/ 
Webservice-InterMine-0.9702
River stage one • 1 direct dependent • 1 total dependent
/ Webservice::InterMine

NAME

Webservice::InterMine - modules for interacting with InterMine datawarehouse webservices

SYNOPSIS

  use Webservice::InterMine;

  my $service  = Webservice::InterMine->new_service($url, $user, $pass);
  my $template = $service->template($name);
  my $results  = $template->results_with(valueA => 'x', valueB => 'y');

OR

  use Webservice::InterMine 'flymine', 'some-username', 'some-password';

  my $query    = Webservice::InterMine->new_query;
  $query->add_view(@views);
  $query->add_constraint(
                  path  => $path,
                  op    => $op,
                  value => $value,
                  );
  my $results  = $query->results;

DESCRIPTION

This distribution is the client interface to any implementation of the InterMine Datawarehousing WebService (www.intermine.org). Primarily used for biological genomic databases, the webservice allows the user to easily write and execute structured queries.

This module allows you to interact with one or more webservices by providing a url to an InterMine implementation.

INSTALLATION AND DEPENDENCIES

This package can be installed using the following commands (Module::Build >= 0.36 is required):

perl Build.PL
./Build test
sudo ./Build install

If any runtime dependencies are missing, you can use the following command to install them:

sudo ./Build installdeps

IMPORT STATEMENTS

In the example above the modules are imported with the following statements:

use Webservice::InterMine;

and

  use Webservice::InterMine 'flymine', 'some-username', 'some-password';

Calling use Webservice::InterMine without any parameters simply means you need to either specify the webservice url on every call, or call the methods on a service directly.

If you call use Webservice::InterMine $mine, [$user, $pass], a default service will be set, meaning method calls will not require the webservice url. Unless you are intending to access multiple services, this form is recommended.

METHODS

new_query( [from => \@service_args], [%query_args] )

returns a new query object for you to fill in with constraints before being run to get its results.

Parameters:

  • from => [url, user, pass]

    An array ref of arguments to pass to get_service. This information can be used to specify a different service than the one named on import, or to specify one when none was named on import.

  • %query_args

    Key value pairs of arguments to pass to the query constructor in Webservice::InterMine::Service. This methid serves as sugar for the factory method in that class.

Please see Webservice::InterMine::Query, Webservice::InterMine::Service.

new_list( %list_args, [from => \@service_args] )

Creates a new list with the content specified by the list arguments. The content key-word parameter will always be required. For a full specification of creating lists, see: Webservice::InterMine::Service.

Parameters:

  • from => [url, user, pass]

    An array ref of arguments to pass to get_service. This information can be used to specify a different service than the one named on import, or to specify one when none was named on import.

  • %list_args

    Key value pairs of arguments to pass to the list constructor in Webservice::InterMine::Service. This methid serves as sugar for the factory method in that class.

get_list( $list_name, [from => \@service_args] )

Get the list of the given name from the default service, or the given service if details are supplied.

load_query([\@service_args], source_file|source_string => $source, %opts )

Returns a query object based on xml you have previously saved, either as a string or as a file. For a file pass:

load_query(source_file => $file);

For a string:

load_query(source_string => $string);

If you want a specific service, call it thus:

load_query(from => [$name, $user, $pass], source_string => $string);

OR:

load_query(from => [$name, $user, $pass], source_string => $string);

Please see Webservice::InterMine::Query::Saved

template( $name, [from => \@service_args], [%opts] )

returns the named template (if it exists - if not it returns undef). If you pass a url, it returns the named template from the specified webservice.

Please see Webservice::InterMine::Query::Template

saved_query( $name, [from => \@service_args], %options ) NOT IMPLEMENTED YET

returns the named saved_query (if it exists - if not it returns undef). If you pass a url, it returns the named query from the specified webservice.

This method requires you to have provided a username and password to the webservice for authentication.

Please see Webservice::InterMine::Query::Saved

get_service( $url, $user, $pass )

returns a webservice object, which is used to construct queries and fetch templates and saved queries. If a url is passed, the webservice for that url is returned, otherwise the service for the url given to use is returned.

If a service for a url has been created previously, that one is returned, even if different login details are provided.

Please see: Webservice::InterMine::Service

get_saved_user_info($mine_name/$mine_url)

Returns saved user name and passwords from the webservice config file if it exists. This file should be located at ~/.intermine-webservices.config, and should have the following format:

flymine                        user@somewhere.edu password
metabolicmine                  user@somewhere.edu another-password
http://yeastmine.org/yeastmine user@somewhere.org A v3rj d1EE!kvlt 0n3

ie., whitespace separated fields. The password may contain whitespace characters, but no new-lines. The mine-name/url needs to identical to the name used to request the service.

clean_temp_lists()

Deletes all automatically created anonymous lists. Any renamed lists will be spared the clean-up. This method is called on system exit, unless the variable $Webservice::InterMine::CLEAN_UP is set to a false value.

get_{minename}(user, pass)

An unknown method preceded with 'get_' will be interpreted as a mine name, and an attempt will be made to return a service with that name.

SEE ALSO

AUTHOR

Alex Kalderimis <dev@intermine.org>

BUGS

Please report any bugs or feature requests to dev@intermine.org.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc Webservice::InterMine

You can also look for information at:

COPYRIGHT AND LICENSE

Copyright 2006 - 2011 FlyMine, all rights reserved.

This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.