PT-225 pt-table-cheksum ignores generated columns

Changelog

@@ -1,5 +1,9 @@
 Changelog for Percona Toolkit
 
+v3.0.6
+
+ * Fixed bug     PT-225: pt-table-checksum ignores generated cols
+
 v3.0.5 released 2017-11-20
 
  * Improvement PMM-1590: Improve MongoDB Profiler for PMM and PT

bin/pt-table-checksum

@@ -10705,7 +10705,7 @@ sub main {
             # TODO: this now happens in 3 places, search for 'columns'.
             my $tbl_struct = $tbl->{tbl_struct};
             my $ignore_col = $o->get('ignore-columns') || {};
-            my $all_cols   = $o->get('columns')        || $tbl_struct->{cols};
+            my $all_cols   = $o->get('columns')        || $tbl_struct->{non_generated_cols};
             my @cols       = map  { lc $_ }
                              grep { !$ignore_col->{$_} }
                              @$all_cols;

t/pt-table-checksum/pt-225.t

@@ -0,0 +1,75 @@
+#!/usr/bin/env perl
+
+BEGIN {
+   die "The PERCONA_TOOLKIT_BRANCH environment variable is not set.\n"
+      unless $ENV{PERCONA_TOOLKIT_BRANCH} && -d $ENV{PERCONA_TOOLKIT_BRANCH};
+   unshift @INC, "$ENV{PERCONA_TOOLKIT_BRANCH}/lib";
+};
+
+use strict;
+use warnings FATAL => 'all';
+use English qw(-no_match_vars);
+use Test::More;
+
+use PerconaTest;
+use Sandbox;
+use SqlModes;
+require "$trunk/bin/pt-table-checksum";
+
+my $dp  = new DSNParser(opts=>$dsn_opts);
+my $sb  = new Sandbox(basedir => '/tmp', DSNParser => $dp);
+my $dbh = $sb->get_dbh_for('master');
+
+if ( !$dbh ) {
+   plan skip_all => 'Cannot connect to sandbox master';
+}
+else {
+   plan tests => 3;
+}
+
+diag("loading samples");
+
+$sb->load_file('master', 't/pt-table-checksum/samples/pt-225.sql');
+
+# The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
+# so we need to specify --set-vars innodb_lock_wait_timeout=3 else the tool will die.
+# And --max-load "" prevents waiting for status variables.
+my $master_dsn = $sb->dsn_for('master');
+diag("setting up the slaves");
+my $slave_dbh = $sb->get_dbh_for('slave1');
+# Create differences
+
+$slave_dbh->do('DELETE FROM `test`.`sbtest1` WHERE id > 15');
+$slave_dbh->do('FLUSH TABLES');
+
+my @args       = ($master_dsn, "--set-vars", "innodb_lock_wait_timeout=50", 
+                               "--ignore-databases", "mysql,sys,sakila,percona_test",
+                               "--nocheck-replication-filters"); 
+my $output;
+my $exit_status;
+
+# Test #1 
+$output = output(
+   sub { $exit_status = pt_table_checksum::main(@args) },
+   stderr => 1,
+);
+
+isnt(
+   $exit_status,
+   0,
+   "PT-225 virtual/generated columns are ignored - exit status",
+);
+
+like(
+    $output,
+    qr/1\s+\d+\s+\d+\s+\d+\s+.*test.sbtest1/,
+    "PT-225 virtual/generated columns were ignored",
+);
+
+
+# #############################################################################
+# Done.
+# #############################################################################
+$sb->wipe_clean($dbh);
+ok($sb->ok(), "Sandbox servers") or BAIL_OUT(__FILE__ . " broke the sandbox");
+exit;

t/pt-table-checksum/samples/pt-225.sql

@@ -0,0 +1,42 @@
+DROP DATABASE IF EXISTS test;
+CREATE DATABASE test;
+
+USE test;
+
+CREATE TABLE `sbtest1` (
+  `id` int(11) NOT NULL AUTO_INCREMENT,
+  `k` int(11) NOT NULL DEFAULT '0',
+  `c` char(120) NOT NULL DEFAULT '',
+  `pad` char(60) NOT NULL DEFAULT '',
+  `json_test_v` json GENERATED ALWAYS AS (json_array(`k`,`c`,`pad`)) VIRTUAL,
+  `json_test_s` json GENERATED ALWAYS AS (json_array(`k`,`c`,`pad`)) STORED,
+  `json_test_index` varchar(255) GENERATED ALWAYS AS (json_array(`k`,`c`,`pad`)) STORED,
+  PRIMARY KEY (`id`),
+  KEY `k_1` (`k`),
+  KEY `json_test_index` (`json_test_index`)
+) ENGINE=InnoDB AUTO_INCREMENT=1001 DEFAULT CHARSET=latin1 COMPRESSION='lz4';
+
+
+/*!40000 ALTER TABLE `sbtest1` DISABLE KEYS */;
+INSERT INTO `sbtest1` (`id`, `k`, `c`, `pad`) VALUES 
+(01,583532949,'at non eaque sint velit enim facilis quisquam nam quaerat.','impedit quae hic possimus ullam est eos totam qui.'),
+(02,583532949,'eos exercitationem quisquam saepe totam dolore consequatur.','sit commodi consequatur neque qui.'),
+(03,1342458479,'et quia sunt eum eveniet non eum nobis quia est mollitia.','corrupti minima et quibusdam.'),
+(04,280366509,'ab minima laudantium!','est sed autem quia nobis suscipit pariatur modi!'),
+(05,1801160058,'perspiciatis tenetur minima accusantium consequatur in et.','rerum quo molestiae voluptates harum aspernatur sunt.'),
+(06,914091476,'quas aut nostrum a.','harum tempora adipisci et et.'),
+(07,1022430181,'qui voluptates inventore voluptatem voluptas numquam blanditiis corporis illum doloremque aut!','dicta neque laboriosam voluptatibus.'),
+(08,165910161,'voluptas molestiae harum quis quod.','voluptatem deleniti dolor blanditiis est earum.'),
+(09,1255569388,'consequuntur nihil non veniam et possimus sunt.','est est possimus recusandae ab.'),
+(10,1375471152,'doloribus quasi quasi eum hic et laborum autem laudantium saepe veritatis.','enim earum et placeat animi ut.'),
+(11,1705409249,'eveniet recusandae expedita est consectetur ut laudantium temporibus.','et asperiores porro id sunt totam maiores eum quidem.'),
+(12,2003588754,'debitis molestias voluptatibus quia.','sint est voluptatem nihil et.'),
+(13,1714682759,'voluptas officiis culpa quaerat sit quis.','vitae omnis repellat rerum consectetur ex.'),
+(14,1898674299,'et est quibusdam!','aut est labore.'),
+(15,1698116023,'similique nisi quisquam pariatur minus repudiandae ducimus.','eveniet rem nihil voluptatibus voluptatem non.'),
+(16,1310715836,'expedita ipsum aut veniam!','incidunt at officia nisi.'),
+(17,472875023,'numquam et quaerat voluptatibus.','commodi natus consequatur reiciendis adipisci ut.'),
+(18,1153628287,'aut quam quia vel molestiae qui.','eos voluptas quod doloremque!'),
+(19,525456967,'dignissimos quibusdam aut et.','laborum reprehenderit eius consequatur qui.'),
+(20,1396416465,'aperiam sint et.','fugiat neque impedit cumque soluta.'),
+(21,1640670520,'nisi repellendus et velit ab.','incidunt quo eligendi.');