Class: Bioroebe::Biomart::Server

Inherits:
Object
  • Object
show all
Includes:
Bioroebe::Biomart
Defined in:
lib/bioroebe/biomart/server.rb

Instance Method Summary collapse

Methods included from Bioroebe::Biomart

#request

Constructor Details

#initialize(url) ⇒ Server

#

initialize

#

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# File 'lib/bioroebe/biomart/server.rb', line 22

def initialize(url)
  @url = url or raise ArgumentError, 'must pass :url'
  unless @url =~ /martservice/
    @url = @url+'/martservice'
  end
  reset
end

Instance Method Details

#alive? ⇒ Boolean

#

alive?

Simple heartbeat function to test that a Biomart server is online. Returns true/false.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/biomart/server.rb', line 114

def alive?
  begin
    @databases = {} # reset the databases store
    self.list_databases
  rescue Biomart::BiomartError => error
    pp error
    return false
  else
    return true
  end
end

#databases? ⇒ Hash Also known as: databases

#

databases?

Returns a hash (keyed by the biomart 'name' for the database) of all of the Biomart::Database objects belonging to this server.

database name.

#

Returns:

  • (Hash) —

    A hash of Biomart::Database objects keyed by the


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# File 'lib/bioroebe/biomart/server.rb', line 75

def databases?
  if @databases.empty?
    fetch_databases
  end
  return @databases
end

#datasets? ⇒ Boolean Also known as: datasets

#

datasets?

Returns a hash (keyed by the biomart 'name' for the dataset) of all of the Biomart::Dataset objects belonging to this server.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/biomart/server.rb', line 101

def datasets?
  if @datasets.empty?
    fetch_datasets
  end
  return @datasets
end

#list_databases ⇒ Array

#

list_databases

Returns an array of the database names (biomart 'name') for this dataset.

#

Returns:

  • (Array) —

    An array of database names


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# File 'lib/bioroebe/biomart/server.rb', line 52

def list_databases
  if @databases.empty?
    fetch_databases
  end
  return @databases.keys
end

#list_datasets ⇒ Object

#

list_datasets

Returns an array of the dataset names (biomart 'name') for this dataset.

#

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# File 'lib/bioroebe/biomart/server.rb', line 88

def list_datasets
  if @datasets.empty?
    fetch_datasets
  end
  return @datasets.keys
end

#reset ⇒ Object

#

reset

#

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# File 'lib/bioroebe/biomart/server.rb', line 33

def reset
  # ======================================================================= #
  # === @databases
  # ======================================================================= #
  @databases = {}
  # ======================================================================= #
  # === @datasets
  # ======================================================================= #
  @datasets  = {}
end

#url? ⇒ Boolean Also known as: url

#

url?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/biomart/server.rb', line 62

def url?
  @url
end