Commits for kate

v341_base to v342_preview (2016-11-07 to 2016-11-14) v342

280cec9d1154fc2613fcf127a988b5252c9fa824 Wed Sep 28 16:42:40 2016 -0700

• First cut CGI with body map illustration for tissue selection: GTEx track config. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 110, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 184, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 977, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 22, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text

cbbb309fcbc6b5a8709f42c8ace1280f1a2c3cd3 Tue Oct 4 14:08:18 2016 -0700

• Support JWest page design w/o banner. Per JK suggestion reviewing GTEx track settings page with body map. refs #17639
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 8, context: html, text, full: html, text
  • src/hg/inc/web.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 23, context: html, text, full: html, text

771b3b9d95995491d03e9d543609ac5e3e3f4bfd Thu Oct 6 12:30:33 2016 -0700

• Add UCSC logo to menu bar. Improve appearance (layout, margins). CSS/HTML cleanup to follow. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 166, context: html, text, full: html, text
  • src/hg/htdocs/style/makefile - lines changed 1, context: html, text, full: html, text

135c5c06f4aa65c8d660b621f682ef88559c5f59 Thu Oct 6 14:19:39 2016 -0700

• Improvements to visual layout of tissue table, using design from Jeff West (DRAFT03c_BodyMapBrowserPage.pdf). refs #17639
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 88, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 19, context: html, text, full: html, text

1b6890714b9e09a3cba18068f5e3b726484548b1 Thu Oct 6 16:03:13 2016 -0700

• Crop whitespace and remove cruft from illustration. Related layout tweaks. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 1331, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 10, context: html, text, full: html, text

89de213f460f60dcc7fcf7d6e0370401d7c3ed25 Thu Oct 6 16:37:33 2016 -0700

• More small layout tweaks. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 6, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 3, context: html, text, full: html, text

d702c482f45bd3f97716f555bdf11caef9491252 Fri Oct 7 10:06:28 2016 -0700

• Added ids and font list. refs #17369
  • src/hg/htdocs/images/bodyMap.svg - lines changed 116, context: html, text, full: html, text

38fe0330488867c168c817169bbf1c49806c5cfb Fri Oct 7 15:32:40 2016 -0700

• Move tissue table to code for flexibility/maintenance. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 54, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 88, context: html, text, full: html, text

ea41056f39eb940ef5ce1ad4e83512e2550bb647 Sat Oct 8 16:43:44 2016 -0700

• First steps to animage tissue selection panel that includes bodymap and table. Hover and click over tissue names and set all/clear all mostly working. Also some corrections to svg (missing colon sub-tissues, oddity in aorta id naming). refs 17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 21, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 135, context: html, text, full: html, text

a0901833881cdac3b2d194b91ccbfa484bac3df0 Sat Oct 8 17:12:14 2016 -0700

• Animate arteryAorta example mouseover ( leader line and white outline on hover ) . refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 35, context: html, text, full: html, text

03728506f98789fc4375911a2e3726f1c61d297d Sat Oct 8 22:44:12 2016 -0700

• Add hover and click handling to bodyMap. Rough cut code for usability review. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 58, context: html, text, full: html, text

def53e877b0ec5eaa779e540bd0568c10104688e Mon Oct 10 10:18:11 2016 -0700

• Remove search box. Would require significant work to implement and adds little value. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 2, context: html, text, full: html, text

16a124688058c010d943b185944e5ae795583b43 Mon Oct 10 13:27:06 2016 -0700

• Header change, suggested by Cath. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 1, context: html, text, full: html, text

1a8f6f1c1791b0d2b48bbea782cd7ee390159418 Mon Oct 10 18:23:09 2016 -0700

• More streamlining, for Cath's review. #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 22, context: html, text, full: html, text

3813a7e3eea7f27539bc67db740579af4b4806ac Mon Oct 10 18:48:01 2016 -0700

• Add sub-panel labels as per Cath suggestion. Early commit (not yet complete). refs #17639
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 4, context: html, text, full: html, text

453c5a463c5d2c1dcd85cf018c7c8912a48a28b8 Tue Oct 11 11:38:29 2016 -0700

• Layout tweaks, input from Cath. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 15, context: html, text, full: html, text

918bf07cb0a69e5a45192639b6d868cc056e494b Tue Oct 11 12:18:14 2016 -0700

• Layout with panel labels for body map and tissue table, as per Cath suggestion. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 9, context: html, text, full: html, text

a8eae0028b061e668072852bbc0fe2072f34229a Tue Oct 11 12:22:42 2016 -0700

• Layout with panel labels for body map and tissue table, as per Cath suggestion. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 12, context: html, text, full: html, text

fbccbe8c3660e3021e5e9d5e1418de0ab81766b4 Mon Oct 17 14:41:41 2016 -0700

• Another layout. Moves config into side panel. Preferred by Cath and Jeff W. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 54, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 31, context: html, text, full: html, text

624776f628c3257193e39187f02b5624d3b58b53 Mon Oct 17 16:36:51 2016 -0700

• Add track description. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 24, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 31, context: html, text, full: html, text

13b15ae7d313d66a036d1e291796178f9d79e888 Mon Oct 17 16:39:14 2016 -0700

• Change hg19 'badge' to look as on Gateway page. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 1, context: html, text, full: html, text

8658c9d49e2b66327b4bfcdb39cbf39c35cb8903 Mon Oct 17 18:33:55 2016 -0700

• Add navigation to track description and back to top. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 9, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 9, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 22, context: html, text, full: html, text

1707e42ef82fc3d38811178598bc3e0b31e0b794 Thu Oct 20 11:43:29 2016 -0700

• Draft 4 illustration export, with post-processing as in hgGtexTrackSettings/README.txt. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 56, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 2589, context: html, text, full: html, text

9da293adea7360f6521ce9e6d07317aa038d3c32 Thu Oct 20 11:44:22 2016 -0700

• Corrections to ID's (some mis-spellings, some missing ids). Jeff W notified so he can incorporate in his original. refs #17369
  • src/hg/htdocs/images/bodyMap.svg - lines changed 17, context: html, text, full: html, text

8ff13070d2da7a7b709da2bbb8c1043d99ecd8c9 Thu Oct 20 12:33:07 2016 -0700

• Style tweaks. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 5, context: html, text, full: html, text

bb14db8215e66c2848385af6442f6e76dcb13f9f Thu Oct 20 13:56:22 2016 -0700

• 1. Fix some identifier naming errors (notified Jeff). Tweaked fonts to match GB (revisit this later). refs #17369
  • src/hg/htdocs/images/bodyMap.svg - lines changed 11, context: html, text, full: html, text

f9cbf216c6f273ff4403779d1fe40c5605c5f7f4 Thu Oct 20 17:00:48 2016 -0700

• More SVG cleanup. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 3, context: html, text, full: html, text

a812abb853ad86bf636d934f1394c2473735cc6f Thu Oct 20 17:01:26 2016 -0700

• More SVG cleanup. refs #17369
  • src/hg/htdocs/images/bodyMap.svg - lines changed 4, context: html, text, full: html, text

e04944e2ed12d0ad5a722755bb9a7fd0f2a3ba2d Thu Oct 20 17:02:39 2016 -0700

• Click handling on individual tissues and set all/clear all now works with DRAFT 04. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 2, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 85, context: html, text, full: html, text

4830cdd0baa82503411b2c3e2828cd65b6704c73 Thu Oct 20 17:53:30 2016 -0700

• Mouseover to highlight tissues on DRAFT 04 bodyMap largely working. Some tissues aren't popping up properly and tissue table not yet connected up fully. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 24, context: html, text, full: html, text

ae9a65f97412a6522e2e3ff4c5884895375ca5f2 Fri Oct 21 11:14:00 2016 -0700

• Fixes to click handling. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 11, context: html, text, full: html, text

ced6299cd30cba4ed8cde8b4765bbf08147613f9 Fri Oct 21 11:24:22 2016 -0700

• Mouseover tissue table now highlights organs in bodymap. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 38, context: html, text, full: html, text

b05548d6d1608de50964509c1185497bf4192b97 Mon Oct 24 14:56:06 2016 -0700

• Add hover event handler to tissue shapes. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 13, context: html, text, full: html, text

4d1bafe4de39413f4ab1a9cd7183c64655b01e0a Mon Oct 24 14:59:31 2016 -0700

• Temporarily hardcode hg19 for review purposes. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 14, context: html, text, full: html, text

ead07b2aa201b1b7dbc812dd98ef155e1714f23c Tue Oct 25 14:19:32 2016 -0700

• Draft 05 from Jeff West, with corrections found during animation of Draft 04. Exported and post-processed as described in hgGtexTrackSettings/README.txt. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 413, context: html, text, full: html, text

359363b36f72d88528e47cb067935b61e964e23f Tue Oct 25 16:56:00 2016 -0700

• Correct id problems in draft 5. refs #17369
  • src/hg/htdocs/images/bodyMap.svg - lines changed 10, context: html, text, full: html, text

8a64798246e9ce75f8ce7c350096ef2f0c6532f6 Tue Oct 25 16:57:02 2016 -0700

• Improve mouseover viz. Draw tissue and highlight last so they pop to top. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 14, context: html, text, full: html, text

194a6dd93807d0100740f324e6a3fe5837847199 Tue Oct 25 16:57:20 2016 -0700

• Correct id problems in draft 5. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 4, context: html, text, full: html, text

b1b6338b01cffb734c6e1694f7120855d024c0fa Wed Oct 26 15:37:55 2016 -0700

• Display tweaks; 1. Leader lines visible always, highlighted on mouseover (JK request). Border highlights on tissue table color patches on mouseover. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 4, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 54, context: html, text, full: html, text

f380603812bf58efc0b6314f1a61b55416a758b0 Wed Oct 26 15:44:07 2016 -0700

• Fade out leader line color, as we are now keeping visible (not just on mouseover). refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 1, context: html, text, full: html, text

cfed2e78dcef652dc85360454f81d7558aa1b678 Thu Oct 27 18:05:04 2016 -0700

• Implement config panel cart vars. Moved from .html mockup to C code. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 288, context: html, text, full: html, text
  • src/hg/hgGtexTrackSettings/makefile - lines changed 9, context: html, text, full: html, text

5ab325050856f28fa3ed1a297afb5a22d49a51c7 Thu Oct 27 18:06:08 2016 -0700

• Fix extension to JWest-style shell. refs #17369
  • src/hg/lib/web.c - lines changed 1, context: html, text, full: html, text

578933212e6c900f4cda77f4d9cd1e7d01b9ace1 Thu Nov 3 16:09:25 2016 -0700

• Initialize tissues from cart. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/cart.h - lines changed 3, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 16, context: html, text, full: html, text

d4a2892366004d7f58c232ab93bd46c37bc95e0d Thu Nov 3 16:09:58 2016 -0700

• Tweak SVG processing. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 1, context: html, text, full: html, text

11db7ea49d8fb79b428a1add7e21ace39c7aac73 Thu Nov 3 16:46:29 2016 -0700

• Get score filter form cart. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 7, context: html, text, full: html, text

46cde8738a468e47a7d39a988dde632eb533aca2 Thu Nov 3 17:22:33 2016 -0700

• Hook new GTEx body map track settings in to browser, in place of hgTrackUi. refs #17369
  • src/hg/hgTracks/hgTracks.c - lines changed 5, context: html, text, full: html, text

9a3d804d4836f8508ed10a5372e3cc50c4c5ff64 Thu Nov 3 20:50:16 2016 -0700

• Finish connection to hgTracks; create form and submit button, and get tissues into cart. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 17, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 2, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 20, context: html, text, full: html, text

d84f0465b2a1fb8b2ac9cd20f5202a5c0c8ce637 Mon Nov 7 09:59:19 2016 -0800

• Adding GTEx body map track settings CGI. refs #17369
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text

ed22a783cddcbbf9ff41d2d939ee48ba5e5bd36f Mon Nov 7 10:04:38 2016 -0800

• Fix coord problem in experimental track. Thanks Angie for catching this. (But track is old (pilot) V4 so I will retire it in favor of a V6 version).
  • src/hg/makeDb/doc/gtex/V4.txt - lines changed 1, context: html, text, full: html, text

4275e302d217370b4eb756d45842f03e1ada9ae1 Tue Nov 8 11:50:38 2016 -0800

• Changes to colorPatch in tissue table to better distinguish selected tissues: switch to white patch with tissue color border. Also fix to problem with select/deselect of tissues from SVG. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 6, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 28, context: html, text, full: html, text

f3e281ea29cd25805890d53e0cdba63e4ab55f3c Tue Nov 8 16:29:58 2016 -0800

• First round code cleanup. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 54, context: html, text, full: html, text

ad2c455833e131ab3fcfb22889803e88f6cadb96 Wed Nov 9 17:03:34 2016 -0800

• Major JS code cleanup and refactor. Also fixed some event handling. refs #17369
  • src/hg/htdocs/style/hgGtexTrackSettings.css - lines changed 5, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 304, context: html, text, full: html, text

94ae7e1c166c598a2e7ea7659eff36efd332fbfe Wed Nov 9 17:09:23 2016 -0800

• Prune long lines. refs #17369
  • src/hg/js/hgGtexTrackSettings.js - lines changed 6, context: html, text, full: html, text

1888f6dd81f220f2ccd0e49c9b8a9a817ae0618c Thu Nov 10 15:59:18 2016 -0800

• Cleanup C code. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 393, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 82, context: html, text, full: html, text
  • src/hg/lib/jWestBanner.html - lines changed 19, context: html, text, full: html, text
  • src/hg/lib/jWestHeader.html - lines changed 18, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 1, context: html, text, full: html, text

66e096cba6f2b2da5feaf6fd270f74da61ab64b6 Thu Nov 10 16:17:17 2016 -0800

• Add hg.conf setting to enable new GTEx trackUI. For removal when new CGI is fully released. refs #17369
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text

190ba8082f1e7f99ab7ee3038b1b2eefb5791357 Thu Nov 10 17:26:32 2016 -0800

• Resolving merge conflicts
  • src/hg/makefile - lines changed 2, context: html, text, full: html, text

6f2a90bd53461985041dae109cf5b7921dd520bc Thu Nov 10 17:30:29 2016 -0800

• Resolving merge conflict

4282fb2d1cb60a12f8b70a9c9524d92828a485df Sat Nov 12 17:23:24 2016 -0800

• Fix truncated label by widening viewport. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 1, context: html, text, full: html, text

78d777539cda826871e6b60e9287536f9f5879f1 Sat Nov 12 20:05:15 2016 -0800

• Tweak layout of track controls. refs #17369
  • src/hg/lib/gtexUi.c - lines changed 3, context: html, text, full: html, text

c83b730a18186bcddc4fe008a48317ac577d9bde Sat Nov 12 20:17:41 2016 -0800

• Fix twitchy highlights. refs #17369
  • src/hg/hgGtexTrackSettings/README.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/images/bodyMap.svg - lines changed 6, context: html, text, full: html, text
  • src/hg/js/hgGtexTrackSettings.js - lines changed 69, context: html, text, full: html, text

58f75643f74cae771b15e359a322a4bb93933f60 Sat Nov 12 20:18:10 2016 -0800

• Fix double label. refs #17369
  • src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c - lines changed 2, context: html, text, full: html, text