Module: Exodb

Defined in:
lib/exodb/constant.rb,
lib/exodb.rb,
lib/exodb/extra.rb,
lib/exodb/utils.rb,
lib/exodb/rositza.rb,
lib/exodb/version.rb,
lib/exodb/exception.rb,
lib/exodb/usermanage.rb,
lib/exodb/dbconnection.rb,
lib/exodb/extra/upload.rb,
lib/exodb/rositza/load.rb,
lib/exodb/datamodel/region.rb,
lib/exodb/datamodel/source.rb,
lib/exodb/utils/miriamrest.rb,
lib/exodb/utils/upload_var.rb,
lib/exodb/datamodel/generef.rb,
lib/exodb/datamodel/isoform.rb,
lib/exodb/datamodel/variant.rb,
lib/exodb/utils/ensemblrest.rb,
lib/exodb/datamodel/reference.rb,
lib/exodb/datamodel/xrefsfield.rb,
lib/exodb/extra/upload_generef.rb,
lib/exodb/datamodel/varlocfield.rb,
lib/exodb/datamodel/genelocfield.rb

Overview

raise “Please, use ruby 1.9.0 or later.” if RUBY_VERSION < “1.9.0”

Defined Under Namespace

Modules: Ensembl, GeneLocationField, Miriam, Utils, VarLocationField, XrefsField Classes: Aa, Cell, Change, Chrref, CreateUserError, Dataset, Gene, Generef, InvalidResponse, Isoform, Lossgain, Mapping, Occurrent, Offexon, Onexon, Reference, Region, Source, Splice, Utr, Variant, Variantref

Constant Summary collapse

VERSION = 
"0.1.3"
NAIUPAC = 
{
	'Y'	=> 'CT',
	'R'	=> 'AG',
	'W'	=> 'AT',
	'S'	=> 'CG',
	'K'	=> 'GT',
	'M'	=> 'AC',
	
	'B'	=> 'CGT',
	'D'	=> 'AGT',
	'H'	=> 'ACT',
	'V'	=> 'ACG',
	
	'N'	=> 'ACGT',
	
	'A'	=> 'A',
	'T'	=> 'T',
	'G'	=> 'G',
	'C'	=> 'C',
	'U'	=> 'U',
	
	'CT' => 'Y',
	'AG' => 'R',
	'AT' => 'W',
	'CG' => 'S',
	'GT' => 'K',
	'AC' => 'M',
	
	'CGT' => 'B',
	'AGT' => 'D',
	'ACT' => 'H',
	'ACG' => 'V',
	
	'ACGT' => 'N'
}
ASSEMBLY = 
{
	'hg19' => 'GRCh37',
	'hg38' => 'GRCh38',
	'GRCh37' => 'GRCh37',
	'GRCh38' => 'GRCh38',
	'grch37' => 'GRCh37',
	'grch38' => 'GRCh38'
}
DEFAULTASSEMBLY = 
'GRCh37'
LATESTASSEMBLY = 
'GRCh38'
HGVPATTERN = 
/^([^:]+):g\.([\-_\d]+)([ATGC]>[ATCG]|del[ATCG]*|ins[ATCG]*)$/
@@verbose = 
true

Class Method Summary collapse

Class Method Details

.assembly(str) ⇒ Object 



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# File 'lib/exodb.rb', line 67

def assembly(str)
	return Exodb::ASSEMBLY[str.downcase]
end

.connect(connectionstr = {}) ⇒ Object

Parameters:

  • Connection (Hash, String) —

    string or a Hash in format { database: ‘exodus’, hosts: [‘localhost:27017’], username: ‘xxx’, options: {}}



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# File 'lib/exodb/dbconnection.rb', line 30

def connect(connectionstr = {})
	
	settings = { database: 'exodus', hosts: ['localhost:27017'], options: {}}
	
	if connectionstr.is_a?(Hash)
		connectionstr.each_pair {|k, v| settings[k.to_sym] = k.to_sym == :hosts ? [v].flatten : v}
	elsif connectionstr.is_a?(String)
		split1 = connectionstr.split('@')
		settings[:username] = split1[0] if split1.length > 1
		split2 = split1[-1].split('/')
		settings[:database] = split2[1] if split2.length > 1
		settings[:hosts] = [split2[0]].flatten
	end
	
	password = ask("Password:  ") { |q| q.echo = "*" } if settings[:username] && !settings[:password]
	
	Mongoid::Sessions.disconnect
	Mongoid::Sessions.clear
	Mongoid.load_configuration({"sessions"=>{"default"=> password ? settings.merge({password: password}) : settings}})
	
	return "#EXODB:INFO Connection with #{settings}" if Pry.current
end

.create_admin(username, database) ⇒ Object

To create an admin user

Parameters:

  • user (String) —

    name to be created

  • database (String) —

    that user created



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# File 'lib/exodb/usermanage.rb', line 59

def create_admin(username, database)
	
	create_user(username, database, "readWrite", "dbAdmin", "userAdmin")
	
end

.create_rouser(username) ⇒ Object

To create a read-only user

Parameters:

  • user (String) —

    name to be created

  • database (String) —

    that user created



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# File 'lib/exodb/usermanage.rb', line 78

def create_rouser(username)
	
	create_user(username, Mongoid.session(:default).options[:database], "read")
	
end

.create_rwuser(username) ⇒ Object

To create a rw user

Parameters:

  • user (String) —

    name to be created

  • database (String) —

    that user created



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# File 'lib/exodb/usermanage.rb', line 69

def create_rwuser(username)
	
	create_user(username, Mongoid.session(:default).options[:database], "readWrite")
	
end

.create_user(username, database, *roles) ⇒ Object

General command for creating a user

Parameters:

  • user (String) —

    name to be created

  • database (String) —

    that user created

  • roles (Array) —

    to be assigned to the user



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# File 'lib/exodb/usermanage.rb', line 22

def create_user(username, database, *roles)
	
	if database != 'admin'
		
		password = nil
		confirmed = nil
		
		while !password || password != confirmed
			password = ask("New password:  ") { |q| q.echo = "*" }
			confirmed = ask("Confirm password:  ") { |q| q.echo = "*" }
			
			puts "Password not match!\n" if password != confirmed
			
		end
		
		if database
			Mongoid.session(:default).with(database: database).command(
				createUser: username,
				pwd: password,
				roles: roles.flatten
			)
		else
			Mongoid.session(:default).command(
				createUser: username,
				pwd: password,
				roles: roles.flatten
			)
		end
	else
		raise CreateUserError, 'Cannot create user on admin database'
	end
end

.current_database ⇒ String

Return the current database name

Returns:

  • (String) —

    the database name



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# File 'lib/exodb/dbconnection.rb', line 79

def current_database
	self.session.options[:database]
end

.noverbose ⇒ Object 



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# File 'lib/exodb.rb', line 55

def noverbose()
	@@verbose = false
end

.putst(str) ⇒ Object 



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# File 'lib/exodb.rb', line 63

def putst(str)
	puts "Exodb:STATUS #{str}"
end

.putstv(str) ⇒ Object 



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# File 'lib/exodb.rb', line 59

def putstv(str)
	putst(str) if @@verbose == true
end

.session ⇒ String

Return the session setting

Returns:

  • (String) —

    the session setting



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# File 'lib/exodb/dbconnection.rb', line 72

def session
	Mongoid.session(:default)
end

.sessionload!(sessionfile = nil) ⇒ Object

load session file

Parameters:

  • path (String) —

    to session file



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# File 'lib/exodb/dbconnection.rb', line 19

def sessionload!(sessionfile = nil)
		if sessionfile && File.exist?(sessionfile)
			Mongoid.load!(sessionfile, :production)
		else
			Mongoid.load!("#{Dir.pwd}/session.yml", :production) if File.exist?("#{Dir.pwd}/session.yml")
		end
end

.verbose ⇒ Object 



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# File 'lib/exodb.rb', line 51

def verbose()
	@@verbose = true
end