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Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 2 22:19:45 2006 UTC (13 years, 9 months ago) by overbeek
Branch: MAIN
CVS Tags: HEAD, mgrast_dev_02212011, mgrast_dev_02222011, mgrast_dev_03252011, mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_dev_05262011, mgrast_dev_06072011, mgrast_dev_08022011, mgrast_dev_08112011, mgrast_dev_10262011, mgrast_dev_12152011, mgrast_rel_2008_0625, mgrast_rel_2008_0806, mgrast_rel_2008_0917, mgrast_rel_2008_0919, mgrast_rel_2008_0923, mgrast_rel_2008_0924, mgrast_rel_2008_1110, mgrast_rel_2008_1110_v2, mgrast_release_3_0, mgrast_release_3_0_1, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_4, mgrast_release_3_1_0, mgrast_release_3_1_1, mgrast_release_3_1_2, mgrast_version_3_2, myrast_33, myrast_rel40, rast_2008_0924, rast_rel_2008_04_23, rast_rel_2008_06_16, rast_rel_2008_06_18, rast_rel_2008_07_21, rast_rel_2008_08_07, rast_rel_2008_09_29, rast_rel_2008_09_30, rast_rel_2008_10_09, rast_rel_2008_10_29, rast_rel_2008_11_24, rast_rel_2008_12_18, rast_rel_2009_02_05, rast_rel_2009_03_26, rast_rel_2009_05_18, rast_rel_2009_07_09, rast_rel_2009_0925, rast_rel_2010_0118, rast_rel_2010_0526, rast_rel_2010_0827, rast_rel_2010_0928, rast_rel_2010_1206, rast_rel_2011_0119, rast_rel_2011_0928, rast_rel_2014_0729, rast_rel_2014_0912, rast_release_2008_09_29
Changes since 1.26: +9 -5 lines
Diff to previous 1.26
Fix extra-args option to go at teh start of the list.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 6 20:20:40 2006 UTC (13 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: caBIG-05Apr06-00, caBIG-13Feb06-00
Changes since 1.25: +75 -14 lines
Diff to previous 1.25
Add support for using system  mysql installation.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 3 20:52:38 2006 UTC (13 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.24: +4 -0 lines
Diff to previous 1.24
SQLite support.

#CVS: ----------------------------------------------------------------------

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 5 19:06:30 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.23: +17 -0 lines
Diff to previous 1.23
Added license words.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 22 17:24:17 2005 UTC (14 years ago) by olson
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22
Don't use innodb by default for mysql.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 16 19:41:12 2005 UTC (14 years, 3 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00, caBIG-dataload-0
Changes since 1.21: +4 -2 lines
Diff to previous 1.21
NMPDR updates

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 27 17:56:13 2005 UTC (14 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.20: +8 -0 lines
Diff to previous 1.20
In mysql server startup, force server to create innodb tables.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 24 21:40:16 2005 UTC (14 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Changes since 1.19: +0 -20 lines
Diff to previous 1.19
Moved vacuum method from DBrtns to DBKernel. Changed so that it also does an analysis in MySQL.

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 15 16:24:37 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
CVS Tags: Root-bobdev_news
Branch point for: Branch-bobdev_news
Changes since 1.18: +3 -2 lines
Diff to previous 1.18
Add support for specification of a database host.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 9 18:34:16 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.17: +26 -247 lines
Diff to previous 1.17
*** empty log message ***

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 1 01:18:50 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.16: +1 -1 lines
Diff to previous 1.16
install precomputed functional coupling data

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 17 16:04:08 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.15: +23 -13 lines
Diff to previous 1.15
Bundle of misc bob changes, including sim computation code and search-for-substring.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 11 18:43:19 2005 UTC (14 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.14: +16 -1 lines
Diff to previous 1.14
some changes for mysql/cluster stuff.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 21 17:56:29 2005 UTC (14 years, 7 months ago) by disz
Branch: MAIN
Changes since 1.13: +2 -2 lines
Diff to previous 1.13
added genome package analyzer

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 12 22:58:32 2005 UTC (14 years, 8 months ago) by redwards
Branch: MAIN
Changes since 1.12: +5 -3 lines
Diff to previous 1.12
debugging load_attributes

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 08:32:10 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11
Allow whitespace at the start of a select in SQL method.

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 17:31:59 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.10: +26 -0 lines
Diff to previous 1.10
add get_inserted_id

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Feb 27 14:05:58 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.9: +7 -0 lines
Diff to previous 1.9
On postgres, use DROP  TABLE <name> CASCADE so that we can drop tables that
have foreign key constraints set up.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 23:32:45 2005 UTC (14 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.8: +12 -1 lines
Diff to previous 1.8
Add backtrace to non-select SQL calls.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 04:44:22 2005 UTC (14 years, 10 months ago) by redwards
Branch: MAIN
Changes since 1.7: +4 -2 lines
Diff to previous 1.7
Minor changes to DBrtns to clarify the weird error I was getting and to include how to fix it in the error code

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 18:59:39 2005 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.6: +9 -3 lines
Diff to previous 1.6
I ran into a bug today where I was using by_alias to look up aliases
for the peg-mapping code, and one of the aliases was DR6', with a
single-quote. Because the code in by_alias doesn't quote its argument,
the SQL failed with a syntax error.

The perl DBI library has a mechanism designed to solve this
problem. If you use ? in a sql string where you want to substitute an
argument from code, DBI will do the appropriate quoting for you. I've
made this accessible via the SQL method in the DBrtns module, so the
by_alias code now looks like this:

    if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = ? )", undef, $alias))

and works properly in the face of $alias having a single-quote in
it. I believe this mechanism is also more efficient. Note the second
argument of SQL is a verbose flag, which means that any bound
variables (to replace ?s in the query) have to start at the third
argument.

I've also made a change in the SQL method such that the query is done
inside an eval{} block, and if it fails, the error is reraised using
confess so that it is possible to see the full backtrace so you can
find in the source where the bad query was.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Nov 7 23:07:34 2004 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.5: +2 -0 lines
Diff to previous 1.5
DB params needed for gendb.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 1 20:20:09 2004 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.4: +153 -0 lines
Diff to previous 1.4
Add database server manipulation routines.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 27 15:04:10 2004 UTC (15 years, 1 month ago) by olson
Branch: MAIN
Changes since 1.3: +15 -1 lines
Diff to previous 1.3
fixes for mysql

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 1 21:16:34 2004 UTC (15 years, 5 months ago) by olson
Branch: MAIN
Changes since 1.2: +48 -4 lines
Diff to previous 1.2
add get_tables, table_exists

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 6 11:52:31 2004 UTC (15 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.1: +3 -2 lines
Diff to previous 1.1
translate auto_assignments

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 1 16:54:26 2003 UTC (16 years ago) by efrank
Branch: MAIN
Branch point for: initial
Initial revision

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