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Webservice-InterMine-0.9815
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/ Webservice::InterMine::Query::Roles::Runnable

NAME

Webservice::InterMine::Query::Roles::Runnable - Composable behaviour for runnable queries

DESCRIPTION

This module provides composable behaviour for running a query against a webservice and getting the results.

METHODS

results_iterator

Returns a results iterator for use with a query.

The following options are available:

  • as => $format

    Possible values: (string|tsv|csv|arrayrefs|hashrefs|jsonobjects|jsonrows|count)

    The format to request results in. The default is arrayrefs

  • size => $size

    The number of results to return. Leave undefined for "all" (default).

  • start => $start

    The first result to return (starting at 0). The default is 0.

  • columnheaders => 0/1/friendly/path

    Whether to return the column headers at the top of TSV/CSV results. The default is false. There are two styles - friendly: "Gene > pathways > name" and path: "Gene.pathways.name". The default style is friendly if a true value is entered and it is not "path".

  • json => $json_processor

    Possible values: (inflate|instantiate|raw|perl)

    What to do with JSON results. The results can be returned as inflated objects, full instantiated Moose objects, a raw json string, or as a perl data structure. (default is perl).

  • summaryPath => $path

    The path of the query to summarise (see summarise).

    If a value for this is supplied, then (as => 'jsonrows') is implied. Also, unlike the " summarise " method, this option will return a list of item/count pairs, as below:

    [
  { item => "the-best", count => 100 },
  { item => "the-runner-up", count => 99 },
  { item => "the-wooden-spoon", count => 98 },
]

    This is best when you care more about the top of the summary list, or which value is at the top than what the value of particular item is. If you are using this method with a big result set it is best to use size as well.

summarise($path, <%opts>) / summarize($path, <%opts>)

Get a column summary for a path in the query. For numerical values this returns a hash reference with four keys: average , stdev , min , and max . These may be accessed as so:

my $average = $query->summarise("length")->{average};

For non-numerical paths, the summary provides a hash from item => count, so the number of occurrences of an item may be accessed as so:

my $no_on_chr2 = $query->summarise("chromosome.primaryIdentifier")->{2};

Obviously you can sort the hash yourself, but if you want this information in order, or just a particular subset (the top 100 perhaps), then you should use results() instead.

Any further options will be passed along to the result-iterator as is, although the one that makes the most sense is size, when you don't want all the results from a very large result set.

results( %options )

returns the results from a query in the result format specified.

The following options are available:

  • as => $format

    Possible values: (tsv|csv|arrayrefs|hashrefs|jsonobjects|jsonrows|count)

    The format to request results in. The default is arrayrefs

  • size => $size

    The number of results to return. Leave undefined for "all" (default).

  • start => $start

    The first result to return (starting at 0). The default is 0.

  • addheaders => 0/1/friendly/path

    Whether to return the column headers at the top of TSV/CSV results. The default is false. There are two styles - friendly: "Gene > pathways > name" and path: "Gene.pathways.name". The default style is friendly if a true value is entered and it is not "path".

  • json => $json_processor

    Possible values: (inflate|instantiate|perl)

    What to do with JSON results. The results can be returned as inflated objects, full instantiated Moose objects, a raw json string, or as a perl data structure. (default is perl).

all(%options)

Return all rows of results. This method takes the same options as results, but any start and size arguments given are ignored. Note that the server code limits result-sets to 10,000,000 rows in size, no matter what.

first(%options)

Return the first result (row or object). This method takes the same options as results, but any size arguments given are ignored. May return undef if there are no results.

one(%options)

Return one result (row or result object), throwing an error if more than one is received.

get_count

A convenience method that returns the number of result rows a query returns.

count

Alias for get_count

url

Get the url for a webservice resource.

get_upload_url

get the url to use to upload queries to the webservice.

save

Save this query in the user's history in the connected webservice. For queries this will be saved into query history, and templates will be saved into your personal collection of private templates.

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::Query::Roles::Runnable

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.

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