[Bio] / FigKernelPackages / Subsystem.pm Repository:
ViewVC logotype

Log of /FigKernelPackages/Subsystem.pm

Parent Directory Parent Directory


Links to HEAD: (view) (download) (as text) (annotate)
Links to caBIG-00-00-00: (view) (download) (as text) (annotate)
Sticky Tag:

Revision 1.74 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 21:03:16 2005 UTC (14 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: caBIG-00-00-00
Changes since 1.73: +4 -2 lines
Diff to previous 1.73
Broad minor fixes to make the SEED use relative paths throughout.

(The motivation this is to fully enable hiding the actual location of a running SEED system behind a web proxy so that things like NMPDR protein page references can be made stable across multiple releases).

This involved things like the following:

Changing $cgi->url() to $cgi->url(-relative => 1)
Changing $cgi->self_url() to $cgi->url(-relative => 1, -query => 1, -path_info => 1)

Changing the definition of FIG::cgi_url() to return "." (this may break something, but I haven't found it yet).

Revision 1.73 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 12 02:45:35 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.72: +271 -92 lines
Diff to previous 1.72
Upgraded the documentation.

Revision 1.72 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 3 20:00:13 2005 UTC (14 years, 6 months ago) by redwards
Branch: MAIN
CVS Tags: caBIG-dataload-0
Changes since 1.71: +2 -0 lines
Diff to previous 1.71
removing leading/trailing spaces

Revision 1.71 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 19:04:46 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.70: +1 -1 lines
Diff to previous 1.70
Remove debug print.

Revision 1.70 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 18:47:58 2005 UTC (14 years, 6 months ago) by olson
Branch: MAIN
Changes since 1.69: +267 -61 lines
Diff to previous 1.69
Careful cleanup of subsystem indexing. Patched a bunch of spots where needed updates didn't happen.

Add variant code to subsystem index.

Revision 1.69 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 15 14:33:49 2005 UTC (14 years, 6 months ago) by parrello
Branch: MAIN
Changes since 1.68: +696 -696 lines
Diff to previous 1.68
Converted tabs to spaces.

Revision 1.68 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 16:25:28 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.67: +5 -5 lines
Diff to previous 1.67
Add a force_backups option to write_subsystem.

Revision 1.67 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 10 12:03:36 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.66: +51 -7 lines
Diff to previous 1.66
More logging and sanity checks on diagram code.

Revision 1.66 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 9 18:08:41 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.65: +22 -1 lines
Diff to previous 1.65
Use system and an array to do the rm -r so we don't get bashed by ()s.

Revision 1.65 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 21:54:39 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.64: +111 -26 lines
Diff to previous 1.64
More diagram changes.

Add new simple start page.

Revision 1.64 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 8 20:05:08 2005 UTC (14 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.63: +3 -3 lines
Diff to previous 1.63
Fixed module attributes that were causing massive compile warnings.

Revision 1.63 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 4 13:27:40 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.62: +1 -1 lines
Diff to previous 1.62
fix bad bug in db_synch for subsystems

Revision 1.62 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 21:16:29 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.61: +36 -5 lines
Diff to previous 1.61
Support gif/png/jpeg file type detection on diagram upload.
Support the multiple file types on packaging for clearinghouse.

Revision 1.61 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Aug 3 17:40:42 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.60: +140 -18 lines
Diff to previous 1.60
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.

Revision 1.60 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 1 22:22:13 2005 UTC (14 years, 8 months ago) by parrello
Branch: MAIN
Changes since 1.59: +81 -81 lines
Diff to previous 1.59
Changed attributes to capital-case in order to prevent the avalanche of compile-time warnings.

Revision 1.59 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Jul 30 13:02:31 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.58: +10 -3 lines
Diff to previous 1.58
fixes to reactions in subsystems

Revision 1.58 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 19:31:21 2005 UTC (14 years, 8 months ago) by overbeek
Branch: MAIN
Changes since 1.57: +54 -1 lines
Diff to previous 1.57
add reactions to subsystems

Revision 1.57 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 29 18:13:45 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.56: +9 -2 lines
Diff to previous 1.56
Make index_subsystems use file load instead of inserts.

Revision 1.56 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 21 18:38:58 2005 UTC (14 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.55: +3 -0 lines
Diff to previous 1.55
Convert space to _ in constructor.

Revision 1.55 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 12 21:08:09 2005 UTC (14 years, 9 months ago) by redwards
Branch: MAIN
Changes since 1.54: +6 -2 lines
Diff to previous 1.54
improved subsys_vectors.cgi

Revision 1.54 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 8 23:05:21 2005 UTC (14 years, 10 months ago) by overbeek
Branch: MAIN
CVS Tags: Root-bobdev_news, merge-bobdev_news-1, merge-bobdev_news-2, merge-bodev_news-3, merge-trunktag-bobdev_news-1, merge-trunktag-bobdev_news-2, merge-trunktag-bodev_news-3
Branch point for: Branch-bobdev_news
Changes since 1.53: +1 -0 lines
Diff to previous 1.53
major change to BBHs (use precomputed)

Revision 1.53 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 10 12:03:39 2005 UTC (14 years, 11 months ago) by overbeek
Branch: MAIN
Changes since 1.52: +3 -1 lines
Diff to previous 1.52
fixes to using trees under subsystems

Revision 1.52 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Apr 25 19:59:11 2005 UTC (14 years, 11 months ago) by olson
Branch: MAIN
Changes since 1.51: +48 -1 lines
Diff to previous 1.51
add get_sorted_rows.

Fix get_subsetC to not fail on empty subsets.

Revision 1.51 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Apr 8 20:22:23 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.50: +1 -1 lines
Diff to previous 1.50
changed tag/value pairs completely. Ooops!

Revision 1.50 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Apr 7 19:16:10 2005 UTC (15 years ago) by redwards
Branch: MAIN
Changes since 1.49: +8 -4 lines
Diff to previous 1.49
many changes to key/value pairs to make them work

Revision 1.49 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Apr 5 18:24:34 2005 UTC (15 years ago) by overbeek
Branch: MAIN
Changes since 1.48: +4 -0 lines
Diff to previous 1.48
strip leading/trailing spaces on subsystem aabr and names

Revision 1.48 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Mar 12 20:30:38 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.47: +24 -0 lines
Diff to previous 1.47
Changed Subsystems to allow selection of active_subsetR (rows) based on tag/value pairs

Revision 1.47 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 26 11:01:13 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.46: +14 -6 lines
Diff to previous 1.46
add reset_curator.cgi

Revision 1.46 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Feb 24 22:02:39 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.45: +4 -2 lines
Diff to previous 1.45
add set_variants.cgi and fixes to Subsystems.pm

Revision 1.45 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Feb 14 18:22:14 2005 UTC (15 years, 1 month ago) by overbeek
Branch: MAIN
Changes since 1.44: +1 -0 lines
Diff to previous 1.44
initialize classification data when creating subsystem

Revision 1.44 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Feb 12 18:18:14 2005 UTC (15 years, 1 month ago) by redwards
Branch: MAIN
Changes since 1.43: +31 -0 lines
Diff to previous 1.43
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.

Revision 1.43 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jan 26 23:46:20 2005 UTC (15 years, 2 months ago) by overbeek
Branch: MAIN
Changes since 1.42: +9 -0 lines
Diff to previous 1.42
fix bug in removing genomes from a subsystem

Revision 1.42 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Nov 30 17:06:13 2004 UTC (15 years, 4 months ago) by olson
Branch: MAIN
Changes since 1.41: +36 -1 lines
Diff to previous 1.41
Add support for sending a list of genomes to billogix extension code.

Revision 1.41 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Nov 12 03:48:02 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.40: +6 -0 lines
Diff to previous 1.40
fix bug in -save parm for align_with_clustal

Revision 1.40 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Oct 25 20:32:35 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.39: +4 -2 lines
Diff to previous 1.39
add document on exchange of annotations and assignments

Revision 1.39 - (view) (download) (as text) (annotate) - [select for diffs]
Sat Oct 16 20:42:28 2004 UTC (15 years, 5 months ago) by overbeek
Branch: MAIN
Changes since 1.38: +5 -2 lines
Diff to previous 1.38
fixes to generalize chromosomal_clusters.cgi for UniProt

Revision 1.38 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Oct 12 11:56:23 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.37: +7 -3 lines
Diff to previous 1.37
updates to subsys.cgi

Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Oct 10 17:13:55 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.36: +62 -17 lines
Diff to previous 1.36
many fixes to subsystems code

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Oct 6 21:37:02 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.35: +5 -2 lines
Diff to previous 1.35
fix bug in copying a subsystem

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 28 20:39:39 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.34: +18 -10 lines
Diff to previous 1.34
fix subset and sorting problems in subsys.cgi

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 23 19:58:28 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.33: +7 -0 lines
Diff to previous 1.33
subsys.cgi was not letting the user delete genomes or set variants

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Sep 17 00:56:04 2004 UTC (15 years, 6 months ago) by overbeek
Branch: MAIN
Changes since 1.32: +8 -2 lines
Diff to previous 1.32
fixes to subsys.cgi

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 9 00:00:09 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.31: +1 -1 lines
Diff to previous 1.31
minor fixes

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Sep 7 02:54:16 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.30: +71 -11 lines
Diff to previous 1.30
add new subsystem interface

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Sep 1 18:39:23 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.29: +30 -0 lines
Diff to previous 1.29
Add set/get active subsets.

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Sun Aug 29 18:36:05 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.28: +17 -2 lines
Diff to previous 1.28
add roles_with_abbrevations

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 17:57:17 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.27: +1 -1 lines
Diff to previous 1.27
darn typos

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 17:55:45 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.26: +1 -1 lines
Diff to previous 1.26
Fix typo.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 27 15:36:29 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.25: +110 -0 lines
Diff to previous 1.25
Added get/set_notes, set_pegs_in_cell, functionality for importing notes
from copied subsystem.

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 26 21:26:52 2004 UTC (15 years, 7 months ago) by olson
Branch: MAIN
Changes since 1.24: +974 -41 lines
Diff to previous 1.24
Massive changes to suppor new subsystem editor.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 16 22:10:55 2004 UTC (15 years, 7 months ago) by overbeek
Branch: MAIN
Changes since 1.23: +0 -2 lines
Diff to previous 1.23
straighten out FIG.pm

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Aug 3 19:13:25 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.22: +131 -54 lines
Diff to previous 1.22
Add chunked execution of subsystem extension.

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 20 18:20:14 2004 UTC (15 years, 8 months ago) by olson
Branch: MAIN
Changes since 1.21: +12 -0 lines
Diff to previous 1.21
changes to delete subsystem_index entries when a subsystem is deleted

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 24 19:28:23 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.20: +8 -8 lines
Diff to previous 1.20
scalar decls

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 24 19:14:57 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.19: +7 -0 lines
Diff to previous 1.19
add call to get role from abbreviation

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 24 18:41:39 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.18: +39 -1 lines
Diff to previous 1.18
Check for existence of rows file after prolog run finishes

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 23 21:32:24 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.17: +3 -0 lines
Diff to previous 1.17
ELimiate spaces from subsystem name used in jobid, should help in
assignment stuff.

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 18 14:48:55 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.16: +35 -0 lines
Diff to previous 1.16
Changes for new clearing house display.

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 17 18:31:45 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.15: +4 -3 lines
Diff to previous 1.15
subsystem extension filename tweaks

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 17:33:53 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.14: +1 -1 lines
Diff to previous 1.14
Fix dumb typo.

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 16:52:10 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.13: +78 -2 lines
Diff to previous 1.13
Modifications to fix & finish up the automated subsystem extension.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 16 14:05:42 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.12: +46 -1 lines
Diff to previous 1.12
Add support to allow only one subsystem extension to run for a given subsystem.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 14 22:04:35 2004 UTC (15 years, 9 months ago) by olson
Branch: MAIN
Changes since 1.11: +129 -1 lines
Diff to previous 1.11
Add subsystem extension support

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jun 10 13:40:07 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.10: +1 -1 lines
Diff to previous 1.10
remove missing subsystem warning for now

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 8 15:02:15 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.9: +4 -1 lines
Diff to previous 1.9
Add capability for :scalar :list :remote annotations to FIG interface. This works with
modules that are declared as subclasses of FIGAttributes.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jun 7 19:58:21 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.8: +0 -2 lines
Diff to previous 1.8
mods for removing empty seqs from export

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 4 16:26:13 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.7: +2 -2 lines
Diff to previous 1.7
fix filename used for area table

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jun 4 16:21:10 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.6: +132 -2 lines
Diff to previous 1.6
Add diagram api

Revision 1.6 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:30:14 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.5: +3 -1 lines
Diff to previous 1.5
Use DBI's prepare/execute to insert stuff, to get around quoting problems.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 1 20:22:03 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.4: +65 -1 lines
Diff to previous 1.4
add db_sync, initialization of data structrues on load

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Thu May 27 19:27:53 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.3: +8 -1 lines
Diff to previous 1.3
add get_role_abbr, fix loading of abbrevs

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 22:34:24 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.2: +21 -0 lines
Diff to previous 1.2
add more accessors

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Tue May 25 16:19:23 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Changes since 1.1: +158 -42 lines
Diff to previous 1.1
more docs, more accessors

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon May 24 21:55:18 2004 UTC (15 years, 10 months ago) by olson
Branch: MAIN
Beginning of sim queueing stuff.
First implementation of Subsystem object, with FIG::peg_in_subsystem_cell
implemented in terms of it.

This form allows you to request diffs between any two revisions of this file. For each of the two "sides" of the diff, select a symbolic revision name using the selection box, or choose 'Use Text Field' and enter a numeric revision.

  Diffs between and
  Type of Diff should be a

Sort log by:

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3