All File Changes

v379_base to v380_preview (2019-03-18 to 2019-03-25) v380

• confs/preview.hg.conf
  • lines changed 4, context: html, text, full: html, text
    715e092a3be50cde09c8b180901f7ecae399125a Sun Mar 24 01:11:45 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    c248d6a10bcbdadcd7f2c7cfb0272dd73334faaf Fri Mar 22 23:33:49 2019 -0700
    check that the file exists first. fixes bug in cdwWebBrowse when meta.txt is not found. discovered on public cirm with kriegsteinBrainOrganoid1.
• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 127, context: html, text, full: html, text
    c03ae3b5f1473ccaa41dc3fb2804d701e90e321d Wed Mar 20 16:33:31 2019 -0700
    Adding new column for imaging data. Changing info icons to not be links.
  • lines changed 19, context: html, text, full: html, text
    b45d635495635e7a591fd00a0a1b1b5e404d7d80 Wed Mar 20 17:26:11 2019 -0700
    Adding links to dataset summary pages for newly public datasets. refs #23156
  • lines changed 7, context: html, text, full: html, text
    0d54e39488e729efe378dc599f9388d2c3bce9b1 Thu Mar 21 13:26:46 2019 -0700
    Changes based on feed back from Will. Yeo lab link opens in new tab. Add descriptions for a Chi and a Corn dataset. Fix link to dataset summary page for a Corn dataset. refs #23172
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    3f62a4af0857b281468ddb912b7e7d2a3fe180f6 Thu Mar 21 11:50:21 2019 -0700
    Removing old url line from AllenBrains section, #23144
• src/hg/hgSession/hgSession.c
  • lines changed 5, context: html, text, full: html, text
    23b10b9fed9b850a60b7f601c6275811caa812e6 Mon Dec 3 11:43:50 2018 -0800
    Don't reuse trash files where it can be avoided -- make new cart files when there are changes, so that we don't have to copy files every time we save or load a session. refs #22440
  • lines changed 3, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/hgSession/hgSession.h
  • lines changed 5, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/hgSession/makefile
  • lines changed 1, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/hgSession/sessionData.c
  • lines changed 456, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 56, context: html, text, full: html, text
    5aba268172742caf3772a7f1e6e194d26e901ee9 Mon Mar 18 16:55:38 2019 -0700
    Fixing CR changes plus a few other FAQgenes ref#23141
  • lines changed 4, context: html, text, full: html, text
    2178fc298d3dd0cb7e400ccd0d944c5132b6026f Mon Mar 18 17:01:48 2019 -0700
    Minor changes to unreleased FAQgenes ref#22696
  • lines changed 19, context: html, text, full: html, text
    a86827f92ed8795e87539b2829821c0d824b5f36 Tue Mar 19 15:07:51 2019 -0700
    More work on unreleased FAQgenes page ref#22696
  • lines changed 64, context: html, text, full: html, text
    3df056201a1057053451c8ea38cb72419f3e75a1 Wed Mar 20 11:13:48 2019 +0100
    genes faq page intro change, #22696
  • lines changed 83, context: html, text, full: html, text
    317dbfc227692ade3bc42d0de919155f67e139e7 Wed Mar 20 11:16:25 2019 -0700
    Minor modifications and new section to unreleased FAQgenes page ref#22696
  • lines changed 3, context: html, text, full: html, text
    b3ee4097a9c129570ba2f8f7d7b376834d9ef4d0 Wed Mar 20 11:20:23 2019 -0700
    Minor modifications to FAQgenes ref#22696
  • lines changed 13, context: html, text, full: html, text
    b851c545e4701e24096f34a522318e3d22054493 Wed Mar 20 13:33:09 2019 -0700
    Final edits to FAQgenes page ref#22696
  • lines changed 32, context: html, text, full: html, text
    55817ba932466fcc3142bfcd3261a7d91bed1c3a Thu Mar 21 11:20:56 2019 +0100
    adding to faq genes page, refs #22696
  • lines changed 37, context: html, text, full: html, text
    9b780ead5d124e051e12c1be725eadc6ca7d76ae Thu Mar 21 11:25:19 2019 +0100
    adding counts to genes faq, refs #22696
• src/hg/htdocs/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    3ebf428309843449546e4e71612f34f9d2fc1e89 Mon Mar 18 11:16:46 2019 -0700
    Adding link to FAQgenes from index ref#22696
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    345027cdb289975c1d0907aad756b4abfe9fe76d Thu Mar 21 11:48:21 2019 -0700
    Changing formulate to format on customTrack.html, #23144
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    5aba268172742caf3772a7f1e6e194d26e901ee9 Mon Mar 18 16:55:38 2019 -0700
    Fixing CR changes plus a few other FAQgenes ref#23141
  • lines changed 28, context: html, text, full: html, text
    10495f58d26155308dd4f24c7e3fed7e8202ea3e Thu Mar 21 15:23:16 2019 -0700
    Adding new section to newarch.html for mastermind release, #21895
  • lines changed 2, context: html, text, full: html, text
    6e768e1ac93b7a2df9e69f7c2808cdba6b4d3eeb Fri Mar 22 08:21:45 2019 -0700
    Editing mastermind news announcements, refs #21895
  • lines changed 13, context: html, text, full: html, text
    d5007f4b43d2ae5c833533fdba6388d8a19e81a8 Fri Mar 22 13:20:37 2019 -0700
    Editing announcement for Mastermind release, refs #21895
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 7, context: html, text, full: html, text
    b29517e40fcf83d015309063ff9347b99258ff7f Mon Mar 18 15:24:42 2019 -0700
    Adding more full verbose list of authors on pubs.html
• src/hg/htdocs/images/ComprehensiveSet.png
  • lines changed 0, context: html, text, full: html, text
    3f6adf1abdca64a38af7870150505b52b7660d84 Tue Mar 19 14:04:12 2019 -0700
    Adding images for FAQgenes page ref#22696
• src/hg/htdocs/images/SpliceVariants.png
  • lines changed 0, context: html, text, full: html, text
    3f6adf1abdca64a38af7870150505b52b7660d84 Tue Mar 19 14:04:12 2019 -0700
    Adding images for FAQgenes page ref#22696
• src/hg/htdocs/inc/dataApi.html
  • lines changed 42, context: html, text, full: html, text
    d7823be63582aafb32001891aafe2573bd550b91 Fri Mar 22 15:31:47 2019 -0700
    help text for API interface refs #18869
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    3fb2b3e094bfd2d6e9a6173ad4298a08220893fc Thu Mar 21 15:27:55 2019 -0700
    Adding mastermind section to indexNews, 21895
• src/hg/hubApi/apiUtils.c
  • lines changed 19, context: html, text, full: html, text
    d2429b17bb096f6c406a2ae03fb5593f27fa53c1 Mon Mar 18 14:17:07 2019 -0700
    hash up the output properly for hubPublic and dbDb outputs refs #18869
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    d2429b17bb096f6c406a2ae03fb5593f27fa53c1 Mon Mar 18 14:17:07 2019 -0700
    hash up the output properly for hubPublic and dbDb outputs refs #18869
  • lines changed 1, context: html, text, full: html, text
    f6772f5e8a7399f1430561d708c3dcf033241cc8 Wed Mar 20 15:27:49 2019 -0700
    consolidate the tableDataOutput functions refs #18869
  • lines changed 16, context: html, text, full: html, text
    b7749ec648f88880da646bca0bba1a14f288639c Wed Mar 20 18:13:15 2019 -0700
    adding hubPublic.c and .h to library refs #18869
  • lines changed 7, context: html, text, full: html, text
    9c28afc6ca0b8e2b4404ab7a894925e8f5fcf62b Thu Mar 21 11:11:54 2019 -0700
    begin round of consolidation and simplification refs #18869
  • lines changed 3, context: html, text, full: html, text
    046c975630f6576722e8cbfa843e68f6068d854e Thu Mar 21 15:06:42 2019 -0700
    somewhat better for sample data URLs refs #18869
• src/hg/hubApi/getData.c
  • lines changed 3, context: html, text, full: html, text
    d2429b17bb096f6c406a2ae03fb5593f27fa53c1 Mon Mar 18 14:17:07 2019 -0700
    hash up the output properly for hubPublic and dbDb outputs refs #18869
  • lines changed 44, context: html, text, full: html, text
    0f8ec54de20313713243e8d359449f28cfb4514d Tue Mar 19 14:22:48 2019 -0700
    object data outputs refs #18869
  • lines changed 1, context: html, text, full: html, text
    f72d8b57a77755e64ef594ae2d4395a12c19712d Tue Mar 19 21:46:37 2019 -0700
    now showing a sample getData URL for supported tracks refs #18869
  • lines changed 114, context: html, text, full: html, text
    f6772f5e8a7399f1430561d708c3dcf033241cc8 Wed Mar 20 15:27:49 2019 -0700
    consolidate the tableDataOutput functions refs #18869
  • lines changed 88, context: html, text, full: html, text
    046c975630f6576722e8cbfa843e68f6068d854e Thu Mar 21 15:06:42 2019 -0700
    somewhat better for sample data URLs refs #18869
  • lines changed 10, context: html, text, full: html, text
    4d72ed9554069edb885ff2f793add75e422a5459 Thu Mar 21 15:58:39 2019 -0700
    error catch aroung bbi file open and better sample getData links refs #18869
  • lines changed 28, context: html, text, full: html, text
    5194786c88bd4ab5e802eec79089897461389fe9 Fri Mar 22 14:52:22 2019 -0700
    getting a little bit better refs #18869
• src/hg/hubApi/hubApi.c
  • lines changed 1, context: html, text, full: html, text
    d2429b17bb096f6c406a2ae03fb5593f27fa53c1 Mon Mar 18 14:17:07 2019 -0700
    hash up the output properly for hubPublic and dbDb outputs refs #18869
  • lines changed 40, context: html, text, full: html, text
    dc68ca87c184d7a6d4112e293073bddb34a9e913 Tue Mar 19 10:36:54 2019 -0700
    full reporting of all track names in html display even when not in detail mode refs #18869
  • lines changed 150, context: html, text, full: html, text
    f72d8b57a77755e64ef594ae2d4395a12c19712d Tue Mar 19 21:46:37 2019 -0700
    now showing a sample getData URL for supported tracks refs #18869
  • lines changed 58, context: html, text, full: html, text
    e27f427561241ab8dd9e881f082c1e68007e6dfe Wed Mar 20 09:48:44 2019 -0700
    correctly exclude vars for hgwdev-api URL functions refs #18869
  • lines changed 17, context: html, text, full: html, text
    f6772f5e8a7399f1430561d708c3dcf033241cc8 Wed Mar 20 15:27:49 2019 -0700
    consolidate the tableDataOutput functions refs #18869
  • lines changed 114, context: html, text, full: html, text
    b7749ec648f88880da646bca0bba1a14f288639c Wed Mar 20 18:13:15 2019 -0700
    adding hubPublic.c and .h to library refs #18869
  • lines changed 173, context: html, text, full: html, text
    9c28afc6ca0b8e2b4404ab7a894925e8f5fcf62b Thu Mar 21 11:11:54 2019 -0700
    begin round of consolidation and simplification refs #18869
  • lines changed 103, context: html, text, full: html, text
    046c975630f6576722e8cbfa843e68f6068d854e Thu Mar 21 15:06:42 2019 -0700
    somewhat better for sample data URLs refs #18869
  • lines changed 61, context: html, text, full: html, text
    4d72ed9554069edb885ff2f793add75e422a5459 Thu Mar 21 15:58:39 2019 -0700
    error catch aroung bbi file open and better sample getData links refs #18869
  • lines changed 240, context: html, text, full: html, text
    5194786c88bd4ab5e802eec79089897461389fe9 Fri Mar 22 14:52:22 2019 -0700
    getting a little bit better refs #18869
  • lines changed 26, context: html, text, full: html, text
    bbed927851c49abc7a66c8ed6350dfa99cebb189 Fri Mar 22 15:11:31 2019 -0700
    clean up some long duplicated strings refs #18869
  • lines changed 54, context: html, text, full: html, text
    0e2add24701b51d27afce7581ad3c54789f6d23e Fri Mar 22 15:35:14 2019 -0700
    help text now in include file refs #18869
• src/hg/hubApi/list.c
  • lines changed 58, context: html, text, full: html, text
    d2429b17bb096f6c406a2ae03fb5593f27fa53c1 Mon Mar 18 14:17:07 2019 -0700
    hash up the output properly for hubPublic and dbDb outputs refs #18869
  • lines changed 65, context: html, text, full: html, text
    0dbf3efc8d7c425510c124204883708273691ec8 Tue Mar 19 13:36:44 2019 -0700
    correctly listing full set of tracks for a hub or database with all attributes refs #18869
  • lines changed 1, context: html, text, full: html, text
    b7749ec648f88880da646bca0bba1a14f288639c Wed Mar 20 18:13:15 2019 -0700
    adding hubPublic.c and .h to library refs #18869
  • lines changed 2, context: html, text, full: html, text
    9c28afc6ca0b8e2b4404ab7a894925e8f5fcf62b Thu Mar 21 11:11:54 2019 -0700
    begin round of consolidation and simplification refs #18869
• src/hg/inc/cart.h
  • lines changed 4, context: html, text, full: html, text
    23b10b9fed9b850a60b7f601c6275811caa812e6 Mon Dec 3 11:43:50 2018 -0800
    Don't reuse trash files where it can be avoided -- make new cart files when there are changes, so that we don't have to copy files every time we save or load a session. refs #22440
  • lines changed 4, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/inc/customTrack.h
  • lines changed 2, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/inc/hubPublic.h
  • lines changed 87, context: html, text, full: html, text
    377a0776897437992e3b9080c73d8c78f7fc7470 Wed Mar 20 18:11:40 2019 -0700
    adding hubPublic.c and .h refs #18869
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    7a2a65c7811a54a9a055b78e07ea4ac4e19b1b0b Fri Mar 22 11:25:47 2019 -0700
    Correcting a comment and removing declaration of a function that is no longer defined in jksql.c.
• src/hg/lib/cart.c
  • lines changed 47, context: html, text, full: html, text
    23b10b9fed9b850a60b7f601c6275811caa812e6 Mon Dec 3 11:43:50 2018 -0800
    Don't reuse trash files where it can be avoided -- make new cart files when there are changes, so that we don't have to copy files every time we save or load a session. refs #22440
  • lines changed 18, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/lib/customFactory.c
  • lines changed 4, context: html, text, full: html, text
    a8273be9da3b7a87a8d829d3efb79bce66e22039 Wed Jan 23 17:42:02 2019 -0800
    New hg.conf settings sessionDataDir and sessionDataDbPrefix enable hgSession to move saved session trash files and customTrash tables into safe storage, so trash cleaner can be simpler. refs #22440 When hgSession saves a session to namedSessionDb: * If sessionDataDir is set in hg.conf (e.g. /data/apache/userdata on hgwdev), trash paths in cart variable values and in the contents of ctfile_$db and customComposite-$db files are replaced with paths in a directory hierarchy under sessionDataDir. Files are moved from trash into the new directories and symlinks are made from trash locations to new locations. * If sessionDataDbPrefix is set in hg.conf (e.g. customData), customTrash tables named in dbTableName settings in ctfile_$db are moved to a <sessionDataDbPrefix><dayOfMonth> database (e.g. customData03 on the third day of the month). dbTableName settings are updated to point to the new locations. If sessionDataDir is also set and a table contains a trash path, then the table is updated to contain to the new path under sessionDataDir. sessionDataDir must be an absolute path to keep the symlinks straightforward. The new directory hierarchy under sessionDataDir is A/B/C/D where A-D are defined as follows: * A: the first two characters of the hex string md5sum of namedSessionDb.userName, i.e. the URI-encoded username truncated to varchar(32) (there can be tens of thousands of userNames; using this mini-hash distributes them across up to 256 subdirectories of sessionDataDir) * B: the URI-encoded userName * C: the first 8 characters of the hex string md5sum of namedSessionDb.sessionName, i.e. the URI-encoded session name truncated to varchar(255) * D: the original path below ../trash/ So, for example, the file ../trash/ct/ct_hgwdev_angie_11fc0_2b5970.maf could be moved to /data/apache/userdata/fb/AngieHinrichs/cf2a2304/ct/ct_hgwdev_angie_11fc0_2b5970.maf
• src/hg/lib/customTrack.c
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    23b10b9fed9b850a60b7f601c6275811caa812e6 Mon Dec 3 11:43:50 2018 -0800
    Don't reuse trash files where it can be avoided -- make new cart files when there are changes, so that we don't have to copy files every time we save or load a session. refs #22440
• src/hg/lib/hubPublic.c
  • lines changed 259, context: html, text, full: html, text
    377a0776897437992e3b9080c73d8c78f7fc7470 Wed Mar 20 18:11:40 2019 -0700
    adding hubPublic.c and .h refs #18869
• src/hg/lib/hubPublic.sql
  • lines changed 1, context: html, text, full: html, text
    377a0776897437992e3b9080c73d8c78f7fc7470 Wed Mar 20 18:11:40 2019 -0700
    adding hubPublic.c and .h refs #18869
• src/hg/lib/jksql.c
  • lines changed 93, context: html, text, full: html, text
    4919a9ebc4669d592f68cb4feb7c00c650a371d8 Thu Mar 21 12:04:08 2019 -0700
    Add support for 'db.table' notation where necessary. refs #22440 Most jksql.c functions with table as a parameter already support 'db.table' notation (as opposed to just 'table', e.g. 'hgFixed.cds' as opposed to 'cds'). Here I'm adding a oneShot test program to test all jksql functions that take table as a param; for functions that don't already support 'db.table', parse db.table and temporarily change database for the table query. The motivation is to support using the customTrash connection for safe-storage customData* databases that will appear as 'db.table' e.g. 'customData01.t1_hgwdev_...'.
• src/hg/lib/makefile
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    626dbc4d58f93cea274d5e4ff4ceba59c0ed40b7 Wed Mar 20 18:11:54 2019 -0700
    adding hubPublic.c and .h refs #18869
• src/hg/lib/tablesTables.c
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    20db82d64258c81a94f963629028e6f09eccf629 Sat Mar 16 01:17:20 2019 -0700
    Fixing See N More count for faceted search. refs#23074.
• src/hg/makeDb/trackDb/augustusGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/ccdsGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
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    e042a25d7400331eb0c2f7aa26bf81c59e35907d Fri Mar 22 09:06:06 2019 -0700
    Updating http to https for galGal3, uiLinks cronjob
• src/hg/makeDb/trackDb/chicken/galGal3/phastConsElements7way.html
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    e042a25d7400331eb0c2f7aa26bf81c59e35907d Fri Mar 22 09:06:06 2019 -0700
    Updating http to https for galGal3, uiLinks cronjob
• src/hg/makeDb/trackDb/drosophila/chainDm1.html
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    f583064309c06d4b0c428f1bdd116e0545b1ad2e Wed Mar 20 09:07:53 2019 -0700
    Updating redirected links for dp2, uiLinks cronjob.
• src/hg/makeDb/trackDb/ensGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/genscan.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/human/hg19/acembly.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/human/hg19/mastermind.html
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    d57c9e28fe9c467d15c84c2eb9eec5f02e71a711 Fri Mar 22 13:22:35 2019 -0700
    Editing mastermind description page to remove incorrect link mention, refs #21895
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    a7f44666e333421e59850a290c01a1a7b3390cbe Mon Mar 25 09:26:15 2019 -0700
    Editing grammar on mastermind description page, refs #21895
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    69cb0429fa36c20c0e1d4a7d8d395098771b3a34 Fri Mar 22 13:32:56 2019 -0700
    Adding pennantIcon and removing release tags from mastermind track, refs #21895
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    de5c6e452ed7bb3cc18c3c9907117e41a9752ede Mon Mar 25 09:27:13 2019 -0700
    removing release tags for mastermind track, refs #21895
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/knownGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/mouse/GRCm38B/trackDb.ra
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    febab8f238e57a9ac1974aee9737c223027e8f9b Sat Mar 23 19:08:14 2019 -0700
    added temporary tracks to GRCm38B temporary assemble
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    40b7e2a3e86f9633d0800d1ae5fed25c38a4e342 Mon Mar 25 06:36:58 2019 -0700
    removed pslToBigPsl warning about missing CDS, as this is an expected occurance for non-coding genes which can generate tens of thousands of warnings
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/mouse/mm9/knownGene.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/netDm1.html
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    f583064309c06d4b0c428f1bdd116e0545b1ad2e Wed Mar 20 09:07:53 2019 -0700
    Updating redirected links for dp2, uiLinks cronjob.
• src/hg/makeDb/trackDb/refSeqComposite.html
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    7584423dc9148b9d1ca4203a3785fb471220ddea Wed Mar 20 13:38:42 2019 -0700
    Adding links to FAQgenes page from many genes track descriptions #22696
• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
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    d040d37e8a69e8f8ca5976d9ef3addfa1c931da3 Thu Mar 21 10:30:58 2019 -0700
    Updating redirected links for cb1, uiLinks cronjob.
• src/hg/near/hgNear/customColumn.c
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    23b10b9fed9b850a60b7f601c6275811caa812e6 Mon Dec 3 11:43:50 2018 -0800
    Don't reuse trash files where it can be avoided -- make new cart files when there are changes, so that we don't have to copy files every time we save or load a session. refs #22440
• src/hg/oneShot/testSqlDbDotTable/makefile
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    4919a9ebc4669d592f68cb4feb7c00c650a371d8 Thu Mar 21 12:04:08 2019 -0700
    Add support for 'db.table' notation where necessary. refs #22440 Most jksql.c functions with table as a parameter already support 'db.table' notation (as opposed to just 'table', e.g. 'hgFixed.cds' as opposed to 'cds'). Here I'm adding a oneShot test program to test all jksql functions that take table as a param; for functions that don't already support 'db.table', parse db.table and temporarily change database for the table query. The motivation is to support using the customTrash connection for safe-storage customData* databases that will appear as 'db.table' e.g. 'customData01.t1_hgwdev_...'.
• src/hg/oneShot/testSqlDbDotTable/testSqlDbDotTable.c
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    4919a9ebc4669d592f68cb4feb7c00c650a371d8 Thu Mar 21 12:04:08 2019 -0700
    Add support for 'db.table' notation where necessary. refs #22440 Most jksql.c functions with table as a parameter already support 'db.table' notation (as opposed to just 'table', e.g. 'hgFixed.cds' as opposed to 'cds'). Here I'm adding a oneShot test program to test all jksql functions that take table as a param; for functions that don't already support 'db.table', parse db.table and temporarily change database for the table query. The motivation is to support using the customTrash connection for safe-storage customData* databases that will appear as 'db.table' e.g. 'customData01.t1_hgwdev_...'.
• src/hg/utils/hubCheck/hubCheck.c
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    2ad067dae732bef5b7ab5ddc463fbaa68a33fca3 Wed Mar 20 15:42:23 2019 -0700
    initialize htslib to use UDC
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
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    40b7e2a3e86f9633d0800d1ae5fed25c38a4e342 Mon Mar 25 06:36:58 2019 -0700
    removed pslToBigPsl warning about missing CDS, as this is an expected occurance for non-coding genes which can generate tens of thousands of warnings
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    fc1790a9a6117cfa0768ac691b0ba1d9bc1ea43b Tue Mar 19 22:05:00 2019 -0700
    version 42. hDisconnectCentral(&conn) should never have been there. moving the other line for code clarity.
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
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    8a575379eee18e0d94bd4fa4a8330eca6ca043d5 Wed Mar 20 10:34:14 2019 -0700
    Initialize udcDir (provide command line option) and call knetUdcInstall to use udc instead of htslib network lib. refs #23127
• src/product/mirrorDocs/makefile
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    569ad8eeb1784010b04d8cc664f1f37a23ac1efb Tue Mar 19 11:16:34 2019 +0100
    tiny makefile change to mirror docs, no redmine
• src/utils/findMotif/tests/expected/test1.txt.gz
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/findMotif/tests/expected/test2.txt.gz
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/findMotif/tests/expected/test3.txt.gz
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/findMotif/tests/expected/test4.txt.gz
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/findMotif/tests/expected/test7.txt.gz
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/findMotif/tests/makefile
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    0639a91e1aee8fa54c7834eb8012c16a4accd877 Tue Mar 19 08:38:36 2019 -0700
    eliminate source version from outputs and expected no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    61f2aaabcc3065c5a9378fbe2fae8c6359d5de5e Mon Mar 25 10:09:54 2019 -0700
    v380 preview1, refs #23070

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• files changed: 114