Class: Constants
- Inherits:
-
Object
show all
- Includes:
- Singleton
- Defined in:
- lib/protk/constants.rb
Instance Attribute Summary collapse
Instance Method Summary
collapse
Constructor Details
Read the global constants file and initialize our class @env variable Initialize loggers
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# File 'lib/protk/constants.rb', line 128
def initialize()
@data_lib_dir="#{File.dirname(__FILE__)}/data"
@protk_dir="#{Dir.home}/.protk"
if ( ENV['PROTK_INSTALL_DIR']!=nil )
p "Using protk install dir from shell"
@protk_dir=ENV['PROTK_INSTALL_DIR']
end
default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil
user_config_yml = nil
user_config_yml = YAML.load_file "#{@protk_dir}/config.yml" if File.exist? "#{@protk_dir}/config.yml"
if ( user_config_yml !=nil )
@env = default_config_yml.merge user_config_yml
else
@env=default_config_yml
end
protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]
protk_paths=[]
protk_tool_dirs.each do |tooldir|
env_value = ENV["PROTK_#{tooldir.upcase}_ROOT"]
if ( env_value!=nil)
protk_paths<<env_value
end
protk_paths<<"#{@protk_dir}/tools/#{tooldir}"
end
original_path=ENV['PATH']
protk_paths<<original_path
ENV['PATH']=protk_paths.join(":")
throw "No data found in config file" unless @env!=nil
@info_level="fatal"
@info_level=default_config_yml['message_level'] unless default_config_yml['message_level'].nil?
end
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Dynamic Method Handling
This class handles dynamic methods through the method_missing method
#method_missing(method) ⇒ Object
Provides direct access to constants through methods of the same name This will be used for all constants other than paths
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# File 'lib/protk/constants.rb', line 38
def method_missing(method)
from_env = @env[method.to_s]
throw "#{method} is undefined" unless from_env!=nil
from_env
end
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Instance Attribute Details
#data_lib_dir ⇒ Object
Returns the value of attribute data_lib_dir.
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# File 'lib/protk/constants.rb', line 32
def data_lib_dir
@data_lib_dir
end
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#info_level ⇒ Object
Returns the value of attribute info_level.
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# File 'lib/protk/constants.rb', line 30
def info_level
@info_level
end
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#protk_dir ⇒ Object
Returns the value of attribute protk_dir.
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# File 'lib/protk/constants.rb', line 31
def protk_dir
@protk_dir
end
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Instance Method Details
#bin ⇒ Object
Some constants are paths. They need to be translated into real paths before being returned
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# File 'lib/protk/constants.rb', line 49
def bin
return "#{@protk_dir}/bin"
end
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#blast_root ⇒ Object
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# File 'lib/protk/constants.rb', line 111
def blast_root
"#{@protk_dir}/tools/blast"
end
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#blastdbcmd ⇒ Object
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# File 'lib/protk/constants.rb', line 88
def blastdbcmd
path=%x[which blastdbcmd]
path.chomp
end
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#current_database_for_name(dbname) ⇒ Object
Based on the database shortname and global database path, find the most current version of the required database If dbname corresponds to a folder in the dbroot this function returns the path of the database with an extension appropriate to the database type
If dbname is a full path to a file this tool will first import the file as a temporary database and will then return its full path
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# File 'lib/protk/constants.rb', line 247
def current_database_for_name(dbname)
dbroot=self.protein_database_root
throw "Protein database directory not specified" unless dbroot!=nil
throw "Protein database directory #{dbroot} does not exist" unless Pathname(dbroot).exist?
dbroot.sub!(/(\/*\s*)$/,"")
return path_for_builtin_database(dbname)
end
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#database_downloads ⇒ Object
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# File 'lib/protk/constants.rb', line 107
def database_downloads
return "#{self.protein_database_root}/downloads"
end
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#dbexist?(dbname) ⇒ Boolean
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# File 'lib/protk/constants.rb', line 236
def dbexist?(dbname)
Pathname.new("#{self.protein_database_root}/#{dbname}").exist?
end
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#import_fasta_database(dbroot, path_to_fasta_file) ⇒ Object
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# File 'lib/protk/constants.rb', line 283
def import_fasta_database(dbroot,path_to_fasta_file)
tmp_dbroot=Pathname.new("#{dbroot}/tmp/")
dest_fasta_file_name=Pathname.new(path_to_fasta_file).basename
dest_fasta_file_path=Pathname.new("#{tmp_dbroot}#{dest_fasta_file_name}")
if ( !dest_fasta_file_path.exist? )
Dir.mkdir(tmp_dbroot) unless tmp_dbroot.exist? && tmp_dbroot.directory?
throw "Unable to make temporary database directory #{tmp_dbroot}" unless tmp_dbroot.exist?
link_cmd = "ln -s #{path_to_fasta_file} #{dest_fasta_file_path}"
result= %x[#{link_cmd}]
p result
end
check_cmd="#{self.ncbi_tools_bin}/blastdbcmd -info -db #{dest_fasta_file_path}"
result = %x[#{check_cmd}]
if ( result=="")
throw "Unable to create temporary database #{dest_fasta_file_path}" unless dest_fasta_file_path.exist?
cmd="#{self.makeblastdb} -in #{dest_fasta_file_path} -parse_seqids"
p cmd
self.run_local(cmd)
end
return dest_fasta_file_path.to_s
end
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#initialize_loggers ⇒ Object
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# File 'lib/protk/constants.rb', line 195
def initialize_loggers
log_dir = Pathname.new(self.log_file).dirname
log_dir.mkpath unless log_dir.exist?
@stdout_logger=Logger.new(STDOUT)
@file_logger=Logger.new(self.log_file)
throw "Unable to create file logger at path #{self.log_file}" unless @file_logger!=nil
throw "Unable to create stdout logger " unless @stdout_logger!=nil
case @info_level
when /info/i
@stdout_logger.level=Logger::INFO
when /debug/i
@stdout_logger.level=Logger::DEBUG
when /warn/i
@stdout_logger.level=Logger::WARN
when /fatal/i
@stdout_logger.level=Logger::FATAL
else
throw "Unknown log level #{@info_level}"
end
end
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#log(message, level) ⇒ Object
Write a message to all logger objects
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# File 'lib/protk/constants.rb', line 222
def log(message,level)
if ( @stdout_logger == nil || @file_logger == nil)
initialize_loggers
end
@stdout_logger.send(level,message)
@file_logger.send(level,message)
end
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#log_file ⇒ Object
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# File 'lib/protk/constants.rb', line 115
def log_file
path=@env['log_file']
if ( path =~ /^\// )
return path
else
return "#{@protk_dir}/#{@env['log_file']}"
end
end
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#makeblastdb ⇒ Object
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# File 'lib/protk/constants.rb', line 83
def makeblastdb
makeblastdbpath=%x[which makeblastdb]
makeblastdbpath.chomp
end
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#mascot2xml ⇒ Object
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# File 'lib/protk/constants.rb', line 93
def mascot2xml
path=%x[which Mascot2XML]
path.chomp
end
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#msgfplus_root ⇒ Object
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# File 'lib/protk/constants.rb', line 62
def msgfplus_root
"#{@protk_dir}/tools/msgfplus"
end
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#msgfplusjar ⇒ Object
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# File 'lib/protk/constants.rb', line 66
def msgfplusjar
msgfplus_path=%x[which MSGFPlus.jar]
msgfplus_path.chomp
end
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#omssa_root ⇒ Object
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# File 'lib/protk/constants.rb', line 58
def omssa_root
"#{@protk_dir}/tools/omssa"
end
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#openms_root ⇒ Object
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# File 'lib/protk/constants.rb', line 75
def openms_root
"#{@protk_dir}/tools/openms"
end
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#path_for_builtin_database(dbname) ⇒ Object
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# File 'lib/protk/constants.rb', line 231
def path_for_builtin_database(dbname)
"#{self.protein_database_root}/#{dbname}/current.fasta"
end
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#protein_database_root ⇒ Object
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# File 'lib/protk/constants.rb', line 98
def protein_database_root
path=@env['protein_database_root']
if ( path =~ /^\// )
return path
else
return "#{@protk_dir}/#{@env['protein_database_root']}"
end
end
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#pwiz_root ⇒ Object
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# File 'lib/protk/constants.rb', line 71
def pwiz_root
return "#{@protk_dir}/tools/pwiz"
end
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#run_local(command_string) ⇒ Object
Runs the given command in a local shell
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# File 'lib/protk/constants.rb', line 264
def run_local(command_string)
self.log("Command: #{command_string} started",:info)
status = Open4::popen4("#{command_string} ") do |pid, stdin, stdout, stderr|
puts "PID #{pid}"
stdout.each { |line| self.log(line.chomp,:info) }
stderr.each { |line| self.log(line.chomp,:warn) }
end
if ( status!=0 )
self.log( "Command: #{command_string} exited with status #{status.to_s}",:error)
else
self.log( "Command: #{command_string} exited with status #{status.to_s}",:info)
end
status
end
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#tandem_root ⇒ Object
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# File 'lib/protk/constants.rb', line 79
def tandem_root
"#{@protk_dir}/tools/tandem"
end
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#tpp_root ⇒ Object
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# File 'lib/protk/constants.rb', line 53
def tpp_root
"#{@protk_dir}/tools/tpp"
end
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#update_user_config(dict) ⇒ Object
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# File 'lib/protk/constants.rb', line 184
def update_user_config(dict)
user_config_yml = YAML.load_file "#{self.protk_dir}/config.yml" if File.exist? "#{self.protk_dir}/config.yml"
if ( user_config_yml !=nil )
dict = user_config_yml.merge dict
end
File.open("#{self.protk_dir}/config.yml", "w") {|file| file.puts(dict.to_yaml) }
end
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