class Bio::SRA::Connection
Public Class Methods
connect(sra_metadb_path=File.join(File.dirname(__FILE__),'..','..','..','db','SRAmetadb.sqlite'))
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Connect to a metadata database.
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sra_metadb_path: a path to the gunzipped SRAmetadb.sqlite file which is the database. By default this is in the db/ directory of this gem, but that probably isn’t where the db file is.
You can download the file like so:
$ wget http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz # gunzip SRAmetadb.sqlite.gz
# File lib/bio/sra/connect.rb, line 18 def self.connect(sra_metadb_path=File.join(File.dirname(__FILE__),'..','..','..','db','SRAmetadb.sqlite')) log = Bio::Log::LoggerPlus['bio-sra'] log.info "Attempting to connect to database #{sra_metadb_path}" # default: # adapter: sqlite3 # database: db/SRAmetadb.sqlite # pool: 5 # timeout: 5000 options = { :adapter => 'sqlite3', :database => sra_metadb_path, :pool => 5, :timeout => 5000, } establish_connection(options) end