2 instead of index1_data2 as paired_ends description for 10x-v2 and drop-seq.
  • src/hca/toHca/hcaStormToBundles/test.tags - lines changed 1, context: html, text, full: html, text

e1a3e66b150100bcb49a4d995aeb38ff95fe43d2 Thu Jun 8 23:28:29 2017 -0700

• Made nextStringBetween for when you are looking repeatedly for a pattern.
  • src/inc/common.h - lines changed 6, context: html, text, full: html, text
  • src/lib/common.c - lines changed 18, context: html, text, full: html, text

16313e67e6b0d8ab72b914a352a8cca2d81c4fa1 Thu Jun 8 23:28:49 2017 -0700

• Allowing '.' in a field name.
  • src/lib/rqlParse.c - lines changed 16, context: html, text, full: html, text

409f0020af91f29da08f529db1b4bb95158db435 Thu Jun 8 23:29:43 2017 -0700

• Adding reverseStanzas option.
  • src/tagStorm/tagStormReformat/tagStormReformat.c - lines changed 15, context: html, text, full: html, text

6a7f1c0079c6959aad2c38688c56f64bf3f71016 Fri Jun 9 00:10:34 2017 -0700

• Improving commening and making protocols go into an array.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 56, context: html, text, full: html, text

ce3b570cf3c96344383503946cd71e05a2e29870 Fri Jun 9 11:57:35 2017 -0700

• Starting a local uuid module with makeUuidString.
  • src/inc/uuid.h - lines changed 11, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/uuid.c - lines changed 20, context: html, text, full: html, text

255671c6b58617b6309ab4d1a2ccf09edca53e74 Fri Jun 9 14:30:53 2017 -0700

• Lots of little fixes to vocabulary. Adding donor.uuid.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c - lines changed 52, context: html, text, full: html, text

92fa558a39565702960b8ff54d3d9b0250e05410 Fri Jun 9 20:13:45 2017 -0700

• Adding constant for UUID_STRING_SIZE
  • src/inc/uuid.h - lines changed 3, context: html, text, full: html, text

d4227924efd51f8fd1f88b373653cbc475e06ec3 Fri Jun 9 20:14:30 2017 -0700

• Linking with uuid library.
  • src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/makefile - lines changed 1, context: html, text, full: html, text

05aac510eef09c3873d1885b49a660259c19fb92 Fri Jun 9 20:14:57 2017 -0700

• Fixing reversal of stanzas.
  • src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c - lines changed 1, context: html, text, full: html, text

0090d76d39cafaa67b70ae78ade2cccdd3ea88b4 Fri Jun 9 20:15:29 2017 -0700

• Adding makeUuidString to library.
  • src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c - lines changed 13, context: html, text, full: html, text

ffa70570b6ea9aa319297d1fc83cd7f6f3aee7ba Fri Jun 9 20:16:08 2017 -0700

• Moving makeUuidString to library.
  • src/hca/oneShot/hcaTsvToJson2/hcaTsvToJson2.c - lines changed 11, context: html, text, full: html, text

4da8f87d4bff04bfcc27509e10ac97739a32b46c Fri Jun 9 20:16:59 2017 -0700

• Moving protocols to an array.
  • src/hca/toHca/hcaStormToBundles/test.tags - lines changed 2, context: html, text, full: html, text

05686549b44546d1095e575291d5356007408e51 Fri Jun 9 20:17:34 2017 -0700

• Printing out an assay.json after test.
  • src/hca/toHca/hcaStormToBundles/testIt - lines changed 1, context: html, text, full: html, text

1873efca603354ee97fddf8947f564244fc65a2b Fri Jun 9 20:18:36 2017 -0700

• Fixing double write of files array. Treating urls as a special directory where the data just lives somewhere on the web.
  • src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c - lines changed 70, context: html, text, full: html, text