Provided by: libbio-perl-perl_1.7.8-1_all 
NAME
Bio::AnalysisI - An interface to any (local or remote) analysis tool
SYNOPSIS
This is an interface module - you do not instantiate it. Use "Bio::Tools::Run::Analysis"
module:
use Bio::Tools::Run::Analysis;
my $tool = Bio::Tools::Run::Analysis->new(@args);
DESCRIPTION
This interface contains all public methods for accessing and controlling local and remote
analysis tools. It is meant to be used on the client side.
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::AnalysisI" object you will
get a not implemented error message. You need to call them on a
"Bio::Tools::Run::Analysis" object instead.
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".
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):
<!ELEMENT DsLSRAnalysis (analysis)+>
<!ELEMENT analysis (description?, input*, output*, extension?)>
<!ATTLIST analysis
type CDATA #REQUIRED
name CDATA #IMPLIED
version CDATA #IMPLIED
supplier CDATA #IMPLIED
installation CDATA #IMPLIED>
<!ELEMENT description ANY>
<!ELEMENT extension ANY>
<!ELEMENT input (default?, allowed*, extension?)>
<!ATTLIST input
type CDATA #REQUIRED
name CDATA #REQUIRED
mandatory (true|false) "false">
<!ELEMENT default (#PCDATA)>
<!ELEMENT allowed (#PCDATA)>
<!ELEMENT output (extension?)>
<!ATTLIST output
type CDATA #REQUIRED
name CDATA #REQUIRED>
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",
"Bio::AnalysisI|run", and/or "Bio::AnalysisI|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
("Bio::AnalysisI|run" and "Bio::AnalysisI|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;
Module Bio::AnalysisI::JobI
An interface to the public methods provided by "Bio::Tools::Run::Analysis::Job" objects.
The "Bio::Tools::Run::Analysis::Job" objects represent a created, running, or finished
execution of an analysis tool.
The factory for these objects is module "Bio::Tools::Run::Analysis" where the following
methods return an "Bio::Tools::Run::Analysis::Job" object:
create_job (returning a prepared job)
run (returning a running job)
wait_for (returning a finished job)
id
Usage : $job->id;
Returns : this job ID
Args : none
Each job (an execution) is identifiable by this unique ID which can be used later to re-
create the same job (in other words: to re-connect to the same job). It is useful in cases
when a job takes long time to finish and your client program does not want to wait for it
within the same session.
Bio::AnalysisI::JobI::run
Usage : $job->run
Returns : itself
Args : none
It starts previously created job. The job already must have all input data filled-in.
This differs from the method of the same name of the "Bio::Tools::Run::Analysis" object
where the "Bio::AnalysisI::JobI::run" method creates also a new job allowing to set input
data.
Bio::AnalysisI::JobI::wait_for
Usage : $job->wait_for
Returns : itself
Args : none
It waits until a previously started execution of this job finishes.
terminate
Usage : $job->terminate
Returns : itself
Args : none
Stop the currently running job (represented by this object). This is a definitive stop,
there is no way to resume it later.
last_event
Usage : $job->last_event
Returns : an XML string
Args : none
It returns a short XML document showing what happened last with this job. This is the used
DTD:
<!-- place for extensions -->
<!ENTITY % event_body_template "(state_changed | heartbeat_progress | percent_progress | time_progress | step_progress)">
<!ELEMENT analysis_event (message?, (%event_body_template;)?)>
<!ATTLIST analysis_event
timestamp CDATA #IMPLIED>
<!ELEMENT message (#PCDATA)>
<!ELEMENT state_changed EMPTY>
<!ENTITY % analysis_state "created | running | completed | terminated_by_request | terminated_by_error">
<!ATTLIST state_changed
previous_state (%analysis_state;) "created"
new_state (%analysis_state;) "created">
<!ELEMENT heartbeat_progress EMPTY>
<!ELEMENT percent_progress EMPTY>
<!ATTLIST percent_progress
percentage CDATA #REQUIRED>
<!ELEMENT time_progress EMPTY>
<!ATTLIST time_progress
remaining CDATA #REQUIRED>
<!ELEMENT step_progress EMPTY>
<!ATTLIST step_progress
total_steps CDATA #IMPLIED
steps_completed CDATA #REQUIRED>
Here is an example what is returned after a job was created and started, but before it
finishes (note that the example uses an analysis 'showdb' which does not need any input
data):
use Bio::Tools::Run::Analysis;
print new Bio::Tools::Run::Analysis (-name => 'display.showdb')
->run
->last_event;
It prints:
<?xml version = "1.0"?>
<analysis_event>
<message>Mar 3, 2003 5:14:46 PM (Europe/London)</message>
<state_changed previous_state="created" new_state="running"/>
</analysis_event>
The same example but now after it finishes:
use Bio::Tools::Run::Analysis;
print new Bio::Tools::Run::Analysis (-name => 'display.showdb')
->wait_for
->last_event;
<?xml version = "1.0"?>
<analysis_event>
<message>Mar 3, 2003 5:17:14 PM (Europe/London)</message>
<state_changed previous_state="running" new_state="completed"/>
</analysis_event>
status
Usage : $job->status
Returns : string describing the job status
Args : none
It returns one of the following strings (and perhaps more if a server implementation
extended possible job states):
CREATED
RUNNING
COMPLETED
TERMINATED_BY_REQUEST
TERMINATED_BY_ERROR
created
Usage : $job->created (1)
Returns : time when this job was created
Args : optional
Without any argument it returns a time of creation of this job in seconds, counting from
the beginning of the UNIX epoch (1.1.1970). With a true argument it returns a formatted
time, using rules described in "Bio::Tools::Run::Analysis::Utils::format_time".
started
Usage : $job->started (1)
Returns : time when this job was started
Args : optional
See "created".
ended
Usage : $job->ended (1)
Returns : time when this job was terminated
Args : optional
See "created".
elapsed
Usage : $job->elapsed
Returns : elapsed time of the execution of the given job
(in milliseconds), or 0 of job was not yet started
Args : none
Note that some server implementations cannot count in millisecond - so the returned time
may be rounded to seconds.
times
Usage : $job->times ('formatted')
Returns : a hash reference with all time characteristics
Args : optional
It is a convenient method returning a hash reference with the following keys:
created
started
ended
elapsed
See "create" for remarks on time formatting.
An example - both for unformatted and formatted times:
use Data::Dumper;
use Bio::Tools::Run::Analysis;
my $rh = Bio::Tools::Run::Analysis->new(-name => 'nucleic_cpg_islands.cpgplot')
->wait_for ( { 'sequence_usa' => 'embl:hsu52852' } )
->times (1);
print Data::Dumper->Dump ( [$rh], ['Times']);
$rh = Bio::Tools::Run::Analysis->new(-name => 'nucleic_cpg_islands.cpgplot')
->wait_for ( { 'sequence_usa' => 'embl:AL499624' } )
->times;
print Data::Dumper->Dump ( [$rh], ['Times']);
$Times = {
'ended' => 'Mon Mar 3 17:52:06 2003',
'started' => 'Mon Mar 3 17:52:05 2003',
'elapsed' => '1000',
'created' => 'Mon Mar 3 17:52:05 2003'
};
$Times = {
'ended' => '1046713961',
'started' => '1046713926',
'elapsed' => '35000',
'created' => '1046713926'
};
results
Usage : $job->results (...)
Returns : one or more results created by this job
Args : various, see belou
This is a complex method trying to make sense for all kinds of results. Especially it
tries to help to put binary results (such as images) into local files. Generally it deals
with fhe following facts:
• Each analysis tool may produce more results.
• Some results may contain binary data not suitable for printing into a terminal window.
• Some results may be split into variable number of parts (this is mainly true for the
image results that can consist of more *.png files).
Note also that results have names to distinguish if there are more of them. The names can
be obtained by method "result_spec".
Here are the rules how the method works:
Retrieving NAMED results:
-------------------------
results ('name1', ...) => return results as they are, no storing into files
results ( { 'name1' => 'filename', ... } ) => store into 'filename', return 'filename'
results ( 'name1=filename', ...) => ditto
results ( { 'name1' => '-', ... } ) => send result to the STDOUT, do not return anything
results ( 'name1=-', ...) => ditto
results ( { 'name1' => '@', ... } ) => store into file whose name is invented by
this method, perhaps using RESULT_NAME_TEMPLATE env
results ( 'name1=@', ...) => ditto
results ( { 'name1' => '?', ... } ) => find of what type is this result and then use
{'name1'=>'@' for binary files, and a regular
return for non-binary files
results ( 'name=?', ...) => ditto
Retrieving ALL results:
-----------------------
results() => return all results as they are, no storing into files
results ('@') => return all results, as if each of them given
as {'name' => '@'} (see above)
results ('?') => return all results, as if each of them given
as {'name' => '?'} (see above)
Misc:
-----
* any result can be returned as a scalar value, or as an array reference
(the latter is used for results consisting of more parts, such images);
this applies regardless whether the returned result is the result itself
or a filename created for the result
* look in the documentation of the C<panalysis[.PLS]> script for examples
(especially how to use various templates for inventing file names)
result
Usage : $job->result (...)
Returns : the first result
Args : see 'results'
remove
Usage : $job->remove
Returns : 1
Args : none
The job object is not actually removed in this time but it is marked (setting 1 to
"_destroy_on_exit" attribute) as ready for deletion when the client program ends
(including a request to server to forget the job mirror object on the server side).