Commits for kent

v312_base to v313_preview (2015-02-16 to 2015-02-23) v313

• Refactoring web.c code so as to have my own menubar. Will hopefully get rid of the nested tables bit soon too.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 60, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 581, context: html, text, full: html, text
• Got rid of some old Drupal stuff. Everything I need still seems to work.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 6, context: html, text, full: html, text
• Moving to strict rather than loose transitional HTML 4.01 in DOCTYPE.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 12, context: html, text, full: html, text
• Refactored part of menuBar function into menuBarAddUiVars for reuse with another menu bar.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 6, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 12, 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 54, context: html, text, full: html, text
• Repositioning menuBar output so that page closes. Breaking page into parts that you see when you select various menu items.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 110, context: html, text, full: html, text
• Replacing localMenuBar() with library routine recently refactored in web.c.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 65, context: html, text, full: html, text
• Refactored a few routines out of the webStartInternal demon for reuse in cdwWebBrowse.
  
  • src/hg/inc/web.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 70, context: html, text, full: html, text
• Making it work with latest cdw tags spec better.
  
  • src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c - lines changed 5, context: html, text, full: html, text
• Ifdeffing out some unused stuff.
  
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 4, context: html, text, full: html, text
• Reducing delay before menu drops down.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 25, context: html, text, full: html, text
• Replacing a lot of duplicated code with calls to stuff factored out of existing libraries. SImplifying in general.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 100, context: html, text, full: html, text
• Adding the menubar html file to makefile. I need to consult with Hiram though, as the .c file needs to get recompiled when the menubar html file is touched and currently it doesn't.
  
  • src/hg/cirm/cdw/cdwWebBrowse/makefile - lines changed 5, context: html, text, full: html, text
• Adding implementation for Browse/Files. Adding lab count to home page.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 92, context: html, text, full: html, text
• Updating comment.
  
  • src/inc/tagStorm.h - lines changed 1, context: html, text, full: html, text
• Making validator look to cdwMetaTags.tags as well as just tags.
  
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 23, context: html, text, full: html, text
• Providing parent tags from cdwMetaTags.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 12, context: html, text, full: html, text
• Putting back most of the delay in hopes of reducing a flickering menu bug.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 1, context: html, text, full: html, text
• Adding initial implementation for browsing labs, data sets, and formats. Moving tables from ascii edge to web 1.0.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 60, context: html, text, full: html, text
• Fixing bug in inequalities.
  
  • src/lib/rqlParse.c - lines changed 4, context: html, text, full: html, text
• Adding cdwLab table.
  
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 70, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 10, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 170, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 12, context: html, text, full: html, text
• Rearranging menus.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 6, context: html, text, full: html, text
• Rearranging menus, making summary part of home page. Deleting some old code.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 355, context: html, text, full: html, text
• Adding routine for sorting elements from a hashInt type hash.
  
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 9, context: html, text, full: html, text
• Adding a helper function to parse from a string as opposed to a file.
  
  • src/inc/rql.h - lines changed 3, context: html, text, full: html, text
  • src/lib/rqlParse.c - lines changed 9, context: html, text, full: html, text
• Updating some old tagTree names to be tagStorm. Adding tagStormCountTagVals function that summarizes values of a given tag in storm.
  
  • src/inc/tagStorm.h - lines changed 8, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 32, context: html, text, full: html, text
• Allowing files without metadata past their own tags into cdwTagStorm.
  
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 5, context: html, text, full: html, text
• tagStanzasMatchingQuery function moved to cdwLib from cdwWebBrowse
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 15, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 59, context: html, text, full: html, text
• Updating tagTree names to tagStorm names
  
  • src/hg/cirm/cdw/cdwQuery/cdwQuery.c - lines changed 1, context: html, text, full: html, text
• Moving a bunch of code to cdwLib.c, tagStorm.c and even hash.c. Updating version string. Updating help.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 137, context: html, text, full: html, text
• Moving limit to separate part of query page
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 17, context: html, text, full: html, text
• Making a better browseFormats page.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 38, context: html, text, full: html, text
• Separating out RQL statement, enforcing it always select from files. The field selector and the where selector are in separate CGI variables.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 25, context: html, text, full: html, text
• Utility to make a cdwFileTags table that is a real but sparse mysql table out of all the tags.
  
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 135, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwMakeFileTags/makefile - lines changed 4, context: html, text, full: html, text
• Switching browseFiles page to using cdwFileTags table rather than building tagStorm.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 99, context: html, text, full: html, text
• Making it so you can change sort by clicking on label names in browse files
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 31, context: html, text, full: html, text
• Refactoring so that use fieldedTable rather than a list of tagStanzas as intermediate part of browse file table redering.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 185, context: html, text, full: html, text
• Making browse labs use the showFieldedTable code.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 109, context: html, text, full: html, text
• Moving tagListIncludingParents to library.
  
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 24, context: html, text, full: html, text
  • src/inc/tagStorm.h - lines changed 3, context: html, text, full: html, text
  • src/lib/tagStorm.c - lines changed 23, context: html, text, full: html, text
• Adding routine to fetch list of formats and their descriptions.
  
  • src/hg/cirm/cdw/inc/cdwValid.h - lines changed 4, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 44, context: html, text, full: html, text
  • src/hg/inc/web.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 23, context: html, text, full: html, text
• Making doBrowseFormat use new sortable tables.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 31, context: html, text, full: html, text
• Making browse tags and the home page use the sortable tables. Making the sortable tables work as expected on numeric fields.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 99, context: html, text, full: html, text
• Polishing help text and selected fields.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 26, context: html, text, full: html, text
• These cirm style sheets are no longer used.
  
  • src/hg/htdocs/style/cirm.css - lines changed 8194, context: html, text, full: html, text
  • src/hg/htdocs/style/cirmUcsc.css - lines changed 58, context: html, text, full: html, text
• Utility to help transport versioned .css and .js to cirm-01.
  
  • src/hg/oneShot/getVersionedCssJs/getVersionedCssJs.c - lines changed 73, context: html, text, full: html, text
  • src/hg/oneShot/getVersionedCssJs/makefile - lines changed 3, context: html, text, full: html, text
• Sanitizing a supposivedly numerical value before sticking it into a SQL query. Removing lab_quake_markers from default display.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 12, context: html, text, full: html, text
• Making it so that you can browse all tags for a file, or all values for a tag.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 157, context: html, text, full: html, text
• Adding a free form filter line to file browse (not sure it's a good idea, it's a where clause from SQL. Also making various tags value listers use it to make link to file browseron just files that match given tag value.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 29, context: html, text, full: html, text
• Moving sql where-clause sanity checking to library for reuse in CIRM routines.
  
  • src/hg/hgTables/filterFields.c - lines changed 136, context: html, text, full: html, text
  • src/hg/inc/sqlSanity.h - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/sqlSanity.c - lines changed 149, context: html, text, full: html, text
• Putting in a sanity check on filter. Bumping version.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 5, context: html, text, full: html, text
• Adding paging to browse file
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 87, context: html, text, full: html, text
• MOving paging to under table. Removing free form query.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 51, context: html, text, full: html, text
• Removed some unimportant links from home page. Bumped version number.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 4, context: html, text, full: html, text
• Making it make purely numeric columns stay that way.
  
  • src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c - lines changed 94, context: html, text, full: html, text
• Making this a fraction less hostile on the command line.
  
  • src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c - lines changed 5, context: html, text, full: html, text
• First cut of browseTracks command, will launch browser with a custom track. Label needs improvement.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 136, context: html, text, full: html, text
• Utility to link bam and vcf index files to appropriate location.
  
  • src/hg/cirm/cdw/fix/cdwFixInvisibleIndexFiles/cdwFixInvisibleIndexFiles.c - lines changed 76, context: html, text, full: html, text
• Little fix applied.
  
  • src/hg/cirm/cdw/fix/cdwFix5/cdwFix5.c - lines changed 65, context: html, text, full: html, text
  • src/hg/cirm/cdw/fix/cdwFix5/makefile - lines changed 4, context: html, text, full: html, text
• Adding isNumericString function.
  
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text
  • src/lib/common.c - lines changed 8, context: html, text, full: html, text
• Fixed transposed words in symbol in comment.
  
  • src/inc/tagStorm.h - lines changed 1, context: html, text, full: html, text
• Adding cdwTrackViz table to support browseTracks in cdwWebBrowse.
  
  • src/hg/cirm/cdw/inc/cdw.h - lines changed 72, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.as - lines changed 12, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.c - lines changed 175, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdw.sql - lines changed 13, context: html, text, full: html, text
• Starting to build up a track table as well as the file table.
  
  • src/hg/cirm/cdw/cdwMakeTrackViz/cdwMakeTrackViz.c - lines changed 290, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwMakeTrackViz/makefile - lines changed 4, context: html, text, full: html, text
• Adding file_id to storm. Also for some reason changing ef var to cf.
  
  • src/hg/cirm/cdw/lib/cdwTagStorm.c - lines changed 16, context: html, text, full: html, text
• Adding bam index validation.
  
  • src/hg/cirm/cdw/inc/cdwValid.h - lines changed 3, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 7, context: html, text, full: html, text
• Adding cdwValidFileFromLicensePlate and cdwFindInSameSubmitDir functinos.
  
  • src/hg/cirm/cdw/inc/cdwLib.h - lines changed 9, context: html, text, full: html, text
  • src/hg/cirm/cdw/lib/cdwLib.c - lines changed 24, context: html, text, full: html, text
• Adding -format option to control output of cdwQuery. Now can get tab or tags output as well as the original ra.
  
  • src/hg/cirm/cdw/cdwQuery/cdwQuery.c - lines changed 63, context: html, text, full: html, text
• Permitting bam.bai and vcf.gz.tbi as formats. Getting rid of old unused
  code. Putting in a prefetch check that will catch ungzipped fastqs.
  + "bam.bai", "vcf.gz.tbi",
  
  • src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c - lines changed 127, context: html, text, full: html, text
• Starting to process bam.bai and vcf.gz.tbi indexes.
  
  • src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c - lines changed 32, context: html, text, full: html, text
• Second cut of browseTracks command. Handes VCF this time. Labels are improved but could still be better.
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 38, context: html, text, full: html, text
• Adding browseTracks command
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwNavBar.html - lines changed 2, context: html, text, full: html, text
• Bumping version (up to 20 since will distribute)
  
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text
• Removing cirm css dependencies.
  
  • src/hg/htdocs/style/makefile - lines changed 1, context: html, text, full: html, text