MARQ 0.0.1

data/merb/app/views/results/error.html.haml

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+:javascript
+  current = 'error';
+
+%center
+  %p= @message

data/merb/app/views/results/explore_hits.html.haml

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+:javascript
+  current = '#{@job}';
+
+%h2#title
+  Results for: 
+  %a.job{:href => "/#{ @job }"}= @job
+  > 
+  %span.jobname== #{ @name }
+
+
+- genes = []
+#hits
+  #canvas
+
+  #genes_hits
+    %table#table_genes_headers
+      %thead
+        %tr
+          %th.name Name
+          %th.synonyms Synonyms
+          %th.hit Pos.
+    %div.table_scroller
+      %table#table_genes
+        %tbody
+          - @hits.each do |p|
+            - genes << p[0][0]
+            %tr{:id => p[0][0]}
+              %td.name
+                - if p[0][0] != p[0][1]
+                  - name = "#{p[0][0]} (#{p[0][1]})"
+                - else
+                  - name = p[0][0]
+                - url = gene_url(@org, p[0][1])
+                - if ! url.nil?
+                  %a.geneurl{:href => "#{url}", :blank => "_target"}= name
+                - else
+                  = name
+                - if @gds
+                  %a.button.profile{:href => "http://www.ncbi.nlm.nih.gov/sites/entrez?db=geo&term=#{@gds}[ACCN]+(#{@translations[p[0][1]].join("OR ")})", :blank => "_target"} GDS
+              %td.synonyms=@synonyms[p[0][1]].uniq.join(", ")
+              %td.hit=p[1]
+
+    .menu_links
+      %a.selected_genes.button{:href => '#'} Get selected genes
+      %a.logratios_hits.button{:href => %"/logratios?experiment=#{escapeURI(@name)}&job=#{@job}&genes=#{genes.join(",")}"} Get logratios
+      - if @name !~ /\[ratio\]/
+        %a.ts_hits.button{:href => "/ts?experiment=#{escapeURI(@name)}&job=#{@job}&genes=#{genes.join(",")}"} Get t-values
+      .clear_floats
+
+:javascript
+
+  var total_genes = #{@total}
+
+  $(start_results_hits);

data/merb/app/views/results/images.html.haml

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+#images
+
+  %h1= @experiment
+
+  - upfile = "/results/images/#{@name}/up/#{@hash}.png"
+  - downfile = "/results/images/#{@name}/down/#{@hash}.png"
+
+  %p
+  - if File.exist? File.join('public', upfile)
+    %h2 Up
+    %p
+      %img{:src => upfile}
+
+  - if File.exist? File.join('public', downfile)
+    %h2 Down
+    %p
+      %img{:src =>downfile}
+

data/merb/app/views/results/main.html.haml

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+:javascript
+  current = '#{@name}';
+
+%h2#title
+  Results for: 
+  %span.jobname= @name
+  %span#status Loading Signature Table
+:javascript
+  var working = false;
+  var status_callback = null;
+  function set_status(text){
+    working = true;
+    $('#status').html(text).show();
+  }
+
+  function hide_status(){
+    working = false;
+    $('#status').hide();
+    if (status_callback != null){
+      status_callback();
+    }
+  }
+
+#results
+  #canvas
+ 
+  #table
+    
+    #annotations_menu
+      = partial 'partials/annotations'
+    
+    
+    .menu_links
+      %a#annotations_menu_link.button{:href => '#'} Annotations Menu
+      :javascript
+        $('#annotations_menu').hide()
+        $('#annotations_menu_link').click(function(){$('#annotations_menu').toggle('slow');return false;})
+      
+      %a#compare_link.button{:href => '#'} Compare signatures
+      .clear_floats
+      
+
+
+    %table#table_results_headers
+      %thead
+        %tr
+          %th.experiment Experiment
+          %th.score Score
+          %th.pvalue P-Val
+          %th.select Compare 
+          /  ↑ / ↓
+    - total = @results.length
+    %div.table_scroller
+      %table#table_results
+        %tbody
+          - @results.each_with_index do |item,i|
+            - if i % (total/10) == 9 
+              - percent = ((100 * i) / total).to_i 
+              :javascript
+                set_status("Loading Signature Table  #{ percent }%")
+            - experiment = item[0]
+            - info       = item[1]
+
+            - if experiment =~ /^GDS|GSE/
+              - gds, condition, name = Info::parse_experiment(experiment).values_at(:gds, :condition, :name) 
+              - title, description = Info::GDS_info(gds).values_at(:title, :description)
+
+              %tr{:id => experiment}
+                %td.experiment
+                  %a.toggle{:href =>"#"} [+]
+                  %span.gds
+                    %span.title= span_words(title)
+                    -if gds =~ /GSE/
+                      %a.dataset{:href =>"http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=#{gds}",:target => "_blank"} [GEO]
+                    -else
+                      %a.dataset{:href =>"http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=#{gds}",:target => "_blank"} [GEO]
+                  %span.test
+                    = span_words(name)
+                    %span.condition== (#{ condition })
+                %td.score= "%1.3g" % info[:score] 
+                - if info[:pvalue] <= 0.05
+                  %td.pvalue.significant= print_pvalue info[:pvalue]
+                - else
+                  %td.pvalue= print_pvalue info[:pvalue]
+                %td.select
+                  %label{:for => "#{i}_up"} &uarr;
+                  %input.compare_select{:type => 'checkbox', :name => experiment, :id=> "#{i}_up" }
+                  %label{:for => "#{i}_down"} &nbsp;&nbsp;&darr;
+                  %input.compare_invert{:type => 'checkbox', :name => experiment, :id=> "#{i}_down"}
+            - else
+              - gds, condition, name = Info::parse_experiment(experiment).values_at(:gds, :condition, :name) 
+              - title, description, gpl = Info::CustomDS_info(gds).values_at(:title, :description, :gpl)
+              %tr{:id => experiment}
+                %td.experiment
+                  %a.toggle{:href =>"#"} [+]
+                  %span.gds
+                    %span.title= span_words(title)
+                    == (#{gds}) 
+                  %span.test  
+                    = span_words(name)
+                    %span.condition== (#{ condition })
+                %td.score= "%1.3g" % info[:score] 
+                - if info[:pvalue] <= 0.05
+                  %td.pvalue.significant= print_pvalue info[:pvalue]
+                - else
+                  %td.pvalue= "%1.3g" % info[:pvalue]
+                %td.select
+                  %label{:for => "#{i}_up"} &uarr;
+                  %input.compare_select{:type => 'checkbox', :name => experiment, :id=> "#{i}_up" }
+                  %label{:for => "#{i}_down"} &nbsp;&nbsp;&darr;
+                  %input.compare_invert{:type => 'checkbox', :name => experiment, :id=> "#{i}_down"}
+    %a#reset.button{:href =>"#", :onclick => "reset_checkboxes()"} Reset 
+
+
+:javascript
+  set_status("Resizing Table...")
+  var job = "#{@name}";
+  
+  var annotations = [];
+  var enrichment = [];
+
+  
+  $(start_results_main);
+  
+  

data/merb/app/views/results/wait.html.haml

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+:javascript
+  current = '#{@name}';
+
+%head  
+  %meta{ 'http-equiv' => 'refresh', :content => "15" }
+
+%center
+  %h2== Job #{@name} is being processed
+  %h4= @message
+  %img{:src =>"images/wait.gif"}

data/merb/app/views/series/main.html.haml

@@ -0,0 +1,99 @@
+:javascript
+  var series = "#{@series}";
+  current = 'series';
+#series
+  %form{:action => "/series", :method => 'post'}
+    %p
+      The server needs to retrieve all the sample data from GEO the first time, this might take a few minutes...
+    %p
+      %input{:name => "series", :value => @series}
+      %input{:type => 'submit'}
+  
+    - if @series
+      %dl
+    
+        %dt Series
+        %dd
+          %a{:href =>"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#{@series}"}= @series
+        - if @gds
+          %dt Dataset
+          %dd This series has a GDS
+        %dt Platform
+        %dd
+          %a{:href =>"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=#{@series_info[:platform]}"}= @series_info[:platform] 
+        %dt Title
+        %dd= @series_info[:title]
+        %dt Description
+        %dd= @series_info[:description]
+      
+      %a.add.button{:href =>'#'} add new condition
+      %table#samples
+        %thead
+          %tr
+            %th Sample
+            %th Title
+            %th.phenotype
+              %input{:value => 'condition', :size => '6'}
+              %a.del{:href =>'#'} del
+        %tbody
+          - @series_info[:samples].each do |gsm|
+            %tr{:id => gsm}
+              %td.gsm{'data-description' => @sample_info[gsm][:description]}= gsm
+              %td= @sample_info[gsm][:title]
+              %td.value
+                %input{:size => '8'}
+     
+      %a.gen.button{:href =>'#'} Generate description file
+      
+:javascript
+  function add(){
+    table = $('table#samples');
+    table.find('thead tr').append(tag('th').addClass('phenotype').append(tag('input').attr('value','condition').attr('size',8)).append(tag('a').addClass('del').attr('href','#').html('del')));
+    table.find('tbody tr').append(tag('td').addClass('value').append(tag('input').attr('size', 10)));
+    $('a.del').click(del);
+    return(false);
+  }
+
+  function del(){
+    $(this).parents('th').attr('data-selected', true);
+    i = 1;
+    $(this).parents('tr').find('th').each(function(){
+      if ($(this).attr('data-selected'))
+        return(false);
+      i += 1;
+    })
+
+    position = i;
+
+    table = $('table#samples');
+    table.find('thead tr th:nth-child(' + position + ')').remove()
+    table.find('tbody tr td:nth-child(' + position + ')').remove()
+    return(false);
+  }
+
+  function description_file(){
+
+    var conditions = [];
+    $('table thead tr th.phenotype input').each(function(){
+     conditions.push($(this).val());
+    })
+
+    var  values = [];
+    $('table tbody tr td.value input').each(function(){
+     values.push($(this).val());
+    })
+
+
+    window.location = "/series?series=" + series + "&conditions=" + conditions.join("|") + "&values=" + values.join("|")
+    return(false);
+  }
+
+
+  $(function(){
+    $('a.add').click(add);
+    $('a.del').click(del);
+    $('a.gen').click(description_file);
+  })
+
+
+ 

data/merb/autotest/discover.rb

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+Autotest.add_discovery { "merb" }

data/merb/autotest/merb.rb

@@ -0,0 +1,149 @@
+# Adapted from Autotest::Rails
+require 'autotest'
+
+class Autotest::Merb < Autotest
+  
+  # +model_tests_dir+::      the directory to find model-centric tests
+  # +controller_tests_dir+:: the directory to find controller-centric tests
+  # +view_tests_dir+::       the directory to find view-centric tests
+  # +fixtures_dir+::         the directory to find fixtures in
+  attr_accessor :model_tests_dir, :controller_tests_dir, :view_tests_dir, :fixtures_dir
+  
+  def initialize
+    super
+    
+    initialize_test_layout
+    
+    # Ignore any happenings in these directories
+    add_exception %r%^\./(?:doc|log|public|tmp)%
+    
+    # Ignore any mappings that Autotest may have already set up
+    clear_mappings
+    
+    # Any changes to a file in the root of the 'lib' directory will run any 
+    # model test with a corresponding name.
+    add_mapping %r%^lib\/.*\.rb% do |filename, _|
+      files_matching Regexp.new(["^#{model_test_for(filename)}$"])
+    end
+    
+    # Any changes to a fixture will run corresponding view, controller and 
+    # model tests
+    add_mapping %r%^#{fixtures_dir}/(.*)s.yml% do |_, m|
+      [
+        model_test_for(m[1]), 
+        controller_test_for(m[1]), 
+        view_test_for(m[1])
+      ]
+    end
+    
+    # Any change to a test or test will cause it to be run
+    add_mapping %r%^test/(unit|models|integration|controllers|views|functional)/.*rb$% do |filename, _|
+      filename
+    end
+    
+    # Any change to a model will cause it's corresponding test to be run
+    add_mapping %r%^app/models/(.*)\.rb$% do |_, m|
+      model_test_for(m[1])
+    end
+    
+    # Any change to the global helper will result in all view and controller 
+    # tests being run
+    add_mapping %r%^app/helpers/global_helpers.rb% do
+      files_matching %r%^test/(views|functional|controllers)/.*_test\.rb$%
+    end
+    
+    # Any change to a helper will run it's corresponding view and controller 
+    # tests, unless the helper is the global helper. Changes to the global 
+    # helper run all view and controller tests.
+    add_mapping %r%^app/helpers/(.*)_helper(s)?.rb% do |_, m|
+      if m[1] == "global" then
+        files_matching %r%^test/(views|functional|controllers)/.*_test\.rb$%
+      else
+        [
+          view_test_for(m[1]), 
+          controller_test_for(m[1])
+        ]
+      end
+    end
+    
+    # Changes to views result in their corresponding view and controller test 
+    # being run
+    add_mapping %r%^app/views/(.*)/% do |_, m|
+      [
+        view_test_for(m[1]), 
+        controller_test_for(m[1])
+      ]
+    end
+    
+    # Changes to a controller result in its corresponding test being run. If 
+    # the controller is the exception or application controller, all 
+    # controller tests are run.
+    add_mapping %r%^app/controllers/(.*)\.rb$% do |_, m|
+      if ["application", "exception"].include?(m[1])
+        files_matching %r%^test/(controllers|views|functional)/.*_test\.rb$%
+      else
+        controller_test_for(m[1])
+      end
+    end
+
+    # If a change is made to the router, run all controller and view tests
+    add_mapping %r%^config/router.rb$% do # FIX
+      files_matching %r%^test/(controllers|views|functional)/.*_test\.rb$%
+    end
+
+    # If any of the major files governing the environment are altered, run 
+    # everything
+    add_mapping %r%^test/test_helper.rb|config/(init|rack|environments/test.rb|database.yml)% do # FIX
+      files_matching %r%^test/(unit|models|controllers|views|functional)/.*_test\.rb$%
+    end
+  end
+  
+private
+
+  # Determines the paths we can expect tests or specs to reside, as well as 
+  # corresponding fixtures.
+  def initialize_test_layout
+    self.model_tests_dir      = "test/unit"
+    self.controller_tests_dir = "test/functional"
+    self.view_tests_dir       = "test/views"
+    self.fixtures_dir         = "test/fixtures"
+  end
+  
+  # Given a filename and the test type, this method will return the 
+  # corresponding test's or spec's name.
+  # 
+  # ==== Arguments
+  # +filename+<String>:: the file name of the model, view, or controller
+  # +kind_of_test+<Symbol>:: the type of test we that we should run
+  # 
+  # ==== Returns
+  # String:: the name of the corresponding test or spec
+  # 
+  # ==== Example
+  # 
+  #   > test_for("user", :model)
+  #   => "user_test.rb"
+  #   > test_for("login", :controller)
+  #   => "login_controller_test.rb"
+  #   > test_for("form", :view)
+  #   => "form_view_spec.rb" # If you're running a RSpec-like suite
+  def test_for(filename, kind_of_test)
+    name  = [filename]
+    name << kind_of_test.to_s if kind_of_test == :view
+    name << "test"
+    return name.join("_") + ".rb"
+  end
+  
+  def model_test_for(filename)
+    [model_tests_dir, test_for(filename, :model)].join("/")
+  end
+  
+  def controller_test_for(filename)
+    [controller_tests_dir, test_for(filename, :controller)].join("/")
+  end
+  
+  def view_test_for(filename)
+    [view_tests_dir, test_for(filename, :view)].join("/")
+  end
+  
+end