compatible w/ latest mysql

misc_utilities/gff3_file_toString.pl

@@ -24,7 +24,8 @@
     
     foreach my $gene_id (@gene_ids) {
         my $gene_obj_ref = $gene_obj_indexer_href->{$gene_id};
-		
+
+        print "// $asmbl_id, gene: $gene_id\n";
         print $gene_obj_ref->toString();
 
     }

schema/cdna_alignment_mysqlschema

@@ -110,7 +110,7 @@ CREATE TABLE alt_splice_tokens (
 
 CREATE TABLE annotation_admin (
   version_id int(11) NOT NULL auto_increment,
-  date datetime NOT NULL default '0000-00-00 00:00:00',
+  date datetime NOT NULL,
   PRIMARY KEY  (version_id)
 ) ;
 
@@ -120,7 +120,7 @@ CREATE TABLE annotation_admin (
 
 CREATE TABLE annotation_compare (
   compare_id int(11) NOT NULL auto_increment,
-  date datetime NOT NULL default '0000-00-00 00:00:00',
+  date datetime NOT NULL,
   annotation_version int(10) unsigned NOT NULL default '0',
   PRIMARY KEY  (compare_id)
 ) ;

schema/notes

@@ -18,8 +18,6 @@ Using the backticks instead of single quotes in the db name pattern is mandatory
 create user 'pasa_access' identified by 'pasa_access';
 create user 'pasa_write' identified by '...';
 
-grant select on *.* to 'pasa_access@%';
-grant all on *.* to 'pasa_write@%';
+grant select on *.* to 'pasa_access';
+grant all on *.* to 'pasa_write';
 
-grant select on *.* to 'pasa_access'@'localhost' identified by 'pasa_access';
-grant all on *.* to 'pasa_write'@'localhost' identified by '...';

scripts/cDNA_annotation_comparer.dbi

@@ -1444,7 +1444,7 @@ sub get_annotated_gene_models_on_contig {
     my @models;
     
     # get the annotated working models for that chromosome:
-    my $query = "select a.gene_id, min(a.lend), max(a.rend), a.orient from annotation_store a where a.annotdb_asmbl_id = ? and annotation_version = ? group by a.gene_id\n";
+    my $query = "select a.gene_id, min(a.lend), max(a.rend), a.orient from annotation_store a where a.annotdb_asmbl_id = ? and annotation_version = ? group by a.gene_id, a.orient\n";
     my @results = &Mysql_connect::do_sql_2D($dbproc, $query, $asmbl_id, $annot_version);
     
     foreach my $result (@results) {