All File Changes

v337_preview to v337_preview2 (2016-08-01 to 2016-08-08) v337

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    db20179a265f3bf06eea5a3ee9da75f0e60d1265 Sun Aug 7 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    db20179a265f3bf06eea5a3ee9da75f0e60d1265 Sun Aug 7 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    db20179a265f3bf06eea5a3ee9da75f0e60d1265 Sun Aug 7 01:11:52 2016 -0700
    Installing updated hg.conf files from UCSC servers
    
• src/blat/makefile
  • lines changed 1, context: html, text, full: html, text
    d2268a67d14ffbdfe295f07b5fda09e8a7c3c9b0 Thu Aug 4 10:48:36 2016 -0700
    new htslib compile on make requires some extra -lz library links refs #17833
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 7, context: html, text, full: html, text
    102acb1e520a68eed9cca59f1a39a0cfc3de84ab Fri Aug 5 14:57:31 2016 -0700
    fixing gbib speed problem after refseq change, refs #17842
    
• src/hg/cirm/cdw/cdwReallyRemoveFiles/cdwReallyRemoveFiles.c
  • lines changed 4, context: html, text, full: html, text
    1fe9e7113a5e738c2522cbce34a8394c83805970 Wed Aug 3 13:26:24 2016 -0700
    Refactoring cdwReallyRemoveFiles.c to share code that deletes records on files in QA tables in database with cdwFileResetTags. Made records from cdwGroupFiles get removed as need be too.
    
• src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
  • lines changed 8, context: html, text, full: html, text
    2d63308251a04de8faf667f20e1f302980f23627 Wed Aug 3 19:12:01 2016 -0700
    Making it behave better when there are multiple files with same md5 sum in submission.
    
  • lines changed 5, context: html, text, full: html, text
    8f3bafddc2b381dd1b55ca51f8bac710a6f0bdc9 Fri Aug 5 10:35:46 2016 -0700
    adding in an automatic cdw database backup, refs #17334
    
• src/hg/cirm/cdw/cdwSummary/cdwSummary
  • lines changed 1939, context: html, text, full: html, text
    c5cba6f47e775308f8d2ef9303857423ff9f6561 Mon Aug 1 14:23:34 2016 -0700
    adding tool to create CIRM CDW summary page. It creates a plot with cells placed on a 2D-space, so similar cells are located close together (T-SNE dimensionality reduction, Seurat package). This a python command line tool that creates R scripts and finally outputs a static html page with lots of D3 javascript in it. An unusual architecture, but I did not find a better solution that is compatible with our security constraints in the CIRM project
    
  • lines changed 7, context: html, text, full: html, text
    493e6392ace2fe0653519c2753e3d81622d0ee1a Fri Aug 5 09:22:46 2016 -0700
    cosmetic changes in cdwSummary, no redmine
    
• src/hg/cirm/cdw/cdwSummary/makefile
  • lines changed 9, context: html, text, full: html, text
    c5cba6f47e775308f8d2ef9303857423ff9f6561 Mon Aug 1 14:23:34 2016 -0700
    adding tool to create CIRM CDW summary page. It creates a plot with cells placed on a 2D-space, so similar cells are located close together (T-SNE dimensionality reduction, Seurat package). This a python command line tool that creates R scripts and finally outputs a static html page with lots of D3 javascript in it. An unusual architecture, but I did not find a better solution that is compatible with our security constraints in the CIRM project
    
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 43, context: html, text, full: html, text
    de1276834030ebf345be51b4c7d1f1008c10684d Mon Aug 1 15:28:43 2016 -0700
    for the CIRM CDW, make the download button put files into the appropriate subdirectories, creating them on the way
    
  • lines changed 12, context: html, text, full: html, text
    f96ae7c4d8f747d1eba8728c2263870f0f6d2c16 Mon Aug 1 15:40:09 2016 -0700
    make sure that CDW CIRM download all button does not write into unexpected directories
    
  • lines changed 1, context: html, text, full: html, text
    df83ccb73d649fdc14703e3b7cb7081845ce2085 Mon Aug 1 16:09:09 2016 -0700
    adding multithreading to the CIRM CDW new download option
    
• src/hg/cirm/cdw/cdwWebCreateUser/cdwWebCreateUser.c
  • lines changed 72, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/cdwWebCreateUser/makefile
  • lines changed 16, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/cdwWebDeprecate/cdwWebDeprecate.c
  • lines changed 209, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/cdwWebDeprecate/makefile
  • lines changed 16, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/cdwWebSubmit/cdwWebSubmit.c
  • lines changed 352, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/cdwWebSubmit/makefile
  • lines changed 16, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 4, context: html, text, full: html, text
    1fe9e7113a5e738c2522cbce34a8394c83805970 Wed Aug 3 13:26:24 2016 -0700
    Refactoring cdwReallyRemoveFiles.c to share code that deletes records on files in QA tables in database with cdwFileResetTags. Made records from cdwGroupFiles get removed as need be too.
    
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 67, context: html, text, full: html, text
    1fe9e7113a5e738c2522cbce34a8394c83805970 Wed Aug 3 13:26:24 2016 -0700
    Refactoring cdwReallyRemoveFiles.c to share code that deletes records on files in QA tables in database with cdwFileResetTags. Made records from cdwGroupFiles get removed as need be too.
    
• src/hg/cirm/cdw/makefile
  • lines changed 6, context: html, text, full: html, text
    5486a8d17ff11540ba33be8080778c628adf8acd Mon Aug 1 10:35:49 2016 -0700
    Removing some unused cgi's.
    
  • lines changed 2, context: html, text, full: html, text
    f23010bc56ecdde272386fa12559ec5ba7d9f0e7 Mon Aug 1 16:36:59 2016 -0700
    adding cdwCheckValidation and cdwCheckDataset to the makefile
    
• src/hg/cirm/cdw/utils/cdwFastqPolyFilter/cdwFastqPolyFilter.c
  • lines changed 4, context: html, text, full: html, text
    49f17e05e9df68df3af5ac6940b258af7145c253 Mon Aug 1 15:06:11 2016 -0700
    Adding in a polyT trim as well
    
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 1, context: html, text, full: html, text
    2f0ca0ada7fa54e0584aa53eb39f801b036c8be4 Mon Aug 1 13:24:52 2016 -0700
    Updating query for mouse genome link in uniProt database to account for MGD/MGI change.
    
• src/hg/hgGene/hgGeneData/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    4036b5220ce14488be1392e09e6ad5704e85ccd3 Wed Aug 3 13:27:16 2016 -0700
    Updating an embedded SQL query to cope with change of MGD to MGI in UniProt database.
    
• src/hg/hgPublicSessions/hgPublicSessions.c
  • lines changed 1, context: html, text, full: html, text
    08b158826eabd5c5f1cf06722ced56961c62255a Tue Aug 2 14:54:33 2016 -0700
    Forgot to remove debugging limit on number of sessions returned from query, refs #17825
    
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 27, context: html, text, full: html, text
    f5ba6de31304850e1650c1a785f717971cbfa4a8 Tue Aug 2 12:28:30 2016 -0700
    fix problem with bigBed code calling SQL code during parallel load.
    This causes a crash because SQL code is not thread safe.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 29, context: html, text, full: html, text
    8cb0eb5850ff9883a1a278c1607998f0a6046bcb Thu Aug 4 08:56:32 2016 -0700
    adding internal ability to draw multiple highlights.
    refs #14951. There is no way to set these currently in the UI,
    as this would be a whole project of its own. Also, in multi-exon
    mode, it will only draw the first region, if multiple ones are defined.
    
  • lines changed 6, context: html, text, full: html, text
    bd8c3d3124817d7ec82a33b9f27a9a9d56df8ef4 Fri Aug 5 14:24:37 2016 -0700
    hotkey fix, refs #17844
    
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    d63b7e753345e199748030d83e1d3aa497b350f9 Tue Aug 2 22:24:07 2016 -0700
    fix problem in bigPsl with '-' as strand for target sequence #17829
    
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 1, context: html, text, full: html, text
    dc9f6fee2303bf11b52578e7d00de63f3e35920e Thu Aug 4 12:57:54 2016 -0700
    Making small typo fixes to bigChain bigMaf html file..bb to file.bb
    
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 1, context: html, text, full: html, text
    dc9f6fee2303bf11b52578e7d00de63f3e35920e Thu Aug 4 12:57:54 2016 -0700
    Making small typo fixes to bigChain bigMaf html file..bb to file.bb
    
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 8, context: html, text, full: html, text
    7bd3ab2b92d48520bf463fd43eeda13318dbe7cb Wed Aug 3 12:13:27 2016 -0700
    make the doc and AS file for bigPsl a little more explicit about the
    file contents
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    8cb0eb5850ff9883a1a278c1607998f0a6046bcb Thu Aug 4 08:56:32 2016 -0700
    adding internal ability to draw multiple highlights.
    refs #14951. There is no way to set these currently in the UI,
    as this would be a whole project of its own. Also, in multi-exon
    mode, it will only draw the first region, if multiple ones are defined.
    
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 263, context: html, text, full: html, text
    80d798ffe7ddc03b856415338be1783025b87c68 Mon Aug 1 12:21:24 2016 -0700
    product/isntaller makefile now creates gbic.html in src tree and prints reminder message to user to commit both files, also changes from code review, refs #17767
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 8, context: html, text, full: html, text
    7cf81f9887e699b4177d3bbdfd59b719e80f3c07 Wed Aug 3 07:16:31 2016 -0700
    trying to improve documentation of special variables in urls, refs #17785
    
• src/hg/htdocs/makefile
  • lines changed 3, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/pandoc/installer/makefile
  • lines changed 33, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/pandoc/installer/staticPage.html
  • lines changed 34, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/pandoc/mirrorDocs/makefile
  • lines changed 12, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/pandoc/mirrorDocs/staticPage.html
  • lines changed 34, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/pandoc/mirrorDocs/staticPage.lua
  • lines changed 424, context: html, text, full: html, text
    284b199b7b48ccea38ce21225898bfaf7172a7cd Mon Aug 1 11:07:17 2016 -0700
    Removing pandoc dependency from htdocs makefile, no refs
    
• src/hg/htdocs/training/index.html
  • lines changed 7, context: html, text, full: html, text
    813dec87ba98017372ce1c4f53992c89a5eb59f4 Thu Aug 4 13:17:35 2016 -0700
    removed Bar Harbor workshop
    
• src/hg/inc/bigPsl.h
  • lines changed 5, context: html, text, full: html, text
    7bd3ab2b92d48520bf463fd43eeda13318dbe7cb Wed Aug 3 12:13:27 2016 -0700
    make the doc and AS file for bigPsl a little more explicit about the
    file contents
    
• src/hg/js/hgTracks.js
  • lines changed 9, context: html, text, full: html, text
    8cb0eb5850ff9883a1a278c1607998f0a6046bcb Thu Aug 4 08:56:32 2016 -0700
    adding internal ability to draw multiple highlights.
    refs #14951. There is no way to set these currently in the UI,
    as this would be a whole project of its own. Also, in multi-exon
    mode, it will only draw the first region, if multiple ones are defined.
    
• src/hg/lib/bigPsl.as
  • lines changed 3, context: html, text, full: html, text
    7bd3ab2b92d48520bf463fd43eeda13318dbe7cb Wed Aug 3 12:13:27 2016 -0700
    make the doc and AS file for bigPsl a little more explicit about the
    file contents
    
• src/hg/lib/bigPsl.c
  • lines changed 8, context: html, text, full: html, text
    d63b7e753345e199748030d83e1d3aa497b350f9 Tue Aug 2 22:24:07 2016 -0700
    fix problem in bigPsl with '-' as strand for target sequence #17829
    
  • lines changed 3, context: html, text, full: html, text
    7bd3ab2b92d48520bf463fd43eeda13318dbe7cb Wed Aug 3 12:13:27 2016 -0700
    make the doc and AS file for bigPsl a little more explicit about the
    file contents
    
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    b333eb9809c523502a638a910e17abc47e2c2d09 Wed Aug 3 07:09:48 2016 -0700
    again trying to fix an issue with handling of ${, $}, refs #17785, #15480
    
• src/hg/makeDb/doc/galGal5/lastzRuns.txt
  • lines changed 59, context: html, text, full: html, text
    a468d05863ec4b02a0606f3d802e3a37dc765748 Thu Aug 4 21:52:36 2016 -0700
    lastz done to pelSin1 refs #17168
    
• src/hg/makeDb/doc/gorGor5/initialBuild.txt
  • lines changed 73, context: html, text, full: html, text
    271c01c105164ce102a3920e09101afdd7cd46e4 Thu Aug 4 21:51:03 2016 -0700
    genbank finally finished, liftOvers to and from gorGor4, augustus done, refs #17580
    
• src/hg/makeDb/doc/hg18.txt
  • lines changed 78, context: html, text, full: html, text
    72a6556b59b841454746ccfb60607ca5b4e8e656 Wed Aug 3 08:39:05 2016 -0700
    liftOver to panPan1 per user request refs #17776
    
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 74, context: html, text, full: html, text
    70999cafd8ac208d538f05c8faa164a33978f51b Thu Aug 4 21:41:05 2016 -0700
    lastz run to panTro5 refs #17817
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 64, context: html, text, full: html, text
    522bd043902bb034b50bd004550de23953307918 Thu Aug 4 21:33:11 2016 -0700
    lastz chain net on panTro5 refs #17817
    
• src/hg/makeDb/doc/orcOrc1/lastzRuns.txt
  • lines changed 2, context: html, text, full: html, text
    71b909c8408071f0212343b4a51ad727996f4351 Thu Aug 4 22:02:05 2016 -0700
    finished lastz turTru2 to orcOrc1 refs #17425
    
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 161, context: html, text, full: html, text
    4753820862f79c9cd5e5f8e229860010cc4c31a6 Thu Aug 4 21:38:33 2016 -0700
    liftOver to panTro5 and some user requested lastz runs refs #17817
    
• src/hg/makeDb/doc/panTro5/initialBuild.txt
  • lines changed 768, context: html, text, full: html, text
    138ca64c20c808794cd930815016fe72545ef5fa Mon Aug 1 21:59:36 2016 -0700
    starting panTro5 build refs 17817
    
  • lines changed 266, context: html, text, full: html, text
    22879614cd1b3c208e12bbf436d6ed02ce2b2ff6 Thu Aug 4 21:55:00 2016 -0700
    almost everything done, genbank loading, liftOvers to panTro3 and 4, blat server setup refs #17817
    
• src/hg/makeDb/doc/panTro5/lastzRuns.txt
  • lines changed 78, context: html, text, full: html, text
    4518da752aef97439e239b46d06c855c6a6fbdf0 Thu Aug 4 21:55:53 2016 -0700
    lastz to gorGor5 underway refs #17817 #17580
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    48a94b926805e755347fd2e97fb5af41adafb510 Thu Aug 4 11:08:38 2016 -0700
    Added gorGor5 - Gorilla - refs #17580
    
  • lines changed 1, context: html, text, full: html, text
    42061eaf5e7526eae52a264c7378259568c0bae3 Mon Aug 8 09:01:00 2016 -0700
    Added panTro5 - chimp - Pan troglodytes refs #17817
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 20, context: html, text, full: html, text
    4560c66e919bcf4dee0edfff4a2670ac2189414b Tue Aug 2 08:57:08 2016 -0700
    adding panTro5 - Chimp refs #17817
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    48a94b926805e755347fd2e97fb5af41adafb510 Thu Aug 4 11:08:38 2016 -0700
    Added gorGor5 - Gorilla - refs #17580
    
  • lines changed 2, context: html, text, full: html, text
    42061eaf5e7526eae52a264c7378259568c0bae3 Mon Aug 8 09:01:00 2016 -0700
    Added panTro5 - chimp - Pan troglodytes refs #17817
    
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • lines changed 1, context: html, text, full: html, text
    7d49a2cb857d1cad62c92eecc6b05b51ac39df52 Sat Aug 6 13:46:48 2016 -0700
    align genbank dbs in the order they're given.
    
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 3, context: html, text, full: html, text
    00ea644ada0eb396a9a763e078062121b2a0bf3a Fri Aug 5 11:20:25 2016 -0700
    don't remove top level work directory in gbDbLoadStep since it
    interferes with more than one load working at a time
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    bfb80b7452b6bef82648c7669dd18494f7d9ef02 Fri Aug 5 08:20:21 2016 -0700
    adding panTro5 and gorGor5 refs #17817
    
• src/hg/makeDb/trackDb/chicken/galGal5/gold.html
  • lines changed 2, context: html, text, full: html, text
    7ace3b197d6426643ddf834845ad291c7ed00c03 Fri Aug 5 15:29:51 2016 -0700
    Fixing URLs on chicken gold page, refs #17168
    
• src/hg/makeDb/trackDb/chimp/panTro5/description.html
  • lines changed 64, context: html, text, full: html, text
    25a69a8e77d57796a6bfb2c49086d1cc1a39ef39 Mon Aug 1 21:16:05 2016 -0700
    adding panTro5 to the build refs #17817
    
• src/hg/makeDb/trackDb/chimp/panTro5/gap.html
  • lines changed 32, context: html, text, full: html, text
    25a69a8e77d57796a6bfb2c49086d1cc1a39ef39 Mon Aug 1 21:16:05 2016 -0700
    adding panTro5 to the build refs #17817
    
• src/hg/makeDb/trackDb/chimp/panTro5/gold.html
  • lines changed 36, context: html, text, full: html, text
    25a69a8e77d57796a6bfb2c49086d1cc1a39ef39 Mon Aug 1 21:16:05 2016 -0700
    adding panTro5 to the build refs #17817
    
• src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    25a69a8e77d57796a6bfb2c49086d1cc1a39ef39 Mon Aug 1 21:16:05 2016 -0700
    adding panTro5 to the build refs #17817
    
• src/hg/makeDb/trackDb/cow/snp148.html
  • lines changed 36, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/cow/snp148.shared.html
  • lines changed 428, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/cow/snp148Common.html
  • lines changed 28, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/cow/snp148Flagged.html
  • lines changed 29, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/cow/snp148Mult.html
  • lines changed 25, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    c1457cdcd08e188c4b93e81d2ed440ff53ac2c3a Tue Aug 2 20:45:52 2016 -0700
    Initial commit of snp148 docs for bosTau8, refs #16846
    
• src/hg/makeDb/trackDb/human/chainNetPanTro4.ra
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    ee46dd2bd382e119fcdab2087d2f441df4119854 Thu Aug 4 10:19:25 2016 -0700
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