RubyGems - lazar-gui - Versions diffs - 1.3.1 → 1.4.0.pre.0 - Mend

lazar-gui 1.3.1 → 1.4.0.pre.0

Files changed (130) hide show

checksums.yaml +4 -4
data/.gitignore +3 -0
data/FAQ.md +9 -6
data/Gemfile +2 -2
data/README.md +19 -8
data/VERSION +1 -1
data/api/api.json +1000 -0
data/application.rb +269 -206
data/config.ru +7 -2
data/docker/Dockerfile +73 -0
data/docker/start.sh +12 -0
data/docker/swagger.html +107 -0
data/helper.rb +46 -1
data/lazar-gui.gemspec +6 -6
data/lib/api.rb +29 -0
data/lib/compound.rb +68 -0
data/lib/dataset.rb +33 -0
data/lib/endpoint.rb +23 -0
data/lib/feature.rb +29 -0
data/lib/model.rb +152 -0
data/lib/report.rb +29 -0
data/lib/substance.rb +34 -0
data/lib/swagger.rb +3 -0
data/lib/validation.rb +67 -0
data/public/fonts/FontAwesome.otf +0 -0
data/public/fonts/fontawesome-webfont.eot +0 -0
data/public/fonts/fontawesome-webfont.svg +2671 -0
data/public/fonts/fontawesome-webfont.ttf +0 -0
data/public/fonts/fontawesome-webfont.woff +0 -0
data/public/fonts/fontawesome-webfont.woff2 +0 -0
data/public/images/orn-logo.jpg +0 -0
data/public/javascripts/bootstrap.js +3944 -0
data/public/javascripts/google_analytics_lazar.js +2 -2
data/public/javascripts/jquery.min.js +2 -0
data/public/javascripts/lazar-gui.js +313 -0
data/public/javascripts/pagination.min.js +11 -0
data/public/javascripts/popper.min.js +5 -0
data/public/stylesheets/bootstrap.min.css +7 -0
data/public/stylesheets/bootstrap.min.css.map +1 -0
data/public/stylesheets/font-awesome.min.css +4 -0
data/public/stylesheets/pagination.css +1 -0
data/qmrf_report.rb +64 -14
data/task.rb +68 -0
data/unicorn.rb +0 -1
data/views/batch.haml +48 -107
data/views/details.haml +10 -2
data/views/error.haml +4 -5
data/views/faq.haml +6 -2
data/views/help.haml +68 -0
data/views/info.haml +3 -2
data/views/layout.haml +68 -78
data/views/model_details.haml +179 -144
data/views/neighbors.haml +98 -80
data/views/predict.haml +43 -178
data/views/prediction.haml +109 -102
data/views/style.scss +44 -37
data/views/upload.haml +28 -0
metadata +51 -105
data/public/css/bootstrap-theme.min.css +0 -5
data/public/css/bootstrap.min.css +0 -5
data/public/css/bootstrap.vertical-tabs.min.css +0 -1
data/public/css/images/black-asc.gif +0 -0
data/public/css/images/black-desc.gif +0 -0
data/public/css/images/black-unsorted.gif +0 -0
data/public/css/images/bootstrap-black-unsorted.png +0 -0
data/public/css/images/bootstrap-white-unsorted.png +0 -0
data/public/css/images/dragtable-handle.png +0 -0
data/public/css/images/dragtable-handle.svg +0 -7
data/public/css/images/dropbox-asc-hovered.png +0 -0
data/public/css/images/dropbox-asc.png +0 -0
data/public/css/images/dropbox-desc-hovered.png +0 -0
data/public/css/images/dropbox-desc.png +0 -0
data/public/css/images/first.png +0 -0
data/public/css/images/green-asc.gif +0 -0
data/public/css/images/green-desc.gif +0 -0
data/public/css/images/green-header.gif +0 -0
data/public/css/images/green-unsorted.gif +0 -0
data/public/css/images/ice-asc.gif +0 -0
data/public/css/images/ice-desc.gif +0 -0
data/public/css/images/ice-unsorted.gif +0 -0
data/public/css/images/last.png +0 -0
data/public/css/images/loading.gif +0 -0
data/public/css/images/metro-black-asc.png +0 -0
data/public/css/images/metro-black-desc.png +0 -0
data/public/css/images/metro-loading.gif +0 -0
data/public/css/images/metro-unsorted.png +0 -0
data/public/css/images/metro-white-asc.png +0 -0
data/public/css/images/metro-white-desc.png +0 -0
data/public/css/images/next.png +0 -0
data/public/css/images/prev.png +0 -0
data/public/css/images/white-asc.gif +0 -0
data/public/css/images/white-desc.gif +0 -0
data/public/css/images/white-unsorted.gif +0 -0
data/public/css/jquery-ui.css +0 -1225
data/public/css/jquery-ui.theme.min.css +0 -5
data/public/css/theme.bootstrap.css +0 -158
data/public/css/theme.bootstrap.min.css +0 -1
data/public/css/theme.default.min.css +0 -1
data/public/fonts/glyphicons-halflings-regular.eot +0 -0
data/public/fonts/glyphicons-halflings-regular.svg +0 -288
data/public/fonts/glyphicons-halflings-regular.ttf +0 -0
data/public/fonts/glyphicons-halflings-regular.woff +0 -0
data/public/fonts/glyphicons-halflings-regular.woff2 +0 -0
data/public/images/Email.png +0 -0
data/public/images/Facebook.png +0 -0
data/public/images/Google+.png +0 -0
data/public/images/LinkedIn.png +0 -0
data/public/images/OpenToxEuro2013_small.png +0 -0
data/public/images/Twitter.png +0 -0
data/public/images/arrow_down_float.png +0 -0
data/public/images/arrow_left_float.png +0 -0
data/public/images/arrow_right_float.png +0 -0
data/public/images/arrow_up_float.png +0 -0
data/public/images/asc.gif +0 -0
data/public/images/bg.gif +0 -0
data/public/images/desc.gif +0 -0
data/public/images/gray_jean.png +0 -0
data/public/images/info_white.png +0 -0
data/public/javascripts/bootstrap.min.js +0 -7
data/public/javascripts/jquery-1.11.2.min.js +0 -4
data/public/javascripts/jquery-1.8.3.min.js +0 -2
data/public/javascripts/jquery-ui-1.10.3.custom.min.js +0 -6
data/public/javascripts/jquery.bpopup.min.js +0 -7
data/public/javascripts/jquery.tablesorter.min.js +0 -2
data/public/javascripts/jquery.tablesorter.widgets.js +0 -2678
data/public/javascripts/jquery.tools.min.js +0 -5
data/public/rect.png +0 -0
data/test/lazarweb.rb +0 -193
data/test/setup.rb +0 -7
data/views/significant_fragments.haml +0 -66

data/config.ru CHANGED Viewed

@@ -1,6 +1,11 @@
+ENV["BATCH_MODE"] = "true"
 ENV["LAZAR_ENV"] = "production"
-require 'bundler'
-Bundler.require
+require "lazar"
+require "qsar-report"
+require "sinatra"
+require "haml"
+require "sass"
+require "rdiscount"
 require File.expand_path './application.rb'
 require "sinatra/reloader" if development?
 run Sinatra::Application

data/docker/Dockerfile ADDED Viewed

@@ -0,0 +1,73 @@
+FROM				archlinux/base
+MAINTAINER  in-silico toxicology Gmbh
+RUN         pacman-db-upgrade
+RUN         pacman -Syyu --noconfirm
+RUN         pacman -S --noconfirm \
+            base-devel \
+            boost-libs \
+            cmake \
+            eigen3 \
+            fontconfig \
+            gcc-fortran \
+            git \
+            gsl \
+            jre10-openjdk-headless \
+            r \
+            ruby \
+            swig \
+            python-pip \
+            catdoc \
+            wget
+RUN         pacman -Scc --noconfirm
+RUN         R -e "install.packages('Rserve', repos='http://rforge.net/')"
+RUN         pip install xlsx2csv
+RUN         useradd -ms /bin/bash ist
+# mongodb has been removed from main repositories
+USER        ist
+WORKDIR     /home/ist
+RUN         mkdir data
+RUN         mkdir src
+WORKDIR     /home/ist/src
+RUN         wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz
+RUN         tar -xvzf mongodb-bin.tar.gz
+WORKDIR     /home/ist/src/mongodb-bin
+RUN         makepkg -s --noconfirm
+# installation requires root
+USER        root
+RUN         pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz
+# install lazar-gui gem
+RUN         echo 'gem: --no-document' > /etc/gemrc
+#RUN         gem install lazar-gui
+RUN         gem install lazar
+RUN         gem install qsar-report
+RUN         gem install sinatra haml sass rdiscount unicorn
+USER        ist
+WORKDIR     /home/ist
+RUN         rm -r src
+# lazar-gui
+RUN         git clone https://git.in-silico.ch/lazar-gui
+WORKDIR     lazar-gui
+RUN         git checkout prerelease
+# SWAGGER for API
+WORKDIR     /home/ist
+RUN         git clone https://github.com/swagger-api/swagger-ui.git
+COPY        swagger.html /home/ist/swagger-ui/dist/index.html
+# TODO adjust to lazar-gui gem path
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js /home/ist/lazar-gui/public/swagger-ui-bundle.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js /home/ist/lazar-gui/public/swagger-ui-standalone-preset.js
+RUN         ln -s /home/ist/swagger-ui/dist/swagger-ui.css /home/ist/lazar-gui/public/swagger-ui.css
+# start script
+COPY        start.sh /home/ist/start.sh
+ENTRYPOINT  ["/home/ist/start.sh"]

data/docker/start.sh ADDED Viewed

@@ -0,0 +1,12 @@
+#!/bin/sh
+# start basic services
+mongod --bind_ip 127.0.0.1 --dbpath ~/data &
+R CMD Rserve --vanilla &
+# import data
+ruby -e "require 'lazar'; include OpenTox; Import.public_data"
+# start lazar service
+cd $HOME/lazar-gui
+unicorn -p 8088 -E production

data/docker/swagger.html ADDED Viewed

@@ -0,0 +1,107 @@
+<!-- HTML for static distribution bundle build -->
+<!DOCTYPE html>
+<html lang="en">
+  <head>
+    <meta charset="UTF-8">
+    <title>Swagger UI</title>
+    <link href="https://fonts.googleapis.com/css?family=Open+Sans:400,700|Source+Code+Pro:300,600|Titillium+Web:400,600,700" rel="stylesheet">
+    <link rel="stylesheet" type="text/css" href="./swagger-ui.css" >
+    <link rel="icon" type="image/png" href="./favicon-32x32.png" sizes="32x32" />
+    <link rel="icon" type="image/png" href="./favicon-16x16.png" sizes="16x16" />
+    <style>
+      html
+      {
+        box-sizing: border-box;
+        overflow: -moz-scrollbars-vertical;
+        overflow-y: scroll;
+      }
+      *,
+      *:before,
+      *:after
+      {
+        box-sizing: inherit;
+      }
+      body
+      {
+        margin:0;
+        background: #fafafa;
+      }
+    </style>
+  </head>
+  <body>
+    <div id="swagger-ui"></div>
+    <script src="./swagger-ui-bundle.js"> </script>
+    <script src="./swagger-ui-standalone-preset.js"> </script>
+    <script>
+    window.onload = function() {
+      // Build a system
+      var base_url = window.location.origin;
+      var swagger_url = base_url + "/api/api.json";
+      const ui = SwaggerUIBundle({
+        url: swagger_url,
+        dom_id: '#swagger-ui',
+        deepLinking: true,
+        presets: [
+          SwaggerUIBundle.presets.apis,
+          SwaggerUIStandalonePreset
+        ],
+        plugins: [
+          SwaggerUIBundle.plugins.DownloadUrl
+        ],
+        layout: "StandaloneLayout"
+      })
+      window.ui = ui;
+      document.getElementsByClassName('topbar')[0].style.backgroundColor = "#fafafa";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].alt = "IST";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].src = "./IST_logo_s.png";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].width = "90";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].height = "35";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('img')[0].style.marginRight = "20px";
+      document.getElementsByClassName('topbar-wrapper')[0].getElementsByTagName('span')[0].innerHTML = "lazar-rest-api";
+    };
+    // add link for docs
+    setTimeout(function() {
+      var base_url = window.location.origin;
+      var section = document.getElementsByClassName("info")[0];
+      var node = document.createElement("docs");
+      var heading = document.createElement('h2');
+      var headingtext = document.createTextNode("Documentation");
+      var link = document.createElement('a');
+      var linktext = document.createTextNode("See curl examples for a typical workflow.");
+      heading.appendChild(headingtext);
+      link.appendChild(linktext);
+      link.title = "curl examples";
+      link.href = "https://github.com/OpenRiskNet/home/blob/master/openshift/deployments/lazar#curl-examples";
+      link.target = "javascript:void(0);";
+      node.appendChild(heading);
+      node.appendChild(link);
+      section.appendChild(node);
+    }, 1000);
+    // add link for gui
+    setTimeout(function() {
+      var base_url = window.location.origin;
+      var section = document.getElementsByClassName("info")[0];
+      var node = document.createElement("gui");
+      var heading = document.createElement('h2');
+      var headingtext = document.createTextNode("Lazar Graphical User Interface");
+      var link = document.createElement('a');
+      var linktext = document.createTextNode("Lazar (GUI)");
+      heading.appendChild(headingtext);
+      link.appendChild(linktext);
+      link.title = "GUI link";
+      link.href = base_url = "/predict";
+      link.target = "javascript:void(0);";
+      node.appendChild(heading);
+      node.appendChild(link);
+      section.appendChild(node);
+    }, 1000);
+  </script>
+  </body>
+</html>

data/helper.rb CHANGED Viewed

@@ -1,3 +1,48 @@
 helpers do
+  def embedded_svg image, options={}
+    doc = Nokogiri::HTML::DocumentFragment.parse image
+    svg = doc.at_css 'svg'
+    title = doc.at_css 'title'
+    if options[:class].present?
+      svg['class'] = options[:class]
+    end
+    if options[:title].present?
+      if options[:title] == "x"
+        title.children.remove
+      else
+        title.children.remove
+        text_node = Nokogiri::XML::Text.new(options[:title], doc)
+        title.add_child(text_node)
+      end
+    end
+    doc.to_html.html_safe
+  end
+  def is_mongoid?
+    self.match(/^[a-f\d]{24}$/i) ? true : false
+  end
+  def remove_task_data(pid)
+    task = Task.find_by(:pid => pid)
+    if task and !task.subTasks.blank?
+      task.subTasks.each_with_index do |task_id,idx|
+        t = Task.find task_id
+        predictionDataset = Dataset.find t.dataset_id if t.dataset_id
+        if predictionDataset && idx == 0
+          trainingDataset = Dataset.find predictionDataset.source
+          predictionDataset.delete
+          # delete training dataset unless it is one used for prediction models
+          models = Model::Validation.all
+          training_datasets = models.collect{|m| m.training_dataset.id.to_s}
+          trainingDataset.delete unless training_datasets.include?(trainingDataset.id.to_s)
+        elsif predictionDataset
+          predictionDataset.delete
+        end
+        t.delete
+      end
+    end
+    task.delete if task
+  end
 end

data/lazar-gui.gemspec CHANGED Viewed

@@ -5,23 +5,23 @@ Gem::Specification.new do |s|
   s.version     = File.read("./VERSION")
   s.authors     = ["Christoph Helma","Denis Gebele"]
   s.email       = ["helma@in-silico.ch","gebele@in-silico.ch"]
-  s.homepage    = "http://github.com/opentox/lazar-gui"
+  s.homepage    = "http://git.in-silico.ch/lazar-gui"
   s.summary     = %q{lazar-gui}
-  s.description = %q{Graphical User Interface for Lazar Toxicology Predictions}
+  s.description = %q{Graphical User Interface for Lazar Toxicity Predictions}
   s.license     = 'GPL-3.0'
   s.executables = ["lazar-start", "lazar-stop"]
   s.rubyforge_project = "lazar-gui"
   s.files       = `git ls-files`.split("\n")
-  s.add_runtime_dependency "lazar"
+  s.add_runtime_dependency "lazar", "~> 1.1"
+  s.add_runtime_dependency "qsar-report", "~> 1.0"
   s.add_runtime_dependency "sinatra"
-  s.add_runtime_dependency "sinatra-reloader"
   s.add_runtime_dependency "rdiscount"
   s.add_runtime_dependency "haml"
   s.add_runtime_dependency "sass"
   s.add_runtime_dependency "unicorn"
-  s.add_runtime_dependency "qsar-report"
-  s.add_runtime_dependency "gem-path"
+  s.add_development_dependency "sinatra-reloader"
+  #s.add_runtime_dependency "gem-path"
   s.post_install_message = %q{
   Service commands:

data/lib/api.rb ADDED Viewed

@@ -0,0 +1,29 @@
+get "/api" do
+  api_file = File.join("api", "api.json")
+  `sed -i 's/SERVER_URI/#{request.env['HTTP_HOST']}/' #{api_file}`
+  halt 400, "API Documentation in Swagger JSON is not implemented." unless File.exists?(api_file)
+  case @accept
+  when "text/html"
+    response['Content-Type'] = "text/html"
+    index_file = File.join(ENV['HOME'],"swagger-ui/dist/index.html")
+    return File.read(index_file)
+  when "application/json"
+    redirect("/api/api.json")
+  else
+    halt 400, "unknown MIME type '#{@accept}'"
+  end
+end
+get "/api/api.json" do
+  api_file = File.join("api", "api.json")
+  `sed -i 's/SERVER_URI/#{request.env['HTTP_HOST']}/' #{api_file}`
+  case @accept
+  when "text/html"
+    response['Content-Type'] = "application/json"
+    return File.read(api_file)
+  when "application/json"
+    return File.read(api_file)
+  else
+    halt 400, "unknown MIME type '#{@accept}'"
+  end
+end

data/lib/compound.rb ADDED Viewed

@@ -0,0 +1,68 @@
+# Get a list of a single or all descriptors
+# @param [Header] Accept one of text/plain, application/json
+# @param [Path] Descriptor name or descriptor ID (e.G.: Openbabel.HBA1, 5755f8eb3cf99a00d8fedf2f)
+# @return [text/plain, application/json] list of all prediction models
+get "/api/compound/descriptor/?:descriptor?" do
+  case @accept
+  when "application/json"
+    return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} "  unless params[:descriptor]
+    return PhysChem.find_by(:name => params[:descriptor]).to_json if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return PhysChem.find(params[:descriptor]).to_json if PhysChem.find(params[:descriptor])
+  else
+    return PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor]
+    return PhysChem::DESCRIPTORS[params[:descriptor]] if PhysChem::DESCRIPTORS.include?(params[:descriptor])
+    return "#{PhysChem.find(params[:descriptor]).name}: #{PhysChem.find(params[:descriptor]).description}" if PhysChem.find(params[:descriptor])
+  end
+end
+post "/api/compound/descriptor/?" do
+  bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor]
+  descriptors = params['descriptor'].split(',')
+  compound = Compound.from_smiles params[:identifier]
+  physchem_descriptors = []
+  descriptors.each do |descriptor|
+    physchem_descriptors << PhysChem.find_by(:name => descriptor)
+  end
+  result = compound.calculate_properties physchem_descriptors
+  csv = (0..result.size-1).collect{|i| "\"#{physchem_descriptors[i].name}\",#{result[i]}"}.join("\n")
+  csv = "SMILES,\"#{params[:identifier]}\"\n#{csv}" if params[:identifier]
+  case @accept
+  when "text/csv","application/csv"
+    return csv
+  when "application/json"
+    result_hash = (0..result.size-1).collect{|i| {"#{physchem_descriptors[i].name}" => "#{result[i]}"}}
+    data = {"compound" => {"SMILES" => "#{params[:identifier]}"}}
+    data["compound"]["InChI"] = "#{compound.inchi}" if compound.inchi
+    data["compound"]["results"] = result_hash
+    return JSON.pretty_generate(data)
+  end
+end
+get %r{/api/compound/(InChI.+)} do |input|
+  compound = Compound.from_inchi URI.unescape(input)
+  if compound
+    response['Content-Type'] = @accept
+    case @accept
+    when "application/json"
+      c = {"compound": {"id": compound.id, "inchi": compound.inchi, "smiles": compound.smiles, "warnings": compound.warnings}}
+      return JSON.pretty_generate JSON.parse(c.to_json)
+    when "chemical/x-daylight-smiles"
+      return compound.smiles
+    when "chemical/x-inchi"
+      return compound.inchi
+    when "chemical/x-mdl-sdfile"
+      return compound.sdf
+    when "chemical/x-mdl-molfile"
+    when "image/png"
+      return compound.png
+    when "image/svg+xml"
+      return compound.svg
+    #when "text/plain"
+      #return "#{compound.names}\n"
+    else
+      halt 400, "Content type #{@accept} not supported."
+    end
+  else
+    halt 400, "Compound with #{input} not found.".to_json
+  end
+end

data/lib/dataset.rb ADDED Viewed

@@ -0,0 +1,33 @@
+# Get all datasets
+get "/api/dataset/?" do
+  datasets = Dataset.all #.limit(100)
+  case @accept
+  when "application/json"
+    list = datasets.collect{|dataset| uri("/api/dataset/#{dataset.id}")}.to_json
+    return list
+  else
+    halt 400, "Mime type #{@accept} is not supported."
+  end
+end
+# Get a dataset
+get "/api/dataset/:id/?" do
+  dataset = Dataset.find :id => params[:id]
+  halt 400, "Dataset with id: #{params[:id]} not found." unless dataset
+  case @accept
+  when "text/csv", "application/csv"
+    return File.read dataset.source
+  else
+    bad_request_error "Mime type #{@accept} is not supported."
+  end
+end
+# Get a dataset attribute. One of compounds, nanoparticles, substances, features
+get "/api/dataset/:id/:attribute/?" do
+  dataset = Dataset.find :id => params[:id]
+  halt 400,  "Dataset with id: #{params[:id]} not found." unless dataset
+  attribs = ["compounds", "nanoparticles", "substances", "features"]
+  return "Attribute '#{params[:attribute]}' is not available. Choose one of #{attribs.join(', ')}." unless attribs.include? params[:attribute]
+  out = dataset.send("#{params[:attribute]}")
+  return out.to_json
+end

data/lib/endpoint.rb ADDED Viewed

@@ -0,0 +1,23 @@
+# Get a list of all endpoints
+# @param [Header] Accept one of text/uri-list,
+# @return [text/uri-list] list of all prediction models
+get "/api/endpoint/?" do
+  models = Model::Validation.all
+  endpoints = models.collect{|m| m.endpoint}.uniq
+  case @accept
+  when "text/uri-list"
+    return endpoints.join("\n") + "\n"
+  when "application/json"
+    return endpoints.to_json
+  else
+    halt 400, "Mime type #{@accept} is not supported."
+  end
+end
+get "/api/endpoint/:endpoint/?" do
+  models = Model::Validation.where(endpoint: params[:endpoint])
+  list = []
+  models.each{|m| list << {m.species => uri("/api/model/#{m.id}")} }
+  halt 404, "Endpoint: #{params[:endpoint]} not found." if models.blank?
+  return list.to_json
+end