All File Changes

v291_preview to v291_preview2 (2013-10-07 to 2013-10-14) v291

• python/lib/ucscGb/encode/track.py
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    small updates to ra library in gbData
• python/lib/ucscGb/gbData/ra/raFile.py
  • lines changed 21, context: html, text, full: html, text
    small updates to ra library in gbData
• python/lib/ucscGb/gbData/ra/raStanza.py
  • lines changed 49, context: html, text, full: html, text
    small updates to ra library in gbData
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 2, context: html, text, full: html, text
    Making this treat 'pooled' as a synonym for blank and 'n/a' and 'both' in the replicate field.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
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    Adding new update parameter to edwAddSubmitJob.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 41, context: html, text, full: html, text
    Moving some logic inside of a errCatch block so that the error message actually makes it to the corresponding field of the edwSubmit table. Setting value of edwSubmit.metaChangeCount to help user know something happened when the do an update with new tags on old files.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 63, context: html, text, full: html, text
    Adding user drop down and # to view button. Maybe fixing bug that makes it show up as stalled sometimes.
  • lines changed 2, context: html, text, full: html, text
    Moving div with log in button outside of form. This seems to fix Bug #752
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
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    Base on the Jim's CR 11880 feedbaci note #1:looks good except for edwUserNameFromFileId(struct sqlConnection *conn, int fId). I'd rather this continue to return NULL if the user is not found, and maybe, if you like, have a wrapper function (or the caller function) that converts this NULL to the "an unknown user" This is so that things that want to take a different action for when the user is not found to not have to know what string to search for.
    
    edwUserNameFromFileId will return edwUser or NULL if the user is not found.
    A new wrapper function edwFindOwnerNameFromFileId(struct sqlConnection *conn, int fId) will return either the user name or "an unknown user" if user is not found. edwWebDeprecate will use this new function instead of
    edwUserNameFromFileId.
    
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 6, context: html, text, full: html, text
    Adding a check box that lets them update file tags for an already submitted file. If unchecked it will complain when manifest contains a file already in the warehouse unless the tags match exactly.
  • lines changed 1, context: html, text, full: html, text
    Improving text associated with new 'Update' button
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Adding new update parameter to edwAddSubmitJob.
  • lines changed 6, context: html, text, full: html, text
    Base on the Jim's CR 11880 feedbaci note #1:looks good except for edwUserNameFromFileId(struct sqlConnection *conn, int fId). I'd rather this continue to return NULL if the user is not found, and maybe, if you like, have a wrapper function (or the caller function) that converts this NULL to the "an unknown user" This is so that things that want to take a different action for when the user is not found to not have to know what string to search for.
    
    edwUserNameFromFileId will return edwUser or NULL if the user is not found.
    A new wrapper function edwFindOwnerNameFromFileId(struct sqlConnection *conn, int fId) will return either the user name or "an unknown user" if user is not found. edwWebDeprecate will use this new function instead of
    edwUserNameFromFileId.
    
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 5, context: html, text, full: html, text
    Adding a few new fields - edwSubmit.metaChangeCount and edwValidFile*QaStatus
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 2, context: html, text, full: html, text
    Adding new update parameter to edwAddSubmitJob.
  • lines changed 10, context: html, text, full: html, text
    Base on the Jim's CR 11880 feedbaci note #1:looks good except for edwUserNameFromFileId(struct sqlConnection *conn, int fId). I'd rather this continue to return NULL if the user is not found, and maybe, if you like, have a wrapper function (or the caller function) that converts this NULL to the "an unknown user" This is so that things that want to take a different action for when the user is not found to not have to know what string to search for.
    
    edwUserNameFromFileId will return edwUser or NULL if the user is not found.
    A new wrapper function edwFindOwnerNameFromFileId(struct sqlConnection *conn, int fId) will return either the user name or "an unknown user" if user is not found. edwWebDeprecate will use this new function instead of
    edwUserNameFromFileId.
    
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 3, context: html, text, full: html, text
    Adding a few new fields - edwSubmit.metaChangeCount and edwValidFile*QaStatus
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 25, context: html, text, full: html, text
    Adding a few new fields - edwSubmit.metaChangeCount and edwValidFile*QaStatus
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 3, context: html, text, full: html, text
    Adding a few new fields - edwSubmit.metaChangeCount and edwValidFile*QaStatus
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 14, context: html, text, full: html, text
    Fixed braney's allergy as per redmine 11889. Long lists of assemblies were not wrapping in the HTML table because there were no spaces. So this now insures spaces in the list.
• src/hg/hgTables/galaxy.c
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    Updating links to Galaxy. refs #11898
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    Updating links to Galaxy. refs #11898
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    Updating links to Galaxy. refs #11898
• src/hg/hgTables/usage.c
  • lines changed 1, context: html, text, full: html, text
    Updating links to Galaxy. refs #11898
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    leave room for the duplication bars in the pack mode
  • lines changed 21, context: html, text, full: html, text
    upgrade to Glenn's new API which allows me to only request what I need.
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    fixing problem when spaces where in the ID list, #10956
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    Adding news release item about DGV update track refs #11200
  • lines changed 1, context: html, text, full: html, text
    Making Variant into Variation per Angies feedback refs #11200
• src/hg/htdocs/indexNews.html
  • lines changed 53, context: html, text, full: html, text
    Adding news release item about DGV update track refs #11200
  • lines changed 1, context: html, text, full: html, text
    Making Variant into Variation per Angies feedback refs #11200
• src/hg/js/ajax.js
  • lines changed 4, context: html, text, full: html, text
    Fix for regex which scrapes out json objects as per redmine 11873. Some IPSs are stripping newlines so regex must tolerate that. This problem was found by Rachel working from England.
• src/hg/lib/annoGratorGpVar.c
  • lines changed 4, context: html, text, full: html, text
    Fixing unsigned int underflow (affects variants in first 5000 bases of chrom).
• src/hg/lib/annoStreamDb.c
  • lines changed 3, context: html, text, full: html, text
    Found one more place where a resetMergeState was necessary.Without the reset, large-bin items from the previous chrom could
    still be hanging out in bigItemQueue when we query the next chrom.
    
  • lines changed 24, context: html, text, full: html, text
    Calling asdDoQueryChunking from way down in nextRowFromBuffer wasn'ta good idea because nextRowFromBuffer might have a caller that assumes
    we're done merging... but after calling asdDoQueryChunking, we need
    to start over with the merging. So, return NULL, but set self->needQuery;
    then, way up in asdNextRow, if we get a NULL, then check self->needQuery,
    and try again if necessary.
    
• src/hg/lib/gpFx.c
  • lines changed 12, context: html, text, full: html, text
    Fix for the latest bug uncovered by the tenacious users of MLQ #11775:a deletion that spans the UTR/CDS boundary was something I hadn't tested
    against yet.
    refs #11775
    
  • lines changed 4, context: html, text, full: html, text
    Don't add splice_region_variant for a variant that falls at beginningor end of transcript -- only for actual splice regions.
    
• src/hg/lib/haplotypes.c
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    Removed an invalid assert. The assert was that the only valid case of a single haplotype for a gene model was where there was no variation from reference. However for gene uc010rxh.2 the single hapl;otype is for no variation from non-reference. This is for redmine #11894.
• src/hg/lib/hui.c
  • lines changed 13, context: html, text, full: html, text
    let people put a treeImage in the composite matrix (for snakes)
• src/hg/makeDb/doc/hg19.txt
  • lines changed 69, context: html, text, full: html, text
    lastz done to phyCat1 Sperm whale refs #10272
  • lines changed 43, context: html, text, full: html, text
    getting ready for pushq of clinvar tracks, rm #10956 and #11228
  • lines changed 109, context: html, text, full: html, text
    fixing simple merge conflict in doc/hg19.txt
    Conflicts:
    src/hg/makeDb/doc/hg19.txt
    
• src/hg/makeDb/genbank/etc/dbload
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    adding max hours to genbank load
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 4, context: html, text, full: html, text
    copy binaries from rrnfs1 which is binary compatible with the euronode
  • lines changed 1, context: html, text, full: html, text
    a couple of tweaks to the eurotoad scripts
• src/hg/makeDb/genbank/etc/euronode-dbload
  • lines changed 4, context: html, text, full: html, text
    copy binaries from rrnfs1 which is binary compatible with the euronode
  • lines changed 1, context: html, text, full: html, text
    a couple of tweaks to the eurotoad scripts
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    fix xenTro1 multiz upstream table
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 12, context: html, text, full: html, text
    make a prioritized list for genbank loading on the rr.
  • lines changed 131, context: html, text, full: html, text
    fiddle with assembly priority again
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 14, context: html, text, full: html, text
    add maxHours option
  • lines changed 6, context: html, text, full: html, text
    adding max hours to genbank load
• src/hg/makeDb/genbank/src/lib/gbCommon.sh
  • lines changed 5, context: html, text, full: html, text
    tweak to allow a prioritized list for rr.dbs
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Since macEug1 is no longer active on the RR, removed it from several groups as it was causing unnecessary errors in joinerCheck
  • lines changed 2, context: html, text, full: html, text
    Added ClinVar Variants tables to hg19 tablesIgnored (redmine #10956)
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 8, context: html, text, full: html, text
    Made some edits to the details page (redmine #10956)
• src/hg/makeDb/trackDb/human/dgvPlus.html
  • lines changed 2, context: html, text, full: html, text
    Punctuation code revew change to dgvPlus.html refs #11879
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Changing trackDb.ra to remove dgv from hg18 and hg19, adding entry in hg17/trackDb.ra to preserve on hg17, for dgvPlus hg17/hg19 release refs # 11200
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
  • lines changed 1, context: html, text, full: html, text
    Adding American to alligator on hg19vertChainNet.html and matrix for page, code review refs #11879
  • lines changed 1, context: html, text, full: html, text
    Capitalizing Alligator, code review #11879
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 2, context: html, text, full: html, text
    Adding American to alligator on hg19vertChainNet.html and matrix for page, code review refs #11879
  • lines changed 2, context: html, text, full: html, text
    Capitalizing Alligator, code review #11879
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    getting ready for pushq of clinvar tracks, rm #10956 and #11228
  • lines changed 15, context: html, text, full: html, text
    Changing trackDb.ra to remove dgv from hg18 and hg19, adding entry in hg17/trackDb.ra to preserve on hg17, for dgvPlus hg17/hg19 release refs # 11200
  • lines changed 4, context: html, text, full: html, text
    Edited short/long labels for uniformity and space considerations (redmine #10956)
  • lines changed 3, context: html, text, full: html, text
    Per Max, removed NCBI from the track long labels (redmine #10956)
• src/lib/annoGrator.c
  • lines changed 2, context: html, text, full: html, text
    qTail->start should be compared to region end only when it's on the same chrom.
• src/utils/calc/calc.c
  • lines changed 9, context: html, text, full: html, text
    rm #11884: change to calc, the most important tool of all
  • lines changed 5, context: html, text, full: html, text
    small change after rm #11884
  • lines changed 1, context: html, text, full: html, text
    fixed typo
  • lines changed 3, context: html, text, full: html, text
    moving curly brackets for brian
• src/utils/qa/checkTableStatus.csh
  • lines changed 3, context: html, text, full: html, text
    replacing the hard-coded location of the genbank TABLE STATUS dump files to the global qaConfig-defined one. Sometimes they are on rrnfs1 and sometimes they are on hgnfs1
• src/utils/qa/getRRdatabases.csh
  • lines changed 1, context: html, text, full: html, text
    removed 2 nonexistent rr machines
  • lines changed 1, context: html, text, full: html, text
    switching hard-coded nfs1 fileserver name for qaConfig variable
• src/utils/qa/getRRdumpfile.csh
  • lines changed 4, context: html, text, full: html, text
    switching hard-coded nfs1 fileserver name for qaConfig variable
• src/utils/qa/getRRtableStatus.csh
  • lines changed 2, context: html, text, full: html, text
    switching hard-coded nfs1 fileserver name for qaConfig variable
• src/utils/qa/getRRtables.csh
  • lines changed 2, context: html, text, full: html, text
    switching hard-coded nfs1 fileserver name for qaConfig variable
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    removed tableDumpDates from the makefile since I removed the script from the repository
• src/utils/qa/qaConfig.bash
  • lines changed 1, context: html, text, full: html, text
    adding a qascript-wide variable to these two qaConfig files for the location of the genank TABLE STATUS dump files. Sometimes they are located on rrnfs1 and sometimes on hgnfs1. This will keep it all in one place. I will also edit all of the qascript files that look for those dumpfiles to use this variable instead.
  • lines changed 1, context: html, text, full: html, text
    the quotes worked better for the csh version, so I'm hoping they do for the bash version as well
• src/utils/qa/qaConfig.csh
  • lines changed 1, context: html, text, full: html, text
    adding a qascript-wide variable to these two qaConfig files for the location of the genank TABLE STATUS dump files. Sometimes they are located on rrnfs1 and sometimes on hgnfs1. This will keep it all in one place. I will also edit all of the qascript files that look for those dumpfiles to use this variable instead.
  • lines changed 1, context: html, text, full: html, text
    I think this will work better with a quoted string
• src/utils/qa/tableDumpDates.csh
  • lines changed 36, context: html, text, full: html, text
    removing this script. it is a holdout from when each rr node had its own MySQL server.

• lines changed: 979
• files changed: 83