[Gmod-schema-cmts] SF.net SVN: gmod:[25172] schema/trunk/chado/bin/gmod_chado_properties.pl

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

Revision: 25172
          http://gmod.svn.sourceforge.net/gmod/?rev=25172&view=rev
Author:   scottcain
Date:     2011-09-01 18:01:43 +0000 (Thu, 01 Sep 2011)
Log Message:
-----------
making it so that if the chado_properties cv doesn't exist when the version is to be updated, it gets created

Modified Paths:
--------------
    schema/trunk/chado/bin/gmod_chado_properties.pl

Modified: schema/trunk/chado/bin/gmod_chado_properties.pl
===================================================================
--- schema/trunk/chado/bin/gmod_chado_properties.pl	2011-09-01 17:16:36 UTC (rev 25171)
+++ schema/trunk/chado/bin/gmod_chado_properties.pl	2011-09-01 18:01:43 UTC (rev 25172)
@@ -30,6 +30,9 @@
 schema updates.  It can also get any named property (based on the cvterm in
 the chadoprop table), or a list of all properties in the chadoprop table.
 
+In older (pre-1.2) versions of Chado, updating the schema version has the 
+side effect of creating the chadoprop table and a chado_properties cv.
+
 =head1 AUTHOR
 
 Scott Cain E<lt>sc...@cp...E<gt>
@@ -78,15 +81,51 @@
     my $dbh     = shift;
 
     if (looks_like_number($version) and $version > 1.19){
-        my $set_query = "INSERT INTO chadoprop (type_id, value) VALUES ((SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version'),?)";
-        my $sth = $dbh->prepare($set_query);
-        $sth->execute($version) or die "database error: $!";
+        #first make sure the chado_properties cv is available
+        my $cp_query = "SELECT cv_id FROM cv WHERE name = 'chado_properties'";
+        my $sth = $dbh->prepare($cp_query);
+        $sth->execute();
+        my ($cv_id) = $sth->fetchrow_array;
+
+        my $cvterm_id;
+        unless ($cv_id) {
+            #chado_properties is not available, so create it
+            my $cv_insert = "insert into cv (name,definition) values ('chado_properties','Terms that are used in the chadoprop table to describe the state of the database')";
+            $dbh->do($cv_insert);
+
+            insert_version_term($dbh);
+        }
+
+        #check that the version term is available
+        my $version_query = "SELECT cvterm_id FROM cvterm WHERE cv_id in (SELECT cv_id FROM cv WHERE name = 'chado_properties') AND name = 'version'";
+        $sth = $dbh->prepare($version_query);
+        $sth->execute();
+        ($cvterm_id) = $sth->fetchrow_array;
+
+        unless ($cvterm_id) {
+            insert_version_term($dbh); 
+
+            $sth->execute();
+            ($cvterm_id) = $sth->fetchrow_array;
+        }
+
+        my $set_query = "INSERT INTO chadoprop (type_id, value) VALUES (?,?)";
+        $sth = $dbh->prepare($set_query);
+        $sth->execute($cvterm_id,$version) or die "database error: $!";
     }
     else {
         die "$version doesn't look like a valid version number.";
     }
 }
 
+sub insert_version_term {
+    my $dbh = shift;
+
+    $dbh->do("insert into dbxref (db_id,accession) values ((select db_id from db where name='null'), 'chado_properties:version')");
+    $dbh->do("insert into cvterm (name,definition,cv_id,dbxref_id) values ('version','Chado schema version',(select cv_id from cv where name = 'chado_properties'),(select dbxref_id from dbxref where accession='chado_properties:version'));");
+
+}
+
 sub determine_version {
     my $dbh = shift;
 

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