Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail Class Reference

Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail:

Public Member Functions
public	param_defaults ()
public	fetch_input ()
public	run ()
public	write_output ()
public	format_table ()
Public Member Functions inherited from Bio::EnsEMBL::Hive::Process
public	new ()
public	life_cycle ()
public	say_with_header ()
public	enter_status ()
public	warning ()
public	param_defaults ()
public	fetch_input ()
public	run ()
public	write_output ()
public Bio::EnsEMBL::Hive::Worker	worker ()
public	execute_writes ()
public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor	db ()
public Bio::EnsEMBL::Hive::DBSQL::DBConnection	dbc ()
public Bio::EnsEMBL::Hive::DBSQL::DBConnection	data_dbc ()
public Returns	run_system_command ()
public Bio::EnsEMBL::Hive::AnalysisJob	input_job ()
public	input_id ()
public	param ()
public	param_required ()
public	param_exists ()
public	param_is_defined ()
public	param_substitute ()
public	dataflow_output_id ()
public	dataflow_output_ids_from_json ()
public	throw ()
public This	complete_early ()
public Int	debug ()
public	worker_temp_directory ()
public	cleanup_worker_temp_directory ()

Detailed Description

Synopsis

This is a RunnableDB module that implements Bio::EnsEMBL::Hive::Process interface
and is ran by Workers during the execution of eHive pipelines.
It is not generally supposed to be instantiated and used outside of this framework.
 
Please refer to Bio::EnsEMBL::Hive::Process documentation to understand the basics of the RunnableDB interface.
 
Please refer to Bio::EnsEMBL::Hive::PipeConfig::* pipeline configuration files to understand how to configure pipelines.

Description

This RunnableDB module will send you a short notification email message per
each job.  You can either dataflow into it, or simply create standalone
jobs.

The main body of the email is expected in the "text" parameter. If the
"is_html" parameter is set, the body is expected to be in HTML.

Attachments such as diagrams, images, PDFs have to be listed in the
'attachments' parameter.

format_table provides a simple method to stringify a table of data. If
you need more options to control the separators, the alignment, etc, have a
look at the very comprehensive Text::Table.

Note: this module uses Email::Sender to send the email, which by default
uses sendmail but has other backends configured. As such, it depends
heavily on the implementation of your compute farm. Please make sure it
works as intended before using this module in complex pipelines.

Definition at line 40 of file NotifyByEmail.pm.

Member Function Documentation

fetch_input()

public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::fetch_input

(

)

    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
                  Here we have nothing to do.

Code:

format_table()

public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::format_table

(

)

The same type of table could be generated with Text::Table:

  my $first_column_name = shift $columns;
  my $tb = Text::Table->new(\'| ', $first_column_name, (map { +(\' | ', $_) } $columns), \' |',);
  $tb->load($results);
  my $rule = $tb->rule('-', '+');
  return $title . "\n" . $rule . $tb->title() . $rule .  $tb->body() . $rule;

Code:

param_defaults()

public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::param_defaults

(

)

Undocumented method

Code:

run()

public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::run

(

)

    Description : Implements run() interface method of Bio::EnsEMBL::Hive::Process that is used to perform the main bulk of the job (minus input and output).
                  Here the actual sending of the email message happens in run() though one may argue it is technically 'output'.

    param('email'):   The email address to send the message to.

    param('subject'): The (optional) 'Subject:' line.

    param('text'):    Text of the email message. It will undergo parameter substitution.

    param('is_html'): Boolean. Whether the content of 'text' is in HTML

    param('attachments'): Array of paths for files to attach.

    param('*'):       Any other parameters can be freely used for parameter substitution.

Code:

write_output()

public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::write_output

(

)

    Description : Implements write_output() interface method of Bio::EnsEMBL::Hive::Process that is used to deal with job's output after the execution.
                  Here we have nothing to do.

Code:

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The documentation for this class was generated from the following file:

• modules/Bio/EnsEMBL/Hive/RunnableDB/NotifyByEmail.pm