lazar-gui 1.0.0

data/test/lazarweb.rb

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+require 'minitest/autorun'
+require 'capybara'
+require 'capybara-webkit'
+
+ENV['DISPLAY'] ="localhost:1.0"
+
+Capybara.register_driver :webkit do |app|
+  Capybara::Webkit::Driver.new(app).tap{|d| d.browser.ignore_ssl_errors}
+end
+Capybara.default_driver = :webkit
+Capybara.default_max_wait_time = 20
+Capybara.javascript_driver = :webkit
+Capybara.run_server = false
+Capybara.app_host = "http://localhost:8088" 
+
+begin
+  puts "Service URI is: http://localhost:8088"
+rescue
+  puts "Unable to start service."
+  exit
+end
+
+class LazarWebTest < MiniTest::Test
+  
+  def self.test_order
+    :sorted
+  end
+  
+  include Capybara::DSL
+
+  def test_00_xsetup
+    `Xvfb :1 -screen 0 1024x768x16 2>/dev/null &`
+    sleep 2
+  end
+
+  def test_01_visit
+    visit('/predict')
+    assert page.has_content?('Lazar Toxicity Predictions')
+    assert page.has_content?("Draw a chemical structure")
+    assert page.has_content?("enter")
+    assert page.has_content?("upload")
+    assert page.has_content?("Select one or more endpoints")
+    assert page.has_content?("Acute toxicity")
+    assert page.has_content?("Fathead minnow")
+    assert page.has_content?("Carcinogenicity")
+    assert page.has_content?("Rat")
+    assert page.has_content?("Rodents (multiple species/sites)")
+    assert page.has_content?("Mouse")
+    assert page.has_content?("Maximum Recommended Daily Dose")
+    assert page.has_content?("Human")
+    assert page.has_content?("Predict")
+  end
+
+  def test_02_insert_wrong_smiles
+    visit('/')
+    page.fill_in 'identifier', :with => "blahblah"
+    check('selection[Rat]')
+    first(:button, '>>').click
+    assert page.has_content?('Attention')
+  end
+
+  def test_03_check_all_links_exists
+    visit('/')
+    links = ["Details | Validation", "SMILES", "toxicology gmbh 2004 - #{Time.now.year.to_s}"]
+    links.each{|l| assert page.has_link?(l), "true"}
+  end
+
+  def test_04_model_details
+    visit("/")
+    details = page.all('a', :text => 'Details | Validation')
+    details[0].click
+    assert page.has_content?('Model:')
+    assert page.has_content?('Source: http://www.epa.gov/comptox/dsstox/sdf_epafhm.html')
+    assert page.has_content?('Algorithm: LAZAR')
+    assert page.has_content?('Type: regression')
+    assert page.has_content?('Training dataset: EPAFHM.csv')
+    assert page.has_content?('Training compounds: 617')
+    assert page.has_content?('Validation:')
+    assert page.has_content?('Num folds: 10')
+    details[0].click
+    #
+    details[1].click
+    assert page.has_content?('Model:')
+    assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
+    assert page.has_content?('Algorithm: LAZAR')
+    assert page.has_content?('Type: classification')
+    assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_Rat.csv')
+    assert page.has_content?('Training compounds: 1195')
+    assert page.has_content?('Validation:')
+    assert page.has_content?('Num folds: 10')
+    details[1].click
+    #
+    details[2].click
+    assert page.has_content?('Model:')
+    assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
+    assert page.has_content?('Algorithm: LAZAR')
+    assert page.has_content?('Type: classification')
+    assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv')
+    assert page.has_content?('Training compounds: 1116')
+    assert page.has_content?('Validation:')
+    assert page.has_content?('Num folds: 10')
+    details[2].click
+    #
+    details[3].click
+    assert page.has_content?('Model:')
+    assert page.has_content?('Source: http://www.epa.gov/ncct/dsstox/sdf_cpdbas.html')
+    assert page.has_content?('Algorithm: LAZAR')
+    assert page.has_content?('Type: classification')
+    assert page.has_content?('Training dataset: DSSTox_Carcinogenic_Potency_DBS_Mouse.csv')
+    assert page.has_content?('Training compounds: 973')
+    assert page.has_content?('Validation:')
+    assert page.has_content?('Num folds: 10')
+    details[3].click
+    #
+    details[4].click
+    assert page.has_content?('Model:')
+    assert page.has_content?('Source: http://www.epa.gov/comptox/dsstox/sdf_fdamdd.html')
+    assert page.has_content?('Algorithm: LAZAR')
+    assert page.has_content?('Type: regression')
+    assert page.has_content?('Training dataset: FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv')
+    assert page.has_content?('Training compounds: 1216')
+    assert page.has_content?('Validation:')
+    assert page.has_content?('Num folds: 10')
+    details[4].click
+  end 
+
+  def test_05_predict
+    visit('/')
+    page.fill_in('identifier', :with => "NNc1ccccc1")
+    check('selection[Rat]')
+    first(:button, '>>').click
+    assert page.has_content?('Carcinogenicity (Rat)'), "true"
+    assert page.has_content?('Type: Classification'), "true"
+    assert page.has_content?('Prediction: active'), "true"
+    assert page.has_content?('Confidence: 0.019'), "true"
+    assert page.has_content?('Neighbors'), "true"
+    assert page.has_content?('Compound'), "true"
+    assert page.has_content?('Measured Activity'), "true"
+    assert page.has_content?('Similarity'), "true"
+=begin
+    assert page.has_link?('Significant fragments'), "true"
+    assert page.has_link?('v'), "true"
+     open 'significant fragments' view
+    find_link('linkPredictionSf').click
+    sleep 5
+    within_frame('details_overview') do
+      assert page.has_content?('Predominantly in compounds with activity "inactive"'), "true"
+      assert page.has_content?('Predominantly in compounds with activity "active"'), "true"
+      assert page.has_content?('p value'), "true"
+      # inactive
+      assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]-[#7&A]'), "true"
+      assert page.has_content?('0.98674'), "true"
+      assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a]:[#6&a]:[#6&a])'), "true"
+      assert page.has_content?('0.97699'), "true"
+      assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a]:[#6&a])'), "true"
+      assert page.has_content?('0.97699'), "true"
+      assert page.has_content?('[#6&a]:[#6&a](-[#7&A])(:[#6&a])'), "true"
+      assert page.has_content?('0.97699'), "true"
+      assert page.has_content?('[#6&a]:[#6&a]'), "true"
+      assert page.has_content?('0.99605'), "true"
+      assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]'), "true"
+      assert page.has_content?('0.99791'), "true"
+      assert page.has_content?('[#6&a]:[#6&a]:[#6&a]:[#6&a]:[#6&a]'), "true"
+      assert page.has_content?('0.99985'), "true"
+      # active
+      assert page.has_content?('[#7&A]-[#7&A]'), "true"
+      assert page.has_content?('0.99993'), "true"
+      # close 'significant fragments' view
+      find_button('closebutton').click
+    end
+    find_link('link0').click
+    sleep 2
+    assert page.has_content?('Supporting information'), "true"
+    first(:link, 'linkCompound').click
+    sleep 5
+    within_frame('details_overview') do
+      assert page.has_content?('SMILES:'), "true"
+      assert page.has_content?('c1ccc(cc1)NN'), "true"
+      assert page.has_content?('InChI:'), "true"
+      assert page.has_content?('1S/C6H8N2/c7-8-6-4-2-1-3-5-6/h1-5,8H,7H2'), "true"
+      assert page.has_content?('Names:'), "true"
+      assert page.has_content?('Phenylhydrazine'), "true"
+      assert page.has_link?('PubChem read across'), "true"
+    end
+=end
+  end
+
+  def test_99_kill
+    `pidof Xvfb|xargs kill`
+  end
+
+end
+

data/test/setup.rb

@@ -0,0 +1,7 @@
+require 'minitest/autorun'
+require_relative '../lib/lazar.rb'
+include OpenTox
+TEST_DIR ||= File.expand_path(File.dirname(__FILE__))
+DATA_DIR ||= File.join(TEST_DIR,"data")
+#$mongo.database.drop
+#$gridfs = $mongo.database.fs # recreate GridFS indexes

data/unicorn.rb

@@ -0,0 +1,7 @@
+#worker_processes 4
+timeout 6000
+listen 8088
+log_dir = "#{ENV['HOME']}"
+log_file = File.join log_dir, "lazar.log"
+stderr_path log_file
+stdout_path log_file

data/views/batch.haml

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+%div.well
+  %a.btn.btn-warning{:href => to('/predict')}
+    %span.glyphicon.glyphicon-menu-left{:aria=>{:hidden=>"true"}}
+    New Prediction
+  / displays all prediction result in first table
+  %div.table-responsive
+    %table.table.table-bordered{:id=>"batch", :style=>"background-color:white;"}
+      %thead
+        %tr
+          %h3.col-md-4{:style=>"padding-left:0;"} Batch Prediction Results:
+          %h3.col-md-8= @filename
+        %tr
+          %span.btn.btn-default
+            %a{:href=>"#{to("/predict/#{@filename}")}", :title=>"download"}
+              %span.glyphicon.glyphicon-download-alt{:aria=>{:hidden=>"true"}}
+                CSV
+      %tbody
+      / key = compound, values = array of arrays with model, prediction
+      - @batch.each do |key, values|
+        - compound = key
+        - mw = compound.molecular_weight
+        %tr
+          %td{:style=>"vertical-align:top;"}
+            %p= compound.svg
+            %p= compound.smiles
+          / array = single prediction [endpoint, result]
+          - values.each_with_index do |array,i|
+            %td{:style=>"vertical-align:top;white-space:nowrap;"}
+              - model = array[0]
+              - prediction = array[1]
+              %b{:class => "title"}
+                = "#{model.endpoint.gsub('_', ' ')} (#{model.species})"
+              %p
+              - if prediction[:confidence] == "measured"
+                %p
+                  %b Measured activity:
+                - if prediction[:value].is_a?(Array)
+                  = prediction[:value][0].numeric? ? prediction[:value].collect{|v| weight = compound.mmol_to_mg(v, mw); '%.2e' % v + " (#{model.unit})"+" | #{'%.2e' % weight} (mg/kg_bw/day)"}.join("</br>") : prediction[:value].join(", ")
+                - else
+                  = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %p 
+                %b Compound is part of the training dataset
+              - elsif prediction[:neighbors].size > 0
+                %p
+                / model type (classification|regression)
+                %b Type:
+                = model.model.class.to_s.match("Classification") ? "Classification" : "Regression"
+                %br
+                %b Prediction:
+                = prediction[:value].numeric? ? "#{'%.2e' % prediction[:value]} (#{model.unit}) | #{'%.2e' % compound.mmol_to_mg(prediction[:value], mw)} (mg/kg_bw/day)" : prediction[:value]
+                %br
+                / TODO probability
+                %b Confidence:
+                = prediction[:confidence].round(3)
+                %p
+              - else
+                %p
+                  = "Not enough similar compounds </br>in training dataset."

data/views/details.haml

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+%div.modal-body{:style=>"padding:10px;"}
+  %button.close{ :type=>" button", data: { dismiss:"modal"}} ×
+  %h3
+    Names and synonyms:
+  %img.img-responsive{:src=>"#{@compound.uri}/image", :alt=>"Compound image not available", :width=>"300px", :heigth=>"300px", :style=>"float:left;"}
+  %p
+  %b="SMILES:"
+  %p= @smiles
+  %br
+  %b="InChI:"
+  %p= @inchi
+  %br
+  %b="Names:"
+  %p{:style=>"padding-left:0.5em;"}
+  - if @names !~ /^no names/i
+    = @names.join("; ")
+  - else
+    = @names
+  %hr
+  %p{:style=>"padding-left:0.5em;"}
+    / pubchem link
+    %a.btn.btn-primary{:href=>"http://aop.in-silico.ch/", :title=>"Link opens in new window.", :alt=>"pubchem read across", :target=>"_blank"} PubChem read across 
+    %i (experimental)
+  %br

data/views/error.haml

@@ -0,0 +1,8 @@
+%div.well
+  %a.btn.btn-warning{:href => to('/predict')}
+    %i.glyphicon.glyphicon-menu-left
+    Back
+  %hr
+  %div.well{:style=>"width:100%;margin-bottom:2em;"}
+    = @error_report
+      

data/views/faq.haml

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+%div.well.faq
+  = @faq

data/views/faq_layout.haml

@@ -0,0 +1,67 @@
+!!!
+%html{:xmlns => "http://www.w3.org/1999/xhtml", "xml:lang" => "en", :lang => "en"}
+  %head
+    %meta{'charset'=>"utf-8"}
+    %meta{'http-equiv'=>"X-UA-Compatible", :content=>"IE=edge"}
+    %meta{'name'=>"viewport", :content=>"width=device-width, initial-scale=1"}
+    %title Lazar GUI FAQ
+    %link{:rel=>'icon', :type=>'image/x-icon', :href=>'/images/favicon.ico'}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/bootstrap.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.default.min.css'}"}
+    %link{:rel=>'stylesheet', :href=>"#{'/css/theme.bootstrap.min.css'}"}
+    %link{ :href=>"/style.css", :rel=>"stylesheet"}
+    %link{ :href=>"/stylesheets/jquery-ui.css", :rel=>"stylesheet"}
+    %script{:src=>"/javascripts/jquery-1.11.2.min.js"}
+    %script{:src=>"/javascripts/bootstrap.min.js"}
+    %script{ :src=>"/javascripts/lazar-gui.js"}
+  %body
+    %noscript
+      %div{ :style=>"width: 22em; position: absolute; left: 50%; margin-left: -11em; color: red; background-color: white; border: 1px solid red; padding: 4px; font-family: sans-serif"}
+      Your web browser must have JavaScript enabled in order for this application to display correctly.
+    %header.page-header
+      %div.row
+        %div.col-md-2
+          %a{:href=> to("/predict")}
+            %img.media-object{:src=>"/images/ist_logo.png", :alt=>"logo", :style=>"margin:0 3em 0 2em;"}
+        %div.col-md-10
+          %h1.media-heading{:style=>"margin: 0 0 0 1em;display:inline;"} Lazar GUI
+          A Graphical User Interface for the <a href="http://github.com/opentox/lazar">Lazar</a> framework
+    
+    %div.container-fluid
+      :javascript
+        $(document).ready(function(){
+          $("#back-top").hide();
+          $(".blind").error(function(){
+            $(this).attr('src', '/images/blind.png');
+          });
+        });
+          
+      = yield
+    
+    %footer.footer
+      %div.container-fluid
+        %p.text-muted
+          &copy; 
+          %a{:href => 'http://www.in-silico.ch', :rel => "external"} <i style="font-family: serife">in silico</i> toxicology gmbh 2004 - #{Time.now.year.to_s}
+
+    #back-top{:style => "z-index:100;position:fixed;bottom:1%;right:1%;"}
+      %a{:href => "", :style=>"text:decoration:none;color:#ccc;"}
+        %span.glyphicon.glyphicon-circle-arrow-up{:style => "font-size:3em;color:black;"}
+    :javascript
+      $("#back-top").hide();
+      $(function () {
+        $(window).scroll(function () {
+          if ($(this).scrollTop() > 600) {
+            $('#back-top').fadeIn();
+          } else {
+            $('#back-top').fadeOut();
+          }
+        });
+        // scroll body to 0px on click
+        $('#back-top a').click(function () {
+          $('body,html').animate({
+            scrollTop: 0
+          }, 500);
+          return false;
+        });
+      });

data/views/info.haml

@@ -0,0 +1,2 @@
+%div.info
+  currently no models available

data/views/jme_help.html

@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html>
+<head>
+  <meta name="generator" content=
+  "HTML Tidy for Linux/x86 (vers 12 April 2005), see www.w3.org">
+  <meta http-equiv="content-type" content=
+  "text/html; charset=us-ascii">
+
+  <title>JME Help</title>
+  <meta name="author" content="Peter Ertl, Novartis Pharma AG">
+  <link rel="stylesheet" href="../style.css" type="text/css">
+<style type="text/css">
+ body {
+  background-color: white;
+ }
+ h2.c3 {text-align: center}
+ p.c2 {font-style: italic; text-align: right}
+ p.c1 {text-align: center}
+</style>
+</head>
+
+<body>
+<h1>JME Molecular Editor</h1>
+
+        <p class="c2">Written by Peter Ertl, Novartis Pharma
+        AG</p>
+
+        <h2 class="c3">Basic Instructions</h2>
+
+        <p>This editor is intended to be used without any special
+        documentation or training, but there are some tricks which
+        can help you to work with it more efficiently.</p>
+
+        <h3>Menu Buttons</h3>
+
+        <ul>
+          <li><b>D-R</b> deletes functional groups - choose this
+          option and then click on the bond connecting the group
+          with the main skeleton</li>
+
+          <li><b>UDO</b> undo last editing step</li>
+
+          <li><b>QRY</b> (if enabled in the param tag) allows easy
+          specification of atomic queries for substructure
+          searches</li>
+
+          <li><b>Stereo bonds</b> - the type of stereo bond (up,
+          down) may be changed by clicking on the already created
+          stereo bond; this cycles through two / four possible
+          stereo bond types</li>
+
+          <li><b>Atomic charges</b> may be changed by the
+          <b>+/-</b> button. Editor enables modification of charges
+          only in "reasonable" cases. If you are not satisfied with
+          the editor's inteligence (concerning charges and the
+          explicit number of hydrogens) you can force your will by
+          using the <b>X</b> button</li>
+
+          <li><b>"Non-organic" atoms</b> or atoms with nonstandard
+          valence may be entered with help of <b>X</b> button by
+          specifying atomic SMILES (without [ ] brackets, i.e. Si,
+          Fe++, NH3+).</li>
+        </ul>
+
+        <h3>Keyboard Shortcuts</h3>
+
+        <p>Most of the commands may be accessed also by keyboard
+        shortcuts. It is possible to:</p>
+
+        <ul>
+          <li>change <b>atom type</b> by pressing <b>C</b>,
+          <b>N</b>, <b>O</b>, <b>S</b>, <b>F</b>, <b>L</b> (for Cl)
+          <b>B</b> (for Br) <b>I</b>, <b>P</b>, <b>H</b>, <b>X</b>,
+          <b>R</b> and clicking the respective atom</li>
+
+          <li>choose <b>bond order</b>: <b>-</b> for single bond,
+          <b>=</b> for double bond, <b>#</b> for triple bond</li>
+
+          <li>choose <b>ring type</b> by pressing <b>3</b>,
+          <b>4</b>, <b>5</b>, <b>6</b>, <b>7</b>, <b>8</b>,
+          <b>9</b> or <b>1</b> for phenyl, <b>0</b> for furyl</li>
+
+          <li>start <b>delete mode</b> by pressing <b>D</b> or
+          <b>Del</b> and</li>
+
+          <li>return to the <b>standard state</b> (carbon, single
+          bond) with <b>Esc</b></li>
+        </ul>
+
+        <p><b>common functional groups</b> may also be added by
+        keyboard shortcuts. Use <b>t</b> for t-butyl, <b>ft</b> for
+        trifluoromethyl, <b>lt</b> for trichloromethyl, <b>a</b>
+        for COOH, <b>z</b> for SO2Me and <b>y</b> for nitro, and
+        then click the atom where the group should be
+        connected.</p>
+
+        <h3>Moving and Rotation</h3>
+
+        <p>You can move molecule by "dragging free space" with the
+        left mouse button and rotate it by using the left mouse
+        button and <b>Shift</b> key (or left and right mouse
+        buttons together).</p>
+
+        <h3>Adding rings</h3>
+
+        <p>When a ring template is selected and multivalent atom is
+        clicked, a new ring will be created connected by single
+        bond to this atom. When spiro ring is required, the
+        <b>Shift</b> key must be pressed when clicking on the atom.
+        Spiro ring may be added only to atom with 2 single
+        bonds.</p>
+
+        <h3>Multivalent nitrogen groups</h3>
+
+        <p>Multivalent nitrogen groups, such as nitro, azide,
+        N-oxide, nitrile etc, should be drawn with a pentavalent
+        nitrogen as shown below.</p>
+
+        <p class="c1"><img src="images/nitro.gif" alt=
+        "nitro stuff"></p>
+
+        <p>The program automatically converts polar form of these
+        groups into non-polar one with pentavalent nitrogen. If you
+        prefer polar nitro (and similar) groups, use keyword
+        "polarnitro" in the applet param tag.</p>
+
+        <h3>Stereochemistry</h3>
+
+        <p>Stereochemistry at C4 centers, double bonds and allenes
+        is supported. Use the up/down wedge bonds to indicate
+        stereochemistry at the C4 centers. Remember, that only
+        bonds with a "sharp point" towards the atom are considered.
+        When creating SMILES the editor tries to guess missing
+        stereo features, in unresolvable cases an error message is
+        issued and the SMILES without stereo information is
+        created.</p>
+
+        <p>When the autoez keyword is set, SMILES with E,Z
+        stereochemistry on all non-ring double bonds is generated
+        automatically. Without this keyword (or for ring double
+        bonds) you have to mark a double bond as stereo by clicking
+        on it with the stereo bond button selected. The bond color
+        will change to violet.</p>
+
+        <p>Stereochemistry may be completely disabled by the
+        "nostereo" option in the param tag.</p>
+
+        <h3>Input of Multipart Structures</h3>
+
+        <p>By default only non-disconnected structures are allowed.
+        This may be changed by a "multipart" option in the applet
+        param tag. A button <b>NEW</b> appears in the JME menu.
+        Creation of a new molecule may be started only after
+        clicking the <b>NEW</b> button, selecting a proper template
+        (atom, ring, bond) and clicking free space in the drawing
+        area. Without <b>NEW</b> button the click on the free space
+        has the same effect as in the standard mode (i.e moving or
+        rotation of the last touched molecule). In the multipart
+        mode <b>CLR</b> button deletes the last touched
+        molecule.</p>
+
+        <h3>Atom Numbering</h3>
+
+        <p>Atom numbering (marking) is enabled with the option
+        "number" in the applet param tag (for reaction input this
+        is default). Button <b>123</b> appears in the JME menu. To
+        mark an atom press the <b>123</b> button and then the atom.
+        You can mark more atoms with the same number when pressing
+        <b>Shift</b> while clicking the 2nd and further atoms.
+        Second click on the marked atom deletes the number.</p>
+
+        <h3>Reaction Input</h3>
+
+        <p>Reaction input is enabled with the option "reaction" in
+        the applet param tag. Button with an arrow, <b>NEW</b>
+        button and <b>123</b> button appear in the JME menu and
+        arrow appears also in the drawing area. Now simply draw
+        reactant(s), product(s) and modulator(s) (modulators have
+        to be above the arrow) as explained in the description of
+        input of multipart structures. The arrow button enables
+        simplified input of reactions. After clicking it, the
+        reactant will be copied to the product (including atom
+        numbering, if any). When the <b>Shift</b> is pressed during
+        this action all atoms will be automatically numbered.</p>
+
+        <h3>Query Features</h3>
+
+        <p>Query button (when enabled in the option tag) launches a
+        query window which allows creation of SMARTS atom queries
+        by combining various atom attributes. Create a SMARTS query
+        and then click the respective atom in the
+        molecule.</p>
+</body>
+</html>
+
+