All File Changes

v388_base to v389_preview (2019-09-23 to 2019-09-30) v389

• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
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    9f32d767827f01c3d380b57787d174aabbc6a4c0 Wed Sep 18 20:17:33 2019 -0700
    Fixed an edge case around missing contributor.
• src/hca/hcat/hcatTabUpdate/hcatTabUpdate.c
  • lines changed 26, context: html, text, full: html, text
    2fe474a25e247a186d1ba8890c9c70028fbad0e2 Wed Sep 18 20:19:17 2019 -0700
    Adding contributors to contact in hopes of unrolling them all and avoiding interns cutting and pasting long author lists.
• src/hca/hcat/mysite/hcat/admin.py
  • lines changed 3, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
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    0ffc5d285457b0063015175086d20fbb0155feef Wed Sep 25 17:13:29 2019 -0700
    Getting rid of AssayType and some of the fields wranglers didn't want. Moved wrangling section to bottom. Overall maybe half way through wrangler requests that don't involve a new view.
  • lines changed 11, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/hcat/api.py
  • lines changed 144, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 15, context: html, text, full: html, text
    3efeb7ddb50d2fe9ad54cde63f0d6d5048cd7aec Wed Sep 25 17:16:10 2019 -0700
    Stripping out return of contact info other than name from public API pending discussion at least. Making project comments and contacts visible.
  • lines changed 8, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/hcat/api_urls.py
  • lines changed 20, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 1, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/hcat/models.py
  • lines changed 23, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 109, context: html, text, full: html, text
    24780d64efc50758fa6360857db108ae821529bb Wed Sep 25 17:12:26 2019 -0700
    Added doc strings to all classes. Rearranged things per wranglers linking a bit, simplifying the wrangling aspects of a project. Separating wrangling_state from the main project state.
  • lines changed 18, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/hcat/urls.py
  • lines changed 8, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 9, context: html, text, full: html, text
    243b5608315974e6830f2314908489fcf88084d1 Wed Sep 25 21:07:05 2019 -0700
    Removing old hcat/api urls since now have straight api urls.
  • lines changed 1, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/hcat/views.py
  • lines changed 134, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 127, context: html, text, full: html, text
    243b5608315974e6830f2314908489fcf88084d1 Wed Sep 25 21:07:05 2019 -0700
    Removing old hcat/api urls since now have straight api urls.
• src/hca/hcat/mysite/mysite/urls.py
  • lines changed 1, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
• src/hca/hcat/mysite/templates/admin/base_site.html
  • lines changed 1, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
• src/hca/hcat/mysite/templates/hcat/project_list.html
  • lines changed 1, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 2, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hca/hcat/mysite/versions.txt
  • lines changed 20, context: html, text, full: html, text
    6c9260361fe78a7fff407ddadf1ad99a5fea21f2 Wed Sep 18 20:21:24 2019 -0700
    Version 7 production/Version 8 dev begin checkin for Tuatara.
  • lines changed 9, context: html, text, full: html, text
    3d73498b2c0eaa16c71676f6a88f3e2d9d6315bd Wed Sep 25 17:17:00 2019 -0700
    Documenting changes so far in V0.8
  • lines changed 10, context: html, text, full: html, text
    8aaa6e02216f5a454a7bd64c180181dee2eab5cd Fri Sep 27 11:21:08 2019 -0700
    Implementing wrangler requests as described in versions.txt. Mostly this is trimming some things they felt were unneeded, renaming some fields, splitting apart project-status and wrangling-status, and moving the biological information up to a more visible part of the project details page in the admin. Also there is a tiny bit of experimenting on non-admin views.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 255, context: html, text, full: html, text
    bdd18de186c0f34406ca395e7ba9b1b88980587d Mon Sep 23 16:44:07 2019 -0700
    Optimizing the jstree on hgHubConnect by writing out a javascript object and letting ajax load the nodes of the tree on an as-needed basis. Also adding measureTiming to hgHubConnect, refs #23812
  • lines changed 15, context: html, text, full: html, text
    daf6b6d8252538b7cc1c8aaad253d5a6fb1aaec4 Tue Sep 24 12:35:44 2019 -0700
    Fixing dumb mistake in hub search where I initialized a variable in two different spots, refs #23812
  • lines changed 1, context: html, text, full: html, text
    1c1634ecde5730e83e599863eb4455d97cf80cd4 Wed Sep 25 09:45:03 2019 -0700
    Fixing two bugs with hub searching, one where I forgot to htmlEncode a result and one where I was preventing single click expand of the results tree, refs #23812
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    e12ac8fea086d17ed824392a2bb3e425090ecb2d Fri Sep 27 16:17:32 2019 -0700
    Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842
• src/hg/hgTables/hic.c
  • lines changed 25, context: html, text, full: html, text
    e12ac8fea086d17ed824392a2bb3e425090ecb2d Fri Sep 27 16:17:32 2019 -0700
    Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842
• src/hg/hgTables/mainPage.c
  • lines changed 4, context: html, text, full: html, text
    e12ac8fea086d17ed824392a2bb3e425090ecb2d Fri Sep 27 16:17:32 2019 -0700
    Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842
• src/hg/hgTracks/barChartTrack.c
  • lines changed 441, context: html, text, full: html, text
    f96fa3ebcc5514dbd65078df1ac4955748d27af5 Tue Sep 17 13:55:51 2019 -0700
    Long-needed refactoring. Prior to implementing new setting to limit chart size. refs #24161
  • lines changed 13, context: html, text, full: html, text
    e37bc753fd4ecbc758ea232a79905a139909e75b Tue Sep 17 15:44:38 2019 -0700
    Add barChartMaxSize setting to limit size of charts (override semantic zoom). Values are small/medium/large (defaults to large). refs #24161
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 15, context: html, text, full: html, text
    3122e477cca8eacc6dc51bdf96544641877a904a Tue Sep 24 15:03:24 2019 -0700
    allow filtering on first three fields of bigBed. Label filtered tracks as filtered
  • lines changed 5, context: html, text, full: html, text
    e260a83c1023f097f5fb1f3c0a8b3d464c536c3c Wed Sep 25 20:52:50 2019 -0700
    support <columnName>.Filter* format for trackDb filtering variables
• src/hg/hgTracks/hgTracks.c
  • lines changed 136, context: html, text, full: html, text
    faf17a6ad5e1cf7379a375b106f4900990d35c2d Tue Apr 23 16:10:51 2019 -0700
    Support for summary file to improve performance of collapseEmptySubtracks setting. This implementation is first cut for the feature (w/o UI). refs #23365
  • lines changed 6, context: html, text, full: html, text
    d24ed481a58b99783bcaad71d5aee510b4572a29 Tue Sep 24 16:26:01 2019 -0700
    Rename trackDb setting for hiding empty subtracks (w/ backward compatibility). refs #23365
  • lines changed 142, context: html, text, full: html, text
    f5ba7e5371b8bcf6c260d065b971e57c09eca1ad Wed Sep 25 10:56:06 2019 -0700
    Merging
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    64b2c5bd9ab0e2bd59360c39298ae54e97615407 Thu Sep 26 13:30:43 2019 -0700
    Add UI control to hide empty subtracks. refs #23365
  • lines changed 1, context: html, text, full: html, text
    7a54bcbfa0fc17fdfbd9153262408a2417b9868e Fri Sep 27 09:40:30 2019 -0700
    comment out a non-existant include file
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    faf17a6ad5e1cf7379a375b106f4900990d35c2d Tue Apr 23 16:10:51 2019 -0700
    Support for summary file to improve performance of collapseEmptySubtracks setting. This implementation is first cut for the feature (w/o UI). refs #23365
  • lines changed 3, context: html, text, full: html, text
    f5ba7e5371b8bcf6c260d065b971e57c09eca1ad Wed Sep 25 10:56:06 2019 -0700
    Merging
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    f5ba7e5371b8bcf6c260d065b971e57c09eca1ad Wed Sep 25 10:56:06 2019 -0700
    Merging
  • lines changed 1, context: html, text, full: html, text
    64b2c5bd9ab0e2bd59360c39298ae54e97615407 Thu Sep 26 13:30:43 2019 -0700
    Add UI control to hide empty subtracks. refs #23365
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 8, context: html, text, full: html, text
    94beebccbdcae3b709516cdacd2f42e2372ebae2 Wed Sep 25 16:26:39 2019 -0700
    Adding a note to other help pages about the 'useOneFile on' hub setting, refs #19383
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 69, context: html, text, full: html, text
    1824a9440d559df44bb22c204fbc62ab260df7aa Wed Sep 25 14:31:05 2019 -0700
    Documenting the 'useOneFile on' hub setting on the Browser Documentation page, Docs #19383
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 4, context: html, text, full: html, text
    94beebccbdcae3b709516cdacd2f42e2372ebae2 Wed Sep 25 16:26:39 2019 -0700
    Adding a note to other help pages about the 'useOneFile on' hub setting, refs #19383
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 4, context: html, text, full: html, text
    94beebccbdcae3b709516cdacd2f42e2372ebae2 Wed Sep 25 16:26:39 2019 -0700
    Adding a note to other help pages about the 'useOneFile on' hub setting, refs #19383
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 173, context: html, text, full: html, text
    539de8508531fab6a834a300830e17b6b8e64afa Tue Sep 24 15:11:14 2019 -0700
    Adding a first draft of the searchable Track hub documentaion, still needing to correct paths #20881
  • lines changed 150, context: html, text, full: html, text
    1c9a945ecbd1b022c8d70a3c047c08cc6e9f8f57 Fri Sep 27 13:51:34 2019 -0700
    Committing final draft of searchable hub guide #20881
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    da5716e1c78af89c9b39a989701c7e4ba8c236e2 Tue Sep 24 15:40:56 2019 -0700
    Document barChartMaxSize setting. refs #23691
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 5, context: html, text, full: html, text
    da5716e1c78af89c9b39a989701c7e4ba8c236e2 Tue Sep 24 15:40:56 2019 -0700
    Document barChartMaxSize setting. refs #23691
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 9, context: html, text, full: html, text
    da5716e1c78af89c9b39a989701c7e4ba8c236e2 Tue Sep 24 15:40:56 2019 -0700
    Document barChartMaxSize setting. refs #23691
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 4, context: html, text, full: html, text
    94beebccbdcae3b709516cdacd2f42e2372ebae2 Wed Sep 25 16:26:39 2019 -0700
    Adding a note to other help pages about the 'useOneFile on' hub setting, refs #19383
• src/hg/htdocs/images/FAM87bSearchResult.pdf
  • lines changed 0, context: html, text, full: html, text
    09fe84f92030a8f110f5b98069807992b996ec8b Fri Sep 27 13:00:08 2019 -0700
    Committing image files for Quick Start Search guide #20881
• src/hg/htdocs/images/FAM87bSearchResult.png
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    4c767b3653a06bbb113bc773efb31347c56f7914 Fri Sep 27 13:37:35 2019 -0700
    Adding image files for #20881
• src/hg/htdocs/images/defaultViewSearchTracks.pdf
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    09fe84f92030a8f110f5b98069807992b996ec8b Fri Sep 27 13:00:08 2019 -0700
    Committing image files for Quick Start Search guide #20881
• src/hg/htdocs/images/defaultViewSearchTracks.png
  • lines changed 0, context: html, text, full: html, text
    4c767b3653a06bbb113bc773efb31347c56f7914 Fri Sep 27 13:37:35 2019 -0700
    Adding image files for #20881
• src/hg/htdocs/images/fam87bSearchOutput.png
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    c9d25904387139e2d6d5413240fba500b911c523 Fri Sep 27 13:46:03 2019 -0700
    Adding another search image #20881
• src/hg/htdocs/images/searchingFAM87b.png
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    09fe84f92030a8f110f5b98069807992b996ec8b Fri Sep 27 13:00:08 2019 -0700
    Committing image files for Quick Start Search guide #20881
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    1647f408f61d470ce25dd8ac39472788faab1648 Tue Sep 24 11:32:33 2019 -0700
    Adding JSON API mention to hgdownload's 'download' drop-down menu, refs #24202
• src/hg/htdocs/training/index.html
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    16ab1a313abfee9a5f155ea778ba47addfc0cd81 Tue Sep 24 14:46:10 2019 -0700
    added U of Oregon workshop to long list
• src/hg/hubApi/apiUtils.c
  • lines changed 11, context: html, text, full: html, text
    26501d3ac1d4eea1d3c539dbbd13e15e46737759 Tue Sep 24 11:57:57 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    74f1ce41ab30aa506ea6c1bd879e6d42ac596d55 Wed Sep 25 12:24:12 2019 -0700
    hard code a list of tables to check for protected data refs #24208
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    26501d3ac1d4eea1d3c539dbbd13e15e46737759 Tue Sep 24 11:57:57 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    74f1ce41ab30aa506ea6c1bd879e6d42ac596d55 Wed Sep 25 12:24:12 2019 -0700
    hard code a list of tables to check for protected data refs #24208
• src/hg/hubApi/getData.c
  • lines changed 2, context: html, text, full: html, text
    26501d3ac1d4eea1d3c539dbbd13e15e46737759 Tue Sep 24 11:57:57 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    e3a5a9df62a97b39cec661b69786f2807005ee70 Tue Sep 24 13:20:44 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    74f1ce41ab30aa506ea6c1bd879e6d42ac596d55 Wed Sep 25 12:24:12 2019 -0700
    hard code a list of tables to check for protected data refs #24208
• src/hg/hubApi/hubApi.c
  • lines changed 10, context: html, text, full: html, text
    26501d3ac1d4eea1d3c539dbbd13e15e46737759 Tue Sep 24 11:57:57 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    74f1ce41ab30aa506ea6c1bd879e6d42ac596d55 Wed Sep 25 12:24:12 2019 -0700
    hard code a list of tables to check for protected data refs #24208
• src/hg/hubApi/list.c
  • lines changed 8, context: html, text, full: html, text
    26501d3ac1d4eea1d3c539dbbd13e15e46737759 Tue Sep 24 11:57:57 2019 -0700
    correctly recognize the "tableBrowser off" entry in trackDb for protected tables refs #24208
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    74f1ce41ab30aa506ea6c1bd879e6d42ac596d55 Wed Sep 25 12:24:12 2019 -0700
    hard code a list of tables to check for protected data refs #24208
• src/hg/hubApi/tests/expected/err01.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err40.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err41.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err42.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err43.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err44.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err45.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/err46.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/hubApi/tests/expected/list03.gz
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    f921e3058c0e62331cb11326cd31cd7b0e754955 Tue Sep 24 13:22:41 2019 -0700
    updated genbank track listings refs #23589
• src/hg/hubApi/tests/expected/list09.gz
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    f921e3058c0e62331cb11326cd31cd7b0e754955 Tue Sep 24 13:22:41 2019 -0700
    updated genbank track listings refs #23589
• src/hg/hubApi/tests/expected/test41.gz
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    9604beb496eccd393ad5473f4ab21fd69ffdd231 Wed Sep 25 12:25:21 2019 -0700
    correctly checking all protected data tables refs #24208
• src/hg/inc/barChartUi.h
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    e37bc753fd4ecbc758ea232a79905a139909e75b Tue Sep 17 15:44:38 2019 -0700
    Add barChartMaxSize setting to limit size of charts (override semantic zoom). Values are small/medium/large (defaults to large). refs #24161
• src/hg/inc/hgFind.h
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    f0d475ddc991cec778b896f0621b5bfa75cc7d55 Thu Sep 26 16:39:12 2019 -0700
    bigBedFind: support searchIndex in the search spec (not just trackDb); default to name if there is an index on name; support padding. refs #23283 Calling addHighlight from bigBedFind caused a lot of utils (e.g. hgTrackDb) to get linker errors about functions in hgFind.c that reference a global cart, so I made cart a param instead of a global in hgFind.c.
• src/hg/inc/hicUi.h
  • lines changed 6, context: html, text, full: html, text
    e12ac8fea086d17ed824392a2bb3e425090ecb2d Fri Sep 27 16:17:32 2019 -0700
    Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    e260a83c1023f097f5fb1f3c0a8b3d464c536c3c Wed Sep 25 20:52:50 2019 -0700
    support <columnName>.Filter* format for trackDb filtering variables
  • lines changed 10, context: html, text, full: html, text
    64b2c5bd9ab0e2bd59360c39298ae54e97615407 Thu Sep 26 13:30:43 2019 -0700
    Add UI control to hide empty subtracks. refs #23365
• src/hg/js/hgHubConnect.js
  • lines changed 87, context: html, text, full: html, text
    bdd18de186c0f34406ca395e7ba9b1b88980587d Mon Sep 23 16:44:07 2019 -0700
    Optimizing the jstree on hgHubConnect by writing out a javascript object and letting ajax load the nodes of the tree on an as-needed basis. Also adding measureTiming to hgHubConnect, refs #23812
  • lines changed 8, context: html, text, full: html, text
    daf6b6d8252538b7cc1c8aaad253d5a6fb1aaec4 Tue Sep 24 12:35:44 2019 -0700
    Fixing dumb mistake in hub search where I initialized a variable in two different spots, refs #23812
  • lines changed 6, context: html, text, full: html, text
    1c1634ecde5730e83e599863eb4455d97cf80cd4 Wed Sep 25 09:45:03 2019 -0700
    Fixing two bugs with hub searching, one where I forgot to htmlEncode a result and one where I was preventing single click expand of the results tree, refs #23812
• src/hg/lib/bed3Sources.as
  • lines changed 9, context: html, text, full: html, text
    faf17a6ad5e1cf7379a375b106f4900990d35c2d Tue Apr 23 16:10:51 2019 -0700
    Support for summary file to improve performance of collapseEmptySubtracks setting. This implementation is first cut for the feature (w/o UI). refs #23365
• src/hg/lib/bigBedFind.c
  • lines changed 54, context: html, text, full: html, text
    f0d475ddc991cec778b896f0621b5bfa75cc7d55 Thu Sep 26 16:39:12 2019 -0700
    bigBedFind: support searchIndex in the search spec (not just trackDb); default to name if there is an index on name; support padding. refs #23283 Calling addHighlight from bigBedFind caused a lot of utils (e.g. hgTrackDb) to get linker errors about functions in hgFind.c that reference a global cart, so I made cart a param instead of a global in hgFind.c.
  • lines changed 21, context: html, text, full: html, text
    73b1cfe6f896f7830c2286ab0733a97ede5b641d Thu Sep 26 17:24:48 2019 -0700
    In my previous change to bigBedFind.c, I opened a bbi but forgot to errCatch & close it. So, errCatch & close it; also reuse it instead of reopening it for each index. refs #23283
• src/hg/lib/hgFind.c
  • lines changed 28, context: html, text, full: html, text
    f0d475ddc991cec778b896f0621b5bfa75cc7d55 Thu Sep 26 16:39:12 2019 -0700
    bigBedFind: support searchIndex in the search spec (not just trackDb); default to name if there is an index on name; support padding. refs #23283 Calling addHighlight from bigBedFind caused a lot of utils (e.g. hgTrackDb) to get linker errors about functions in hgFind.c that reference a global cart, so I made cart a param instead of a global in hgFind.c.
• src/hg/lib/hicUi.c
  • lines changed 24, context: html, text, full: html, text
    e12ac8fea086d17ed824392a2bb3e425090ecb2d Fri Sep 27 16:17:32 2019 -0700
    Adding table browser selectors for normalization and resolution in .hic tracks, refs #18842
• src/hg/lib/hui.c
  • lines changed 57, context: html, text, full: html, text
    62abffb9b3bc4dc77214ea9128636037686fb7b7 Wed Sep 25 15:08:09 2019 -0700
    Minor code refactor to remove duplication before adding new feature. refs #23365
  • lines changed 34, context: html, text, full: html, text
    e260a83c1023f097f5fb1f3c0a8b3d464c536c3c Wed Sep 25 20:52:50 2019 -0700
    support <columnName>.Filter* format for trackDb filtering variables
  • lines changed 70, context: html, text, full: html, text
    64b2c5bd9ab0e2bd59360c39298ae54e97615407 Thu Sep 26 13:30:43 2019 -0700
    Add UI control to hide empty subtracks. refs #23365
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    8e3f3a01dbb1b2ac9d3c7fed4fb2840dcb6014f6 Sat Sep 28 10:09:20 2019 -0700
    allow trackDb variables to have an empty value, useful for filters
• src/hg/lib/wiggleCart.c
  • lines changed 1, context: html, text, full: html, text
    0c0c2f708b2972bf78b5cc4341396bca1d9c6e34 Tue Aug 8 13:02:50 2017 -0700
    Support for max height in barChart (reusing from wiggle). refs #19872
• src/hg/makeDb/doc/encode3/tfbs.txt
  • lines changed 79, context: html, text, full: html, text
    faf17a6ad5e1cf7379a375b106f4900990d35c2d Tue Apr 23 16:10:51 2019 -0700
    Support for summary file to improve performance of collapseEmptySubtracks setting. This implementation is first cut for the feature (w/o UI). refs #23365
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 20, context: html, text, full: html, text
    6c02988b8ef7077f418bd3185126666f612759b1 Thu Sep 26 10:28:41 2019 -0700
    import of gencode V32 final
  • lines changed 2, context: html, text, full: html, text
    ba8b284fa2d2a06ef112c06ecfacf5a135c7742d Thu Sep 26 10:35:36 2019 -0700
    import of gencode V32 final
• src/hg/makeDb/doc/mm10.txt
  • lines changed 2, context: html, text, full: html, text
    6c02988b8ef7077f418bd3185126666f612759b1 Thu Sep 26 10:28:41 2019 -0700
    import of gencode V32 final
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    6c02988b8ef7077f418bd3185126666f612759b1 Thu Sep 26 10:28:41 2019 -0700
    import of gencode V32 final
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    71820b924c4289d2213eab2ddb429afa95b6c056 Fri Sep 27 09:56:27 2019 -0700
    some tweaks for mouse M20
  • lines changed 2, context: html, text, full: html, text
    07892d76d0c99f0a2130083b81287881fb048449 Fri Sep 27 10:35:44 2019 -0700
    fix retro tables again
  • lines changed 9, context: html, text, full: html, text
    9d3d295f183b11cd6c6c7f45292b66114ac27b5a Fri Sep 27 12:56:37 2019 -0700
    more Gencode V32 changes
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 14, context: html, text, full: html, text
    5084982f891b8abffe273249949613cd8e592765 Mon Sep 23 16:20:54 2019 -0700
    Add a Data Access section to the GeneHancer track html refs #22504
• src/hg/makeDb/trackDb/human/hg38/encode3.ra
  • lines changed 1, context: html, text, full: html, text
    faf17a6ad5e1cf7379a375b106f4900990d35c2d Tue Apr 23 16:10:51 2019 -0700
    Support for summary file to improve performance of collapseEmptySubtracks setting. This implementation is first cut for the feature (w/o UI). refs #23365
  • lines changed 13197, context: html, text, full: html, text
    189bd07809d0dc4125ef2c43b6a8e9a6a4ebf872 Mon Jul 29 09:52:44 2019 -0700
    Gave up on merging this
• src/hg/makeDb/trackDb/human/mastermind.html
  • lines changed 6, context: html, text, full: html, text
    2a16ed67395107fb7a5104a88101107c8a3f9633 Tue Sep 24 13:57:09 2019 -0700
    Touching up MM descriptions page refs #24157
  • lines changed 4, context: html, text, full: html, text
    5a185db3a16a454b4e9b6c39e803b3c88aa58b33 Wed Sep 25 02:27:16 2019 -0700
    fix suggested by qa, refs #24157
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    3deac615bc1604caf7e97bfe8c9dc97b15ca1332 Wed Sep 25 13:00:10 2019 -0700
    Fixing MM github URL refs #24157
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8feb86631ca19310cb56aff6970a63e69747f86e Thu Sep 26 03:16:18 2019 -0700
    fixing mastermind otto based on feedback from QA, refs #24157
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
  • lines changed 14, context: html, text, full: html, text
    0e21ffef07796a9f33cf7500d120eb480eec7072 Mon Sep 23 14:40:46 2019 -0700
    Adjust default tracks based on input from D. Gorkin. refs #23970
• src/hg/makeDb/trackDb/mouse/mm10/encode3.chromHmm.ra
  • lines changed 4, context: html, text, full: html, text
    4ce8f539c0427437858ef3a8590ae184f049030f Mon Sep 23 13:48:15 2019 -0700
    Adjust defaults, based on input from D. Gorkin. refs #24128
• src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra
  • lines changed 23, context: html, text, full: html, text
    0d7d207d6124780140c7c8427c638e986a475442 Mon Sep 23 14:41:07 2019 -0700
    Adjust default tracks based on input from D. Gorkin. refs #23693
  • lines changed 563, context: html, text, full: html, text
    8b9477ba0a31209d16910db2c6b228aee3e1b7f8 Mon Sep 23 15:12:50 2019 -0700
    Cleanup
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.html
  • lines changed 44, context: html, text, full: html, text
    f7acf08a5582e5a898faaa8c9735c1c44b2825f3 Tue Sep 24 14:51:40 2019 -0700
    Add summary methods, draft of data access and credits. refs #23881
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 2, context: html, text, full: html, text
    a2f154d98e17a25dbd18718b9ae4a29070efb1d7 Mon Sep 23 14:40:10 2019 -0700
    Adjust ordering of tracks in supertrack. refs #23880
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 3, context: html, text, full: html, text
    49e44093b6e7e6613583676454b7916b1831b8e6 Fri Sep 27 10:54:36 2019 -0700
    Updating http to https for ornAna1 (platypus), uiLinks cronjob.
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
  • lines changed 1, context: html, text, full: html, text
    49e44093b6e7e6613583676454b7916b1831b8e6 Fri Sep 27 10:54:36 2019 -0700
    Updating http to https for ornAna1 (platypus), uiLinks cronjob.
• src/hg/makeDb/trackDb/platypus/ornAna1/wssdCoverage.html
  • lines changed 1, context: html, text, full: html, text
    49e44093b6e7e6613583676454b7916b1831b8e6 Fri Sep 27 10:54:36 2019 -0700
    Updating http to https for ornAna1 (platypus), uiLinks cronjob.
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    03f8972539f5ed48dd9026c8dd95be2764514e3e Mon Sep 30 08:57:51 2019 -0700
    Updating http to https for sacCer3, uiLinks cronjob
• src/hg/makeDb/trackDb/sacCer/transRegCode.html
  • lines changed 1, context: html, text, full: html, text
    03f8972539f5ed48dd9026c8dd95be2764514e3e Mon Sep 30 08:57:51 2019 -0700
    Updating http to https for sacCer3, uiLinks cronjob
• src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
  • lines changed 1, context: html, text, full: html, text
    03f8972539f5ed48dd9026c8dd95be2764514e3e Mon Sep 30 08:57:51 2019 -0700
    Updating http to https for sacCer3, uiLinks cronjob
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    7a975046edd84e2742f808cab2498691657dd5ba Mon Sep 23 15:13:06 2019 -0700
    Add missing type
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    20ec2e933ac40fff5932e1bf01d0285a2da9bf45 Tue Sep 24 16:14:47 2019 -0700
    Add new barCHart setting. refs #23691
  • lines changed 1, context: html, text, full: html, text
    d24ed481a58b99783bcaad71d5aee510b4572a29 Tue Sep 24 16:26:01 2019 -0700
    Rename trackDb setting for hiding empty subtracks (w/ backward compatibility). refs #23365
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 3, context: html, text, full: html, text
    7aaad12993fcbdb0e2619a12d2df61ca47710855 Wed Sep 25 08:56:24 2019 -0700
    Updating http to https for danRer7, uiLinks cronjob.
• src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
  • lines changed 1, context: html, text, full: html, text
    7aaad12993fcbdb0e2619a12d2df61ca47710855 Wed Sep 25 08:56:24 2019 -0700
    Updating http to https for danRer7, uiLinks cronjob.
• src/hg/pyLib/hgLib.py
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    444eff44f7651c6c3029cb807a33012329f5dbcf Thu Sep 26 03:02:23 2019 -0700
    adding hogExit message when blocking IP to hgGeneGraph, refs #24094
• src/hg/utils/hicInfo/hicInfo.c
  • lines changed 73, context: html, text, full: html, text
    7cb1d45d2ab54a8556d73748d41246df932bcb42 Fri Sep 27 16:23:47 2019 -0700
    Initial commit of hicInfo utility for displaying header info from .hic files, refs #22316
• src/hg/utils/hicInfo/makefile
  • lines changed 3, context: html, text, full: html, text
    7cb1d45d2ab54a8556d73748d41246df932bcb42 Fri Sep 27 16:23:47 2019 -0700
    Initial commit of hicInfo utility for displaying header info from .hic files, refs #22316
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 2, context: html, text, full: html, text
    45f102e1f2780bf665ea9ece8afdbd6967eaea2f Wed Sep 25 11:48:23 2019 -0700
    When hubCheck is actually going out and getting bigDataUrls, we still want those errors in html output mode too, bug reported by Lou
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    7cb1d45d2ab54a8556d73748d41246df932bcb42 Fri Sep 27 16:23:47 2019 -0700
    Initial commit of hicInfo utility for displaying header info from .hic files, refs #22316
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 18, context: html, text, full: html, text
    1fbf0a4bf3e1a40b9a117893d61b395561779d7a Mon Sep 23 13:45:20 2019 -0700
    Adding archiving commands to otto build scripts, refs #21825
• src/hg/utils/otto/geneReviews/checkGeneReviews.sh
  • lines changed 17, context: html, text, full: html, text
    1fbf0a4bf3e1a40b9a117893d61b395561779d7a Mon Sep 23 13:45:20 2019 -0700
    Adding archiving commands to otto build scripts, refs #21825
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 17, context: html, text, full: html, text
    1fbf0a4bf3e1a40b9a117893d61b395561779d7a Mon Sep 23 13:45:20 2019 -0700
    Adding archiving commands to otto build scripts, refs #21825
• src/hg/utils/otto/isca/checkISCA.sh
  • lines changed 38, context: html, text, full: html, text
    1fbf0a4bf3e1a40b9a117893d61b395561779d7a Mon Sep 23 13:45:20 2019 -0700
    Adding archiving commands to otto build scripts, refs #21825
• src/hg/utils/otto/mastermind/buildMastermind.sh
  • lines changed 8, context: html, text, full: html, text
    8feb86631ca19310cb56aff6970a63e69747f86e Thu Sep 26 03:16:18 2019 -0700
    fixing mastermind otto based on feedback from QA, refs #24157
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    027e5fe9c53369f8b09c68b6f6529bd7f22facaa Thu Sep 26 05:04:56 2019 -0700
    adding license and README to archive, refs #24157
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 16, context: html, text, full: html, text
    1fbf0a4bf3e1a40b9a117893d61b395561779d7a Mon Sep 23 13:45:20 2019 -0700
    Adding archiving commands to otto build scripts, refs #21825
• src/inc/bigBed.h
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    3ba9819d796643362d5bdbc6996b21ee16dfd6eb Tue Sep 24 15:08:16 2019 -0700
    add a new function to bigBed to get any field's column
• src/lib/bigBed.c
  • lines changed 18, context: html, text, full: html, text
    3ba9819d796643362d5bdbc6996b21ee16dfd6eb Tue Sep 24 15:08:16 2019 -0700
    add a new function to bigBed to get any field's column
• src/lib/net.c
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    2c221d2db31c68228249bfa07ccc134ef85d1989 Mon Sep 23 14:21:02 2019 -0700
    After code review with Jonathn, response codes 300 and 303 we cannot currently support anyways and we do not want to try. Nobody is using these codes, removed 300 and 303. Cleanup.
• src/utils/qa/weeklybld/buildEnv.csh
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    a617f0789415db12a98c32ea2b093956639e7a45 Mon Sep 30 10:01:58 2019 -0700
    v389 preview1, refs #24138

• lines changed: 17113
• files changed: 150