Commits for angie
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v379_base to v380_preview (2019-03-18 to 2019-03-25) v380
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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/hg/utils/vcfToHgvs/vcfToHgvs.c - lines changed 11, 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.
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/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/oneShot/testSqlDbDotTable/testSqlDbDotTable.c - lines changed 134, 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
- src/hg/hgSession/hgSession.c - lines changed 5, context: html, text, full: html, text
- src/hg/lib/customTrack.c - lines changed 12, context: html, text, full: html, text
- src/hg/near/hgNear/customColumn.c - lines changed 15, 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.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgSession/hgSession.h - lines changed 5, context: html, text, full: html, text
- src/hg/hgSession/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgSession/sessionData.c - lines changed 456, context: html, text, full: html, text
- src/hg/inc/customTrack.h - lines changed 2, context: html, text, full: html, text
- src/hg/lib/customFactory.c - lines changed 4, context: html, text, full: html, text
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