Class: MartSearch::FileSystemDataSource

Inherits:

DataSource

• Object
• DataSource
• MartSearch::FileSystemDataSource

show all

Defined in:

lib/martsearch/data_source_file_system.rb

Overview

Instance Attribute Summary (collapse)

• - (Object) fs_location readonly

  The location on the file system of this dataset.

Instance Method Summary (collapse)

• - (Object) data_origin_url(query, conf)

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

• - (Object) fetch_all_terms_for_indexing(conf)

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

• - (FileSystemDataSource) initialize(conf) constructor

  A new instance of FileSystemDataSource.

• - (Boolean) is_alive?

  Simple heartbeat function to check that the datasource is online.

• - (Object) search(query, conf)

  Function to search a biomart datasource given an appropriate configuration.

Methods inherited from DataSource

#name

Methods included from Utils

#build_http_client, #convert_array_to_hash

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

def initialize( conf )
  super
  @fs_location = "#{MARTSEARCH_PATH}#{@conf[:location]}"
  
  unless File.exists?(@fs_location) and File.directory?(@fs_location)
    raise MartSearch::InvalidConfigError, "#{@fs_location} does not exist, or is not a directory!"
  end
end

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

def fs_location
  @fs_location
end

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# File 'lib/martsearch/data_source_file_system.rb', line 81

def data_origin_url( query, conf )
  nil
end

- THIS FEATURE HAS NOT BEEN IMPLEMENTED FOR THIS CLASS.

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# File 'lib/martsearch/data_source_file_system.rb', line 34

def fetch_all_terms_for_indexing( conf )
  raise NotImplementedError, "This feature has not been implemented for the FileSystemDataSource class."
end

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# File 'lib/martsearch/data_source_file_system.rb', line 25

def is_alive?
  true
end

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# File 'lib/martsearch/data_source_file_system.rb', line 42

def search( query, conf )
  MartSearch::Controller.instance().logger.debug("[MartSearch::FileSystemDataSource] '#{self.name}' ::search - running search( '#{query}', conf )")
  unless conf[:file_globs]
    raise MartSearch::DataSourceError, "You have not specifed any 'glob' patterns!"
  end
  
  results   = []
  file_list = []
  pwd       = Dir.pwd
  
  begin
    Dir.chdir(@fs_location)
    conf[:file_globs].each do |glob_str|
      Dir.glob(glob_str).each do |file|
        file_list.push( file )
      end
    end
  rescue => error
    Dir.chdir(pwd)
    raise MartSearch::DataSourceError, "Error querying file system: #{error}"
  end
  
  Dir.chdir(pwd)
  
  file_list.each do |file|
    query.each do |string|
      if file.include?(string)
        results.push({ conf[:joined_index_field].to_sym => string, :file => file })
      end
    end
  end
  
  return results.uniq
end