AnalysisI documentation.

 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.
Here is an example output:

  Analysis 'edit.seqret':
        installation => EMBL-EBI
        description => Reads and writes (returns) sequences
        supplier => EMBOSS
        version => 2.6.0
        type => edit
        name => seqret

describe

 Usage   : $tool->analysis_spec;
 Returns : an XML detailed description of this analysis
 Args    : none

The returned XML string contains metadata describing this analysis
service. It includes also metadata returned (and easier used) by
method analysis_spec, input_spec and result_spec.
The DTD used for returned metadata is based on the adopted standard
(BSA specification for analysis engine):

But the DTD may be extended by provider-specific metadata. For
example, the EBI experimental SOAP-based service on top of EMBOSS uses
DTD explained at http://www.ebi.ac.uk/~senger/applab.

input_spec

 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 service with the input data (the
inputs are given to methods create_job, run, and/or wait_for
as name/value pairs).
Here is a (slightly shortened) example of an input specification:

 $input_spec = [
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'sequence_usa'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'sequence_direct_data'
          },
          {
            'mandatory' => 'false',
            'allowed_values' => [
                                  'gcg',
                                  'gcg8',
                                  ...
                                  'raw'
                                ],
            'type' => 'String',
            'name' => 'sformat'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'sbegin'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'send'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'sprotein'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'snucleotide'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'sreverse'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'slower'
          },
          {
            'mandatory' => 'false',
            'type' => 'String',
            'name' => 'supper'
          },
          {
            'mandatory' => 'false',
            'default' => 'false',
            'type' => 'String',
            'name' => 'firstonly'
          },
          {
            'mandatory' => 'false',
            'default' => 'fasta',
            'allowed_values' => [
                                  'gcg',
                                  'gcg8',
                                  'embl',
                                  ...
                                  'raw'
                                ],
            'type' => 'String',
            'name' => 'osformat'
          }
        ];

result_spec

 Usage   : $tool->result_spec;
 Returns : a hash reference with result names as keys
           and result types as values
 Args    : none

The analysis results are named and can be retrieved using their names
by methods results and result.
Here is an example of the result specification (again for the service
edit.seqret):

  $result_spec = {
          'outseq' => 'String',
          'report' => 'String',
          'detailed_status' => 'String'
        };

create_job

 Usage   : $tool->create_job ( {'sequence'=>'tatat'} )
 Returns : Bio::Tools::Run::Analysis::Job
 Args    : data and parameters for this execution
           (in various formats)

Create an object representing a single execution of this analysis
tool.
Call this method if you wish to "stage the scene" - to create a job
with all input data but without actually running it. This method is
called automatically from other methods (run and wait_for) so
usually you do not need to call it directly.
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.

scalar

In this case, the parameter represents a job ID obtained in some
previous invocation - such job already exists on the server side, and
we are just re-creating it here using the same job ID.
TBD: here we should allow the same by using a reference to the
Bio::Tools::Run::Analysis::Job object.

undef

Finally, if the parameter is undefined, ask server to create an empty
job. The input data may be added later using set_data...
method(s) - see scripts/papplmaker.PLS for details.

run

 Usage   : $tool->run ( ['sequence=@my.seq', 'osformat=embl'] )
 Returns : Bio::Tools::Run::Analysis::Job,
           representing started job (an execution)
 Args    : the same as for create_job

Create a job and start it, but do not wait for its completion.

wait_for

 Usage   : $tool->wait_for ( { 'sequence' => '@my,file' } )
 Returns : Bio::Tools::Run::Analysis::Job,
           representing finished job
 Args    : the same as for create_job

Create a job, start it and wait for its completion.
Note that this is a blocking method. It returns only after the
executed job finishes, either normally or by an error.
Usually, after this call, you ask for results of the finished job:

    $analysis->wait_for (...)->results;

Methods code

BEGIN

BEGIN {

    $Revision = q[AnalysisI.pm,v 1.7.2.1 2005/10/09 15:16:18 jason Exp];

}

analysis_name

sub analysis_name {

 shift->throw_not_implemented();

}

analysis_spec

sub analysis_spec {

 shift->throw_not_implemented();

}

describe

sub describe {

 shift->throw_not_implemented();

}

input_spec

sub input_spec {

 shift->throw_not_implemented();

}

result_spec

sub result_spec {

 shift->throw_not_implemented();

}

create_job

sub create_job {

 shift->throw_not_implemented();

}

run

sub run {

 shift->throw_not_implemented();

}

wait_for

sub wait_for {

 shift->throw_not_implemented();

}

General documentation

FEEDBACK

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Report bugs to the Bioperl bug tracking system to help us keep track
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web:

  http://bugzilla.bioperl.org/

AUTHOR

Martin Senger (martin.senger@gmail.com)

DISCLAIMER