All File Changes

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

• confs/hgwbeta.hg.conf
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    3fede7ba7791d3bebc3499aee3fc8bd4376f9f48 Sun Sep 8 01:11:37 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c
  • lines changed 23, 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/hcat/hcatTabUpdate/hcatTabUpdate.c
  • lines changed 298, 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
  • lines changed 72, 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
  • lines changed 65, 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.
  • lines changed 5, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
  • lines changed 4, context: html, text, full: html, text
    48b8f1204bddf90e7a578d985df17de877fc5e8c Sun Sep 1 17:11:17 2019 -0700
    Making output tables have the old hcat_ prefix.
  • lines changed 1, context: html, text, full: html, text
    20a082c2ea3b931b061a716135c29368befcf472 Sun Sep 1 17:38:58 2019 -0700
    Fixing mistaken plural in hcat_contibutors
  • lines changed 21, 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.
  • lines changed 8, context: html, text, full: html, text
    5db640d61b5495fb5a644885753ea37ff61dbb31 Mon Sep 2 08:46:09 2019 -0700
    Fixing field names in output.
  • lines changed 11, context: html, text, full: html, text
    d8a1130659866e272cd481848b48c6134fac7e02 Mon Sep 2 10:23:35 2019 -0700
    Fixing some of the @ and @@ field names.
  • lines changed 39, context: html, text, full: html, text
    9fd1c6fa1c7581d60eacdc0eb14c5afda0d35e9b Mon Sep 2 11:41:17 2019 -0700
    Generating organ table if need be.
  • lines changed 196, 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/makefile
  • lines changed 3, 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/tests/doTest.csh
  • lines changed 5, context: html, text, full: html, text
    3a065d997b16bf72f96a84e5d08323d5fa7adde0 Sun Sep 1 17:03:29 2019 -0700
    Adding test script driver.
• src/hca/hcat/hcatTabUpdate/tests/expected/contributors.tsv
  • lines changed 5, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
  • 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/hcat_assaytype.tsv
  • lines changed 2, 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_contributor.tsv
  • lines changed 5, context: html, text, full: html, text
    20a082c2ea3b931b061a716135c29368befcf472 Sun Sep 1 17:38:58 2019 -0700
    Fixing mistaken plural in hcat_contibutors
  • lines changed 5, context: html, text, full: html, text
    5db640d61b5495fb5a644885753ea37ff61dbb31 Mon Sep 2 08:46:09 2019 -0700
    Fixing field names in output.
  • lines changed 2, 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_contributors.tsv
  • lines changed 5, context: html, text, full: html, text
    af164773eb7cf94de29afde3484a0dd3ceb1c8bb Sun Sep 1 17:08:22 2019 -0700
    Changing expected output file names.
  • lines changed 5, 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/tests/expected/hcat_disease.tsv
  • lines changed 2, 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_lab.tsv
  • lines changed 2, context: html, text, full: html, text
    af164773eb7cf94de29afde3484a0dd3ceb1c8bb Sun Sep 1 17:08:22 2019 -0700
    Changing expected output file names.
  • lines changed 1, 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.
  • lines changed 1, context: html, text, full: html, text
    5db640d61b5495fb5a644885753ea37ff61dbb31 Mon Sep 2 08:46:09 2019 -0700
    Fixing field names in output.
  • 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_organ.tsv
  • lines changed 2, 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_organpart.tsv
  • lines changed 2, 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_project.tsv
  • lines changed 2, context: html, text, full: html, text
    af164773eb7cf94de29afde3484a0dd3ceb1c8bb Sun Sep 1 17:08:22 2019 -0700
    Changing expected output file names.
  • lines changed 1, 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.
  • lines changed 1, context: html, text, full: html, text
    5db640d61b5495fb5a644885753ea37ff61dbb31 Mon Sep 2 08:46:09 2019 -0700
    Fixing field names in output.
  • lines changed 2, 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_publication.tsv
  • lines changed 2, 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/lab.tsv
  • lines changed 2, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
  • lines changed 2, 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/project.tsv
  • lines changed 2, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
  • lines changed 2, 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/in/hcat_project.tsv
  • lines changed 2, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
  • lines changed 2, context: html, text, full: html, text
    9fd1c6fa1c7581d60eacdc0eb14c5afda0d35e9b Mon Sep 2 11:41:17 2019 -0700
    Generating organ table if need be.
  • lines changed 2, context: html, text, full: html, text
    6151600bec314ebdfea3af87232e9d3be24161fe Wed Sep 4 14:36:58 2019 -0700
    Updating test set with new features.
• src/hca/hcat/hcatTabUpdate/tests/in/hcat_sample.tsv
  • lines changed 421, context: html, text, full: html, text
    9cd188d4f3c3aa9cee5d24e9d75fbe8c6bcebf73 Sun Sep 1 17:02:30 2019 -0700
    Removing a few debugging statements.
• src/hca/hcat/mysite/hcat/admin.py
  • lines changed 13, 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/migrations/0001_initial.py
  • lines changed 77, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0002_auto_20190829_0853.py
  • lines changed 44, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0003_auto_20190829_1841.py
  • lines changed 49, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0004_auto_20190829_1844.py
  • lines changed 15, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0005_auto_20190829_1856.py
  • lines changed 24, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0006_auto_20190829_1204.py
  • lines changed 24, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0007_auto_20190829_1220.py
  • lines changed 27, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0008_auto_20190829_1233.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0009_auto_20190829_1308.py
  • lines changed 20, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0010_auto_20190829_1323.py
  • lines changed 22, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0011_auto_20190829_1332.py
  • lines changed 19, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0012_auto_20190829_1348.py
  • lines changed 67, context: html, text, full: html, text
    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0013_auto_20190829_1416.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0014_auto_20190829_1420.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0015_auto_20190829_1438.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0016_auto_20190829_1505.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0017_auto_20190829_1506.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0018_auto_20190829_1518.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0019_auto_20190829_1540.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0020_auto_20190829_1542.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/0021_auto_20190829_1544.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/migrations/__init__.py
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    cbf0073ee8015d4a347eb2ba9a5015ca100d4997 Wed Sep 4 14:36:03 2019 -0700
    Removing migrations.
• src/hca/hcat/mysite/hcat/models.py
  • lines changed 9, 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/templates/admin/base_site.html
  • lines changed 1, 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/hg/cirm/gateway/htdocs/examples/datasetPageExample.html
  • lines changed 199, context: html, text, full: html, text
    a17b96a39394a3d6de05b5be3db061e09745f9d6 Thu Sep 5 11:16:34 2019 -0700
    Adding template and example implementation of new dataset summary page layout to source tree. no redmine.
• src/hg/cirm/gateway/htdocs/examples/datasetPageTemplate.html
  • lines changed 227, context: html, text, full: html, text
    a17b96a39394a3d6de05b5be3db061e09745f9d6 Thu Sep 5 11:16:34 2019 -0700
    Adding template and example implementation of new dataset summary page layout to source tree. no redmine.
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 1, context: html, text, full: html, text
    b754e9dee364c085968f348a97462c3a63394911 Thu Sep 5 11:18:22 2019 -0700
    Minor typo correction for Weissman lab dataset. no redmine.
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    402544fcf638ed533286eee1939579994e3577e4 Wed Aug 28 14:19:43 2019 -0700
    Fix cluster display in multi-region mode. refs #22422
  • lines changed 120, context: html, text, full: html, text
    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
    add cumulative auto-scaling to composites and views. Remove REMOTE_TRACK_AJAX_CALLBACK stuff that was apparently an experiment from ten years ago.
  • lines changed 16, context: html, text, full: html, text
    ebb119f63d024ea706a6922adf67bb9956d5f049 Tue Sep 3 16:33:52 2019 -0700
    More fixes for multi-region (cross-chrom and non-cluster mode). refs #22422
  • lines changed 9, context: html, text, full: html, text
    29c87a7aa6537003cfc8a44b2100a58573696422 Wed Sep 4 13:06:15 2019 -0700
    Style hgTracks position box to appear as pressed button when in multi-region mode. Also add more informative mouseover text when in MR mode. And style cursor for consistency with other buttons. refs #22422
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    402544fcf638ed533286eee1939579994e3577e4 Wed Aug 28 14:19:43 2019 -0700
    Fix cluster display in multi-region mode. refs #22422
  • lines changed 14, context: html, text, full: html, text
    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
    add cumulative auto-scaling to composites and views. Remove REMOTE_TRACK_AJAX_CALLBACK stuff that was apparently an experiment from ten years ago.
  • lines changed 6, context: html, text, full: html, text
    ebb119f63d024ea706a6922adf67bb9956d5f049 Tue Sep 3 16:33:52 2019 -0700
    More fixes for multi-region (cross-chrom and non-cluster mode). refs #22422
• src/hg/hgTracks/interactTrack.c
  • lines changed 20, context: html, text, full: html, text
    402544fcf638ed533286eee1939579994e3577e4 Wed Aug 28 14:19:43 2019 -0700
    Fix cluster display in multi-region mode. refs #22422
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    5f6b07f6ef00d7a59ca4e454d7336205eede6055 Wed Aug 28 16:03:23 2019 -0700
    Add ifdef to force interaction display to linked features mode (no curves) when in multi-region view. Awaiting JK input. refs #22422
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    7729449a6ca86ac9953a6274dbea550d01195355 Tue Sep 3 14:58:20 2019 -0700
    Add region size to Multi-region ranges popup. Helpful for interact multi-region feature. refs #22422
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    ebb119f63d024ea706a6922adf67bb9956d5f049 Tue Sep 3 16:33:52 2019 -0700
    More fixes for multi-region (cross-chrom and non-cluster mode). refs #22422
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    aea31ed3dfad99bed299624e281260966d808792 Wed Aug 28 14:23:24 2019 -0700
    Minor optimization. refs #22422
  • lines changed 38, context: html, text, full: html, text
    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
    add cumulative auto-scaling to composites and views. Remove REMOTE_TRACK_AJAX_CALLBACK stuff that was apparently an experiment from ten years ago.
  • lines changed 10, context: html, text, full: html, text
    ebb119f63d024ea706a6922adf67bb9956d5f049 Tue Sep 3 16:33:52 2019 -0700
    More fixes for multi-region (cross-chrom and non-cluster mode). refs #22422
• src/hg/hgTracks/wigTrack.c
  • lines changed 42, context: html, text, full: html, text
    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
    add cumulative auto-scaling to composites and views. Remove REMOTE_TRACK_AJAX_CALLBACK stuff that was apparently an experiment from ten years ago.
• src/hg/hgc/interactClick.c
  • lines changed 7, context: html, text, full: html, text
    48b920782dcf3eff2151fa74078be1622ecbb9f4 Wed Aug 28 15:22:22 2019 -0700
    Avoid duplicating regions when nested. refs #22422
  • lines changed 4, context: html, text, full: html, text
    918ed323bb2a24640f3f08b61a7431a5f1fa6c6c Tue Sep 3 15:58:03 2019 -0700
    Fix problem with interchromosomal multi-region. refs #22422
  • lines changed 1, context: html, text, full: html, text
    ebb119f63d024ea706a6922adf67bb9956d5f049 Tue Sep 3 16:33:52 2019 -0700
    More fixes for multi-region (cross-chrom and non-cluster mode). refs #22422
  • lines changed 42, context: html, text, full: html, text
    8c86cfcdfb9447faf474101662d0c846dfa25981 Wed Sep 4 17:23:18 2019 -0700
    Interact track multi-region link now adds a custom track showing where multi-regions are located. refs #22422
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 2, context: html, text, full: html, text
    10c3680ae0bc23f666f067f473249a6008d0cecd Tue Sep 3 15:07:02 2019 -0700
    Removing sentence about us considering to continue knwonGene pipeline refs#24069
• src/hg/htdocs/FAQ/FAQreleases.html
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    be75d87257907a1a651b6dbac2f1c12b1d518737 Wed Sep 4 11:41:46 2019 -0700
    Adding new assembly rheMac10 to FAQreleases #23771
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    7d9184716dc20689e28ab957e9d7ed6ed9c28887 Wed Sep 4 11:58:25 2019 -0700
    Adding new assembly rheMac10 to credits.html #23771
• src/hg/htdocs/goldenPath/credits.html
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    7d9184716dc20689e28ab957e9d7ed6ed9c28887 Wed Sep 4 11:58:25 2019 -0700
    Adding new assembly rheMac10 to credits.html #23771
• src/hg/htdocs/goldenPath/help/mysql.html
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    641f9ebc4932cfb9493e386062678c7ba821234d Thu Sep 5 10:29:43 2019 -0700
    Adding a link to the .hg.conf file on the mysql.html page, refs #21766
• src/hg/htdocs/goldenPath/history.html
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    a91282409ef8b3ef8fb6fe7932e5910a94714a9a Wed Sep 4 16:45:15 2019 -0700
    Updating hard-coded links to UCSC to be relative links. Fixing a misspelled 'target' HTML attribute for EBI. CR #24083
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    0a1cd358605c0737979f9bc735ab6bfb67196045 Fri Sep 6 12:44:30 2019 -0700
    Restructuring an introductory paragraph for the history.html page, refs #20314
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    5b156a144f9b6370354acb5e242fc64be5575af4 Fri Sep 6 13:07:46 2019 -0700
    Adding some headers to split the introduciton to genomics section from the more complex features of the Genome Browser, refs #20314
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    c5e232d6f6bcec33a0531b083848a3c5b9e70fa9 Fri Sep 6 14:08:39 2019 -0700
    Adding a note that we surpassed 200 assemblies in 2018. Ann provided the comment, but the date and number still need to be fact checked. refs #20314
• src/hg/htdocs/goldenPath/newsarch.html
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    23688dbba6229bdf678dee3d1f07f763e5751d41 Wed Sep 4 14:21:02 2019 -0700
    Adding new assembly rheMac10 to newsArch page #23771
• src/hg/htdocs/indexNews.html
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    8564f0a9d2f4fcde46287534f3189d9ace2407f8 Wed Sep 4 14:25:23 2019 -0700
    Adding new assembly rheMac10 to newsArch page #23771
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    7b47af799470692a85fc71777d65a36fe777ebf7 Tue Sep 3 05:25:29 2019 -0700
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    29c87a7aa6537003cfc8a44b2100a58573696422 Wed Sep 4 13:06:15 2019 -0700
    Style hgTracks position box to appear as pressed button when in multi-region mode. Also add more informative mouseover text when in MR mode. And style cursor for consistency with other buttons. refs #22422
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• src/hg/inc/hui.h
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    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
    add cumulative auto-scaling to composites and views. Remove REMOTE_TRACK_AJAX_CALLBACK stuff that was apparently an experiment from ten years ago.
• src/hg/inc/trackDb.h
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    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
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• src/hg/js/hgTracks.js
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    7729449a6ca86ac9953a6274dbea550d01195355 Tue Sep 3 14:58:20 2019 -0700
    Add region size to Multi-region ranges popup. Helpful for interact multi-region feature. refs #22422
• src/hg/lib/hgFind.c
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    a3e70739aa74b73a688d2638013eab96c2692dea Thu Sep 5 11:46:00 2019 -0700
    Use the string "Gencode Genes" instead of "Known Genes" in hgFind if the track is Gencode
• src/hg/lib/hui.c
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    12d023ae3337d8909508d543d9d78c99758b25c5 Mon Sep 2 10:29:34 2019 -0700
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• src/hg/makeDb/doc/GRCm38B/initialBuild.txt
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    d8751b5445ffe3667e72aeb5041b724a1877a392 Mon Sep 9 10:00:16 2019 -0700
    initial build is sufficient for Mark.s testing refs #22271
• src/hg/makeDb/doc/VGP/README.txt
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    4fdac1a09cb6a154a2f739885b02fc8f0e40a00d Mon Sep 9 09:57:59 2019 -0700
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    4fdac1a09cb6a154a2f739885b02fc8f0e40a00d Mon Sep 9 09:57:59 2019 -0700
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• src/hg/makeDb/doc/VGP/hub.txt
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    first instance of hub is complete refs #23734
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
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    249b307f8e7edcaa916870d673678044c478e953 Mon Sep 9 09:59:05 2019 -0700
    Adding Ensembl alias with v95 release refs #22425
• src/hg/makeDb/doc/hg19.txt
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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    7873ad671c469a1c6c8b6d249dc4123e6d82e361 Wed Sep 4 08:35:13 2019 -0700
    lastz chainNet hg19 to rheMac10 refs #23771
• src/hg/makeDb/doc/hg38/gencode.txt
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    d13887bf1bc4a13e590d7c1ff16b2d81b2cdb18e Mon Sep 9 10:01:11 2019 -0700
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    f630e910fa3bf0edff8347bd8c914606318c041e Mon Sep 9 10:02:02 2019 -0700
    liftOver to rheMac10 refs #23771
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
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    79124adf60b5a8e99e4025e8f982389e13db955e Wed Sep 4 15:09:02 2019 -0700
    starting V32 of hg38 knownGene
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    decef64a3ad7fb887848c70df9dd1d95a5d05cef Fri Sep 6 14:14:09 2019 -0700
    mostly done with GencodeV32 knownGene
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    792dd8a3abcda4a6d4a9f236bd434c2e76a543f4 Mon Sep 2 15:06:54 2019 -0700
    Turning on GenBank updates for new assembly #23771
• src/hg/makeDb/kgAllocId/kgAllocId.c
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    79124adf60b5a8e99e4025e8f982389e13db955e Wed Sep 4 15:09:02 2019 -0700
    starting V32 of hg38 knownGene
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    79124adf60b5a8e99e4025e8f982389e13db955e Wed Sep 4 15:09:02 2019 -0700
    starting V32 of hg38 knownGene
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/schema/all.joiner
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
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    66b5c5da59e6f7a59d559c0f68f37841cad1eb4b Mon Sep 2 11:38:37 2019 -0700
    Nesting new rheMac10 assembly in proper conservation track refs #23771
• src/hg/makeDb/trackDb/human/hg19/encode3.ra
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    6b5d39f2748635a2ba42c7dfaa5a111bbf35323a Mon Sep 2 11:31:46 2019 -0700
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• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV32lift37.html
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV32lift37.ra
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
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    6b5d39f2748635a2ba42c7dfaa5a111bbf35323a Mon Sep 2 11:31:46 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/gdcCancer.ra
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• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    7f3fbe8639b9eecae13d8e2c3637a748b746f147 Thu Sep 5 07:11:47 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    7f3fbe8639b9eecae13d8e2c3637a748b746f147 Thu Sep 5 07:11:47 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV32.html
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV32.ra
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
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    6b5d39f2748635a2ba42c7dfaa5a111bbf35323a Mon Sep 2 11:31:46 2019 -0700
    Removing stale pennantIcons
• src/hg/makeDb/trackDb/mouse/mm10/chainNetRheMac10.ra
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    877fbdf0bd82de39aafcd89c731889a9b8143368 Tue Sep 3 08:49:26 2019 -0700
    Nesting new rheMac10 release in mm10 conservation refs #23771
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
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    66b5c5da59e6f7a59d559c0f68f37841cad1eb4b Mon Sep 2 11:38:37 2019 -0700
    Nesting new rheMac10 assembly in proper conservation track refs #23771
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gencode.ra
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM23.html
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM23.ra
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    778cb733e935272196ce9dc65f51bdc38ebccebb Tue Sep 3 10:51:42 2019 -0700
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• src/hg/makeDb/trackDb/rat/regenRn1/description.html
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    39cf3af89847e9fd3ecda1fdcd6453abb52f9590 Sun Sep 8 17:24:52 2019 -0700
    initial files from makeGenomeDb.pl refs #21579
• src/hg/makeDb/trackDb/rat/regenRn1/gap.html
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    39cf3af89847e9fd3ecda1fdcd6453abb52f9590 Sun Sep 8 17:24:52 2019 -0700
    initial files from makeGenomeDb.pl refs #21579
• src/hg/makeDb/trackDb/rat/regenRn1/gold.html
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    39cf3af89847e9fd3ecda1fdcd6453abb52f9590 Sun Sep 8 17:24:52 2019 -0700
    initial files from makeGenomeDb.pl refs #21579
• src/hg/makeDb/trackDb/rat/regenRn1/trackDb.ra
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    39cf3af89847e9fd3ecda1fdcd6453abb52f9590 Sun Sep 8 17:24:52 2019 -0700
    initial files from makeGenomeDb.pl refs #21579
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    4685bc3c351c5e1dd1f0b91be90a36cc2eac92d6 Wed Sep 4 13:29:50 2019 -0700
    Updating http to https for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce10/gap.html
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    4685bc3c351c5e1dd1f0b91be90a36cc2eac92d6 Wed Sep 4 13:29:50 2019 -0700
    Updating http to https for ce10, uiLinks cronjob.
• src/hg/makeDb/trackDb/worm/ce10/gold.html
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    4685bc3c351c5e1dd1f0b91be90a36cc2eac92d6 Wed Sep 4 13:29:50 2019 -0700
    Updating http to https for ce10, uiLinks cronjob.
• src/hg/oneShot/freen/freen.c
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    aab2d99a685cdf228873d86290ffee434361aedc Wed Sep 4 12:59:24 2019 -0700
    Freen explores sqlEscapeString.
• src/hg/pyLib/hgLib.py
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    216ce3dce7eb7f0f4ad401e50f301136b17bc89a Mon Sep 9 07:17:42 2019 -0700
    now outputing 429 when blocking in hgGeneGraph, refs #24094
• src/hg/sqlUpdateRelated/makefile
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    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/sqlUpdateRelated.c
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    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
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    a2b75cac670b61deb2664261984bd24e1971242f Mon Sep 2 10:21:11 2019 -0700
    Adding relationship table updates to multi-multi handling.
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    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.doc
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    e59a222a6acfae7632d0de9f11cf72b787d890e7 Wed Sep 4 09:06:27 2019 -0700
    Adding a doc file to this new utility.
• src/hg/sqlUpdateRelated/tests/doTest.csh
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    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/expectedDb.sql
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    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/hcat_assaytype.tsv
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    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/hcat_contributor.tsv
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    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/hcat_disease.tsv
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    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/hcat_lab.tsv
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    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/hcat_organ.tsv
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    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/hcat_organpart.tsv
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    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/hcat_project.tsv
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    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/hcat_publication.tsv
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    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/inDb.sql
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    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/utils/otto/clinvar/clinVarToBed
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    9a26b7380a408f1ed968d72f1b3cff18f2a1e054 Mon Sep 9 02:41:20 2019 -0700
    fixing clinvar typo added in last commit and also a missing _mouseOver field (very strange problem, possibly have not committed this file for a long time?)
• src/hg/utils/otto/clinvar/clinvar.as
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    9a26b7380a408f1ed968d72f1b3cff18f2a1e054 Mon Sep 9 02:41:20 2019 -0700
    fixing clinvar typo added in last commit and also a missing _mouseOver field (very strange problem, possibly have not committed this file for a long time?)
• src/inc/fieldedTable.h
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    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.
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    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/lib/fieldedTable.c
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    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.
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    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/tabFile/tabToTabDir/tabToTabDir.c
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    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.
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    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/tests/input/inSpec.ra
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    7b47af799470692a85fc71777d65a36fe777ebf7 Tue Sep 3 05:25:29 2019 -0700
    fixing merge a conflict in HGStyle.css
• src/utils/qa/weeklybld/buildEnv.csh
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    1fc980dbe4d0907a809564f5d2d83c1e0835741c Mon Sep 9 10:07:24 2019 -0700
    v388 preview1, refs #24021

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• files changed: 206