bio-polymarker_db_batch 0.4.0 → 0.5.0

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.4.0
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+ 0.5.0
@@ -12,7 +12,7 @@ options = {}
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  OptionParser.new do |opts|
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- opts.banner = "Usage: run_pending_polymarker.rb [options]"
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+ opts.banner = "Usage: monitor_running_polymarker.rb [options]"
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  opts.on("-p", "--preferences FILE" "File with the preferences") do |o|
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  options[:preferences] = o
@@ -25,13 +25,10 @@ pol=Bio::DB::Polymarker.new(options[:preferences])
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  #pol.mysql_version
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  pol.each_running do |row|
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- #puts row.join(",")
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- #puts row.inspect
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  pol.review_running_status(row[0], row[1])
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  end
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  pol.each_timeout do |row|
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- #puts "Timeouts: #{row[0]}"
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  pol.update_error_status(row[0], "Timeout")
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  end
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@@ -4,7 +4,7 @@ class Bio::DB::Polymarker
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  def initialize( props)
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  @properties =Hash[*File.read(props).split(/[=\n]+/)]
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- #puts @properties.inspect
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+ puts @properties.inspect
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  end
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  def mysql_version
@@ -54,7 +54,7 @@ class Bio::DB::Polymarker
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  def each_snp_in_file(file_id)
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  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;"
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  ret = 0
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- puts query
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+ #puts query
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  if block_given?
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  ret = execute_query(query){|row| yield row }
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  else
@@ -64,21 +64,38 @@ class Bio::DB::Polymarker
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  end
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  def write_output_file_and_execute(file_id, filename)
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- puts "Writting: #{file_id}_#{filename}"
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+ #puts "Writting: #{file_id}_#{filename}"
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  path =@properties["execution_path"]+"/#{file_id}_#{filename}"
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  puts "Writting: #{path}"
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  f=File.open(path, "w")
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-
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  each_snp_in_file(file_id) do |row|
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  f.puts(row.join(","))
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  end
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- execute_polymarker(path)
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- update_status(file_id, "SUBMITTED")
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  f.close
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+ execute_polymarker(file_id, path)
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+ update_status(file_id, "SUBMITTED")
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+
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+ end
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+
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+ def get_preferences(file_id)
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+ query="SELECT name, value FROM preferences \
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+ join snp_file_preferences on preferenceID = preferences_preferenceID \
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+ where snp_file_snp_file_id = #{file_id};"
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+ preferences = Hash.new
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+ execute_query(query) do |row|
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+ preferences[row[0].to_sym] = row[1]
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+ end
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+ return preferences
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  end
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- def execute_polymarker(snp_file)
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- cmd="#{@properties['wrapper_prefix'] } polymarker.rb -m #{snp_file} -o #{snp_file}_out -c #{@properties['path_to_chromosomes']} #{@properties['wrapper_suffix'] }"
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+ def execute_polymarker(file_id, snp_file)
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+
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+ preferences = get_preferences(file_id)
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+
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+ cmd=@properties['wrapper_prefix']
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+ cmd << "polymarker.rb -m #{snp_file} -o #{snp_file}_out "
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+ cmd << "-c #{@properties['path_to_chromosomes']}/#{preferences[:reference]} "
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+ cmd << @properties['wrapper_suffix']
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  #polymarker.rb -m 1_GWAS_SNPs.csv -o 1_test -c /Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa
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  execute_command(cmd)
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  end
@@ -101,8 +118,6 @@ class Bio::DB::Polymarker
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  def update_error_status(snp_file_id, error_message)
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  snp_file = get_snp_file(snp_file_id)
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  return if snp_file['status'] == "ERROR"
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-
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-
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  pst = con.prepare "UPDATE snp_file SET status = 'ERROR', error=? WHERE snp_file_id = ?"
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  puts "update_error_status: #{pst}"
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  pst.execute error_message, snp_file_id
@@ -161,7 +176,7 @@ END_OF_MESSAGE
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  lines.each do |l|
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  error = l.include?("ERROR") unless error
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- error_message << l if error
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+ error_message << lines if error
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  end
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  end
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@@ -222,7 +237,7 @@ END_OF_MESSAGE
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  return n_rows unless block_given?
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  return ret
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  end
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- raise "Unsuported query #{query}"
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+ raise "Unsuported query '#{query}'"
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  end
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metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-polymarker_db_batch
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  version: !ruby/object:Gem::Version
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- version: 0.4.0
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+ version: 0.5.0
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  platform: ruby
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  authors:
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  - Ricardo H. Ramirez-Gonzalez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-10-14 00:00:00.000000000 Z
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+ date: 2015-03-05 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio-polyploid-tools