Article:		Relational Modeling of Biological Data: Trees and Graphs
Subject:		fetch() without execute() error in Example 1
Date:		2003-06-14 16:24:32
From:		gee
I've been looking most of the day for a script like the one in Example 1 (converting adjacency list to nested set) to fix a mysql table that I fubared this morning. Fortunately, I had the foresight to track parent id's as well as record left and right id's thinking I might need to repair a mistake sometime. Unfortunately, I can't get the script in Example 1 to run correctly. The error I get is: DBD::mysql::st fetchrow_array failed: fetch() without execute() at ./fixnest line 33. I have determined error occurs once the script begins to process a leaf node -- one that does not have any children. After that, I confess I am stumped, this being my first exposure to the DBI module. Has anyone else encountered this problem? If so, is there a workaround to suggest? At the very least, is there a confirmed case of the script above working (perhaps there is a line left out in the published version)? Thanks in advance for any help -- feel free to write direct to geestarr at the domain geedev dot com. I'll summarize any solutions here.

Showing messages 1 through 3 of 3.

• fetch() without execute() error in Example 1
  2003-06-15 11:49:37  anonymous2 [View]
  
  
  Aaron generously offered a solution via email:
  
  In the script, replace the following line:
  
  while(my ($id) = $children->fetchrow_array) {
  
  With this:
  
  for my $row (@{$children->fetchall_arrayref}) {
  my ($id) = @$row;
  
  Thanks, Aaron!
  
• fetch() without execute() error in Example 1
  2004-01-11 11:31:44  anonymous2 [View]
  
  
  It took several days(more than a week) on a pentium-4 freebsd machine to run this code for entire ncbi taxonomy. Is there anything I should check with my MySql or table structure? I have indexed the taxon_id and the parent_id.
• fetch() without execute() error in Example 1
  2006-02-06 10:55:01  Aaron Mackey | [View]
  
  
  The $children statement needs an additional clause, as follows:
  
  
my $children = $dbh->prepare("SELECT id
FROM taxon
WHERE parent_id = ?
AND id <> parent_id");