All File Changes

v340_preview to v340_preview2 (2016-10-03 to 2016-10-10) v340

• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 11, context: html, text, full: html, text
    e24d100ca539e3d25bc5f06bed240c2f4de1ab7a Wed Oct 5 15:26:57 2016 -0700
    Adding in a new table for joint datasets, refs #17870
    
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    4e84edcbf2bd31c87f184b2c63c92ad8691638a7 Thu Oct 6 01:35:15 2016 -0700
    hgGateway needs early warn handlers. htmshell.c needs to also write error to stderr on early errors.
    
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
  • lines changed 1, context: html, text, full: html, text
    7503efba2f496789a0108e7dcfecb55b5b402bec Wed Oct 5 10:53:16 2016 -0700
    Correction per code review refs #18166
    
• src/hg/lib/annoFormatVep.c
  • lines changed 9, context: html, text, full: html, text
    4baafe0977277f8efefc24f9d2c864c76af51596 Fri Oct 7 11:51:12 2016 -0700
    dbNSFP v3.1a format changed slightly: comma-sep lists of the same code or same score were collapsed, so were no longer strictly parallel with other comma-sep lists.
    For example, "B,B,B" is now collapsed to "B". Accomodate that by returning the single value if we are looking for an item in a comma-sep list but it has no commas.
    There's still a pre-existing issue that sometimes multiple scores and codes are reported for the same aaPos (in different UniProt sequences), but we only report the
    first one that we encounter.
    refs #18199
    
• src/hg/lib/cart.c
  • lines changed 11, context: html, text, full: html, text
    c68d2c9b63b22488a6746004246a235c65a1dec9 Wed Oct 5 17:25:13 2016 -0700
    Fixes problem with crashing in hgTables, hgIntegrator and hgSession when bogus XSS hgsid is given. It had been generating an errAbort with the wrong handler such that the content-type never appeared in the output. also did minor removal of commented out code cleanup. refs #18163.
    
• src/hg/lib/hui.c
  • lines changed 45, context: html, text, full: html, text
    be3dc2f7f8a22768c79f2ec27dbea7fc78a2bd95 Thu Oct 6 14:14:13 2016 -0700
    first pass at supporting tagStorm in track hubs.
    
• src/hg/lib/mafGene.c
  • lines changed 3, context: html, text, full: html, text
    bd8427c06c3c63aa073850539abcb6ea284d43b5 Fri Oct 7 10:52:30 2016 -0700
    fix a problem in mafGene with translated 1bp exons.
    
• src/hg/lib/trackHub.c
  • lines changed 9, context: html, text, full: html, text
    be3dc2f7f8a22768c79f2ec27dbea7fc78a2bd95 Thu Oct 6 14:14:13 2016 -0700
    first pass at supporting tagStorm in track hubs.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    f84a60bd2562df48b0f53b7f8929c84812168ecf Mon Oct 3 16:05:51 2016 -0700
    Adding crispr tables to tablesIgnored for all dbs, refs #17235
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html
  • lines changed 1, context: html, text, full: html, text
    e72e20df096a06cccdadbc9d48d1a48ee972e2e8 Thu Oct 6 10:17:22 2016 -0700
    Fixup of green monkey gateway page, refs #11172
    
• src/hg/makeDb/trackDb/crispr.html
  • lines changed 47, context: html, text, full: html, text
    8c18a1c4534664581f19b1848ca0002ece416c02 Mon Oct 3 16:28:03 2016 -0700
    Reordering references for crispr tracks, refs #17325
    
  • lines changed 10, context: html, text, full: html, text
    3a6eeda3924568f11cc19e9ff005a4a85317af6b Tue Oct 4 10:22:16 2016 -0700
    Escaping some chars and some grammar fixes, refs #17235
    
  • lines changed 2, context: html, text, full: html, text
    438075e9742409d3fc96945c655563827f0f641d Tue Oct 4 10:33:10 2016 -0700
    Changes as per code review, refs #18169
    
  • lines changed 3, context: html, text, full: html, text
    dfd790b4a5b029fe47f80bce7a12d2fc45f93c68 Tue Oct 4 11:30:16 2016 -0700
    Fixing a few typos in crispr description page, refs #17235
    
• src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
  • lines changed 10, context: html, text, full: html, text
    3ac47e15a13d8106abd5c3cd0dc48f9e095cdc1d Tue Oct 4 15:06:56 2016 -0700
    Removing release tags from knownGene bigGenePred stuff, refs #15259
    
• src/hg/makeDb/trackDb/human/hg19/crispr.html
  • lines changed 47, context: html, text, full: html, text
    8c18a1c4534664581f19b1848ca0002ece416c02 Mon Oct 3 16:28:03 2016 -0700
    Reordering references for crispr tracks, refs #17325
    
  • lines changed 11, context: html, text, full: html, text
    3a6eeda3924568f11cc19e9ff005a4a85317af6b Tue Oct 4 10:22:16 2016 -0700
    Escaping some chars and some grammar fixes, refs #17235
    
  • lines changed 2, context: html, text, full: html, text
    438075e9742409d3fc96945c655563827f0f641d Tue Oct 4 10:33:10 2016 -0700
    Changes as per code review, refs #18169
    
  • lines changed 3, context: html, text, full: html, text
    dfd790b4a5b029fe47f80bce7a12d2fc45f93c68 Tue Oct 4 11:30:16 2016 -0700
    Fixing a few typos in crispr description page, refs #17235
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    3ac47e15a13d8106abd5c3cd0dc48f9e095cdc1d Tue Oct 4 15:06:56 2016 -0700
    Removing release tags from knownGene bigGenePred stuff, refs #15259
    
• src/hg/makeDb/trackDb/human/hg38/crispr.html
  • lines changed 12, context: html, text, full: html, text
    3a6eeda3924568f11cc19e9ff005a4a85317af6b Tue Oct 4 10:22:16 2016 -0700
    Escaping some chars and some grammar fixes, refs #17235
    
  • lines changed 2, context: html, text, full: html, text
    438075e9742409d3fc96945c655563827f0f641d Tue Oct 4 10:33:10 2016 -0700
    Changes as per code review, refs #18169
    
  • lines changed 3, context: html, text, full: html, text
    dfd790b4a5b029fe47f80bce7a12d2fc45f93c68 Tue Oct 4 11:30:16 2016 -0700
    Fixing a few typos in crispr description page, refs #17235
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 23, context: html, text, full: html, text
    3ac47e15a13d8106abd5c3cd0dc48f9e095cdc1d Tue Oct 4 15:06:56 2016 -0700
    Removing release tags from knownGene bigGenePred stuff, refs #15259
    
• src/hg/makeDb/trackDb/mouse/mm10/defaultPriority.ra
  • lines changed 7, context: html, text, full: html, text
    3ac47e15a13d8106abd5c3cd0dc48f9e095cdc1d Tue Oct 4 15:06:56 2016 -0700
    Removing release tags from knownGene bigGenePred stuff, refs #15259
    
• src/hg/makeDb/trackDb/mouse/mm9/defaultPriority.ra
  • lines changed 7, context: html, text, full: html, text
    3ac47e15a13d8106abd5c3cd0dc48f9e095cdc1d Tue Oct 4 15:06:56 2016 -0700
    Removing release tags from knownGene bigGenePred stuff, refs #15259
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7a460f30564abdace57c36f0c03ddb31533f62f1 Wed Oct 5 11:08:08 2016 -0700
    Removing release tag for crispr track, refs #17235
    
• src/hg/phyloPng/phyloPng.c
  • lines changed 3, context: html, text, full: html, text
    54394882d8acb424d954899ede629d6b9dd522e8 Wed Oct 5 16:54:11 2016 -0700
    removing comment.
    
• src/lib/cheapcgi.c
  • lines changed 8, context: html, text, full: html, text
    8ed54eda44eba3788b50aba97a70080dad274e90 Fri Oct 7 18:27:15 2016 -0700
    Added a useful comment about tricky textarea newlines.
    
• src/lib/htmshell.c
  • lines changed 21, context: html, text, full: html, text
    3de82ff7fd9de5151f140a8282713eaed47881c2 Sat Oct 1 11:57:01 2016 -0700
    Fixing bug with textarea. Because browser submits linefeeds as CRLF and even converts CR to CRLF, and we were converting LF to an html entity neglecting CR, we got a strange expansion of newlines (and pipe chars under ff) every time hgVai is submitted. It looks like old code that is safe to remove, so the html-entity encoding of LF in htmlEncode is gone. This is intended to simplify things. Refs#17782.
    
  • lines changed 1, context: html, text, full: html, text
    4080635571d545e38ec5d6d363bac9c5c9e8bd42 Mon Oct 3 14:46:49 2016 -0700
    Refs #17782. html encode title for some codepaths in htmshell.c.
    
  • lines changed 123, context: html, text, full: html, text
    89cacc8b69a80a7e2787aaf9082782a83352d789 Tue Oct 4 14:34:03 2016 -0700
    refs #18175. more elegant code for the hex decoder for attr css js url. Thanks Angie.
    
  • lines changed 7, context: html, text, full: html, text
    4e84edcbf2bd31c87f184b2c63c92ad8691638a7 Thu Oct 6 01:35:15 2016 -0700
    hgGateway needs early warn handlers. htmshell.c needs to also write error to stderr on early errors.
    
• src/lib/tagStorm.c
  • lines changed 5, context: html, text, full: html, text
    be3dc2f7f8a22768c79f2ec27dbea7fc78a2bd95 Thu Oct 6 14:14:13 2016 -0700
    first pass at supporting tagStorm in track hubs.
    
• src/lib/tests/testDecodedString.c
  • lines changed 5, context: html, text, full: html, text
    89cacc8b69a80a7e2787aaf9082782a83352d789 Tue Oct 4 14:34:03 2016 -0700
    refs #18175. more elegant code for the hex decoder for attr css js url. Thanks Angie.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    ebd34e37ddff51cf23ef6d01c92ede2f3e562906 Mon Oct 10 10:24:15 2016 -0700
    v340 preview2
    

• lines changed: 481
• files changed: 36