NAME¶
Bio::SimpleAnalysisI - A simple interface to any (local or remote) analysis tool
SYNOPSIS¶
This is an interface module - you do not instantiate it. Use other modules
instead (those that implement this interface).
DESCRIPTION¶
This interface contains public methods for accessing and controlling local and
remote analysis tools. It is meant to be used on the client side. The
interface consists only of a necessary set of methods for synchronous
invocation of analysis tools. For more complex set, including an asynchronous
access, see interface "Bio::AnalysisI" (which inherits from this
one, by the way).
FEEDBACK¶
Mailing Lists¶
User feedback is an integral part of the evolution of this and other Bioperl
modules. Send your comments and suggestions preferably to the Bioperl mailing
list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support¶
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive
experts will be able look at the problem and quickly address it. Please
include a thorough description of the problem with code and data examples if
at all possible.
Reporting Bugs¶
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs
and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR¶
Martin Senger (martin.senger@gmail.com)
COPYRIGHT¶
Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.
This module is free software; you can redistribute it and/or modify it under the
same terms as Perl itself.
DISCLAIMER¶
This software is provided "as is" without warranty of any kind.
SEE ALSO¶
- •
- http://www.ebi.ac.uk/Tools/webservices/soaplab/guide
APPENDIX¶
This is actually the main documentation...
If you try to call any of these methods directly on this
"Bio::SimpleAnalysisI" object you will get a
not implemented
error message.
analysis_name¶
Usage : $tool->analysis_name;
Returns : a name of this analysis
Args : none
analysis_spec¶
Usage : $tool->analysis_spec;
Returns : a hash reference describing this analysis
Args : none
The returned hash reference uses the following keys (not all of them always
present, perhaps others present as well): "name", "type",
"version", "supplier", "installation",
"description".
Usage : $tool->input_spec;
Returns : an array reference with hashes as elements
Args : none
The analysis input data are named, and can be also associated with a default
value, with allowed values and with few other attributes. The names are
important for feeding the analysis with the input data (the inputs are given
to methods "run" and "wait_for" as name/value pairs).
result_spec¶
Usage : $tool->result_spec;
Returns : a hash reference with result names as keys
and result types as values
Args : none
An analysis can produce several results, or the same result in several different
formats. All such results are named and can be retrieved using their names by
metod "result".
Here is an example of the result specification:
$result_spec = {
'outseq' => 'String',
'report' => 'String',
'detailed_status' => 'String'
};
run¶
Usage : $tool->run ( ['sequence=@my.seq', 'osformat=embl'] )
Returns : $self
Args : data and parameters for this execution
(in various formats)
Create a job, start it, and wait for its completion. The method is identical to
the method "wait_for". Why there are two methods doing the same?
Because it is expected that the sub-classes may implement them differently (an
example is an interface "Bio::AnalysisI" which uses method
"run" for an asynchronous execution and method "wait_for"
for a synchronous one.
Usually, after this call, you ask for results of the finished job:
$analysis->run (...)->result;
The input data and prameters for this execution can be specified in various
ways:
- array reference
- The array has scalar elements of the form
name = [[@]value]
where "name" is the name of an input data or input parameter (see
method "input_spec" for finding what names are recognized by
this analysis) and "value" is a value for this data/parameter.
If "value" is missing a 1 is assumed (which is convenient for
the boolean options). If "value" starts with "@" it is
treated as a local filename, and its contents is used as the
data/parameter value.
- hash reference
- The same as with the array reference but now there is no need to use an
equal sign. The hash keys are input names and hash values their data. The
values can again start with a "@" sign indicating a local
filename.
wait_for¶
Usage : $tool->wait_for ( { 'sequence' => '@my,file' } )
Returns : $self
Args : the same as for method 'run'
Create a job, start it and wait for its completion. The method is identical to
the method "run". See details in the "run" method.
status¶
Usage : $tool->status
Returns : string describing a status of the execution
Args : none
It returns one of the following strings (and perhaps more if a server
implementation extended possible job states):
CREATED (not run yet)
COMPLETED (run and finished normally)
TERMINATED_BY_ERROR (run and finished with an error or a signal)
result¶
Usage : $job->result (...)
Returns : a result created by running an analysis
Args : none (but an implementation may choose
to add arguments for instructions how to process
the raw result)
The method returns a scalar representing a result of an executed job. If the job
was terminated by an error the result may contain an error message instead of
the real data (or both, depending on the implementation).