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Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 31 20:03:07 2011 UTC (8 years, 10 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_03312011, mgrast_dev_04012011, mgrast_dev_04052011, mgrast_dev_04082011, mgrast_dev_04132011, mgrast_release_3_0_3, mgrast_release_3_0_4
Changes since 1.72: +1 -1 lines
Diff to previous 1.72 , to selected 1.47
New method for features expressed in a given fraction of the experiments.

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 17 21:32:30 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_03252011, myrast_33
Changes since 1.71: +8 -2 lines
Diff to previous 1.71 , to selected 1.47
More debugging fixes.

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 17 20:30:01 2011 UTC (8 years, 11 months ago) by olson
Branch: MAIN
CVS Tags: mgrast_release_3_0_2
Changes since 1.70: +8 -0 lines
Diff to previous 1.70 , to selected 1.47
Make STDERR stay local for FCGI

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 17 18:40:41 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.69: +4 -4 lines
Diff to previous 1.69 , to selected 1.47
Update to expressed_genomes. Turned off activity warnings.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 16 15:57:16 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.68: +5 -3 lines
Diff to previous 1.68 , to selected 1.47
Hacked in some tracking stuff.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 15 19:06:08 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.67: +16 -10 lines
Diff to previous 1.67 , to selected 1.47
Added eval protection to the YAML encoding.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 21:11:21 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.66: +1 -1 lines
Diff to previous 1.66 , to selected 1.47
*** empty log message ***

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 21:04:25 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.65: +3 -4 lines
Diff to previous 1.65 , to selected 1.47
*** empty log message ***

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Mar 14 20:57:19 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.64: +27 -0 lines
Diff to previous 1.64 , to selected 1.47
Added a logging hack.

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 23 21:45:52 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
CVS Tags: mgrast_release_3_0, mgrast_release_3_0_1
Changes since 1.63: +1 -1 lines
Diff to previous 1.63 , to selected 1.47
Fixed missing method problem.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Feb 22 19:19:22 2011 UTC (8 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.62: +71 -65 lines
Diff to previous 1.62 , to selected 1.47
Enhanced to do method checks on the server side for applications that bypass ClientThing.

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 9 17:56:09 2011 UTC (9 years ago) by parrello
Branch: MAIN
CVS Tags: mgrast_dev_02212011, mgrast_dev_02222011
Changes since 1.61: +7 -1 lines
Diff to previous 1.61 , to selected 1.47
Changed to store the CGI object in the server object.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 15:32:08 2011 UTC (9 years ago) by dejongh
Branch: MAIN
Changes since 1.60: +1 -1 lines
Diff to previous 1.60 , to selected 1.47
fix handling of server name

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 25 22:44:43 2011 UTC (9 years ago) by chenry
Branch: MAIN
Changes since 1.59: +12 -2 lines
Diff to previous 1.59 , to selected 1.47
Added small change to code to handle ModelSEED::FBAMODEL package.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jan 11 15:03:02 2011 UTC (9 years, 1 month ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2011_0119
Changes since 1.58: +3 -1 lines
Diff to previous 1.58 , to selected 1.47
Fix to reduce Sapling dependence.

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 30 13:52:58 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_1206
Changes since 1.57: +39 -2 lines
Diff to previous 1.57 , to selected 1.47
New Sapling update support.

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 21 13:03:16 2010 UTC (9 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.56: +2 -6 lines
Diff to previous 1.56 , to selected 1.47
Enhanced "subsystems_for_role", removed reverse-arrow check for correspondence files.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 14 17:28:49 2010 UTC (9 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.55: +58 -0 lines
Diff to previous 1.55 , to selected 1.47
Expression vector support methods.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 29 17:35:51 2010 UTC (9 years, 6 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0827, rast_rel_2010_0928
Changes since 1.54: +2 -0 lines
Diff to previous 1.54 , to selected 1.47
Added support for using SAS_SERVER environment variable to configure the appropriate server.

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 13 18:49:09 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.53: +13 -10 lines
Diff to previous 1.53 , to selected 1.47
Fixed so that if no parameter is specified, it is not parsed.

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 8 20:15:39 2010 UTC (9 years, 7 months ago) by parrello
Branch: MAIN
Changes since 1.52: +65 -0 lines
Diff to previous 1.52 , to selected 1.47
Updates for new expression-data method.

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 14:36:02 2010 UTC (9 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.51: +28 -7 lines
Diff to previous 1.51 , to selected 1.47
Updates for auxiliary role filtering.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 28 15:46:38 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0526
Changes since 1.50: +10 -4 lines
Diff to previous 1.50 , to selected 1.47
*** empty log message ***

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 28 15:31:12 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.49: +2 -1 lines
Diff to previous 1.49 , to selected 1.47
Fixed an error in the Java interface.

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Apr 28 14:02:11 2010 UTC (9 years, 9 months ago) by parrello
Branch: MAIN
Changes since 1.48: +53 -3 lines
Diff to previous 1.48 , to selected 1.47
Added JSON support.

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 16 21:39:51 2010 UTC (9 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.47: +1 -1 lines
Diff to previous 1.47
Push down max requests.

Revision 1.47 - (view) (download) (as text) (annotate) - [selected]
Tue Apr 13 20:05:49 2010 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.46: +33 -2 lines
Diff to previous 1.46
Updated for computing previously-mapped genomes.

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Mar 31 17:09:15 2010 UTC (9 years, 10 months ago) by parrello
Branch: MAIN
Changes since 1.45: +1 -1 lines
Diff to previous 1.45 , to selected 1.47
Added module name to the documentation page titles.

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 18:27:07 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.44: +1 -1 lines
Diff to previous 1.44 , to selected 1.47
*** empty log message ***

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 15:08:27 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.43: +9 -6 lines
Diff to previous 1.43 , to selected 1.47
*** empty log message ***

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 03:43:08 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.42: +2 -2 lines
Diff to previous 1.42 , to selected 1.47
*** empty log message ***

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 19 00:15:05 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.41: +1 -1 lines
Diff to previous 1.41 , to selected 1.47
*** empty log message ***

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 18 23:06:48 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.40: +40 -2 lines
Diff to previous 1.40 , to selected 1.47
Fixed a bug in the corresponding-genes code.

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 16 20:24:05 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.39: +9 -3 lines
Diff to previous 1.39 , to selected 1.47
Added option to include reverse correspondences in correspondence map output.

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Mar 16 19:50:43 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.38: +27 -3 lines
Diff to previous 1.38 , to selected 1.47
Made gene correspondence submission more robust.

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 14 14:30:12 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.37: +1 -1 lines
Diff to previous 1.37 , to selected 1.47
*** empty log message ***

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Mar 14 13:26:32 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.36: +430 -49 lines
Diff to previous 1.36 , to selected 1.47
Updates for new gene correspondence system.

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 25 20:30:10 2010 UTC (9 years, 11 months ago) by parrello
Branch: MAIN
Changes since 1.35: +78 -0 lines
Diff to previous 1.35 , to selected 1.47
Added enhanced support for gene correspondence maps.

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jan 29 16:08:29 2010 UTC (10 years ago) by parrello
Branch: MAIN
Changes since 1.34: +29 -20 lines
Diff to previous 1.34 , to selected 1.47
Fixed an error in the handling of optional identifier lists.

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 20:57:35 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2010_0118
Changes since 1.33: +0 -1 lines
Diff to previous 1.33 , to selected 1.47
Fixed so that the ETracing parameter overrides the environment variable.

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 20:50:31 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.32: +1 -0 lines
Diff to previous 1.32 , to selected 1.47
Testing hack.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 16 18:49:10 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.31: +19 -15 lines
Diff to previous 1.31 , to selected 1.47
Modified so that errors will appear in the trace file by default.

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Dec 14 20:59:35 2009 UTC (10 years, 2 months ago) by disz
Branch: MAIN
Changes since 1.30: +51 -1 lines
Diff to previous 1.30 , to selected 1.47
Added LineNumberize

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 11 21:21:04 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.29: +10 -2 lines
Diff to previous 1.29 , to selected 1.47
Server database recovery fix.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 19:12:21 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.28: +2 -2 lines
Diff to previous 1.28 , to selected 1.47
Increased request limit to 5000. Streamlined tracing at level 2.

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 17:23:23 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27 , to selected 1.47
*** empty log message ***

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 17:09:22 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26 , to selected 1.47
*** empty log message ***

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 16:40:12 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.25: +5 -5 lines
Diff to previous 1.25 , to selected 1.47
*** empty log message ***

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 15:34:10 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.24: +4 -13 lines
Diff to previous 1.24 , to selected 1.47
*** empty log message ***

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 10 15:13:51 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.23: +1 -0 lines
Diff to previous 1.23 , to selected 1.47
Trying to trace the FastCGI problem.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Dec 9 21:43:59 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22 , to selected 1.47
Changed to accept CGI request only if the request limit has not yet been reached.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Dec 8 14:53:52 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.21: +11 -4 lines
Diff to previous 1.21 , to selected 1.47
Converted subsystem filtering from "unusable" to "usable".

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Dec 6 18:21:07 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.20: +64 -0 lines
Diff to previous 1.20 , to selected 1.47
Added new subsystem methods.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 4 19:23:43 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.19: +1 -1 lines
Diff to previous 1.19 , to selected 1.47
Fixed bad URL in "ProducePod".

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Dec 3 15:34:16 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.18: +25 -11 lines
Diff to previous 1.18 , to selected 1.47
Added server to search for roles and/or functions in a genome.

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 18:08:25 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.17: +3 -2 lines
Diff to previous 1.17 , to selected 1.47
Made memory tracing better.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 17:50:25 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.16: +1 -0 lines
Diff to previous 1.16 , to selected 1.47
Added optional memory tracing.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 17:39:47 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.15: +1 -1 lines
Diff to previous 1.15 , to selected 1.47
Removed trace hacks.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 12:47:36 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.14: +7 -5 lines
Diff to previous 1.14 , to selected 1.47
Added task IDs to trace messages.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Nov 30 11:44:50 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.13: +1 -0 lines
Diff to previous 1.13 , to selected 1.47
Added a memory trace for fast CGI mode.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 25 22:34:35 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.12: +62 -66 lines
Diff to previous 1.12 , to selected 1.47
Fixed to only allocate the server object once during a FASTCGI loop.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 25 21:52:02 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.11: +1 -1 lines
Diff to previous 1.11 , to selected 1.47
*** empty log message ***

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 25 21:38:05 2009 UTC (10 years, 2 months ago) by parrello
Branch: MAIN
Changes since 1.10: +9 -2 lines
Diff to previous 1.10 , to selected 1.47
Added maximum number of requests.

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 3 21:20:07 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.9: +44 -12 lines
Diff to previous 1.9 , to selected 1.47
Error handling restructure.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Oct 29 18:26:59 2009 UTC (10 years, 3 months ago) by parrello
Branch: MAIN
Changes since 1.8: +231 -100 lines
Diff to previous 1.8 , to selected 1.47
Final server updates.

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 30 15:34:28 2009 UTC (10 years, 4 months ago) by parrello
Branch: MAIN
Changes since 1.7: +82 -1 lines
Diff to previous 1.7 , to selected 1.47
Moved DocUtils so that it is only included if needed.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 9 15:20:54 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_0925
Changes since 1.6: +1 -1 lines
Diff to previous 1.6 , to selected 1.47
Fixed CSS link.

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 27 19:44:45 2009 UTC (10 years, 5 months ago) by parrello
Branch: MAIN
Changes since 1.5: +60 -15 lines
Diff to previous 1.5 , to selected 1.47
Converted to handle Fast CGI requests.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 4 18:41:56 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.4: +8 -6 lines
Diff to previous 1.4 , to selected 1.47
Changed handling of documentation URL.

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 4 18:19:59 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.3: +67 -43 lines
Diff to previous 1.3 , to selected 1.47
Added documentation functions to the Sapling server.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 3 21:31:42 2009 UTC (10 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.2: +11 -1 lines
Diff to previous 1.2 , to selected 1.47
Updated to Sapling Server for Berkeley.

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 30 20:11:54 2009 UTC (10 years, 7 months ago) by parrello
Branch: MAIN
CVS Tags: rast_rel_2009_07_09
Changes since 1.1: +5 -2 lines
Diff to previous 1.1 , to selected 1.47
Additional functionality for sapling server.

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 16 16:37:23 2009 UTC (10 years, 8 months ago) by parrello
Branch: MAIN
Diff to selected 1.47
New Sapling server support.

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