Commits for kent

v388_preview to v388_preview2 (2019-09-09 to 2019-09-16) v388

b115bef91d8de7132ccdbeca330a9941a5ffee65 Thu Sep 5 16:27:05 2019 -0700

• Fixed a few typos in comments and docs.
  • src/inc/strex.h - lines changed 1, context: html, text, full: html, text
  • src/lib/strex.doc - lines changed 2, context: html, text, full: html, text

0512731f08d36248257c4ed6682f1abdafcfee3b Thu Sep 5 16:27:50 2019 -0700

• Describing changes since last production release.
  • src/hca/hcat/mysite/versions.txt - lines changed 23, context: html, text, full: html, text

3a16297829778f22d084827214ed1b6b650e866c Thu Sep 5 16:31:51 2019 -0700

• Making comments just text fields. Making wranglers, curators, and software developers as separate tables with a link to plain old contributors. A bunch of more minor changes that were easy to implement described in the 0.5 section of version.txt.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 74, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 89, context: html, text, full: html, text

45339e6f4ac8777701d3ecad108d8eee2b942ed8 Thu Sep 5 16:33:00 2019 -0700

• Updating docs which had drifted a little from implementation, in the comments.
  • src/lib/strex.c - lines changed 5, context: html, text, full: html, text

87b7cd26d44ee9fee02081c5ae0d346a19be2178 Fri Sep 6 13:40:00 2019 -0700

• Adding in descriptions of changes from Paris' requests.
  • src/hca/hcat/mysite/versions.txt - lines changed 3, context: html, text, full: html, text

e61dee7bb39246a91885ef62078d45818559bedd Fri Sep 6 14:01:59 2019 -0700

• Switching date/deliverable order so lines up pretty. Changing some things in response to Paris's requests.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 14, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 25, context: html, text, full: html, text

a0ed68b1fddb7782e86481e27b972fa14caec97e Fri Sep 6 14:03:30 2019 -0700

• Recording latest mods.
  • src/hca/hcat/mysite/versions.txt - lines changed 2, context: html, text, full: html, text

552331b42c93f88781b16183d733f9f48d07802f Fri Sep 6 14:05:56 2019 -0700

• dealing with change of project_role to be a foreign key into contributorType. Removing contact from lab until I figure out how to do it right. Fixed a lab_contributor mixup.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 11, context: html, text, full: html, text

3e6c9b3323a9875d9163e6f4fc28c35c92717985 Fri Sep 6 14:07:07 2019 -0700

• Making it optionally tolerate missing files in the command line without complaint.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 5, context: html, text, full: html, text

c4c03a112fa516468b6ce875108c5b1749e11104 Fri Sep 6 14:08:20 2019 -0700

• Making it so that a newField can have a ? before it, in which case if the corresponding oldField is missing it is not an error, it simply is skipped.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 22, context: html, text, full: html, text

e28685060d11d006ed870d8b3030e251bb63076b Thu Sep 12 17:02:26 2019 -0700

• First commit of program to import JSON from Parth's tracker into hcat. Needs to generate table headers, but the table columns are looking good by visual inspection at least.
  • src/hca/hcat/hcatParseParth/hcatParseParth.c - lines changed 275, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/makefile - lines changed 3, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/testExpected/hcat_contributor.tsv - lines changed 64, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/testExpected/hcat_project.tsv - lines changed 25, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/testIn.json - lines changed 2473, context: html, text, full: html, text

aea3d32ec26cf8d333ba7af1d27964addad961c4 Thu Sep 12 22:15:48 2019 -0700

• Produces header lines in the output files now. This version used to preload hcat with the older data, but not yet parsing out the status bits.
  • src/hca/hcat/hcatParseParth/hcatParseParth.c - lines changed 31, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/testExpected/hcat_contributor.tsv - lines changed 65, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/testExpected/hcat_project.tsv - lines changed 26, context: html, text, full: html, text

f75e51cbc8d0fa611902086582672ea627ab643f Thu Sep 12 22:20:45 2019 -0700

• Adding uuid field to project.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/mysite/versions.txt - lines changed 10, context: html, text, full: html, text

12f8b1f11a6bc0d7a9694a7b64163123f8ad3e8e Thu Sep 12 22:22:47 2019 -0700

• Starting to tinker on non-admin views.
  • src/hca/hcat/mysite/hcat/urls.py - lines changed 4, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/views.py - lines changed 19, context: html, text, full: html, text
  • src/hca/hcat/mysite/templates/hcat/project_detail.html - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/mysite/templates/hcat/project_list.html - lines changed 9, context: html, text, full: html, text

9caa48dc0a1f42140f778d262c7efadd506351e3 Thu Sep 12 22:23:36 2019 -0700

• Some renaming from HCAT to Tuatara.
  • src/hca/hcat/mysite/templates/admin/base_site.html - lines changed 2, context: html, text, full: html, text

de60f72591d3d1dac467019d1cfc6e7a21edf31a Fri Sep 13 07:11:35 2019 -0700

• Got rid of search_fields that involve foreign keys or multis as they just crash Django.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 7, context: html, text, full: html, text

285594d7319101feb853a740494f511e37c5c180 Sat Sep 14 14:25:49 2019 -0700

• Adding an update option which parallels the conditional option in some ways.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 54, context: html, text, full: html, text

6f32b1ba12ffa50bdffefd5cc88ea12141f1334a Sat Sep 14 14:33:04 2019 -0700

• Started to document how fields work in usage message. Not complete. My, this code could use a couple of functions broken up too - logic is a little tortured and long now. Alas it's gonna be the sort of refactor where the functions are going to have 8 parameters each if I break up the big one.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 10, context: html, text, full: html, text

867a3f8e1801a5e150dcc054a9f8b7b05fe6f428 Sat Sep 14 14:34:55 2019 -0700

• Decided to go with a separate table for the tracker info since project was getting so big. No regrets!
  • src/hca/hcat/hcatParseParth/hcatParseParth.c - lines changed 83, context: html, text, full: html, text

efb20cbb23e6e1a8d09ef36c69c6367e86fcbb52 Sat Sep 14 14:36:30 2019 -0700

• New Tracker model and stuff to show it in the admin.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 31, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 23, context: html, text, full: html, text

96656d98549f8f0bb4ad2931330f35110ee8b857 Sat Sep 14 14:37:02 2019 -0700

• Documenting changes since last version.
  • src/hca/hcat/mysite/versions.txt - lines changed 15, context: html, text, full: html, text

0890e2c3c68649027aa95195fe82ca2e1101e82e Sun Sep 15 11:42:11 2019 -0700

• Adding -uncsv as an option. Actually it used to be the default so I had to throw it on in the test set. The csv/array vs. normal commas in free text are a weak point of the system. Between that and the SQL you can't escape escaping it seems!
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 26, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/doTest.csh - lines changed 1, context: html, text, full: html, text

b76d22919942bde7b254eb6155dd93f32b825437 Sun Sep 15 12:13:27 2019 -0700

• Saving some shell scripts that I'll probably use again though there's not much to them.
  • src/hca/hcat/hcatParseParth/doTest.csh - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/fetchAndParse.csh - lines changed 3, context: html, text, full: html, text
  • src/hca/hcat/hcatParseParth/updateProd.csh - lines changed 4, context: html, text, full: html, text

0b7fc0972a745005ac329190569f51b12877ebe0 Sun Sep 15 15:24:53 2019 -0700

• Adding unroll for unpacking csv arrays into a table with multiple rows. The driving use case is the contacts/contributors merge for HCA.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 67, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/unroll_test.tsv - lines changed 4, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/input/spec.txt - lines changed 4, context: html, text, full: html, text

ff2d32fb46b3b97bcf6bf061ef0f8fd888556e64 Sun Sep 15 17:47:57 2019 -0700

• Making all the series.contact_ prefixed fields get expanded to have one item (blank alas except in case of contact_name) for all the contributors. This and the new tabToTabDir unroll type is enough to save the curators from a separate cut and paste for each person n the project, which can get tedious.
  • src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c - lines changed 69, context: html, text, full: html, text

dd17da0c5dfbf9cf7e7aa4cde8fdc8ba14389663 Sun Sep 15 17:48:50 2019 -0700

• Showing submit_date instead of title. Looks cleaner and more informative.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 1, context: html, text, full: html, text

52312aa9e2d2642c8ab02602f43941db285c1742 Sun Sep 15 17:49:41 2019 -0700

• Bumping visible version on dev site.
  • src/hca/hcat/mysite/templates/admin/base_site.html - lines changed 1, context: html, text, full: html, text