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