File Changes for tdreszer

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• src/hg/hgGateway/hgGateway.c
  • lines changed 3, context: html, text, full: html, text
    Insignificant change from FONT tags to CSS.
• src/hg/hgTables/usage.c
  • lines changed 1, context: html, text, full: html, text
    Removed a <P> tag to keep line spacing the same as when we used DOCTYPE 3.2.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/hgTracks/hgTracks.c
  • lines changed 11, context: html, text, full: html, text
    Insignificant change from FONT tags to CSS.
• src/hg/hgTracks/searchTracks.c
  • lines changed 95, context: html, text, full: html, text
    Removed a lot of ifdef'd out code. We are not going to revive fileSearch as a tab on trackSearch (unfortunately)
  • lines changed 2, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/inc/cv.h
  • lines changed 3, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
• src/hg/inc/mdb.h
  • lines changed 1, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
• src/hg/js/hui.js
  • lines changed 9, context: html, text, full: html, text
    redmine 1411. One more tweek to martix CB graying. This was found by Katrina when already on beta.
• src/hg/lib/cv.c
  • lines changed 42, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
• src/hg/lib/fileUi.c
  • lines changed 313, context: html, text, full: html, text
    Adding CGI support for mdb fimeName being a comma delimited list. Also includes support for md5sum as comma delimited list.
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    Adding CGI support for mdb fimeName being a comma delimited list. Also includes support for md5sum as comma delimited list.
  • lines changed 1, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
  • lines changed 10, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/lib/mdb.c
  • lines changed 13, context: html, text, full: html, text
    When in doubt, should always prefer the sandbox table.
  • lines changed 4, context: html, text, full: html, text
    Temprarily block experimentify from creating expId's in encodeExp table. Cricket will manage expId creation with Kate's tool for now. mdbUpdate can still create accessions in encodeExp table when expId already exists.
  • lines changed 16, context: html, text, full: html, text
    Changes so that -accession -test will work. Also made some experimentify errors more prominent.
  • lines changed 6, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
  • lines changed 30, context: html, text, full: html, text
    Cleaned up some mesages in experimentify mdbPrint command
• src/hg/lib/web.c
  • lines changed 130, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • lines changed 75, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • lines changed 46, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 76, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 194, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 20, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
  • lines changed 9, context: html, text, full: html, text
    Simplified the encodeExp table option
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 21, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
  • lines changed 1, context: html, text, full: html, text
    Changes so that -accession -test will work. Also made some experimentify errors more prominent.
  • lines changed 9, context: html, text, full: html, text
    Simplified the encodeExp table option
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Extended typeOfTerm hidden var to hide from beta,public
  • lines changed 1, context: html, text, full: html, text
    Hopefully fixed a bad regex on dccAccession
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    Added the common name of this cute little fellow.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 1099, context: html, text, full: html, text
    Added expId's and dccAccessions to Broad Histone hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 19, context: html, text, full: html, text
    Added expIds and dccAccessions for Broad HMM hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 1067, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
  • lines changed 2, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1861, context: html, text, full: html, text
    Added expId's and dccAccessions to Broad Histone hg18 and hg19
  • lines changed 211, context: html, text, full: html, text
    Changed antibody=Control to the standard antibody=Input. Removed expIds and dccAccessions for those as well.
  • lines changed 91, context: html, text, full: html, text
    45 of 70 antobody=Input experiment objects got proper expId's matching hg18.
  • lines changed 41, context: html, text, full: html, text
    Revived the legitimate hg19 only antibody=Input experiments which had been screwed up by antibody=Control.
  • lines changed 11, context: html, text, full: html, text
    One more exp where antibody should not have been Control
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 19, context: html, text, full: html, text
    Added expIds and dccAccessions for Broad HMM hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 555, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 657, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 363, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 8, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 2767, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 1, context: html, text, full: html, text
    Updated fileSortOrder for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 1046, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 1225, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 695, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 16, context: html, text, full: html, text
    Added a validation level filter and changed coloring and wording to clarify the difference between OC code and validation level.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 24, context: html, text, full: html, text
    Added a validation level filter and changed coloring and wording to clarify the difference between OC code and validation level.
• src/lib/common.c
  • lines changed 4, context: html, text, full: html, text
    startsWithWordByDelimit failed when the line only contained the word.
• src/lib/htmshell.c
  • lines changed 4, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
  • lines changed 1, context: html, text, full: html, text
    Need the 'f' param for fput.
• src/lib/ra.c
  • lines changed 1, context: html, text, full: html, text
    Changed a wrong comment that Angie pointed out.
• src/lib/seqOut.c
  • lines changed 4, context: html, text, full: html, text
    Insignificant change from FONT tags to CSS.