Commits for chmalee

v450_preview to v450_preview2 (2023-06-12 to 2023-06-20) v450

e17ab1abdfd35d012ce831f46c24e972d52517db Thu Feb 16 16:20:49 2023 -0800

• Strip hub_id when making api requests for hub tracks/genomes, refs #30024
  • src/hg/js/hgTracks.js - lines changed 3, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 20, context: html, text, full: html, text

a18f2d0e8a33b79825dfb45c0761d8c4193daf8c Thu Feb 16 16:27:26 2023 -0800

• Merge branch 'master' into chmalee_hgTracksTutorial

13a71608b50408e504d9c0e88526264e43e4be20 Fri Feb 17 12:28:47 2023 -0800

• Proof of concept tutorial overlay done
  • src/hg/hgTracks/hgTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/htmshell.c - lines changed 2, context: html, text, full: html, text

70b8a142600a4211810d41aa258b43cb2cea9e8c Thu Mar 2 11:22:03 2023 -0800

• Add file that controls the tutorial, refs #30670
  • src/hg/js/tutorial.js - lines changed 69, context: html, text, full: html, text

b2970a8f4cde332dbf5be4635245c99954bd0f58 Thu Mar 2 11:27:20 2023 -0800

• Merge branch 'master' into chmalee_hgTracksTutorial

eb8483343ae0c285f9b74f7ebbc96d2abcb9816c Thu Mar 23 11:46:25 2023 -0700

• Merge branch 'master' into chmalee_hgTracksTutorial
  • src/hg/js/hgTracks.js - lines changed 15, context: html, text, full: html, text

8f399a09d7b39a87eadc3cc0a89c33598ddc5d2a Wed Apr 5 11:16:22 2023 -0700

• First attempt at surfacing up hub errors when the requested hub database doesn't exist, refs #30832
  • src/hg/lib/hubConnect.c - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 6, context: html, text, full: html, text

7ea5ed7d0c917304cdf903d3acdc12d937e1d7cb Fri May 19 10:36:46 2023 -0700

• Merge branch 'master' into chmalee_hgTracksTutorial
  • src/hg/js/hgTracks.js - lines changed 44, context: html, text, full: html, text

cda1904f5a784ef6a94ee2ad8cfbcc3c0d0d4bef Fri May 19 11:23:11 2023 -0700

• Temporary commit generalizing the notification box
  • src/hg/js/hgTracks.js - lines changed 22, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 39, context: html, text, full: html, text

752ca37b9f0031e59abc0dedef4752b7eb890946 Fri May 19 12:11:41 2023 -0700

• Generalize the notification box setups so we can have multiple of them. Starting on getting the tutorial to show up conditionally
  • src/hg/htdocs/style/HGStyle.css - lines changed 1, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 11, context: html, text, full: html, text
  • src/hg/js/utils.js - lines changed 11, context: html, text, full: html, text

edb9731b4634655aba9aae9707a6aa8c9a1457cb Fri May 19 16:31:53 2023 -0700

• Don't show tutorial until a link is clicked, hide/show tutorial correctly. TODO: when tutorial is finished set the localStorage correctly
  • src/hg/js/hgTracks.js - lines changed 7, context: html, text, full: html, text

f77196f3a66db3bb1bce1913a2e7d6223db94c0b Mon May 22 15:58:42 2023 -0700

• Make tutorial login dependent, add a link to view the tutorial under Help
  • src/hg/hgTracks/hgTracks.c - lines changed 6, context: html, text, full: html, text
  • src/hg/js/hgTracks.js - lines changed 14, context: html, text, full: html, text
  • src/hg/js/tutorial.js - lines changed 1, context: html, text, full: html, text

6c13a4db99ad6efef393ab837b3cbefacde6bd14 Mon May 22 16:02:29 2023 -0700

• Fix truthiness syntax after checking localStorage
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text

966a8c19f18ac15df06580c18bb7515c6af258fd Tue Jun 13 12:23:26 2023 -0700

• Fixing merge conflict
  • src/hg/lib/trackHub.c - lines changed 7, context: html, text, full: html, text

13d78f3b0149c4d9216fb78f28fbd9f91c088237 Tue Jun 13 15:50:10 2023 -0700

• Remove sample level high repro region beds and replace with a single overlapped item bed, refs #31122
  • src/hg/makeDb/doc/hg38/problematic.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/problematic.ra - lines changed 63, context: html, text, full: html, text

3765ac407abd18d240ad41ee087e39fd5ef3d3d4 Tue Jun 13 16:36:29 2023 -0700

• Add a description of the highly reproducible regions tracks to the problematic regions track, get release tags working so description doesn't go out until the track is ready, refs #31122
  • src/hg/makeDb/trackDb/human/hg38/problematic.alpha.ra - lines changed 143, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/problematic.ra - lines changed 102, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/problematicDev.html - lines changed 142, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

f697b7634598c60ac8ccef17e988867512d1d94a Wed Jun 14 09:47:16 2023 -0700

• Change test hub genome to a real one so as not to bring up spurious errors, refs build email
  • src/hg/utils/hubCheck/tests/input/badType.txt - lines changed 1, context: html, text, full: html, text

78aafe96d19a48bef4bb7e4a1fc7401eb65a7daa Wed Jun 14 10:11:53 2023 -0700

• Fix merge conflict
  • src/hg/js/hgTracks.js - lines changed 53, context: html, text, full: html, text
  • src/lib/htmshell.c - lines changed 3, context: html, text, full: html, text

f929ce1c8f6ee0325d755d63920d3fe60cce6bbc Wed Jun 14 10:15:37 2023 -0700

• Merge branch 'chmalee_hgTracksTutorial' of hgwdev.gi.ucsc.edu:/data/git/kent into chmalee_hgTracksTutorial

007a55145057933e9253a401d91b2a51bb3e0750 Wed Jun 14 11:11:46 2023 -0700

• Merge branch 'chmalee_hgTracksTutorial'

2bdb4c4bf6c6b3525de22edaf18815061acd800b Wed Jun 14 13:43:45 2023 -0700

• Change highRepro bed track to a bigBed 9 so filters can work, refs #31122
  • src/hg/makeDb/doc/hg38/problematic.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/problematic.alpha.ra - lines changed 4, context: html, text, full: html, text

a415b46e764f69b880f0cb1220964c92c76e4914 Thu Jun 15 11:00:04 2023 -0700

• Don't show notification box on configure page of hgTracks, no refs
  • src/hg/js/utils.js - lines changed 2, context: html, text, full: html, text

661ec62ccfe5864b48b9dbfd5e9f720a60e7c45e Thu Jun 15 11:06:30 2023 -0700

• Fix missing braces typo when deciding whether to include the hg.conf controlled tutorial on hgTracks, no refs
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text