All File Changes

v298_base to v299_preview (2014-04-07 to 2014-04-14) v299

• src/browserbox/README.txt
  • lines changed 8, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/apache2/ports.conf
  • lines changed 24, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/at.deny
  • lines changed 25, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/default/grub
  • lines changed 36, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/default/rcS
  • lines changed 27, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/init/tty1.conf
  • lines changed 14, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/issue
  • lines changed 18, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/mysql/debian.cnf
  • lines changed 14, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/mysql/my.cnf
  • lines changed 143, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/sudoers.d/README
  • lines changed 21, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/sudoers.d/browserbox
  • lines changed 5, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/sudoers.d/sudoNoPass
  • lines changed 2, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/etc/trashCleaner
  • lines changed 3, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/home/browser/.bashrc
  • lines changed 132, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/home/browser/.hg.conf
  • lines changed 412, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/home/browser/downloadTools
  • lines changed 3, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/home/browser/updateBrowser
  • lines changed 2, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/packages.txt
  • lines changed 394, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/addTools
  • lines changed 4, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/dirStatsFromFind.pl
  • lines changed 229, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/fileStatsFromFind.pl
  • lines changed 64, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/measureTrash.sh
  • lines changed 73, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/trashCleanMonitor.sh
  • lines changed 150, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/trashCleaner.bash
  • lines changed 390, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/trashSizeMonitor.sh
  • lines changed 117, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/browserLogs/scripts/virtualBox.txt
  • lines changed 138, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/changes.txt
  • lines changed 58, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/cleanVm.sh
  • lines changed 53, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/cronCleanTmp.sh
  • lines changed 12, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/cronUpdate.sh
  • lines changed 14, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/lastUpdateTime.flag
  • lines changed 0, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/mirrorTrack
  • lines changed 10, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/testCleaner.sh
  • lines changed 25, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/updateBrowser.sh
  • lines changed 145, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/urlIsNotNewerThanFile
  • lines changed 41, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/root/zeroVm
  • lines changed 17, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 426, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/usr/local/apache/htdocs/folders
  • lines changed 1, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/usr/local/apache/trash
  • lines changed 1, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/usr/local/apache/userdata
  • lines changed 1, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/var/lib/mysql
  • lines changed 1, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/browserbox/var/spool/cron/crontabs/root
  • lines changed 33, context: html, text, full: html, text
    Committing all config files for the browserbox, refs #11957
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 9, context: html, text, full: html, text
    Handle missing controls better. Thanks to Tim code review.
• src/hg/hgGene/geneReviews.c
  • lines changed 7, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
  • lines changed 6, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/hgMirror/hgMirror
  • lines changed 14, context: html, text, full: html, text
    moving code to suppress some tracks from item search into hgMirror so itis executed after each mirroring. refs #11957
    
  • lines changed 1, context: html, text, full: html, text
    fixing typo in previous commit.
• src/hg/hgTracks/snakeTrack.c
  • lines changed 185, context: html, text, full: html, text
    make snakes more compact
• src/hg/hgc/geneReviewsClick.c
  • lines changed 22, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
  • lines changed 7, context: html, text, full: html, text
    Remove the "NVBI book id" column from geneReviews detail page display.See Bob's note http://redmine.soe.ucsc.edu/issues/11226#note-27
    in Track #11226 for more details.
    
  • lines changed 5, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
  • lines changed 1, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 4, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 5, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    adding entries for balAcu1, refs #12977
• src/hg/htdocs/cite.html
  • lines changed 4, context: html, text, full: html, text
    Updated Miga et al., Raney et al., and a few other references to reflect latest publication status.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
  • lines changed 49, context: html, text, full: html, text
    adding entries for balAcu1, refs #12977
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    Adding announcements for the release of mm10 UCSC Genes (redmine #12639)
  • lines changed 36, context: html, text, full: html, text
    Fixed incorrect format for a few name tags.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 32, context: html, text, full: html, text
    Updated Miga et al., Raney et al., and a few other references to reflect latest publication status.
• src/hg/htdocs/indexNews.html
  • lines changed 66, context: html, text, full: html, text
    Adding announcements for the release of mm10 UCSC Genes (redmine #12639)
  • lines changed 2, context: html, text, full: html, text
    Fixed a formatting issue in one of the archive headers
  • lines changed 1, context: html, text, full: html, text
    Updated Miga et al., Raney et al., and a few other references to reflect latest publication status.
• src/hg/inc/hubConnect.h
  • lines changed 2, context: html, text, full: html, text
    first cut at writing out search terms from public hubs #11633
• src/hg/inc/trackHub.h
  • lines changed 7, context: html, text, full: html, text
    first cut at writing out search terms from public hubs #11633
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    removed jquery.js from the static_files list, as the rsync can potentially break the soft links built by cpAndLinkToResourceFiles.pl
• src/hg/lib/geneReviewsGeneGRshortNBKidGRtitle.sql
  • lines changed 7, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/lib/geneReviewsGrshortNBKid.sql
  • lines changed 1, context: html, text, full: html, text
    CR #13033 feed back from kate
  • lines changed 1, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/lib/geneReviewsGrshortTitleNBKid.sql
  • lines changed 1, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/lib/hdb.c
  • lines changed 16, context: html, text, full: html, text
    again, changing the way 2bits are replacing nib files. refs #11957
  • lines changed 1, context: html, text, full: html, text
    small changes after code review, refs #13038
• src/hg/lib/hubConnect.c
  • lines changed 34, context: html, text, full: html, text
    first cut at writing out search terms from public hubs #11633
• src/hg/lib/jksql.c
  • lines changed 3, context: html, text, full: html, text
    small changes after code review, refs #13038
• src/hg/lib/trackHub.c
  • lines changed 72, context: html, text, full: html, text
    first cut at writing out search terms from public hubs #11633
• src/hg/makeDb/doc/criGri1.txt
  • lines changed 415, context: html, text, full: html, text
    in the pushQ 007215 refs #6506
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 6, context: html, text, full: html, text
    Corrections to track description (add Pol2) from Steve Wilder. refs #12259
  • lines changed 4, context: html, text, full: html, text
    Fix to downloads dir structure for ENCODE Seg track. RM #12259
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 1704, context: html, text, full: html, text
    in the pushQ 007216 refs #9419
• src/hg/makeDb/doc/hg18.txt
  • lines changed 59, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
  • lines changed 4, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 178, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
  • lines changed 7, context: html, text, full: html, text
    Feed back from CR #13033Rename geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail
    Add a comment in the geneReviewsGrshortNBKid.sql and geneReviewsGrshortTitleNBKid.sql
    to let reader know they are temp files used by track build.
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added criGri1 to daily hgwdev build refs #6506
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding criGri1 Chinese hamster refs #6506
  • lines changed 1, context: html, text, full: html, text
    enable new mm10 CCDS
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding balAcu1, refs #12977
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added criGri1 to daily hgwdev build refs #6506
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding balAcu1, refs #12977
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding criGri1 Chinese hamster refs #6506
• src/hg/makeDb/schema/all.joiner
  • lines changed 15, context: html, text, full: html, text
    adding rules for criGri1 refs #6506
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Changing entries for balAcu1 CpG island super track, refs #12977
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 14, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMapRelease2.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • lines changed 7, context: html, text, full: html, text
    Added citation for Derrien et al. at the request of AndyP.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra
  • lines changed 15, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg19/encMapability.html
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of mappability.
  • lines changed 7, context: html, text, full: html, text
    Added citation for Derrien et al. at the request of AndyP.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 7, context: html, text, full: html, text
    Corrections to track description (add Pol2) from Steve Wilder. refs #12259
  • lines changed 61, context: html, text, full: html, text
    Remove much repetitive info from ENCODE Seg track description. refs #12259
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.ra
  • lines changed 1, context: html, text, full: html, text
    Take some dev tracks off default on genome-test
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 5, context: html, text, full: html, text
    Fixed spelling of mappability.
  • lines changed 7, context: html, text, full: html, text
    Added citation for Derrien et al. at the request of AndyP.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.ra
  • lines changed 4, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Take some dev tracks off default on genome-test
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
  • lines changed 27, context: html, text, full: html, text
    Updated Miga et al. citation and link.
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 4, context: html, text, full: html, text
    Updated Miga et al. citation and link.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    must also specify release alpha in the sub-track of a super track alpha release refs #12803
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    UCSC GB Track #11226Change the geneReviews tables of hg19 and hg18 to match NCBI.
    
• src/hg/makeDb/trackDb/mouse/mm9/mapability.html
  • lines changed 3, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/mouse/mm9/mapability.ra
  • lines changed 7, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.html
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed spelling of mappability.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    must also specify release alpha in the sub-track of a super track alpha release refs #12803
  • lines changed 1, context: html, text, full: html, text
    Changing entries for balAcu1 CpG island super track, refs #12977
  • lines changed 18, context: html, text, full: html, text
    adding rmskUpdate track for refs #12522 investigation
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 2, context: html, text, full: html, text
    fix problem with tRNA gene symbols not having a null terminator. #12832
  • lines changed 1, context: html, text, full: html, text
    oops... one other place needs null termination for tRNA genes intxGeneXref.c
    
  • lines changed 99, context: html, text, full: html, text
    make sure that the descriptions in kgXref correspond to what's in theGenbank record for the id we choose as the primary id. #12832
    
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 12, context: html, text, full: html, text
    first cut at writing out search terms from public hubs #11633
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 23, context: html, text, full: html, text
    fix hubPublicCheck to not put spurious 1_ prefix on assembly hub nameswhen adding a new url, also check dbList to make sure it's right when
    checking hubs
    
• src/hg/utils/overlapSelect/usage.txt
  • lines changed 4, context: html, text, full: html, text
    fixed incomplete description in overlapSelect usage message
• src/hg/utils/phyloTrees/120way.commonNames.nh
  • lines changed 1, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/120way.scientificNames.nh
  • lines changed 1, context: html, text, full: html, text
    adding serCan1 cynSem1 refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/122way.commonNames.nh
  • lines changed 122, context: html, text, full: html, text
    adding serCan1 cynSem1 refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/122way.nh
  • lines changed 122, context: html, text, full: html, text
    adding serCan1 cynSem1 refs #10272
• src/hg/utils/phyloTrees/122way.scientificNames.nh
  • lines changed 122, context: html, text, full: html, text
    adding serCan1 cynSem1 refs #10272
  • lines changed 1, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/123way.commonNames.nh
  • lines changed 123, context: html, text, full: html, text
    adding Japanese eel angJap1 refs @10272
  • lines changed 4, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/123way.nh
  • lines changed 123, context: html, text, full: html, text
    adding Japanese eel angJap1 refs @10272
• src/hg/utils/phyloTrees/123way.scientificNames.nh
  • lines changed 123, context: html, text, full: html, text
    adding Japanese eel angJap1 refs @10272
  • lines changed 4, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/129way.commonNames.nh
  • lines changed 129, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/129way.nh
  • lines changed 129, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/129way.scientificNames.nh
  • lines changed 129, context: html, text, full: html, text
    adding genomes to catch up with NCBI FTP site
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 2, context: html, text, full: html, text
    adding serCan1 cynSem1 refs #10272
  • lines changed 2, context: html, text, full: html, text
    adding Japanese eel angJap1 refs @10272
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    adding genomes to catch up with NCBI FTP site
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