Commits for kent

v387_base to v388_preview (2019-09-02 to 2019-09-09) v388

dd06af8866cf7caca22463089b2c78a6cfa60dee Sat Aug 31 18:26:33 2019 -0700

• Adding -id and -startId options to fieldedTable to get steadily incrementing numerical id's for django.
  • src/inc/fieldedTable.h - lines changed 5, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 20, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 14, context: html, text, full: html, text

f1902465c9b73714073acdaa9356dc5d15f647af Sun Sep 1 08:39:54 2019 -0700

• Fixed bug that was causing 'zip/postal_code' to appear in a field name inside a system that can't deal with '/' inside of a field name!
  • src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c - lines changed 23, context: html, text, full: html, text

3cbffa5fa5e6432fa9a0aed338a7c6aa4ac80875 Sun Sep 1 11:41:08 2019 -0700

• Starting to work on a utility to help load things from GEO into HCAT
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 298, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/makefile - lines changed 3, context: html, text, full: html, text

ca4919c8dda0799f1bc1b68de0741b6a38172381 Sun Sep 1 14:07:38 2019 -0700

• Starting to process fields like organ and organ_part that come from sample
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 72, context: html, text, full: html, text

55f0ab3d708b3c9898830d1d962f010730b43cfd Sun Sep 1 16:55:17 2019 -0700

• Mangling the field names of the foreign keys and multi/multis.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 65, context: html, text, full: html, text

9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700

• Removing a few debugging statements.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/contributors.tsv - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/lab.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/project.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/in/hcat_project.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/in/hcat_sample.tsv - lines changed 421, context: html, text, full: html, text

3a065d997b16bf72f96a84e5d08323d5fa7adde0 Sun Sep 1 17:03:29 2019 -0700

• Adding test script driver.
  • src/hca/hcat/hcatTabUpdate/tests/doTest.csh - lines changed 5, context: html, text, full: html, text

af164773eb7cf94de29afde3484a0dd3ceb1c8bb Sun Sep 1 17:08:22 2019 -0700

• Changing expected output file names.
  • src/hca/hcat/hcatTabUpdate/tests/expected/contributors.tsv - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_contributors.tsv - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_lab.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_project.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/lab.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/project.tsv - lines changed 2, context: html, text, full: html, text

48b8f1204bddf90e7a578d985df17de877fc5e8c Sun Sep 1 17:11:17 2019 -0700

• Making output tables have the old hcat_ prefix.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 4, context: html, text, full: html, text

743f3715fea786aeb0939f645d7e681ac11db115 Sun Sep 1 17:14:23 2019 -0700

• Swapping around order of the multi-multi @ barrage to be same as the foreignKey @ barrage at the end.
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_lab.tsv - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_project.tsv - lines changed 1, context: html, text, full: html, text

20a082c2ea3b931b061a716135c29368befcf472 Sun Sep 1 17:38:58 2019 -0700

• Fixing mistaken plural in hcat_contibutors
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_contributor.tsv - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_contributors.tsv - lines changed 5, context: html, text, full: html, text

72ce237deec6e71abc9588bee0a94caba887e052 Mon Sep 2 07:19:55 2019 -0700

• Getting rid of some fields of contributor that HCAT doesn't support yet. Unkinking some of the CSV handling. Copying with an inconsistency in Django underbars.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 21, context: html, text, full: html, text

e907713dd4d0dad8934b23ec55c2d937b9085482 Mon Sep 2 08:44:52 2019 -0700

• Starting to work. Creates normal, conditional and foreign key inserts. Still to do - the multi to multi
  • src/hg/sqlUpdateRelated/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 295, context: html, text, full: html, text

5db640d61b5495fb5a644885753ea37ff61dbb31 Mon Sep 2 08:46:09 2019 -0700

• Fixing field names in output.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 8, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_contributor.tsv - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_lab.tsv - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_project.tsv - lines changed 1, context: html, text, full: html, text

a2b75cac670b61deb2664261984bd24e1971242f Mon Sep 2 10:21:11 2019 -0700

• Adding relationship table updates to multi-multi handling.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 59, context: html, text, full: html, text

d8a1130659866e272cd481848b48c6134fac7e02 Mon Sep 2 10:23:35 2019 -0700

• Fixing some of the @ and @@ field names.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 11, context: html, text, full: html, text

9fd1c6fa1c7581d60eacdc0eb14c5afda0d35e9b Mon Sep 2 11:41:17 2019 -0700

• Generating organ table if need be.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 39, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/in/hcat_project.tsv - lines changed 2, context: html, text, full: html, text

42616d3f95e6b0ca9b8ab64fd02e4ebcd154ad4c Tue Sep 3 15:45:48 2019 -0700

• Improving usage message and commenting. Took out the lies about strex, which actually isn't used here after all, just in the previous step.
  • src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c - lines changed 196, context: html, text, full: html, text

b3aaca25eddcf6ab159bb4e5ca80b52e2c30a52e Tue Sep 3 22:31:41 2019 -0700

• Improving commenting a hair and fixing some lines that are too long. Could still use a little more of this.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 2, context: html, text, full: html, text

20710d4500737f2022bed8e3935ee8428fd88702 Wed Sep 4 08:05:28 2019 -0700

• Adding test files and script. Test script isn't perfect yet, it's a little tricky working with stuff that modifies a database like this.
  • src/hg/sqlUpdateRelated/tests/doTest.csh - lines changed 8, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/expectedDb.sql - lines changed 1912, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_assaytype.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_contributor.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_disease.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_lab.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_organ.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_organpart.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_project.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/hcat_publication.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/sqlUpdateRelated/tests/inDb.sql - lines changed 1914, context: html, text, full: html, text

e59a222a6acfae7632d0de9f11cf72b787d890e7 Wed Sep 4 09:06:27 2019 -0700

• Adding a doc file to this new utility.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.doc - lines changed 113, context: html, text, full: html, text

aab2d99a685cdf228873d86290ffee434361aedc Wed Sep 4 12:59:24 2019 -0700

• Freen explores sqlEscapeString.
  • src/hg/oneShot/freen/freen.c - lines changed 8, context: html, text, full: html, text

751106c544e4499ef9e7c3f9292834da52d3b39b Wed Sep 4 13:00:20 2019 -0700

• Doing more error checking on field names before attempting to commit anything to the database.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.c - lines changed 46, context: html, text, full: html, text

730e30d353962933ce8286de4fb9f46f58a7440e Wed Sep 4 13:02:37 2019 -0700

• Added a new small function aking to fieldedTableMustFindFieldIx, but without the must. Just returns a -1 on problem rather than errAborting.
  • src/inc/fieldedTable.h - lines changed 3, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 7, context: html, text, full: html, text

2c3a2f69934f13b659261dfa516ad9d1d14c03cc Wed Sep 4 14:28:55 2019 -0700

• Adding a bunch of fields to contributor. Making more lab fields optional.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 13, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 9, context: html, text, full: html, text

018fb36b8981de4687ad462781b6254aeb7e42f5 Wed Sep 4 14:29:51 2019 -0700

• Making the bit on my home dir be the developmental branch.
  • src/hca/hcat/mysite/templates/admin/base_site.html - lines changed 1, context: html, text, full: html, text

34f53f8b38b45c7d8992e43e997a42bc568e6799 Wed Sep 4 14:33:41 2019 -0700

• Updating test set with new features.
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_assaytype.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_contributor.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_disease.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_lab.tsv - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_organ.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_organpart.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_project.tsv - lines changed 2, context: html, text, full: html, text
  • src/hca/hcat/hcatTabUpdate/tests/expected/hcat_publication.tsv - lines changed 2, context: html, text, full: html, text

cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700

• Removing migrations.
  • src/hca/hcat/mysite/hcat/migrations/0001_initial.py - lines changed 77, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0002_auto_20190829_0853.py - lines changed 44, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0003_auto_20190829_1841.py - lines changed 49, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0004_auto_20190829_1844.py - lines changed 15, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0005_auto_20190829_1856.py - lines changed 24, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0006_auto_20190829_1204.py - lines changed 24, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0007_auto_20190829_1220.py - lines changed 27, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0008_auto_20190829_1233.py - lines changed 33, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0009_auto_20190829_1308.py - lines changed 20, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0010_auto_20190829_1323.py - lines changed 22, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0011_auto_20190829_1332.py - lines changed 19, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0012_auto_20190829_1348.py - lines changed 67, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0013_auto_20190829_1416.py - lines changed 17, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0014_auto_20190829_1420.py - lines changed 31, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0015_auto_20190829_1438.py - lines changed 18, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0016_auto_20190829_1505.py - lines changed 26, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0017_auto_20190829_1506.py - lines changed 23, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0018_auto_20190829_1518.py - lines changed 23, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0019_auto_20190829_1540.py - lines changed 17, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0020_auto_20190829_1542.py - lines changed 18, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/0021_auto_20190829_1544.py - lines changed 22, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/migrations/__init__.py - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

6151600bec314ebdfea3af87232e9d3be24161fe Wed Sep 4 14:36:58 2019 -0700

• Updating test set with new features.
  • src/hca/hcat/hcatTabUpdate/tests/in/hcat_project.tsv - lines changed 2, context: html, text, full: html, text