Commits for galt

v339_preview2 to v339_base (2016-09-19 to 2016-09-26) v339

850b7d8ce4c1b5f779a7eaddd51ae3da9122d6a4 Mon Sep 19 13:37:32 2016 -0700

• adding missing detail in webBlat.cfg example
  
  • src/hg/htdocs/goldenPath/help/blatSpec.html - lines changed 2, context: html, text, full: html, text

e771ca271fbf50808a1496fe610fbd6cb4342d2e Mon Sep 19 13:51:58 2016 -0700

• updated webBlat, made it more consistent.
  
  • src/hg/htdocs/goldenPath/help/blatSpec.html - lines changed 11, context: html, text, full: html, text

4f059beb788c0f7685ae2c95958d45e649f2f805 Mon Sep 19 14:10:25 2016 -0700

• updating webBlat docs and making consistent
  
  • src/webBlat/install.txt - lines changed 9, context: html, text, full: html, text
  • src/webBlat/webBlat.cfg - lines changed 4, context: html, text, full: html, text

285c2491df2e77edf845a763afb008a3a733220f Mon Sep 19 16:52:41 2016 -0700

• fixing XSS problem in VisiGene search box
  
  • src/hg/visiGene/hgVisiGene/hgVisiGene.c - lines changed 1, context: html, text, full: html, text

d00bfa06dc2a084d1915779c2175a4d8bff0c879 Mon Sep 19 16:56:07 2016 -0700

• fixing XSS problem in phyloGif
  
  • src/hg/phyloGif/phyloGif.c - lines changed 2, context: html, text, full: html, text

6894b3e9c5590a37147afd1485f21f07285c7ed1 Mon Sep 19 17:10:21 2016 -0700

• Renamed phyloGif to phloPng for greater accuracy in the name. Because when we switched to PNG, only 16-bit color palettes are supported now. We lost the ability to do 8-bit color palette which is needed by GIF.
  
  • src/hg/phyloGif/17way.nh - lines changed 13, context: html, text, full: html, text
  • src/hg/phyloGif/makefile - lines changed 33, context: html, text, full: html, text
  • src/hg/phyloGif/phyloGif.c - lines changed 770, context: html, text, full: html, text
  • src/hg/phyloPng/17way.nh - lines changed 13, context: html, text, full: html, text
  • src/hg/phyloPng/makefile - lines changed 33, context: html, text, full: html, text
  • src/hg/phyloPng/phyloPng.c - lines changed 770, context: html, text, full: html, text

23006734e4b7badfcdce018f6af09e68c6bb8026 Mon Sep 19 17:23:43 2016 -0700

• Renamed phyloGif to phloPng. Fixes #18104.
  
  • src/hg/htdocs/util.html - lines changed 2, context: html, text, full: html, text

aa2868d81e0ceb67d971112ee42118e298c3ee08 Mon Sep 19 17:35:48 2016 -0700

• Renamed phyloGif to phloPng. Refs #18104.
  
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/makePushQSql.pl - lines changed 1, context: html, text, full: html, text
  • src/utils/bdfToGem/menlo/README - lines changed 1, context: html, text, full: html, text

86516ebc28dc4b6c7c96067e66469308880d7502 Wed Sep 21 12:55:16 2016 -0700

• Fixes XSS problem found in hgVisiGene. refs #17782.
  
  • src/lib/cheapcgi.c - lines changed 4, context: html, text, full: html, text

4f1aaa591d14ef02e785e2ae05f86c49129104af Wed Sep 21 14:27:01 2016 -0700

• fix XSS textarea in hgBlat. refs #17782.
  
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text

324f433e00cd05daeba5403195601ba0a03cdbeb Wed Sep 21 16:56:46 2016 -0700

• Fixes oops and adds comment about unfinished XSS issues for javascript parameters. refs #17782.
  
  • src/lib/cheapcgi.c - lines changed 3, context: html, text, full: html, text

42241b695b4f77908324071a230104d5d506e916 Fri Sep 23 11:07:28 2016 -0700

• renamed phyloGif to phyloPng. refs #18104.
  
  • src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat4/cons6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/cons8way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/cons5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/cons5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/multiz10way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/multiz17way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/multiz7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/cons44way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/multiz28way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/multizPrimate.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/cons100way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/cons46way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons100way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons17way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons20way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/cons60way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/cons30way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/multiz9way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn5/cons13way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/cons9way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce11/cons26way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/multiz6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce9/cons10way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html - lines changed 1, context: html, text, full: html, text

165031e4604f8cd4905100753c686a3e66d1ff91 Fri Sep 23 11:29:16 2016 -0700

• rename phyloGif to phyloPng
  
  • src/hg/phyloPng/makefile - lines changed 2, context: html, text, full: html, text