Class: MartSearch::BiomartDataSource

Inherits:
DataSource show all
Defined in:
lib/martsearch/data_source_biomart.rb

Overview

Custom DataSource class for interacting with BioMart based datasources.

Author:

Instance Attribute Summary (collapse)

Instance Method Summary (collapse)

Methods inherited from DataSource

#name

Methods included from Utils

#build_http_client, #convert_array_to_hash

Constructor Details

- (BiomartDataSource) initialize(conf)

A new instance of BiomartDataSource

Parameters:

  • conf (Hash) —

    configuration hash



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# File 'lib/martsearch/data_source_biomart.rb', line 13

def initialize( conf )
  super
  @ds = Biomart::Dataset.new( @url, { :name => @conf[:dataset] } )
end

Instance Attribute Details

- (Object) ds (readonly)

The Biomart::Dataset object for the BiomartDataSource



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# File 'lib/martsearch/data_source_biomart.rb', line 10

def ds
  @ds
end

Instance Method Details

- (Object) data_origin_url(query, conf)

Function to provide a link URL to the original datasource given a dataset query.

See Also:



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# File 'lib/martsearch/data_source_biomart.rb', line 90

def data_origin_url( query, conf )
  MartSearch::Controller.instance().logger.debug("[MartSearch::BiomartDataSource] '#{self.name}' ::data_origin_url - running data_origin_url( '#{query}', conf )")

  url = @url + "/martview?VIRTUALSCHEMANAME=default&VISIBLEPANEL=resultspanel"

  # Filters...
  filters = []

  filters_to_build = { conf[:joined_filter] => query }
  filters_to_build.merge!( conf[:filters] ) unless conf[:filters].nil?

  filters_to_build.each do |key,value|
    filter = "#{@conf[:dataset]}.default.filters.#{key}.""

    if value.is_a?(Array) then filter << "#{CGI::escape(value.join(","))}&quot;"
    else                       filter << "#{CGI::escape(value)}&quot;"
    end

    filters.push(filter)
  end

  url << "&FILTERS=#{filters.join("|")}"

  # Attributes...
  attrs = []

  url << "&ATTRIBUTES="
  conf[:attributes].each do |attribute|
    attrs.push("#{@conf[:dataset]}.default.attributes.#{attribute}")
  end

  url << attrs.join("|")

  MartSearch::Controller.instance().logger.debug("[MartSearch::BiomartDataSource] '#{self.name}' ::data_origin_url - running data_origin_url( '#{query}', conf ) - DONE")
  return url
end

- (Object) ds_attributes 



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# File 'lib/martsearch/data_source_biomart.rb', line 18

def ds_attributes
  @ds_attributes = @ds.attributes if @ds_attributes.nil?
  return @ds_attributes
end

- (Object) fetch_all_terms_for_indexing(conf)

Function to query a biomart datasource and return all of the data ready for indexing.

See Also:



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# File 'lib/martsearch/data_source_biomart.rb', line 33

def fetch_all_terms_for_indexing( conf )
  MartSearch::Controller.instance().logger.debug("[MartSearch::BiomartDataSource] '#{self.name}' ::fetch_all_terms_for_indexing - running fetch_all_terms_for_indexing()")

  attributes = []
  conf[:attribute_map].each do |map|
    attributes.push(map[:attr])
  end

  filters = conf[:filters]
  filters.stringify_keys! unless filters.nil?

  biomart_search_params = {
    :filters    => filters,
    :attributes => attributes.uniq,
    :timeout    => MartSearch::Server.settings.biomart_search_params_timeout
  }

  @ds.search(biomart_search_params)
end

- (Boolean) is_alive?

Simple heartbeat function to check that the datasource is online.

Returns:

  • (Boolean)

See Also:



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# File 'lib/martsearch/data_source_biomart.rb', line 26

def is_alive?
  @ds.alive?
end

- (Object) search(query, conf)

Function to search a biomart datasource given an appropriate configuration.

Raises:

See Also:



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# File 'lib/martsearch/data_source_biomart.rb', line 57

def search( query, conf )
  MartSearch::Controller.instance().logger.debug("[MartSearch::BiomartDataSource] '#{self.name}' ::search - running search( '#{query}', conf )")

  filters = { conf[:joined_filter] => query.join(',') }
  filters.merge!( conf[:filters] ) unless conf[:filters].nil? or conf[:filters].empty?
  filters.stringify_keys!

  search_options = {
    :filters         => filters,
    :attributes      => conf[:attributes],
    :process_results => true,
    :timeout         => MartSearch::Server.settings.biomart_search_options_timeout
  }

  if conf[:required_attributes]
    search_options[:required_attributes] = conf[:required_attributes]
  end

  begin
    results = @ds.search(search_options)
    results.recursively_symbolize_keys!
  rescue Biomart::BiomartError => error
    raise MartSearch::DataSourceError, "Biomart::BiomartError: #{error.message}"
  end

  MartSearch::Controller.instance().logger.debug("[MartSearch::BiomartDataSource] '#{self.name}' ::search - running search( '#{query}', conf ) - DONE")
  return results
end