[Gmod-schema-cmts] schema/chado/modules default_schema.sql,1.37,1.38

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

Update of /cvsroot/gmod/schema/chado/modules
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30683/modules

Modified Files:
	default_schema.sql 
Log Message:
removed double $ quoting--it isn't supported by Pg7.4


Index: default_schema.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/default_schema.sql,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** default_schema.sql	29 Dec 2005 18:30:02 -0000	1.37
--- default_schema.sql	6 Jan 2006 19:24:47 -0000	1.38
***************
*** 876,901 ****
  
  CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT
!  AS $$
    SELECT organism_id 
    FROM organism
    WHERE genus=$1
      AND species=$2
!  $$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT
!  AS $$
  SELECT organism_id
    FROM organism
!   WHERE genus=substring($1,1,position(' ' IN $1)-1)
!     AND species=substring($1,position(' ' IN $1)+1)
!  $$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT
!  AS $$
  SELECT organism_id
    FROM organism
    WHERE substr(genus,1,1)=substring($1,1,1)
!     AND species=substring($1,position(' ' IN $1)+1)
!  $$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) 
--- 876,901 ----
  
  CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR,VARCHAR) RETURNS INT
!  AS '
    SELECT organism_id 
    FROM organism
    WHERE genus=$1
      AND species=$2
!  ' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_organism_id(VARCHAR) RETURNS INT
!  AS ' 
  SELECT organism_id
    FROM organism
!   WHERE genus=substring($1,1,position('' '' IN $1)-1)
!     AND species=substring($1,position('' '' IN $1)+1)
!  ' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_organism_id_abbrev(VARCHAR) RETURNS INT
!  AS '
  SELECT organism_id
    FROM organism
    WHERE substr(genus,1,1)=substring($1,1,1)
!     AND species=substring($1,position('' '' IN $1)+1)
!  ' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION store_organism (VARCHAR,VARCHAR,VARCHAR) 
***************
*** 1752,1756 ****
  CREATE OR REPLACE FUNCTION project_featureloc_up(int,int)
   RETURNS featureloc AS
! $$
  DECLARE
      in_featureloc_id alias for $1;
--- 1752,1756 ----
  CREATE OR REPLACE FUNCTION project_featureloc_up(int,int)
   RETURNS featureloc AS
! '
  DECLARE
      in_featureloc_id alias for $1;
***************
*** 1801,1809 ****
    RETURN in_featureloc;
  END
! $$   
  LANGUAGE 'plpgsql';
  
  CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int)
!  RETURNS INT AS $$
   DECLARE
      in_p             alias for $1;
--- 1801,1809 ----
    RETURN in_featureloc;
  END
! '   
  LANGUAGE 'plpgsql';
  
  CREATE OR REPLACE FUNCTION project_point_g2t(int,int,int)
!  RETURNS INT AS '
   DECLARE
      in_p             alias for $1;
***************
*** 1814,1818 ****
      exon_cvterm_id   INT;
  BEGIN
!  SELECT INTO exon_cvterm_id get_feature_type_id('exon');
   SELECT INTO out_p
    CASE 
--- 1814,1818 ----
      exon_cvterm_id   INT;
  BEGIN
!  SELECT INTO exon_cvterm_id get_feature_type_id(''exon'');
   SELECT INTO out_p
    CASE 
***************
*** 1831,1869 ****
    RETURN in_featureloc;
  END
! $$   
  LANGUAGE 'plpgsql';
  
  
  CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT
!  AS $$SELECT cv_id FROM cv WHERE name='sequence'$$ LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT
!  AS $$SELECT cv_id FROM cv WHERE name='feature_property'$$ LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT
!  AS $$SELECT cv_id FROM cv WHERE name='relationship'$$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT
!  AS $$
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name='sequence'
!  $$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT
!  AS $$
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name='feature_property'
!  $$ LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT
!  AS $$
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name='relationship'
!  $$ LANGUAGE 'sql';
  
  -- depends on sequence-cv-helper
  CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT
!  AS $$
    SELECT feature_id 
    FROM feature
--- 1831,1869 ----
    RETURN in_featureloc;
  END
! '   
  LANGUAGE 'plpgsql';
  
  
  CREATE OR REPLACE FUNCTION get_cv_id_for_feature() RETURNS INT
!  AS 'SELECT cv_id FROM cv WHERE name=''sequence''' LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION get_cv_id_for_featureprop() RETURNS INT
!  AS 'SELECT cv_id FROM cv WHERE name=''feature_property''' LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION get_cv_id_for_feature_relationsgip() RETURNS INT
!  AS 'SELECT cv_id FROM cv WHERE name=''relationship''' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_feature_type_id(VARCHAR) RETURNS INT
!  AS ' 
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name=''sequence''
!  ' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_featureprop_type_id(VARCHAR) RETURNS INT
!  AS '
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name=''feature_property''
!  ' LANGUAGE 'sql';
  
  CREATE OR REPLACE FUNCTION get_feature_relationship_type_id(VARCHAR) RETURNS INT
!  AS '
    SELECT cvterm_id 
    FROM cv INNER JOIN cvterm USING (cv_id)
!   WHERE cvterm.name=$1 AND cv.name=''relationship''
!  ' LANGUAGE 'sql';
  
  -- depends on sequence-cv-helper
  CREATE OR REPLACE FUNCTION get_feature_id(VARCHAR,VARCHAR,VARCHAR) RETURNS INT
!  AS '
    SELECT feature_id 
    FROM feature
***************
*** 1871,1875 ****
      AND type_id=get_feature_type_id($2)
      AND organism_id=get_organism_id($3)
!  $$ LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION store_feature 
  (INT,INT,INT,INT,
--- 1871,1875 ----
      AND type_id=get_feature_type_id($2)
      AND organism_id=get_organism_id($3)
!  ' LANGUAGE 'sql';
  CREATE OR REPLACE FUNCTION store_feature 
  (INT,INT,INT,INT,
***************
*** 2046,2050 ****
  
  CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT)
!  RETURNS TEXT AS $$
  DECLARE v_feature_id ALIAS FOR $1;
  DECLARE v_rtype_id   ALIAS FOR $2;
--- 2046,2050 ----
  
  CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT,INT,INT,INT)
!  RETURNS TEXT AS '
  DECLARE v_feature_id ALIAS FOR $1;
  DECLARE v_rtype_id   ALIAS FOR $2;
***************
*** 2054,2058 ****
  DECLARE seqrow       RECORD;
  BEGIN 
!   subseq = '';
   FOR seqrow IN
     SELECT
--- 2054,2058 ----
  DECLARE seqrow       RECORD;
  BEGIN 
!   subseq = '''';
   FOR seqrow IN
     SELECT
***************
*** 2076,2080 ****
   RETURN subseq;
  END
! $$
  LANGUAGE 'plpgsql';
  
--- 2076,2080 ----
   RETURN subseq;
  END
! '
  LANGUAGE 'plpgsql';
  
***************
*** 2086,2092 ****
  CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT)
   RETURNS TEXT AS
! $$
! SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id('part_of'),0,0)
! $$
  LANGUAGE 'sql';
  
--- 2086,2092 ----
  CREATE OR REPLACE FUNCTION subsequence_by_subfeatures(INT)
   RETURNS TEXT AS
! '
! SELECT subsequence_by_subfeatures($1,get_feature_relationship_type_id(''part_of''),0,0)
! '
  LANGUAGE 'sql';
  
***************
*** 2094,2098 ****
  -- constrained by subfeature.type_id (eg exons of a transcript)
  CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT)
!  RETURNS TEXT AS $$
  DECLARE v_feature_id ALIAS FOR $1;
  DECLARE v_ftype_id   ALIAS FOR $2;
--- 2094,2098 ----
  -- constrained by subfeature.type_id (eg exons of a transcript)
  CREATE OR REPLACE FUNCTION subsequence_by_typed_subfeatures(INT,INT,INT,INT)
!  RETURNS TEXT AS '
  DECLARE v_feature_id ALIAS FOR $1;
  DECLARE v_ftype_id   ALIAS FOR $2;
***************
*** 2102,2106 ****
  DECLARE seqrow       RECORD;
  BEGIN 
!   subseq = '';
   FOR seqrow IN
     SELECT
--- 2102,2106 ----
  DECLARE seqrow       RECORD;
  BEGIN 
!   subseq = '''';
   FOR seqrow IN
     SELECT
***************
*** 2124,2128 ****
   RETURN subseq;
  END
! $$
  LANGUAGE 'plpgsql';
  
--- 2124,2128 ----
   RETURN subseq;
  END
! '
  LANGUAGE 'plpgsql';