InterMine > Webservice-InterMine-1.0300 > Webservice::InterMine::Query

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NAME ^

Webservice::InterMine::Query - an object representation of a query on an InterMine database

SYNOPSIS ^

  # Queries should be created by their webservices, or through
  # the Webservice::InterMine factory module

  my $query = $service->new_query;

  $query->name('Genes_Annotated_Biological_Process');
  $query->description(
      'Get all genes in Drosophilids annotated with GO Terms in the Biological Process namespace'
  );

  $query->add_view(
      'Gene.name',
      'Gene.primaryIdentifier',
      'Gene.goAnnotation.ontologyTerm.name',
  );

  $query->set_sort_order('Gene.primaryIdentifier', 'asc');

  $query->add_constraint(
      path  => 'Gene.goAnnotation.ontologyTerm.namespace',
      op    => '=',
      value => 'biological_process',
  );

  $query->add_constraint(
      path  => 'Gene.organism.name',
      op    => 'CONTAINS',
      value => 'Drosophila',
  );

  my $results = $query->results(as => 'arrayrefs');

  for my $row (@$results) {
      my ($name, $id, $go_term) = @$row;
      print "$name ($id): $go_term\n";
  }

DESCRIPTION ^

This module is allows you to construct complex queries and obtain results from webservices which implement InterMine genomic databases.

METHODS ^

add_view( [@paths] | [$comma_sep_paths] | [$space_sep_paths])

Adds the paths to the view (result columns). If the argument to add_view is a comma or space separated string, it will be split automatically. All paths must be valid for the model being used, or an exception will be thrown.

set_sort_order( $path, [$direction] )

Defines the sort order for the results to be a particular column in the view (this column must already be in the view, or an exception will be thrown). You do not have to set the sort order manually, the default column is the first column of the view, and the default direction is 'asc'.

constraint methods:

add_join(%args or $path)

Adds a join description to the query (see Webservice::InterMine::Cookbook::Recipe4).

add_pathdescription(%args)

Adds a path description to the query (see Webservice::InterMine::Cookbook::Recipe4).

logic

Get the logic for the query as an object. The Logic object is string overloaded to its human readable string representation (also available with ->code).

see: Webservice::InterMine::LogicalSet

set_logic(EXPR or $str)

Sets the current logic for the query. Illegal logic expressions or strings will cause exceptions to be thrown.

Examples:

  # Parse a string
  $query->set_logic("A and (B or C)");

  # Perform boolean logic on constraint objects
  $query->set_logic($conA & ($conB | $conC));

results([as => Str, size => Int, start => Int, columnheaders => Bool])

Gets a page of results (defined by start and size - defaulting to all results from the beginning) in a requested format. (See Webservice::InterMine::Cookbook::Recipe5)

The formats are:

results_iterator

returns a results object that allows you to iterate through the results row by row, in whatever format you choose. Please see Webservice::InterMine::Cookbook::Recipe6 and Webservice::InterMine::Cookbook::Recipe7.

suspend_validation | resume_validation | validate

Queries will by default check for errors in construction as they are being defined. You can choose to turn this off, which might be useful if you don't want to care about the order you add elements to the query (ie. you might call set_sort_order before add_view), or if you are concerned about speed. In most cases the recommendation is to not turn validation off, unless of course, you really know what you are doing. Calling validate at any point will always perform the validation checks, even if you have suspended validation.

to_xml

Returns an xml string representation of the query. This is suitable for serialisation of queries.

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

You can also look for information at:

COPYRIGHT AND LICENSE ^

Copyright 2006 - 2010 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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