MARQ 0.0.1

data/merb/app/controllers/main.rb

@@ -0,0 +1,72 @@
+class Main < Application
+  include CacheHelper
+
+  def index
+    @organisms = {}
+    
+    cache("main") do
+      Organism.all.collect{|org| 
+        [  
+          org, 
+          Organism.name(org), 
+          MARQ.organism_platforms(org).sort{|a,b| 
+            a.sub(/GPL/,'').to_i <=> b.sub(/GPL/,'').to_i
+          }
+        ]
+      }.select{|p| 
+        p[0].to_s != 'worm' &&  # Remove worm, it only has 11 datasets 
+          p[2].any?
+      }.each{|p| 
+        @organisms[p[0]] = [p[1],p[2]]
+      }
+  
+      headers["Expires"] = (Time.now + 31536000).to_s
+      headers['Cache-Control'] = 'public, max-age=31536000'
+  
+  
+      render
+    end
+  end
+
+  def post
+    platform = params[:platform]
+    organism = params[:organism]
+    ids_up   = params[:ids_up].split(/["\s,;]+/).uniq.collect{|gene| gene.strip}
+    ids_down = params[:ids_down].split(/["\s,;]+/).uniq.collect{|gene| gene.strip}
+    name     = params[:name].gsub(/\s/,'_')
+
+    if platform == "cross"
+      name = WS::match_organism(organism, ids_up, ids_down, name || "")
+    else
+      name = WS::match_platform(platform, ids_up, ids_down, name || "")
+    end
+
+
+    ip = request.env['HTTP_X_FORWARDED_FOR'] || request.env['REMOTE_ADDR']
+    JobLog.log(ip, name)
+
+
+    redirect "/#{ name }" 
+  end
+
+  def ajax_partial
+    name = params[:name]
+    job = params[:job]
+    data = params[name.to_sym]
+
+    @name = job
+    partial "partials/#{name}", :with => data, :as => name.to_sym
+  end
+ 
+  def get_genes
+    genes = params[:genes].split("|")
+
+    headers["Content-Type"] =  'text/plain'
+    headers["Content-Disposition"] =  'attachment; filename=genes.txt'
+
+    genes.join("\n")
+  end
+
+
+
+end

data/merb/app/controllers/normalize.rb

@@ -0,0 +1,41 @@
+require 'MARQ/ID'
+
+class Normalize < Application
+  def index
+    @organisms = Organism.all
+    @ids = {}
+    @organisms.each{|org|
+      @ids[org] = Organism.supported_ids(org)
+    }
+    @found ||= []
+    @missing ||= []
+    
+    render :template => 'normalize/index'
+  end
+
+  def post
+    org = params[:org]
+    missing = params[:missing].split(/[\s,]+/)
+    found = params[:found].split(/[\s,]+/)
+    id = params[:id]
+
+
+    translations = ID.translate(org,missing, :to => id )
+
+    
+    p translations
+    @found = @missing = []
+    @found += found
+    missing.zip(translations).each{|p| 
+      if p[1] && p[1] != "NO MATCH"
+        @found << p[1]
+      else
+        @missing << p[0]
+      end
+    }
+
+    @found
+
+    index
+  end
+end

data/merb/app/controllers/results.rb

@@ -0,0 +1,247 @@
+class Results < Application
+  include CacheHelper
+
+  def main
+    name = params[:job]
+
+    @name = name
+
+    begin
+      info = WS::info(name)
+    rescue WS::JobNotFound
+      @message = $!.message
+      return render :template =>  'results/error'
+    end
+
+    @up   = info[:up]
+    @down = info[:down]
+
+    case WS::status(name)
+    when 'done'
+      render_deferred do
+        @title = "[HTML] #{ name }"
+        @message = "Job #{ name } has finished correctly. The results page is been generated"
+        wait = render :template => 'results/wait'
+        cache("#{@name}_results", {:job => @name}, wait ) do
+          @results = WS::sort_results(name)
+          @title = "#{ name }"
+  
+          headers["Expires"] = (Time.now + 31536000).to_s
+          headers['Cache-Control'] = 'public, max-age=31536000'
+  
+          render
+        end
+      end
+    when 'error'
+      @message = WS::messages(name).last
+      render :template =>  'results/error'
+    else
+      @title = "[#{WS::status(name)}] #{ name }"
+      @message = WS::messages(name).last
+
+      render :template =>  'results/wait'
+    end
+
+  end
+  
+  def images
+    @name = params[:job]
+    @experiment = params[:experiment]
+
+    @hash = @experiment.hash_code
+    render
+  end
+
+  def ajax_annotations
+    job = params[:job]
+    type = params[:type]
+    
+    render_deferred do
+      annotations, terms = WS::annotations(job, type)
+      {:annotations => annotations, :terms => terms}.to_json
+    end
+  end
+
+  def images
+    image = params[:image]
+    Open.read(File.join(MARQ.workdir, 'merb', 'tmp', 'images',image))
+  end
+ 
+  def ajax_experiment
+    job = params[:job]
+    experiment = params[:experiment]
+
+    results = WS::results(job)
+    entries = results[experiment][:total_entries]
+    
+    up = results[experiment][:positions_up].select{|p| p !~ /MISSING|PLATFORM/} if results[experiment][:positions_up]
+    down = results[experiment][:positions_down].select{|p| p !~ /MISSING|PLATFORM/} if results[experiment][:positions_down]
+
+    info = {}
+    if up && up.any?
+      up_filename = File.join(MARQ.workdir, 'merb', 'tmp', 'images', (experiment + '_up').hash.to_s)
+      Score.draw_hits(up, entries, up_filename, {:size => 1000, :bg_color => :green})
+      info[:up] = up_filename.sub(/^.*tmp/,'')
+    end
+
+    if down && down.any?
+      down_filename = File.join(MARQ.workdir, 'merb', 'tmp', 'images', (experiment + '_down').hash.to_s)
+      Score.draw_hits(down, entries, down_filename, {:size => 1000, :bg_color => :green})
+      info[:down] = down_filename.sub(/^.*tmp/,'')
+    end
+
+    @job = job
+    @experiment = experiment
+
+    dataset, condition, name = experiment.match(/^(.+?): (.+?): (.*)/).values_at(1,2,3)
+    info[:dataset] = dataset
+    info[:condition] = condition
+    info[:name] = name
+    info[:title] = Info::info(dataset)[:title]
+    info[:description] = Info::info(dataset)[:description]
+    partial 'partials/experiment', :with => info, :as => :info
+  end
+  
+
+  def explore_hits
+    job        = params[:job]
+    experiment = params[:experiment]
+    up         = params[:side] =~ /up/i
+
+    results = WS::results(job)
+    @total = results[experiment][:total_entries]
+    
+    genes = WS::genes(job)
+    
+    if experiment =~ /^(GDS\d+)/
+      gds = $1
+    else
+      gds = nil
+    end
+    @translations = {}
+    if up
+      @hits = genes[:up].zip(results[experiment][:positions_up])
+      native = genes[:up].collect{|p| p.last}
+      native.zip(Info.to_GPL_format(GEO.dataset_platform(gds), native)).each{|p| @translations[p.first] = p.last} if gds
+    else
+      @hits = genes[:down].zip(results[experiment][:positions_down]) 
+      native = genes[:down].collect{|p| p.last}
+      native.zip(Info.to_GPL_format(GEO.dataset_platform(gds), native)).each{|p| @translations[p.first] = p.last} if gds
+    end
+    
+    org = WS::info(job)[:organism]
+    @synonyms = Info::synonyms(org, (genes[:up] + genes[:down]).collect{|p| p[1] }.compact.uniq, WS::info(job)[:platform].nil?)
+
+    @hits = @hits.select{|p| p[1].to_s =~ /\d+/ }.sort{|a,b| 
+      a[1].to_i <=> b[1].to_i
+    }
+
+    @gds = gds
+    @name = experiment
+    @job = job
+    @org = org
+
+    render
+  end
+
+  def logratios
+    job = params[:job]
+    experiment = params[:experiment]
+    genes = params[:genes].split(',')
+    
+    dataset, condition = experiment.match(/^(.*?:) (.*)/).values_at(1,2)
+
+    headers["Content-Type"] =  'text/plain'
+    headers["Content-Disposition"] =  'attachment; filename=logratios.txt'
+
+    if genes && genes.any?
+      translations = WS::translations(job)
+      cross = translations.values_at(*genes)
+      inverse = translations.invert
+      WS::logratios(dataset.sub(/:$/,'_cross_platform'), condition, cross.compact).sort.collect{|l| 
+        code, value = l.chomp.split(/\t/).values_at(0,1)
+        next if inverse[code].nil?
+        "#{inverse[code]}\t#{value}"
+      }.join("\n")
+    else
+      WS::logratios(dataset.sub(/:$/,'_cross_platform'), condition, [])
+    end
+  end
+
+  def ts
+    job = params[:job]
+    experiment = params[:experiment]
+    genes = params[:genes].split(',')
+    
+    dataset, condition = experiment.match(/^(.*?:) (.*)/).values_at(1,2)
+
+    headers["Content-Type"] =  'text/plain'
+    headers["Content-Disposition"] =  'attachment; filename=t-values.txt'
+
+    if genes && genes.any?
+      translations = WS::translations(job)
+      cross = translations.values_at(*genes)
+      inverse = translations.invert
+      WS::ts(dataset.sub(/:$/,'_cross_platform'), condition, cross.compact).sort.collect{|l| 
+        code, value = l.chomp.split(/\t/).values_at(0,1)
+        next if inverse[code].nil?
+        "#{inverse[code]}\t#{value}"
+      }.join("\n")
+    else
+      WS::ts(dataset.sub(/:$/,'_cross_platform'), condition, [])
+    end
+  end
+
+
+  def compare
+    job = params[:job]
+    signatures = params[:experiments].scan(/[^|]+/)
+    invert = (params[:invert] || "").scan(/[^|]+/)
+    format = params[:format]
+
+    @url = "/compare?" + request.env['QUERY_STRING']
+    @job = job
+    
+    render_deferred do
+      genes = WS::genes(job)
+      @genes_up   = genes[:up] || []
+      @genes_down = genes[:down] || []
+  
+      @genes_up.collect!{|p| p[1]}
+      @genes_down.collect!{|p| p[1]}
+      @org = WS::info(job)[:organism]
+  
+  
+  
+      @scores_up, @scores_down = CompareGenes::RankProduct.compare(job, signatures, invert)
+  
+      case
+      when format == 'tsv'
+        filename = CompareGenes::RankProduct.prepare_files(job, signatures, invert, @genes_up, @genes_down)[0]
+        headers["Content-Type"] =  'text/plain'
+        headers["Content-Disposition"] =  'attachment; filename=rankproduct.txt'
+  
+  
+        Open.read(filename)
+      when format == 'excel'
+        filename = CompareGenes::RankProduct.prepare_files(job, signatures, invert, @genes_up, @genes_down)[1]
+        headers['Content-Type'] = "application/vnd.ms-excel"
+        headers['Content-Disposition'] = "attachment; filename=\"rankproduct.xls\""
+        headers['Cache-Control'] = ''
+  
+        Open.read(filename)
+      else
+        cache('compare', params) do
+          threshold = 0.05
+          @sorted_up = @scores_up.select{|gene, info| info[1] < threshold}.sort{|a,b| a[1][0] <=> b[1][0]}
+          @sorted_down = @scores_down.select{|gene, info| info[1] < threshold}.sort{|a,b| a[1][0] <=> b[1][0]}
+          @synonyms = Info::synonyms(WS::info(job)[:organism], @scores_up.keys, true)
+          @translations = WS::translations(job).invert
+          render
+        end
+      end
+    end
+  end
+
+
+end

data/merb/app/controllers/series.rb

@@ -0,0 +1,44 @@
+require 'MARQ/GEO'
+
+class Series < Application
+  def main
+    @series = params[:series]
+
+    if @series
+      @series_info = GEO::GSE_info(@series)
+      @sample_info = {}
+      @gds = GEO::Eutils::GSE_dataset? @series
+      @series_info[:samples].each{|gsm|
+        @sample_info[gsm] = GEO::GSM_info(gsm)
+      }
+      if params[:conditions]
+        info = {}
+        info[:platform] = @series_info[:platform]
+        info[:title] = @series_info[:title]
+        info[:description] = @series_info[:description]
+        info[:arrays] = {}
+        conditions = params[:conditions].split("|")
+        values = params[:values].split("|")
+        @series_info[:samples].each{|sample|
+          ph = {}
+          conditions.each{|c|
+            ph[c.strip] = values.shift.strip
+          }
+          info[:arrays][sample] = ph
+        }
+
+        headers["Content-Type"] =  'text/plain'
+        headers["Content-Disposition"] =  "attachment; filename=#{@series}.yaml"
+
+        info.to_yaml
+      else
+        render_deferred do
+          render
+        end
+      end
+    else
+      render
+    end
+  end
+
+end

data/merb/app/helpers/global_helpers.rb

@@ -0,0 +1,5 @@
+module Merb
+  module GlobalHelpers
+    # helpers defined here available to all views.  
+  end
+end

data/merb/app/helpers/main_helper.rb

@@ -0,0 +1,5 @@
+module Merb
+  module MainHelper
+
+  end
+end # Merb

data/merb/app/helpers/results_helper.rb

@@ -0,0 +1,50 @@
+module Merb
+  module ResultsHelper
+    
+    def span_words(text, stem = true)
+      text.split(/(\w+)/).collect{|w|
+        if stem
+          t = w.downcase.stem
+        else
+          t = w
+        end
+
+       if w =~ /\w/
+          "<span class='word' data-stem='#{t}' >#{ w }</span>" 
+        else
+          w
+        end
+      }.join("")
+    end
+
+    def annotation_term(type, term)
+      case 
+      when type == "GO_up" || type == "GO_down"
+        Info::GO::name(term)
+      else
+        term
+      end
+    end
+
+    def gene_url(org, gene) 
+      case org.to_s
+      when 'sgd':  return "http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=" + gene 
+      when 'cgd':  return "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=" + gene 
+      when 'rgd':  return "http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=" + gene.sub(/RGD:/,'') 
+      when 'mgi':  return "http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=" + gene
+      when 'pombe':  return "http://www.genedb.org/genedb/Search?organism=pombe&isid=true&name=" + gene
+      when 'human':  return "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum&TermToSearch=" + gene
+      else return nil   
+      end
+    end
+
+    def print_pvalue(pvalue, min = 0.001)
+      if pvalue == 0
+        "< #{min}"
+      else
+        "%1.3g" % pvalue
+      end
+    end
+  end
+
+end # Merb