[Bio] View of /BioSimScratch/FnlChartTab.sql

Revision 1.2 - (download) (annotate)
Fri May 9 17:52:54 2003 UTC (16 years, 7 months ago) by efrank
Branch: MAIN
CVS Tags: post-st-migration2, mass-spec-01, sc2004-3, mass-spec-02, ldrd-2003-01, post-st-migration, forRick-14Jul04-1, forRick-14Jul04-0, sc2004-4, sc04-finalDay, sc2004-2, sc2004-1, sc2004-0, HEAD
Changes since 1.1: +8 -3 lines

loadBss.py
   two classes, bss and Reaction_py.
   bss() represents the biosimscratch schema and has methods to load
	data into it.  the methods are guesses at basic operations
	on the database for building models and will stand behind
	a gui at some point.
   Reaction_py: a class that holds info for a reacction.  its got this
	name to distinguish it from RecoReadout/Reaction.hh.  they
        should probably be meged but that takes a language mix.  this
	one knows how to parse a simple ascii rep of a reaction

-- ----------------------------------------------------------------------
drop   table ProcList;
create table ProcList (
--
-- Lists all the processes and assigns a unique ID.  A process
-- is something that happens, e.g., a reaction, set of reactions,
-- set of rules, etc.
-- ----------------------------------------------------------------------
--
	ProcName	varchar2(128)	NOT NULL,
	/* Process name    */
--
	ProcId		Number(10)	NOT NULL,
	/* A unique number */
--
	Model		BFILE,
	/* A file describing the process */
--
        CONSTRAINT ProcList_PK PRIMARY KEY ( ProcId )
);

-- ----------------------------------------------------------------------
drop   table ProcStruct;
create table ProcStruct (
--
-- Lists the immediate descendents of each Process.  Thus,
-- for any process name (Parent), list its parts (ChildProc)
-- ----------------------------------------------------------------------
--
	ParentProc	varchar2(128)	NOT NULL,
	/* Name of proc */
--
	ParentProcId	Number(10)	NOT NULL,
--
	ChildProc	varchar2(128)	NOT NULL,
--
	ChildProcID	Number(10)	NOT NULL
--
);

-- ----------------------------------------------------------------------
drop   table RecoCatalogEntry;
create table RecoCatalogEntry (
--
-- Catalog of reconstructions.  Another table holds a relation
-- tying processes to reconstructions.
-- ----------------------------------------------------------------------
--
	RecoName	varchar2(128)	NOT NULL UNIQUE,
--
	Curator		varchar2(128),
--
	RecoId		Number(10)	NOT NULL,
--
	CONSTRAINT RecoCatalogEntry_PK PRIMARY KEY ( RecoId )
);

-- ----------------------------------------------------------------------
drop   table ProcessInReco;
create table ProcessInReco (
--
-- Lists the processes that are in a reconstruction.  I'm not sure
-- yet if this should mean that you list some nodes and we infer
-- that there descendents are in the reco transitively, or if we
-- list the transitive closure in this table and ask the ProcStruct
-- structural questions.  For the moment, we take the policy that
-- this table just locates the list of top nodes in the reconstruction
-- and we then chase those through the ProcStruct table.--
-- ----------------------------------------------------------------------
--
	RecoId		Number(10)	NOT NULL,
--
	ProcessId	Number(10)	NOT NULL
);

-- ----------------------------------------------------------------------
drop   table ReactionsInProcess;
create table ReactionsInProcess (
--
-- Lists the reactions associated with a process in a reconstruction.
-- This is a weak relation between reaction, recoCatalogEntry,
-- and Process
-- ----------------------------------------------------------------------
--
	RxId		Number(10)	NOT NULL,
--
	ProcessId	Number(10)	NOT NULL,
--
	RecoId		Number(10)	NOT NULL
);