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From: <all...@us...> - 2003-06-03 17:49:18
|
Update of /cvsroot/gmod/schema/chado/modules/general
In directory sc8-pr-cvs1:/tmp/cvs-serv25436/general
Modified Files:
general.sql
Log Message:
renaming contact fk
Index: general.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/general/general.sql,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** general.sql 3 Jun 2003 17:46:46 -0000 1.15
--- general.sql 3 Jun 2003 17:49:14 -0000 1.16
***************
*** 20,26 ****
primary key (db_id),
name varchar(255) not null,
! contact int not null,
! -- this table doesn't exist yet.
! foreign key (contact) references contact (contact_id),
description varchar(255) null,
urlprefix varchar(255) null,
--- 20,25 ----
primary key (db_id),
name varchar(255) not null,
! contact_id int not null,
! foreign key (contact_id) references contact (contact_id),
description varchar(255) null,
urlprefix varchar(255) null,
|
|
From: <all...@us...> - 2003-06-03 17:47:19
|
Update of /cvsroot/gmod/schema/chado/modules/cv/bridges
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/cv/bridges
Modified Files:
godb-bridge.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: godb-bridge.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/cv/bridges/godb-bridge.sql,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** godb-bridge.sql 13 Mar 2003 00:04:50 -0000 1.2
--- godb-bridge.sql 3 Jun 2003 17:46:46 -0000 1.3
***************
*** 72,78 ****
SELECT
cvrelationship_id AS id,
! reltype_id AS relationship_type_id,
! objterm_id AS term1_id,
! subjterm_id AS term2_id
FROM cvrelationship;
--- 72,78 ----
SELECT
cvrelationship_id AS id,
! type_id AS relationship_type_id,
! object_id AS term1_id,
! subject_id AS term2_id
FROM cvrelationship;
***************
*** 82,88 ****
INSERT INTO cvrelationship
(
! reltype_id,
! objterm_id,
! subjterm_id)
VALUES
(
--- 82,88 ----
INSERT INTO cvrelationship
(
! type_id,
! object_id,
! subject_id)
VALUES
(
***************
*** 97,103 ****
UPDATE cvrelationship
SET
! reltype_id = NEW.relationship_type_id,
! objterm_id = NEW.term1_id,
! subjterm_id = NEW.term2_id
WHERE cvrelationship_id = OLD.id;
--- 97,103 ----
UPDATE cvrelationship
SET
! type_id = NEW.relationship_type_id,
! object_id = NEW.term1_id,
! subject_id = NEW.term2_id
WHERE cvrelationship_id = OLD.id;
***************
*** 114,119 ****
cvpath_id AS id,
NULL AS relationship_type_id,
! objterm_id AS term1_id,
! subjterm_id AS term2_id,
pathdistance AS distance
FROM cvpath;
--- 114,119 ----
cvpath_id AS id,
NULL AS relationship_type_id,
! object_id AS term1_id,
! subject_id AS term2_id,
pathdistance AS distance
FROM cvpath;
***************
*** 124,130 ****
INSERT INTO cvpath
(
! reltype_id,
! objterm_id,
! subjterm_id,
pathdistance)
VALUES
--- 124,130 ----
INSERT INTO cvpath
(
! type_id,
! object_id,
! subject_id,
pathdistance)
VALUES
***************
*** 141,147 ****
UPDATE cvpath
SET
! reltype_id = NULL,
! objterm_id = NEW.term1_id,
! subjterm_id = NEW.term2_id,
pathdistance = NEW.distance
WHERE cvpath_id = OLD.id;
--- 141,147 ----
UPDATE cvpath
SET
! type_id = NULL,
! object_id = NEW.term1_id,
! subject_id = NEW.term2_id,
pathdistance = NEW.distance
WHERE cvpath_id = OLD.id;
|
|
From: <all...@us...> - 2003-06-03 17:47:19
|
Update of /cvsroot/gmod/schema/chado/modules/cv
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/cv
Modified Files:
cv.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: cv.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/cv/cv.sql,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** cv.sql 22 Apr 2003 22:39:29 -0000 1.11
--- cv.sql 3 Jun 2003 17:46:45 -0000 1.12
***************
*** 8,15 ****
cv_id serial not null,
primary key (cv_id),
! cvname varchar(255) not null,
! cvdefinition text,
! unique(cvname)
);
--- 8,15 ----
cv_id serial not null,
primary key (cv_id),
! name varchar(255) not null,
! definition text,
! unique(name)
);
***************
*** 24,28 ****
foreign key (cv_id) references cv (cv_id),
name varchar(255) not null,
! termdefinition text,
dbxref_id int,
foreign key (dbxref_id) references dbxref (dbxref_id),
--- 24,28 ----
foreign key (cv_id) references cv (cv_id),
name varchar(255) not null,
! definition text,
dbxref_id int,
foreign key (dbxref_id) references dbxref (dbxref_id),
***************
*** 37,83 ****
-- ================================================
! -- TABLE: cvrelationship
-- ================================================
! create table cvrelationship (
! cvrelationship_id serial not null,
! primary key (cvrelationship_id),
! reltype_id int not null,
! foreign key (reltype_id) references cvterm (cvterm_id),
! subjterm_id int not null,
! foreign key (subjterm_id) references cvterm (cvterm_id),
! objterm_id int not null,
! foreign key (objterm_id) references cvterm (cvterm_id),
! unique(reltype_id, subjterm_id, objterm_id)
);
! create index cvrelationship_idx1 on cvrelationship (reltype_id);
! create index cvrelationship_idx2 on cvrelationship (subjterm_id);
! create index cvrelationship_idx3 on cvrelationship (objterm_id);
-- ================================================
! -- TABLE: cvpath
-- ================================================
! create table cvpath (
! cvpath_id serial not null,
! primary key (cvpath_id),
! reltype_id int,
! foreign key (reltype_id) references cvterm (cvterm_id),
! subjterm_id int not null,
foreign key (subjterm_id) references cvterm (cvterm_id),
! objterm_id int not null,
! foreign key (objterm_id) references cvterm (cvterm_id),
cv_id int not null,
foreign key (cv_id) references cv (cv_id),
pathdistance int,
! unique (subjterm_id, objterm_id)
);
! create index cvpath_idx1 on cvpath (reltype_id);
! create index cvpath_idx2 on cvpath (subjterm_id);
! create index cvpath_idx3 on cvpath (objterm_id);
! create index cvpath_idx4 on cvpath (cv_id);
--- 37,83 ----
-- ================================================
! -- TABLE: cvtermrelationship
-- ================================================
! create table cvtermrelationship (
! cvtermrelationship_id serial not null,
! primary key (cvtermrelationship_id),
! type_id int not null,
! foreign key (type_id) references cvterm (cvterm_id),
! subject_id int not null,
! foreign key (subject_id) references cvterm (cvterm_id),
! object_id int not null,
! foreign key (object_id) references cvterm (cvterm_id),
! unique(type_id, subject_id, object_id)
);
! create index cvtermrelationship_idx1 on cvtermrelationship (type_id);
! create index cvtermrelationship_idx2 on cvtermrelationship (subject_id);
! create index cvtermrelationship_idx3 on cvtermrelationship (object_id);
-- ================================================
! -- TABLE: cvtermpath
-- ================================================
! create table cvtermpath (
! cvtermpath_id serial not null,
! primary key (cvtermpath_id),
! type_id int,
! foreign key (type_id) references cvterm (cvterm_id),
! subject_id int not null,
foreign key (subjterm_id) references cvterm (cvterm_id),
! object_id int not null,
! foreign key (object_id) references cvterm (cvterm_id),
cv_id int not null,
foreign key (cv_id) references cv (cv_id),
pathdistance int,
! unique (subject_id, object_id)
);
! create index cvtermpath_idx1 on cvtermpath (type_id);
! create index cvtermpath_idx2 on cvtermpath (subject_id);
! create index cvtermpath_idx3 on cvtermpath (object_id);
! create index cvtermpath_idx4 on cvtermpath (cv_id);
***************
*** 91,97 ****
cvterm_id int not null,
foreign key (cvterm_id) references cvterm (cvterm_id),
! termsynonym varchar(255) not null,
! unique(cvterm_id, termsynonym)
);
create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id);
--- 91,97 ----
cvterm_id int not null,
foreign key (cvterm_id) references cvterm (cvterm_id),
! synonym varchar(255) not null,
! unique(cvterm_id, synonym)
);
create index cvtermsynonym_idx1 on cvtermsynonym (cvterm_id);
|
|
From: <all...@us...> - 2003-06-03 17:47:18
|
Update of /cvsroot/gmod/schema/chado/modules/companalysis
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/companalysis
Modified Files:
companalysis.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: companalysis.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/companalysis/companalysis.sql,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** companalysis.sql 5 May 2003 20:41:11 -0000 1.22
--- companalysis.sql 3 Jun 2003 17:46:45 -0000 1.23
***************
*** 80,91 ****
analysis_id int not null,
foreign key (analysis_id) references analysis (analysis_id),
! pkey_id int not null,
! foreign key (pkey_id) references cvterm (cvterm_id),
! pval text,
! unique(analysis_id, pkey_id, pval)
);
create index analysisprop_idx1 on analysisprop (analysis_id);
! create index analysisprop_idx2 on analysisprop (pkey_id);
--- 80,91 ----
analysis_id int not null,
foreign key (analysis_id) references analysis (analysis_id),
! type_id int not null,
! foreign key (type_id) references cvterm (cvterm_id),
! value text,
! unique(analysis_id, type_id, value)
);
create index analysisprop_idx1 on analysisprop (analysis_id);
! create index analysisprop_idx2 on analysisprop (type_id);
|
|
From: <all...@us...> - 2003-06-03 17:46:51
|
Update of /cvsroot/gmod/schema/chado/modules/sequence
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/sequence
Modified Files:
sequence.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: sequence.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/sequence/sequence.sql,v
retrieving revision 1.35
retrieving revision 1.36
diff -C2 -d -r1.35 -r1.36
*** sequence.sql 2 Jun 2003 14:46:10 -0000 1.35
--- sequence.sql 3 Jun 2003 17:46:48 -0000 1.36
***************
*** 166,178 ****
feature_id int not null,
foreign key (feature_id) references feature (feature_id),
! pkey_id int not null,
! foreign key (pkey_id) references cvterm (cvterm_id),
! pval text not null default '',
! prank int not null default 0,
! unique(feature_id, pkey_id, pval, prank)
);
create index featureprop_idx1 on featureprop (feature_id);
! create index featureprop_idx2 on featureprop (pkey_id);
--- 166,178 ----
feature_id int not null,
foreign key (feature_id) references feature (feature_id),
! type_id int not null,
! foreign key (type_id) references cvterm (cvterm_id),
! value text not null default '',
! rank int not null default 0,
! unique(feature_id, type_id, value, rank)
);
create index featureprop_idx1 on featureprop (feature_id);
! create index featureprop_idx2 on featureprop (type_id);
|
|
From: <all...@us...> - 2003-06-03 17:46:51
|
Update of /cvsroot/gmod/schema/chado/modules/pub
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/pub
Modified Files:
pub.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: pub.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/pub/pub.sql,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** pub.sql 23 Apr 2003 15:56:58 -0000 1.9
--- pub.sql 3 Jun 2003 17:46:47 -0000 1.10
***************
*** 88,91 ****
--- 88,94 ----
author_id serial not null,
primary key (author_id),
+ contact_id int not null,
+ foreign key (contact_id) references contact (contact_id),
+ -- these fields may be moving to the contact table...
surname varchar(100) not null,
givennames varchar(100),
***************
*** 129,140 ****
pub_id int not null,
foreign key (pub_id) references pub (pub_id),
! pkey_id int not null,
! foreign key (pkey_id) references cvterm (cvterm_id),
! pval text not null,
! prank integer,
! unique(pub_id,pkey_id,pval)
);
create index pubprop_idx1 on pubprop (pub_id);
! create index pubprop_idx2 on pubprop (pkey_id);
--- 132,143 ----
pub_id int not null,
foreign key (pub_id) references pub (pub_id),
! type_id int not null,
! foreign key (type_id) references cvterm (cvterm_id),
! value text not null,
! rank integer,
! unique(pub_id,pkey_id,value)
);
create index pubprop_idx1 on pubprop (pub_id);
! create index pubprop_idx2 on pubprop (type_id);
|
|
From: <all...@us...> - 2003-06-03 17:46:50
|
Update of /cvsroot/gmod/schema/chado/modules/organism
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/organism
Modified Files:
organism.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: organism.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/organism/organism.sql,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** organism.sql 19 May 2003 12:46:44 -0000 1.8
--- organism.sql 3 Jun 2003 17:46:47 -0000 1.9
***************
*** 6,10 ****
organism_id serial not null,
primary key (organism_id),
! abbrev varchar(255) null,
genus varchar(255) not null,
species varchar(255) not null,
--- 6,10 ----
organism_id serial not null,
primary key (organism_id),
! abbreviation varchar(255) null,
genus varchar(255) not null,
species varchar(255) not null,
***************
*** 51,62 ****
organism_id int not null,
foreign key (organism_id) references organism (organism_id),
! pkey_id int not null,
! foreign key (pkey_id) references cvterm (cvterm_id),
! pval text not null default '',
! prank int not null default 0,
! unique(organism_id, pkey_id, pval, prank)
);
create index organismprop_idx1 on organismprop (organism_id);
! create index organismprop_idx2 on organismprop (pkey_id);
--- 51,62 ----
organism_id int not null,
foreign key (organism_id) references organism (organism_id),
! type_id int not null,
! foreign key (type_id) references cvterm (cvterm_id),
! value text not null default '',
! rank int not null default 0,
! unique(organism_id, type_id, value, rank)
);
create index organismprop_idx1 on organismprop (organism_id);
! create index organismprop_idx2 on organismprop (type_id);
|
|
From: <all...@us...> - 2003-06-03 17:46:50
|
Update of /cvsroot/gmod/schema/chado/modules/general
In directory sc8-pr-cvs1:/tmp/cvs-serv23854/general
Modified Files:
general.sql
Log Message:
sweeping changes to tables, fields. also added new tables, fields, and FK
constraints. follow thread "[Gmod-schema] table changes (again)" on
gmod-schema list for the full scoop.
Index: general.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/general/general.sql,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** general.sql 27 May 2003 06:41:35 -0000 1.14
--- general.sql 3 Jun 2003 17:46:46 -0000 1.15
***************
*** 1,2 ****
--- 1,15 ----
+ --
+ -- should this be in pub?
+ --
+ -- ================================================
+ -- TABLE: contact
+ -- ================================================
+ create table contact (
+ contact_id serial not null,
+ primary key (contact_id),
+ -- fields to be added after discussion
+ description varchar(255) null
+ );
+
-- ================================================
-- TABLE: db
***************
*** 4,11 ****
create table db (
! db_id varchar(255) not null,
primary key (db_id),
name varchar(255) not null,
description varchar(255) null,
url varchar(255) null,
unique (name)
--- 17,28 ----
create table db (
! db_id serial not null,
primary key (db_id),
name varchar(255) not null,
+ contact int not null,
+ -- this table doesn't exist yet.
+ foreign key (contact) references contact (contact_id),
description varchar(255) null,
+ urlprefix varchar(255) null,
url varchar(255) null,
unique (name)
***************
*** 20,70 ****
dbxref_id serial not null,
primary key (dbxref_id),
! dbname varchar(255) not null,
foreign key (dbname) references db (db_id),
accession varchar(255) not null,
version varchar(255) not null default '',
! dbxrefdescription text,
unique (dbname, accession, version)
);
-- ================================================
-- TABLE: dbxrefprop
-- ================================================
! create table dbxrefprop (
! dbxrefprop_id serial not null,
! primary key (dbxrefprop_id),
! dbxref_id int not null,
! foreign key (dbxref_id) references dbxref (dbxref_id),
! pkey_id int not null,
! foreign key (pkey_id) references cvterm (cvterm_id),
! pval text not null default '',
! prank int not null default 0,
!
! unique(dbxref_id, pkey_id, pval, prank)
! );
! create index dbxrefprop_idx1 on dbxrefprop (dbxref_id);
! create index dbxrefprop_idx2 on dbxrefprop (pkey_id);
!
-- ================================================
-- TABLE: dbxrefrelationship
-- ================================================
!
! create table dbxrefrelationship (
! dbxrefrelationship_id serial not null,
! primary key (dbxrefrelationship_id),
! reltype_id int not null,
! foreign key (reltype_id) references cvterm (cvterm_id),
! subjterm_id int not null,
! foreign key (subjterm_id) references dbxref (dbxref_id),
! objterm_id int not null,
! foreign key (objterm_id) references dbxref (dbxref_id),
!
! unique(reltype_id, subjterm_id, objterm_id)
! );
! create index dbxrefrelationship_idx1 on dbxrefrelationship (reltype_id);
! create index dbxrefrelationship_idx2 on dbxrefrelationship (subjterm_id);
! create index dbxrefrelationship_idx3 on dbxrefrelationship (objterm_id);
-- ================================================
--- 37,93 ----
dbxref_id serial not null,
primary key (dbxref_id),
! db_id int not null,
foreign key (dbname) references db (db_id),
accession varchar(255) not null,
version varchar(255) not null default '',
! description text,
unique (dbname, accession, version)
);
+ --
+ -- this table pending review
+ --
-- ================================================
-- TABLE: dbxrefprop
-- ================================================
+ --
+ --create table dbxrefprop (
+ -- dbxrefprop_id serial not null,
+ -- primary key (dbxrefprop_id),
+ -- dbxref_id int not null,
+ -- foreign key (dbxref_id) references dbxref (dbxref_id),
+ -- pkey_id int not null,
+ -- foreign key (pkey_id) references cvterm (cvterm_id),
+ -- pval text not null default '',
+ -- prank int not null default 0,
+ --
+ -- unique(dbxref_id, pkey_id, pval, prank)
+ --);
+ --create index dbxrefprop_idx1 on dbxrefprop (dbxref_id);
+ --create index dbxrefprop_idx2 on dbxrefprop (pkey_id);
! --
! -- this table pending review
! --
-- ================================================
-- TABLE: dbxrefrelationship
-- ================================================
! --
! --create table dbxrefrelationship (
! -- dbxrefrelationship_id serial not null,
! -- primary key (dbxrefrelationship_id),
! -- reltype_id int not null,
! -- foreign key (reltype_id) references cvterm (cvterm_id),
! -- subjterm_id int not null,
! -- foreign key (subjterm_id) references dbxref (dbxref_id),
! -- objterm_id int not null,
! -- foreign key (objterm_id) references dbxref (dbxref_id),
! --
! -- unique(reltype_id, subjterm_id, objterm_id)
! --);
! --create index dbxrefrelationship_idx1 on dbxrefrelationship (reltype_id);
! --create index dbxrefrelationship_idx2 on dbxrefrelationship (subjterm_id);
! --create index dbxrefrelationship_idx3 on dbxrefrelationship (objterm_id);
-- ================================================
***************
*** 94,97 ****
primary key (project_id),
name varchar(255) not null,
! description varchar(255) not null
);
--- 117,120 ----
primary key (project_id),
name varchar(255) not null,
! description varchar(255) not null
);
|
|
From: <sco...@us...> - 2003-06-02 14:46:15
|
Update of /cvsroot/gmod/schema/chado/modules/sequence In directory sc8-pr-cvs1:/tmp/cvs-serv32642 Modified Files: sequence.sql Log Message: changed docs for featureloc to agree with code Index: sequence.sql =================================================================== RCS file: /cvsroot/gmod/schema/chado/modules/sequence/sequence.sql,v retrieving revision 1.34 retrieving revision 1.35 diff -C2 -d -r1.34 -r1.35 *** sequence.sql 2 Jun 2003 14:44:04 -0000 1.34 --- sequence.sql 2 Jun 2003 14:46:10 -0000 1.35 *************** *** 100,108 **** -- an awkward fuzzy system -- nbeg, nend are for feature natural begin/end -- by natural begin, end we mean these are the actual -- beginning (5' position) and actual end (3' position) -- rather than the low position and high position, as ! -- these terms are sometimes erroneously used create table featureloc ( --- 100,113 ---- -- an awkward fuzzy system + -- Note that nbeg and nend have been replaced with fmin and fmax, + -- which are the minimum and maximum coordinates of the feature + -- relative to the parent feature. By contrast, -- nbeg, nend are for feature natural begin/end -- by natural begin, end we mean these are the actual -- beginning (5' position) and actual end (3' position) -- rather than the low position and high position, as ! -- these terms are sometimes erroneously used. To compensate ! -- for the removal of nbeg and nend from featureloc, a view ! -- based on featureloc, dfeatureloc, is provided in sequence_views.sql. create table featureloc ( |
|
From: <sco...@us...> - 2003-06-02 14:44:08
|
Update of /cvsroot/gmod/schema/chado/modules/sequence
In directory sc8-pr-cvs1:/tmp/cvs-serv31376
Modified Files:
sequence.sql sequence_views.sql
Log Message:
added fmin/fmax to featureloc and removed nbeg/nend. created dfeatureloc view.
Index: sequence.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/sequence/sequence.sql,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** sequence.sql 2 Jun 2003 13:36:34 -0000 1.33
--- sequence.sql 2 Jun 2003 14:44:04 -0000 1.34
***************
*** 115,122 ****
foreign key (srcfeature_id) references feature (feature_id),
! nbeg int,
! is_nbeg_partial boolean not null default 'false',
! nend int,
! is_nend_partial boolean not null default 'false',
strand smallint,
phase int,
--- 115,122 ----
foreign key (srcfeature_id) references feature (feature_id),
! fmin int,
! is_fmin_partial boolean not null default 'false',
! fmax int,
! is_fmax_partial boolean not null default 'false',
strand smallint,
phase int,
***************
*** 132,136 ****
create index featureloc_idx1 on featureloc (feature_id);
create index featureloc_idx2 on featureloc (srcfeature_id);
! create index featureloc_idx3 on featureloc (srcfeature_id,nbeg,nend);
-- ================================================
--- 132,136 ----
create index featureloc_idx1 on featureloc (feature_id);
create index featureloc_idx2 on featureloc (srcfeature_id);
! create index featureloc_idx3 on featureloc (srcfeature_id,fmin,fmax);
-- ================================================
Index: sequence_views.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/sequence/sequence_views.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** sequence_views.sql 10 Jan 2003 16:28:17 -0000 1.1
--- sequence_views.sql 2 Jun 2003 14:44:04 -0000 1.2
***************
*** 1,3 ****
--- 1,39 ----
--------------------------------
+ ---- dfeatureloc ---------------
+ --------------------------------
+ -- dfeatureloc is meant as an alternate representation of
+ -- the data in featureloc (see the descrption of featureloc
+ -- in sequence.sql). In dfeatureloc, fmin and fmax are
+ -- replaced with nbeg and nend. Whereas fmin and fmax
+ -- are absolute coordinates relative to the parent feature, nbeg
+ -- and nend are the beginning and ending coordinates
+ -- relative to the feature itself. For example, nbeg would
+ -- mark the 5' end of a gene and nend would mark the 3' end.
+
+ CREATE OR REPLACE VIEW dfeatureloc (
+ featureloc_id,
+ feature_id,
+ srcfeature_id,
+ nbeg,
+ is_nbeg_partial,
+ nend,
+ is_nend_partial,
+ strand,
+ phase,
+ residue_info,
+ locgroup,
+ rank
+ ) AS
+ SELECT featureloc_id, feature_id, srcfeature_id, fmin, is_fmin_partial,
+ fmax, is_fmax_partial, strand, phase, residue_info, locgroup, rank
+ FROM featureloc
+ WHERE (strand < 0 or phase < 0)
+ UNION
+ SELECT featureloc_id, feature_id, srcfeature_id, fmax, is_fmax_partial,
+ fmin, is_fmin_partial, strand, phase, residue_info, locgroup, rank
+ FROM featureloc
+ WHERE (strand is NULL or strand >= 0 or phase >= 0) ;
+
+ --------------------------------
---- f_type --------------------
--------------------------------
***************
*** 42,45 ****
--- 78,86 ----
---- f_loc ---------------------
--------------------------------
+ -- Note from Scott: I changed this view to depend on dfeatureloc,
+ -- since I don't know what it is used for. The change should
+ -- be transparent. I also changed dbxrefstr to dbxref_id since
+ -- dbxrefstr is no longer in feature
+
DROP VIEW f_loc;
CREATE VIEW f_loc
***************
*** 47,55 ****
SELECT f.feature_id,
f.name,
! f.dbxrefstr,
fl.nbeg,
fl.nend,
fl.strand
! FROM featureloc fl, f_type f
WHERE f.feature_id = fl.feature_id;
--- 88,96 ----
SELECT f.feature_id,
f.name,
! f.dbxref_id,
fl.nbeg,
fl.nend,
fl.strand
! FROM dfeatureloc fl, f_type f
WHERE f.feature_id = fl.feature_id;
|
|
From: <em...@us...> - 2003-06-02 13:36:39
|
Update of /cvsroot/gmod/schema/chado/modules/sequence
In directory sc8-pr-cvs1:/tmp/cvs-serv17007/modules/sequence
Modified Files:
sequence.sql
Log Message:
Removed synonym_pub table, which has no use
Index: sequence.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/sequence/sequence.sql,v
retrieving revision 1.32
retrieving revision 1.33
diff -C2 -d -r1.32 -r1.33
*** sequence.sql 20 Mar 2003 17:29:54 -0000 1.32
--- sequence.sql 2 Jun 2003 13:36:34 -0000 1.33
***************
*** 257,261 ****
foreign key (pub_id) references pub (pub_id),
! unique(feature_id, cvterm_id, pub_id)
);
create index feature_cvterm_idx1 on feature_cvterm (feature_id);
--- 257,262 ----
foreign key (pub_id) references pub (pub_id),
! unique (feature_id, cvterm_id, pub_id)
!
);
create index feature_cvterm_idx1 on feature_cvterm (feature_id);
***************
*** 316,335 ****
create index feature_synonym_idx2 on feature_synonym (feature_id);
create index feature_synonym_idx3 on feature_synonym (pub_id);
-
-
- -- ================================================
- -- TABLE: synonym_pub
- -- ================================================
-
- create table synonym_pub (
- synonym_pub_id serial not null,
- primary key (synonym_pub_id),
- synonym_id int not null,
- foreign key (synonym_id) references synonym (synonym_id),
- pub_id int not null,
- foreign key (pub_id) references pub (pub_id),
-
- unique(synonym_id, pub_id)
- );
- create index synonym_pub_idx1 on synonym_pub (synonym_id);
- create index synonym_pub_idx2 on synonym_pub (pub_id);
--- 317,318 ----
|
|
From: <pi...@us...> - 2003-05-30 21:24:52
|
Update of /cvsroot/gmod/schema/XMLTools/XORT/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv29721/XORT/bin
Modified Files:
ddl_properties_creator.pl dump.pl
Log Message:
Index: ddl_properties_creator.pl
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/XORT/bin/ddl_properties_creator.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** ddl_properties_creator.pl 28 May 2003 17:21:08 -0000 1.1
--- ddl_properties_creator.pl 30 May 2003 21:15:36 -0000 1.2
***************
*** 243,246 ****
--- 243,247 ----
$tablename=$temp1[0];
print "\ntable name:$tablename";
+ push @tables_pseudo, $tablename;
if ($all_tables){
$all_tables=$all_tables." ".$tablename;
Index: dump.pl
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/XORT/bin/dump.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** dump.pl 28 May 2003 16:58:04 -0000 1.2
--- dump.pl 30 May 2003 21:15:37 -0000 1.3
***************
*** 58,62 ****
"\n -s struct_type :module/single",
"\n -l loadable :1 for loadable, 0 for non_loadable",
! "\n -l app_data :app data for dumpspec if using variable in dumpspec, separate by space for multvalue",
"\n if you provide dumpspec, struct_type, loadable and tables will be ignored",
"\nexample1: $0 -d chado_gadfly5 -g \"/users/zhou/work/API/XORT/Config/dumpspec_gene.xml\" -p \"/export/zhou/dump_gene_no_local_id.xml\" -f no_local_id ",
--- 58,62 ----
"\n -s struct_type :module/single",
"\n -l loadable :1 for loadable, 0 for non_loadable",
! "\n -a app_data :app data for dumpspec if using variable in dumpspec, separate by space for multvalue",
"\n if you provide dumpspec, struct_type, loadable and tables will be ignored",
"\nexample1: $0 -d chado_gadfly5 -g \"/users/zhou/work/API/XORT/Config/dumpspec_gene.xml\" -p \"/export/zhou/dump_gene_no_local_id.xml\" -f no_local_id ",
|
|
From: <pi...@us...> - 2003-05-30 21:19:00
|
Update of /cvsroot/gmod/schema/XMLTools/XORT/Loader
In directory sc8-pr-cvs1:/tmp/cvs-serv29721/XORT/Loader
Modified Files:
XMLParser.pm
Log Message:
Index: XMLParser.pm
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Loader/XMLParser.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** XMLParser.pm 28 May 2003 17:28:42 -0000 1.2
--- XMLParser.pm 30 May 2003 21:15:35 -0000 1.3
***************
*** 83,87 ****
# algorithms to filter out ignore elements: initiately P_pseudo set to -1, for tables_pseudo, increase by 1 at beginning of start_element, decrease by 1 at end of end_element
# if P_pseudo >-1, then do nothing for start_element, end_element, character
! my $TABLES_PSEUDO='tables_pseudo';
my %hash_tables_pseudo;
my $P_pseudo=-1;
--- 83,87 ----
# algorithms to filter out ignore elements: initiately P_pseudo set to -1, for tables_pseudo, increase by 1 at beginning of start_element, decrease by 1 at end of end_element
# if P_pseudo >-1, then do nothing for start_element, end_element, character
! my $TABLES_PSEUDO='table_pseudo';
my %hash_tables_pseudo;
my $P_pseudo=-1;
***************
*** 449,457 ****
if ($P_pseudo==-1 && $element_name ne $APP_DATA_NODE) {
my $data = $properties->{'Data'};
! $data =~ s/\&/\&/g;
! $data =~ s/</\</g;
! $data =~ s/>/\>/g;
! $data =~ s/\"/\"/g;
! $data =~ s/\'/\'/g;
chomp($data);
my $data_length=length $data;
--- 449,468 ----
if ($P_pseudo==-1 && $element_name ne $APP_DATA_NODE) {
my $data = $properties->{'Data'};
! #$data =~ s/\&/\&/g;
! #$data =~ s/</\</g;
! #$data =~ s/>/\>/g;
! #$data =~ s/\"/\"/g;
! #$data =~ s/\'/\'/g;
! #$data =~ s/\\/\\\\/g;
!
!
! $data =~ s/\&/\&/g;
! $data =~ s/\</</g;
! $data =~ s/\>/>/g;
! $data =~ s/\"/\"/g;
! $data =~ s/\'/\'/g;
! $data =~ s/\\\\/\\/g;
! #$data =~ s/\&nbsp;/\s/g;
!
chomp($data);
my $data_length=length $data;
***************
*** 474,478 ****
if (defined $hash_ddl{$parent_element}){
my $hash_ref_cols=&_get_table_columns($parent_element);
! if (defined $hash_ref_cols->{$element_name} && ($data =~/\w/ || $data eq '-') && $data ne "\t"){
my $key=$hash_level_name{$level-1}.".".$element_name;
# treat differently for update and other operation
--- 485,489 ----
if (defined $hash_ddl{$parent_element}){
my $hash_ref_cols=&_get_table_columns($parent_element);
! if (defined $hash_ref_cols->{$element_name} && ($data =~/\w|\W/ || $data eq '-') && $data ne "\t"){
my $key=$hash_level_name{$level-1}.".".$element_name;
# treat differently for update and other operation
***************
*** 480,486 ****
--- 491,499 ----
if ($AoH_op[$level]{$element_name} eq 'update'){
$AoH_data_new[$level]{$key}= $AoH_data_new[$level]{$key}.$data;
+ # $AoH_data_new[$level]{$key}=~ s/ /\s/g;
}
else {
$AoH_data[$level]{$key}= $AoH_data[$level]{$key}.$data;
+ # $AoH_data[$level]{$key}=~ s/ /\s/g;
}
}
***************
*** 488,491 ****
--- 501,505 ----
if ($AoH_op[$level]{$element_name} ne 'update'){
$AoH_data[$level]{$key}= $AoH_data[$level]{$key}.$data;
+ # $AoH_data[$level]{$key}=~ s/ /\s/g;
}
else {
***************
*** 495,499 ****
}
}
! #print "\n\nkey:$key\tvalue:$AoH_data[$level]{$key}\tlevel:$level";
--- 509,513 ----
}
}
! print "\n\nkey:$key\tvalue:$AoH_data[$level]{$key}:\tlevel:$level";
***************
*** 532,535 ****
--- 546,551 ----
}
+
+
# ------------------------------------------------------------
# here come to the end of table
***************
*** 805,810 ****
sub end_document {
#clean the load.log
! system("delete load.log") if -e 'load.log';
$dbh_obj->close();
}
--- 821,829 ----
sub end_document {
#clean the load.log
!
! system(sprintf("delete $log_file")) if (-e $log_file && ($recovery_status eq '0' || $recovery_status ==0));
$dbh_obj->close();
+ print "\n\nbingo ....you success !....";
+ exit(1);
}
***************
*** 828,832 ****
my $start=length $content;
my $key=substr($value, $start);
! # print "\ncontent:$content:value:$value:\tkey:$key:";
$result->{$key}=$hash_ref->{$value};
delete $hash_ref->{$value};
--- 847,853 ----
my $start=length $content;
my $key=substr($value, $start);
!
! #here we modify to get space as value since standard xml will be empty element, so &nbsp; will represent ' '
! $hash_ref->{$value}=~ s/ / /g;
$result->{$key}=$hash_ref->{$value};
delete $hash_ref->{$value};
|
|
From: <pi...@us...> - 2003-05-30 21:19:00
|
Update of /cvsroot/gmod/schema/XMLTools/XORT/Config In directory sc8-pr-cvs1:/tmp/cvs-serv29721/XORT/Config Modified Files: ddl.properties function_view.sql idb-full.ddl Log Message: Index: ddl.properties =================================================================== RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Config/ddl.properties,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** ddl.properties 28 May 2003 17:28:40 -0000 1.4 --- ddl.properties 30 May 2003 21:15:33 -0000 1.5 *************** *** 65,73 **** cvterm_dbxref_non_null_default= ! organism=common_name taxgroup genus abbrev comment species organism_id organism_primary_key=organism_id ! organism_data_type=common_name:varchar;taxgroup:varchar;genus:varchar;abbrev:varchar;comment:text;species:varchar;organism_id:serial ! organism_unique=taxgroup genus species ! organism_non_null_cols=taxgroup genus species organism_non_null_default= --- 65,73 ---- cvterm_dbxref_non_null_default= ! organism=common_name genus abbrev comment species organism_id organism_primary_key=organism_id ! organism_data_type=:;common_name:varchar;genus:varchar;abbrev:varchar;comment:text;species:varchar;organism_id:serial ! organism_unique=genus species ! organism_non_null_cols=genus species organism_non_null_default= *************** *** 591,593 **** synonym_pub:synonym_id_ref_table=synonym ! table_pseudo= \ No newline at end of file --- 591,593 ---- synonym_pub:synonym_id_ref_table=synonym ! table_pseudo=feature_evidence _appdata \ No newline at end of file Index: function_view.sql =================================================================== RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Config/function_view.sql,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** function_view.sql 28 May 2003 17:28:40 -0000 1.4 --- function_view.sql 30 May 2003 21:15:33 -0000 1.5 *************** *** 1,10 **** ! create or replace view feature_evidence(feature_evidence_id, feature_id, evidence_id) as ! select anchor.feature_id||':'||evloc.feature_id, anchor.feature_id, evloc.feature_id ! from featureloc anchor, featureloc evloc, analysisfeature af ! where anchor.srcfeature_id=evloc.srcfeature_id ! and evloc.min>anchor.min ! and evloc.max<anchor.max ! and anchor.strand*evloc.strand>-1 ! and evloc.feature_id = af.feature_id; --- 1,3 ---- ! *************** *** 26,30 **** (srcfeature_id,min,max); ! --- 19,30 ---- (srcfeature_id,min,max); ! create or replace view feature_evidence(feature_evidence_id, feature_id, evidence_id) as ! select anchor.feature_id||':'||evloc.feature_id, anchor.feature_id, evloc.feature_id ! from featureloc anchor, featureloc evloc, analysisfeature af ! where anchor.srcfeature_id=evloc.srcfeature_id ! and evloc.min>anchor.min ! and evloc.max<anchor.max ! and anchor.strand*evloc.strand>-1 ! and evloc.feature_id = af.feature_id; Index: idb-full.ddl =================================================================== RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Config/idb-full.ddl,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** idb-full.ddl 16 May 2003 15:48:48 -0000 1.1 --- idb-full.ddl 30 May 2003 21:15:34 -0000 1.2 *************** *** 150,158 **** abbrev varchar(255) null, genus varchar(255) not null, ! taxgroup varchar(255) not null, species varchar(255) not null, common_name varchar(255) null, comment text null, ! unique(taxgroup, genus, species) ); GRANT ALL on organism_organism_id_seq to PUBLIC; --- 150,158 ---- abbrev varchar(255) null, genus varchar(255) not null, ! species varchar(255) not null, common_name varchar(255) null, comment text null, ! unique(genus, species) ); GRANT ALL on organism_organism_id_seq to PUBLIC; |
|
From: <pi...@us...> - 2003-05-30 21:18:26
|
Update of /cvsroot/gmod/schema/XMLTools/XORT/Dumper
In directory sc8-pr-cvs1:/tmp/cvs-serv29721/XORT/Dumper
Modified Files:
DumperSpec.pm DumperXML.pm
Log Message:
Index: DumperSpec.pm
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Dumper/DumperSpec.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** DumperSpec.pm 15 May 2003 16:51:06 -0000 1.1
--- DumperSpec.pm 30 May 2003 21:15:34 -0000 1.2
***************
*** 13,16 ****
--- 13,19 ----
my $dbh_obj;
+ my $TABLES_PSEUDO='table_pseudo';
+ my %hash_tables_pseudo;
+
#global variable, attribute of test or dump
my $DUMP_ALL='all';
***************
*** 59,62 ****
--- 62,73 ----
$dbh_obj->open();
+ # load the elements which need to be filtered out
+ my @array_pseudo=split(/\s+/, $hash_ddl{$TABLES_PSEUDO});
+ foreach my $value(@array_pseudo){
+ $hash_tables_pseudo{$value}=1;
+ print "\npseudo:$value";
+ }
+
+
bless $self, $type;
return $self;
***************
*** 2275,2279 ****
if ($temp1[1] !~ /int|serial|float|smallint|integer|bigint|decimal|numeric|real|bigserial/ ){
# in case of boolean type, need to replace 0/1 with f/t ?
-
if (defined($hash_ref->{$temp1[0]})){
my $value=$hash_ref->{$temp1[0]};
--- 2286,2289 ----
Index: DumperXML.pm
===================================================================
RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Dumper/DumperXML.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** DumperXML.pm 15 May 2003 16:51:06 -0000 1.1
--- DumperXML.pm 30 May 2003 21:15:34 -0000 1.2
***************
*** 19,22 ****
--- 19,27 ----
# this hash using for checking the avail of refer objectect, any object first time define, it will has all the field, after that, only unique
my %hash_object_id;
+ #here for pseudo table, e.g view, function and _appdata, _sql
+ my $TABLES_PSEUDO='table_pseudo';
+ my %hash_tables_pseudo;
+
+
my $LOCAL_ID="local_id";
my $NO_LOCAL_ID='xml';
***************
*** 96,99 ****
--- 101,108 ----
+
+
+
+
#load the propertity information and open the connection with database
my $property_file=$self->{'dbname'};
***************
*** 105,108 ****
--- 114,125 ----
%hash_ddl=$ddl_pro->get_properties_hash();
+
+ # load the elements which need to be filtered out
+ my @array_pseudo=split(/\s+/, $hash_ddl{$TABLES_PSEUDO});
+ foreach my $value(@array_pseudo){
+ $hash_tables_pseudo{$value}=1;
+ print "\npseudo:$value";
+ }
+
# if there is dumpspec to guide the dumper, then use it
if (defined $dumpspec_obj){
***************
*** 118,122 ****
my $node_name=$node->getNodeName();
print "\nnode_type:$node_type:node_name:$node_name";
! if ($node_type eq ELEMENT_NODE && defined $hash_ddl{$node_name}){
print "\nnode name ", $node->getNodeName();
#the result from get_id($node) is id string separated by '|'
--- 135,139 ----
my $node_name=$node->getNodeName();
print "\nnode_type:$node_type:node_name:$node_name";
! if ($node_type eq ELEMENT_NODE && defined $hash_ddl{$node_name} && !(defined $hash_tables_pseudo{$node_name})){
print "\nnode name ", $node->getNodeName();
#the result from get_id($node) is id string separated by '|'
***************
*** 239,242 ****
--- 256,260 ----
$data =~ s/\'/\'/g;
$data =~ s/\\/\\\\/g;
+ $data =~ s/ /&nbsp;/g if ($data !~/\W|\w|\S/);
$hash_ref->{$key}=$data;
}
|
|
From: <sle...@us...> - 2003-05-30 15:44:21
|
Update of /cvsroot/gmod/schema/chado/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv22389
Modified Files:
ddltrans
Log Message:
added dumpspec and date attrs to outermost tag
Index: ddltrans
===================================================================
RCS file: /cvsroot/gmod/schema/chado/bin/ddltrans,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** ddltrans 29 May 2003 19:15:22 -0000 1.4
--- ddltrans 30 May 2003 15:15:39 -0000 1.5
***************
*** 289,292 ****
--- 289,293 ----
push(@{$tablenames},$tablename); }
print "<!ELEMENT $schemaname ( ", join(" | ", @{$tablenames}), ")*>\n";
+ print "<!ATTLIST $schemaname\n\tdumpspec CDATA #IMPLIED\n\tdata CDATA #IMPLIED>\n\n";
foreach $tablename (@{$tablenames})
{ $table=$schema->{$tablename};
|
|
From: <sle...@us...> - 2003-05-30 15:38:42
|
Update of /cvsroot/gmod/schema/chado/dat
In directory sc8-pr-cvs1:/tmp/cvs-serv22959
Modified Files:
chado.dtd chado.html chado.pl chado.xml
Log Message:
various
Index: chado.dtd
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.dtd,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** chado.dtd 29 May 2003 19:14:46 -0000 1.4
--- chado.dtd 30 May 2003 15:16:15 -0000 1.5
***************
*** 2,6 ****
<!-- ********************** chado XML DTD **************************
! autogenerated on Thu May 29 15:08:25 EDT 2003 by ddltrans
for use with XORT dumper and loader.
--- 2,6 ----
<!-- ********************** chado XML DTD **************************
! autogenerated on Fri May 30 09:35:46 EDT 2003 by ddltrans
for use with XORT dumper and loader.
***************
*** 44,47 ****
--- 44,51 ----
<!ELEMENT chado ( acquisition | acquisitionparam | analysis | analysisfeature | analysisimplementation | analysisimplementationparam | analysisinput | analysisinvocation | analysisinvocationparam | analysisoutput | analysisprop | array | arrayannotation | assay | assay_biomaterial | assay_labeledextract | author | biomaterial | biomaterial_cvterm | biomaterialmeasurement | channel | compositeelementresult | control | cv | cvpath | cvrelationship | cvterm | cvterm_dbxref | cvtermsynonym | db | dbxref | dbxrefprop | eimage | element | elementresult | expression | expression_cvterm | expression_image | expression_pub | feature | feature_cvterm | feature_dbxref | feature_expression | feature_genotype | feature_phenotype | feature_pub | feature_relationship | feature_synonym | featureloc | featuremap | featuremap_pub | featurepos | featureprop | featureprop_pub | featurerange | genotype | interaction | interaction_obj | interaction_subj | labelmethod | magedocumentation | mageml | organism | organism_dbxref | phenotype | phenotype_cvterm | processimplementation | processimplementationparam | processinvocation | processinvocation_quantification | processinvocationparam | processio | processresult | project | projectlink | protocol | protocolparam | pub | pub_author | pub_dbxref | pub_relationship | pubprop | quantification | quantificationparam | relatedacquisition | relatedquantification | study | study_assay | studydesign | studydesign_assay | studydesigndescription | studyfactor | studyfactorvalue | synonym | synonym_pub | tableinfo | treatment | wwwuser | wwwuser_author | wwwuser_cvterm | wwwuser_expression | wwwuser_feature | wwwuser_genotype | wwwuser_interaction | wwwuser_organism | wwwuser_phenotype | wwwuser_project | wwwuser_pub | wwwuserrelationship)*>
+ <!ATTLIST chado
+ dumpspec CDATA #IMPLIED
+ data CDATA #IMPLIED>
+
<!-- ********************* TABLE acquisition *****************************
Index: chado.html
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** chado.html 29 May 2003 19:14:46 -0000 1.4
--- chado.html 30 May 2003 15:16:15 -0000 1.5
***************
*** 1,3 ****
! <em>Schema metadata produced by ddltrans on Thu May 29 15:08:25 EDT 2003</em>
<html>
--- 1,3 ----
! <em>Schema metadata produced by ddltrans on Fri May 30 09:35:47 EDT 2003</em>
<html>
Index: chado.pl
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.pl,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** chado.pl 29 May 2003 19:14:46 -0000 1.4
--- chado.pl 30 May 2003 15:16:15 -0000 1.5
***************
*** 1,3 ****
! # Schema metadata produced by ddltrans on Thu May 29 15:08:26 EDT 2003
$schema = {
'labelmethod' => {
--- 1,3 ----
! # Schema metadata produced by ddltrans on Fri May 30 09:35:47 EDT 2003
$schema = {
'labelmethod' => {
Index: chado.xml
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.xml,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** chado.xml 29 May 2003 19:14:46 -0000 1.4
--- chado.xml 30 May 2003 15:16:15 -0000 1.5
***************
*** 1,3 ****
! <!-- Schema metadata produced by ddltrans on Thu May 29 15:08:27 EDT 2003>
--- 1,3 ----
! <!-- Schema metadata produced by ddltrans on Fri May 30 09:35:49 EDT 2003>
|
|
From: <sle...@us...> - 2003-05-29 19:37:07
|
Update of /cvsroot/gmod/schema/chado/dat
In directory sc8-pr-cvs1:/tmp/cvs-serv9660
Modified Files:
chado.dtd chado.html chado.pl chado.xml
Log Message:
more fixes to generated dtd due to syntax errors caught by TurboXML
Index: chado.dtd
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.dtd,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** chado.dtd 29 May 2003 14:53:17 -0000 1.3
--- chado.dtd 29 May 2003 19:14:46 -0000 1.4
***************
*** 1,6 ****
! <?xml version="1.0" encoding="UTF-8"?>
<!-- ********************** chado XML DTD **************************
! autogenerated on Thu May 29 10:39:49 EDT 2003 by ddltrans
for use with XORT dumper and loader.
--- 1,6 ----
! <?xml version='1.0' encoding='UTF-8' ?>
<!-- ********************** chado XML DTD **************************
[...2037 lines suppressed...]
- <!ELEMENT world_read #PCDATA > <!ATTLIST world_read op (update) #IMPLIED>
<!-- ********************* TABLE wwwuser_pub *****************************
--- 1937,1940 ----
***************
*** 2144,2150 ****
ref CDATA #IMPLIED
op (lookup | insert | update | force | delete) #IMPLIED>
- <!ELEMENT wwwuser_id ( #PCDATA | wwwuser ) > <!ATTLIST wwwuser_id op (update) #IMPLIED>
- <!ELEMENT pub_id ( #PCDATA | pub ) > <!ATTLIST pub_id op (update) #IMPLIED>
- <!ELEMENT world_read #PCDATA > <!ATTLIST world_read op (update) #IMPLIED>
<!-- ********************* TABLE wwwuserrelationship *****************************
--- 1950,1953 ----
***************
*** 2162,2164 ****
<!ELEMENT objwwwuser_id ( #PCDATA | wwwuser ) > <!ATTLIST objwwwuser_id op (update) #IMPLIED>
<!ELEMENT subjwwwuser_id ( #PCDATA | wwwuser ) > <!ATTLIST subjwwwuser_id op (update) #IMPLIED>
- <!ELEMENT world_read #PCDATA > <!ATTLIST world_read op (update) #IMPLIED>
--- 1965,1966 ----
Index: chado.html
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** chado.html 29 May 2003 14:53:17 -0000 1.3
--- chado.html 29 May 2003 19:14:46 -0000 1.4
***************
*** 1,3 ****
! <em>Schema metadata produced by ddltrans on Thu May 29 10:39:50 EDT 2003</em>
<html>
--- 1,3 ----
! <em>Schema metadata produced by ddltrans on Thu May 29 15:08:25 EDT 2003</em>
<html>
***************
*** 1045,1050 ****
<h2>wwwuser</h2>
!
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
</table>
--- 1045,1055 ----
<h2>wwwuser</h2>
! ------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
+ <tr><td>email</td><td>varchar(128)</td><td>no</td><td></td><td></td></tr>
+ <tr><td>username</td><td>varchar(32)</td><td>no</td><td></td><td></td></tr>
+ <tr><td>wwwuser_id</td><td>serial</td><td>no</td><td></td><td><li>wwwuser_feature.wwwuser_id<li>wwwuser_cvterm.wwwuser_id<li>wwwuser_project.wwwuser_id<li>wwwuser_organism.wwwuser_id<li>wwwuser_genotype.wwwuser_id<li>wwwuser_author.wwwuser_id<li>wwwuser_interaction.wwwuser_id<li>wwwuser_phenotype.wwwuser_id<li>wwwuser_pub.wwwuser_id<li>wwwuser_expression.wwwuser_id<li>wwwuserrelationship.objwwwuser_id<li>wwwuserrelationship.subjwwwuser_id</td></tr>
+ <tr><td>profile</td><td>text</td><td>yes</td><td></td><td></td></tr>
+ <tr><td>password</td><td>varchar(32)</td><td>no</td><td></td><td></td></tr>
</table>
***************
*** 1122,1126 ****
<h2>wwwuser_project</h2>
! ------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
<tr><td>wwwuser_id</td><td>int</td><td>no</td><td></td><td>wwwuser.wwwuser_id</td></tr>
--- 1127,1131 ----
<h2>wwwuser_project</h2>
! link wwwuser accounts to projects
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
<tr><td>wwwuser_id</td><td>int</td><td>no</td><td></td><td>wwwuser.wwwuser_id</td></tr>
Index: chado.pl
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.pl,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** chado.pl 29 May 2003 14:53:17 -0000 1.3
--- chado.pl 29 May 2003 19:14:46 -0000 1.4
***************
*** 1,3 ****
! # Schema metadata produced by ddltrans on Thu May 29 10:39:52 EDT 2003
$schema = {
'labelmethod' => {
--- 1,3 ----
! # Schema metadata produced by ddltrans on Thu May 29 15:08:26 EDT 2003
$schema = {
'labelmethod' => {
***************
*** 134,138 ****
'_entity' => 'set'
},
! 'column' => {}
},
'assay_labeledextract' => {
--- 134,236 ----
'_entity' => 'set'
},
! 'name' => 'wwwuser',
! 'comment' => '------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).',
! '_entity' => 'table',
! 'primarykey' => 'wwwuser_id',
! 'column' => {
! 'email' => {
! 'name' => 'email',
! 'allownull' => 'no',
! 'type' => 'varchar(128)',
! '_entity' => 'column'
! },
! 'username' => {
! 'name' => 'username',
! 'allownull' => 'no',
! 'type' => 'varchar(32)',
! '_entity' => 'column',
! 'unique' => 1
! },
! 'wwwuser_id' => {
! 'name' => 'wwwuser_id',
! 'allownull' => 'no',
! 'type' => 'serial',
! 'foreign_references' => [
! {
! 'table' => 'wwwuser_feature',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_cvterm',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_project',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_organism',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_genotype',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_author',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_interaction',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_phenotype',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_pub',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_expression',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuserrelationship',
! 'column' => 'objwwwuser_id'
! },
! {
! 'table' => 'wwwuserrelationship',
! 'column' => 'subjwwwuser_id'
! }
! ],
! '_entity' => 'column',
! 'primarykey' => 'yes'
! },
! 'profile' => {
! 'name' => 'profile',
! 'allownull' => 'yes',
! 'type' => 'text',
! '_entity' => 'column'
! },
! 'password' => {
! 'name' => 'password',
! 'allownull' => 'no',
! 'type' => 'varchar(32)',
! '_entity' => 'column'
! },
! '_order' => [
! 'wwwuser_id',
! 'username',
! 'password',
! 'email',
! 'profile'
! ],
! '_entity' => 'list'
! },
! 'unique' => [
! 'username'
! ]
},
'assay_labeledextract' => {
***************
*** 1727,1731 ****
},
'name' => 'wwwuser_project',
! 'comment' => '------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects',
'_entity' => 'table',
'primarykey' => 'wwwuser_project_id',
--- 1825,1829 ----
},
'name' => 'wwwuser_project',
! 'comment' => 'link wwwuser accounts to projects',
'_entity' => 'table',
'primarykey' => 'wwwuser_project_id',
Index: chado.xml
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** chado.xml 29 May 2003 14:53:17 -0000 1.3
--- chado.xml 29 May 2003 19:14:46 -0000 1.4
***************
*** 1,3 ****
! <!-- Schema metadata produced by ddltrans on Thu May 29 10:39:58 EDT 2003>
--- 1,3 ----
! <!-- Schema metadata produced by ddltrans on Thu May 29 15:08:27 EDT 2003>
***************
*** 86,95 ****
<\column>
<\table>
! <index>
! <columns>username</columns>
! <name>wwwuser_idx1</name>
! <\index>
! <column>
! </column>
<table>
<name>assay_labeledextract</name>
--- 86,159 ----
<\column>
<\table>
! <table>
! <name>wwwuser</name>
! <comment>------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).</comment>
! <column>
! <name>wwwuser_id</name>
! <type>serial</type>
! <allownull>no</allownull>
! <foreign_references>
! <li>
! <table>wwwuser_feature</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_cvterm</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_project</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_organism</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_genotype</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_author</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_interaction</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_phenotype</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_pub</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_expression</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuserrelationship</table>
! <column>objwwwuser_id</column><\li>
! <li>
! <table>wwwuserrelationship</table>
! <column>subjwwwuser_id</column><\li>
! </foreign_references>
! <\column>
! <column>
! <name>username</name>
! <type>varchar(32)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>password</name>
! <type>varchar(32)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>email</name>
! <type>varchar(128)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>profile</name>
! <type>text</type>
! <allownull>yes</allownull>
! <\column>
! <unique>
! <li>username<\li>
! </unique>
! <\table>
<table>
<name>assay_labeledextract</name>
***************
*** 1033,1037 ****
<table>
<name>wwwuser_project</name>
! <comment>------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects</comment>
<column>
<name>wwwuser_project_id</name>
--- 1097,1101 ----
<table>
<name>wwwuser_project</name>
! <comment>link wwwuser accounts to projects</comment>
<column>
<name>wwwuser_project_id</name>
|
|
From: <sle...@us...> - 2003-05-29 19:22:57
|
Update of /cvsroot/gmod/schema/chado/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv10056
Modified Files:
ddltrans
Log Message:
fixed syntax errors in generated dtd
Index: ddltrans
===================================================================
RCS file: /cvsroot/gmod/schema/chado/bin/ddltrans,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** ddltrans 29 May 2003 14:52:30 -0000 1.3
--- ddltrans 29 May 2003 19:15:22 -0000 1.4
***************
*** 134,140 ****
{ # ignore
}
! elsif(/^create /i)
{ # ignore
! if($_ !~ /;$/){ while(<>){ last if /;$/; }}
}
else { warn "Unrecognized sql: $_\n"; if($_ !~ /;$/){ while(<>){ last if /;$/; }}}
--- 134,140 ----
{ # ignore
}
! elsif(/^\s*create /i)
{ # ignore
! if($_ !~ /;$/){ while(<>){ last if /;\s*$/; }}
}
else { warn "Unrecognized sql: $_\n"; if($_ !~ /;$/){ while(<>){ last if /;$/; }}}
***************
*** 241,245 ****
my($schema, $tables)=@_;
! print '<?xml version="1.0" encoding="UTF-8"?>', "\n\n";
print "<!-- ********************** $schemaname XML DTD **************************
autogenerated on $date by ddltrans
--- 241,245 ----
my($schema, $tables)=@_;
! print "<?xml version='1.0' encoding='UTF-8' ?>\n\n";
print "<!-- ********************** $schemaname XML DTD **************************
autogenerated on $date by ddltrans
***************
*** 288,292 ****
next if $tablename =~ /_audit$/;
push(@{$tablenames},$tablename); }
! print "<!ELEMENT xort ( ", join(" | ", @{$tablenames}), ")*>\n";
foreach $tablename (@{$tablenames})
{ $table=$schema->{$tablename};
--- 288,292 ----
next if $tablename =~ /_audit$/;
push(@{$tablenames},$tablename); }
! print "<!ELEMENT $schemaname ( ", join(" | ", @{$tablenames}), ")*>\n";
foreach $tablename (@{$tablenames})
{ $table=$schema->{$tablename};
***************
*** 307,329 ****
print " ************************************************************************* -->\n";
# print table element
! print "<!ELEMENT $tablename (";
# column subelements
! $dlm="";
! for $colname (@{$colnames})
! { next if $colname eq $table->{primarykey};
! # Cardinality of table fields:
! # if part of a unique key, may appear twice in an update context: once to refer, once to modify
! # if a foreign key, may be ommitted due to hierarchy rule
! # if a non-null field, may still be ommitted in an update or delete context.
! $card="?";
! if( defined($table->{column}->{$colname}->{unique}) ) { $card="*"; }
! print "$dlm$colname"; $dlm = " | "; }
! print ")* ";
!
# linking table subelements
my($joins)=$table->{column}->{$table->{primarykey}}->{foreign_references};
if(@{$joins}+0)
! { print "\n\t( ", $dlm = "";
$printed={};
foreach $join (@{$joins})
--- 307,332 ----
print " ************************************************************************* -->\n";
# print table element
! print "<!ELEMENT $tablename ";
# column subelements
! if(@{$colnames}){
! print "(";
! $dlm="";
! for $colname (@{$colnames})
! { next if $colname eq $table->{primarykey};
! # Cardinality of table fields:
! # if part of a unique key, may appear twice in an update context: once to refer, once to modify
! # if a foreign key, may be ommitted due to hierarchy rule
! # if a non-null field, may still be ommitted in an update or delete context.
! $card="?";
! if( defined($table->{column}->{$colname}->{unique}) ) { $card="*"; }
! print "$dlm$colname"; $dlm = " | "; }
! print ")* ";
! }
!
# linking table subelements
my($joins)=$table->{column}->{$table->{primarykey}}->{foreign_references};
if(@{$joins}+0)
! { print "\n\t, ( ", $dlm = "";
$printed={};
foreach $join (@{$joins})
***************
*** 347,356 ****
{ if($def ne $defined{$colname}->{to})
{ next if canonical_type( $def ) eq canonical_type( $defined{$colname}->{to});
! warn "Warning: Incompatible definitions of column `$colname':\n\tin table $defined{$colname}->{from} as $defined{$colname}->{to}\n\tin table $tablename as $def\n";
! next; }}
$defined{$colname}={from=>$tablename, to=>$def};
print "<!ELEMENT $colname ";
if($col->{fk_table}){ print "( #PCDATA | $col->{fk_table} )"; }
! else { print "#PCDATA"; }
print " >";
print "\t<!ATTLIST $colname op (update) #IMPLIED>";
--- 350,359 ----
{ if($def ne $defined{$colname}->{to})
{ next if canonical_type( $def ) eq canonical_type( $defined{$colname}->{to});
! warn "Warning: Incompatible definitions of column `$colname':\n\tin table $defined{$colname}->{from} as $defined{$colname}->{to}\n\tin table $tablename as $def\n"; }
! next; }
$defined{$colname}={from=>$tablename, to=>$def};
print "<!ELEMENT $colname ";
if($col->{fk_table}){ print "( #PCDATA | $col->{fk_table} )"; }
! else { print "(#PCDATA)"; }
print " >";
print "\t<!ATTLIST $colname op (update) #IMPLIED>";
|
|
From: <sle...@us...> - 2003-05-29 14:53:21
|
Update of /cvsroot/gmod/schema/chado/dat
In directory sc8-pr-cvs1:/tmp/cvs-serv31791
Modified Files:
chado.ddl chado.dtd chado.html chado.pl chado.xml
Log Message:
regenerated after fixing extra paren bug in ddltrans
Index: chado.ddl
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.ddl,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** chado.ddl 9 May 2003 18:18:34 -0000 1.1
--- chado.ddl 29 May 2003 14:53:17 -0000 1.2
***************
*** 2260,2263 ****
--- 2260,2295 ----
WHERE fp.pkey_id = c.cvterm_id;
+
+ /* feature before (?)deletion trigger implements the following rules:
+
+ -if feature to be deleted is a
+
+ transcript:
+ -delete any exons having this as their only related transcript
+ -delete any proteins having this as their only related transcript
+ -prevent deletion if there are any alleles of the transcript?
+
+ gene:
+ -prevent deletion if there are any alleles of the gene? or other info?
+ -delete all transcripts that are related only to this gene
+
+ what needs to be preserved about dbxrefs, etc.?
+ */
+
+ CREATE OR REPLACE FUNCTION feature_del_tr () RETURNS TRIGGER AS '
+ body goes here
+
+
+
+
+ ' LANGUAGE SQL (?);
+ or language plpgsql;
+
+ CREATE TRIGGER name { BEFORE | AFTER } { event [OR ...] }
+ ON table FOR EACH { ROW | STATEMENT }
+ EXECUTE PROCEDURE func ( arguments )
+
+ CREATE TRIGGER feature_del_tr BEFORE DELETE ON feature FOR EACH { ROW | STATEMENT }
+ EXECUTE PROCEDURE feature_del_tr ;
-- ================================================
-- TABLE: wwwuser
Index: chado.dtd
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.dtd,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** chado.dtd 13 May 2003 15:26:07 -0000 1.2
--- chado.dtd 29 May 2003 14:53:17 -0000 1.3
***************
*** 2,6 ****
<!-- ********************** chado XML DTD **************************
! autogenerated on Tue May 13 11:18:29 EDT 2003 by ddltrans
for use with XORT dumper and loader.
--- 2,6 ----
<!-- ********************** chado XML DTD **************************
! autogenerated on Thu May 29 10:39:49 EDT 2003 by ddltrans
for use with XORT dumper and loader.
[...1418 lines suppressed...]
<!ATTLIST wwwuser_pub
--- 2138,2142 ----
* world_read smallint not null default 1
************************************************************************* -->
! <!ELEMENT wwwuser_pub (wwwuser_id | pub_id | world_read)* >
<!ATTLIST wwwuser_pub
***************
*** 2165,2169 ****
* world_read smallint not null default 1
************************************************************************* -->
! <!ELEMENT wwwuserrelationship (objwwwuser_id | subjwwwuser_id | world_read)* )>
<!ATTLIST wwwuserrelationship
--- 2154,2158 ----
* world_read smallint not null default 1
************************************************************************* -->
! <!ELEMENT wwwuserrelationship (objwwwuser_id | subjwwwuser_id | world_read)* >
<!ATTLIST wwwuserrelationship
Index: chado.html
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** chado.html 13 May 2003 15:26:07 -0000 1.2
--- chado.html 29 May 2003 14:53:17 -0000 1.3
***************
*** 1,3 ****
! <em>Schema metadata produced by ddltrans on Tue May 13 11:18:30 EDT 2003</em>
<html>
--- 1,3 ----
! <em>Schema metadata produced by ddltrans on Thu May 29 10:39:50 EDT 2003</em>
<html>
***************
*** 1045,1055 ****
<h2>wwwuser</h2>
! ------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
- <tr><td>email</td><td>varchar(128)</td><td>no</td><td></td><td></td></tr>
- <tr><td>username</td><td>varchar(32)</td><td>no</td><td></td><td></td></tr>
- <tr><td>wwwuser_id</td><td>serial</td><td>no</td><td></td><td><li>wwwuser_feature.wwwuser_id<li>wwwuser_cvterm.wwwuser_id<li>wwwuser_project.wwwuser_id<li>wwwuser_organism.wwwuser_id<li>wwwuser_genotype.wwwuser_id<li>wwwuser_author.wwwuser_id<li>wwwuser_interaction.wwwuser_id<li>wwwuser_phenotype.wwwuser_id<li>wwwuser_pub.wwwuser_id<li>wwwuser_expression.wwwuser_id<li>wwwuserrelationship.objwwwuser_id<li>wwwuserrelationship.subjwwwuser_id</td></tr>
- <tr><td>profile</td><td>text</td><td>yes</td><td></td><td></td></tr>
- <tr><td>password</td><td>varchar(32)</td><td>no</td><td></td><td></td></tr>
</table>
--- 1045,1050 ----
<h2>wwwuser</h2>
!
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
</table>
***************
*** 1127,1131 ****
<h2>wwwuser_project</h2>
! link wwwuser accounts to projects
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
<tr><td>wwwuser_id</td><td>int</td><td>no</td><td></td><td>wwwuser.wwwuser_id</td></tr>
--- 1122,1126 ----
<h2>wwwuser_project</h2>
! ------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects
<table border=1><tr><th>Name</th><th>Type</th><th>NULL?</th><th>Comment</th><th>References</th></tr>
<tr><td>wwwuser_id</td><td>int</td><td>no</td><td></td><td>wwwuser.wwwuser_id</td></tr>
Index: chado.pl
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.pl,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** chado.pl 13 May 2003 15:26:07 -0000 1.2
--- chado.pl 29 May 2003 14:53:17 -0000 1.3
***************
*** 1,3 ****
! # Schema metadata produced by ddltrans on Tue May 13 11:18:30 EDT 2003
$schema = {
'labelmethod' => {
--- 1,3 ----
! # Schema metadata produced by ddltrans on Thu May 29 10:39:52 EDT 2003
$schema = {
'labelmethod' => {
***************
*** 134,236 ****
'_entity' => 'set'
},
! 'name' => 'wwwuser',
! 'comment' => '------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).',
! '_entity' => 'table',
! 'primarykey' => 'wwwuser_id',
! 'column' => {
! 'email' => {
! 'name' => 'email',
! 'allownull' => 'no',
! 'type' => 'varchar(128)',
! '_entity' => 'column'
! },
! 'username' => {
! 'name' => 'username',
! 'allownull' => 'no',
! 'type' => 'varchar(32)',
! '_entity' => 'column',
! 'unique' => 1
! },
! 'wwwuser_id' => {
! 'name' => 'wwwuser_id',
! 'allownull' => 'no',
! 'type' => 'serial',
! 'foreign_references' => [
! {
! 'table' => 'wwwuser_feature',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_cvterm',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_project',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_organism',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_genotype',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_author',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_interaction',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_phenotype',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_pub',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuser_expression',
! 'column' => 'wwwuser_id'
! },
! {
! 'table' => 'wwwuserrelationship',
! 'column' => 'objwwwuser_id'
! },
! {
! 'table' => 'wwwuserrelationship',
! 'column' => 'subjwwwuser_id'
! }
! ],
! '_entity' => 'column',
! 'primarykey' => 'yes'
! },
! 'profile' => {
! 'name' => 'profile',
! 'allownull' => 'yes',
! 'type' => 'text',
! '_entity' => 'column'
! },
! 'password' => {
! 'name' => 'password',
! 'allownull' => 'no',
! 'type' => 'varchar(32)',
! '_entity' => 'column'
! },
! '_order' => [
! 'wwwuser_id',
! 'username',
! 'password',
! 'email',
! 'profile'
! ],
! '_entity' => 'list'
! },
! 'unique' => [
! 'username'
! ]
},
'assay_labeledextract' => {
--- 134,138 ----
'_entity' => 'set'
},
! 'column' => {}
},
'assay_labeledextract' => {
***************
*** 1825,1829 ****
},
'name' => 'wwwuser_project',
! 'comment' => 'link wwwuser accounts to projects',
'_entity' => 'table',
'primarykey' => 'wwwuser_project_id',
--- 1727,1731 ----
},
'name' => 'wwwuser_project',
! 'comment' => '------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects',
'_entity' => 'table',
'primarykey' => 'wwwuser_project_id',
Index: chado.xml
===================================================================
RCS file: /cvsroot/gmod/schema/chado/dat/chado.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** chado.xml 13 May 2003 15:26:07 -0000 1.2
--- chado.xml 29 May 2003 14:53:17 -0000 1.3
***************
*** 1,3 ****
! <!-- Schema metadata produced by ddltrans on Tue May 13 11:18:32 EDT 2003>
--- 1,3 ----
! <!-- Schema metadata produced by ddltrans on Thu May 29 10:39:58 EDT 2003>
***************
*** 86,159 ****
<\column>
<\table>
! <table>
! <name>wwwuser</name>
! <comment>------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ keep track of www users. this may also be useful in an audit module at some point (?).</comment>
! <column>
! <name>wwwuser_id</name>
! <type>serial</type>
! <allownull>no</allownull>
! <foreign_references>
! <li>
! <table>wwwuser_feature</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_cvterm</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_project</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_organism</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_genotype</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_author</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_interaction</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_phenotype</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_pub</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuser_expression</table>
! <column>wwwuser_id</column><\li>
! <li>
! <table>wwwuserrelationship</table>
! <column>objwwwuser_id</column><\li>
! <li>
! <table>wwwuserrelationship</table>
! <column>subjwwwuser_id</column><\li>
! </foreign_references>
! <\column>
! <column>
! <name>username</name>
! <type>varchar(32)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>password</name>
! <type>varchar(32)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>email</name>
! <type>varchar(128)</type>
! <allownull>no</allownull>
! <\column>
! <column>
! <name>profile</name>
! <type>text</type>
! <allownull>yes</allownull>
! <\column>
! <unique>
! <li>username<\li>
! </unique>
! <\table>
<table>
<name>assay_labeledextract</name>
--- 86,95 ----
<\column>
<\table>
! <index>
! <columns>username</columns>
! <name>wwwuser_idx1</name>
! <\index>
! <column>
! </column>
<table>
<name>assay_labeledextract</name>
***************
*** 1097,1101 ****
<table>
<name>wwwuser_project</name>
! <comment>link wwwuser accounts to projects</comment>
<column>
<name>wwwuser_project_id</name>
--- 1033,1037 ----
<table>
<name>wwwuser_project</name>
! <comment>------------------------------ -- f_type -------------------- ------------------------------ ------------------------------ -- fnr_type ------------------ ------------------------------ ------------------------------ -- f_loc --------------------- ------------------------------ ------------------------------ -- fp_key ------------------- ------------------------------ link wwwuser accounts to projects</comment>
<column>
<name>wwwuser_project_id</name>
|
|
From: <sle...@us...> - 2003-05-29 14:52:33
|
Update of /cvsroot/gmod/schema/chado/bin
In directory sc8-pr-cvs1:/tmp/cvs-serv31379
Modified Files:
ddltrans
Log Message:
Fixed extra paren at end of table entity
Index: ddltrans
===================================================================
RCS file: /cvsroot/gmod/schema/chado/bin/ddltrans,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** ddltrans 13 May 2003 15:26:07 -0000 1.2
--- ddltrans 29 May 2003 14:52:30 -0000 1.3
***************
*** 333,337 ****
print ")*\n "; }
! print ")>\n"; # end table element
# Table element ttribute list
--- 333,337 ----
print ")*\n "; }
! print ">\n"; # end table element
# Table element ttribute list
|
|
From: <sco...@us...> - 2003-05-28 19:16:31
|
Update of /cvsroot/gmod/schema/chado/modules/sequence/gff-bridge
In directory sc8-pr-cvs1:/tmp/cvs-serv474
Added Files:
sequence-gff-funcs.pgsql sequence-gff-views.sql
Log Message:
added a view and function for getting GFF-style attributes
--- NEW FILE: sequence-gff-funcs.pgsql ---
-- FUNCTION gfffeatureatts (integer) is a function to get
-- data in the same format as the gffatts view so that
-- it can be easily converted to GFF attributes.
CREATE FUNCTION gfffeatureatts (integer)
RETURNS SETOF gffatts
AS
'
SELECT feature_id, ''cvterm'' AS type, s.name AS attribute
FROM cvterm s, feature_cvterm fs
WHERE fs.feature_id= $1 AND fs.cvterm_id = s.cvterm_id
UNION
SELECT feature_id, ''dbxref'' AS type, dbname || '':'' || s.accession AS attribute
FROM dbxref s, feature_dbxref fs
WHERE fs.feature_id= $1 AND fs.dbxref_id = s.dbxref_id
UNION
SELECT feature_id, ''expression'' AS type, s.description AS attribute
FROM expression s, feature_expression fs
WHERE fs.feature_id= $1 AND fs.expression_id = s.expression_id
UNION
SELECT feature_id, ''genotype'' AS type, s.description AS attribute
FROM genotype s, feature_genotype fs
WHERE fs.feature_id= $1 AND fs.genotype_id = s.genotype_id
UNION
SELECT feature_id, ''phenotype'' AS type, s.description AS attribute
FROM phenotype s, feature_phenotype fs
WHERE fs.feature_id= $1 AND fs.phenotype_id = s.phenotype_id
UNION
SELECT feature_id, ''synonym'' AS type, s.name AS attribute
FROM synonym s, feature_synonym fs
WHERE fs.feature_id= $1 AND fs.synonym_id = s.synonym_id
UNION
SELECT feature_id, ''pub'' AS type, s.series_name || '':'' || s.title AS attribute
FROM pub s, feature_pub fs
WHERE fs.feature_id= $1 AND fs.pub_id = s.pub_id
'
LANGUAGE SQL;
--- NEW FILE: sequence-gff-views.sql ---
-- 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
) AS
SELECT feature_id, 'cvterm' AS type, s.name AS attribute
FROM cvterm s, feature_cvterm fs
WHERE fs.cvterm_id = s.cvterm_id
UNION ALL
SELECT feature_id, 'dbxref' AS type, dbname || ':' || s.accession AS attribute
FROM dbxref s, feature_dbxref fs
WHERE fs.dbxref_id = s.dbxref_id
UNION ALL
SELECT feature_id, 'expression' AS type, s.description AS attribute
FROM expression s, feature_expression fs
WHERE fs.expression_id = s.expression_id
UNION ALL
SELECT feature_id, 'genotype' AS type, s.description AS attribute
FROM genotype s, feature_genotype fs
WHERE fs.genotype_id = s.genotype_id
UNION ALL
SELECT feature_id, 'phenotype' AS type, s.description AS attribute
FROM phenotype s, feature_phenotype fs
WHERE fs.phenotype_id = s.phenotype_id
UNION ALL
SELECT feature_id, 'synonym' AS type, s.name AS attribute
FROM synonym s, feature_synonym fs
WHERE fs.synonym_id = s.synonym_id
UNION ALL
SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute
FROM pub s, feature_pub fs
WHERE fs.pub_id = s.pub_id;
|
|
From: <sco...@us...> - 2003-05-28 19:15:32
|
Update of /cvsroot/gmod/schema/chado/modules/sequence/gff-bridge In directory sc8-pr-cvs1:/tmp/cvs-serv32716/gff-bridge Log Message: Directory /cvsroot/gmod/schema/chado/modules/sequence/gff-bridge added to the repository |
|
From: <sco...@us...> - 2003-05-28 19:09:41
|
Update of /cvsroot/gmod/schema/chado/modules/gff-bridge In directory sc8-pr-cvs1:/tmp/cvs-serv30400/gff-bridge Log Message: Directory /cvsroot/gmod/schema/chado/modules/gff-bridge added to the repository |
|
From: <pi...@us...> - 2003-05-28 17:49:38
|
Update of /cvsroot/gmod/schema/XMLTools/XORT/Doc In directory sc8-pr-cvs1:/tmp/cvs-serv21656/XORT/Doc Modified Files: readme_xort Log Message: Index: readme_xort =================================================================== RCS file: /cvsroot/gmod/schema/XMLTools/XORT/Doc/readme_xort,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** readme_xort 27 May 2003 18:08:08 -0000 1.4 --- readme_xort 28 May 2003 17:28:41 -0000 1.5 *************** *** 4,8 **** ! 2. create the ddl.properties file by running CodeBase/XORT/bin/ddl_properties_creater.pl, it will create the ddl.properties in CodeBase/XORT/Config --- 4,10 ---- ! 2. create the ddl.properties file by running CodeBase/XORT/bin/ddl_properties_creator.pl, it will create the ddl.properties in CodeBase/XORT/Config ! before go further step, view CodeBase.XORT/Config/ddl.properties to see whether it make sense, if not, normally means that your ddl file DOES NOT have same format as samle ddl:CodeBase/XORT/Config/idb-full.ddl ! for all view/function, you need to MAKE one create TABLE statement for each view/function in another file(refer to CodeBase/XORT/Config/function_view.sql & function_view.ddl), this will be argument -v to ddl_properties_creator.pl *************** *** 10,14 **** 4. log into the target database and execute CodeBase/XORT/Config/function_view.sql to synchronize the database ! here will create the necessary view, also because the current dump from Berkeley didn't have featureloc.min and featureloc.max, so need o add those two cols, if in the future you get the dump which already implement those change, then you can comment those sql statement which modify featureloc table. 5. run CodeBase/XORT/bin/dump.pl loader.pl validator.pl with -h for how to use it. --- 12,16 ---- 4. log into the target database and execute CodeBase/XORT/Config/function_view.sql to synchronize the database ! here will create the necessary view, also because the current dump from Berkeley didn't have featureloc.min and featureloc.max, so need o add those two cols, if in the future you get the dump which already implement those change, then you can comment those sql statement which modify featureloc table. Refering CodeBase/XORT/Config/function_view.sql and function_view.ddl for how convert function and view into ddl format. 5. run CodeBase/XORT/bin/dump.pl loader.pl validator.pl with -h for how to use it. |
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