File Changes for kent

v312_preview2 to v312_base (2015-02-09 to 2015-02-16) v312

• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
  • lines changed 51, context: html, text, full: html, text
    Putting in validators for cram, jpg, text, and html files.
    
• src/hg/cirm/cdw/cdwQuery/cdwQuery.c
  • lines changed 32, context: html, text, full: html, text
    Expanding wildcards in field list, so allowing select *. Also implementing count(*) function.
    
  • lines changed 125, context: html, text, full: html, text
    Reworking to get metadata tags from cdwMetaTags table rather than tagStorm file.
    
  • lines changed 92, context: html, text, full: html, text
    Moving tagStormFromDatabase into cdwTabStorm library function. Making count(*) queries work.
    
  • lines changed 1, context: html, text, full: html, text
    Sorting field list.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Fixing cdwFileName for manifest.txt and meta.txt files.
    
  • lines changed 34, context: html, text, full: html, text
    Adding support for cram, jpg, html, and text files. Checking all tags are defined in meta.txt.
    
  • lines changed 94, context: html, text, full: html, text
    Saving metadata tags in cdwMetaTags table.
    
  • lines changed 20, context: html, text, full: html, text
    Updating metadata on old files during resubmissions.
    
• src/hg/cirm/cdw/cdwSwapInSymLink/cdwSwapInSymLink.c
  • lines changed 68, context: html, text, full: html, text
    Utility to swap symlinks into warehouse for submitted files seems to work mostly.
    
• src/hg/cirm/cdw/cdwSwapInSymLink/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to swap symlinks into warehouse for submitted files seems to work mostly.
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 2, context: html, text, full: html, text
    Just changing some text visible to user to be more consistent.
    
  • lines changed 199, context: html, text, full: html, text
    Reworking away from a submission oriented view to an executive summary. Also letting you query with RQL.
    
• src/hg/cirm/cdw/fix/cdwFixCdwFileNamePath/cdwFixCdwFileNamePath.c
  • lines changed 55, context: html, text, full: html, text
    Fixing cdwFileName.
    
• src/hg/cirm/cdw/fix/cdwFixCdwFileNamePath/makefile
  • lines changed 4, context: html, text, full: html, text
    Fixing cdwFileName.
    
• src/hg/cirm/cdw/fix/cdwFixUpdateTime/cdwFixUpdateTime.c
  • lines changed 62, context: html, text, full: html, text
    Fix utility to restore update times seems to work.
    
• src/hg/cirm/cdw/fix/cdwFixUpdateTime/makefile
  • lines changed 4, context: html, text, full: html, text
    Fix utility to restore update times seems to work.
    
• src/hg/cirm/cdw/inc/cdw.h
  • lines changed 71, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 7, context: html, text, full: html, text
    Moving cdwTagStorm to library and polishing it a little.
    
• src/hg/cirm/cdw/inc/cdwValid.h
  • lines changed 18, context: html, text, full: html, text
    Implementing file recognizers for jpg and cram files. Restricting tags to just ones that are documented.
    
• src/hg/cirm/cdw/lib/cdw.as
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
    
  • lines changed 9, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdw.c
  • lines changed 169, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdw.sql
  • lines changed 12, context: html, text, full: html, text
    Adding cdwMetaTags table, and a field that refers to it in cdwFile.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 2, context: html, text, full: html, text
    Fixing a part/file_part mixup, and ''/NULL mixup.
    
  • lines changed 136, context: html, text, full: html, text
    Moving cdwTagStorm to library and polishing it a little.
    
  • lines changed 140, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
• src/hg/cirm/cdw/lib/cdwTagStorm.c
  • lines changed 234, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
  • lines changed 30, context: html, text, full: html, text
    Adding map_to_ribosome and map_to_repeat tags.
    
  • lines changed 36, context: html, text, full: html, text
    Adding map_to_ contaminant tags.
    
  • lines changed 44, context: html, text, full: html, text
    Adding info from cdwBamFile
    
• src/hg/cirm/cdw/lib/cdwValid.c
  • lines changed 97, context: html, text, full: html, text
    Implementing file recognizers for jpg and cram files. Restricting tags to just ones that are documented.
    
  • lines changed 3, context: html, text, full: html, text
    Adding seq_sample, data_set_id, and keywords to acceptable tags.
    
• src/hg/cirm/cdw/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Moving cdwTagStorm function to it's own file and expanding it to include additional tags.
    
• src/hg/cirm/quakeLab/quakeFakeMouseManifest/quakeFakeMouseManifest.c
  • lines changed 21, context: html, text, full: html, text
    Coming up with a unique identifier for the sample-level data. Changing tag names to fit documentation where they differed.
    
  • lines changed 9, context: html, text, full: html, text
    Adjusting metadata to new cdw way.
    
• src/hg/htdocs/style/cirm.css
  • lines changed 8194, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/htdocs/style/cirmUcsc.css
  • lines changed 58, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding cirm css initially as a clone of encode3.css. Hmm. So huge!
    
• src/hg/js/cdwPersona.js
  • lines changed 45, context: html, text, full: html, text
    Making the little authentication by persona stuff work for cdw web works.
    
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Making the little authentication by persona stuff work for cdw web works.
    
• src/hg/oneShot/freen/freen.c
  • lines changed 46, context: html, text, full: html, text
    Freen tests cgiParseNext.
    
• src/inc/cheapcgi.h
  • lines changed 13, context: html, text, full: html, text
    Adding cgiEncodeHash and cgiParseNext functions.
    
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added wildExpandList() function.
    
• src/inc/fieldedTable.h
  • lines changed 6, context: html, text, full: html, text
    Added functions to index a field.
    
• src/inc/ra.h
  • lines changed 1, context: html, text, full: html, text
    Adding missing part to the 'only include me once' bracketing of this include file.
    
• src/inc/rql.h
  • lines changed 1, context: html, text, full: html, text
    Switching rql's integral type from int to long long since it's dealing some with file sizes that overflow 32 bits.
    
• src/inc/tagStorm.h
  • lines changed 19, context: html, text, full: html, text
    Adding functions to get all fields mentioned in a tagStorm.
    
  • lines changed 1, context: html, text, full: html, text
    Changed tagStormNew's parameter name from fileName to more generic name, since they are built in memory sometimes too.
    
  • lines changed 8, context: html, text, full: html, text
    Adding function for adding long long integer or double values to storm.
    
• src/lib/cheapcgi.c
  • lines changed 56, context: html, text, full: html, text
    Adding cgiEncodeHash and cgiParseNext functions.
    
• src/lib/fieldedTable.c
  • lines changed 39, context: html, text, full: html, text
    Added functions to index a field.
    
• src/lib/rqlEval.c
  • lines changed 1, context: html, text, full: html, text
    Switching rql's integral type from int to long long since it's dealing some with file sizes that overflow 32 bits.
    
• src/lib/rqlParse.c
  • lines changed 2, context: html, text, full: html, text
    Updating code for long long vs. int.
    
• src/lib/tagStorm.c
  • lines changed 64, context: html, text, full: html, text
    Adding functions to get all fields mentioned in a tagStorm.
    
  • lines changed 2, context: html, text, full: html, text
    Changed tagStormNew's parameter name from fileName to more generic name, since they are built in memory sometimes too.
    
  • lines changed 18, context: html, text, full: html, text
    Adding function for adding long long integer or double values to storm.
    
• src/lib/wildcmp.c
  • lines changed 54, context: html, text, full: html, text
    Added wildExpandList() function.
    
• src/tagStorm/tagStormInfo/c
  • lines changed 0, context: html, text, full: html, text
    Adding a comment.
    
  • lines changed 0, context: html, text, full: html, text
    Removing stray file
    
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 1, context: html, text, full: html, text
    Adding a comment.
    
• src/tagStorm/tagStormJoinTab/more.tab
  • lines changed 26, context: html, text, full: html, text
    A test case for the append option.
    
• src/tagStorm/tagStormQuery/tagStormQuery.c
  • lines changed 52, context: html, text, full: html, text
    Making it so that you can have wildcards on the field list, and so that it will abort if the field list in the query contains fields not in the tag storm.
    
  • lines changed 39, context: html, text, full: html, text
    Moving wildExpandList to library.
    
  • lines changed 10, context: html, text, full: html, text
    Supporting count command in addition to select.