File Changes for kent

v283_preview to v283_preview2 (2013-04-23 to 2013-04-30) v283

• src/hg/autoSql/autoSql.c
  • lines changed 12, context: html, text, full: html, text
    Adding xxxCommaSepFieldNames output.
• src/hg/autoSql/tests/expected/doc.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc2.c
  • lines changed 12, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/doc2.h
  • lines changed 8, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/hardTest.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/hardTest.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/mainTest.c
  • lines changed 18, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/mainTest.h
  • lines changed 12, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/newTest.c
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/newTest.h
  • lines changed 4, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/polyTest.c
  • lines changed 9, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/polyTest.h
  • lines changed 6, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/simpleTest.c
  • lines changed 27, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/simpleTest.h
  • lines changed 18, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/symTest.c
  • lines changed 3, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/autoSql/tests/expected/symTest.h
  • lines changed 2, context: html, text, full: html, text
    Updating autoSql test cases to tolerate new comma separated string output.
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/edwCreateUser.c
  • lines changed 46, context: html, text, full: html, text
    Moving most of the work to a library routine shared with edwWebCreateUser. Removing password from command line.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 2, context: html, text, full: html, text
    Making replica hunting use fileId rather than valid file ID to avoid a validation race condition that sometimes caused a replicate not to be found.
  • lines changed 14, context: html, text, full: html, text
    Moving findElderReplicates to library.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless parameter to shuffleArrayOfChars.
  • lines changed 6, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/edwResetPassword.c
  • lines changed 56, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 284, context: html, text, full: html, text
    Trying a daemon that will poll database table, but wake up early if it gets a signal.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/makefile
  • lines changed 4, context: html, text, full: html, text
    Trying a daemon that will poll database table, but wake up early if it gets a signal.
• src/hg/encode3/encodeDataWarehouse/edwRunner/edwRunner.c
  • lines changed 1, context: html, text, full: html, text
    Marking edwRunner and edwSubmitSpooler as obsoleted by edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 4, context: html, text, full: html, text
    Removing old unused code.
  • lines changed 36, context: html, text, full: html, text
    Adding an error catcher so that file in manifest that have gone missing leave an error message in the edwSubmit record.
  • lines changed 12, context: html, text, full: html, text
    Moving sevral functions from applications to library.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makefile
  • lines changed 17, context: html, text, full: html, text
    Adapting makefile to Hiram's new minimal style.
• src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/edwSubmitSpooler.c
  • lines changed 1, context: html, text, full: html, text
    Marking edwRunner and edwSubmitSpooler as obsoleted by edwRunDaemon.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c
  • lines changed 90, context: html, text, full: html, text
    A Persona authentication checker web service. Seems to work. WiStill need to figure out how not to recompile it for hgwdev, hgwdev-kent, and so forth.
  • lines changed 6, context: html, text, full: html, text
    Removing hard-coding of hgwdev-kent in favor of HTTP_HOST.
  • lines changed 14, context: html, text, full: html, text
    Switching from HTTP_HOST to SERVER_NAME as it's more secure.
  • lines changed 5, context: html, text, full: html, text
    Tightening up security a bit per Laurence's suggestions.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/makefile
  • lines changed 16, context: html, text, full: html, text
    A Persona authentication checker web service. Seems to work. WiStill need to figure out how not to recompile it for hgwdev, hgwdev-kent, and so forth.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/edwWebAuthLogout.c
  • lines changed 14, context: html, text, full: html, text
    Persona logout helper.
  • lines changed 1, context: html, text, full: html, text
    Simplifying output nobody will read.
  • lines changed 1, context: html, text, full: html, text
    Adding another cookie besides email to make it harder for a user to spoof somebody else's email by altering their own browser cookies. This was Laurence's suggestion.
• src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/makefile
  • lines changed 16, context: html, text, full: html, text
    Persona logout helper.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 285, context: html, text, full: html, text
    Adding submission browser.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/makefile
  • lines changed 16, context: html, text, full: html, text
    Adding submission browser.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
  • lines changed 55, context: html, text, full: html, text
    Making a CGI that lets old users add new users.
  • lines changed 11, context: html, text, full: html, text
    A little polish - making sure it really is one of our users, not just someone with a persona account.
  • lines changed 3, context: html, text, full: html, text
    Adding log out button. Improving security.
  • lines changed 1, context: html, text, full: html, text
    Just improving html readability with a newline user won't see.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/makefile
  • lines changed 16, context: html, text, full: html, text
    Making a CGI that lets old users add new users.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 32, context: html, text, full: html, text
    Changing to Persona authentication.
  • lines changed 11, context: html, text, full: html, text
    Adding log out button. Improving security.
  • lines changed 48, context: html, text, full: html, text
    Improving edwWebSubmit status output particularly for errors. Adding button to browse submissions. Moving fifo to a place where all engineers sandboxes and the alpha will share same fifo, which is good, since the point of the fifo is to avoid overloading the system.
  • lines changed 125, context: html, text, full: html, text
    Changing submission fifo, and making it so user can see how many people in submit fifo ahead of them.
  • lines changed 3, context: html, text, full: html, text
    Adding a half second delay to give daemons a little change to process before we present status page for first time.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 9, context: html, text, full: html, text
    Adding a few functions related to Persona and creating users.
  • lines changed 32, context: html, text, full: html, text
    Removing some unused security stuff and replacing it with a little more Persona based security stuff.
  • lines changed 37, context: html, text, full: html, text
    Moving sevral functions from applications to library.
  • lines changed 3, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 4, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 108, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 47, context: html, text, full: html, text
    Adding a few functions related to Persona and creating users.
  • lines changed 80, context: html, text, full: html, text
    Removing some unused security stuff and replacing it with a little more Persona based security stuff.
  • lines changed 3, context: html, text, full: html, text
    Moving edwPerson.js to be included earlier. Seems to work and the firefox developers tools were fussing about having the script tag outside of the html.
  • lines changed 87, context: html, text, full: html, text
    Moving sevral functions from applications to library.
  • lines changed 22, context: html, text, full: html, text
    Turns out we need to keep the sample bed files indefinitely, we never really know when we'll get another replicate. Therefore moving them out of main temp dir, which would otherwise get too big.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 10, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 11, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 37, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 232, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h
  • lines changed 1195, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 14, context: html, text, full: html, text
    Removing several fields from edwUser table since Persona handling authentication. Adding a few more indexes. Having to take away length qualifiers on indexes of md5 and format fields since this makes MySQL want to call it's built in functions of same name.
  • lines changed 12, context: html, text, full: html, text
    Adding edwSubmitJob table in preparation for shifting edwSubmitSpooler to use a queue in database rather than just fifo.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 5, context: html, text, full: html, text
    Adjusting to new persona based authentication, and adding Mike, Cricket, and Venkat to automatically added users.
  • lines changed 1, context: html, text, full: html, text
    Adding mm10.
  • lines changed 1, context: html, text, full: html, text
    Adding Esther on database startup.
  • lines changed 35, context: html, text, full: html, text
    Changing to edwRunDaemon
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding new programs to edw web works.
  • lines changed 2, context: html, text, full: html, text
    Removing no longer needed edwResetPassword.
  • lines changed 1, context: html, text, full: html, text
    Adding edwRunDaemon.
  • lines changed 2, context: html, text, full: html, text
    Removing some obsolete now programs from build.
  • lines changed 1, context: html, text, full: html, text
    Removing directory that was never checked in.
• src/hg/encode3/importEncode2/README
  • lines changed 1, context: html, text, full: html, text
    Marking some stuff as unused in docs.
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 21, context: html, text, full: html, text
    Adding a copy of non-bigified bed to what gets in encode2->encode3 staging area per wrangler request.
• src/hg/encode3/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding encodeDataWarehouse to parent directory make file.
• src/hg/hgTables/bam.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/hgTables/vcf.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/js/edwPersona.js
  • lines changed 45, context: html, text, full: html, text
    Code for ENCODE Data Warehouse login via Persona.
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    Code for ENCODE Data Warehouse login via Persona.
  • lines changed 2, context: html, text, full: html, text
    Fixing merge conflict - Tim also added a new javascript module.
• src/hg/lib/encode3/encode2Manifest.c
  • lines changed 3, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/hg/lib/tests/expected/spDbTest
  • lines changed 20, context: html, text, full: html, text
    Updating test expected output.
• src/hg/lib/tests/spDbTest.c
  • lines changed 1, context: html, text, full: html, text
    Removing some slow parts of spDbTest.c
• src/hg/mouseStuff/regionPicker/regionPicker.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/oneShot/freen/freen.c
  • lines changed 25, context: html, text, full: html, text
    Testing around system call results and exit results as returned by wait.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/hg/visiGene/gensat/gensatRandomXml/gensatRandomXml.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/inc/meta.h
  • lines changed 1, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/inc/net.h
  • lines changed 4, context: html, text, full: html, text
    Making new library function netWaitForData that is a minor refactoring of a private existing net.c function.
• src/inc/obscure.h
  • lines changed 4, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/lib/log.c
  • lines changed 8, context: html, text, full: html, text
    Making logDaemonize code be a little more robust.
• src/lib/meta.c
  • lines changed 2, context: html, text, full: html, text
    Making meta and manifest readers work with URLs.
• src/lib/net.c
  • lines changed 14, context: html, text, full: html, text
    Making new library function netWaitForData that is a minor refactoring of a private existing net.c function.
• src/lib/obscure.c
  • lines changed 5, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.
• src/parasol/para/para.c
  • lines changed 2, context: html, text, full: html, text
    Fixing compile error that is making me wonder if para.c gets compiles usually.
• src/parasol/paraHub/paraHub.c
  • lines changed 1, context: html, text, full: html, text
    Fixing compile error that is making me wonder if para.c gets compiles usually.
• src/utils/shuffleLines/shuffleLines.c
  • lines changed 1, context: html, text, full: html, text
    Removing useless shuffleCount parameter from shuffleList, shuffleArrayOfChars and shuffleArrayOfPointers functions in response to code review feedback.