quorum 0.1.0

data/app/controllers/quorum/jobs_controller.rb

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+module Quorum
+  class JobsController < ApplicationController
+
+    respond_to :html, :json
+    before_filter :set_blast_dbs, :only => [:new, :create]
+
+    def index
+      redirect_to :action => "new"
+    end
+
+    def new
+      @job = Job.new
+      @job.build_blastn_job
+      @job.build_blastx_job
+      @job.build_tblastn_job
+      @job.build_blastp_job
+    end
+
+    def create
+      if params[:job][:sequence_file]
+        file = params[:job][:sequence_file].read
+        params[:job].delete(:sequence_file)
+      end
+
+      @job = Job.new(params[:job])
+
+      if file
+        @job.sequence = ""
+        @job.sequence << file
+      end
+
+      unless @job.save
+        @job.build_blastn_job  if @job.blastn_job.nil?
+        @job.build_blastx_job  if @job.blastx_job.nil?
+        @job.build_tblastn_job if @job.tblastn_job.nil?
+        @job.build_blastp_job  if @job.blastp_job.nil?
+        render :action => "new"
+        return 
+      end
+      redirect_to job_path(@job.id)
+    end
+
+    def show
+      begin
+        @jobs = Job.find(params[:id])
+      rescue ActiveRecord::RecordNotFound => e
+        set_flash_message(:notice, :data_not_found)
+        redirect_to :action => "new"
+      end        
+    end
+
+    #
+    # Returns Resque worker results.
+    #
+    def get_quorum_search_results
+      valid = ["blastn", "blastx", "tblastn", "blastp"]
+      empty = [{ :results => false }].to_json
+
+      json = empty
+
+      if valid.include? params[:algo]
+        queued = "#{params[:algo]}_job".to_sym
+        report = "#{params[:algo]}_job_reports".to_sym
+
+	      begin
+	        job = Job.find(params[:id])
+	      rescue ActiveRecord::RecordNotFound => e
+	        json = empty
+	      else
+	        if job.method(queued).call.present?
+	          if job.method(report).call.present?
+              if params[:query]
+                json = job.method(report).call.by_query(params[:query]).default_order
+              else
+                json = job.method(report).call.default_order
+              end
+            else
+              json = []
+            end
+	        end
+	      end
+      end
+
+      respond_with json
+    end
+
+    private
+
+    #
+    # Blast Database options for select.
+    #
+    def set_blast_dbs
+      @blast_dbs = {
+        :blastn  => Quorum.blastn,
+        :blastx  => Quorum.blastx, 
+        :tblastn => Quorum.tblastn, 
+        :blastp  => Quorum.blastp
+      }
+    end
+
+  end
+end

data/app/helpers/quorum/application_helper.rb

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+module Quorum
+  module ApplicationHelper
+  end
+end

data/app/models/quorum/blastn_job.rb

@@ -0,0 +1,111 @@
+module Quorum
+  class BlastnJob < ActiveRecord::Base
+
+    before_save :set_optional_params, :set_blast_dbs
+
+    belongs_to :job
+    has_many :blastn_job_reports, 
+      :dependent   => :destroy,
+      :foreign_key => :blastn_job_id,
+      :primary_key => :job_id
+
+    attr_accessible :expectation, :max_score, :min_bit_score,
+      :filter,  :gapped_alignments, :gap_opening_penalty,
+      :gap_extension_penalty, :gap_opening_extension, :queue,
+      :blast_dbs
+
+    validates_format_of :expectation,
+      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :message     => " - Valid formats (12, 32.05, 43e-123)",
+      :allow_blank => true
+    validates_numericality_of :max_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :min_bit_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_opening_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_extension_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_presence_of :blast_dbs, :if => :queue
+    validate :gap_opening_extension_exists
+
+    #
+    # Gapped alignment helper.
+    #
+    def gapped_alignment?
+      self.gapped_alignments
+    end
+
+    #
+    # Valid gap opening and extension values.
+    #
+    def gap_opening_extension_values
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    end
+
+    #
+    # Virtual attribute getter.
+    #
+    def gap_opening_extension
+      [gap_opening_penalty, gap_extension_penalty].join(',')
+    end
+
+    #
+    # Virtual attribute setter.
+    #
+    def gap_opening_extension=(value)
+      v = value.split(',')
+      self.gap_opening_penalty   = v.first
+      self.gap_extension_penalty = v.last
+    end
+
+    private
+
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
+      end
+    end
+
+    def set_optional_params
+      self.expectation   = "5e-10" if self.expectation.blank?
+      self.max_score     ||= 25
+      self.min_bit_score ||= 0
+      unless self.gapped_alignments
+        self.gap_opening_penalty   = 0
+        self.gap_extension_penalty = 0
+      end
+    end
+
+    #
+    # Add error if gapped_alignment? without gap_opening_extension.
+    #
+    def gap_opening_extension_exists
+      if gap_opening_extension.split(',').blank? && gapped_alignment?
+        errors.add(
+          :gap_opening_extension,
+          " - Please select a value."
+        )
+      end
+    end
+
+  end
+end

data/app/models/quorum/blastn_job_report.rb

@@ -0,0 +1,7 @@
+module Quorum
+  class BlastnJobReport < ActiveRecord::Base
+    belongs_to :blastn_job
+    scope :default_order, order("query ASC, bit_score DESC")
+    scope :by_query, lambda { |query| where("query = ?", query) }
+  end
+end

data/app/models/quorum/blastp_job.rb

@@ -0,0 +1,111 @@
+module Quorum
+  class BlastpJob < ActiveRecord::Base
+
+    before_save :set_optional_params, :set_blast_dbs
+
+    belongs_to :job
+    has_many :blastp_job_reports, 
+      :dependent   => :destroy,
+      :foreign_key => :blastp_job_id,
+      :primary_key => :job_id
+
+    attr_accessible :expectation, :max_score, :min_bit_score,
+      :filter,  :gapped_alignments, :gap_opening_penalty,
+      :gap_extension_penalty, :gap_opening_extension, :queue,
+      :blast_dbs
+
+    validates_format_of :expectation,
+      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :message     => " - Valid formats (12, 32.05, 43e-123)",
+      :allow_blank => true
+    validates_numericality_of :max_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :min_bit_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_opening_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_extension_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_presence_of :blast_dbs, :if => :queue
+    validate :gap_opening_extension_exists
+
+    #
+    # Gapped alignment helper.
+    #
+    def gapped_alignment?
+      self.gapped_alignments
+    end
+
+    #
+    # Valid gap opening and extension values.
+    #
+    def gap_opening_extension_values
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    end
+
+    #
+    # Virtual attribute getter.
+    #
+    def gap_opening_extension
+      [gap_opening_penalty, gap_extension_penalty].join(',')
+    end
+
+    #
+    # Virtual attribute setter.
+    #
+    def gap_opening_extension=(value)
+      v = value.split(',')
+      self.gap_opening_penalty   = v.first
+      self.gap_extension_penalty = v.last
+    end
+
+    private
+
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
+      end
+    end
+
+    def set_optional_params
+      self.expectation   = "5e-20" if self.expectation.blank?
+      self.max_score     ||= 25
+      self.min_bit_score ||= 0
+      unless self.gapped_alignments
+        self.gap_opening_penalty   = 0
+        self.gap_extension_penalty = 0
+      end
+    end
+
+    #
+    # Add error if gapped_alignment? without gap_opening_extension.
+    #
+    def gap_opening_extension_exists
+      if gap_opening_extension.split(',').blank? && gapped_alignment?
+        errors.add(
+          :gap_opening_extension,
+          " - Please select a value."
+        )
+      end
+    end
+
+  end
+end

data/app/models/quorum/blastp_job_report.rb

@@ -0,0 +1,7 @@
+module Quorum
+  class BlastpJobReport < ActiveRecord::Base
+    belongs_to :blastp_job
+    scope :default_order, order("query ASC, bit_score DESC")
+    scope :by_query, lambda { |query| where("query = ?", query) }
+  end
+end

data/app/models/quorum/blastx_job.rb

@@ -0,0 +1,111 @@
+module Quorum
+  class BlastxJob < ActiveRecord::Base
+
+    before_save :set_optional_params, :set_blast_dbs
+
+    belongs_to :job
+    has_many :blastx_job_reports, 
+      :dependent   => :destroy,
+      :foreign_key => :blastx_job_id,
+      :primary_key => :job_id
+
+    attr_accessible :expectation, :max_score, :min_bit_score,
+      :filter,  :gapped_alignments, :gap_opening_penalty,
+      :gap_extension_penalty, :gap_opening_extension, :queue,
+      :blast_dbs
+
+    validates_format_of :expectation,
+      :with        => /^[+-]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/,
+      :message     => " - Valid formats (12, 32.05, 43e-123)",
+      :allow_blank => true
+    validates_numericality_of :max_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :min_bit_score,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_opening_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_numericality_of :gap_extension_penalty,
+      :only_integer => true,
+      :allow_blank  => true
+    validates_presence_of :blast_dbs, :if => :queue
+    validate :gap_opening_extension_exists
+
+    #
+    # Gapped alignment helper.
+    #
+    def gapped_alignment?
+      self.gapped_alignments
+    end
+
+    #
+    # Valid gap opening and extension values.
+    #
+    def gap_opening_extension_values
+      [
+        ['--Select--', ''],
+        ['32767, 32767', '32767,32767'],
+        ['11, 2', '11,2'],
+        ['10, 2', '10,2'],
+        ['9, 2', '9,2'],
+        ['8, 2', '8,2'],
+        ['7, 2', '7,2'],
+        ['6, 2', '6,2'],
+        ['13, 1', '13,1'],
+        ['12, 1', '12,1'],
+        ['11, 1', '11,1'],
+        ['10, 1', '10,1'],
+        ['9, 1', '9,1']
+      ]
+    end
+
+    #
+    # Virtual attribute getter.
+    #
+    def gap_opening_extension
+      [gap_opening_penalty, gap_extension_penalty].join(',')
+    end
+
+    #
+    # Virtual attribute setter.
+    #
+    def gap_opening_extension=(value)
+      v = value.split(',')
+      self.gap_opening_penalty   = v.first
+      self.gap_extension_penalty = v.last
+    end
+
+    private
+
+    def set_blast_dbs
+      if self.blast_dbs.present?
+        self.blast_dbs = self.blast_dbs.join(';')
+      end
+    end
+
+    def set_optional_params
+      self.expectation   = "5e-20" if self.expectation.blank?
+      self.max_score     ||= 25
+      self.min_bit_score ||= 0
+      unless self.gapped_alignments
+        self.gap_opening_penalty   = 0
+        self.gap_extension_penalty = 0
+      end
+    end
+
+    #
+    # Add error if gapped_alignment? without gap_opening_extension.
+    #
+    def gap_opening_extension_exists
+      if gap_opening_extension.split(',').blank? && gapped_alignment?
+        errors.add(
+          :gap_opening_extension,
+          " - Please select a value."
+        )
+      end
+    end
+
+  end
+end

data/app/models/quorum/blastx_job_report.rb

@@ -0,0 +1,7 @@
+module Quorum
+  class BlastxJobReport < ActiveRecord::Base
+    belongs_to :blastx_job
+    scope :default_order, order("query ASC, bit_score DESC")
+    scope :by_query, lambda { |query| where("query = ?", query) }
+  end
+end

data/app/models/quorum/job.rb

@@ -0,0 +1,164 @@
+module Quorum
+  class Job < ActiveRecord::Base
+  
+    include Quorum::Sequence
+
+    after_save :queue_workers
+
+    has_one :blastn_job, :dependent => :destroy
+    has_many :blastn_job_reports, :through => :blastn_job, 
+      :dependent => :destroy
+
+    has_one :blastx_job, :dependent => :destroy
+    has_many :blastx_job_reports, :through => :blastx_job, 
+      :dependent => :destroy
+
+    has_one :tblastn_job, :dependent => :destroy
+    has_many :tblastn_job_reports, :through => :tblastn_job, 
+      :dependent => :destroy
+
+    has_one :blastp_job, :dependent => :destroy
+    has_many :blastp_job_reports, :through => :blastp_job, 
+      :dependent => :destroy
+
+    accepts_nested_attributes_for :blastn_job, :blastx_job, :tblastn_job,
+      :blastp_job,
+      :reject_if => proc { |attributes| attributes['queue'] == '0' }
+
+    attr_accessible :sequence, :na_sequence, :aa_sequence, 
+      :blastn_job_attributes, :blastx_job_attributes, :tblastn_job_attributes,
+      :blastp_job_attributes
+
+    validates_associated :blastn_job, :blastx_job, :tblastn_job, :blastp_job
+
+    validate :filter_input_sequences, :algorithm_selected
+
+    private
+
+    #
+    # Filter input sequences by type (AA or NA) and place each in it's
+    # appropriate attribute.
+    #
+    def filter_input_sequences
+      # Ensure the sequences are in plain text.
+      begin
+        ActiveSupport::Multibyte::Unicode.u_unpack(self.sequence)
+      rescue ActiveSupport::Multibyte::EncodingError => e
+        logger.error e.message
+        errors.add(
+          :sequence, 
+          "Please enter your sequence(s) in Plain Text as FASTA."
+        )
+        self.sequence = ""
+        return
+      end
+
+      hash = create_hash(self.sequence)
+      tmp  = File.join(::Rails.root.to_s, 'tmp')
+
+      # Ensure the sequences are FASTA via #write_input_sequence_to_file.
+      begin
+        write_input_sequence_to_file(tmp, hash, self.sequence)
+      rescue Exception => e
+        errors.add(:sequence, e.message)
+        return
+      else
+        fasta = File.read(File.join(tmp, hash + ".fa"))
+      ensure
+        File.delete(File.join(tmp, hash + ".fa"))
+        File.delete(File.join(tmp, hash + ".seq"))
+      end
+
+      self.na_sequence = ""
+      self.aa_sequence = ""
+
+      # Split the sequences on >, check the type (AA or NA) and separate. 
+      seqs = fasta.split('>')
+      seqs.delete_if { |s| s.empty? }
+      seqs.each do |s|
+        type = discover_input_sequence_type(s)
+        if type == "nucleic_acid"
+          self.na_sequence << ">" << s
+        end
+        if type == "amino_acid"
+          self.aa_sequence << ">" << s
+        end 
+      end   
+
+      self.na_sequence = nil if self.na_sequence.empty?
+      self.aa_sequence = nil if self.aa_sequence.empty?
+    end
+
+    #
+    # Make sure an algorithm is selected.
+    #
+    def algorithm_selected
+      in_queue = false
+      if (self.blastn_job && self.blastn_job.queue) || 
+        (self.blastx_job && self.blastx_job.queue) ||
+        (self.tblastn_job && self.tblastn_job.queue) || 
+        (self.blastp_job && self.blastp_job.queue)
+        in_queue = true
+      end
+      unless in_queue
+        errors.add(
+          :algorithm, 
+          " - Please select at least one algorithm to continue."
+        )
+      end
+    end
+
+    #
+    # Queue Resque workers.
+    #
+    def queue_workers
+      jobs = []
+      if self.blastn_job && self.blastn_job.queue
+        jobs << create_system_command("blastn")
+      end
+      if self.blastx_job && self.blastx_job.queue
+        jobs << create_system_command("blastx")
+      end
+      if self.tblastn_job && self.tblastn_job.queue
+        jobs << create_system_command("tblastn")
+      end
+      if self.blastp_job && self.blastp_job.queue
+        jobs << create_system_command("blastp")
+      end
+     
+      unless jobs.blank?
+        jobs.each do |j|
+          Resque.enqueue(
+            Workers::System, j, Quorum.blast_remote, 
+            Quorum.blast_ssh_host, Quorum.blast_ssh_user, 
+            Quorum.blast_ssh_options
+          )
+        end
+      end
+    end
+
+    #
+    # Create system commands based on config/quorum_settings.yml
+    #
+    def create_system_command(algorithm)
+      # System command
+      cmd = ""
+
+      if Quorum::BLAST_ALGORITHMS.include?(algorithm)
+        cmd << "#{Quorum.blast_script} -l #{Quorum.blast_log_dir} " <<
+          "-m #{Quorum.blast_tmp_dir} -b #{Quorum.blast_db} " <<
+          "-t #{Quorum.blast_threads} "
+      else
+        return cmd
+      end
+
+      cmd << "-s #{algorithm} -i #{self.id} " <<
+        "-d #{ActiveRecord::Base.configurations[::Rails.env.to_s]['database']} " <<
+        "-a #{ActiveRecord::Base.configurations[::Rails.env.to_s]['adapter']} " <<
+        "-k #{ActiveRecord::Base.configurations[::Rails.env.to_s]['host']} " <<
+        "-u #{ActiveRecord::Base.configurations[::Rails.env.to_s]['username']} " <<
+        "-p #{ActiveRecord::Base.configurations[::Rails.env.to_s]['password']} "
+    end
+
+  end
+end