Class: Bio::DB::Polymarker

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-polymarker_db_batch/polymarker_db_batch.rb

Instance Method Summary collapse

Constructor Details

#initialize(props) ⇒ Polymarker

Returns a new instance of Polymarker.



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 5

def initialize( props)
  @properties =Hash[*File.read(props).split(/[=\n]+/)]
  puts @properties.inspect
end

Instance Method Details

#each_running ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 30

def each_running
  query="SELECT snp_file_id, filename FROM snp_file WHERE status IN ('SUBMITTED', 'RUNNING');"
  ret = 0
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#each_snp_in_file(file_id) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 54

def each_snp_in_file(file_id)
  query="SELECT name, chromosome, sequence FROM snp, snp_file_snp WHERE snp_file_snp.snpList_snpId = snp.snpId AND snp_file_snp.snp_file_snp_file_id = '#{file_id}' AND snp.process = 1;"
  ret = 0
  #puts query
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#each_timeout ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 41

def each_timeout
  #TODO: validate the timeouts. 
  #SELECT * FROM snp_file WHERE datediff(NOW(), lastChange) > 3 and status != 'DONE';
  query="SELECT snp_file_id, filename FROM snp_file WHERE datediff(NOW(), submitted) > 3 AND status IN ('NEW', 'SUBMITTED', 'RUNNING');"
  ret = 0
  if block_given?
     ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#each_to_run ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 19

def each_to_run
  query="SELECT snp_file_id, filename FROM snp_file WHERE status = 'NEW';"
  ret = 0
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#execute_polymarker(file_id, snp_file) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 91

def execute_polymarker(file_id, snp_file)
  
  preferences = get_preferences(file_id)

  cmd=@properties['wrapper_prefix']
  cmd << "polymarker.rb -m #{snp_file} -o #{snp_file}_out "
  cmd << "-c #{@properties['path_to_chromosomes']}/#{preferences[:reference]} "
  cmd << @properties['wrapper_suffix']
  #polymarker.rb -m 1_GWAS_SNPs.csv -o 1_test -c /Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa
  execute_command(cmd)
end

#get_preferences(file_id) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 80

def get_preferences(file_id)
  query="SELECT name, value FROM preferences \
  join snp_file_preferences on preferenceID = preferences_preferenceID \
  where snp_file_snp_file_id = #{file_id};"
  preferences = Hash.new
  execute_query(query) do |row|
    preferences[row[0].to_sym] = row[1]
  end
  return preferences
end

#get_snp_file(id) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 14

def get_snp_file(id)
 results = con.query "SELECT * FROM snp_file WHERE snp_file_id=#{id}"
 results.fetch_hash
end

#mysql_version ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 10

def mysql_version
  con.get_server_info
end

#review_running_status(file_id, filename) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 160

def review_running_status(file_id, filename)
  out_folder=@properties["execution_path"]+"/#{file_id}_#{filename}_out"
  started=File.exist?(out_folder)
  done=false
  

  error_message = ""
  error = false

  if started
    lines = IO.readlines("#{out_folder}/status.txt")
    puts lines.inspect

  lines.each do |l| 
    done = l.split(",").include?("DONE\n")
  end
    
    lines.each do |l|  
      error = l.include?("ERROR") unless error
      error_message << lines if error
    end 
  end


  if done 
    exons_filename="#{out_folder}/exons_genes_and_contigs.fa"
    output_primers="#{out_folder}/primers.csv"
    read_file_to_snp_file("mask_fasta", file_id, exons_filename )
    read_file_to_snp_file("polymarker_output", file_id, output_primers )
    update_status(file_id, "DONE")
  elsif error
     update_error_status(file_id, error_message)
  elsif started
    update_status(file_id, "RUNNING")
  end
end

#send_email(to, id, status) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 140

def send_email(to,id, status)
  options = @properties

  msg = <<END_OF_MESSAGE
From: #{options['email_from_alias']} <#{options['email_from']}>
To: <#{to}>
Subject: Polymarker #{id} #{status}

The current status of your request (#{id}) is #{status}
The latest status and results (when done) are available in: #{options['web_domain']}/status?id=#{id}


END_OF_MESSAGE
  smtp = Net::SMTP.new options["email_server"], 587
  smtp.enable_starttls
  smtp.start( options["email_domain"], options["email_user"], options["email_pwd"], :login) do
    smtp.send_message(msg, options["email_from"], to)
  end
end

#update_error_status(snp_file_id, error_message) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 118

def update_error_status(snp_file_id, error_message)
  snp_file = get_snp_file(snp_file_id)
  return if snp_file['status'] == "ERROR"
  pst = con.prepare "UPDATE snp_file SET status = 'ERROR', error=? WHERE snp_file_id = ?"
  puts "update_error_status: #{pst}"
  pst.execute error_message, snp_file_id
  con.commit
  new_status = "ERROR: #{error_message}"
    hashed_id = "#{snp_file_id}:#{snp_file['hash']}"
  begin
    send_email(snp_file['email'], hashed_id,  new_status)
  rescue Exception => e  
    puts "Error sending email to #{snp_file['email']}: #{e.message}"
  end
    
  begin
    send_email(@properties['email_from'], hashed_id, new_status)
  rescue Exception => e  
    puts "Error sending email to #{@properties['email_from']}: #{e.message}"
  end
end

#update_status(snp_file_id, new_status) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 103

def update_status(snp_file_id, new_status)
  raise "Invalid status #{new_status}" unless ["NEW", "SUBMITTED", "RUNNING", "DONE", "ERROR"].include?(new_status)
  snp_file = get_snp_file(snp_file_id)
  return if snp_file['status'] == new_status
  pst = con.prepare "UPDATE snp_file SET status = ? WHERE snp_file_id = ?"
  pst.execute new_status, snp_file_id
  con.commit
  begin
    hashed_id = "#{snp_file_id}:#{snp_file['hash']}"
    send_email(snp_file['email'],hashed_id, new_status)
  rescue
    puts "Error sending email. "
  end
end

#write_output_file_and_execute(file_id, filename) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 66

def write_output_file_and_execute(file_id, filename)
  #puts "Writting: #{file_id}_#{filename}"
  path =@properties["execution_path"]+"/#{file_id}_#{filename}"
  puts "Writting: #{path}"
  f=File.open(path, "w")
  each_snp_in_file(file_id) do |row|
    f.puts(row.join(","))
  end
  f.close
  execute_polymarker(file_id, path)
  update_status(file_id, "SUBMITTED")
 
end