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Revision 1.37 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 13 17:41:10 2004 UTC (15 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: HEAD, MigrateToNewPackage, V00-00-03, mass-spec-01, mass-spec-02, mass-spec-03
Changes since 1.36: +2 -7 lines
Diff to previous 1.36 , to selected 1.6
Adding a bu

Revision 1.36 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 14 20:45:24 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
CVS Tags: forRick-14Jul04-1
Changes since 1.35: +2 -2 lines
Diff to previous 1.35 , to selected 1.6
migrate to new plugin interface.
fix onLeftClick for SetLabel -> setValue

Revision 1.35 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jul 13 21:15:07 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
CVS Tags: forRick-14Jul04-0
Changes since 1.34: +4 -12 lines
Diff to previous 1.34 , to selected 1.6
Schema:
	o change size of Function column from 64 to 128.
	  More reasonable size and avoids a crash.
	o RebuldDb...runs all the steps of rebuilding the database.
	o biuldNewBssCatalog:  go to new BssFactory ctor

CatalogServices:
	o remove setFoundryId from DataFactoryBase.  Now expect that info
	  to be in the DB itself and for ctor of derivative to set it.

FaST:
	o Migrate to new DbManager from DBconnect.  Includes moving to
	  new nextSeqVal().
	o Now get fid from database
PyGui:
	o Changed to follow mods above.
	o

Revision 1.34 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 12 20:38:19 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.33: +4 -11 lines
Diff to previous 1.33 , to selected 1.6
KahOM/KahDataMgr:
	first pass at top level data manager to be returned from catalogentry read

Schema:
	added KahDatabaseInfo to put fid into database.
	create- changed so that no long initialize name of top catalogEntry (see below)
	destroyBss- changed !#/usr/bin/py to env py

FaST:
	txMgr - fixed close()...added self
	BssFactory - now gets fid via kahDatabaseInfo in database

PyGUI
	change so that something or another

Revision 1.33 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 9 19:08:13 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.32: +9 -7 lines
Diff to previous 1.32 , to selected 1.6
Had a loop between catalogpanel putting a factory into the catalog
in loadCatalog() and the callback handler in MainLayout for added factories
trying to call into loadCatalog().

got rid of the adding of factories in loadCatalog().

now factory is added in very topmost level (ModelEditor).  the callback
chain/observer takes care of the rest.

Revision 1.32 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 9 15:29:36 2004 UTC (15 years, 5 months ago) by sheradon
Branch: MAIN
Changes since 1.31: +4 -6 lines
Diff to previous 1.31 , to selected 1.6

Catalogpanel.py
	change catalog load so that a) turn off localhost seed b) stuff
 i don't remember

MainLayout:
	in callback for newDataFactory in catalog:  remember to get catalog
	loaded

MainMenuBar:

Revision 1.31 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jul 7 16:24:48 2004 UTC (15 years, 5 months ago) by hwang
Branch: MAIN
Changes since 1.30: +2 -1 lines
Diff to previous 1.30 , to selected 1.6
	BssFactory.py
		fixed indentation error
	Catalogpanel.py
		allows the path label to be set
	MainLayout.py
		fixed the layout of Catalog panel

Revision 1.30 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Jul 2 22:08:02 2004 UTC (15 years, 5 months ago) by hwang
Branch: MAIN
Changes since 1.29: +4 -3 lines
Diff to previous 1.29 , to selected 1.6
	To maintain state, self was taken out of local variables

Revision 1.29 - (view) (download) (as text) (annotate) - [select for diffs]
Tue Jun 29 16:12:19 2004 UTC (15 years, 5 months ago) by hwang
Branch: MAIN
CVS Tags: larrys-08jul04
Changes since 1.28: +3 -0 lines
Diff to previous 1.28 , to selected 1.6
	Changes to combobox in MainLayout
	Catalogpanel takes in BssFactoryProxy - but commented out

Revision 1.28 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 23 19:19:10 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.27: +2 -2 lines
Diff to previous 1.27 , to selected 1.6
migrate import statements to follow move of Recoelem, Reaction, Reactant
from FaST to KahOM

Revision 1.27 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 23 19:02:51 2004 UTC (15 years, 5 months ago) by efrank
Branch: MAIN
Changes since 1.26: +21 -137 lines
Diff to previous 1.26 , to selected 1.6
Migrate data classes to really use FoundryItem.
gut a bunch of old dead code.
merge what used to be separate seed/bss into single.

Revision 1.26 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Jun 9 22:36:10 2004 UTC (15 years, 6 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-02, forKubal-15Jun04
Changes since 1.25: +54 -46 lines
Diff to previous 1.25 , to selected 1.6
o clean up double foundryId problem in FoundryItems
o change names in CatalogEntry to read() and write()
o write the write() method just mentioned
o get writing to work again, propagate changes into PyGUI
o add plugin capability to modelEditor

Revision 1.25 - (view) (download) (as text) (annotate) - [select for diffs]
Wed May 26 01:38:25 2004 UTC (15 years, 6 months ago) by efrank
Branch: MAIN
Changes since 1.24: +251 -28 lines
Diff to previous 1.24 , to selected 1.6
Lots of work aimed at getting catalog services to work, incorporating
catalog editing into the model editor, and simplifying the api
for going form path to model in hand to work with.

CatalogEntryTop was changed to CatalogEntrBase and made base of CatalogEntry
rather than other way around to break a dependency loop that was causing
python import problems.  CatalogEntry is still the base class to use
for extending to new data factories.

changed open() to return catalogEntry rather than foundryItemKey.  simpler
for the user and more opportunity to encapsulate.

made catalogEntry able to read a recoElem and return it.  all done in
terms of arch abstractions.  this is temorary.  we will add a Navigator
or Manager class and that will be returned from the CatalogEntry rather
than recoElem.  that's becausee Recoelem is just one of many things
that will be present, e.g., conditions data.

PyGui/MainMenuBar.  split out to help stay sane for when that becomes
more complex.

Moved add seed server to menu bar so that right click in catalog panel
coudl be used to pull up catalog editing tools.

Revision 1.24 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 26 17:12:46 2004 UTC (15 years, 8 months ago) by efrank
Branch: MAIN
Changes since 1.23: +11 -10 lines
Diff to previous 1.23 , to selected 1.6
Modifications to install the new Catalog code, FoundryId stuff.  I ripped
out old code as well:  the list of foundryComboBoxes is gone since we now
have just one combo box.

the notion of FoundryId's intVal is gone.  at least for the moment.  it's too hard
at the mment to have a (bottleneck!) central authority to manage the intVals.

so, starting now, foundryId's are based on strings that are notionally URLs and
its up to the dataFoundry manager to make sure all distinct instances at his
site have distinct urls.

this also means that if a foundry moves, then the history information that
refers to it becomes incorrect.

Revision 1.23 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Mar 25 00:49:56 2004 UTC (15 years, 8 months ago) by efrank
Branch: MAIN
Changes since 1.22: +1 -1 lines
Diff to previous 1.22 , to selected 1.6
Migrating to new Catalog, Catlogentry, etc.  This is an intermediary
sync

Revision 1.22 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Mar 5 19:30:38 2004 UTC (15 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.21: +3 -32 lines
Diff to previous 1.21 , to selected 1.6
	Catalogpanel.py
		Got rid of the "Load to Navigator" button
	FontManager.py
		fixed variable consistancy
	MainLayout.py
		Added combobox label and got rid of "Load to Navigator" button

Revision 1.21 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Feb 25 17:08:17 2004 UTC (15 years, 9 months ago) by hwang
Branch: MAIN
Changes since 1.20: +5 -4 lines
Diff to previous 1.20 , to selected 1.6
     Changed all the files so that the past inconsistancies of variable and classes names
 are consistant. I.E. MainLayout import MainLayout.
     In MainLayout, separate functions are made for each panel.

Revision 1.20 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Dec 19 15:46:52 2003 UTC (15 years, 11 months ago) by hwang
Branch: MAIN
Changes since 1.19: +2 -3 lines
Diff to previous 1.19 , to selected 1.6
	Catalogpanel.py
		added the double click
	MainLayout.py
		catalog_tree is not modifible

Revision 1.19 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 21:41:08 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: SC-01, SC-02, sc-14Nov03-linux-01, sc-14Nov03-linux-02
Changes since 1.18: +6 -1 lines
Diff to previous 1.18 , to selected 1.6
duplicate server error trapped

Revision 1.18 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 19:21:46 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.17: +1 -1 lines
Diff to previous 1.17 , to selected 1.6
back to localhost for init

Revision 1.17 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Nov 13 01:41:16 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: sc-12Nov03-linux-02
Changes since 1.16: +9 -2 lines
Diff to previous 1.16 , to selected 1.6

RecoElemPanel:
	fix a few bugs related to menu commands.  most related to problems
	not detecting special cases like "nothing selected" or "this node
	i9s special because its the root"


CatalogPanel:
	make the Seed part of the tree include a node, "Spontaneous Reactions"
	which olds all the spontaneous reactions in Seed (those without enzymes)

Revision 1.16 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 12 22:56:33 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.15: +5 -0 lines
Diff to previous 1.15 , to selected 1.6
Lots of changes to start port to mac.  lots of fiddling with layout because
we are doing something wrong, and it shows up on Mac.

Also alot of work to make enzymes work, including EC.  focus is on seed.

Revision 1.15 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 5 21:30:08 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: sc-06Nov03-linuxLeft-01, sc-12Nov03-linux-01
Changes since 1.14: +1 -0 lines
Diff to previous 1.14 , to selected 1.6
cursor busy was not being turned off in one case

Revision 1.14 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 5 21:07:55 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
Changes since 1.13: +89 -15 lines
Diff to previous 1.13 , to selected 1.6

Catalogpanel:
	Extend so that multiple Seed servers can be used.  A right click in the
	panel brings up a menu in which there is an "Add Server" entry.  Selecting
	that prompts for a server name.  that server is connected to, the org
	list is read, ettc., and all are put into the catalog.

Revision 1.13 - (view) (download) (as text) (annotate) - [select for diffs]
Wed Nov 5 02:28:44 2003 UTC (16 years, 1 month ago) by efrank
Branch: MAIN
CVS Tags: efrank-initialSeed-04Nov03, sc-works-00
Changes since 1.12: +17 -12 lines
Diff to previous 1.12 , to selected 1.6
Modifications to read data from Seed.  Now can read all the reactions/compounds
data associatd with a reconstrruction.  In ross' terms, we're reading out
the formal rconstruction.

Revision 1.12 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Oct 17 20:25:57 2003 UTC (16 years, 2 months ago) by efrank
Branch: MAIN
Changes since 1.11: +43 -0 lines
Diff to previous 1.11 , to selected 1.6
Add catalog for reading from FIG/Seed
Requires updated FaST/

Revision 1.11 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Sep 25 23:48:06 2003 UTC (16 years, 2 months ago) by hwang
Branch: MAIN
Changes since 1.10: +19 -0 lines
Diff to previous 1.10 , to selected 1.6
	Added enzyme buttons/text/grid
	Added exit button to allow user to exit normally

Revision 1.10 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 18 15:55:57 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: V00-00-00, V00-00-01
Changes since 1.9: +11 -0 lines
Diff to previous 1.9 , to selected 1.6
Start documenting the code a trifle.  All files have been modified by adding
the list of def'd methods at the top of the class.  Must add description
strings, but this is a start.

Revision 1.9 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 7 19:14:27 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.8: +1 -1 lines
Diff to previous 1.8 , to selected 1.6
*** empty log message ***

Revision 1.8 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Aug 7 02:39:46 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.7: +1 -1 lines
Diff to previous 1.7 , to selected 1.6
adding to Metabolite panel so that we can search for metabolites.
main.py: move some init stuff out of main.py into associated panel.
mainlayout: clean up and reorg a bit.  lots of renames
rxpanel: commented out to speed up startup.

Revision 1.7 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Aug 4 16:18:47 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.6: +0 -5 lines
Diff to previous 1.6
more tweaks for making things work.  no fundamental changes.  oh...except
in RecoElemPanel where we now use wxTreeCtrl EVT_TREE_SEL_CHANGED to figure
out when there's a hit on something.  Before, we were not picking up
selections on the top nodes.  That meant that a recoElem with no kids but
*with* reactions could not have its reactions listed.

Revision 1.6 - (view) (download) (as text) (annotate) - [selected]
Mon Aug 4 12:46:49 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.5: +52 -26 lines
Diff to previous 1.5
sync with kaitlyn's mods.  add new fn'ality:

Catalogpanel.py:
   o include Wit as Datasource via FaST/WitFactory
   o Catalog tree of data sources expands to basic level at startup
   o to handle multiple data sources:
        We use EVT_TREE_SEL_CHANGED to know when a user has chosen something.
        At that point, we remember the data associated with tree item that was
        set when the item was added to the tree.  That data is a tuple comprising
        (ptr-to-function, arg list). When the load button is hit, it looks at
        this tuple and evaluates ptr-to-fnction on the arg list.  The idea is
        that when the catalog tree is built, it is built by various data-base
        specific functions.  Those functions know the database they are dealing
        with, so they can load the (func, args) correctly to achieve the correct
        behavior.  The point here is that wxPython only allows you set a single
        selection-handler per tree, not per tree item.  Thus we build our own
        little dispatch handler as just described since our tree is really
        heterogeneous.  Get it?

MainLayout.py:
   o Just some name changes, like the title of the window.

Revision 1.5 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 1 20:53:06 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.4: +14 -7 lines
Diff to previous 1.4 , to selected 1.6
catalogPanel:
	change so that EVT_TREE_SEL_CHANGED rather than EVT_LEFT_DCLICK so that
	we work through tree as single click.

mainLayout:
	had to latch the Id fro the catalog_tree control
	changed text in some buttons and tabs

Revision 1.4 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 1 18:54:31 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
Changes since 1.3: +72 -12 lines
Diff to previous 1.3 , to selected 1.6
Catalogpanel:
	modify so that the catalog is a tree.  the top level nodes in the tree
	list the data factories, e.g., Bss, Wit, etc.

main.py
	to match above.

Revision 1.3 - (view) (download) (as text) (annotate) - [select for diffs]
Fri Aug 1 15:33:39 2003 UTC (16 years, 4 months ago) by hwang
Branch: MAIN
Changes since 1.2: +7 -4 lines
Diff to previous 1.2 , to selected 1.6
*** empty log message ***

Revision 1.2 - (view) (download) (as text) (annotate) - [select for diffs]
Thu Jul 31 15:54:29 2003 UTC (16 years, 4 months ago) by efrank
Branch: MAIN
CVS Tags: efrank-worksBeforeCatalogTree
Changes since 1.1: +16 -10 lines
Diff to previous 1.1 , to selected 1.6
1) change so that when an item is selected, the load does not start right away.  instead,
   we just rcord which thing was selected.
2) wire in the LOAD button.  the load button handler does the recoelem load refered
   to in 1)
3) stifle some printouts

Revision 1.1 - (view) (download) (as text) (annotate) - [select for diffs]
Mon Jul 28 22:31:13 2003 UTC (16 years, 4 months ago) by hwang
Branch: MAIN
Diff to selected 1.6
*** empty log message ***

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