All File Changes

v286_base to v287_preview (2013-07-09 to 2013-07-16) v287

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 13, context: html, text, full: html, text
    Removed -o option, fixed HTML appearing in -p output, refs #10192
• src/hg/encode3/validateManifest/makefile
  • lines changed 2, context: html, text, full: html, text
    this has changes for 1.6 (except still need to add types IDAT,RCC,unknown)
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 27, context: html, text, full: html, text
    this has changes for 1.6 (except still need to add types IDAT,RCC,unknown)
  • lines changed 34, context: html, text, full: html, text
    adding types idat and rcc which just check for fileSize > 0
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    some cleanup of assembly hubs: require organism and defaultPos, tolerate missing scientificName, groups, htmlPath and orderKey. Fix weird bug with wikiTrack missing a settingsHash.
• src/hg/hgLogin/hgLogin.c
  • lines changed 3, context: html, text, full: html, text
    Feature #9526 tweak wording on hgLogin messages.
  • lines changed 1, context: html, text, full: html, text
    Fixed hgLogin.c:401: warning: unused variable 'sendMailContain'
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    some cleanup of assembly hubs: require organism and defaultPos, tolerate missing scientificName, groups, htmlPath and orderKey. Fix weird bug with wikiTrack missing a settingsHash.
• src/hg/hgTables/wikiTrack.c
  • lines changed 1, context: html, text, full: html, text
    some cleanup of assembly hubs: require organism and defaultPos, tolerate missing scientificName, groups, htmlPath and orderKey. Fix weird bug with wikiTrack missing a settingsHash.
• src/hg/hgTracks/menu.c
  • lines changed 5, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
• src/hg/hgc/hgc.c
  • lines changed 49, context: html, text, full: html, text
    adding iframeUrl and iframeOptions trackDb options to hgc. They allow to show an external webpage directly on the hgc page
  • lines changed 3, context: html, text, full: html, text
    fixing merge conflict
  • lines changed 1, context: html, text, full: html, text
    forgot one line in merge conflict
  • lines changed 3, context: html, text, full: html, text
    fixing oops somebody made losing my changes.
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 11, context: html, text, full: html, text
    Adding comment to suggest use of Track Hubs for genome-euro refs #3000
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 0, context: html, text, full: html, text
    Minor edits for code review. refs #11255.
  • lines changed 0, context: html, text, full: html, text
    Correcting tiny typo, refs #11255
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 1, context: html, text, full: html, text
    Minor edits for code review. refs #11255.
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 2, context: html, text, full: html, text
    Minor edits for code review. refs #11255.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 6, context: html, text, full: html, text
    made an image a bit smaller so the page wraps better when browser is narrow. Stops the scroll bar from appearing and keeps the left margin from disappearing. thanks Jonathan for figuring it out!
• src/hg/htdocs/indexNews.html
  • lines changed 5, context: html, text, full: html, text
    Minor edits for code review. refs #11255.
• src/hg/htdocs/style/nice_menu.css
  • lines changed 8, context: html, text, full: html, text
    Removed references to non-existent arrow-down.png and arrow-right.png, refs #11170
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
• src/hg/lib/hgFind.c
  • lines changed 4, context: html, text, full: html, text
    some cleanup of assembly hubs: require organism and defaultPos, tolerate missing scientificName, groups, htmlPath and orderKey. Fix weird bug with wikiTrack missing a settingsHash.
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
• src/hg/lib/mdb.c
  • lines changed 51, context: html, text, full: html, text
    Previously I missed a place where subqueries were created in code. This is proving enormously inefficient in MySql >5.0.89, which means on the RR. I have converted the subqueries to JOINs and also reducced the number of queries needed to 'render tabs' in trackSearch. This should solve redmine #11155.
• src/hg/lib/trackHub.c
  • lines changed 5, context: html, text, full: html, text
    resolve newly introduced error in menu bar, notify users that hgVai doesn't work with assembly hubs, and resolve caching problems with assembly hubs (set udc cache timeout before opening hubs (otherwise the default is 0), don't open 2bit files until they are actually used)
  • lines changed 15, context: html, text, full: html, text
    some cleanup of assembly hubs: require organism and defaultPos, tolerate missing scientificName, groups, htmlPath and orderKey. Fix weird bug with wikiTrack missing a settingsHash.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    done with lastz for tupChi1 and octDeg1 refs #10272
  • lines changed 14, context: html, text, full: html, text
    finishing off lastz runs for choHof1 oryAfe1 chrAsi1 dasNov3 refs #10272
  • lines changed 240, context: html, text, full: html, text
    swapping eriEur2 starting lastz on sarHar1 macEug2 triMan1 conCri1 refs #10272
  • lines changed 23, context: html, text, full: html, text
    finished with lastz for eriEur2 and continuing oryAfe1 and chrAsi1 refs #10272
  • lines changed 13, context: html, text, full: html, text
    lastz swaps for oryAfe1 chrAsi1 dasNov3 refs #10272
  • lines changed 17, context: html, text, full: html, text
    finishing up lastz for chrAsi1 eleEdw1 dasNov3 refs #10272
  • lines changed 16, context: html, text, full: html, text
    finishing lastz for oryAfe1 eleEdw1 conCri1 refs #10272
  • lines changed 29, context: html, text, full: html, text
    finishing off lastz for sarHar1 triMan1 conCri1 refs #10272
  • lines changed 180, context: html, text, full: html, text
    starting lastz for lepWed1 felCat5 musFur1 refs #10272
  • lines changed 4, context: html, text, full: html, text
    swapping macEug2 refs #10272
  • lines changed 146, context: html, text, full: html, text
    wrapping up lastz for macEug2 lepWed1 musFur1 and starting camFer1 and odoRosDiv1 refs #10272
  • lines changed 11, context: html, text, full: html, text
    finishing up lepWed1 musFur1 and felCat5 lastz runs refs #10272
  • lines changed 17, context: html, text, full: html, text
    finishing off lastz for felCat5 camFer1 odoRosDiv1 refs #10272
  • lines changed 14, context: html, text, full: html, text
    done with camFer1 and odoRosDiv1 lastz chain net refs #10272
  • lines changed 10, context: html, text, full: html, text
    done with lastz felCat5 refs #10272
  • lines changed 375, context: html, text, full: html, text
    lastz runs started on panPan1 latCha1 jacJac1 panHod1 capHir1 hetGla2 refs #10272
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • lines changed 1, context: html, text, full: html, text
    correction after code review #11258
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    adding oviAri3 to the rule set refs #9409
  • lines changed 1, context: html, text, full: html, text
    Missed one of the 'pg%' tables in tablesIgnored in a36d941448. Nice catch by Jonathan. refs #11204.
• src/hg/makeDb/trackDb/human/hg19/chainCanFam2.ra
  • lines changed 7, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel1.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel2.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal3.ra
  • lines changed 15, context: html, text, full: html, text
    adding galGal4 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal4.ra
  • lines changed 15, context: html, text, full: html, text
    adding galGal4 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra
  • lines changed 51, context: html, text, full: html, text
    adding galGal4 and legacy out galGal3 refs #10272
  • lines changed 20, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
  • lines changed 38, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
  • lines changed 54, context: html, text, full: html, text
    adding gorGor1 nomLeu1 rheMac2 to legacy chainNet refs #10272
  • lines changed 86, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
  • lines changed 16, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
  • lines changed 16, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
  • lines changed 16, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri1.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri3.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
  • lines changed 443, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
  • lines changed 14, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
  • lines changed 15, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
  • lines changed 15, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra
  • lines changed 204, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
  • lines changed 0, context: html, text, full: html, text
    adding gorGor1 nomLeu1 rheMac2 to legacy chainNet refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRn4.ra
  • lines changed 15, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRn5.ra
  • lines changed 15, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
  • lines changed 306, context: html, text, full: html, text
    move vertebrate chainNet into separate file and adding Budgerigar refs #10272
  • lines changed 15, context: html, text, full: html, text
    adding galGal4 and legacy out galGal3 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac1.ra
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac2.ra
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/netCanFam2.ra
  • lines changed 7, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 7, context: html, text, full: html, text
    Grammar and punctuation tweaks from code review. refs #11204.
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 34, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
  • lines changed 290, context: html, text, full: html, text
    move vertebrate chainNet into separate file and adding Budgerigar refs #10272
  • lines changed 2, context: html, text, full: html, text
    adding galGal4 and legacy out galGal3 refs #10272
  • lines changed 470, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
  • lines changed 214, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    experimenting with genbank DNA support, need to checkin to get onto alpha
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 1, context: html, text, full: html, text
    better short title for aged-out/legacy chain net refs #10272
  • lines changed 34, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
  • lines changed 1, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 14, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    forgot iframeUrl tagtype
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    adding mysqlSecurityCheck to makefile
• src/hg/utils/mysqlSecurityCheck/makefile
  • lines changed 14, context: html, text, full: html, text
    Initial commit of new utility mysqlSecurityCheck which can be used to make sure that CGI mysql users do not have access to the mysql meta database where the mysql.user.password values must be protected from hacking.
• src/hg/utils/mysqlSecurityCheck/mysqlSecurityCheck.c
  • lines changed 254, context: html, text, full: html, text
    Initial commit of new utility mysqlSecurityCheck which can be used to make sure that CGI mysql users do not have access to the mysql meta database where the mysql.user.password values must be protected from hacking.
  • lines changed 5, context: html, text, full: html, text
    some little improvements to mysqlSecurityCheck output
• src/hg/utils/phyloTrees/110way.commonNames.nh
  • lines changed 110, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/110way.nh
  • lines changed 110, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/110way.scientificNames.nh
  • lines changed 110, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
  • lines changed 100, context: html, text, full: html, text
    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
  • lines changed 100, context: html, text, full: html, text
    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
  • lines changed 100, context: html, text, full: html, text
    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 3, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 8, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
  • lines changed 8, context: html, text, full: html, text
    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 3, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/lib/errabort.c
  • lines changed 44, context: html, text, full: html, text
    Fixing multi-threaded race condition in errAbort.c on pidInUse by adding another mutex.
  • lines changed 1, context: html, text, full: html, text
    make sure that the rlimit out of memory errAbort still works
  • lines changed 1, context: html, text, full: html, text
    After discussing with Angie, its probably OK to allow atexit cleanup
• src/lib/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    make sure that the rlimit out of memory errAbort still works
• src/lib/tests/testOutOfMem.c
  • lines changed 65, context: html, text, full: html, text
    make sure that the rlimit out of memory errAbort still works
• src/product/README.install
  • lines changed 4, context: html, text, full: html, text
    To Do 9403 remove reference to 32 bit CGI build.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v287 preview1

• lines changed: 5093
• files changed: 117