Protect generate_graph.pl in table-drawing mode from printing too many rows...

Protect generate_graph.pl in table-drawing mode from printing too many rows (by setting a limit in JSON config)

hive_config.json

@@ -69,7 +69,7 @@
 
         "DisplayStats"          : "barchart",   # show analysis statistics using "barchart", "text" or "" (don't show statistics)
         "DisplayJobs"           : 0,            # if nonzero, represents the max number of jobs to show in each analysis node
-        "DisplayData"           : 0,
+        "DisplayData"           : 0,            # if nonzero, represents the max number of data rows to show in each table node
 
         "DisplayDetails"        : 1,
         "DisplayStretched"      : 0,

modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm

@@ -157,6 +157,8 @@ sub fetch_all {
             # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:
         if($constraint=~/\bJOIN\b/i) {
             $sql = 'SELECT ' . join(', ', map { "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name $constraint";
+        } elsif($constraint=~/^LIMIT|ORDER|GROUP/) {
+            $sql .= ' '.$constraint;
         } else {
             $sql .= ' WHERE '.$constraint;
         }

modules/Bio/EnsEMBL/Hive/Utils/Graph.pm

@@ -452,15 +452,20 @@ sub _add_table_node {
     my ($self, $table_node, $table_name) = @_;
 
     my $node_fontname    = $self->config_get('Node', 'Table', 'Font');
-    my (@column_names, $columns, $table_data);
+    my (@column_names, $columns, $table_data, $data_limit, $hit_limit);
 
-    if( $self->config_get('DisplayData') ) {
+    if( $data_limit = $self->config_get('DisplayData') ) {
         my $adaptor = $self->dba->get_NakedTableAdaptor();
         $adaptor->table_name( $table_name );
 
         @column_names = sort keys %{$adaptor->column_set};
         $columns = scalar(@column_names);
-        $table_data = $adaptor->fetch_all( );
+        $table_data = $adaptor->fetch_all( 'LIMIT '.($data_limit+1) );
+
+        if(scalar(@$table_data)>$data_limit) {
+            pop @$table_data;
+            $hit_limit = 1;
+        }
     }
 
     my $table_label = '<<table border="0" cellborder="0" cellspacing="0" cellpadding="1"><tr><td colspan="'.($columns||1).'">'.$table_name.'</td></tr>';
@@ -471,6 +476,9 @@ sub _add_table_node {
         foreach my $row (@$table_data) {
             $table_label .= '<tr>'.join('', map { qq{<td>$_</td>} } @{$row}{@column_names}).'</tr>';
         }
+        if($hit_limit) {
+            $table_label  .= qq{<tr><td colspan="$columns">[ more data ]</td></tr>};
+        }
     }
     $table_label .= '</table>>';