lazar-gui 1.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 63fad5e104b2e9a3d87993b4ce490de848ab14ac
+  data.tar.gz: 4f50c319f247c6716c0df6490c8d63a592d9202c
+SHA512:
+  metadata.gz: 177829a3a7d2025d2ac5819a37a7b87ec3e659ab427758a1305d8aa3c62bee0c3e445b0a976ac72f8bc404d0be004c1ff79545fd022bbd32fb40513fd7b11303
+  data.tar.gz: ea8728c578e29b430a4a0d4a7192c6ce53bb45f9af2e0a8320159db26dec2dd182234d445396b99ea082244489a85dfe36f6c8064cf8384f7e3530e2c345dabb

data/.gitignore

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+Gemfile.lock
+.sass-cache/
+tmp/*

data/FAQ.md

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+Frequently Asked Questions
+==========================
+<br>
+####How does this prediction works?
+>
+
+####You talk about significant fragments. Where can I find them?
+> We will show up those significant fragments in a further version.
+
+####What is endpoint details about?
+> You get the source from where we took compounds for the endpoint. The type and the number of compounds we used.
+
+####What is three times independent validation about?
+>
+
+####Do you consider providing plots for the validation results?
+> In a further version we will show up confidence and correlation plots.
+
+####What does 'Not enough similar compounds in training dataset' mean?
+> Lazar uses neighbors from the training dataset of the endpoint to predict your compound. If there are not enough neighbors for Lazar it is not possible to make a prediction.
+
+####Is there a minimum number of necessary neighbors to make a prediction?
+>  
+
+####How can I activate the 'batch prediction' option?
+> Please contact us directly via [mail](mailto:support@in-silico.ch).
+
+####Not the right answers for me. Is there a way to contact you or report problems.
+> You can always ask your questions via [mail](mailto:support@in-silico.ch). If you run into problems with the GUI please post your issue [here](https://github.com/opentox/lazar-gui/issues). If you would like to post any other issue e.g. about an expected prediction result please use this [form](https://github.com/opentox/lazar/issues).

data/Gemfile

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+source "https://rubygems.org"
+gemspec
+gem "lazar"
+gem "gem-path"
+gem "sinatra"
+gem "haml"
+gem "sass"

data/README.md

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+IST Software&Services GUI
+=========================
+
+Installation:
+-------------
+    bundle install
+
+Usage:
+------
+    sudo /etc/init.d/mongod start
+    unicorn -D
+
+Visit:
+------
+    http://localhost:8080

data/VERSION

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+1.0.0

data/application.rb

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+#require_relative 'helper.rb'
+#require 'rdiscount'
+include OpenTox
+#require File.join(ENV["HOME"],".opentox","config","lazar-gui.rb") # until added to ot-tools
+
+# DG: workaround for https://github.com/sinatra/sinatra/issues/808
+# Date: 18/11/2013
+#set :protection, :except => :path_traversal
+
+configure :development do
+  $logger = Logger.new(STDOUT)
+end
+
+helpers do
+  class Numeric
+    def percent_of(n)
+      self.to_f / n.to_f * 100.0
+    end
+  end
+
+end
+
+get '/?' do
+  redirect to('/predict') 
+end
+
+get '/predict/?' do
+  @models = OpenTox::Model::Prediction.all
+  @endpoints = @models.collect{|m| m.endpoint}.sort.uniq
+  @models.count <= 0 ? (haml :info) : (haml :predict)
+end
+
+get '/predict/modeldetails/:model' do
+  model = OpenTox::Model::Prediction.find params[:model]
+  crossvalidations = model.crossvalidations
+  #confidence_plots = crossvalidations.collect{|cv| [cv.id, cv.confidence_plot]}
+  #confidence_plots.each do |confp|
+  #  File.open(File.join('public', "confp#{confp[0]}.svg"), 'w'){|file| file.write(confp[1])} unless File.exists? File.join('public', "confp#{confp[0]}.svg")
+  #end
+  #if model.regression?
+  #  correlation_plots = crossvalidations.collect{|cv| [cv.id, cv.correlation_plot]}
+  #  correlation_plots.each do |corrp|
+  #    File.open(File.join('public', "corrp#{corrp[0]}.svg"), 'w'){|file| file.write(corrp[1])} unless File.exists? File.join('public', "corrp#{corrp[0]}.svg")
+  #  end
+  #end
+
+  return haml :model_details, :layout=> false, :locals => {:model => model}
+end
+
+get '/jme_help/?' do
+  File.read(File.join('views','jme_help.html'))
+end
+
+# get individual compound details
+get '/prediction/:neighbor/details/?' do
+  @compound = OpenTox::Compound.new params[:neighbor]
+  @smiles = @compound.smiles
+  task = OpenTox::Task.run("Get names for '#{@smiles}'.") do
+    names = @compound.names
+  end
+  task.wait
+  
+  case task[RDF::OT.hasStatus]
+  when "Error"
+    @names = "No names for this compound available."
+  when "Completed"
+    @names = @compound.names
+  else
+    @names = "No names for this compound available."
+  end
+  @inchi = @compound.inchi.gsub("InChI=", "")
+
+  haml :details, :layout => false
+end
+=begin
+# sdf representation for datasets
+#TODO fix 502 errors from compound service
+get '/predict/:dataset_uri/sdf/?' do
+  uri = CGI.unescape(params[:dataset_uri])
+  $logger.debug uri
+  bad_request_error "Not a dataset uri." unless URI.dataset? uri
+  dataset = OpenTox::Dataset.find uri
+  @compounds = dataset.compounds
+  @data_entries = dataset.data_entries
+  sum=""
+  @compounds.each_with_index{ |c, idx|
+    sum << c.inchi
+    sum << c.sdf.sub(/\n\$\$\$\$/,'')
+    @data_entries[idx].each{ |f,v|
+      sum << "> <\"#{f}\">\n"
+      sum << v.join(", ")
+      sum << "\n\n"
+    }
+    sum << "$$$$\n"
+  }
+  send_file sum, :filename => "#{dataset.title}.sdf"
+end
+=end
+# fingerprints for compound in predictions
+get '/prediction/:model_uri/:type/:compound_uri/fingerprints/?' do
+  @type = params[:type]
+  model = OpenTox::Model::Lazar.find params[:model_uri]
+  feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset]
+  @compound = OpenTox::Compound.new params[:compound_uri]
+  @significant_fragments = []
+  if @type =~ /classification/i
+    # collect all feature values with fingerprint
+    fingerprints = OpenTox::Algorithm::Descriptor.send("smarts_match", [@compound], feature_dataset.features.collect{ |f| f[RDF::DC.title]})[@compound.uri]
+    #$logger.debug "fingerprints:\t#{fingerprints}\n"
+
+    # collect fingerprints with value 1
+    @fingerprint_values = fingerprints.collect{|smarts, value| [smarts, value] if value > 0}
+    
+    # collect all features from feature_dataset
+    @features = feature_dataset.features.collect{|f| f }
+    
+    # search for each fingerprint in all features and collect feature values( effect, smarts, pValue )
+    @fingerprint_values.each{ |fi, v| @features.each{ |f| @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue]] if fi == f[RDF::OT.smarts] } }
+    
+    # pass value_map, important to interprete effect value
+    prediction_feature_uri = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "prediction_feature_uri"
+        prediction_feature_uri = p[RDF::OT.paramValue].object
+      end
+    }
+    prediction_feature = OpenTox::Feature.find prediction_feature_uri
+    @value_map = prediction_feature.value_map
+
+  else #regression
+    feature_calc_algo = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "feature_calculation_algorithm"
+        feature_calc_algo = p[RDF::OT.paramValue].object
+      end
+    }
+
+    @desc = []
+    fingerprints = OpenTox::Algorithm::Descriptor.send( feature_calc_algo, [ @compound ], feature_dataset.features.collect{ |f| f[RDF::DC.title] } )
+    fingerprints.each{|x, h| h.each{|descriptor, value| @desc << [descriptor, [value]]}}
+    
+    pc_descriptor_titles_descriptions = {}
+    feature_dataset.features.collect{ |f|
+      pc_descriptor_titles_descriptions[f[RDF::DC.title]]= f[RDF::DC.description]
+    }
+
+    @desc.each{|d, v| @significant_fragments << [pc_descriptor_titles_descriptions[d], v] }
+  end
+
+  haml :significant_fragments, :layout => false
+end
+
+get '/prediction/:model_uri/:type/:neighbor/significant_fragments/?' do
+  @type = params[:type]
+  @compound = OpenTox::Compound.new params[:neighbor]
+  model = OpenTox::Model::Lazar.find params[:model_uri]
+  #$logger.debug "model for significant fragments:\t#{model.uri}"
+  
+  feature_dataset = OpenTox::Dataset.find model[RDF::OT.featureDataset]
+  $logger.debug "feature_dataset_uri:\t#{feature_dataset.uri}\n"
+  
+  # load all compounds
+  feature_dataset.compounds
+  
+  # load all features
+  @features = feature_dataset.features.collect{|f| f}
+  
+  # find all features and values for a neighbor compound
+  @significant_fragments = []
+  # check type first
+  if @type =~ /classification/i
+    # get compound index in feature dataset
+    c_idx = feature_dataset.compound_indices @compound.uri
+
+    # collect feature uris with value
+    @feat = @features.collect{|f| [feature_dataset.data_entry_value(c_idx[0], f.uri), f.uri]}
+    #$logger.debug "@feat:\t#{@feat}\n"
+
+    # pass feature uris if value > 0
+    @feat.each do |f|
+      # search relevant features
+      if f[0] > 0
+        f = OpenTox::Feature.find f[1]
+        # pass relevant features with [ effect, smarts, pValue ] 
+        @significant_fragments << [f[RDF::OT.effect].to_i, f[RDF::OT.smarts], f[RDF::OT.pValue].to_f.round(3)]
+      end
+    end
+    # pass value_map, important to interprete effect value
+    prediction_feature_uri = ""
+    model.parameters.each {|p|
+      if p[RDF::DC.title].to_s == "prediction_feature_uri"
+        prediction_feature_uri = p[RDF::OT.paramValue].object
+      end
+    }
+    prediction_feature = OpenTox::Feature.find prediction_feature_uri
+    @value_map = prediction_feature.value_map
+
+  else # regression
+    # find a value in feature dataset by compound and feature
+    @values = @features.collect{|f| feature_dataset.values(@compound, f)}
+    #$logger.debug "values in fd:\t#{@values}"
+    
+    @features.each_with_index{|f, i| @significant_fragments << [f.description, @values[i]]}
+  end  
+  #$logger.debug "significant fragments:\t#{@significant_fragments}\n"
+  
+  haml :significant_fragments, :layout => false
+end
+
+get '/predict/?:csv?' do
+  response['Content-Type'] = "text/csv"
+  @csv = "\"Compound\",\"Endpoint\",\"Type\",\"Prediction\",\"Confidence\"\n"
+  @@batch.each do |key, values|
+    values.each do |array|
+      model = array[0]
+      prediction = array[1]
+      compound = key.smiles
+      mw = key.molecular_weight
+      endpoint = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
+      if prediction[:confidence] == "measured"
+        if prediction[:value].is_a?(Array)
+          prediction[:value].each do |value|
+            type = ""
+            weight = Compound.from_smiles(compound).mmol_to_mg(value, mw)
+            pred = value.numeric? ? "#{'%.2e' % value} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : value
+            confidence = "measured activity"
+            @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n"
+          end
+        else
+          type = ""
+          weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw)
+          pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
+          confidence = "measured activity"
+        end
+      elsif prediction[:neighbors].size > 0
+        weight = Compound.from_smiles(compound).mmol_to_mg(prediction[:value], mw)
+        type = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
+        pred = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % weight} (mg/kg_bw/day)" : prediction[:value]
+        confidence = prediction[:confidence]
+      else
+        type = ""
+        pred = "Not enough similar compounds in training dataset."
+        confidence = ""
+      end
+      @csv += "\"#{compound}\",\"#{endpoint}\",\"#{type}\",\"#{pred}\",\"#{confidence}\"\n" unless prediction[:value].is_a?(Array)
+    end
+  end
+  @csv
+end
+
+post '/predict/?' do
+
+  # process batch prediction
+  if !params[:fileselect].blank?
+    if params[:fileselect][:filename] !~ /\.csv$/
+      @error_report = "Please submit a csv file."
+      return haml :error
+    end
+    File.open('tmp/' + params[:fileselect][:filename], "w") do |f|
+      f.write(params[:fileselect][:tempfile].read)
+    end
+    @filename = params[:fileselect][:filename]
+    input = OpenTox::Dataset.from_csv_file File.join "tmp", params[:fileselect][:filename]
+    dataset = OpenTox::Dataset.find input.id 
+    @compounds = dataset.compounds
+    if @compounds.size == 0
+      @error_report = "No valid SMILES submitted."
+      dataset.delete
+      return haml :error
+    end
+    @batch = {}
+    @compounds.each do |compound|
+      @batch[compound] = []
+      params[:selection].keys.each do |model_id|
+        model = Model::Prediction.find model_id
+        prediction = model.predict(compound)
+        @batch[compound] << [model, prediction]
+      end
+    end
+    @@batch = @batch
+    dataset.delete
+    return haml :batch
+  end
+
+  # validate identifier input
+  # transfered input
+  if !params[:identifier].blank?
+    @identifier = params[:identifier]
+    $logger.debug "input:#{@identifier}"
+    # get compound from SMILES
+    @compound = Compound.from_smiles @identifier
+    if @compound.blank?
+      @error_report = "Attention, '#{@identifier}' is not a valid SMILES string."
+      return haml :error
+    end
+
+    @models = []
+    @predictions = []
+    params[:selection].keys.each do |model_id|
+      model = Model::Prediction.find model_id
+      @models << model
+      @predictions << model.predict(@compound)
+    end
+    haml :prediction
+  end
+end
+=begin
+get '/faq' do
+  @faq = RDiscount.new(File.read("FAQ.md")).to_html
+  haml :faq, :layout => :faq_layout
+end
+=end
+get '/style.css' do
+  headers 'Content-Type' => 'text/css; charset=utf-8'
+  scss :style
+end
+

data/bin/lazar-start

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+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'lazar-start.sh')
+
+`#{shell_script_path}`

data/bin/lazar-start.sh

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+#!/bin/bash
+sudo mongod &
+R CMD Rserve
+LAZARPATH=$(gem path lazar-gui)
+cd $LAZARPATH
+unicorn -c unicorn.rb -E production -D
+
+exit 0

data/bin/lazar-stop

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+#!/usr/bin/env ruby
+bin_dir = File.expand_path(File.dirname(__FILE__))
+shell_script_path = File.join(bin_dir, 'lazar-stop.sh')
+
+`#{shell_script_path}`
+

data/bin/lazar-stop.sh

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+#!/bin/bash
+grep_lazar=`ps aux | grep -v grep | grep lazar-start`
+grep_mongo=`ps aux | grep -v grep | grep mongod`
+grep_rserve=`ps aux | grep -v grep | grep Rserve`
+grep_unicorn=`ps aux | grep -v grep | grep unicorn`
+
+# lazar
+if [ ${#grep_lazar} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep lazar-start | awk '{ print $1 }'`
+  for i in "${PID}"
+  do
+    `kill $i`
+  done
+else
+  echo "Lazar is stopped."
+fi
+
+# mongod
+if [ ${#grep_mongo} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep mongod | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `sudo kill $i`
+  done
+else
+  echo "MongoDB is not running."
+fi
+
+# rserve
+if [ ${#grep_rserve} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep Rserve | awk '{ print $1 }'`
+  for i in "${PID}"
+  do 
+    `kill $i`
+  done
+else
+  echo "Rserve is not running."
+fi
+
+# unicorn
+if [ ${#grep_unicorn} -gt 0 ]
+then
+  PID=`ps ax | grep -v grep | grep unicorn | awk '{ print $1 }'`
+  `kill ${PID[0]}`
+else
+  echo "Unicorn is not running."
+fi
+
+exit 0