PT-2140 - Update modules in the main branch (#570)

* PT-2140 - Update modules in the main branch

Updated modules for:
- pt-align
- pt-archiver
- pt-config-diff
- pt-deadlock-logger
- pt-diskstats
- pt-duplicate-key-checker
- pt-fifo-split
- pt-find
- pt-fingerprint
- pt-fk-error-logger
- pt-heartbeat
- pt-index-usage
- pt-ioprofile
- pt-kill
- pt-mext
- pt-mysql-summary
- pt-online-schema-change
- pt-pmp
- pt-query-digest
- pt-show-grants
- pt-sift
- pt-slave-delay
- pt-slave-find
- pt-slave-restart
- pt-summary
- pt-table-sync
- pt-upgrade
- pt-variable-advisor

Added execute bit for pt-query-digest

* PT-2140 Update modules in the main branch

Fixed Daemon.pm plugin usage
Updated all tests, related to the Daemon plugin.
I intentionally did not fix failing tests, not related to Daemon plugin,
to avoid making this PR too big.

- bin/pt-archiver
	- PT-2141 - Fixed usage of Daemon.pm
	- PT-2141 - Updated t/pt-archiver/standard_options.t
- bin/pt-deadlock-logger
	- PT-2143 - Fixed usage of Daemon.pm
	- PT-2143 - Updated t/pt-deadlock-logger/standard_options.t
- bin/pt-fifo-split
	- PT-2144 - Fixed usage of Daemon.pm
	- PT-2144 - Updated t/pt-fifo-split/pt-fifo-split.t
- bin/pt-find
	- PT-2145 - Fixed usage of Daemon.pm
	- PT-2145 - Updated t/pt-find/pt-find.t
- bin/pt-fk-error-logger
	- PT-2146 - Fixed usage of Daemon.pm
	- PT-2146 - Updated t/pt-fk-error-logger/basics.t
- bin/pt-heartbeat
	- PT-2147 - Fixed usage of Daemon.pm
	- PT-2147 - Updated t/pt-heartbeat/standard_options.t, t/pt-heartbeat/basics.t
- bin/pt-kill
	- PT-2148 - Fixed usage of Daemon.pm
	- PT-2148 - Updated t/pt-kill/standard_options.t
- bin/pt-show-grants
	- PT-2152 - Fixed usage of Daemon.pm
	- PT-2152 - Updated t/pt-show-grants/standard_options.t
- bin/pt-slave-delay
	- Fixed usage of Daemon.pm
	- Updated t/pt-slave-delay/standard_options.t
- bin/pt-slave-find
	- PT-2153 - Fixed usage of Daemon.pm
	- PT-2153 -Updated t/pt-slave-find/pt-slave-find.t
- bin/pt-slave-restart
	- Fixed usage of Daemon.pm
	- Updated t/pt-slave-restart/pt-slave-restart.t
- bin/pt-table-sync
	- PT-2154 - Fixed usage of Daemon.pm
	- PT-2154 -Updated t/pt-table-sync/standard_options.t

t/pt-archiver/standard_options.t

@@ -101,7 +101,7 @@ $output = output(
 
 like(
    $output,
-   qr{PID file $pid_file already exists},
+   qr{PID file $pid_file exists},
    'Dies if PID file already exists (issue 391)'
 );
 

t/pt-deadlock-logger/standard_options.t

@@ -67,7 +67,7 @@ $output = output(
 
 like(
    $output,
-   qr{PID file $pid_file already exists},
+   qr{PID file $pid_file exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 
@@ -82,6 +82,8 @@ $sb->load_file('master', 't/pt-deadlock-logger/samples/deadlocks_tbl.sql', 'test
 
 $output = `$trunk/bin/pt-deadlock-logger $dsn --dest D=test,t=deadlocks --daemonize --run-time 10 --interval 1 --pid $pid_file 1>/dev/null 2>/dev/null`;
 
+#REMOVEME
+`echo "test 3" >>/tmp/REMOVEME`;
 PerconaTest::wait_for_files($pid_file);
 
 $output = `ps x | grep 'pt-deadlock-logger $dsn' | grep -v grep`;
@@ -91,6 +93,8 @@ like(
    'It lives daemonized'
 ) or diag($output);
 
+#REMOVEME
+`echo "test 4" >>/tmp/REMOVEME`;
 my ($pid) = $output =~ /(\d+)/;
 
 ok(
@@ -127,7 +131,7 @@ $output = output(
 
 like(
    $output,
-   qr/PID file $pid_file already exists/,
+   qr/PID file $pid_file exists/,
    'Does not run if PID file already exists'
 );
 

t/pt-fifo-split/pt-fifo-split.t

@@ -153,7 +153,7 @@ diag(`touch $pid_file`);
 $output = `$cmd --pid $pid_file 2>&1`;
 like(
    $output,
-   qr{PID file $pid_file already exists},
+   qr{PID file $pid_file exists},
    'Dies if PID file already exists (issue 391)'
 );
 

t/pt-find/pt-find.t

@@ -288,7 +288,7 @@ $dbh->do("DROP DATABASE sakila_test");
 $output = `$cmd mysql --pid /tmp/mk-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-script.pid already exists},
+   qr{PID file /tmp/mk-script.pid exists},
    'Dies if PID file already exists (issue 391)'
 );
 `rm -rf /tmp/mk-script.pid`;

t/pt-fk-error-logger/basics.t

@@ -193,7 +193,7 @@ $output = `$trunk/bin/pt-fk-error-logger h=127.1,P=12345,u=msandbox,p=msandbox -
 
 like(
    $output,
-   qr{PID file $pid_file already exists},
+   qr{PID file $pid_file exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 

t/pt-heartbeat/basics.t

@@ -109,6 +109,7 @@ like($output, qr/$cmd/, 'It is running');
 ok(-f $pid_file, 'PID file created');
 my ($pid) = $output =~ /^\s*(\d+)\s+/;
 $output = `cat $pid_file` if -f $pid_file;
+chomp($output);
 is($output, $pid, 'PID file has correct PID');
 
 $output = `$cmd -D test --monitor --run-time 1s`;

t/pt-heartbeat/standard_options.t

@@ -42,7 +42,7 @@ my $cmd = "$trunk/bin/pt-heartbeat -F $cnf ";
 $output = `$cmd --host 127.1 -u msandbox -p msandbox --port 12345 -D test --check --recurse 1 --pid /tmp/mk-script.pid --create-table --master-server-id 12345 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-script.pid already exists},
+   qr{PID file /tmp/mk-script.pid exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 `rm -rf /tmp/mk-script.pid`;

t/pt-kill/standard_options.t

@@ -64,7 +64,7 @@ diag(`touch /tmp/pt-script.pid`);
 $output = `$cmd --test-matching $trunk/t/lib/samples/pl/recset006.txt --match-state Locked  --print --pid /tmp/pt-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/pt-script.pid already exists},
+   qr{PID file /tmp/pt-script.pid exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 diag(`rm -rf /tmp/pt-script.pid 2>/dev/null`);

t/pt-show-grants/standard_options.t

@@ -23,7 +23,7 @@ my $output;
 $output = `$trunk/bin/pt-show-grants -F /tmp/12345/my.sandbox.cnf --drop --pid /tmp/mk-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-script.pid already exists},
+   qr{PID file /tmp/mk-script.pid exists},
    'Dies if PID file already exists (issue 391)'
 );
 `rm -rf /tmp/mk-script.pid`;

t/pt-slave-delay/standard_options.t

@@ -91,7 +91,7 @@ like(
 $output = `$cmd --run-time 1s --interval 1s --use-master --pid /tmp/mk-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-script.pid already exists},
+   qr{PID file /tmp/mk-script.pid exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 `rm -rf /tmp/mk-script.pid`;

t/pt-slave-find/pt-slave-find.t

@@ -99,7 +99,7 @@ like (
 $output = `$trunk/bin/pt-slave-find -h 127.0.0.1 -P 12345 -u msandbox -p msandbox --pid /tmp/mk-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-script.pid already exists},
+   qr{PID file /tmp/mk-script.pid exists},
    'Dies if PID file already exists (issue 391)'
 );
 `rm -rf /tmp/mk-script.pid`;

t/pt-slave-restart/pt-slave-restart.t

@@ -57,6 +57,7 @@ ok(-f '/tmp/pt-slave-restart.log', 'Log file created');
 
 my ($pid) = $output =~ /^\s*(\d+)\s+/;
 $output = `cat /tmp/pt-slave-restart.pid`;
+chomp($output);
 is($output, $pid, 'PID file has correct PID');
 
 diag(`$trunk/bin/pt-slave-restart --stop -q`);
@@ -107,7 +108,7 @@ unlike(
 $output = `$trunk/bin/pt-slave-restart --max-sleep 0.25 -h 127.0.0.1 -P 12346 -u msandbox -p msandbox --pid /tmp/pt-script.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/pt-script.pid already exists},
+   qr{PID file /tmp/pt-script.pid exists},
    'Dies if PID file already exists (--pid without --daemonize) (issue 391)'
 );
 `rm -rf /tmp/pt-script.pid`;

t/pt-table-sync/standard_options.t

@@ -48,7 +48,7 @@ EOF
 $output = `$trunk/bin/pt-table-sync h=127.1,P=12346,u=msandbox,p=msandbox --sync-to-master --print --no-check-triggers --pid /tmp/mk-table-sync.pid 2>&1`;
 like(
    $output,
-   qr{PID file /tmp/mk-table-sync.pid already exists},
+   qr{PID file /tmp/mk-table-sync.pid exists},
    'Dies if PID file already exists (issue 391)'
 );