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Showing content from http://www.ensembl.org/info/docs/webcode/dev/debugging.html below:

Debugging and profiling

In your plugins you can set the value of the EnsEMBL debug flags so that you can control what messages appear in the error logs.

  ## Turn on Perl profiling output.
  $SiteDefs::ENSEMBL_DEBUG_FLAGS |= $SiteDefs::ENSEMBL_PERL_PROFILER;
  ## Turn off Long process warnings
  $SiteDefs::ENSEMBL_DEBUG_FLAGS &= ~$SiteDefs::ENSEMBL_DEBUG_LONG_PROCESS;

A full list of flags are:

$SiteDefs::ENSEMBL_DEBUG_JAVASCRIPT_DEBUG

Include a Debug div in the webpage in which errors warnings and timings are logged.

$SiteDefs::ENSEMBL_DEBUG_MAGIC_MESSAGES

EnsEMBL::Web::Magic module displays a textual description of each request if this flag is set.

$SiteDefs::ENSEMBL_DEBUG_REFERER

For debugging AJAX etc - print out the parsed web-request

$SiteDefs::ENSEMBL_DEBUG_TREE_DUMPS

Textual dump of the image configuration trees.

$SiteDefs::ENSEMBL_DEBUG_TIMESTAMPED_LOGS

If set log files are stamped with the time the server is started.

$SiteDefs::ENSEMBL_DEBUG_PERL_PROFILER

At various points in the code there are in built profiling statements - set this flag to dump them to the logs at the end of the request.

$SiteDefs::ENSEMBL_DEBUG_LONG_PROCESS

Display information about requests that last more than a certain number of seconds.

$SiteDefs::ENSEMBL_DEBUG_HANDLER_ERRORS

Include some detailed error messages while the server is routing the request.

$SiteDefs::ENSEMBL_DEBUG_SD_AUTOLOADER

Various shouts in the EnsEMBL::Web::SpeciesDefs AUTOLOAD function.

$SiteDefs::ENSEMBL_DEBUG_DRAWING_CODE

Informational messages from the drawing code.

$SiteDefs::ENSEMBL_DEBUG_GENERAL_ERRORS

Show some general error messages

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