Commits for kent

v314_preview to v314_preview2 (2015-03-16 to 2015-03-23) v314

• Removing cwwMakeWigSpotQa, since doesn't compile and can look at code in edwMakeWigSpotQa.
  
  • src/hg/cirm/cdw/cdwMakeWigSpotQa/cdwMakeWigSpotQa.c - lines changed 124, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwMakeWigSpotQa/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/makefile - lines changed 5, context: html, text, full: html, text
• Fixing it so touching .html file remakes .c as well as .h
  
  • src/hg/cirm/cdw/cdwWebBrowse/makefile - lines changed 3, context: html, text, full: html, text
• Adding a test case.
  
  • src/tagStorm/tagStormHoist/expected.out - lines changed 122, context: html, text, full: html, text
  • src/tagStorm/tagStormHoist/test.in - lines changed 146, context: html, text, full: html, text
• Adding info from cdwVcfFile to storm. Calculating amount of vcf that is explained by common snps by looking up common_snp in cdwEnrich.
  
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 45, context: html, text, full: html, text
• Making program not worry about a few new types.
  
  • src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c - lines changed 7, context: html, text, full: html, text
• Making it output a header line when out=tab. Rearranged sort so * is still alphabetical, but when fields are explicitly listed the listed order is kept. Things are only alphabetically ordered within a wildcard expansion of the field list.
  
  • src/hg/cirm/cdw/cdwQuery/cdwQuery.c - lines changed 14, context: html, text, full: html, text
• Adding chrom back in track table and bumping version.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 2, context: html, text, full: html, text
• Making utility to add a group.
  
  • src/hg/cirm/cdw/cdwCreateGroup/cdwCreateGroup.c - lines changed 46, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwCreateGroup/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 8, context: html, text, full: html, text
• Utility to add users to a group seems to work.
  
  • src/hg/cirm/cdw/cdwGroupUser/cdwGroupUser.c - lines changed 83, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwGroupUser/makefile - lines changed 4, context: html, text, full: html, text
• Utility to add group associations to files seems to work.
  
  • src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c - lines changed 110, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwGroupFile/makefile - lines changed 4, context: html, text, full: html, text
• Adding testing helper.
  
  • src/hg/cirm/cdw/cdwFreen/cdwFreen.c - lines changed 49, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwFreen/makefile - lines changed 4, context: html, text, full: html, text
• A little refactoring so can reuse login system for CIRM.
  
  • src/hg/inc/wikiLink.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/wikiLink.c - lines changed 31, context: html, text, full: html, text
• Doing little bit of resource freeing, but not to matter in the absense of a vcfRecordFree. This utility currently leaks memory. On the 1000 genomes data was up to using 400 Gig on chr1 before I killed it.
  
  • src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c - lines changed 1, context: html, text, full: html, text
• Saving a line of code by using a newr library routine.
  
  • src/hg/cirm/cdw/cdwQuery/cdwQuery.c - lines changed 2, context: html, text, full: html, text
• Simplifying command line so you just need the boolean part of the where clause.
  
  • src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c - lines changed 19, context: html, text, full: html, text
• Saving a couple of lines of code by using a library routine.
  
  • src/hg/cirm/cdw/cdwGroupUser/cdwGroupUser.c - lines changed 3, context: html, text, full: html, text
• Implementing first pass of file access control including login system (hgLogin) and user/group/all access controls, a system for managing groups for access, and overviews of access on the web display home page, and access controlling Genome Browser links elsewhere in the web display.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 28, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 94, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 208, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 22, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 26, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 470, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 31, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 61, context: html, text, full: html, text
• Making cdwQuickCheckAccess for quicker checking when doing more than one file. Breakeven point at a guess is about 5 files. It gets about 100x faster for thousands of files though.
  
  • src/hg/cirm/cdw/cdwFreen/cdwFreen.c - lines changed 29, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 17, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 85, context: html, text, full: html, text
• Utility to change access attributes of files matching a query seems to work.
  
  • src/hg/cirm/cdw/cdwChangeAccess/cdwChangeAccess.c - lines changed 143, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwChangeAccess/makefile - lines changed 4, context: html, text, full: html, text
• Adding routines to get list of all good cdwFiles, and also to limit tag storm to what a user can access.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 6, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 17, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 46, context: html, text, full: html, text
• Restricting files and tracks and tags browsing to files you have access to.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 76, context: html, text, full: html, text
• Adding remove option.
  
  • src/hg/cirm/cdw/cdwGroupFile/cdwGroupFile.c - lines changed 22, context: html, text, full: html, text
• Adding printWithGreekByte, just a wrapper around sprintWithGreekByte.
  
  • src/inc/obscure.h - lines changed 3, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 8, context: html, text, full: html, text
• Freen does reality speed check on loading all exons for a chrom into a rangeTree.
  
  • src/hg/oneShot/freen/freen.c - lines changed 23, context: html, text, full: html, text
• Adding 'shortVal' parameter to webTableOutputWrapperType. This is so can use the full value for constructing urls and the like, but display the short value in the table so as to keep it from getting too wide.
  
  • src/hg/inc/tablesTables.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 3, context: html, text, full: html, text
• Commenting out some statistics gathering that I feared was making things too slow. Making it free up memory from time to time.
  
  • src/hg/cirm/cdw/utils/cdwVcfStats/cdwVcfStats.c - lines changed 19, context: html, text, full: html, text
• Adding cdwAccessibleFileList function to get list of all accessible files for a users.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 36, context: html, text, full: html, text
• Exploring a little how to merge different meta.txt files.
  
  • src/hg/cirm/cdw/cdwFreen/cdwFreen.c - lines changed 86, context: html, text, full: html, text
• Adding remove option.
  
  • src/hg/cirm/cdw/cdwGroupUser/cdwGroupUser.c - lines changed 35, context: html, text, full: html, text
• Avoiding crash on null assembly for vcf.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 1, context: html, text, full: html, text
• Having it revalidate when metadata pointed to by metaId changes. Adding command line option to not revalidate. Removing unused 'believe' command line option.
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 21, context: html, text, full: html, text
• Restricting oneTag page to only showing info from accessible files. Changing home page total size reports to use GB, TB, PB rather than full number with many commas. Fixed bug when clicking on links on an item that was abbreviated to fit in a table.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 66, context: html, text, full: html, text
• No need for persona in cdw it looks like.
  
  • src/hg/js/cdwPersona.js - lines changed 45, context: html, text, full: html, text
• Starting to have suggest javascript going on in filter row
  
  • src/hg/lib/tablesTables.c - lines changed 34, context: html, text, full: html, text
• Exploring some suggest stuff in CIRM data warehouse.
  
  • src/hg/js/cdwSuggest.js - lines changed 85, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
• Making it just print out list of all fields.
  
  • src/hg/cirm/cdw/cdwFreen/cdwFreen.c - lines changed 81, context: html, text, full: html, text
• Working on two main features - printing a line of descriptive text about a tag in the doOneTag page, and experimenting with javascript autosuggest for filters.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 86, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h - lines changed 46, context: html, text, full: html, text
• Added doTest command.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 1, context: html, text, full: html, text
• Adding suggestHash to tables so they can do suggestions.
  
  • src/hg/inc/tablesTables.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 49, context: html, text, full: html, text
• Some tinkering, but generally looks like won't be using this module for long. Most of the logic has moved.
  
  • src/hg/js/cdwSuggest.js - lines changed 1, context: html, text, full: html, text
• Refactoring to expose cdwUserTagStormFromList function, which will help keep us from generating some expensive data structures twice.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 21, context: html, text, full: html, text
• Putting suggest onto the filters controls where appropriate. Tinkering with test page a little.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 114, context: html, text, full: html, text
• No longer useing cdwSuggest.js
  
  • src/hg/js/cdwSuggest.js - lines changed 86, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
• Librarifying accessForUser to become cdwAccessTreeForUser thinking it might get reused.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 5, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 19, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 19, context: html, text, full: html, text
• Speeding up code that generates suggestions a bunch by making it use cdwFileTags rather than making a tagStorm.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 91, context: html, text, full: html, text
• Adding skipTable option.
  
  • src/hg/makeDb/schema/dbSnoop/dbSnoop.c - lines changed 5, context: html, text, full: html, text
• Putting in but then ifdefing out some watermark code that looked nice, but left the word 'filter' printed all over the cart. Will try and fix soon. Wordsmithing one line of instructions a little.
  
  • src/hg/lib/tablesTables.c - lines changed 15, context: html, text, full: html, text
• Moving cartSaveSession() to inside of a form so that it actually does save the session ID.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 5, context: html, text, full: html, text
• Fixing browse files when there are accessible files, which I just had broken fixing browser files when there are no accessible files.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 16, context: html, text, full: html, text
• Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
  
  • src/hg/js/jquery.watermark.js - lines changed 625, context: html, text, full: html, text
• Adding a watermark (grayed out text to serve as mini-instructions in a text input control) from a jquery library that's better about not submitting the watermark than the older jquery.watermarkinput.gs.
  
  • src/hg/js/makefile - lines changed 1, context: html, text, full: html, text
• Trying another shot at watermarks on the filter row. Seems to work with new library.
  
  • src/hg/lib/tablesTables.c - lines changed 14, context: html, text, full: html, text
• Trying new watermark code on test page. Seems to work.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 10, context: html, text, full: html, text
• Making it work behind a firewall/VPN where there is effectively no domain.
  
  • src/hg/lib/cart.c - lines changed 7, context: html, text, full: html, text
• Making it deal with situations like under a VPN where the web address is not qualified with . anything, and effectively there is thus no domain to use for the cookies.
  
  • src/hg/hgLogin/hgLogin.c - lines changed 23, context: html, text, full: html, text
• Adding up or down arrow after a column we sort on.
  
  • src/hg/lib/omiciaUi.c - lines changed 55, context: html, text, full: html, text
  • src/hg/lib/oregannoOther.c - lines changed 591, context: html, text, full: html, text
  • src/hg/lib/tablesTables.c - lines changed 14, context: html, text, full: html, text
• Oops, did not mean to add these!
  
  • src/hg/lib/omiciaUi.c - lines changed 55, context: html, text, full: html, text
  • src/hg/lib/oregannoOther.c - lines changed 591, context: html, text, full: html, text
• Correcting age_unit to be singular the way t_unit is.
  
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 1, context: html, text, full: html, text
• Checking out some of the available graphics in the test page and bumping versino number.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 30, context: html, text, full: html, text
• Second pass at tag descriptions.
  
  • src/hg/cirm/cdw/cdwWebBrowse/tagDescriptions.h - lines changed 53, context: html, text, full: html, text
• Adding a pie chart maker that is pretty nice and depends on D3.
  
  • src/hg/js/d3pie.min.js - lines changed 9, context: html, text, full: html, text
• Swapping out list of graphic images in test for a pie experiment, and then integrating pie chart into main page.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 135, context: html, text, full: html, text
• Utility that creates full text index for cdwFileTags seems to work.
  
  • src/hg/cirm/cdw/cdwTextForIndex/cdwTextForIndex.c - lines changed 121, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwTextForIndex/makefile - lines changed 4, context: html, text, full: html, text
• Adding a stem cell photo.
  
  • src/hg/htdocs/images/stem-cell-talk-57210.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Making it print numerical fields right justified. Tweaking instructiona line a little.
  
  • src/hg/lib/tablesTables.c - lines changed 14, context: html, text, full: html, text
• Fixing a bug where was crashing if you weren't logged in.
  
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 4, context: html, text, full: html, text
• Making numerical ID rather than accession be used to in search results.
  
  • src/hg/cirm/cdw/cdwTextForIndex/cdwTextForIndex.c - lines changed 6, context: html, text, full: html, text
• cdwFreen prints out table description.
  
  • src/hg/cirm/cdw/cdwFreen/cdwFreen.c - lines changed 8, context: html, text, full: html, text
• Implementing trix search. Polishing pie charts on home page.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 73, context: html, text, full: html, text
• Making use of periods more consistent in descriptions.
  
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 8, context: html, text, full: html, text
• Making URL an actual link in doLabs page.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 14, context: html, text, full: html, text