quorum 0.1.0 → 0.2.0

data/app/models/quorum/job.rb

@@ -33,6 +33,34 @@ module Quorum
 
     validate :filter_input_sequences, :algorithm_selected
 
+    #
+    # Fetch Blast hit_id, hit_display_id, queue Resque worker and 
+    # return worker's meta_id.
+    #
+    def fetch_quorum_blast_sequence(algo, algo_id)
+      job    = "#{algo}_job".to_sym
+      report = "#{algo}_job_reports".to_sym
+
+      blast_dbs = self.method(job).call.blast_dbs
+
+      job_report = self.method(report).call.where(
+        "quorum_#{algo}_job_reports.id = ?", algo_id
+      ).first
+
+      hit_id          = job_report.hit_id
+      hit_display_id  = job_report.hit_display_id
+
+      cmd = create_blast_fetch_command(blast_dbs, hit_id, hit_display_id, algo)
+
+      data = Workers::System.enqueue(
+        cmd, Quorum.blast_remote, 
+        Quorum.blast_ssh_host, Quorum.blast_ssh_user, 
+        Quorum.blast_ssh_options, true
+      )
+
+      Workers::System.get_meta(data.meta_id)
+    end
+
     private
 
     #
@@ -114,22 +142,22 @@ module Quorum
     def queue_workers
       jobs = []
       if self.blastn_job && self.blastn_job.queue
-        jobs << create_system_command("blastn")
+        jobs << create_search_command("blastn")
       end
       if self.blastx_job && self.blastx_job.queue
-        jobs << create_system_command("blastx")
+        jobs << create_search_command("blastx")
       end
       if self.tblastn_job && self.tblastn_job.queue
-        jobs << create_system_command("tblastn")
+        jobs << create_search_command("tblastn")
       end
       if self.blastp_job && self.blastp_job.queue
-        jobs << create_system_command("blastp")
+        jobs << create_search_command("blastp")
       end
      
       unless jobs.blank?
         jobs.each do |j|
-          Resque.enqueue(
-            Workers::System, j, Quorum.blast_remote, 
+          Workers::System.enqueue(
+            j, Quorum.blast_remote, 
             Quorum.blast_ssh_host, Quorum.blast_ssh_user, 
             Quorum.blast_ssh_options
           )
@@ -138,14 +166,29 @@ module Quorum
     end
 
     #
-    # Create system commands based on config/quorum_settings.yml
+    # Create fetch command based on config/quorum_settings.yml
+    #
+    def create_blast_fetch_command(db_names, hit_id, hit_display_id, algo)
+      # System command
+      cmd = ""
+
+      fetch = File.join(Quorum.blast_bin, "fetch")
+      cmd << "#{fetch} -f blastdbcmd -l #{Quorum.blast_log_dir} " <<
+        "-m #{Quorum.blast_tmp_dir} -d #{Quorum.blast_db} " <<
+        "-n '#{db_names}' -b '#{hit_id}' -s '#{hit_display_id}' " <<
+        "-a #{algo}"
+    end
+
+    #
+    # Create search command based on config/quorum_settings.yml
     #
-    def create_system_command(algorithm)
+    def create_search_command(algorithm)
       # System command
       cmd = ""
 
       if Quorum::BLAST_ALGORITHMS.include?(algorithm)
-        cmd << "#{Quorum.blast_script} -l #{Quorum.blast_log_dir} " <<
+        search = File.join(Quorum.blast_bin, "search")
+        cmd << "#{search} -l #{Quorum.blast_log_dir} " <<
           "-m #{Quorum.blast_tmp_dir} -b #{Quorum.blast_db} " <<
           "-t #{Quorum.blast_threads} "
       else

data/app/views/quorum/jobs/new.html.erb

@@ -4,29 +4,30 @@
     <%= render "shared/error_messages", :target => @job %>
     <div>
       <%= f.text_area :sequence, 
-        :title => "Paste nucleic and amino acid FASTA sequence(s) here or upload a file below.",
+        :title => "Paste nucleic and amino acid FASTA sequence(s) here " << 
+          "or upload a file below.",
         :class => "auto-hint" %>
     </div>
     <div>
       <%= f.file_field :sequence_file %>
     </div>
     <!-- Search Algorithms -->
-    <!-- Comment out an alorithm below to remove it from the form. -->
+    <!-- Comment out an algorithm below to remove it from the form. -->
 
     <!-- blastn -->
-    <%= render :partial => "blastn_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastn_form", :locals => { 
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- blastx -->
-    <%= render :partial => "blastx_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastx_form", :locals => { 
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- tblastn -->
-    <%= render :partial => "tblastn_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/tblastn_form", :locals => { 
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- blastp -->
-    <%= render :partial => "blastp_form", :locals => { 
+    <%= render :partial => "quorum/jobs/form/blastp_form", :locals => { 
       :f => f, :blast_dbs => @blast_dbs } %>
 
     <!-- End Search Algorithms -->

data/app/views/quorum/jobs/show.html.erb

@@ -16,28 +16,28 @@
     <div id="tabs-1">
       <h2>Blastn</h2>
       <div id="blastn-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
     <div id="tabs-2">
       <h2>Blastx</h2>
       <div id="blastx-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
     <div id="tabs-3">
       <h2>Tblastn</h2>
       <div id="tblastn-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
 
     <div id="tabs-4">
       <h2>Blastp</h2>
       <div id="blastp-results">
-        Searching... <%= image_tag "quorum/knight_rider.gif" %> 
+        Searching... <%= image_tag "quorum/loading.gif" %> 
       </div>
     </div>
   </div>
@@ -54,120 +54,9 @@
   </p>
 </div>
 
-<!-- Blast Results Template -->
-<script type="text/template" id="blast_template">
-  {{ if (data[0].results === false) { }}
-    <p><strong>Your search returned 0 hits.</strong></p>
-  {{ } else { }}
-	  <table class="results">
-	    <tr>
-	      <th>Query Accession</th>
-	      <th>Query Length</th>
-	      <th>Hit Length</th>
-	      <th>Qstrand / Hstrand</th>
-	      <th>Hit Accession</th>
-	      <th>Hit Description</th>
-	      <th>Alignment Length</th>
-        <th>
-          <a class="bit-score"
-            onclick="openWindow(
-              'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app8/',
-              'Bit Score',
-              800,
-              300
-            )">
-            Bit Score
-          </a>
-        </th>
-        <th>
-          <a class="e-value"
-            onclick="openWindow(
-              'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app42/',
-              'E-value',
-              800,
-              300
-            )">
-            E-value
-          </a>
-        </th>
-	    </tr>
-	    {{ var i = 1; var style = "" }}
-	    {{ _.each(data, function(v) { }}
-	      {{ i % 2 == 0 ? style = "even" : style = "odd" }}
-        {{ var qstrand = v.query_frame }}
-        {{ var hstrand = v.hit_frame }}
-	      <tr class="{{= style }}">
-	        <td>{{= v.query }}</td>
-	        <td class="right">{{= v.query_len }}</td>
-	        <td class="right">{{= v.hit_len }}</td>
-          <td>{{= formatStrand(qstrand, hstrand) }}</td>
-          <td>{{= v.hit_id }}</td>
-          <td>{{= v.hit_def.trunc(20) }}</td>
-	        <td class="right">{{= v.align_len }}</td>
-	        <td class="right">{{= v.bit_score }}</td>
-          <td class="right">
-            <a class="detailed_report" 
-              onclick="viewDetailedReport(
-                <%= @jobs.id %>, 
-                {{= v.id }}, 
-                '{{= v.query }}', 
-                '{{= algo }}')">
-              {{= v.evalue }}
-            </a>
-          </td>
-	      </tr>
-	      {{ i++ }}
-	    {{ }); }}
-	  </table>
-  {{ } }}
-</script>
-
-<!-- Detailed Report Template -->
-<script type="text/template" id="detailed_report_template">
-  <h3>Query Accession {{= query }}</h3>
-  {{ _.each(data, function(v) { }}
-    {{ var id        = v.id }}
-    {{ var qseq      = v.qseq }}
-    {{ var midline   = v.midline }}
-    {{ var hseq      = v.hseq }}
-    {{ var q_from    = v.query_from }}
-    {{ var q_to      = v.query_to }}
-    {{ var h_from    = v.hit_from }} 
-    {{ var h_to      = v.hit_to }} 
-    {{ var qstrand   = v.query_frame }}
-    {{ var hstrand   = v.hit_frame }}
-    {{ var hsp_group = v.hsp_group }}
-    <div id="{{= id }}">
-      <p class="small">{{= displayHspLinks(id, hsp_group, data) }}</p>
-      <p class="small">Hit Accession: {{= v.hit_id }}</p>
-      <p class="small">Hit Description: {{= v.hit_def }}</p>
-	    <table class="report_details">
-	      <tr>
-	        <td>E-value: {{= v.evalue }}</td>
-	        <td>Bit Score: {{= v.bit_score }}</td>
-          <td></td>
-	      </tr>
-	      <tr>
-	        <td>Alignment Length: {{= v.align_len }}</td>
-	        <td>Qstrand / Hstrand: {{= formatStrand(qstrand, hstrand) }}</td>
-          <td></td>
-	      </tr>
-	      <tr>
-          <td>Query Length: {{= v.query_len }}</td>
-	        <td>Query From: {{= v.query_from }}</td>
-	        <td>Query To: {{= v.query_to }}</td>
-	      </tr>
-	      <tr>
-          <td>Hit Length: {{= v.hit_len }}</td>
-	        <td>Hit From: {{= v.hit_from }}</td>
-	        <td>Hit To: {{= v.hit_to }}</td>
-	      </tr>
-	    </table>
-	    {{= formatSequenceReport(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) }}
-    </div>
-    <hr />
-  {{ }); }}
-</script>
+<!-- Templates -->
+<%= render :partial => "quorum/jobs/templates/blast_template" %>
+<%= render :partial => "quorum/jobs/templates/blast_detailed_report_template" %>
 
 <script type="text/javascript">
   $(function() {

data/app/views/quorum/jobs/templates/_blast_detailed_report_template.html.erb

@@ -0,0 +1,53 @@
+<!-- Detailed Report Template -->
+<script type="text/template" id="detailed_report_template">
+  <h3>Query Accession {{= query }}</h3>
+  {{ _.each(data, function(v) { }}
+    {{ var id        = v.id }}
+    {{ var qseq      = v.qseq }}
+    {{ var midline   = v.midline }}
+    {{ var hseq      = v.hseq }}
+    {{ var q_from    = v.query_from }}
+    {{ var q_to      = v.query_to }}
+    {{ var h_from    = v.hit_from }} 
+    {{ var h_to      = v.hit_to }} 
+    {{ var qstrand   = v.query_frame }}
+    {{ var hstrand   = v.hit_frame }}
+    {{ var hsp_group = v.hsp_group }}
+    <div id="{{= id }}">
+      <p class="small">{{= displayHspLinks(id, hsp_group, data) }}</p>
+      <p class="small">Hit Accession: {{= v.hit_display_id }}</p>
+      <p class="small">Hit Description: {{= v.hit_def }}</p>
+	    <table class="report_details">
+	      <tr>
+	        <td>E-value: {{= v.evalue }}</td>
+	        <td>Bit Score: {{= v.bit_score }}</td>
+          <td></td>
+	      </tr>
+	      <tr>
+	        <td>Alignment Length: {{= v.align_len }}</td>
+	        <td>Qstrand / Hstrand: {{= formatStrand(qstrand, hstrand) }}</td>
+          <td></td>
+	      </tr>
+	      <tr>
+          <td>Query Length: {{= v.query_len }}</td>
+	        <td>Query From: {{= v.query_from }}</td>
+	        <td>Query To: {{= v.query_to }}</td>
+	      </tr>
+	      <tr>
+          <td>Hit Length: {{= v.hit_len }}</td>
+	        <td>Hit From: {{= v.hit_from }}</td>
+	        <td>Hit To: {{= v.hit_to }}</td>
+	      </tr>
+	    </table>
+      <p class="small">
+        <a id="download_sequence_{{= id }}" 
+          onclick="downloadSequence(<%= @jobs.id %>, {{= id }}, '{{= algo }}', this)">
+          Download Sequence
+        </a>
+      </p>
+      {{= formatSequenceReport(qseq, midline, hseq, q_from, q_to, h_from, h_to, algo) }}
+    </div>
+    <hr />
+  {{ }); }}
+</script>
+

data/app/views/quorum/jobs/templates/_blast_template.html.erb

@@ -0,0 +1,68 @@
+<!-- Blast Results Template -->
+<script type="text/template" id="blast_template">
+  {{ if (data[0].results === false) { }}
+    <p><strong>Your search returned 0 hits.</strong></p>
+  {{ } else { }}
+	  <table class="results">
+	    <tr>
+	      <th>Query Accession</th>
+	      <th>Query Length</th>
+	      <th>Hit Length</th>
+	      <th>Qstrand / Hstrand</th>
+	      <th>Hit Accession</th>
+	      <th>Hit Description</th>
+	      <th>Alignment Length</th>
+        <th>
+          <a class="bit-score"
+            onclick="openWindow(
+              'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app8/',
+              'Bit Score',
+              800,
+              300
+            )">
+            Bit Score
+          </a>
+        </th>
+        <th>
+          <a class="e-value"
+            onclick="openWindow(
+              'http://www.ncbi.nlm.nih.gov/books/NBK21106/def-item/app42/',
+              'E-value',
+              800,
+              300
+            )">
+            E-value
+          </a>
+        </th>
+	    </tr>
+	    {{ var i = 1; var style = "" }}
+	    {{ _.each(data, function(v) { }}
+	      {{ i % 2 == 0 ? style = "even" : style = "odd" }}
+        {{ var qstrand = v.query_frame }}
+        {{ var hstrand = v.hit_frame }}
+	      <tr class="{{= style }}">
+	        <td>{{= v.query }}</td>
+	        <td class="right">{{= v.query_len }}</td>
+	        <td class="right">{{= v.hit_len }}</td>
+          <td>{{= formatStrand(qstrand, hstrand) }}</td>
+          <td>{{= v.hit_display_id }}</td>
+          <td>{{= v.hit_def.trunc(20) }}</td>
+	        <td class="right">{{= v.align_len }}</td>
+	        <td class="right">{{= v.bit_score }}</td>
+          <td class="right">
+            <a class="detailed_report" 
+              onclick="viewDetailedReport(
+                <%= @jobs.id %>, 
+                {{= v.id }}, 
+                '{{= v.query }}', 
+                '{{= algo }}')">
+              {{= v.evalue }}
+            </a>
+          </td>
+	      </tr>
+	      {{ i++ }}
+	    {{ }); }}
+	  </table>
+  {{ } }}
+</script>
+

data/config/routes.rb

@@ -2,6 +2,8 @@ Quorum::Engine.routes.draw do
   resources :jobs, :only => [:index, :show, :new, :create] do
     member do
       get :get_quorum_search_results
+      get :get_quorum_blast_hit_sequence
+      get :send_quorum_blast_hit_sequence
     end
   end
 

data/db/migrate/20120109232446_add_hit_display_id_to_blast_reports.rb

@@ -0,0 +1,8 @@
+class AddHitDisplayIdToBlastReports < ActiveRecord::Migration
+  def change
+    add_column :quorum_blastn_job_reports, :hit_display_id, :string
+    add_column :quorum_blastx_job_reports, :hit_display_id, :string
+    add_column :quorum_tblastn_job_reports, :hit_display_id, :string
+    add_column :quorum_blastp_job_reports, :hit_display_id, :string
+  end
+end

data/lib/generators/quorum/images_generator.rb

@@ -0,0 +1,18 @@
+module Quorum
+  module Generators
+    class ImagesGenerator < Rails::Generators::Base
+      source_root File.expand_path("../../../../app/assets/images", __FILE__)
+      desc "Copy quorum images to your application."
+
+      IMAGE_DIRECTORIES = [
+        "quorum"
+      ]
+
+      def copy_images
+        IMAGE_DIRECTORIES.each do |d|
+          directory d.to_s, "app/assets/images/#{d.to_s}"
+        end
+      end
+    end
+  end
+end

data/lib/generators/quorum/install_generator.rb

@@ -1,21 +1,26 @@
 module Quorum
   module Generators
     class InstallGenerator < Rails::Generators::Base
+
+      include Quorum::Helpers::Colors
+
       source_root File.expand_path("../../templates", __FILE__)
 
-      desc "Creates Quorum initializer, settings and " <<
-           "search tool files."
+      desc "Creates Quorum initializer, settings and search " <<
+           "/ fetch tool files."
 
       DEPENDENCIES = ["makeblastdb", "seqret"]
 
-      def copy_initializer
+      def copy_quorum
         template "quorum_initializer.rb", 
           "config/initializers/quorum_initializer.rb"
         template "quorum_settings.yml", "config/quorum_settings.yml"
         template "search", "quorum/bin/search"
+        template "fetch", "quorum/bin/fetch"
         template "trollop.rb", "quorum/lib/trollop.rb"
         template "logger.rb", "quorum/lib/logger.rb"
         template "blast.rb", "quorum/lib/search_tools/blast.rb"
+        template "blast_db.rb", "quorum/lib/fetch_tools/blast_db.rb"
       end
 
       def copy_locale
@@ -23,8 +28,9 @@ module Quorum
       end
 
       def change_file_permissions
-        f = File.new("quorum/bin/search", "r")
-        f.chmod(0755)
+        Dir.glob(File.join("quorum", "bin", "*")).each do |f|
+          File.new(f, "r").chmod(0755)
+        end
       end
 
       def create_quorum_tmp_dir
@@ -35,12 +41,30 @@ module Quorum
         Dir.mkdir("quorum/log") unless File.directory?("quorum/log")
       end
 
+      def set_mount_engines
+        @quorum = %Q(mount Quorum::Engine => "/quorum")
+        @resque = %Q(mount Resque::Server.new, :at => "/quorum/resque")
+      end
+      
+      def read_routes_file
+        @routes = File.open(File.join("config", "routes.rb"), "r")
+        @routes = @routes.read
+      end
+
+      def mount_engine_exists?
+        @routes.include?(@quorum)
+      end
+
       def add_mount_engine
-        route %Q(mount Quorum::Engine => "/quorum")
+        route @quorum unless mount_engine_exists? 
+      end
+
+      def resque_mount_engine_exists?
+        @routes.include?(@resque)
       end
 
       def add_resque_mount_engine
-        route %Q(mount Resque::Server.new, :at => "/quorum/resque")
+        route @resque unless resque_mount_engine_exists?
       end
 
       def check_dependencies
@@ -49,14 +73,18 @@ module Quorum
         messages = []
         DEPENDENCIES.each do |b|
           system("which #{b} > /dev/null 2>&1")
-          if $?.exitstatus > 0
-            messages << "Please add `#{b}` to your PATH."
-          end
+          messages << b if $?.exitstatus > 0
         end
         unless messages.empty?
-          puts "*** Warning: Quorum system dependencies not found ***"
-          messages.each { |m| puts m }
-          puts ""
+          puts bold(
+            red("*** Warning: Quorum system dependencies not found ***")
+          )
+          puts bold(
+            red("Please add the below to your PATH.")
+          )
+          messages.each { |m| puts bold(red(m)) }
+        else
+          puts "All good! Yay!!"
         end
       end
 

data/lib/generators/templates/README

@@ -1,5 +1,5 @@
 
-ZOMG!! Thanks for installing Quorum!!
+Thanks for installing Quorum!!
 
 ==============================================================================
 

data/lib/generators/templates/blast.rb

@@ -11,6 +11,8 @@ module Quorum
     class Blast
 
       class QuorumJob < ActiveRecord::Base
+        set_table_name "quorum_jobs"
+
         has_one :quorum_blastn_job, 
           :foreign_key => "job_id"
         has_many :quorum_blastn_job_reports, 
@@ -33,38 +35,46 @@ module Quorum
       end
 
       class QuorumBlastnJob < ActiveRecord::Base
+        set_table_name "quorum_blastn_jobs"
         belongs_to :quorum_job
         has_many :quorum_blastn_job_reports
       end
 
       class QuorumBlastnJobReport < ActiveRecord::Base
+        set_table_name "quorum_blastn_job_reports"
         belongs_to :quorum_blastn_job
       end
 
       class QuorumBlastxJob < ActiveRecord::Base
+        set_table_name "quorum_blastx_jobs"
         belongs_to :quorum_job
         has_many :quorum_blastx_job_reports
       end
 
       class QuorumBlastxJobReport < ActiveRecord::Base
+        set_table_name "quorum_blastx_job_reports"
         belongs_to :quorum_blastx_job
       end
 
       class QuorumTblastnJob < ActiveRecord::Base
+        set_table_name "quorum_tblastn_jobs"
         belongs_to :quorum_job
         has_many :quorum_tblastn_job_reports
       end
 
       class QuorumTblastnJobReport < ActiveRecord::Base
+        set_table_name "quorum_tblastn_job_reports"
         belongs_to :quorum_tblastn_job
       end
 
       class QuorumBlastpJob < ActiveRecord::Base
+        set_table_name "quorum_blastp_jobs"
         belongs_to :quorum_job
         has_many :quorum_blastp_job_reports
       end
 
       class QuorumBlastpJobReport < ActiveRecord::Base
+        set_table_name "quorum_blastp_job_reports"
         belongs_to :quorum_blastp_job
       end
 
@@ -235,26 +245,26 @@ module Quorum
       end
 
       #
-      # Format Blast report hit_id and hit_def.
+      # Format Blast report hit_display_id and hit_def.
       #
       # For added flexibility, Quorum doesn't parse seqids or deflines.
       # Instead, format_hit splits the hit_def on whitespace and
-      # reports hit_id as the first element and hit_def as the second.
+      # reports hit_display_id as the first element and hit_def as the second.
       #
       def format_hit(str)
-        hit_id  = ""
+        hit_display_id  = ""
         hit_def = ""
 
         hit = str.split(" ", 2)
         if hit.length < 2
-          hit_id  = hit.first
+          hit_display_id  = hit.first
           hit_def = "None"
         else
-          hit_id  = hit.first
+          hit_display_id  = hit.first
           hit_def = hit.last
         end
 
-        return hit_id, hit_def
+        return hit_display_id, hit_def
       end
 
       #
@@ -275,8 +285,9 @@ module Quorum
             @data[:query_len] = iteration.query_len
 
             iteration.each do |hit|
-              @data[:hit_id], @data[:hit_def] = format_hit(hit.hit_def)
+              @data[:hit_display_id], @data[:hit_def] = format_hit(hit.hit_def)
 
+              @data[:hit_id]        = hit.hit_id
               @data[:hit_accession] = hit.accession
               @data[:hit_len]       = hit.len