UserSpecies changes rever.

modules/Bio/Otter/Server/UserSpecies.pm

@@ -31,25 +31,25 @@ sub species_group{
 
  # Connect to MySQL database
  my $dbh = DBI->connect($dsn, $username, $password, \%attr);
-
+ 
  # Set up hash of species for each user
  my %final_species_groups = query_links($dbh);
-
+ 
  # Setting up 'dev','main', 'restricted' and 'mouse_strain' species groups
  $final_species_groups{'species_groups'}{'dev'} = [ 'human_test'];
- $final_species_groups{'species_groups'}{'main'} = ['c_elegans', 'cat', 'chicken', 'chimp', 'cow', 'dog', 'drosophila', 'gibbon', 'gorilla', 'human', 'lemur', 'marmoset', 'medicago', 'mouse', 'mus_spretus', 'opossum', 'pig', 'platypus', 'rat', 'sheep', 'sordaria', 'tas_devil', 'tomato', 'tropicalis', 'wallaby', 'wheat', 'zebrafish'];
+ $final_species_groups{'species_groups'}{'main'} = ['c_elegans', 'cat', 'chicken', 'chimp', 'cow', 'dog', 'drosophila', 'gibbon', 'gorilla', 'human', 'lemur', 'marmoset', 'medicago', 'mouse', 'mus_spretus', 'opossum', 'pig', 'platypus', 'rat', 'sheep', 'sordaria', 'tas_devil', 'tomato', 'tropicalis', 'wallaby', 'wheat', 'zebrafish']; 
  $final_species_groups{'species_groups'}{'mouse_strains'} = ['mouse-SPRET-EiJ', 'mouse-PWK-PhJ', 'mouse-CAST-EiJ', 'mouse-WSB-EiJ', 'mouse-NZO-HlLtJ', 'mouse-C57BL-6NJ', 'mouse-NOD-ShiLtJ', 'mouse-FVB-NJ', 'mouse-DBA-2J', 'mouse-CBA-J', 'mouse-C3H-HeJ', 'mouse-AKR-J', 'mouse-BALB-cJ', 'mouse-A-J', 'mouse-LP-J', 'mouse-129S1-SvImJ', 'mouse-C57BL-6NJ_v1_test'];
  $final_species_groups{'species_groups'}{'restricted'} =['human_test','mouse_test'];
-
+ 
  # Disconnect from the MySQL database
  $dbh->disconnect();
  return \%final_species_groups;
 }
 
-sub query_links{
+sub query_links{ 
  my ($dbh) = @_;
  my %data_group;
-
+ 
   # Query the database
   my $sql_user_group = "SELECT username, species_write, species_read FROM otter_species_access";
   my $sth_user_group = $dbh->prepare($sql_user_group)
@@ -62,32 +62,32 @@ sub query_links{
         # Setting up read and write species for each user
         my $username = $array_ref->[0];
         $data_group{'user_groups'}{$username.'.data'}{'users'} = $username;
-
-        my $species_write_string = $array_ref->[1];
+ 
+        my $species_write_string = $array_ref->[1];  
         if ($species_write_string){
             @species_write_array = split ',', $species_write_string;
         }
         else{
             @species_write_array = ();
-        }
-        $data_group{'user_groups'}{$username.'.data'}{'write'} = [@species_write_array];
+        }        
+        $data_group{'user_groups'}{$username.'.data'}{'write'} = [@species_write_array]; 
 
-        my $species_read_string = $array_ref->[2];
+        my $species_read_string = $array_ref->[2]; 
         if ($species_read_string){
-             @species_read_array = split ',', $species_read_string;
+             @species_read_array = split ',', $species_read_string; 
         }
         else{
-            @species_read_array = ();
-        }
+            @species_read_array = (); 
+        } 
 #        $data_group{'user_groups'}{$username.'.data'}{'read'} = [@species_read_array]; #Uncomment this line when READONLY datasets are available
   }
   die "Error in fetchrow_array(): ", $sth_user_group->errstr(), "\n"
         if $sth_user_group->err();
 
-  $sth_user_group->finish();
-
-  return %data_group;
+  $sth_user_group->finish();            
 
+  return %data_group;      
+  
 }
 
 1;