Class: MiGA::SQLite

Inherits:
MiGA
  • Object
show all
Defined in:
lib/miga/sqlite.rb

Overview

SQLite3 wrapper for MiGA.

Constant Summary

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from Common::Path

#root_path, #script_path

Methods included from Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from Common::Net

#download_file_ftp, #known_hosts, #remote_connection

Methods included from Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

#initialize(path, opts = {}) ⇒ SQLite

Create MiGA::SQLite with database in path (without opening a connection) and options opts (see .default_opts)



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# File 'lib/miga/sqlite.rb', line 31

def initialize(path, opts = {})
  @opts = MiGA::SQLite.default_opts(opts)
  @path = File.absolute_path(path)
  MiGA::MiGA.DEBUG("Accessing database: #{path}")
end

Instance Attribute Details

#opts ⇒ Object (readonly)

Options hash



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# File 'lib/miga/sqlite.rb', line 22

def opts
  @opts
end

#path ⇒ Object (readonly)

Database absolute path



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# File 'lib/miga/sqlite.rb', line 26

def path
  @path
end

Class Method Details

.default_opts(opts = {}) ⇒ Object

Default parsing options. Supported opts keys:

  • :busy_attempts: Number of times to retry when database is busy (default: 3)



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# File 'lib/miga/sqlite.rb', line 14

def default_opts(opts = {})
  opts[:busy_attempts] ||= 3
  opts
end

Instance Method Details

#run(*cmd) ⇒ Object

Executes cmd and returns the result. Alternatively, if a block is passed, the commands are ignored and the block is executed with a single parameter of the database connection



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# File 'lib/miga/sqlite.rb', line 41

def run(*cmd)
  if block_given?
    run_block { |conn| yield(conn) }
  else
    y = nil
    run_block { |conn| y = conn.execute(*cmd) }
    y
  end
end

#run_block(&blk) ⇒ Object

Executes blk that accepts a single parameter for the database connection



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# File 'lib/miga/sqlite.rb', line 54

def run_block(&blk)
  busy_attempts ||= 0
  io_attempts ||= 0
  SQLite3::Database.new(path) { |conn| blk[conn] }
rescue SQLite3::BusyException => e
  busy_attempts += 1
  raise "Database busy #{path}: #{e.message}" if busy_attempts >= 3

  sleep(1)
  retry
rescue SQLite3::IOException => e
  io_attempts += 1
  raise "Database I/O error #{path}: #{e.message}" if io_attempts >= 3

  sleep(1)
  retry
end