[Gmod-schema-cmts] schema/chado/modules default_nofuncs.sql,NONE,1.1 default_schema.sql,1.20,1.21 extension.modules,1.9,1.10

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/modules
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15268/modules

Modified Files:
	default_schema.sql extension.modules 
Added Files:
	default_nofuncs.sql 
Log Message:
many fixes to get the default schema and related files up to date.


Index: extension.modules
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/extension.modules,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** extension.modules	18 Dec 2003 16:41:58 -0000	1.9
--- extension.modules	21 Mar 2005 21:13:04 -0000	1.10
***************
*** 1,5 ****
  sequence/gff-bridge/sequence-gff-views.sql
  expression/rad.sql
- expression/expression.sql
  #pathway/pathway.sql
  #www/www.sql
--- 1,4 ----

--- NEW FILE: default_nofuncs.sql ---
-- ================================================
-- TABLE: tableinfo
-- ================================================

create table tableinfo (
    tableinfo_id serial not null,
    primary key (tableinfo_id),
    name varchar(30) not null,
    primary_key_column varchar(30) null,
    is_view int not null default 0,
    view_on_table_id int null,
    superclass_table_id int null,
    is_updateable int not null default 1,
    modification_date date not null default now(),
    constraint tableinfo_c1 unique (name)
);

COMMENT ON TABLE tableinfo IS NULL;

[...2433 lines suppressed...]
create index studyfactor_idx1 on studyfactor (studydesign_id);
create index studyfactor_idx2 on studyfactor (type_id);

COMMENT ON TABLE studyfactor IS NULL;

create table studyfactorvalue (
    studyfactorvalue_id serial not null,
    primary key (studyfactorvalue_id),
    studyfactor_id int not null,
    foreign key (studyfactor_id) references studyfactor (studyfactor_id) on delete cascade INITIALLY DEFERRED,
    assay_id int not null,
    foreign key (assay_id) references assay (assay_id) on delete cascade INITIALLY DEFERRED,
    factorvalue text null,
    name text null,
    rank int not null default 0
);
create index studyfactorvalue_idx1 on studyfactorvalue (studyfactor_id);
create index studyfactorvalue_idx2 on studyfactorvalue (assay_id);

COMMENT ON TABLE studyfactorvalue IS NULL;

Index: default_schema.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/default_schema.sql,v
retrieving revision 1.20
retrieving revision 1.21
diff -C2 -d -r1.20 -r1.21
*** default_schema.sql	18 Mar 2005 19:59:55 -0000	1.20
--- default_schema.sql	21 Mar 2005 21:13:04 -0000	1.21
***************
*** 1811,1812 ****
--- 1811,3506 ----
  create index library_feature_idx2 on library_feature (feature_id);
  
+ -- VIEW gffatts: a view to get feature attributes in a format that
+ -- will make it easy to convert them to GFF attributes
+ 
+ CREATE OR REPLACE VIEW gffatts (
+     feature_id,
+     type,
+     attribute
[...1667 lines suppressed...]
+       IF slen > char_length(s) THEN
+         return_data.fmin = fmin;
+         return_data.fmax = featureloc_data.fmin + (slen - char_length(s));
+ 
+         --if the string started with a match, return it,
+         --otherwise, trim the gaps first (ie do not return this iteration)
+         RETURN NEXT return_data;
+       END IF;
+ 
+       --trim off leading gap
+       s = trim(leading ''-'' from s);
+ 
+       fmin = featureloc_data.fmin + (slen - char_length(s));
+     END LOOP;
+   END LOOP;
+ 
+   RETURN;
+ 
+ END;
+ ' LANGUAGE 'plpgsql';