v345

Code changes:

• In order to prevent XSS javascript injection into genome browser web pages generated by our CGIs, Content Security Policy (CSP) has been implemented. Version 2 is supported by all browsers (except IE). This technique tells the browser what javascript was legitimately generated by us. Foreign javascript from hackers is not allowed to run (#18538). Galt.
• Allow arbitrary fields within bigBeds to be used as labels in hgTracks (#18782). Brian
• Changes and fixes for new static doc style rollout (#18504, #18621). Kate
• Improve hgTables: in output download file name, replace '/' with '_' (#18810). Angie
• GTEx hgc and hgGtexTrackSettings fixes. Kate
• Minor fixes related to new CSP support: Angie
  • cart.js: use window.hgsid after initialization, not during, so inline-at-end JS can set hgsid
  • add back globalNavBar.inc inline JS until v345 (CSP) has been released on RR
  • increase buffer size for new CSP JS string in hgSession
• Small bug fix hgGateway: use time-stamped JS links to avoid browser caching. Angie
• Small bug fix HGVS search: map c. upstream changes instead of showing whole transcript. Angie
• Small bug fix checkHgFindSpec: display searchPriority to help with reordering. Angie
• Ongoing work on blat results to custom track (#2811). Brian
• Fix bedToBigBed to write out zoom level information. Brian
• The doDbSnp.pl pipeline now knows how to handle contigs that dbSNP uses in the reverse orientation from an assembly (#16847). Jonathan
• doDbSnp.pl now creates a bigBed file of SNP positions for use by hgVai (#18239). Jonathan
• CIRM cdwFlowCharts.c - new code to support multiple analysis steps and have updated all the code to work with CSP enhancements (#17544). Chris
• CIRM cdwWebBrowse.c - Updated the analysis joint data page's code to run on the same logic as the browse data set page that Jim just re did (#17870). Chris
• CIRM maniMani - Incorporated feedback from the group, some new options and reworking of old options/usage statements (#16113). Chris

Data changes:

• Massive overhaul of static doc pages to use new style (#18504). Donna
• Rebuilt UCSC Gene Pfam on mm10 (#18742). Brian
• TransMap tracks work (#18818). Mark
• Initial release of chicken galGal5 SNP track, from dbSNP b147 (#16847). Jonathan
• Another all.joiner id-order change to support knownGene -> OMIM tables (#18586). Angie
• Adding photographs to htdocs/images/ in preparation for future browser builds refs (#18785). Hiram
• Added chain/net tracks to danRer10 mm10 xenTro7 tetNig2 fr3 oryLat2 gasAcu1 refs (#18809). Hiram