All File Changes

v294_base to v295_preview (2014-01-13 to 2014-01-20) v295

• src/hg/altSplice/altSplice/orthoSplice.c
  • lines changed 1, context: html, text, full: html, text
    remove useless extra parentheses refs #12209
• src/hg/checkTableCoords/checkTableCoords.c
  • lines changed 8, context: html, text, full: html, text
    remove always false if() statement due to unsigned int compare to < 0 refs #12209
• src/hg/encode3/eap/README
  • lines changed 2, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/eapDaemon/eapDaemon.c
  • lines changed 375, context: html, text, full: html, text
    Easy to misspell daemon.
  • lines changed 24, context: html, text, full: html, text
    Refactoring in preparation for moving some code to library.
  • lines changed 55, context: html, text, full: html, text
    Since startTime is now indexed, look for startTime=0 across whole table, not just for recent IDs. Moving some of the parasol interface stuff to eapLib.c
• src/hg/encode3/eap/eapDaemon/eapDeamon.c
  • lines changed 375, context: html, text, full: html, text
    Moving encodeDataWarehouse/edwAnalysisDaemon to eap/eapDaemon
  • lines changed 7, context: html, text, full: html, text
    Renaming edwAnalysisDaemon to eapDaemon
  • lines changed 375, context: html, text, full: html, text
    Easy to misspell daemon.
• src/hg/encode3/eap/eapDaemon/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving encodeDataWarehouse/edwAnalysisDaemon to eap/eapDaemon
  • lines changed 2, context: html, text, full: html, text
    Renaming edwAnalysisDaemon to eapDaemon
  • lines changed 1, context: html, text, full: html, text
    Linking with local library.
• src/hg/encode3/eap/eapFinish/eapFinish.c
  • lines changed 342, context: html, text, full: html, text
    Renaming edwFinishAnalysis to the more elegant eapFinish
  • lines changed 10, context: html, text, full: html, text
    Added -keepFailing option.
• src/hg/encode3/eap/eapFinish/edwFinishAnalysis.c
  • lines changed 342, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
  • lines changed 2, context: html, text, full: html, text
    adjusting to new position in source tree.
  • lines changed 6, context: html, text, full: html, text
    simple symbol substitution
  • lines changed 342, context: html, text, full: html, text
    Renaming edwFinishAnalysis to the more elegant eapFinish
• src/hg/encode3/eap/eapFinish/makefile
  • lines changed 4, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
  • lines changed 2, context: html, text, full: html, text
    Renaming edwFinishAnalysis to the more elegant eapFinish
• src/hg/encode3/eap/eapMonitor/eapMonitor.c
  • lines changed 51, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
  • lines changed 183, context: html, text, full: html, text
    Implementing status, chill, and cull commands.
  • lines changed 67, context: html, text, full: html, text
    Added info command. Polishing and extending status command.
  • lines changed 194, context: html, text, full: html, text
    Implementing err and errFile commands.
  • lines changed 176, context: html, text, full: html, text
    Implementing steps,errlist, and scrounge commands.
  • lines changed 155, context: html, text, full: html, text
    Making errList command have optional days and step parameters. Making status command list top three batches sorted by # of jobs running mostly. Making results have a more proper constructor.
  • lines changed 80, context: html, text, full: html, text
    Improving several things. Including node job was run on in errList. Removed nearly useless Youngest Job information item.
• src/hg/encode3/eap/eapMonitor/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 743, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
  • lines changed 120, context: html, text, full: html, text
    Trying to add macs2 chip-seq.
  • lines changed 4, context: html, text, full: html, text
    Fixed bug in input tyeps for scheduleMacsChip. Got rid of some uglyfs.
• src/hg/encode3/eap/eapSchedule/edwScheduleAnalysis.c
  • lines changed 747, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
  • lines changed 747, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/eapSchedule/makefile
  • lines changed 4, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
  • lines changed 2, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/inc/eapLib.h
  • lines changed 22, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
  • lines changed 12, context: html, text, full: html, text
    Adding routines to get list of running jobs from Parasol, to put that list intoa a hash, and also a command to extract the 'step' out of a command line.
• src/hg/encode3/eap/lib/eapLib.c
  • lines changed 29, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
  • lines changed 61, context: html, text, full: html, text
    Adding routines to get list of running jobs from Parasol, to put that list intoa a hash, and also a command to extract the 'step' out of a command line.
• src/hg/encode3/eap/lib/makefile
  • lines changed 11, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/makefile
  • lines changed 49, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/eap/notes/sampleBam/makefile
  • lines changed 3, context: html, text, full: html, text
    Moving encPipe directory to be eap/notes
• src/hg/encode3/eap/notes/sampleBam/sampleBam.c
  • lines changed 109, context: html, text, full: html, text
    Moving encPipe directory to be eap/notes
• src/hg/encode3/encPipe/sampleBam/makefile
  • lines changed 3, context: html, text, full: html, text
    Moving encPipe directory to be eap/notes
• src/hg/encode3/encPipe/sampleBam/sampleBam.c
  • lines changed 109, context: html, text, full: html, text
    Moving encPipe directory to be eap/notes
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c
  • lines changed 1, context: html, text, full: html, text
    Added an assert suggested in code review. Matches an assert elsewhere in a similar situation.
• src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/edwAnalysisDaemon.c
  • lines changed 287, context: html, text, full: html, text
    Making it clean up temp dir when done, but there's a noClean option still. Doing a 'mv' via shell instead of a 'rename' via C library to put files into the warehouse, since it turns out rename doesn't work across devices. Removing some code that was a weak old attempt at making it possible to run this program in parallel. It must be run serially.
  • lines changed 15, context: html, text, full: html, text
    telling parasol about our job size. Clarifying name of var.
  • lines changed 11, context: html, text, full: html, text
    Making paraHost a command line option. Rearranging debugging statements. Adding 1 second sleep. Upping processor use to 3.
  • lines changed 128, context: html, text, full: html, text
    Refactoring to remove fifo and simplify command line. Bypassing stderr file copying which is being flaky since it's trying to go straight from dev to one of the paraNodes.
  • lines changed 33, context: html, text, full: html, text
    Making it so that parasol add job is done serially, just wait for results in parallel.
  • lines changed 40, context: html, text, full: html, text
    Handling copy over of stderr from node to db table. Cleaned up a lot of debugging code.
  • lines changed 92, context: html, text, full: html, text
    Got out one more run time kink I think. It was having trouble collecting stderr. I moved the collection to the serial side in hopes that ssh will like it better.
  • lines changed 22, context: html, text, full: html, text
    Adding version number to logging. Failing more softly if cant fetch stderr file from parasol node.
  • lines changed 16, context: html, text, full: html, text
    Making it retry the ssh to paraHub 6 times over the course of a minute before giving up.
  • lines changed 303, context: html, text, full: html, text
    Almost complete reworking that now meshes well with parasol. Only a single copy of the daemon exists, in a boring 2-way polling loop. It looks for new jobs in database table and sends them to paraHub daemon on remote machine. It looks for new lines in a results file to see what jobs parasol has finished. It transports information from the results file back into the database table.
  • lines changed 3, context: html, text, full: html, text
    Adding a level-1 verbose status message, and bumping the version number.
  • lines changed 5, context: html, text, full: html, text
    Making dirs on path to the results file.
  • lines changed 58, context: html, text, full: html, text
    Fixing bug so cpusRequested actually gets passe to hub. Making it use different queues for different analysis steps.
  • lines changed 91, context: html, text, full: html, text
    When daemon restarts it does a pretty good job of trying to reconnect with exiting running jobs or ones that finished when it was down.
  • lines changed 8, context: html, text, full: html, text
    Improving commenting.
  • lines changed 375, context: html, text, full: html, text
    Moving encodeDataWarehouse/edwAnalysisDaemon to eap/eapDaemon
• src/hg/encode3/encodeDataWarehouse/edwAnalysisDaemon/makefile
  • lines changed 4, context: html, text, full: html, text
    Making it clean up temp dir when done, but there's a noClean option still. Doing a 'mv' via shell instead of a 'rename' via C library to put files into the warehouse, since it turns out rename doesn't work across devices. Removing some code that was a weak old attempt at making it possible to run this program in parallel. It must be run serially.
  • lines changed 1, context: html, text, full: html, text
    Linking in with parasol libraries.
  • lines changed 4, context: html, text, full: html, text
    Moving encodeDataWarehouse/edwAnalysisDaemon to eap/eapDaemon
• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c
  • lines changed 1, context: html, text, full: html, text
    Adding new argument to edwFileResetTags.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c
  • lines changed 36, context: html, text, full: html, text
    Changing program so that it can add new tags as well as change existing ones.
  • lines changed 5, context: html, text, full: html, text
    Adding noRevalidate option. Most of work is in library.
• src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/edwFinishAnalysis.c
  • lines changed 57, context: html, text, full: html, text
    Making it clean up temp dir when done, but there's a noClean option still. Doing a 'mv' via shell instead of a 'rename' via C library to put files into the warehouse, since it turns out rename doesn't work across devices. Removing some code that was a weak old attempt at making it possible to run this program in parallel. It must be run serially.
  • lines changed 1, context: html, text, full: html, text
    Free pass for idat and rcc. Fixing typo in temp dir.
  • lines changed 342, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
• src/hg/encode3/encodeDataWarehouse/edwFinishAnalysis/makefile
  • lines changed 4, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
• src/hg/encode3/encodeDataWarehouse/edwJob/edwJob.c
  • lines changed 156, context: html, text, full: html, text
    Utility to look at a job table.
• src/hg/encode3/encodeDataWarehouse/edwJob/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to look at a job table.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
  • lines changed 12, context: html, text, full: html, text
    Giving free pass to unknown, idat, rcc,
  • lines changed 18, context: html, text, full: html, text
    Adding a little logic to make enrichments work in spite of assemblies like 'male.hg19'. Specifically made a routine that returns the root 'hg19' in cases like this.
  • lines changed 21, context: html, text, full: html, text
    Adding looseBed to formats. Making enrichmentAssembly into a library routine with a more meaningful name.
  • lines changed 2, context: html, text, full: html, text
    Changing looseBed to customTrack.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c
  • lines changed 21, context: html, text, full: html, text
    Making it sole responsibility of younger member of pair to make edwQaPairedEndFastq record. Creating Record in a single transaction.
  • lines changed 3, context: html, text, full: html, text
    Improving logging statements.
• src/hg/encode3/encodeDataWarehouse/edwMakeRepeatQa/edwMakeRepeatQa.c
  • lines changed 124, context: html, text, full: html, text
    QA routines to check alignments against repeat library and save to database.
• src/hg/encode3/encodeDataWarehouse/edwMakeRepeatQa/makefile
  • lines changed 4, context: html, text, full: html, text
    QA routines to check alignments against repeat library and save to database.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 1, context: html, text, full: html, text
    Adding looseBed format
  • lines changed 2, context: html, text, full: html, text
    Changing looseBed to customTrack.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 19, context: html, text, full: html, text
    Making it take constant prefix to license plate from settings table rather than being a hardcoded 'ENCFF'.
  • lines changed 56, context: html, text, full: html, text
    Librarifying edwFileFieldsFromTags and edwValidFileUpdateDb. AMaking revalidation an option for edwFileResetTags rather than always happening.
  • lines changed 45, context: html, text, full: html, text
    Changing looseBed to customTrack and allowing track and browser lines
• src/hg/encode3/encodeDataWarehouse/edwQaEvaluate/edwQaEvaluate.c
  • lines changed 41, context: html, text, full: html, text
    Version 5 - mostly to let Encode2 in with lower standards.
  • lines changed 18, context: html, text, full: html, text
    Adding in ChiaPet thresholds.
  • lines changed 2, context: html, text, full: html, text
    Improved comment.
• src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/edwReallyRemoveFiles.c
  • lines changed 17, context: html, text, full: html, text
    Adding a bunch of new linked tables to what gets deleted.
• src/hg/encode3/encodeDataWarehouse/edwRetryJob/edwRetryJob.c
  • lines changed 31, context: html, text, full: html, text
    Reworking so that it will retry if the most recent attempt at a command failed.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 6, context: html, text, full: html, text
    Adding delay as a command line parameter.
  • lines changed 8, context: html, text, full: html, text
    Somehow the status demangling slipped out. I put it back in. Also put info on what version we are as first log message.
• src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/edwScheduleAnalysis.c
  • lines changed 254, context: html, text, full: html, text
    Several changes. This version is tuned to schedule bwa alignments on hg38 mostly.
  • lines changed 11, context: html, text, full: html, text
    Removing some debugging statements. Making it schedule only single-end bwa.
  • lines changed 11, context: html, text, full: html, text
    Adding a dry option that just lists command that would get run.
  • lines changed 45, context: html, text, full: html, text
    Adding retry and ignoreQa options. Shifting analysis from bam to fastq.
  • lines changed 42, context: html, text, full: html, text
    Fixing merge conflicts
  • lines changed 45, context: html, text, full: html, text
    Changing human target from hg38 to hg19. Making already scheduled queries sensitive to target.
  • lines changed 38, context: html, text, full: html, text
    Rearranging ifdefs to decide what to schedule.
  • lines changed 747, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
• src/hg/encode3/encodeDataWarehouse/edwScheduleAnalysis/makefile
  • lines changed 4, context: html, text, full: html, text
    Part of the eap spinning out of the edw.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 31, context: html, text, full: html, text
    Adding looseBed to formats.
  • lines changed 1, context: html, text, full: html, text
    Changing looseBed to customTrack.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/makk
  • lines changed 1, context: html, text, full: html, text
    Adding commented out beta site
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTarget2/edwFixTarget2.c
  • lines changed 115, context: html, text, full: html, text
    Another fixer. This one for downstream effects of not respecting BAM file ucscDb when running Macs2.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTarget2/makefile
  • lines changed 4, context: html, text, full: html, text
    Another fixer. This one for downstream effects of not respecting BAM file ucscDb when running Macs2.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTargetSeq/edwFixTargetSeq.c
  • lines changed 82, context: html, text, full: html, text
    Fix to add targets seems to work.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTargetSeq/makefile
  • lines changed 4, context: html, text, full: html, text
    Fix to add targets seems to work.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRepsFromTarballs/edwFixTechRepsFromTarballs.c
  • lines changed 90, context: html, text, full: html, text
    Fixer seems to work.
  • lines changed 7, context: html, text, full: html, text
    Making the outputType be 'rejected_reads' in the rejected case.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 1, context: html, text, full: html, text
    Removing unused eapTempDir variable.
  • lines changed 8, context: html, text, full: html, text
    Exporting a few local functions for wider use.
  • lines changed 4, context: html, text, full: html, text
    Creating new library function edwOneLineSystemAttempt
  • lines changed 8, context: html, text, full: html, text
    Two steps forward one step back.
  • lines changed 11, context: html, text, full: html, text
    Librarifying edwFileFieldsFromTags and edwValidFileUpdateDb. AMaking revalidation an option for edwFileResetTags rather than always happening.
  • lines changed 4, context: html, text, full: html, text
    Adding edwSimpleAssemblyName.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 137, context: html, text, full: html, text
    Adding edwBiosample and edwSettings tables.
  • lines changed 5, context: html, text, full: html, text
    Correcting index on edwQaPairedEndFastq which could not be unique after all. Added parasolId to the edwAnalysisJob table, and added cpusRequested to both edwAnalysisJob and edwAnalysisStep
  • lines changed 5, context: html, text, full: html, text
    Adding targetBaseCount and targetSeqCount fields to edwBamFile and seqCount to edwAssembly to help match assemblies to bam files.
  • lines changed 2, context: html, text, full: html, text
    Adding control field to experiment. Adding indexes to several fields.
• src/hg/encode3/encodeDataWarehouse/lib/eapLib.c
  • lines changed 15, context: html, text, full: html, text
    New micro start of analyis library.
  • lines changed 15, context: html, text, full: html, text
    Moving several edw programs into eap land. If it needs to talk to Parasol it's here. So are the programs eapSchedule and eapFinish which set up jobs for parasol and store the results respectively.
• src/hg/encode3/encodeDataWarehouse/lib/edwBamFileFromRa.c
  • lines changed 16, context: html, text, full: html, text
    Adding targetBaseCount and targetSeqCount fields.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 2, context: html, text, full: html, text
    Removing unused eapTempDir variable.
  • lines changed 3, context: html, text, full: html, text
    Exporting a few local functions for wider use.
  • lines changed 11, context: html, text, full: html, text
    Creating new library function edwOneLineSystemAttempt
  • lines changed 69, context: html, text, full: html, text
    Continued messing to get pipes reliable. Improving logic that finds matching pair fastq. Deleting some old unused code.
  • lines changed 1, context: html, text, full: html, text
    Removed some debugging.
  • lines changed 88, context: html, text, full: html, text
    Librarifying edwFileFieldsFromTags and edwValidFileUpdateDb. AMaking revalidation an option for edwFileResetTags rather than always happening.
  • lines changed 17, context: html, text, full: html, text
    Adding edwSimpleAssemblyName.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 16, context: html, text, full: html, text
    Adding edwBiosample and edwSettings tables.
  • lines changed 5, context: html, text, full: html, text
    Correcting index on edwQaPairedEndFastq which could not be unique after all. Added parasolId to the edwAnalysisJob table, and added cpusRequested to both edwAnalysisJob and edwAnalysisStep
  • lines changed 3, context: html, text, full: html, text
    Adding targetBaseCount and targetSeqCount fields to edwBamFile and seqCount to edwAssembly to help match assemblies to bam files.
  • lines changed 5, context: html, text, full: html, text
    Adding control field to experiment. Adding indexes to several fields.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 313, context: html, text, full: html, text
    Adding edwBiosample and edwSettings tables.
  • lines changed 27, context: html, text, full: html, text
    Removed some debugging.
  • lines changed 25, context: html, text, full: html, text
    Adding targetBaseCount and targetSeqCount fields to edwBamFile and seqCount to edwAssembly to help match assemblies to bam files.
  • lines changed 13, context: html, text, full: html, text
    Adding control field to experiment. Adding indexes to several fields.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 22, context: html, text, full: html, text
    Adding edwBiosample and edwSettings tables.
  • lines changed 3, context: html, text, full: html, text
    Correcting index on edwQaPairedEndFastq which could not be unique after all. Added parasolId to the edwAnalysisJob table, and added cpusRequested to both edwAnalysisJob and edwAnalysisStep
  • lines changed 5, context: html, text, full: html, text
    Adding targetBaseCount and targetSeqCount fields to edwBamFile and seqCount to edwAssembly to help match assemblies to bam files.
  • lines changed 1, context: html, text, full: html, text
    Adding control field to experiment. Adding indexes to several fields.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    New micro start of analyis library.
  • lines changed 1, context: html, text, full: html, text
    Moving several things from edw to eap.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 15, context: html, text, full: html, text
    Fixing time format in a view. Adding hg38 stuff.
• src/hg/encode3/encodeDataWarehouse/lib/restartDaemons
  • lines changed 1, context: html, text, full: html, text
    Bumping up analysis jobs since running remotely.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 2, context: html, text, full: html, text
    Utility to look at a job table.
  • lines changed 10, context: html, text, full: html, text
    Fixing merge conflicts
  • lines changed 6, context: html, text, full: html, text
    Adding 4 missing directories and alphabetizing.
  • lines changed 3, context: html, text, full: html, text
    Moving several things from edw to eap.
  • lines changed 6, context: html, text, full: html, text
    Moved to eap.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/cellTypeSlim.tab
  • lines changed 447, context: html, text, full: html, text
    It's painful enough to reproduce this table I'll put it under source code control. It is a few fields from the encode2 cellType - just sex and organism.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 58, context: html, text, full: html, text
    Faking up a biosample table based on term,organism, and sex fields from encode2.
  • lines changed 117, context: html, text, full: html, text
    Bringing in biosamples from Stanford too.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/makefile
  • lines changed 3, context: html, text, full: html, text
    Faking up a biosample table based on term,organism, and sex fields from encode2.
  • lines changed 1, context: html, text, full: html, text
    Bringing in biosamples from Stanford too.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 72, context: html, text, full: html, text
    Bringing in encode2 metadata too.
  • lines changed 37, context: html, text, full: html, text
    Adding code to find control experiment. So far, just the Stanford side.
  • lines changed 59, context: html, text, full: html, text
    Seem to find controls for ChIP-seq on the UCSC side now.
  • lines changed 2, context: html, text, full: html, text
    Removing some debugging.
  • lines changed 1, context: html, text, full: html, text
    Trying to avoid using control sets as target sets for peak callers.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 4, context: html, text, full: html, text
    Changed spelling to match database.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c
  • lines changed 8, context: html, text, full: html, text
    Fixing zero-divide.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/edwSamRepeatAnalysis.c
  • lines changed 85, context: html, text, full: html, text
    Tool to parse out sam file run against repeatmasker library.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamRepeatAnalysis/makefile
  • lines changed 4, context: html, text, full: html, text
    Tool to parse out sam file run against repeatmasker library.
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/edwSolexaToSangerFastq.c
  • lines changed 123, context: html, text, full: html, text
    Utility to convert quality scores in fastqs from Solexa to Sanger style seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSolexaToSangerFastq/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to convert quality scores in fastqs from Solexa to Sanger style seems to work.
• src/hg/genePredCheck/genePredCheck.c
  • lines changed 1, context: html, text, full: html, text
    initialize variable to avoid compiler complaint refs #12209
• src/hg/hgGene/alleles.c
  • lines changed 1, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/hgMirror/hgMirror
  • lines changed 336, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 5, context: html, text, full: html, text
    making sure that trackDb actually exists before changing it
  • lines changed 2, context: html, text, full: html, text
    forgot to always mirror the slowest table of all, trackDb.
  • lines changed 15, context: html, text, full: html, text
    not trying to parse rsync log anymore, just checking at-queue now
• src/hg/hgTables/gffOut.c
  • lines changed 4, context: html, text, full: html, text
    Fixes #12513. hgTables gtf output problem when table is a split-table. For example, dm3.rmsk
• src/hg/hgTables/intersect.c
  • lines changed 1, context: html, text, full: html, text
    eliminate useless compare of an unsigned int with < 0 refs #12209
• src/hg/hgTablesTest/hgTablesTest.c
  • lines changed 5, context: html, text, full: html, text
    fixup potential use of unset variable and better localize variables refs #12209
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 1, context: html, text, full: html, text
    eliminate a useless self to self assignment statement refs #12209
• src/hg/hgTracks/factorSource.c
  • lines changed 1, context: html, text, full: html, text
    fix a broken if() statement that allowed always TRUE behavior refs #12209
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    adding cpgIslandExtUnmasked track handler refs #11681
• src/hg/hgTracks/snakeTrack.c
  • lines changed 4, context: html, text, full: html, text
    draw the pale yellow for N's in snakes
  • lines changed 3, context: html, text, full: html, text
    color mismatches with N's a pale yellow if the N is in the query, or notat all if there is an N in the reference
    
• src/hg/hgTracks/variation.c
  • lines changed 7, context: html, text, full: html, text
    fixup enum type casts refs #12209
• src/hg/hgTracks/variation.h
  • lines changed 1, context: html, text, full: html, text
    sumValues can be negative now using an int instead of unsigned refs #12209
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixup broken if() statement, was always drawing chains where it should not refs @12209
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    fixup enum types conversions and eliminate useless duplicate parentheses refs #12209
  • lines changed 25, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/hgVai/hgVai.c
  • lines changed 11, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    open link to GENCODE tags descirpiton in another tab
  • lines changed 12, context: html, text, full: html, text
    don't include GENCODE links to APPRIS, PDB, or SwissProt if it is not a protein coding transcript
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    eliminate always TRUE condition of if() statement refs @12209
• src/hg/hgc/pubs.c
  • lines changed 12, context: html, text, full: html, text
    breaking long lines in fasta view of pubs tracks, adding better sequenceIDs (refs #12212)
    
• src/hg/htdocs/cite.html
  • lines changed 145, context: html, text, full: html, text
    Redid the format of this page to shorten it and hopefully make it more usable. Added refs for big*, track hubs, and gene sorter, and updated a few of the other entries.
• src/hg/htdocs/contacts.html
  • lines changed 218, context: html, text, full: html, text
    Reorganized page, updated info, added twitter link.
  • lines changed 13, context: html, text, full: html, text
    Added staff picture to top of page.
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
  • lines changed 1, context: html, text, full: html, text
    tiny change to readme file
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 18, context: html, text, full: html, text
    adding intro to containers in trackDb doc, refs #12486
  • lines changed 19, context: html, text, full: html, text
    fiddling again with the trackDb container intro, adding examples
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 13, context: html, text, full: html, text
    adding intro to containers in trackDb doc, refs #12486
  • lines changed 18, context: html, text, full: html, text
    fiddling again with the trackDb container intro, adding examples
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4, context: html, text, full: html, text
    changing wording after code review rm #12486
  • lines changed 5, context: html, text, full: html, text
    adding intro to containers in trackDb doc, refs #12486
  • lines changed 2, context: html, text, full: html, text
    fixing stray div, refs #12079
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 40, context: html, text, full: html, text
    Adding E coli hub announcements, refs #11889
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 22, context: html, text, full: html, text
    Updated a few citations.
• src/hg/htdocs/images/browserStaff13.jpg
  • lines changed 0, context: html, text, full: html, text
    Added staff picture to top of page.
• src/hg/htdocs/indexNews.html
  • lines changed 75, context: html, text, full: html, text
    Adding E coli hub announcements, refs #11889
• src/hg/htdocs/license/index.html
  • lines changed 27, context: html, text, full: html, text
    Added exceptions to commercial licensing requirements.
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/inc/wiggle.h
  • lines changed 1, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/lib/ggGraph.c
  • lines changed 1, context: html, text, full: html, text
    remove useless self assignment refs #12209
• src/hg/lib/ggTypes.c
  • lines changed 5, context: html, text, full: html, text
    casting enum to avoid compile warnings refs #12209
• src/hg/lib/haplotypes.c
  • lines changed 5, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/lib/hdb.c
  • lines changed 135, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 2, context: html, text, full: html, text
    A recent change introduced a case in which fullName could be useduninitialized. Give it the sensible default value first, and
    override if there's an unusual case. refs #12352
    
• src/hg/lib/hgFind.c
  • lines changed 24, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/lib/jksql.c
  • lines changed 335, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 5, context: html, text, full: html, text
    fixing null pointer bug in jksql introduced with my last commit
  • lines changed 8, context: html, text, full: html, text
    not adding failover connections to the connection pool, as they aremanaged by their "parent". This lead to invalid pointers when failover
    was activated in the sqlCleanup step upon exit. Also fixing a debug
    message.
    
  • lines changed 3, context: html, text, full: html, text
    adding additional null pointer checks, just in case
  • lines changed 36, context: html, text, full: html, text
    Changing handling of sqlConnect to allow a db that exists onlyon the failover server, not on the main one.
    
  • lines changed 5, context: html, text, full: html, text
    handling the show table status command with failover connections
• src/hg/lib/pubsArticle.as
  • lines changed 17, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsBingArticle.as
  • lines changed 17, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsBingArticle.sql
  • lines changed 5, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsBingBlat.as
  • lines changed 30, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
  • lines changed 1, context: html, text, full: html, text
    fixing typo
  • lines changed 3, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBingBlat.sql
  • lines changed 13, context: html, text, full: html, text
    fixing stray div, refs #12079
  • lines changed 2, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBingBlatPsl.as
  • lines changed 26, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
  • lines changed 1, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBingBlatPsl.sql
  • lines changed 1, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBingSequenceAnnot.as
  • lines changed 12, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
  • lines changed 1, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBingSequenceAnnot.sql
  • lines changed 1, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBlat.as
  • lines changed 19, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
  • lines changed 1, context: html, text, full: html, text
    fixing typo
  • lines changed 12, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBlat.sql
  • lines changed 13, context: html, text, full: html, text
    fixed some more typos in pubs as/sql files
• src/hg/lib/pubsBlatPsl.as
  • lines changed 26, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsBlatPsl.sql
  • lines changed 28, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerAnnot.as
  • lines changed 12, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerAnnot.sql
  • lines changed 1, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerBand.as
  • lines changed 9, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerBand.sql
  • lines changed 1, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerGene.as
  • lines changed 9, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerGene.sql
  • lines changed 1, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsMarkerSnp.as
  • lines changed 9, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/pubsSequenceAnnot.as
  • lines changed 12, context: html, text, full: html, text
    adding .as files for publications track, ref #12212
• src/hg/lib/search.c
  • lines changed 8, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/hg/lib/snp125Ui.c
  • lines changed 1, context: html, text, full: html, text
    remove useless enum compare to less than zero never possible refs #12209
• src/hg/lib/sqlProg.c
  • lines changed 5, context: html, text, full: html, text
    I found that when hgsql's mysql child process exited with an error,hgsql was still exiting with status==0, so the failure did not halt my
    script as expected. Fix: propagate child's exit status after parent
    checks that it completed normally (i.e. execvp didn't fail).
    
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    fill in a db description for assembly hubs even if it's not set in thegenomes.txt file
    
• src/hg/lib/wigDataStream.c
  • lines changed 11, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 2, context: html, text, full: html, text
    addressing gcc warnings
• src/hg/lib/wiggleCart.c
  • lines changed 2, context: html, text, full: html, text
    casting enum to avoid compile warnings refs #12209
• src/hg/liftAgp/liftAgp.c
  • lines changed 2, context: html, text, full: html, text
    fixup argument declaration to match actual use refs #12209
• src/hg/liftUp/liftUp.c
  • lines changed 1, context: html, text, full: html, text
    clarify genepred types in usage message refs #11681
• src/hg/makeDb/doc/hg38.txt
  • lines changed 55, context: html, text, full: html, text
    cpgIslands done blat server on default position set refs #11681
  • lines changed 70, context: html, text, full: html, text
    genscan track done on contig hard masked sequence refs #11681
• src/hg/makeDb/doc/mm10.txt
  • lines changed 244, context: html, text, full: html, text
    Added dbSNP build 138 tracks for mm10. refs #12490Enhanced doDbSnp.pl to use an NCBI Assembly Report file to map
    RefSeq assembly contigs used by dbSNP to GenBank assembly contigs
    used in our builds.
    
• src/hg/makeDb/outside/allenBrain/allenCollectSeq/allenCollectSeq.c
  • lines changed 1, context: html, text, full: html, text
    remove bad ascii character from ascii string refs #12209
• src/hg/makeDb/outside/hgFlyBase/hgFlyBase.c
  • lines changed 1, context: html, text, full: html, text
    fix empty if statement, path never taken before refs #12209
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    checking in hg38 definitions refs #11681
  • lines changed 3, context: html, text, full: html, text
    correctly avoiding checks on wormBaseId flyBaseGeneId and sgdCodingId on hg38 refs #11681
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • lines changed 25, context: html, text, full: html, text
    Added -justSchema option, to suppress information depending on contents as opposed to structure of database. Comparing dbSnoop -justSchema output of two databases is an easy way to see if the databases are synchonized (including indexes).
• src/hg/makeDb/trackDb/contrastGene.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/esRegGeneToMotif.html
  • lines changed 11, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/fugu/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/horse/equCab2/nscanGene.html
  • lines changed 25, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/human/coriellDelDup.html
  • lines changed 1, context: html, text, full: html, text
    Removed stray </a> tag that was causing hgTablesTest robot error (redmine #12352)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    removing release tag for human pubs track override, refs #12362
  • lines changed 3, context: html, text, full: html, text
    Adding override statement to put hg19 Web Sequences track under the Phenotype and Literature group, refs #12212
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Commiting change to wgEncode.ra hg19 for staging GENCODE V19 on beta refs #12452
  • lines changed 1, context: html, text, full: html, text
    Staging V19 Gencode for public release refs #12452
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.ra
  • lines changed 1, context: html, text, full: html, text
    changing GencodeV17 to not be default display with V19 release, refs #12452
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 2, context: html, text, full: html, text
    setting default track visibilities refs #11681
• src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html
  • lines changed 63, context: html, text, full: html, text
    now have a superTrack for two CpG Island tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/crossMatchUnique.html
  • lines changed 12, context: html, text, full: html, text
    description pages for the HMMER vs. Cross-Match unique tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 60, context: html, text, full: html, text
    Added a new Assembly Details section with some prelimary info (redmine #11706)
  • lines changed 21, context: html, text, full: html, text
    mention sections to fill in refs #11706
• src/hg/makeDb/trackDb/human/hg38/hmmerUnique.bed
  • lines changed 12, context: html, text, full: html, text
    description pages for the HMMER vs. Cross-Match unique tracks refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 26, context: html, text, full: html, text
    now have a superTrack for two CpG Island tracks refs #11681
  • lines changed 29, context: html, text, full: html, text
    setting default track visibilities refs #11681
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 4, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/pubsBingBlat.html
  • lines changed 2, context: html, text, full: html, text
    Commenting out lines about Individual Sequence matches track, refs #12212
  • lines changed 2, context: html, text, full: html, text
    Adding html names for quotes, and adding missing period after Publications track link, refs #12212
• src/hg/makeDb/trackDb/rat/rn3/ecoresFr1.html
  • lines changed 10, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/rat/rn3/ecoresTetraodon.html
  • lines changed 10, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/rat/rn3/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/rat/sgpGene.html
  • lines changed 6, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
  • lines changed 2, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/sgpGene.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/tetraodon/ecoresHg17.html
  • lines changed 11, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in long label found by contributor. refs #10954
• src/hg/makeDb/trackDb/worm/caeRem3/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 1, context: html, text, full: html, text
    Changes related to code review, refs #12428
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 2, context: html, text, full: html, text
    correct cloneString qName and tName into psl structure to avoid free problem refs #12352
• src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.bed.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/expected/redmine12502.psl.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/redmine12502.lav.gz
  • lines changed 0, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/mouseStuff/lavToPsl/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    add test cases for bug refs #12502
• src/hg/near/hgNearTest/hgNearTest.c
  • lines changed 5, context: html, text, full: html, text
    fixup initialization of variable before use and localize variables refs #12209
• src/hg/oneShot/freen/freen.c
  • lines changed 14, context: html, text, full: html, text
    Freen counts through some big numbers.
• src/hg/phyloGif/phyloGif.c
  • lines changed 7, context: html, text, full: html, text
    Changing output of phyloGif back go actual gif instead of png. I first tried changing stuff to be png, but there were many references in html files that would be a real pain to change back. Besides, the gif code is stable and works well. There is no patents on it anymore, and no reason to not use it when it is convenient, which it is here.
  • lines changed 7, context: html, text, full: html, text
    It turns out that although it compiles,it does not actually work unless one turns off COLOR32 setting in common.mk,
    which is not going to happen.
    I have a local development branch where this works.
    Alternatives such as converting color values from 32-bit to 256 colors for gif saving
    could be explored in the future.
    
    Revert "Changing output of phyloGif back go actual gif instead of png. I first tried changing stuff to be png, but there were many references in html files that would be a real pain to change back. Besides, the gif code is stable and works well. There is no patents on it anymore, and no reason to not use it when it is convenient, which it is here."
    
    This reverts commit 6f8f179499a5fccd49717db4af56d7aec5c9b26c.
    
• src/hg/txGraph/txOrtho/txOrtho.c
  • lines changed 2, context: html, text, full: html, text
    remove useless extra parentheses refs #12209
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 177, context: html, text, full: html, text
    Added dbSNP build 138 tracks for mm10. refs #12490Enhanced doDbSnp.pl to use an NCBI Assembly Report file to map
    RefSeq assembly contigs used by dbSNP to GenBank assembly contigs
    used in our builds.
    
• src/hg/utils/gapToLift/gapToLift.c
  • lines changed 3, context: html, text, full: html, text
    remove always false if() statement due to unsigned int compare to < 0 refs #12209
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 9, context: html, text, full: html, text
    fix up gff3ToPsl to grok NCBI's mappings from the haplotypes to thereference chroms
    
  • lines changed 1, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 1, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes
  • lines changed 26, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/hg/utils/gff3ToPsl/tests/input/locusNameAndSize.txt
  • lines changed 24, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/hg/utils/gff3ToPsl/tests/input/locusToChrom.sed
  • lines changed 24, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    make gff3ToPsl pass its tests.
• src/inc/common.h
  • lines changed 1, context: html, text, full: html, text
    changed BIGNUM to be even bigger because it was casuing a bug inbrowsers with chroms bigger than 0x3ffffff
    
  • lines changed 1, context: html, text, full: html, text
    BIGNUM back to 0x3fffffff per Jim
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
• src/inc/linefile.h
  • lines changed 5, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/inc/portable.h
  • lines changed 3, context: html, text, full: html, text
    Adding mustRemove wrapper around remove.
• src/inc/udc.h
  • lines changed 9, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/lib/cheapcgi.c
  • lines changed 6, context: html, text, full: html, text
    casting enum to avoid compile warnings refs #12209
• src/lib/common.c
  • lines changed 2, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
• src/lib/linefile.c
  • lines changed 42, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 2, context: html, text, full: html, text
    fixing a null pointer bug introduced in earlier commit today
• src/lib/maf.c
  • lines changed 1, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Changing output of phyloGif back go actual gif instead of png. I first tried changing stuff to be png, but there were many references in html files that would be a real pain to change back. Besides, the gif code is stable and works well. There is no patents on it anymore, and no reason to not use it when it is convenient, which it is here.
  • lines changed 1, context: html, text, full: html, text
    It turns out that although it compiles,it does not actually work unless one turns off COLOR32 setting in common.mk,
    which is not going to happen.
    I have a local development branch where this works.
    Alternatives such as converting color values from 32-bit to 256 colors for gif saving
    could be explored in the future.
    
    Revert "Changing output of phyloGif back go actual gif instead of png. I first tried changing stuff to be png, but there were many references in html files that would be a real pain to change back. Besides, the gif code is stable and works well. There is no patents on it anymore, and no reason to not use it when it is convenient, which it is here."
    
    This reverts commit 6f8f179499a5fccd49717db4af56d7aec5c9b26c.
    
• src/lib/osunix.c
  • lines changed 8, context: html, text, full: html, text
    Adding mustRemove wrapper around remove.
• src/lib/psl.c
  • lines changed 11, context: html, text, full: html, text
    fix up gff3ToPsl to grok NCBI's mappings from the haplotypes to thereference chroms
    
• src/lib/udc.c
  • lines changed 11, context: html, text, full: html, text
    library changes for the browser box: This changes mostly hdb and jksql,plus - to a smaller extent - various other places in the code that deal
    with /gbdb/ files. The overall aim is to make it possible to have the
    data remote at UCSC while having the CGIs on a machine far away. At up to
    180msecs distance from UCSC (Europe,Japan), each query can get slow. So
    I tried to reduce the number of queries sent to UCSC while allowing to
    keep some mysql tables on localhost.
    
    I changed four things:
    - extend larry's table cache to include field names. The code uses
    "describe" very often, which is slow from remote. With a table name
    cache these queries can be handled locally. This is configured in
    hg.conf
    - mysql "failover" connections: a mysql connection can have a 2nd
    connection that is used if a query fails, configured in hg.conf
    (I didn't call it "remote" connections, because we use that term already
    in the code)
    - mysql lazy connects: don't connect a sqlConnection right away, but
    only when needed. a mysql connect takes >500msecs from across the
    atlantic.
    - move gbdb: patch various places that use absolute "/gbdb/" pathnames
    to go through a central function that can change the filename of
    gbdb files to something else, as configured in hg.conf
    
    Plus patch 1 or 2 lines for more speed + update the hgMirror script
    
  • lines changed 1, context: html, text, full: html, text
    fixing a null pointer bug introduced in earlier commit today
• src/oneShot/sqlToAs/makefile
  • lines changed 7, context: html, text, full: html, text
    a quick .sql to .as converter
• src/oneShot/sqlToAs/sqlToAs
  • lines changed 98, context: html, text, full: html, text
    a quick .sql to .as converter
• src/parasol/inc/paraMessage.h
  • lines changed 9, context: html, text, full: html, text
    Moving pmSendStringWithRetries and pmHubSingleLineQuery from para application to library, so the edwAnalysisDaemon can use it too.
  • lines changed 7, context: html, text, full: html, text
    Librarified some message-the-hub stuff so can reuse
  • lines changed 1, context: html, text, full: html, text
    Making pmHubMultilineQuery return a slName list instead of a slRef list with string values. This saves about 8 freez() calls and is a bit tidier overall.
  • lines changed 16, context: html, text, full: html, text
    Making paraPstat2Job - a parsed version of parasol pstat2 output - public.
• src/parasol/lib/paraMessage.c
  • lines changed 41, context: html, text, full: html, text
    Moving pmSendStringWithRetries and pmHubSingleLineQuery from para application to library, so the edwAnalysisDaemon can use it too.
  • lines changed 46, context: html, text, full: html, text
    Librarified some message-the-hub stuff so can reuse
  • lines changed 5, context: html, text, full: html, text
    Making pmHubMultilineQuery return a slName list instead of a slRef list with string values. This saves about 8 freez() calls and is a bit tidier overall.
  • lines changed 13, context: html, text, full: html, text
    Making paraPstat2Job - a parsed version of parasol pstat2 output - public.
• src/parasol/para/para.c
  • lines changed 49, context: html, text, full: html, text
    Moving pmSendStringWithRetries and pmHubSingleLineQuery from para application to library, so the edwAnalysisDaemon can use it too.
  • lines changed 40, context: html, text, full: html, text
    Librarified some message-the-hub stuff so can reuse
  • lines changed 40, context: html, text, full: html, text
    Making pmHubMultilineQuery return a slName list instead of a slRef list with string values. This saves about 8 freez() calls and is a bit tidier overall.
• src/parasol/paraHub/paraHub.c
  • lines changed 18, context: html, text, full: html, text
    Adding -all option to list batches, to see finished ones too.
• src/parasol/parasol/parasol.c
  • lines changed 15, context: html, text, full: html, text
    Improving exit code handling.
  • lines changed 6, context: html, text, full: html, text
    Adding -all option to list batches, to see finished ones too.
  • lines changed 7, context: html, text, full: html, text
    Added -printId option, used by edwAnalysisDaemon now. (Wait option no longer used by that daemon.
  • lines changed 4, context: html, text, full: html, text
    Fixing merge conflicts
• src/product/scripts/README.trashCleaning
  • lines changed 17, context: html, text, full: html, text
    indicate that a simple system could be used refs #11957
• src/utils/qa/2bitCompare
  • lines changed 5, context: html, text, full: html, text
    Per Ann, added 'rr' to hgwbeta output lines and adjusted spacing of other output lines to compensate
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v295 preview1 refs #12352
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 11, context: html, text, full: html, text
    correctly copy binaries from hgwdev to hgwbeta after they are build refs #12352

• lines changed: 15555
• files changed: 362