Commits for kent

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

• 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/edwWebAuthLogin/edwWebAuthLogin.c - lines changed 90, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/makefile - lines changed 16, context: html, text, full: html, text
• Persona logout helper.
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/edwWebAuthLogout.c - lines changed 14, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/makefile - lines changed 16, context: html, text, full: html, text
• Removing hard-coding of hgwdev-kent in favor of HTTP_HOST.
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c - lines changed 6, context: html, text, full: html, text
• Switching from HTTP_HOST to SERVER_NAME as it's more secure.
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c - lines changed 14, context: html, text, full: html, text
• Making a CGI that lets old users add new users.
  • src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c - lines changed 55, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/makefile - lines changed 16, 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.
  • src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c - lines changed 11, context: html, text, full: html, text
• Simplifying output nobody will read.
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogout/edwWebAuthLogout.c - lines changed 1, context: html, text, full: html, text
• Adjusting to new persona based authentication, and adding Mike, Cricket, and Venkat to automatically added users.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 5, 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.
  • src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 10, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 37, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 14, context: html, text, full: html, text
• Adding a few functions related to Persona and creating users.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 9, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 47, context: html, text, full: html, text
• Changing to Persona authentication.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 32, context: html, text, full: html, text
• Removing old unused code.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 4, 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/edwCreateUser/edwCreateUser.c - lines changed 46, context: html, text, full: html, text
• Adding new programs to edw web works.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 4, context: html, text, full: html, text
• Removing no longer needed edwResetPassword.
  • src/hg/encode3/encodeDataWarehouse/edwResetPassword/edwResetPassword.c - lines changed 56, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwResetPassword/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 2, context: html, text, full: html, text
• Adding xxxCommaSepFieldNames output.
  • src/hg/autoSql/autoSql.c - lines changed 12, context: html, text, full: html, text
• Adding mm10.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 1, context: html, text, full: html, text
• Removing some unused security stuff and replacing it with a little more Persona based security stuff.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 32, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 80, context: html, text, full: html, text
• Adding log out button. Improving security.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 11, context: html, text, full: html, text
• Adding log out button. Improving security.
  • src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c - lines changed 3, context: html, text, full: html, text
• Tightening up security a bit per Laurence's suggestions.
  • src/hg/encode3/encodeDataWarehouse/edwWebAuthLogin/edwWebAuthLogin.c - lines changed 5, context: html, text, full: html, text
• Code for ENCODE Data Warehouse login via Persona.
  • 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
• Making new library function netWaitForData that is a minor refactoring of a private existing net.c function.
  • src/inc/net.h - lines changed 4, context: html, text, full: html, text
  • src/lib/net.c - lines changed 14, 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/bam.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/bigBed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/vcf.c - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/regionPicker/regionPicker.c - lines changed 1, context: html, text, full: html, text
  • src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c - lines changed 1, context: html, text, full: html, text
  • src/hg/visiGene/gensat/gensatRandomXml/gensatRandomXml.c - lines changed 1, context: html, text, full: html, text
  • src/inc/obscure.h - lines changed 4, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 5, context: html, text, full: html, text
  • src/utils/shuffleLines/shuffleLines.c - lines changed 1, context: html, text, full: html, text
• Adding encodeDataWarehouse to parent directory make file.
  • src/hg/encode3/makefile - lines changed 1, context: html, text, full: html, text
• Marking some stuff as unused in docs.
  • src/hg/encode3/importEncode2/README - lines changed 1, 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/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 21, context: html, text, full: html, text
• Adding Esther on database startup.
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 1, 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/inc/encodeDataWarehouse.h - lines changed 108, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as - lines changed 11, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c - lines changed 232, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h - lines changed 1195, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql - lines changed 12, 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.
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 3, context: html, text, full: html, text
• Adapting makefile to Hiram's new minimal style.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/makefile - lines changed 17, 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.
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 2, context: html, text, full: html, text
• Removing useless parameter to shuffleArrayOfChars.
  • src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c - lines changed 1, 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.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 36, 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/edwWebAuthLogout.c - 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/edwWebCreateUser.c - lines changed 1, 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.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 48, context: html, text, full: html, text
• Updating autoSql test cases to tolerate new comma separated string output.
  • src/hg/autoSql/tests/expected/doc.c - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc.h - lines changed 4, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc2.c - lines changed 12, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/doc2.h - lines changed 8, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/hardTest.c - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/hardTest.h - lines changed 4, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/mainTest.c - lines changed 18, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/mainTest.h - lines changed 12, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.c - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/newTest.h - lines changed 4, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/polyTest.c - lines changed 9, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/polyTest.h - lines changed 6, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/simpleTest.c - lines changed 27, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/simpleTest.h - lines changed 18, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symTest.c - lines changed 3, context: html, text, full: html, text
  • src/hg/autoSql/tests/expected/symTest.h - lines changed 2, context: html, text, full: html, text
• Fixing merge conflict - Tim also added a new javascript module.
  • src/hg/js/makefile - lines changed 2, context: html, text, full: html, text
• Adding submission browser.
  • src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c - lines changed 285, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwWebBrowse/makefile - lines changed 16, 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/edwRunDaemon.c - lines changed 284, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwRunDaemon/makefile - lines changed 4, context: html, text, full: html, text
• Making logDaemonize code be a little more robust.
  • src/lib/log.c - lines changed 8, context: html, text, full: html, text
• Fixing compile error that is making me wonder if para.c gets compiles usually.
  • 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
• Testing around system call results and exit results as returned by wait.
  • src/hg/oneShot/freen/freen.c - lines changed 25, context: html, text, full: html, text
• Marking edwRunner and edwSubmitSpooler as obsoleted by edwRunDaemon.
  • src/hg/encode3/encodeDataWarehouse/edwRunner/edwRunner.c - lines changed 1, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/edwSubmitSpooler/edwSubmitSpooler.c - lines changed 1, context: html, text, full: html, text
• Moving findElderReplicates to library.
  • src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c - lines changed 14, 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.
  • src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c - lines changed 125, context: html, text, full: html, text
• Moving sevral functions from applications to library.
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 37, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 87, context: html, text, full: html, text
• Moving sevral functions from applications to library.
  • src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c - lines changed 12, context: html, text, full: html, text
• Adding edwRunDaemon.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text
• Changing to edwRunDaemon
  • src/hg/encode3/encodeDataWarehouse/lib/resetEdw - lines changed 35, context: html, text, full: html, text
• Removing some slow parts of spDbTest.c
  • src/hg/lib/tests/spDbTest.c - lines changed 1, context: html, text, full: html, text
• Making meta and manifest readers work with URLs.
  • src/hg/lib/encode3/encode2Manifest.c - lines changed 3, context: html, text, full: html, text
  • src/inc/meta.h - lines changed 1, context: html, text, full: html, text
  • src/lib/meta.c - lines changed 2, context: html, text, full: html, text
• Updating test expected output.
  • src/hg/lib/tests/expected/spDbTest - lines changed 20, context: html, text, full: html, text
• Removing some obsolete now programs from build.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 2, 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/edwMakeValidFile/edwMakeValidFile.c - lines changed 6, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/inc/edwLib.h - lines changed 3, context: html, text, full: html, text
  • src/hg/encode3/encodeDataWarehouse/lib/edwLib.c - lines changed 22, 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/edwWebSubmit/edwWebSubmit.c - lines changed 3, context: html, text, full: html, text
• Removing directory that was never checked in.
  • src/hg/encode3/encodeDataWarehouse/makefile - lines changed 1, context: html, text, full: html, text